Warning: Permanently added '2620:52:6:1161:dead:beef:cafe:c160' (ED25519) to the list of known hosts. INFO: Calling: curl -H Pragma: -H 'Accept-Encoding: identity' -o apbs-3.0.0.tar.gz --location --connect-timeout 60 --retry 3 --retry-delay 10 --remote-time --show-error --fail --retry-all-errors https://copr-dist-git.fedorainfracloud.org/repo/pkgs/jplesnik/swig-rebuild/apbs/apbs-3.0.0.tar.gz/md5/f54dff1a670e1dc766d5ad3f775b5de8/apbs-3.0.0.tar.gz % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 25.93M 100 25.93M 0 0 97.44M 0 0 INFO: Reading stdout from command: md5sum apbs-3.0.0.tar.gz Running (timeout=38000): unbuffer mock --spec /var/lib/copr-rpmbuild/workspace/workdir-bw8d8wqg/apbs/apbs.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-bw8d8wqg/apbs --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1785937922.137901 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 6.7 starting (python version = 3.14.5, NVR = mock-6.7-1.fc44), args: /usr/libexec/mock/mock --spec /var/lib/copr-rpmbuild/workspace/workdir-bw8d8wqg/apbs/apbs.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-bw8d8wqg/apbs --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1785937922.137901 -r /var/lib/copr-rpmbuild/results/configs/child.cfg Start(bootstrap): init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish(bootstrap): init plugins Start: init plugins INFO: tmpfs initialized INFO: selinux enabled INFO: chroot_scan: initialized INFO: compress_logs: initialized Finish: init plugins INFO: Signal handler active Start: run INFO: Start(/var/lib/copr-rpmbuild/workspace/workdir-bw8d8wqg/apbs/apbs.spec) Config(fedora-rawhide-ppc64le) Start: clean chroot Finish: clean chroot Mock Version: 6.7 INFO: Mock Version: 6.7 Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1785937922.137901/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata INFO: Guessed host environment type: unknown INFO: Using container image: registry.fedoraproject.org/fedora:rawhide INFO: Pulling image: registry.fedoraproject.org/fedora:rawhide INFO: Tagging container image as mock-bootstrap-a891a8eb-96cb-4e6d-95c2-18df90fef9a9 INFO: Checking that 867877d47af083cab503cf7d25fe9ccdc90264e39ead2c321cb36635eddab017 image matches host's architecture INFO: Copy content of container 867877d47af083cab503cf7d25fe9ccdc90264e39ead2c321cb36635eddab017 to /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1785937922.137901/root INFO: mounting 867877d47af083cab503cf7d25fe9ccdc90264e39ead2c321cb36635eddab017 with podman image mount INFO: image 867877d47af083cab503cf7d25fe9ccdc90264e39ead2c321cb36635eddab017 as /var/lib/containers/storage/overlay/49439f9ba4d11547ee8e4189e6c11ebf90c25c7767a9b8c52f1c7ec18de21201/merged INFO: umounting image 867877d47af083cab503cf7d25fe9ccdc90264e39ead2c321cb36635eddab017 (/var/lib/containers/storage/overlay/49439f9ba4d11547ee8e4189e6c11ebf90c25c7767a9b8c52f1c7ec18de21201/merged) with podman image umount INFO: Removing image mock-bootstrap-a891a8eb-96cb-4e6d-95c2-18df90fef9a9 INFO: Package manager dnf5 detected and used (fallback) INFO: Not updating bootstrap chroot, bootstrap_image_ready=True Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1785937922.137901/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Package manager dnf5 detected and used (direct choice) INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.0.92-2.fc45.ppc64le rpm-sequoia-1.10.2-5.fc45.ppc64le dnf5-5.4.2.1-10.fc45.ppc64le dnf5-plugins-5.4.2.1-10.fc45.ppc64le Start: installing minimal buildroot with dnf5 Updating and loading repositories: Copr repository 100% | 4.7 KiB/s | 4.2 KiB | 00m01s fedora 100% | 11.7 MiB/s | 20.0 MiB | 00m02s Repositories loaded. Package Arch Version Repository Size Installing group/module packages: bash ppc64le 0:5.3.15-2.fc45 fedora 8.9 MiB bzip2 ppc64le 0:1.0.8-24.fc45 fedora 170.8 KiB coreutils ppc64le 0:9.11-6.fc45 fedora 9.6 MiB cpio ppc64le 0:2.15-10.fc45 fedora 1.2 MiB diffutils ppc64le 0:3.12-6.fc45 fedora 1.7 MiB fedora-release-common noarch 0:45-0.8 fedora 4.2 KiB findutils ppc64le 1:4.11.0-2.fc45 fedora 2.1 MiB gawk ppc64le 0:5.4.1-1.fc45 fedora 3.2 MiB glibc-minimal-langpack ppc64le 0:2.44-1.fc45 fedora 0.0 B grep ppc64le 0:3.12-4.fc45 fedora 1.0 MiB gzip ppc64le 0:1.14-4.fc45 fedora 437.4 KiB info ppc64le 0:7.3-3.fc45 fedora 488.1 KiB patch ppc64le 0:2.8-5.fc45 fedora 262.3 KiB redhat-rpm-config noarch 0:344-5.fc45 fedora 184.2 KiB rpm-build ppc64le 0:6.0.92-2.fc45 fedora 679.8 KiB sed ppc64le 0:4.10-2.fc45 fedora 942.3 KiB shadow-utils ppc64le 2:4.20.0-1.fc45 fedora 4.8 MiB tar ppc64le 2:1.35-9.fc45 fedora 3.1 MiB unzip ppc64le 0:6.0-71.fc45 fedora 533.4 KiB util-linux ppc64le 0:2.42.2-3.fc45 fedora 7.0 MiB which ppc64le 0:2.25-2.fc45 fedora 123.4 KiB xz ppc64le 1:5.8.3-2.fc45 fedora 1.5 MiB Installing dependencies: R-srpm-macros noarch 0:1.3.7-3.fc45 fedora 3.5 KiB add-determinism ppc64le 0:0.7.3-3.fc45 fedora 2.3 MiB alternatives ppc64le 0:1.33-6.fc45 fedora 89.9 KiB ansible-srpm-macros noarch 0:1-22.fc45 fedora 35.7 KiB audit-libs ppc64le 0:4.2.1-1.fc45 fedora 550.2 KiB binutils ppc64le 0:2.47-1.fc45 fedora 33.7 MiB build-reproducibility-srpm-macros noarch 0:0.7.3-3.fc45 fedora 1.2 KiB bzip2-libs ppc64le 0:1.0.8-24.fc45 fedora 136.4 KiB ca-certificates noarch 0:2025.2.80_v9.0.304-9.fc45 fedora 2.6 MiB cmake-srpm-macros noarch 0:4.3.0-5.fc45 fedora 524.0 B coreutils-common ppc64le 0:9.11-6.fc45 fedora 10.9 MiB crypto-policies noarch 0:20260713-2.gitc42da77.fc45 fedora 134.3 KiB curl ppc64le 0:8.21.0-4.fc45 fedora 527.9 KiB cyrus-sasl-lib ppc64le 0:2.1.28-37.fc45 fedora 2.9 MiB debugedit ppc64le 0:5.3-3.fc45 fedora 384.4 KiB dwz ppc64le 0:0.17-3.fc45 fedora 386.6 KiB ed ppc64le 0:1.22.5-3.fc45 fedora 221.6 KiB efi-srpm-macros noarch 0:6-9.fc45 fedora 40.3 KiB elfutils ppc64le 0:0.195-3.fc45 fedora 3.4 MiB elfutils-debuginfod-client ppc64le 0:0.195-3.fc45 fedora 143.4 KiB elfutils-libelf ppc64le 0:0.195-3.fc45 fedora 1.2 MiB elfutils-libs ppc64le 0:0.195-3.fc45 fedora 874.3 KiB erlang-srpm-macros noarch 0:0.3.11-2.fc45 fedora 1.9 KiB fedora-gpg-keys noarch 0:45-0.1 fedora 133.4 KiB fedora-release noarch 0:45-0.8 fedora 0.0 B fedora-release-identity-basic noarch 0:45-0.8 fedora 664.0 B fedora-repos noarch 0:45-0.1 fedora 4.9 KiB fedora-repos-rawhide noarch 0:45-0.1 fedora 2.2 KiB file ppc64le 0:5.47-3.fc45 fedora 141.0 KiB file-libs ppc64le 0:5.47-3.fc45 fedora 12.3 MiB filesystem ppc64le 0:3.18-59.fc45 fedora 112.0 B filesystem-srpm-macros noarch 0:3.18-59.fc45 fedora 38.2 KiB fips-provider ppc64le 0:1.5.2-3.fc45 fedora 4.7 MiB fonts-srpm-macros noarch 1:5.0.0-4.fc45 fedora 55.8 KiB forge-srpm-macros noarch 0:0.4.0-5.fc45 fedora 38.9 KiB fpc-srpm-macros noarch 0:1.3-17.fc45 fedora 144.0 B gap-srpm-macros noarch 0:2-3.fc45 fedora 2.1 KiB gdb-minimal ppc64le 0:17.2-4.fc45 fedora 16.3 MiB gdbm-libs ppc64le 1:1.23-12.fc45 fedora 233.3 KiB ghc-srpm-macros noarch 0:1.10-2.fc45 fedora 792.0 B glibc ppc64le 0:2.44-1.fc45 fedora 12.0 MiB glibc-common ppc64le 0:2.44-1.fc45 fedora 1.5 MiB glibc-gconv-extra ppc64le 0:2.44-1.fc45 fedora 18.5 MiB gmp ppc64le 1:6.3.0-6.fc45 fedora 786.1 KiB gnat-srpm-macros noarch 0:7-3.fc45 fedora 1.0 KiB gnome-srpm-macros noarch 0:1.0-2.fc45 fedora 3.5 KiB gnulib-l10n noarch 0:20241231-4.fc45 fedora 655.0 KiB gnupg2 ppc64le 0:2.4.9-17.fc45 fedora 6.8 MiB gnupg2-dirmngr ppc64le 0:2.4.9-17.fc45 fedora 837.9 KiB gnupg2-gpg-agent ppc64le 0:2.4.9-17.fc45 fedora 974.1 KiB gnupg2-gpgconf ppc64le 0:2.4.9-17.fc45 fedora 321.5 KiB gnupg2-keyboxd ppc64le 0:2.4.9-17.fc45 fedora 233.1 KiB gnupg2-verify ppc64le 0:2.4.9-17.fc45 fedora 428.1 KiB gnutls ppc64le 0:3.8.13-3.fc45 fedora 4.1 MiB go-srpm-macros noarch 0:3.8.0-3.fc45 fedora 61.9 KiB gpgverify noarch 0:2.2-5.fc45 fedora 8.7 KiB ima-evm-utils-libs ppc64le 0:1.6.2-12.fc45 fedora 92.5 KiB jansson ppc64le 0:2.14-5.fc45 fedora 156.9 KiB java-srpm-macros noarch 0:1-9.fc45 fedora 870.0 B json-c ppc64le 0:0.18-9.fc45 fedora 138.5 KiB kernel-srpm-macros noarch 0:1.0-30.fc45 fedora 1.9 KiB keyutils-libs ppc64le 0:1.6.3-8.fc45 fedora 97.9 KiB krb5-libs ppc64le 0:1.22.2-9.fc45 fedora 3.0 MiB libacl ppc64le 0:2.4.0-2.fc45 fedora 67.6 KiB libarchive ppc64le 0:3.8.8-3.fc45 fedora 1.3 MiB libassuan ppc64le 0:2.5.7-6.fc45 fedora 215.8 KiB libattr ppc64le 0:2.6.0-2.fc45 fedora 68.0 KiB libblkid ppc64le 0:2.42.2-3.fc45 fedora 354.3 KiB libbrotli ppc64le 0:1.2.0-6.fc45 fedora 1.0 MiB libcap ppc64le 0:2.78-2.fc45 fedora 506.7 KiB libcap-ng ppc64le 0:0.9.3-5.fc45 fedora 160.2 KiB libcbor ppc64le 0:0.14.0-3.fc45 fedora 139.5 KiB libcom_err ppc64le 0:1.47.4-2.fc45 fedora 110.9 KiB libcurl ppc64le 0:8.21.0-4.fc45 fedora 1.3 MiB libeconf ppc64le 0:0.7.9-4.fc45 fedora 80.7 KiB libevent ppc64le 0:2.1.12-19.fc45 fedora 1.3 MiB libfdisk ppc64le 0:2.42.2-3.fc45 fedora 482.8 KiB libffi ppc64le 0:3.5.2-3.fc45 fedora 347.5 KiB libfido2 ppc64le 0:1.17.0-5.fc45 fedora 344.6 KiB libfsverity ppc64le 0:1.7-4.fc45 fedora 68.0 KiB libgcc ppc64le 0:16.1.1-4.fc45.1 fedora 286.4 KiB libgcrypt ppc64le 0:1.12.2-2.fc45 fedora 1.6 MiB libgomp ppc64le 0:16.1.1-4.fc45.1 fedora 657.0 KiB libgpg-error ppc64le 0:1.61-2.fc45 fedora 1.0 MiB libidn2 ppc64le 0:2.3.8-4.fc45 fedora 560.1 KiB libksba ppc64le 0:1.8.0-3.fc45 fedora 535.0 KiB liblastlog2 ppc64le 0:2.42.2-3.fc45 fedora 137.2 KiB libmount ppc64le 0:2.42.2-3.fc45 fedora 548.3 KiB libnghttp2 ppc64le 0:1.69.0-4.fc45 fedora 197.8 KiB libnghttp3 ppc64le 0:1.18.0-1.fc45 fedora 206.7 KiB libpkgconf ppc64le 0:2.5.1-2.fc45 fedora 133.9 KiB libpsl ppc64le 0:0.23.1-1.fc45 fedora 132.1 KiB librtas ppc64le 0:2.0.7-2.fc45 fedora 320.4 KiB libselinux ppc64le 0:3.11-3.fc45 fedora 329.1 KiB libselinux-utils ppc64le 0:3.11-3.fc45 fedora 1.3 MiB libsemanage ppc64le 0:3.11-3.fc45 fedora 423.9 KiB libsepol ppc64le 0:3.11-2.fc45 fedora 1.0 MiB libsmartcols ppc64le 0:2.42.2-3.fc45 fedora 289.4 KiB libssh ppc64le 0:0.12.2-1.fc45 fedora 913.5 KiB libssh-config noarch 0:0.12.2-1.fc45 fedora 277.0 B libstdc++ ppc64le 0:16.1.1-4.fc45.1 fedora 4.1 MiB libtasn1 ppc64le 0:4.21.0-2.fc45 fedora 220.4 KiB libtool-ltdl ppc64le 0:2.5.4-11.fc45 fedora 93.8 KiB libunistring ppc64le 0:1.1-12.fc45 fedora 1.9 MiB libusb1 ppc64le 0:1.0.30-2.fc45 fedora 243.5 KiB libuuid ppc64le 0:2.42.2-3.fc45 fedora 69.2 KiB libverto ppc64le 0:0.3.2-13.fc45 fedora 69.0 KiB libxcrypt ppc64le 0:4.5.2-4.fc45 fedora 336.9 KiB libxml2 ppc64le 0:2.13.9-4.fc45 fedora 2.2 MiB libzstd ppc64le 0:1.5.7-6.fc45 fedora 1.1 MiB linkdupes ppc64le 0:0.7.3-3.fc45 fedora 838.4 KiB lua-libs ppc64le 0:5.5.0-3.fc45 fedora 393.9 KiB lua-srpm-macros noarch 0:1-18.fc45 fedora 1.3 KiB lz4-libs ppc64le 0:1.10.0-5.fc45 fedora 261.0 KiB mpfr ppc64le 0:4.2.2-4.fc45 fedora 913.4 KiB ncurses-base noarch 0:6.6-3.fc45 fedora 329.7 KiB ncurses-libs ppc64le 0:6.6-3.fc45 fedora 1.5 MiB nettle ppc64le 0:4.0-5.fc45 fedora 965.1 KiB ngtcp2 ppc64le 0:1.22.1-3.fc45 fedora 405.1 KiB ngtcp2-crypto-ossl ppc64le 0:1.22.1-3.fc45 fedora 67.1 KiB npth ppc64le 0:1.8-5.fc45 fedora 93.0 KiB ocaml-srpm-macros noarch 0:11-4.fc45 fedora 1.9 KiB openblas-srpm-macros noarch 0:2-22.fc45 fedora 112.0 B openldap ppc64le 0:2.6.13-4.fc45 fedora 891.8 KiB openssl-libs ppc64le 1:4.0.1-5.fc45 fedora 7.1 MiB p11-kit ppc64le 0:0.26.4-2.fc45 fedora 3.3 MiB p11-kit-trust ppc64le 0:0.26.4-2.fc45 fedora 594.0 KiB package-notes-srpm-macros noarch 0:0.20-2.fc45 fedora 1.6 KiB pam-libs ppc64le 0:1.7.2-4.fc45 fedora 286.0 KiB pcre2 ppc64le 0:10.47-1.fc45.2 fedora 841.8 KiB pcre2-syntax noarch 0:10.47-1.fc45.2 fedora 281.9 KiB perl-srpm-macros noarch 0:1-65.fc45 fedora 861.0 B pkgconf ppc64le 0:2.5.1-2.fc45 fedora 116.6 KiB pkgconf-m4 noarch 0:2.5.1-2.fc45 fedora 14.3 KiB pkgconf-pkg-config ppc64le 0:2.5.1-2.fc45 fedora 990.0 B policycoreutils ppc64le 0:3.11-2.fc45 fedora 1.5 MiB popt ppc64le 0:1.19-11.fc45 fedora 208.6 KiB publicsuffix-list-dafsa noarch 0:20260624-2.fc45 fedora 71.3 KiB pyproject-srpm-macros noarch 0:1.23.2-1.fc45 fedora 3.4 KiB python-srpm-macros noarch 0:3.15-2.fc45 fedora 51.6 KiB qt5-srpm-macros noarch 0:5.15.18-3.fc45 fedora 500.0 B qt6-srpm-macros noarch 0:6.11.1-2.fc45 fedora 472.0 B readline ppc64le 0:8.3-5.fc45 fedora 627.3 KiB redhat-systemd-presets noarch 0:102-3.fc45 fedora 1.0 KiB redhat-systemd-presets-common noarch 0:102-3.fc45 fedora 16.9 KiB rpm ppc64le 0:6.0.92-2.fc45 fedora 4.2 MiB rpm-build-libs ppc64le 0:6.0.92-2.fc45 fedora 327.9 KiB rpm-libs ppc64le 0:6.0.92-2.fc45 fedora 1.4 MiB rpm-plugin-selinux ppc64le 0:6.0.92-2.fc45 fedora 67.8 KiB rpm-sequoia ppc64le 0:1.10.2-5.fc45 fedora 4.8 MiB rpm-sign-libs ppc64le 0:6.0.92-2.fc45 fedora 67.5 KiB rust-srpm-macros noarch 0:28.5-2.fc45 fedora 5.5 KiB selinux-policy noarch 0:45.10-1.fc45 fedora 32.1 KiB selinux-policy-targeted noarch 0:45.10-1.fc45 fedora 18.9 MiB setup noarch 0:2.15.1-2.fc45 fedora 725.6 KiB sqlite-libs ppc64le 0:3.53.4-1.fc45 fedora 2.0 MiB systemd-libs ppc64le 0:261.2-1.fc45 fedora 3.3 MiB systemd-standalone-sysusers ppc64le 0:261.2-1.fc45 fedora 1.1 MiB tpm2-tss ppc64le 0:4.2.0-1.fc45 fedora 2.5 MiB tree-sitter-srpm-macros noarch 0:0.4.6-2.fc45 fedora 8.6 KiB util-linux-core ppc64le 0:2.42.2-3.fc45 fedora 2.6 MiB xxhash-libs ppc64le 0:0.8.3-5.fc45 fedora 85.5 KiB xz-libs ppc64le 1:5.8.3-2.fc45 fedora 265.2 KiB zig-srpm-macros noarch 0:1-9.fc45 fedora 1.3 KiB zip ppc64le 0:3.0-46.fc45 fedora 889.2 KiB zlib-ng-compat ppc64le 0:2.3.3-6.fc45 fedora 197.3 KiB zstd ppc64le 0:1.5.7-6.fc45 fedora 562.0 KiB Installing groups: Buildsystem building group Transaction Summary: Installing: 189 packages Total size of inbound packages is 76 MiB. Need to download 76 MiB. After this operation, 287 MiB extra will be used (install 287 MiB, remove 0 B). [ 1/189] bzip2-0:1.0.8-24.fc45.ppc64le 100% | 4.7 MiB/s | 53.3 KiB | 00m00s [ 2/189] cpio-0:2.15-10.fc45.ppc64le 100% | 36.7 MiB/s | 300.7 KiB | 00m00s [ 3/189] coreutils-0:9.11-6.fc45.ppc64 100% | 45.1 MiB/s | 1.3 MiB | 00m00s [ 4/189] diffutils-0:3.12-6.fc45.ppc64 100% | 30.5 MiB/s | 406.0 KiB | 00m00s [ 5/189] fedora-release-common-0:45-0. 100% | 6.1 MiB/s | 18.6 KiB | 00m00s [ 6/189] findutils-1:4.11.0-2.fc45.ppc 100% | 73.7 MiB/s | 603.8 KiB | 00m00s [ 7/189] glibc-minimal-langpack-0:2.44 100% | 29.3 MiB/s | 120.0 KiB | 00m00s [ 8/189] gawk-0:5.4.1-1.fc45.ppc64le 100% | 60.3 MiB/s | 1.2 MiB | 00m00s [ 9/189] grep-0:3.12-4.fc45.ppc64le 100% | 30.1 MiB/s | 308.5 KiB | 00m00s [ 10/189] bash-0:5.3.15-2.fc45.ppc64le 100% | 26.0 MiB/s | 1.9 MiB | 00m00s [ 11/189] gzip-0:1.14-4.fc45.ppc64le 100% | 11.7 MiB/s | 179.5 KiB | 00m00s [ 12/189] info-0:7.3-3.fc45.ppc64le 100% | 15.6 MiB/s | 207.3 KiB | 00m00s [ 13/189] patch-0:2.8-5.fc45.ppc64le 100% | 30.0 MiB/s | 123.0 KiB | 00m00s [ 14/189] redhat-rpm-config-0:344-5.fc4 100% | 25.3 MiB/s | 77.7 KiB | 00m00s [ 15/189] rpm-build-0:6.0.92-2.fc45.ppc 100% | 35.3 MiB/s | 180.9 KiB | 00m00s [ 16/189] sed-0:4.10-2.fc45.ppc64le 100% | 53.3 MiB/s | 327.3 KiB | 00m00s [ 17/189] unzip-0:6.0-71.fc45.ppc64le 100% | 39.6 MiB/s | 202.6 KiB | 00m00s [ 18/189] tar-2:1.35-9.fc45.ppc64le 100% | 61.8 MiB/s | 886.6 KiB | 00m00s [ 19/189] shadow-utils-2:4.20.0-1.fc45. 100% | 55.0 MiB/s | 1.4 MiB | 00m00s [ 20/189] which-0:2.25-2.fc45.ppc64le 100% | 3.8 MiB/s | 43.4 KiB | 00m00s [ 21/189] util-linux-0:2.42.2-3.fc45.pp 100% | 50.9 MiB/s | 1.3 MiB | 00m00s [ 22/189] xz-1:5.8.3-2.fc45.ppc64le 100% | 37.6 MiB/s | 654.1 KiB | 00m00s [ 23/189] ncurses-libs-0:6.6-3.fc45.ppc 100% | 62.1 MiB/s | 381.8 KiB | 00m00s [ 24/189] bzip2-libs-0:1.0.8-24.fc45.pp 100% | 24.1 MiB/s | 49.4 KiB | 00m00s [ 25/189] filesystem-0:3.18-59.fc45.ppc 100% | 49.1 MiB/s | 1.8 MiB | 00m00s [ 26/189] gmp-1:6.3.0-6.fc45.ppc64le 100% | 52.1 MiB/s | 319.9 KiB | 00m00s [ 27/189] 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100% | 21.2 MiB/s | 86.7 KiB | 00m00s [156/189] gnutls-0:3.8.13-3.fc45.ppc64l 100% | 59.8 MiB/s | 1.4 MiB | 00m00s [157/189] libidn2-0:2.3.8-4.fc45.ppc64l 100% | 15.7 MiB/s | 176.6 KiB | 00m00s [158/189] libunistring-0:1.1-12.fc45.pp 100% | 35.1 MiB/s | 574.7 KiB | 00m00s [159/189] nettle-0:4.0-5.fc45.ppc64le 100% | 41.1 MiB/s | 462.5 KiB | 00m00s [160/189] libevent-0:2.1.12-19.fc45.ppc 100% | 40.8 MiB/s | 292.7 KiB | 00m00s [161/189] libtool-ltdl-0:2.5.4-11.fc45. 100% | 12.8 MiB/s | 39.4 KiB | 00m00s [162/189] cyrus-sasl-lib-0:2.1.28-37.fc 100% | 48.1 MiB/s | 886.5 KiB | 00m00s [163/189] fedora-release-0:45-0.8.noarc 100% | 2.5 MiB/s | 12.7 KiB | 00m00s [164/189] gdbm-libs-1:1.23-12.fc45.ppc6 100% | 10.1 MiB/s | 61.9 KiB | 00m00s [165/189] systemd-standalone-sysusers-0 100% | 58.8 MiB/s | 421.2 KiB | 00m00s [166/189] xxhash-libs-0:0.8.3-5.fc45.pp 100% | 6.2 MiB/s | 37.8 KiB | 00m00s [167/189] fedora-release-identity-basic 100% | 6.6 MiB/s | 13.4 KiB | 00m00s [168/189] libcurl-0:8.21.0-4.fc45.ppc64 100% | 63.3 MiB/s | 518.9 KiB | 00m00s [169/189] krb5-libs-0:1.22.2-9.fc45.ppc 100% | 64.5 MiB/s | 859.2 KiB | 00m00s [170/189] libbrotli-0:1.2.0-6.fc45.ppc6 100% | 38.4 MiB/s | 392.9 KiB | 00m00s [171/189] libnghttp2-0:1.69.0-4.fc45.pp 100% | 16.3 MiB/s | 83.2 KiB | 00m00s [172/189] libnghttp3-0:1.18.0-1.fc45.pp 100% | 18.9 MiB/s | 77.4 KiB | 00m00s [173/189] libpsl-0:0.23.1-1.fc45.ppc64l 100% | 16.7 MiB/s | 68.5 KiB | 00m00s [174/189] libssh-0:0.12.2-1.fc45.ppc64l 100% | 44.4 MiB/s | 318.3 KiB | 00m00s [175/189] ngtcp2-0:1.22.1-3.fc45.ppc64l 100% | 20.5 MiB/s | 168.3 KiB | 00m00s [176/189] gdb-minimal-0:17.2-4.fc45.ppc 100% | 73.6 MiB/s | 4.9 MiB | 00m00s [177/189] ngtcp2-crypto-ossl-0:1.22.1-3 100% | 1.1 MiB/s | 27.2 KiB | 00m00s [178/189] keyutils-libs-0:1.6.3-8.fc45. 100% | 1.3 MiB/s | 32.5 KiB | 00m00s [179/189] libcom_err-0:1.47.4-2.fc45.pp 100% | 6.5 MiB/s | 26.8 KiB | 00m00s [180/189] libverto-0:0.3.2-13.fc45.ppc6 100% | 5.3 MiB/s | 21.7 KiB | 00m00s [181/189] publicsuffix-list-dafsa-0:202 100% | 11.9 MiB/s | 61.1 KiB | 00m00s [182/189] libfido2-0:1.17.0-5.fc45.ppc6 100% | 54.8 MiB/s | 112.3 KiB | 00m00s [183/189] libssh-config-0:0.12.2-1.fc45 100% | 2.9 MiB/s | 8.9 KiB | 00m00s [184/189] libcbor-0:0.14.0-3.fc45.ppc64 100% | 18.5 MiB/s | 37.9 KiB | 00m00s [185/189] selinux-policy-0:45.10-1.fc45 100% | 11.3 MiB/s | 34.7 KiB | 00m00s [186/189] policycoreutils-0:3.11-2.fc45 100% | 36.7 MiB/s | 263.0 KiB | 00m00s [187/189] libselinux-utils-0:3.11-3.fc4 100% | 20.7 MiB/s | 127.4 KiB | 00m00s [188/189] rpm-plugin-selinux-0:6.0.92-2 100% | 8.7 MiB/s | 17.8 KiB | 00m00s [189/189] selinux-policy-targeted-0:45. 100% | 111.6 MiB/s | 6.8 MiB | 00m00s -------------------------------------------------------------------------------- [189/189] Total 100% | 99.9 MiB/s | 76.1 MiB | 00m01s Running transaction Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. Importing OpenPGP key 0xF577861E: UserID : "Fedora (45) " Fingerprint: 4F50A6114CD5C6976A7F1179655A4B02F577861E From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-45-primary The key was successfully imported. Importing OpenPGP key 0x6D9F90A6: UserID : "Fedora (44) " Fingerprint: 36F612DCF27F7D1A48A835E4DBFCF71C6D9F90A6 From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-44-primary The key was successfully imported. Importing OpenPGP key 0x91211FCE: UserID : "Fedora (46) " Fingerprint: D924B10D3E810DABDD8B56B596E7E91491211FCE From : file:///usr/share/distribution-gpg-keys/fedora/RPM-GPG-KEY-fedora-46-primary The key was successfully imported. [ 1/191] Verify package files 100% | 157.0 B/s | 189.0 B | 00m01s >>> Running %pretrans scriptlet: filesystem-0:3.18-59.fc45.ppc64le >>> Finished %pretrans scriptlet: filesystem-0:3.18-59.fc45.ppc64le >>> [RPM] failed to open /var/lib/mock/fedora-rawhide-ppc64le-1785937922.137901/root/etc/group for id/name lookup: No such file or directory [ 2/191] Prepare transaction 100% | 1.0 KiB/s | 189.0 B | 00m00s [ 3/191] Installing libgcc-0:16.1.1-4. 100% | 70.3 MiB/s | 288.1 KiB | 00m00s [ 4/191] Installing redhat-systemd-pre 100% | 1.4 MiB/s | 1.5 KiB | 00m00s [ 5/191] Installing redhat-systemd-pre 100% | 17.7 MiB/s | 18.1 KiB | 00m00s [ 6/191] Installing libssh-config-0:0. 100% | 796.9 KiB/s | 816.0 B | 00m00s [ 7/191] Installing publicsuffix-list- 100% | 70.3 MiB/s | 72.0 KiB | 00m00s [ 8/191] Installing fedora-release-ide 100% | 898.4 KiB/s | 920.0 B | 00m00s [ 9/191] Installing fedora-gpg-keys-0: 100% | 12.7 MiB/s | 182.1 KiB | 00m00s [ 10/191] Installing fedora-repos-rawhi 100% | 2.4 MiB/s | 2.4 KiB | 00m00s [ 11/191] Installing fedora-repos-0:45- 100% | 5.6 MiB/s | 5.7 KiB | 00m00s [ 12/191] Installing fedora-release-com 100% | 3.6 MiB/s | 7.4 KiB | 00m00s [ 13/191] Installing fedora-release-0:4 100% | 12.1 KiB/s | 124.0 B | 00m00s >>> Running sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Finished sysusers scriptlet: setup-0:2.15.1-2.fc45.noarch >>> Scriptlet output: >>> Creating group 'adm' with GID 4. >>> Creating group 'audio' with GID 63. >>> Creating group 'cdrom' with GID 11. >>> Creating group 'clock' with GID 103. >>> Creating group 'dialout' with GID 18. >>> Creating group 'disk' with GID 6. >>> Creating group 'floppy' with GID 19. >>> Creating group 'ftp' with GID 50. >>> Creating group 'games' with GID 20. >>> Creating group 'input' with GID 104. >>> Creating group 'kmem' with GID 9. >>> Creating group 'kvm' with GID 36. >>> Creating group 'lock' with GID 54. >>> Creating group 'lp' with GID 7. >>> Creating group 'mail' with GID 12. >>> Creating group 'man' with GID 15. >>> Creating group 'mem' with GID 8. >>> Creating group 'nobody' with GID 65534. >>> Creating group 'render' with GID 105. >>> Creating group 'root' with GID 0. >>> Creating group 'sgx' with GID 106. >>> Creating group 'sys' with GID 3. >>> Creating group 'tape' with GID 33. >>> Creating group 'tty' with GID 5. >>> Creating group 'users' with GID 100. >>> Creating group 'utmp' with GID 22. >>> Creating group 'video' with GID 39. >>> Creating group 'wheel' with GID 10. >>> Creating user 'adm' (adm) with UID 3 and GID 4. >>> Creating group 'bin' with GID 1. >>> Creating user 'bin' (bin) with UID 1 and GID 1. >>> Creating group 'daemon' with GID 2. >>> Creating user 'daemon' (daemon) with UID 2 and GID 2. >>> Creating user 'ftp' (FTP User) with UID 14 and GID 50. >>> Creating user 'games' (games) with UID 12 and GID 100. >>> Creating user 'halt' (halt) with UID 7 and GID 0. >>> Creating user 'lp' (lp) with UID 4 and GID 7. >>> Creating user 'mail' (mail) with UID 8 and GID 12. >>> Creating user 'nobody' (Kernel Overflow User) with UID 65534 and GID 65534. >>> Creating user 'operator' (operator) with UID 11 and GID 0. >>> Creating user 'root' (Super User) with UID 0 and GID 0. >>> Creating user 'shutdown' (shutdown) with UID 6 and GID 0. >>> Creating user 'sync' (sync) with UID 5 and GID 0. >>> [ 14/191] Installing setup-0:2.15.1-2.f 100% | 12.3 MiB/s | 731.3 KiB | 00m00s >>> [RPM] /etc/hosts created as /etc/hosts.rpmnew [ 15/191] Installing filesystem-0:3.18- 100% | 836.9 KiB/s | 253.6 KiB | 00m00s [ 16/191] Installing pkgconf-m4-0:2.5.1 100% | 14.4 MiB/s | 14.7 KiB | 00m00s [ 17/191] Installing pcre2-syntax-0:10. 100% | 69.4 MiB/s | 284.3 KiB | 00m00s [ 18/191] Installing gnulib-l10n-0:2024 100% | 53.9 MiB/s | 661.9 KiB | 00m00s [ 19/191] Installing coreutils-common-0 100% | 114.1 MiB/s | 11.0 MiB | 00m00s [ 20/191] Installing ncurses-base-0:6.6 100% | 21.7 MiB/s | 355.3 KiB | 00m00s [ 21/191] Installing bash-0:5.3.15-2.fc 100% | 82.7 MiB/s | 8.9 MiB | 00m00s [ 22/191] Installing glibc-common-0:2.4 100% | 26.1 MiB/s | 1.5 MiB | 00m00s [ 23/191] Installing glibc-gconv-extra- 100% | 128.2 MiB/s | 18.6 MiB | 00m00s [ 24/191] Installing glibc-0:2.44-1.fc4 100% | 82.8 MiB/s | 12.0 MiB | 00m00s [ 25/191] Installing ncurses-libs-0:6.6 100% | 93.4 MiB/s | 1.5 MiB | 00m00s [ 26/191] Installing glibc-minimal-lang 100% | 121.1 KiB/s | 124.0 B | 00m00s [ 27/191] Installing zlib-ng-compat-0:2 100% | 64.5 MiB/s | 198.1 KiB | 00m00s [ 28/191] Installing bzip2-libs-0:1.0.8 100% | 67.2 MiB/s | 137.5 KiB | 00m00s [ 29/191] Installing libgpg-error-0:1.6 100% | 20.4 MiB/s | 1.0 MiB | 00m00s [ 30/191] Installing libstdc++-0:16.1.1 100% | 128.3 MiB/s | 4.1 MiB | 00m00s [ 31/191] Installing libzstd-0:1.5.7-6. 100% | 109.1 MiB/s | 1.1 MiB | 00m00s [ 32/191] Installing elfutils-libelf-0: 100% | 124.0 MiB/s | 1.2 MiB | 00m00s [ 33/191] Installing libassuan-0:2.5.7- 100% | 70.8 MiB/s | 217.6 KiB | 00m00s [ 34/191] Installing libgcrypt-0:1.12.2 100% | 112.5 MiB/s | 1.6 MiB | 00m00s [ 35/191] Installing readline-0:8.3-5.f 100% | 102.5 MiB/s | 629.5 KiB | 00m00s [ 36/191] Installing gmp-1:6.3.0-6.fc45 100% | 96.2 MiB/s | 788.3 KiB | 00m00s [ 37/191] Installing libacl-0:2.4.0-2.f 100% | 33.4 MiB/s | 68.4 KiB | 00m00s [ 38/191] Installing systemd-libs-0:261 100% | 126.2 MiB/s | 3.3 MiB | 00m00s [ 39/191] Installing libuuid-0:2.42.2-3 100% | 34.3 MiB/s | 70.3 KiB | 00m00s [ 40/191] Installing xz-libs-1:5.8.3-2. 100% | 86.7 MiB/s | 266.3 KiB | 00m00s [ 41/191] Installing popt-0:1.19-11.fc4 100% | 26.3 MiB/s | 215.2 KiB | 00m00s [ 42/191] Installing sqlite-libs-0:3.53 100% | 111.5 MiB/s | 2.0 MiB | 00m00s [ 43/191] Installing npth-0:1.8-5.fc45. 100% | 45.9 MiB/s | 94.1 KiB | 00m00s [ 44/191] Installing elfutils-libs-0:0. 100% | 107.0 MiB/s | 876.2 KiB | 00m00s [ 45/191] Installing libblkid-0:2.42.2- 100% | 86.8 MiB/s | 355.5 KiB | 00m00s [ 46/191] Installing libsepol-0:3.11-2. 100% | 115.8 MiB/s | 1.0 MiB | 00m00s [ 47/191] Installing gnupg2-gpgconf-0:2 100% | 7.5 MiB/s | 323.6 KiB | 00m00s [ 48/191] Installing pcre2-0:10.47-1.fc 100% | 102.9 MiB/s | 843.2 KiB | 00m00s [ 49/191] Installing libselinux-0:3.11- 100% | 80.7 MiB/s | 330.4 KiB | 00m00s [ 50/191] Installing grep-0:3.12-4.fc45 100% | 19.6 MiB/s | 1.0 MiB | 00m00s [ 51/191] Installing sed-0:4.10-2.fc45. 100% | 17.9 MiB/s | 950.8 KiB | 00m00s [ 52/191] Installing findutils-1:4.11.0 100% | 36.3 MiB/s | 2.1 MiB | 00m00s [ 53/191] Installing libxcrypt-0:4.5.2- 100% | 66.3 MiB/s | 339.6 KiB | 00m00s [ 54/191] Installing libtasn1-0:4.21.0- 100% | 72.3 MiB/s | 222.2 KiB | 00m00s [ 55/191] Installing libunistring-0:1.1 100% | 117.0 MiB/s | 1.9 MiB | 00m00s [ 56/191] Installing libidn2-0:2.3.8-4. 100% | 30.7 MiB/s | 566.3 KiB | 00m00s [ 57/191] Installing crypto-policies-0: 100% | 10.4 MiB/s | 159.5 KiB | 00m00s [ 58/191] Installing xz-1:5.8.3-2.fc45. 100% | 24.7 MiB/s | 1.5 MiB | 00m00s [ 59/191] Installing libmount-0:2.42.2- 100% | 89.4 MiB/s | 549.3 KiB | 00m00s [ 60/191] Installing gnupg2-verify-0:2. 100% | 10.0 MiB/s | 429.5 KiB | 00m00s [ 61/191] Installing mpfr-0:4.2.2-4.fc4 100% | 89.4 MiB/s | 915.1 KiB | 00m00s [ 62/191] Installing gawk-0:5.4.1-1.fc4 100% | 47.4 MiB/s | 3.2 MiB | 00m00s [ 63/191] Installing dwz-0:0.17-3.fc45. 100% | 9.0 MiB/s | 388.0 KiB | 00m00s [ 64/191] Installing libksba-0:1.8.0-3. 100% | 87.5 MiB/s | 537.6 KiB | 00m00s [ 65/191] Installing unzip-0:6.0-71.fc4 100% | 11.9 MiB/s | 536.9 KiB | 00m00s [ 66/191] Installing file-libs-0:5.47-3 100% | 183.1 MiB/s | 12.3 MiB | 00m00s [ 67/191] Installing file-0:5.47-3.fc45 100% | 3.4 MiB/s | 142.5 KiB | 00m00s [ 68/191] Installing diffutils-0:3.12-6 100% | 30.1 MiB/s | 1.7 MiB | 00m00s [ 69/191] Installing libattr-0:2.6.0-2. 100% | 33.7 MiB/s | 69.0 KiB | 00m00s [ 70/191] Installing libeconf-0:0.7.9-4 100% | 40.2 MiB/s | 82.4 KiB | 00m00s [ 71/191] Installing libcap-ng-0:0.9.3- 100% | 52.7 MiB/s | 162.0 KiB | 00m00s [ 72/191] Installing audit-libs-0:4.2.1 100% | 90.0 MiB/s | 552.8 KiB | 00m00s [ 73/191] Installing pam-libs-0:1.7.2-4 100% | 70.4 MiB/s | 288.4 KiB | 00m00s [ 74/191] Installing libcap-0:2.78-2.fc 100% | 11.4 MiB/s | 511.9 KiB | 00m00s [ 75/191] Installing libsemanage-0:3.11 100% | 83.1 MiB/s | 425.6 KiB | 00m00s [ 76/191] Installing libsmartcols-0:2.4 100% | 70.9 MiB/s | 290.5 KiB | 00m00s [ 77/191] Installing alternatives-0:1.3 100% | 2.2 MiB/s | 91.5 KiB | 00m00s [ 78/191] Installing lua-libs-0:5.5.0-3 100% | 77.2 MiB/s | 395.4 KiB | 00m00s [ 79/191] Installing libffi-0:3.5.2-3.f 100% | 85.2 MiB/s | 348.9 KiB | 00m00s [ 80/191] Installing p11-kit-0:0.26.4-2 100% | 45.2 MiB/s | 3.3 MiB | 00m00s [ 81/191] Installing p11-kit-trust-0:0. 100% | 11.2 MiB/s | 595.7 KiB | 00m00s [ 82/191] Installing json-c-0:0.18-9.fc 100% | 45.5 MiB/s | 139.7 KiB | 00m00s [ 83/191] Installing ngtcp2-0:1.22.1-3. 100% | 66.2 MiB/s | 406.6 KiB | 00m00s [ 84/191] Installing util-linux-core-0: 100% | 40.2 MiB/s | 2.7 MiB | 00m00s [ 85/191] Installing liblastlog2-0:2.42 100% | 15.1 MiB/s | 139.3 KiB | 00m00s [ 86/191] Installing zip-0:3.0-46.fc45. 100% | 18.2 MiB/s | 893.1 KiB | 00m00s [ 87/191] Installing gnupg2-keyboxd-0:2 100% | 25.4 MiB/s | 234.4 KiB | 00m00s [ 88/191] Installing libpsl-0:0.23.1-1. 100% | 43.4 MiB/s | 133.2 KiB | 00m00s [ 89/191] Installing tar-2:1.35-9.fc45. 100% | 46.7 MiB/s | 3.1 MiB | 00m00s [ 90/191] Installing linkdupes-0:0.7.3- 100% | 17.4 MiB/s | 839.8 KiB | 00m00s [ 91/191] Installing libselinux-utils-0 100% | 25.5 MiB/s | 1.4 MiB | 00m00s [ 92/191] Installing libfdisk-0:2.42.2- 100% | 78.8 MiB/s | 483.9 KiB | 00m00s [ 93/191] Installing fips-provider-0:1. 100% | 126.8 MiB/s | 4.7 MiB | 00m00s [ 94/191] Installing openssl-libs-1:4.0 100% | 125.0 MiB/s | 7.1 MiB | 00m00s [ 95/191] Installing coreutils-0:9.11-6 100% | 79.8 MiB/s | 9.7 MiB | 00m00s [ 96/191] Installing ca-certificates-0: 100% | 807.2 KiB/s | 2.4 MiB | 00m03s [ 97/191] Installing gzip-0:1.14-4.fc45 100% | 9.4 MiB/s | 442.9 KiB | 00m00s [ 98/191] Installing rpm-sequoia-0:1.10 100% | 125.3 MiB/s | 4.8 MiB | 00m00s [ 99/191] Installing libfsverity-0:1.7- 100% | 33.7 MiB/s | 69.0 KiB | 00m00s [100/191] Installing libevent-0:2.1.12- 100% | 115.6 MiB/s | 1.3 MiB | 00m00s [101/191] Installing ngtcp2-crypto-ossl 100% | 33.2 MiB/s | 68.0 KiB | 00m00s [102/191] Installing libxml2-0:2.13.9-4 100% | 38.9 MiB/s | 2.2 MiB | 00m00s [103/191] Installing libusb1-0:1.0.30-2 100% | 18.4 MiB/s | 245.2 KiB | 00m00s >>> Running sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc45.ppc64le >>> Finished sysusers scriptlet: tpm2-tss-0:4.2.0-1.fc45.ppc64le >>> Scriptlet output: >>> Creating group 'tss' with GID 59. >>> Creating user 'tss' (Account used for TPM access) with UID 59 and GID 59. >>> [104/191] Installing tpm2-tss-0:4.2.0-1 100% | 115.7 MiB/s | 2.5 MiB | 00m00s [105/191] Installing ima-evm-utils-libs 100% | 45.8 MiB/s | 93.8 KiB | 00m00s [106/191] Installing gnupg2-gpg-agent-0 100% | 17.7 MiB/s | 978.1 KiB | 00m00s [107/191] Installing nettle-0:4.0-5.fc4 100% | 94.6 MiB/s | 968.2 KiB | 00m00s [108/191] Installing gnutls-0:3.8.13-3. 100% | 122.0 MiB/s | 4.1 MiB | 00m00s [109/191] Installing zstd-0:1.5.7-6.fc4 100% | 12.0 MiB/s | 565.6 KiB | 00m00s [110/191] Installing bzip2-0:1.0.8-24.f 100% | 4.0 MiB/s | 175.4 KiB | 00m00s [111/191] Installing add-determinism-0: 100% | 38.6 MiB/s | 2.3 MiB | 00m00s [112/191] Installing cpio-0:2.15-10.fc4 100% | 21.8 MiB/s | 1.2 MiB | 00m00s [113/191] Installing ed-0:1.22.5-3.fc45 100% | 5.0 MiB/s | 223.9 KiB | 00m00s [114/191] Installing patch-0:2.8-5.fc45 100% | 6.1 MiB/s | 263.8 KiB | 00m00s [115/191] Installing librtas-0:2.0.7-2. 100% | 17.5 MiB/s | 322.5 KiB | 00m00s [116/191] Installing util-linux-0:2.42. 100% | 57.9 MiB/s | 7.1 MiB | 00m00s [117/191] Installing policycoreutils-0: 100% | 20.1 MiB/s | 1.5 MiB | 00m00s [118/191] Installing selinux-policy-0:4 100% | 1.2 MiB/s | 34.5 KiB | 00m00s [119/191] Installing selinux-policy-tar 100% | 56.5 MiB/s | 15.1 MiB | 00m00s [120/191] Installing build-reproducibil 100% | 1.5 MiB/s | 1.5 KiB | 00m00s [121/191] Installing jansson-0:2.14-5.f 100% | 77.3 MiB/s | 158.3 KiB | 00m00s [122/191] Installing lz4-libs-0:1.10.0- 100% | 64.0 MiB/s | 262.1 KiB | 00m00s [123/191] Installing libarchive-0:3.8.8 100% | 105.6 MiB/s | 1.3 MiB | 00m00s [124/191] Installing libgomp-0:16.1.1-4 100% | 107.2 MiB/s | 658.4 KiB | 00m00s [125/191] Installing libpkgconf-0:2.5.1 100% | 65.9 MiB/s | 135.0 KiB | 00m00s [126/191] Installing pkgconf-0:2.5.1-2. 100% | 2.8 MiB/s | 119.1 KiB | 00m00s [127/191] Installing pkgconf-pkg-config 100% | 45.5 KiB/s | 1.8 KiB | 00m00s [128/191] Installing libtool-ltdl-0:2.5 100% | 46.3 MiB/s | 94.9 KiB | 00m00s [129/191] Installing gdbm-libs-1:1.23-1 100% | 76.5 MiB/s | 235.0 KiB | 00m00s [130/191] Installing cyrus-sasl-lib-0:2 100% | 46.3 MiB/s | 2.9 MiB | 00m00s [131/191] Installing openldap-0:2.6.13- 100% | 79.5 MiB/s | 895.6 KiB | 00m00s [132/191] Installing gnupg2-dirmngr-0:2 100% | 14.7 MiB/s | 840.6 KiB | 00m00s [133/191] Installing gnupg2-0:2.4.9-17. 100% | 67.6 MiB/s | 6.8 MiB | 00m00s [134/191] Installing gpgverify-0:2.2-5. 100% | 4.6 MiB/s | 9.4 KiB | 00m00s [135/191] Installing systemd-standalone 100% | 21.6 MiB/s | 1.1 MiB | 00m00s [136/191] Installing rpm-libs-0:6.0.92- 100% | 101.0 MiB/s | 1.4 MiB | 00m00s [137/191] Installing rpm-sign-libs-0:6. 100% | 33.4 MiB/s | 68.4 KiB | 00m00s [138/191] Installing rpm-build-libs-0:6 100% | 80.2 MiB/s | 328.7 KiB | 00m00s [139/191] Installing xxhash-libs-0:0.8. 100% | 42.4 MiB/s | 86.9 KiB | 00m00s [140/191] Installing libbrotli-0:1.2.0- 100% | 101.4 MiB/s | 1.0 MiB | 00m00s [141/191] Installing libnghttp2-0:1.69. 100% | 64.8 MiB/s | 198.9 KiB | 00m00s [142/191] Installing libnghttp3-0:1.18. 100% | 67.7 MiB/s | 208.1 KiB | 00m00s [143/191] Installing keyutils-libs-0:1. 100% | 48.5 MiB/s | 99.3 KiB | 00m00s [144/191] Installing libcom_err-0:1.47. 100% | 54.7 MiB/s | 112.0 KiB | 00m00s [145/191] Installing libverto-0:0.3.2-1 100% | 34.6 MiB/s | 70.8 KiB | 00m00s [146/191] Installing krb5-libs-0:1.22.2 100% | 106.1 MiB/s | 3.0 MiB | 00m00s [147/191] Installing libcbor-0:0.14.0-3 100% | 45.9 MiB/s | 140.9 KiB | 00m00s [148/191] Installing libfido2-0:1.17.0- 100% | 67.6 MiB/s | 346.1 KiB | 00m00s [149/191] Installing libssh-0:0.12.2-1. 100% | 99.3 MiB/s | 915.6 KiB | 00m00s [150/191] Installing libcurl-0:8.21.0-4 100% | 106.1 MiB/s | 1.3 MiB | 00m00s [151/191] Installing elfutils-debuginfo 100% | 3.3 MiB/s | 145.7 KiB | 00m00s [152/191] Installing binutils-0:2.47-1. 100% | 116.8 MiB/s | 33.8 MiB | 00m00s [153/191] Installing elfutils-0:0.195-3 100% | 52.3 MiB/s | 3.5 MiB | 00m00s [154/191] Installing gdb-minimal-0:17.2 100% | 102.4 MiB/s | 16.3 MiB | 00m00s [155/191] Installing debugedit-0:5.3-3. 100% | 8.6 MiB/s | 387.8 KiB | 00m00s [156/191] Installing curl-0:8.21.0-4.fc 100% | 8.9 MiB/s | 530.6 KiB | 00m00s [157/191] Installing rpm-0:6.0.92-2.fc4 100% | 30.3 MiB/s | 2.8 MiB | 00m00s [158/191] Installing cmake-srpm-macros- 100% | 785.2 KiB/s | 804.0 B | 00m00s [159/191] Installing efi-srpm-macros-0: 100% | 20.2 MiB/s | 41.3 KiB | 00m00s [160/191] Installing java-srpm-macros-0 100% | 1.1 MiB/s | 1.1 KiB | 00m00s [161/191] Installing lua-srpm-macros-0: 100% | 1.9 MiB/s | 1.9 KiB | 00m00s [162/191] Installing tree-sitter-srpm-m 100% | 9.4 MiB/s | 9.6 KiB | 00m00s [163/191] Installing zig-srpm-macros-0: 100% | 1.8 MiB/s | 1.9 KiB | 00m00s [164/191] Installing filesystem-srpm-ma 100% | 38.0 MiB/s | 38.9 KiB | 00m00s [165/191] Installing rust-srpm-macros-0 100% | 6.2 MiB/s | 6.4 KiB | 00m00s [166/191] Installing qt6-srpm-macros-0: 100% | 730.5 KiB/s | 748.0 B | 00m00s [167/191] Installing qt5-srpm-macros-0: 100% | 757.8 KiB/s | 776.0 B | 00m00s [168/191] Installing perl-srpm-macros-0 100% | 1.1 MiB/s | 1.1 KiB | 00m00s [169/191] Installing package-notes-srpm 100% | 2.0 MiB/s | 2.1 KiB | 00m00s [170/191] Installing openblas-srpm-macr 100% | 382.8 KiB/s | 392.0 B | 00m00s [171/191] Installing ocaml-srpm-macros- 100% | 214.5 KiB/s | 2.1 KiB | 00m00s [172/191] Installing kernel-srpm-macros 100% | 2.3 MiB/s | 2.3 KiB | 00m00s [173/191] Installing gnome-srpm-macros- 100% | 4.0 MiB/s | 4.1 KiB | 00m00s [174/191] Installing gnat-srpm-macros-0 100% | 1.2 MiB/s | 1.3 KiB | 00m00s [175/191] Installing ghc-srpm-macros-0: 100% | 1.0 MiB/s | 1.0 KiB | 00m00s [176/191] Installing gap-srpm-macros-0: 100% | 2.6 MiB/s | 2.7 KiB | 00m00s [177/191] Installing fpc-srpm-macros-0: 100% | 410.2 KiB/s | 420.0 B | 00m00s [178/191] Installing ansible-srpm-macro 100% | 17.7 MiB/s | 36.2 KiB | 00m00s [179/191] Installing redhat-rpm-config- 100% | 31.0 MiB/s | 190.4 KiB | 00m00s [180/191] Installing forge-srpm-macros- 100% | 19.7 MiB/s | 40.3 KiB | 00m00s [181/191] Installing rpm-build-0:6.0.92 100% | 13.2 MiB/s | 689.8 KiB | 00m00s [182/191] Installing erlang-srpm-macros 100% | 2.4 MiB/s | 2.5 KiB | 00m00s [183/191] Installing pyproject-srpm-mac 100% | 3.9 MiB/s | 4.0 KiB | 00m00s [184/191] Installing fonts-srpm-macros- 100% | 27.8 MiB/s | 57.0 KiB | 00m00s [185/191] Installing go-srpm-macros-0:3 100% | 30.8 MiB/s | 63.0 KiB | 00m00s [186/191] Installing R-srpm-macros-0:1. 100% | 4.3 MiB/s | 4.4 KiB | 00m00s [187/191] Installing python-srpm-macros 100% | 25.9 MiB/s | 52.9 KiB | 00m00s [188/191] Installing rpm-plugin-selinux 100% | 33.6 MiB/s | 68.8 KiB | 00m00s [189/191] Installing which-0:2.25-2.fc4 100% | 2.7 MiB/s | 125.6 KiB | 00m00s [190/191] Installing shadow-utils-2:4.2 100% | 46.9 MiB/s | 4.9 MiB | 00m00s [191/191] Installing info-0:7.3-3.fc45. 100% | 34.6 KiB/s | 488.5 KiB | 00m14s Complete! Finish: installing minimal buildroot with dnf5 Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: R-srpm-macros-1.3.7-3.fc45.noarch add-determinism-0.7.3-3.fc45.ppc64le alternatives-1.33-6.fc45.ppc64le ansible-srpm-macros-1-22.fc45.noarch audit-libs-4.2.1-1.fc45.ppc64le bash-5.3.15-2.fc45.ppc64le binutils-2.47-1.fc45.ppc64le build-reproducibility-srpm-macros-0.7.3-3.fc45.noarch bzip2-1.0.8-24.fc45.ppc64le bzip2-libs-1.0.8-24.fc45.ppc64le ca-certificates-2025.2.80_v9.0.304-9.fc45.noarch cmake-srpm-macros-4.3.0-5.fc45.noarch coreutils-9.11-6.fc45.ppc64le coreutils-common-9.11-6.fc45.ppc64le cpio-2.15-10.fc45.ppc64le crypto-policies-20260713-2.gitc42da77.fc45.noarch curl-8.21.0-4.fc45.ppc64le cyrus-sasl-lib-2.1.28-37.fc45.ppc64le debugedit-5.3-3.fc45.ppc64le diffutils-3.12-6.fc45.ppc64le dwz-0.17-3.fc45.ppc64le ed-1.22.5-3.fc45.ppc64le efi-srpm-macros-6-9.fc45.noarch elfutils-0.195-3.fc45.ppc64le elfutils-debuginfod-client-0.195-3.fc45.ppc64le elfutils-libelf-0.195-3.fc45.ppc64le elfutils-libs-0.195-3.fc45.ppc64le erlang-srpm-macros-0.3.11-2.fc45.noarch fedora-gpg-keys-45-0.1.noarch fedora-release-45-0.8.noarch fedora-release-common-45-0.8.noarch fedora-release-identity-basic-45-0.8.noarch fedora-repos-45-0.1.noarch fedora-repos-rawhide-45-0.1.noarch file-5.47-3.fc45.ppc64le file-libs-5.47-3.fc45.ppc64le filesystem-3.18-59.fc45.ppc64le filesystem-srpm-macros-3.18-59.fc45.noarch findutils-4.11.0-2.fc45.ppc64le fips-provider-1.5.2-3.fc45.ppc64le fonts-srpm-macros-5.0.0-4.fc45.noarch forge-srpm-macros-0.4.0-5.fc45.noarch fpc-srpm-macros-1.3-17.fc45.noarch gap-srpm-macros-2-3.fc45.noarch gawk-5.4.1-1.fc45.ppc64le gdb-minimal-17.2-4.fc45.ppc64le gdbm-libs-1.23-12.fc45.ppc64le ghc-srpm-macros-1.10-2.fc45.noarch glibc-2.44-1.fc45.ppc64le glibc-common-2.44-1.fc45.ppc64le glibc-gconv-extra-2.44-1.fc45.ppc64le glibc-minimal-langpack-2.44-1.fc45.ppc64le gmp-6.3.0-6.fc45.ppc64le gnat-srpm-macros-7-3.fc45.noarch gnome-srpm-macros-1.0-2.fc45.noarch gnulib-l10n-20241231-4.fc45.noarch gnupg2-2.4.9-17.fc45.ppc64le gnupg2-dirmngr-2.4.9-17.fc45.ppc64le gnupg2-gpg-agent-2.4.9-17.fc45.ppc64le gnupg2-gpgconf-2.4.9-17.fc45.ppc64le gnupg2-keyboxd-2.4.9-17.fc45.ppc64le gnupg2-verify-2.4.9-17.fc45.ppc64le gnutls-3.8.13-3.fc45.ppc64le go-srpm-macros-3.8.0-3.fc45.noarch gpg-pubkey-36f612dcf27f7d1a48a835e4dbfcf71c6d9f90a6-6786af3b gpg-pubkey-4f50a6114cd5c6976a7f1179655a4b02f577861e-6888bc98 gpg-pubkey-d924b10d3e810dabdd8b56b596e7e91491211fce-697c9899 gpgverify-2.2-5.fc45.noarch grep-3.12-4.fc45.ppc64le gzip-1.14-4.fc45.ppc64le ima-evm-utils-libs-1.6.2-12.fc45.ppc64le info-7.3-3.fc45.ppc64le jansson-2.14-5.fc45.ppc64le java-srpm-macros-1-9.fc45.noarch json-c-0.18-9.fc45.ppc64le kernel-srpm-macros-1.0-30.fc45.noarch keyutils-libs-1.6.3-8.fc45.ppc64le krb5-libs-1.22.2-9.fc45.ppc64le libacl-2.4.0-2.fc45.ppc64le libarchive-3.8.8-3.fc45.ppc64le libassuan-2.5.7-6.fc45.ppc64le libattr-2.6.0-2.fc45.ppc64le libblkid-2.42.2-3.fc45.ppc64le libbrotli-1.2.0-6.fc45.ppc64le libcap-2.78-2.fc45.ppc64le libcap-ng-0.9.3-5.fc45.ppc64le libcbor-0.14.0-3.fc45.ppc64le libcom_err-1.47.4-2.fc45.ppc64le libcurl-8.21.0-4.fc45.ppc64le libeconf-0.7.9-4.fc45.ppc64le libevent-2.1.12-19.fc45.ppc64le libfdisk-2.42.2-3.fc45.ppc64le libffi-3.5.2-3.fc45.ppc64le libfido2-1.17.0-5.fc45.ppc64le libfsverity-1.7-4.fc45.ppc64le libgcc-16.1.1-4.fc45.1.ppc64le libgcrypt-1.12.2-2.fc45.ppc64le libgomp-16.1.1-4.fc45.1.ppc64le libgpg-error-1.61-2.fc45.ppc64le libidn2-2.3.8-4.fc45.ppc64le libksba-1.8.0-3.fc45.ppc64le liblastlog2-2.42.2-3.fc45.ppc64le libmount-2.42.2-3.fc45.ppc64le libnghttp2-1.69.0-4.fc45.ppc64le libnghttp3-1.18.0-1.fc45.ppc64le libpkgconf-2.5.1-2.fc45.ppc64le libpsl-0.23.1-1.fc45.ppc64le librtas-2.0.7-2.fc45.ppc64le libselinux-3.11-3.fc45.ppc64le libselinux-utils-3.11-3.fc45.ppc64le libsemanage-3.11-3.fc45.ppc64le libsepol-3.11-2.fc45.ppc64le libsmartcols-2.42.2-3.fc45.ppc64le libssh-0.12.2-1.fc45.ppc64le libssh-config-0.12.2-1.fc45.noarch libstdc++-16.1.1-4.fc45.1.ppc64le libtasn1-4.21.0-2.fc45.ppc64le libtool-ltdl-2.5.4-11.fc45.ppc64le libunistring-1.1-12.fc45.ppc64le libusb1-1.0.30-2.fc45.ppc64le libuuid-2.42.2-3.fc45.ppc64le libverto-0.3.2-13.fc45.ppc64le libxcrypt-4.5.2-4.fc45.ppc64le libxml2-2.13.9-4.fc45.ppc64le libzstd-1.5.7-6.fc45.ppc64le linkdupes-0.7.3-3.fc45.ppc64le lua-libs-5.5.0-3.fc45.ppc64le lua-srpm-macros-1-18.fc45.noarch lz4-libs-1.10.0-5.fc45.ppc64le mpfr-4.2.2-4.fc45.ppc64le ncurses-base-6.6-3.fc45.noarch ncurses-libs-6.6-3.fc45.ppc64le nettle-4.0-5.fc45.ppc64le ngtcp2-1.22.1-3.fc45.ppc64le ngtcp2-crypto-ossl-1.22.1-3.fc45.ppc64le npth-1.8-5.fc45.ppc64le ocaml-srpm-macros-11-4.fc45.noarch openblas-srpm-macros-2-22.fc45.noarch openldap-2.6.13-4.fc45.ppc64le openssl-libs-4.0.1-5.fc45.ppc64le p11-kit-0.26.4-2.fc45.ppc64le p11-kit-trust-0.26.4-2.fc45.ppc64le package-notes-srpm-macros-0.20-2.fc45.noarch pam-libs-1.7.2-4.fc45.ppc64le patch-2.8-5.fc45.ppc64le pcre2-10.47-1.fc45.2.ppc64le pcre2-syntax-10.47-1.fc45.2.noarch perl-srpm-macros-1-65.fc45.noarch pkgconf-2.5.1-2.fc45.ppc64le pkgconf-m4-2.5.1-2.fc45.noarch pkgconf-pkg-config-2.5.1-2.fc45.ppc64le policycoreutils-3.11-2.fc45.ppc64le popt-1.19-11.fc45.ppc64le publicsuffix-list-dafsa-20260624-2.fc45.noarch pyproject-srpm-macros-1.23.2-1.fc45.noarch python-srpm-macros-3.15-2.fc45.noarch qt5-srpm-macros-5.15.18-3.fc45.noarch qt6-srpm-macros-6.11.1-2.fc45.noarch readline-8.3-5.fc45.ppc64le redhat-rpm-config-344-5.fc45.noarch redhat-systemd-presets-102-3.fc45.noarch redhat-systemd-presets-common-102-3.fc45.noarch rpm-6.0.92-2.fc45.ppc64le rpm-build-6.0.92-2.fc45.ppc64le rpm-build-libs-6.0.92-2.fc45.ppc64le rpm-libs-6.0.92-2.fc45.ppc64le rpm-plugin-selinux-6.0.92-2.fc45.ppc64le rpm-sequoia-1.10.2-5.fc45.ppc64le rpm-sign-libs-6.0.92-2.fc45.ppc64le rust-srpm-macros-28.5-2.fc45.noarch sed-4.10-2.fc45.ppc64le selinux-policy-45.10-1.fc45.noarch selinux-policy-targeted-45.10-1.fc45.noarch setup-2.15.1-2.fc45.noarch shadow-utils-4.20.0-1.fc45.ppc64le sqlite-libs-3.53.4-1.fc45.ppc64le systemd-libs-261.2-1.fc45.ppc64le systemd-standalone-sysusers-261.2-1.fc45.ppc64le tar-1.35-9.fc45.ppc64le tpm2-tss-4.2.0-1.fc45.ppc64le tree-sitter-srpm-macros-0.4.6-2.fc45.noarch unzip-6.0-71.fc45.ppc64le util-linux-2.42.2-3.fc45.ppc64le util-linux-core-2.42.2-3.fc45.ppc64le which-2.25-2.fc45.ppc64le xxhash-libs-0.8.3-5.fc45.ppc64le xz-5.8.3-2.fc45.ppc64le xz-libs-5.8.3-2.fc45.ppc64le zig-srpm-macros-1-9.fc45.noarch zip-3.0-46.fc45.ppc64le zlib-ng-compat-2.3.3-6.fc45.ppc64le zstd-1.5.7-6.fc45.ppc64le Start: buildsrpm Start: rpmbuild -bs Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1785110400 Wrote: /builddir/build/SRPMS/apbs-3.0.0-38.fc45.src.rpm Finish: rpmbuild -bs INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-ppc64le-1785937922.137901/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-bw8d8wqg/apbs/apbs.spec) Config(child) 0 minutes 52 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot INFO: Start(/var/lib/copr-rpmbuild/results/apbs-3.0.0-38.fc45.src.rpm) Config(fedora-rawhide-ppc64le) Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1785937922.137901/root. INFO: reusing tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-bootstrap-1785937922.137901/root. INFO: calling preinit hooks INFO: enabled root cache INFO: enabled package manager cache Start(bootstrap): cleaning package manager metadata Finish(bootstrap): cleaning package manager metadata Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/fedora-rawhide-ppc64le-1785937922.137901/root. INFO: calling preinit hooks INFO: enabled root cache Start: unpacking root cache Finish: unpacking root cache INFO: enabled package manager cache Start: cleaning package manager metadata Finish: cleaning package manager metadata INFO: enabled HW Info plugin INFO: Buildroot is handled by package management downloaded with a bootstrap image: rpm-6.0.92-2.fc45.ppc64le rpm-sequoia-1.10.2-5.fc45.ppc64le dnf5-5.4.2.1-10.fc45.ppc64le dnf5-plugins-5.4.2.1-10.fc45.ppc64le Finish: chroot init Start: build phase for apbs-3.0.0-38.fc45.src.rpm Start: build setup for apbs-3.0.0-38.fc45.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1785110400 Wrote: /builddir/build/SRPMS/apbs-3.0.0-38.fc45.src.rpm Updating and loading repositories: fedora 100% | 6.0 KiB/s | 2.9 KiB | 00m00s Copr repository 100% | 8.6 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package Arch Version Repository Size Installing: chrpath ppc64le 0:0.16-29.fc45 fedora 102.1 KiB cmake ppc64le 0:4.3.0-5.fc45 fedora 40.1 MiB doxygen ppc64le 2:1.17.0-3.fc45 fedora 22.0 MiB doxygen-latex noarch 2:1.17.0-3.fc45 fedora 0.0 B gcc-c++ ppc64le 0:16.1.1-4.fc45.1 fedora 44.0 MiB graphviz ppc64le 0:15.1.0-5.fc45 fedora 6.0 MiB make ppc64le 1:4.4.1-13.fc45 fedora 1.9 MiB maloc-devel ppc64le 0:1.5-36.fc45 fedora 2.9 MiB python3-devel ppc64le 0:3.15.0~b4-1.fc45 fedora 2.4 MiB python3-numpy ppc64le 1:2.5.1-3.fc45 fedora 40.7 MiB python3-sphinx noarch 1:9.1.0-7.fc45 fedora 14.1 MiB swig ppc64le 0:4.5.0-1.fc45 copr_base 6.8 MiB texlive-adjustbox noarch 12:svn78101-7.fc45 fedora 892.2 KiB texlive-collection-latexrecommended noarch 12:svn78568-4.fc45 fedora 0.0 B texlive-etoc noarch 12:svn78908-7.fc45 fedora 1.2 MiB texlive-hanging noarch 12:svn77682-7.fc45 fedora 188.1 KiB texlive-multirow noarch 12:svn77682-7.fc45 fedora 652.7 KiB texlive-newunicodechar noarch 12:svn77682-7.fc45 fedora 403.6 KiB texlive-sectsty noarch 12:svn77682-7.fc45 fedora 267.6 KiB texlive-stackengine noarch 12:svn75878-7.fc45 fedora 470.6 KiB texlive-tocloft noarch 12:svn77682-7.fc45 fedora 550.3 KiB texlive-ulem noarch 12:svn77682-5.fc45 fedora 186.8 KiB texlive-wasy noarch 12:svn53533-9.fc45 fedora 469.9 KiB texlive-wasysym noarch 12:svn77682-9.fc45 fedora 194.0 KiB zlib-ng-compat-devel ppc64le 0:2.3.3-6.fc45 fedora 107.0 KiB Installing dependencies: aalib-libs ppc64le 0:1.4.0-0.59.rc5.fc45 fedora 231.1 KiB abattis-cantarell-vf-fonts noarch 0:0.301-18.fc45 fedora 192.7 KiB adobe-mappings-cmap noarch 0:20231115-6.fc45 fedora 15.2 MiB adobe-mappings-cmap-deprecated noarch 0:20231115-6.fc45 fedora 582.1 KiB adobe-mappings-pdf noarch 0:20190401-13.fc45 fedora 4.4 MiB annobin-docs noarch 0:13.28-1.fc45 fedora 99.7 KiB annobin-plugin-gcc ppc64le 0:13.28-1.fc45 fedora 785.3 KiB avahi-libs ppc64le 0:0.9~rc2-9.fc45 fedora 293.3 KiB biber noarch 0:2.21-5.fc45 fedora 1.4 MiB bubblewrap ppc64le 0:0.11.2-2.fc45 fedora 182.7 KiB cairo ppc64le 0:1.18.4-9.fc45 fedora 2.1 MiB cairo-gobject ppc64le 0:1.18.4-9.fc45 fedora 66.8 KiB clang-libs ppc64le 0:22.1.8-20.fc45 fedora 117.5 MiB clang-resource-filesystem ppc64le 0:22.1.8-20.fc45 fedora 15.3 KiB cmake-data noarch 0:4.3.0-5.fc45 fedora 9.4 MiB cmake-filesystem ppc64le 0:4.3.0-5.fc45 fedora 0.0 B cmake-rpm-macros noarch 0:4.3.0-5.fc45 fedora 8.4 KiB cpp ppc64le 0:16.1.1-4.fc45.1 fedora 39.1 MiB cups-filesystem noarch 1:2.4.19-4.fc45 fedora 0.0 B cups-libs ppc64le 1:2.4.19-4.fc45 fedora 922.6 KiB dblatex noarch 0:0.3.12-33.fc45 fedora 5.2 MiB dbus-libs ppc64le 1:1.16.2-6.fc45 fedora 461.7 KiB default-fonts-core-sans noarch 0:4.3-3.fc45 fedora 11.9 KiB desktop-file-utils ppc64le 0:0.28-8.fc45 fedora 381.8 KiB docbook-dtds noarch 0:1.0-92.fc45 fedora 6.7 MiB emacs-filesystem ppc64le 1:30.2-3.fc45 fedora 0.0 B expat ppc64le 0:2.8.1-2.fc45 fedora 435.2 KiB flexiblas ppc64le 0:3.5.0-3.fc45 fedora 38.0 KiB flexiblas-netlib ppc64le 0:3.5.0-3.fc45 fedora 18.9 MiB flexiblas-openblas-openmp ppc64le 0:3.5.0-3.fc45 fedora 66.7 KiB fmt ppc64le 0:12.1.0-3.fc45 fedora 400.4 KiB fontconfig ppc64le 0:2.18.2-6.fc45 fedora 1.7 MiB fonts-filesystem noarch 1:5.0.0-4.fc45 fedora 0.0 B freetype ppc64le 0:2.14.3-2.fc45 fedora 1.1 MiB fribidi ppc64le 0:1.0.16-5.fc45 fedora 245.8 KiB gcc ppc64le 0:16.1.1-4.fc45.1 fedora 107.1 MiB gcc-plugin-annobin ppc64le 0:16.1.1-4.fc45.1 fedora 132.8 KiB gdk-pixbuf2 ppc64le 0:2.44.7-3.fc45 fedora 2.7 MiB ghostscript ppc64le 0:10.07.1-2.fc45 fedora 86.6 KiB ghostscript-tools-dvipdf noarch 0:10.07.1-2.fc45 fedora 1.4 KiB ghostscript-tools-fontutils noarch 0:10.07.1-2.fc45 fedora 2.5 KiB ghostscript-tools-printing noarch 0:10.07.1-2.fc45 fedora 3.5 KiB glib2 ppc64le 0:2.89.3-1.fc45 fedora 16.8 MiB glibc-devel ppc64le 0:2.44-1.fc45 fedora 3.7 MiB glycin-libs ppc64le 0:2.1.5-2.fc45 fedora 5.8 MiB glycin-loaders ppc64le 0:2.1.5-2.fc45 fedora 20.4 MiB gobject-introspection ppc64le 0:1.86.0-11.fc45 fedora 445.2 KiB google-droid-sans-fonts noarch 0:20200215-25.fc45 fedora 6.3 MiB google-noto-fonts-common noarch 0:20260601-3.fc45 fedora 17.7 KiB google-noto-sans-vf-fonts noarch 0:20260601-3.fc45 fedora 1.4 MiB gpgme ppc64le 0:2.0.1-6.fc45 fedora 889.0 KiB gpgmepp ppc64le 1:2.0.0-2.fc45 fedora 694.7 KiB gpm-libs ppc64le 0:1.20.7-54.fc45 fedora 67.4 KiB graphite2 ppc64le 0:1.3.14-22.fc45 fedora 302.9 KiB graphviz-libs ppc64le 0:15.1.0-5.fc45 fedora 1.7 MiB groff-base ppc64le 0:1.24.1-2.fc45 fedora 4.8 MiB gts ppc64le 0:0.7.6-53.20121130.fc45 fedora 1.1 MiB harfbuzz ppc64le 0:14.3.0-1.fc45 fedora 3.3 MiB highway ppc64le 0:1.3.0-3.fc45 fedora 1.5 MiB hostname ppc64le 0:3.25-5.fc45 fedora 89.1 KiB jbig2dec-libs ppc64le 0:0.20-9.fc45 fedora 236.8 KiB jbigkit-libs ppc64le 0:2.1-34.fc45 fedora 180.7 KiB js-doxygen noarch 2:1.17.0-3.fc45 fedora 235.3 KiB jsoncpp ppc64le 0:1.9.6-3.fc44 fedora 335.6 KiB kernel-headers ppc64le 0:7.2.0-0.rc6.48.fc45 fedora 7.0 MiB lasi ppc64le 0:1.1.3-19.fc45 fedora 130.2 KiB latexmk noarch 0:4.88-2.fc45 fedora 1.0 MiB lcms2 ppc64le 0:2.16-8.fc45 fedora 548.9 KiB libICE ppc64le 0:1.1.2-5.fc45 fedora 222.2 KiB libSM ppc64le 0:1.2.5-5.fc45 fedora 128.8 KiB libX11 ppc64le 0:1.8.13-2.fc45 fedora 1.6 MiB libX11-common noarch 0:1.8.13-2.fc45 fedora 1.1 MiB libXau ppc64le 0:1.0.12-5.fc45 fedora 120.5 KiB libXaw ppc64le 0:1.0.16-6.fc45 fedora 614.8 KiB libXext ppc64le 0:1.3.6-6.fc45 fedora 145.7 KiB libXft ppc64le 0:2.3.8-11.fc45 fedora 192.2 KiB libXi ppc64le 0:1.8.3-2.fc45 fedora 136.3 KiB libXmu ppc64le 0:1.2.1-6.fc45 fedora 326.6 KiB libXpm ppc64le 0:3.5.19-4.fc45 fedora 212.5 KiB libXrender ppc64le 0:0.9.12-5.fc45 fedora 69.8 KiB libXt ppc64le 0:1.3.1-5.fc45 fedora 541.4 KiB libaom ppc64le 0:3.13.3-3.fc45 fedora 3.5 MiB libasan ppc64le 0:16.1.1-4.fc45.1 fedora 2.2 MiB libatomic ppc64le 0:16.1.1-4.fc45.1 fedora 77.0 KiB libdatrie ppc64le 0:0.2.14-3.fc45 fedora 93.4 KiB libdav1d ppc64le 0:1.5.3-2.fc45 fedora 978.9 KiB libedit ppc64le 0:3.1-60.20260512cvs.fc45 fedora 344.3 KiB libgfortran ppc64le 0:16.1.1-4.fc45.1 fedora 2.8 MiB libgs ppc64le 0:10.07.1-2.fc45 fedora 25.7 MiB libheif ppc64le 0:1.21.2-8.fc45 fedora 2.1 MiB libicu ppc64le 0:78.3-8.fc45 fedora 39.2 MiB libijs ppc64le 0:0.35-27.fc45 fedora 101.4 KiB libjpeg-turbo ppc64le 0:3.1.4.1-2.fc45 fedora 873.4 KiB libjxl ppc64le 1:0.11.2-2.fc45 fedora 3.7 MiB liblerc ppc64le 0:4.2.0-1.fc45 fedora 739.5 KiB libmpc ppc64le 0:1.4.1-2.fc45 fedora 281.6 KiB libopenjph ppc64le 0:0.29.0-2.fc45 fedora 389.7 KiB libpaper ppc64le 1:2.1.1-11.fc45 fedora 96.4 KiB libpng ppc64le 2:1.6.58-2.fc45 fedora 333.6 KiB libquadmath ppc64le 0:16.1.1-4.fc45.1 fedora 426.5 KiB librsvg2 ppc64le 0:2.62.3-3.fc45 fedora 6.1 MiB libseccomp ppc64le 0:2.6.1-3.fc45 fedora 310.1 KiB libstdc++-devel ppc64le 0:16.1.1-4.fc45.1 fedora 41.1 MiB libthai ppc64le 0:0.1.30-3.fc45 fedora 824.8 KiB libtiff ppc64le 0:4.7.2-2.fc45 fedora 787.0 KiB libubsan ppc64le 0:16.1.1-4.fc45.1 fedora 668.9 KiB libuv ppc64le 1:1.52.1-2.fc45 fedora 680.4 KiB libwebp ppc64le 0:1.6.0-4.fc45 fedora 943.5 KiB libxcb ppc64le 0:1.17.0-8.fc45 fedora 2.2 MiB libxcrypt-devel ppc64le 0:4.5.2-4.fc45 fedora 31.0 KiB libxslt ppc64le 0:1.1.43-9.fc45 fedora 611.7 KiB llvm-filesystem ppc64le 0:22.1.8-20.fc45 fedora 0.0 B llvm-libs ppc64le 0:22.1.8-20.fc45 fedora 150.3 MiB lzo ppc64le 0:2.10-17.fc45 fedora 226.5 KiB mailcap noarch 0:2.1.54-11.fc45 fedora 86.0 KiB maloc ppc64le 0:1.5-36.fc45 fedora 326.4 KiB mpdecimal ppc64le 0:4.0.1-4.fc45 fedora 281.1 KiB ncurses ppc64le 0:6.6-3.fc45 fedora 958.6 KiB netpbm ppc64le 0:11.14-2.fc45 fedora 641.2 KiB ninja-build ppc64le 0:1.13.2-6.fc45 fedora 532.7 KiB noopenh264 ppc64le 0:2.6.0-5.fc45 fedora 94.7 KiB nspr ppc64le 0:4.39.0-5.fc45 fedora 548.0 KiB nss ppc64le 0:3.126.0-1.fc45 fedora 2.4 MiB nss-softokn ppc64le 0:3.126.0-1.fc45 fedora 2.6 MiB nss-softokn-freebl ppc64le 0:3.126.0-1.fc45 fedora 1.0 MiB nss-sysinit ppc64le 0:3.126.0-1.fc45 fedora 69.8 KiB nss-util ppc64le 0:3.126.0-1.fc45 fedora 280.8 KiB openblas ppc64le 0:0.3.34-1.fc45 fedora 138.1 KiB openblas-openmp ppc64le 0:0.3.34-1.fc45 fedora 23.4 MiB openjpeg ppc64le 0:2.5.4-4.fc45 fedora 540.2 KiB pango ppc64le 0:1.58.0-2.fc45 fedora 1.5 MiB perl-Authen-SASL noarch 0:2.2000-2.fc45 fedora 133.1 KiB perl-AutoLoader noarch 0:5.74-527.fc45 fedora 20.6 KiB perl-B ppc64le 0:1.92-527.fc45 fedora 557.4 KiB perl-B-Hooks-EndOfScope noarch 0:0.28-6.fc45 fedora 69.3 KiB perl-Business-ISBN noarch 0:3.014-2.fc45 fedora 56.1 KiB perl-Business-ISBN-Data noarch 0:20260804.001-1.fc45 fedora 308.9 KiB perl-Business-ISMN noarch 0:1.205-4.fc45 fedora 36.7 KiB perl-Business-ISSN noarch 0:1.008-4.fc45 fedora 21.7 KiB perl-Carp noarch 0:1.54-527.fc45 fedora 46.6 KiB perl-Class-Accessor noarch 0:0.51-25.fc45 fedora 40.8 KiB perl-Class-Data-Inheritable noarch 0:0.10-5.fc45 fedora 6.3 KiB perl-Class-Inspector noarch 0:1.36-21.fc45 fedora 57.5 KiB perl-Class-Method-Modifiers noarch 0:2.15-9.fc45 fedora 102.5 KiB perl-Class-Singleton noarch 0:1.6-16.fc45 fedora 39.7 KiB perl-Class-Struct noarch 0:0.68-527.fc45 fedora 25.4 KiB perl-Clone ppc64le 0:0.50-3.fc45 fedora 101.0 KiB perl-Clone-PP noarch 0:1.08-16.fc45 fedora 12.9 KiB perl-Compress-Raw-Bzip2 ppc64le 0:2.218-527.fc45 fedora 104.4 KiB perl-Compress-Raw-Zlib ppc64le 0:2.222-528.fc45 fedora 232.0 KiB perl-Convert-ASN1 noarch 0:0.34-8.fc45 fedora 170.0 KiB perl-Crypt-URandom ppc64le 0:0.55-3.fc45 fedora 116.8 KiB perl-Data-Compare noarch 0:1.29-9.fc45 fedora 55.5 KiB perl-Data-Dump noarch 0:1.25-15.fc45 fedora 50.2 KiB perl-Data-Dumper ppc64le 0:2.192-528.fc45 fedora 135.2 KiB perl-Data-OptList noarch 0:0.114-9.fc45 fedora 50.1 KiB perl-Data-Uniqid noarch 0:0.12-39.fc45 fedora 4.2 KiB perl-Date-ISO8601 noarch 0:0.005-25.fc45 fedora 24.5 KiB perl-Date-Manip noarch 0:6.99-2.fc45 fedora 10.8 MiB perl-DateTime ppc64le 2:1.66-7.fc45 fedora 427.0 KiB perl-DateTime-Calendar-Julian noarch 0:0.107-13.fc45 fedora 32.8 KiB perl-DateTime-Format-Builder noarch 0:0.8300-18.fc45 fedora 202.3 KiB perl-DateTime-Format-Strptime noarch 1:1.80-3.fc45 fedora 96.5 KiB perl-DateTime-Locale noarch 0:1.45-4.fc45 fedora 22.8 MiB perl-DateTime-TimeZone noarch 0:2.69-3.fc45 fedora 6.1 MiB perl-DateTime-TimeZone-SystemV noarch 0:0.010-26.fc45 fedora 28.4 KiB perl-DateTime-TimeZone-Tzfile noarch 0:0.011-26.fc45 fedora 24.6 KiB perl-Devel-CallChecker ppc64le 0:0.009-13.fc45 fedora 88.7 KiB perl-Devel-Caller ppc64le 0:2.07-13.fc45 fedora 79.0 KiB perl-Devel-GlobalDestruction noarch 0:0.14-29.fc45 fedora 16.6 KiB perl-Devel-LexAlias ppc64le 0:0.05-44.fc45 fedora 70.7 KiB perl-Devel-StackTrace noarch 1:2.05-8.fc45 fedora 48.9 KiB perl-Digest noarch 0:1.20-527.fc45 fedora 35.2 KiB perl-Digest-HMAC noarch 0:1.05-5.fc45 fedora 29.5 KiB perl-Digest-MD5 ppc64le 0:2.59-527.fc45 fedora 103.2 KiB perl-Digest-SHA ppc64le 1:6.04-528.fc45 fedora 136.0 KiB perl-Dist-CheckConflicts noarch 0:0.11-35.fc45 fedora 31.7 KiB perl-DynaLoader ppc64le 0:1.57-527.fc45 fedora 32.1 KiB perl-DynaLoader-Functions noarch 0:0.004-9.fc45 fedora 19.7 KiB perl-Email-Date-Format noarch 0:1.008-9.fc45 fedora 24.8 KiB perl-Encode ppc64le 4:3.24-527.fc45 fedora 4.8 MiB perl-Encode-Locale noarch 0:1.05-34.fc45 fedora 19.0 KiB perl-English noarch 0:1.12-527.fc45 fedora 6.2 KiB perl-Errno ppc64le 0:1.39-527.fc45 fedora 8.4 KiB perl-Eval-Closure noarch 0:0.14-28.fc45 fedora 33.3 KiB perl-Exception-Class noarch 0:1.45-15.fc45 fedora 92.4 KiB perl-Exporter noarch 0:5.79-527.fc45 fedora 54.2 KiB perl-ExtUtils-MM-Utils noarch 2:7.78-527.fc45 fedora 2.9 KiB perl-Fcntl ppc64le 0:1.20-527.fc45 fedora 92.3 KiB perl-File-Basename noarch 0:2.86-527.fc45 fedora 14.0 KiB perl-File-Compare noarch 0:1.100.800-527.fc45 fedora 5.6 KiB perl-File-Copy noarch 0:2.43-527.fc45 fedora 19.6 KiB perl-File-Find noarch 0:1.44-527.fc45 fedora 42.0 KiB perl-File-Find-Rule noarch 0:0.35-4.fc45 fedora 42.4 KiB perl-File-Listing noarch 0:6.16-8.fc45 fedora 41.2 KiB perl-File-Path noarch 0:2.18-527.fc45 fedora 63.4 KiB perl-File-ShareDir noarch 0:1.118-16.fc45 fedora 56.2 KiB perl-File-Slurper noarch 0:0.014-10.fc45 fedora 28.7 KiB perl-File-Temp noarch 1:0.231.200-527.fc45 fedora 163.7 KiB perl-File-stat noarch 0:1.15-527.fc45 fedora 13.7 KiB perl-FileHandle noarch 0:2.05-527.fc45 fedora 9.4 KiB perl-Filter ppc64le 2:1.65-527.fc45 fedora 363.4 KiB perl-FindBin noarch 0:1.54-527.fc45 fedora 6.8 KiB perl-GSSAPI ppc64le 0:0.28-53.fc45 fedora 176.6 KiB perl-Getopt-Long noarch 1:2.58-527.fc45 fedora 144.5 KiB perl-Getopt-Std noarch 0:1.15-527.fc45 fedora 12.5 KiB perl-Getopt-Tabular noarch 0:0.3-41.fc45 fedora 86.8 KiB perl-HTML-Parser ppc64le 0:3.85-3.fc45 fedora 291.9 KiB perl-HTML-Tagset noarch 0:3.24-6.fc45 fedora 18.7 KiB perl-HTTP-Cookies noarch 0:6.11-8.fc45 fedora 73.4 KiB perl-HTTP-Date noarch 0:6.08-2.fc45 fedora 44.3 KiB perl-HTTP-Message noarch 0:7.04-1.fc45 fedora 216.6 KiB perl-HTTP-Negotiate noarch 0:6.01-43.fc45 fedora 27.6 KiB perl-HTTP-Tiny noarch 0:0.096-528.fc45 fedora 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texlive-dehyph noarch 12:svn48599-8.fc45 fedora 239.9 KiB texlive-diagbox noarch 12:svn77682-7.fc45 fedora 272.2 KiB texlive-dvipdfmx ppc64le 12:svn77942-113.fc45 fedora 3.8 MiB texlive-dvips ppc64le 12:svn77830-113.fc45 fedora 1.7 MiB texlive-ec noarch 12:svn25033-12.fc45 fedora 2.5 MiB texlive-eepic noarch 12:svn77682-4.fc45 fedora 194.5 KiB texlive-enctex noarch 12:svn34957-12.fc45 fedora 572.4 KiB texlive-enumitem noarch 12:svn77682-7.fc45 fedora 268.0 KiB texlive-environ noarch 12:svn77682-7.fc45 fedora 175.8 KiB texlive-epstopdf noarch 12:svn71782-113.fc45 fedora 45.6 KiB texlive-epstopdf-pkg noarch 12:svn77682-5.fc45 fedora 386.5 KiB texlive-eso-pic noarch 12:svn77682-4.fc45 fedora 329.7 KiB texlive-etex noarch 12:svn77830-12.fc45 fedora 519.4 KiB texlive-etex-pkg noarch 12:svn77682-12.fc45 fedora 37.7 KiB texlive-etexcmds noarch 12:svn78101-5.fc45 fedora 321.0 KiB texlive-etoolbox noarch 12:svn77682-5.fc45 fedora 362.7 KiB texlive-euenc noarch 12:svn19795-4.fc45 fedora 187.7 KiB texlive-euler noarch 12:svn77682-4.fc45 fedora 277.5 KiB texlive-euro noarch 12:svn22191-9.fc45 fedora 262.0 KiB texlive-euro-ce noarch 12:svn25714-9.fc45 fedora 41.5 KiB texlive-eurosym noarch 12:svn78101-9.fc45 fedora 522.3 KiB texlive-everyhook noarch 12:svn35675-7.fc45 fedora 138.3 KiB texlive-everysel noarch 12:svn57489-4.fc45 fedora 457.9 KiB texlive-everyshi noarch 12:svn77682-4.fc45 fedora 157.4 KiB texlive-extractbb noarch 12:svn77855-113.fc45 fedora 40.7 KiB texlive-extsizes noarch 12:svn78101-4.fc45 fedora 344.1 KiB texlive-fancybox noarch 12:svn77682-4.fc45 fedora 366.5 KiB texlive-fancyhdr noarch 12:svn78348-5.fc45 fedora 1.3 MiB texlive-fancyref noarch 12:svn77682-4.fc45 fedora 172.5 KiB texlive-fancyvrb noarch 12:svn78721-4.fc45 fedora 289.6 KiB texlive-fandol noarch 12:svn37889-9.fc45 fedora 33.3 MiB texlive-filehook noarch 12:svn77682-4.fc45 fedora 364.6 KiB texlive-finstrut noarch 12:svn21719-7.fc45 fedora 231.6 KiB texlive-firstaid noarch 12:svn76740-5.fc45 fedora 334.7 KiB texlive-fix2col noarch 12:svn38770-5.fc45 fedora 234.4 KiB texlive-fixlatvian noarch 12:svn21631-11.fc45 fedora 193.7 KiB texlive-float noarch 12:svn77682-4.fc45 fedora 160.2 KiB texlive-fmtcount noarch 12:svn77682-7.fc45 fedora 882.7 KiB texlive-fnpara noarch 12:svn25607-7.fc45 fedora 202.9 KiB texlive-font-change-xetex noarch 12:svn40404-11.fc45 fedora 691.6 KiB texlive-fontbook noarch 12:svn23608-11.fc45 fedora 1.5 MiB texlive-fonts-tlwg noarch 12:svn78431-5.fc45 fedora 8.5 MiB texlive-fontspec noarch 12:svn77682-4.fc45 fedora 1.5 MiB texlive-fontwrap noarch 12:svn15878-11.fc45 fedora 386.8 KiB texlive-footmisc noarch 12:svn77682-7.fc45 fedora 732.1 KiB texlive-footnotehyper noarch 12:svn77682-4.fc45 fedora 116.1 KiB texlive-fp noarch 12:svn77682-4.fc45 fedora 361.0 KiB texlive-fpl noarch 12:svn54512-9.fc45 fedora 692.3 KiB texlive-garuda-c90 noarch 12:svn60832-7.fc45 fedora 33.6 KiB texlive-gensymb noarch 12:svn77682-7.fc45 fedora 257.7 KiB texlive-geometry noarch 12:svn78315-5.fc45 fedora 1.0 MiB texlive-gettitlestring noarch 12:svn77682-5.fc45 fedora 338.8 KiB texlive-glyphlist noarch 12:svn54074-113.fc45 fedora 90.3 KiB texlive-graphics noarch 12:svn78282-5.fc45 fedora 3.1 MiB texlive-graphics-cfg noarch 12:svn41448-5.fc45 fedora 4.0 KiB texlive-graphics-def noarch 12:svn76719-12.fc45 fedora 99.7 KiB texlive-grfext noarch 12:svn77682-5.fc45 fedora 327.8 KiB texlive-grffile noarch 12:svn78101-4.fc45 fedora 379.3 KiB texlive-gsftopk ppc64le 12:svn52851-113.fc45 fedora 78.8 KiB texlive-helvetic noarch 12:svn77161-9.fc45 fedora 1.7 MiB texlive-hologo noarch 12:svn78580-4.fc45 fedora 672.9 KiB texlive-hopatch noarch 12:svn65491-5.fc45 fedora 345.8 KiB texlive-hycolor noarch 12:svn77682-5.fc45 fedora 411.7 KiB texlive-hypcap noarch 12:svn77682-5.fc45 fedora 316.8 KiB texlive-hypdoc noarch 12:svn68661-7.fc45 fedora 359.9 KiB texlive-hyperref noarch 12:svn78811-5.fc45 fedora 5.4 MiB texlive-hyph-utf8 noarch 12:svn78069-12.fc45 fedora 388.3 KiB texlive-hyphen-base noarch 12:svn78076-12.fc45 fedora 83.0 KiB texlive-hyphen-english noarch 12:svn78069-7.fc45 fedora 177.2 KiB texlive-hyphenex noarch 12:svn57387-12.fc45 fedora 26.3 KiB texlive-ifmtarg noarch 12:svn77682-7.fc45 fedora 56.1 KiB texlive-ifoddpage noarch 12:svn77682-7.fc45 fedora 163.4 KiB texlive-ifplatform noarch 12:svn77682-12.fc45 fedora 171.0 KiB texlive-iftex noarch 12:svn77682-12.fc45 fedora 266.4 KiB texlive-import noarch 12:svn77682-7.fc45 fedora 249.7 KiB texlive-index noarch 12:svn77682-4.fc45 fedora 323.1 KiB texlive-infwarerr noarch 12:svn77682-4.fc45 fedora 306.3 KiB texlive-intcalc noarch 12:svn77682-5.fc45 fedora 471.6 KiB texlive-interchar noarch 12:svn77682-11.fc45 fedora 143.7 KiB texlive-ipaex noarch 12:svn61719-6.fc45 fedora 40.6 MiB texlive-japanese-otf noarch 12:svn78329-6.fc45 fedora 42.4 MiB texlive-jknapltx noarch 12:svn19440-4.fc45 fedora 55.9 KiB texlive-knuth-lib noarch 12:svn57963-12.fc45 fedora 99.9 KiB texlive-knuth-local noarch 12:svn57963-12.fc45 fedora 106.1 KiB texlive-koma-script noarch 12:svn77575-4.fc45 fedora 14.9 MiB texlive-kotex-utf noarch 12:svn63690-6.fc45 fedora 11.1 MiB texlive-kpathsea ppc64le 12:svn77861-113.fc45 fedora 2.3 MiB texlive-kvdefinekeys noarch 12:svn77682-5.fc45 fedora 314.2 KiB texlive-kvoptions noarch 12:svn77682-5.fc45 fedora 550.0 KiB texlive-kvsetkeys noarch 12:svn77682-5.fc45 fedora 427.4 KiB texlive-l3backend noarch 12:svn78544-5.fc45 fedora 1.1 MiB texlive-l3backend-dev noarch 12:svn77954-7.fc45 fedora 1.1 MiB texlive-l3experimental noarch 12:svn78549-4.fc45 fedora 1.6 MiB texlive-l3kernel noarch 12:svn78545-5.fc45 fedora 15.2 MiB texlive-l3kernel-dev noarch 12:svn78876-7.fc45 fedora 15.2 MiB texlive-l3packages noarch 12:svn76637-5.fc45 fedora 1.9 MiB texlive-lastpage noarch 12:svn77682-7.fc45 fedora 633.5 KiB texlive-latex noarch 12:svn76924-113.fc45 fedora 48.8 MiB texlive-latex-base-dev noarch 12:svn78934-7.fc45 fedora 51.4 MiB texlive-latex-firstaid-dev noarch 12:svn78934-7.fc45 fedora 336.3 KiB texlive-latex-fonts noarch 12:svn28888-5.fc45 fedora 125.5 KiB texlive-latex-lab noarch 12:svn76739-5.fc45 fedora 16.5 MiB texlive-latexbug noarch 12:svn78389-4.fc45 fedora 285.9 KiB texlive-latexconfig noarch 12:svn68923-5.fc45 fedora 22.8 KiB texlive-letltxmacro noarch 12:svn77682-5.fc45 fedora 311.2 KiB texlive-lettrine noarch 12:svn77053-7.fc45 fedora 641.0 KiB texlive-lib ppc64le 12:20260301-113.fc45 fedora 734.7 KiB texlive-linegoal noarch 12:svn21523-7.fc45 fedora 210.4 KiB texlive-lineno noarch 12:svn78315-4.fc45 fedora 1.2 MiB texlive-listings noarch 12:svn77682-4.fc45 fedora 4.4 MiB texlive-listofitems noarch 12:svn77682-5.fc45 fedora 518.1 KiB texlive-lm noarch 12:svn77682-9.fc45 fedora 42.8 MiB texlive-lm-math noarch 12:svn67718-9.fc45 fedora 847.5 KiB texlive-logreq noarch 12:svn53003-9.fc45 fedora 53.5 KiB texlive-ltablex noarch 12:svn77682-7.fc45 fedora 254.2 KiB texlive-ltabptch noarch 12:svn17533-7.fc45 fedora 312.8 KiB texlive-ltx-talk noarch 12:svn78710-4.fc45 fedora 1.2 MiB texlive-ltxcmds noarch 12:svn77682-5.fc45 fedora 446.5 KiB texlive-ltxmisc noarch 12:svn75878-5.fc45 fedora 80.9 KiB texlive-lua-alt-getopt noarch 12:svn78415-12.fc45 fedora 14.9 KiB texlive-lua-uni-algos noarch 12:svn76195-5.fc45 fedora 160.1 KiB texlive-lua-unicode-math noarch 12:svn78498-4.fc45 fedora 258.9 KiB texlive-luabidi noarch 12:svn78654-7.fc45 fedora 188.0 KiB texlive-luacode noarch 12:svn78415-4.fc45 fedora 426.8 KiB texlive-luahbtex ppc64le 12:svn77830-113.fc45 fedora 7.3 MiB texlive-lualatex-math noarch 12:svn77682-4.fc45 fedora 233.0 KiB texlive-lualibs noarch 12:svn78415-4.fc45 fedora 885.6 KiB texlive-luaotfload noarch 12:svn74324-113.fc45 fedora 8.2 MiB texlive-luatex ppc64le 12:svn78218-113.fc45 fedora 10.2 MiB texlive-luatex85 noarch 12:svn77682-4.fc45 fedora 191.3 KiB texlive-luatexbase noarch 12:svn77682-4.fc45 fedora 288.6 KiB texlive-luatexja noarch 12:svn78752-6.fc45 fedora 5.6 MiB texlive-luatexko noarch 12:svn78005-4.fc45 fedora 509.6 KiB texlive-luatextra noarch 12:svn77682-4.fc45 fedora 312.4 KiB texlive-lwarp noarch 12:svn78111-113.fc45 fedora 4.8 MiB texlive-makecmds noarch 12:svn77682-7.fc45 fedora 152.9 KiB texlive-makeindex ppc64le 12:svn75712-113.fc45 fedora 518.4 KiB texlive-makerobust noarch 12:svn78101-7.fc45 fedora 84.5 KiB texlive-manfnt-font noarch 12:svn45777-9.fc45 fedora 42.5 KiB texlive-marvosym noarch 12:svn77682-9.fc45 fedora 671.5 KiB texlive-mathpazo noarch 12:svn77682-9.fc45 fedora 538.4 KiB texlive-mathspec noarch 12:svn77682-4.fc45 fedora 255.4 KiB texlive-mathtools noarch 12:svn78251-4.fc45 fedora 1.3 MiB texlive-mdwtools noarch 12:svn15878-4.fc45 fedora 2.1 MiB texlive-memoir noarch 12:svn77682-4.fc45 fedora 4.8 MiB texlive-metafont ppc64le 12:svn77830-113.fc45 fedora 1.0 MiB texlive-metalogo noarch 12:svn77682-4.fc45 fedora 120.4 KiB texlive-mfirstuc noarch 12:svn77682-7.fc45 fedora 1.1 MiB texlive-mflogo noarch 12:svn77682-12.fc45 fedora 277.4 KiB texlive-mflogo-font noarch 12:svn54512-9.fc45 fedora 39.2 KiB texlive-mfnfss noarch 12:svn77682-5.fc45 fedora 505.2 KiB texlive-mfware ppc64le 12:svn77830-113.fc45 fedora 422.1 KiB texlive-microtype noarch 12:svn78228-4.fc45 fedora 3.1 MiB texlive-minifp noarch 12:svn76924-7.fc45 fedora 514.5 KiB texlive-minitoc noarch 12:svn77682-7.fc45 fedora 9.5 MiB texlive-mnsymbol noarch 12:svn18651-7.fc45 fedora 6.0 MiB texlive-modes noarch 12:svn77365-12.fc45 fedora 380.3 KiB texlive-mptopdf noarch 12:svn78010-113.fc45 fedora 151.3 KiB texlive-multido noarch 12:svn77682-5.fc45 fedora 163.1 KiB texlive-na-position noarch 12:svn55559-11.fc45 fedora 116.6 KiB texlive-natbib noarch 12:svn77682-5.fc45 fedora 622.8 KiB texlive-ncctools noarch 12:svn51810-7.fc45 fedora 3.1 MiB texlive-ncntrsbk noarch 12:svn77161-9.fc45 fedora 937.1 KiB texlive-newfloat noarch 12:svn77682-4.fc45 fedora 234.8 KiB texlive-ninecolors noarch 12:svn76924-7.fc45 fedora 97.9 KiB texlive-norasi-c90 noarch 12:svn60831-7.fc45 fedora 44.5 KiB texlive-notoccite noarch 12:svn77682-7.fc45 fedora 231.7 KiB texlive-ntgclass noarch 12:svn77239-4.fc45 fedora 2.4 MiB texlive-ntheorem noarch 12:svn77682-7.fc45 fedora 531.2 KiB texlive-oberdiek noarch 12:svn78315-113.fc45 fedora 11.2 MiB texlive-overpic noarch 12:svn77682-7.fc45 fedora 420.9 KiB texlive-pagesel noarch 12:svn77682-5.fc45 fedora 354.7 KiB texlive-palatino noarch 12:svn77161-9.fc45 fedora 1.1 MiB texlive-paralist noarch 12:svn77682-7.fc45 fedora 251.9 KiB texlive-parallel noarch 12:svn77682-8.fc45 fedora 177.1 KiB texlive-parskip noarch 12:svn77682-4.fc45 fedora 422.1 KiB texlive-passivetex noarch 12:svn69742-7.fc45 fedora 294.3 KiB texlive-pdfcol noarch 12:svn64469-7.fc45 fedora 345.6 KiB texlive-pdfcolfoot noarch 12:svn77682-4.fc45 fedora 335.8 KiB texlive-pdfcolmk noarch 12:svn78793-7.fc45 fedora 19.6 KiB texlive-pdfescape noarch 12:svn77682-5.fc45 fedora 375.9 KiB texlive-pdflscape noarch 12:svn77682-4.fc45 fedora 341.8 KiB texlive-pdfmanagement noarch 12:svn78778-5.fc45 fedora 6.5 MiB texlive-pdfpages noarch 12:svn78558-4.fc45 fedora 324.7 KiB texlive-pdftex ppc64le 12:svn77868-113.fc45 fedora 7.3 MiB texlive-pdftexcmds noarch 12:svn77682-5.fc45 fedora 423.9 KiB texlive-perltex noarch 12:svn73044-113.fc45 fedora 466.0 KiB texlive-pgf noarch 12:svn78101-4.fc45 fedora 24.8 MiB texlive-philokalia noarch 12:svn45356-11.fc45 fedora 239.8 KiB texlive-placeins noarch 12:svn77682-7.fc45 fedora 258.8 KiB texlive-plain noarch 12:svn75712-12.fc45 fedora 109.4 KiB texlive-platex noarch 12:svn77830-6.fc45 fedora 2.5 MiB texlive-platex-tools noarch 12:svn72097-6.fc45 fedora 649.0 KiB texlive-plautopatch noarch 12:svn77682-6.fc45 fedora 181.2 KiB texlive-polyglossia noarch 12:svn78740-4.fc45 fedora 1.4 MiB texlive-psfrag noarch 12:svn15878-4.fc45 fedora 124.7 KiB texlive-pslatex noarch 12:svn67469-5.fc45 fedora 36.7 KiB texlive-psnfss noarch 12:svn77682-5.fc45 fedora 410.4 KiB texlive-pspicture noarch 12:svn15878-5.fc45 fedora 87.7 KiB texlive-pst-3d noarch 12:svn77682-3.fc45 fedora 192.4 KiB texlive-pst-calculate noarch 12:svn77682-3.fc45 fedora 65.5 KiB texlive-pst-coil noarch 12:svn77682-3.fc45 fedora 3.6 MiB texlive-pst-eps noarch 12:svn77682-3.fc45 fedora 151.5 KiB texlive-pst-fill noarch 12:svn77682-3.fc45 fedora 1.0 MiB texlive-pst-grad noarch 12:svn77682-3.fc45 fedora 298.6 KiB texlive-pst-math noarch 12:svn77682-3.fc45 fedora 305.0 KiB texlive-pst-node noarch 12:svn77682-3.fc45 fedora 1.0 MiB texlive-pst-ovl noarch 12:svn77682-3.fc45 fedora 68.5 KiB texlive-pst-pdf noarch 12:svn77682-113.fc45 fedora 1.3 MiB texlive-pst-plot noarch 12:svn77682-3.fc45 fedora 2.3 MiB texlive-pst-text noarch 12:svn77682-3.fc45 fedora 253.6 KiB texlive-pst-tree noarch 12:svn77682-3.fc45 fedora 279.7 KiB texlive-pstricks noarch 12:svn78101-3.fc45 fedora 13.8 MiB texlive-pstricks-add noarch 12:svn77682-3.fc45 fedora 18.0 MiB texlive-ptex ppc64le 12:svn77830-113.fc45 fedora 1.3 MiB texlive-ptex-base noarch 12:svn64072-6.fc45 fedora 42.3 KiB texlive-ptex-fonts noarch 12:svn64330-6.fc45 fedora 4.8 MiB texlive-ptext noarch 12:svn77682-11.fc45 fedora 164.5 KiB texlive-pxfonts noarch 12:svn77682-9.fc45 fedora 1.4 MiB texlive-ragged2e noarch 12:svn77682-4.fc45 fedora 798.8 KiB texlive-rcs noarch 12:svn15878-4.fc45 fedora 239.2 KiB texlive-realscripts noarch 12:svn77682-7.fc45 fedora 129.2 KiB texlive-refcount noarch 12:svn77682-5.fc45 fedora 348.0 KiB texlive-regexpatch noarch 12:svn77682-7.fc45 fedora 569.4 KiB texlive-rerunfilecheck noarch 12:svn77682-5.fc45 fedora 360.6 KiB texlive-rsfs noarch 12:svn15878-9.fc45 fedora 102.3 KiB texlive-sansmath noarch 12:svn77682-4.fc45 fedora 196.5 KiB texlive-sansmathaccent noarch 12:svn77682-7.fc45 fedora 219.2 KiB texlive-sauerj noarch 12:svn15878-7.fc45 fedora 1.0 MiB texlive-section noarch 12:svn20180-4.fc45 fedora 410.6 KiB texlive-seminar noarch 12:svn77682-4.fc45 fedora 780.1 KiB texlive-sepnum noarch 12:svn20186-4.fc45 fedora 371.6 KiB texlive-setspace noarch 12:svn77682-4.fc45 fedora 236.1 KiB texlive-showexpl noarch 12:svn77682-7.fc45 fedora 644.6 KiB texlive-shtthesis noarch 12:svn62441-11.fc45 fedora 2.2 MiB texlive-simple-resume-cv noarch 12:svn43057-11.fc45 fedora 118.1 KiB texlive-simple-thesis-dissertation noarch 12:svn43058-11.fc45 fedora 267.8 KiB texlive-siunitx noarch 12:svn78712-3.fc45 fedora 1.5 MiB texlive-stmaryrd noarch 12:svn77682-3.fc45 fedora 437.7 KiB texlive-stringenc noarch 12:svn77682-5.fc45 fedora 1.0 MiB texlive-sttools noarch 12:svn77682-7.fc45 fedora 788.2 KiB texlive-subfig noarch 12:svn77682-4.fc45 fedora 751.8 KiB texlive-subfigure noarch 12:svn15878-7.fc45 fedora 443.1 KiB texlive-svn-prov noarch 12:svn77682-7.fc45 fedora 317.8 KiB texlive-symbol noarch 12:svn77161-9.fc45 fedora 83.6 KiB texlive-t2 noarch 12:svn47870-9.fc45 fedora 445.9 KiB texlive-tabu noarch 12:svn77682-7.fc45 fedora 2.5 MiB texlive-tabularray noarch 12:svn78251-7.fc45 fedora 1.8 MiB texlive-tagpdf noarch 12:svn78799-5.fc45 fedora 3.8 MiB texlive-tetragonos noarch 12:svn49732-11.fc45 fedora 1.6 MiB texlive-tex ppc64le 12:svn77830-113.fc45 fedora 524.9 KiB texlive-tex-gyre noarch 12:svn68624-9.fc45 fedora 37.6 MiB texlive-tex-gyre-math noarch 12:svn41264-9.fc45 fedora 3.2 MiB texlive-tex-ini-files noarch 12:svn78524-12.fc45 fedora 13.8 KiB texlive-texlive-common noarch 12:svn78660-12.fc45 fedora 677.7 KiB texlive-texlive-en noarch 12:svn78030-113.fc45 fedora 6.2 MiB texlive-texlive-msg-translations noarch 12:svn78661-12.fc45 fedora 1.4 MiB texlive-texlive-scripts noarch 12:svn78361-113.fc45 fedora 340.4 KiB texlive-texlive-scripts-extra noarch 12:svn78162-113.fc45 fedora 106.4 KiB texlive-texlive.infra noarch 12:svn78313-113.fc45 fedora 1.0 MiB texlive-textcase noarch 12:svn77682-4.fc45 fedora 248.8 KiB texlive-thumbpdf noarch 12:svn62518-113.fc45 fedora 97.0 KiB texlive-tikz-cd noarch 12:svn77682-4.fc45 fedora 357.0 KiB texlive-times noarch 12:svn77161-9.fc45 fedora 994.3 KiB texlive-tipa noarch 12:svn77682-9.fc45 fedora 6.5 MiB texlive-titlesec noarch 12:svn77682-7.fc45 fedora 860.5 KiB texlive-tkz-tab noarch 12:svn66115-4.fc45 fedora 542.0 KiB texlive-tocvsec2 noarch 12:svn77682-7.fc45 fedora 322.2 KiB texlive-tools noarch 12:svn76708-5.fc45 fedora 8.4 MiB texlive-translator noarch 12:svn77682-4.fc45 fedora 500.0 KiB texlive-transparent noarch 12:svn77682-7.fc45 fedora 301.1 KiB texlive-trimspaces noarch 12:svn77682-7.fc45 fedora 191.0 KiB texlive-ttfutils ppc64le 12:svn77830-113.fc45 fedora 1.4 MiB texlive-txfonts noarch 12:svn77682-9.fc45 fedora 2.4 MiB texlive-typehtml noarch 12:svn17134-4.fc45 fedora 224.2 KiB texlive-ucharcat noarch 12:svn78415-4.fc45 fedora 175.8 KiB texlive-ucharclasses noarch 12:svn77682-11.fc45 fedora 201.6 KiB texlive-uhc noarch 12:svn16791-6.fc45 fedora 7.4 MiB texlive-underscore noarch 12:svn77682-4.fc45 fedora 287.3 KiB texlive-undolabl noarch 12:svn77682-7.fc45 fedora 389.9 KiB texlive-unibidi-lua noarch 12:svn78655-4.fc45 fedora 780.7 KiB texlive-unicode-bidi noarch 12:svn77682-11.fc45 fedora 22.0 KiB texlive-unicode-data noarch 12:svn76413-12.fc45 fedora 3.4 MiB texlive-unicode-math noarch 12:svn78251-4.fc45 fedora 3.8 MiB texlive-unimath-plain-xetex noarch 12:svn72498-11.fc45 fedora 1.2 MiB texlive-uniquecounter noarch 12:svn77682-5.fc45 fedora 312.0 KiB texlive-unisugar noarch 12:svn22357-11.fc45 fedora 538.3 KiB texlive-uptex ppc64le 12:svn77830-113.fc45 fedora 3.1 MiB texlive-uptex-base noarch 12:svn77840-6.fc45 fedora 666.7 KiB texlive-uptex-fonts noarch 12:svn74119-6.fc45 fedora 15.7 MiB texlive-url noarch 12:svn77682-5.fc45 fedora 299.5 KiB texlive-utopia noarch 12:svn77682-9.fc45 fedora 546.6 KiB texlive-varwidth noarch 12:svn77682-7.fc45 fedora 64.2 KiB texlive-wadalab noarch 12:svn42428-6.fc45 fedora 21.1 MiB texlive-was noarch 12:svn64691-7.fc45 fedora 364.4 KiB texlive-wasy-type1 noarch 12:svn53534-9.fc45 fedora 332.4 KiB texlive-xcjk2uni noarch 12:svn54958-7.fc45 fedora 2.1 MiB texlive-xcolor noarch 12:svn77682-4.fc45 fedora 1.1 MiB texlive-xdvi ppc64le 12:svn62387-113.fc45 fedora 890.4 KiB texlive-xebaposter noarch 12:svn75290-11.fc45 fedora 1.0 MiB texlive-xechangebar noarch 12:svn77682-11.fc45 fedora 65.1 KiB texlive-xecjk noarch 12:svn77682-11.fc45 fedora 3.1 MiB texlive-xecolor noarch 12:svn77682-11.fc45 fedora 26.0 KiB texlive-xecyr noarch 12:svn77682-11.fc45 fedora 810.8 KiB texlive-xeindex noarch 12:svn77682-11.fc45 fedora 113.6 KiB texlive-xesearch noarch 12:svn77682-11.fc45 fedora 725.9 KiB texlive-xespotcolor noarch 12:svn77682-11.fc45 fedora 180.7 KiB texlive-xetex ppc64le 12:svn77830-113.fc45 fedora 2.6 MiB texlive-xetex-devanagari noarch 12:svn34296-11.fc45 fedora 1.1 MiB texlive-xetex-itrans noarch 12:svn55475-11.fc45 fedora 1.1 MiB texlive-xetex-pstricks noarch 12:svn17055-11.fc45 fedora 2.0 KiB texlive-xetex-tibetan noarch 12:svn28847-11.fc45 fedora 1.1 MiB texlive-xetexconfig noarch 12:svn45845-11.fc45 fedora 19.0 KiB texlive-xetexfontinfo noarch 12:svn15878-11.fc45 fedora 17.7 KiB texlive-xetexko noarch 12:svn77682-11.fc45 fedora 588.1 KiB texlive-xetexref noarch 12:svn73885-11.fc45 fedora 229.6 KiB texlive-xevlna noarch 12:svn77682-11.fc45 fedora 94.7 KiB texlive-xfrac noarch 12:svn77682-4.fc45 fedora 678.0 KiB texlive-xifthen noarch 12:svn77682-7.fc45 fedora 507.7 KiB texlive-xits noarch 12:svn55730-7.fc45 fedora 1.4 MiB texlive-xkeyval noarch 12:svn77682-4.fc45 fedora 677.0 KiB texlive-xltabular noarch 12:svn77682-7.fc45 fedora 300.1 KiB texlive-xltxtra noarch 12:svn77682-4.fc45 fedora 125.5 KiB texlive-xmltex noarch 12:svn76924-113.fc45 fedora 155.3 KiB texlive-xpatch noarch 12:svn77682-7.fc45 fedora 487.4 KiB texlive-xpinyin noarch 12:svn77682-9.fc45 fedora 1.4 MiB texlive-xstring noarch 12:svn77682-7.fc45 fedora 898.5 KiB texlive-xtab noarch 12:svn77682-7.fc45 fedora 394.9 KiB texlive-xunicode noarch 12:svn77682-4.fc45 fedora 220.0 KiB texlive-xurl noarch 12:svn77682-7.fc45 fedora 75.9 KiB texlive-zapfchan noarch 12:svn77161-9.fc45 fedora 183.4 KiB texlive-zapfding noarch 12:svn77161-9.fc45 fedora 84.8 KiB texlive-zbmath-review-template noarch 12:svn59693-11.fc45 fedora 283.2 KiB texlive-zhmetrics noarch 12:svn22207-9.fc45 fedora 5.5 MiB texlive-zhmetrics-uptex noarch 12:svn40728-9.fc45 fedora 7.5 MiB texlive-zhnumber noarch 12:svn77682-9.fc45 fedora 366.6 KiB texlive-zref noarch 12:svn78317-7.fc45 fedora 799.8 KiB tzdata noarch 0:2026b-2.fc45 fedora 1.2 MiB urw-base35-bookman-fonts noarch 0:20200910-29.fc45 fedora 1.4 MiB urw-base35-c059-fonts noarch 0:20200910-29.fc45 fedora 1.4 MiB urw-base35-d050000l-fonts noarch 0:20200910-29.fc45 fedora 84.3 KiB urw-base35-fonts noarch 0:20200910-29.fc45 fedora 5.3 KiB urw-base35-fonts-common noarch 0:20200910-29.fc45 fedora 37.4 KiB urw-base35-gothic-fonts noarch 0:20200910-29.fc45 fedora 1.2 MiB urw-base35-nimbus-mono-ps-fonts noarch 0:20200910-29.fc45 fedora 1.0 MiB urw-base35-nimbus-roman-fonts noarch 0:20200910-29.fc45 fedora 1.4 MiB urw-base35-nimbus-sans-fonts noarch 0:20200910-29.fc45 fedora 2.4 MiB urw-base35-p052-fonts noarch 0:20200910-29.fc45 fedora 1.5 MiB urw-base35-standard-symbols-ps-fonts noarch 0:20200910-29.fc45 fedora 64.9 KiB urw-base35-z003-fonts noarch 0:20200910-29.fc45 fedora 390.8 KiB vim-filesystem noarch 2:9.2.843-1.fc45 fedora 40.0 B web-assets-filesystem noarch 0:5-26.fc45 fedora 34.0 B xapian-core-libs ppc64le 0:1.4.31-2.fc45 fedora 2.3 MiB xdg-utils noarch 0:1.2.1-6.fc45 fedora 346.3 KiB xml-common noarch 0:0.6.3-69.fc45 fedora 78.4 KiB xpdf-libs ppc64le 1:4.06-3.fc45 fedora 2.2 MiB zziplib ppc64le 0:0.13.78-6.fc45 fedora 410.9 KiB Transaction Summary: Installing: 858 packages Total size of inbound packages is 903 MiB. Need to download 903 MiB. After this operation, 2 GiB extra will be used (install 2 GiB, remove 0 B). [ 1/858] chrpath-0:0.16-29.fc45.ppc64l 100% | 4.9 MiB/s | 30.4 KiB | 00m00s [ 2/858] doxygen-latex-2:1.17.0-3.fc45 100% | 5.0 MiB/s | 10.1 KiB | 00m00s [ 3/858] doxygen-2:1.17.0-3.fc45.ppc64 100% | 65.8 MiB/s | 5.6 MiB | 00m00s [ 4/858] graphviz-0:15.1.0-5.fc45.ppc6 100% | 50.1 MiB/s | 1.4 MiB | 00m00s [ 5/858] make-1:4.4.1-13.fc45.ppc64le 100% | 58.8 MiB/s | 601.6 KiB | 00m00s [ 6/858] cmake-0:4.3.0-5.fc45.ppc64le 100% | 64.6 MiB/s | 13.7 MiB | 00m00s [ 7/858] maloc-devel-0:1.5-36.fc45.ppc 100% | 14.4 MiB/s | 1.3 MiB | 00m00s [ 8/858] python3-devel-0:3.15.0~b4-1.f 100% | 42.8 MiB/s | 481.8 KiB | 00m00s [ 9/858] gcc-c++-0:16.1.1-4.fc45.1.ppc 100% | 51.8 MiB/s | 15.5 MiB | 00m00s [ 10/858] texlive-collection-latexrecom 100% | 1.1 MiB/s | 8.9 KiB | 00m00s [ 11/858] python3-sphinx-1:9.1.0-7.fc45 100% | 27.6 MiB/s | 3.1 MiB | 00m00s [ 12/858] texlive-adjustbox-12:svn78101 100% | 26.2 MiB/s | 752.2 KiB | 00m00s [ 13/858] texlive-hanging-12:svn77682-7 100% | 22.1 MiB/s | 158.3 KiB | 00m00s [ 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00m00s [258/860] Installing texlive-l3packages 100% | 135.7 MiB/s | 1.9 MiB | 00m00s [259/860] Installing texlive-fancyhdr-1 100% | 167.9 MiB/s | 1.3 MiB | 00m00s [260/860] Installing texlive-multido-12 100% | 53.7 MiB/s | 165.0 KiB | 00m00s [261/860] Installing texlive-xstring-12 100% | 125.7 MiB/s | 901.1 KiB | 00m00s [262/860] Installing texlive-grfext-12: 100% | 107.1 MiB/s | 329.1 KiB | 00m00s [263/860] Installing texlive-stringenc- 100% | 105.4 MiB/s | 1.1 MiB | 00m00s [264/860] Installing texlive-dvips-12:s 100% | 28.1 MiB/s | 1.7 MiB | 00m00s [265/860] Installing texlive-refcount-1 100% | 113.7 MiB/s | 349.2 KiB | 00m00s [266/860] Installing texlive-wasy-12:sv 100% | 77.3 MiB/s | 475.1 KiB | 00m00s [267/860] Installing texlive-enumitem-1 100% | 87.7 MiB/s | 269.5 KiB | 00m00s [268/860] Installing texlive-booktabs-1 100% | 102.9 MiB/s | 316.1 KiB | 00m00s [269/860] Installing texlive-everysel-1 100% | 112.2 MiB/s | 459.4 KiB | 00m00s [270/860] Installing texlive-setspace-1 100% | 25.8 MiB/s | 237.6 KiB | 00m00s [271/860] Installing texlive-lm-12:svn7 100% | 134.3 MiB/s | 43.0 MiB | 00m00s [272/860] Installing texlive-zapfding-1 100% | 21.5 MiB/s | 88.0 KiB | 00m00s [273/860] Installing texlive-latexconfi 100% | 2.6 MiB/s | 23.8 KiB | 00m00s [274/860] Installing texlive-ec-12:svn2 100% | 27.9 MiB/s | 2.8 MiB | 00m00s [275/860] Installing texlive-lua-alt-ge 100% | 5.6 MiB/s | 17.2 KiB | 00m00s [276/860] Installing texlive-tex-12:svn 100% | 10.9 MiB/s | 526.4 KiB | 00m00s [277/860] Installing texlive-stmaryrd-1 100% | 48.5 MiB/s | 446.8 KiB | 00m00s [278/860] Installing texlive-svn-prov-1 100% | 77.9 MiB/s | 318.9 KiB | 00m00s [279/860] Installing texlive-everyhook- 100% | 68.2 MiB/s | 139.6 KiB | 00m00s [280/860] Installing texlive-xpatch-12: 100% | 119.3 MiB/s | 488.6 KiB | 00m00s [281/860] Installing texlive-tagpdf-12: 100% | 140.8 MiB/s | 3.8 MiB | 00m00s [282/860] Installing texlive-bitset-12: 100% | 129.6 MiB/s | 663.5 KiB | 00m00s [283/860] Installing texlive-footmisc-1 100% | 119.5 MiB/s | 734.4 KiB | 00m00s [284/860] Installing texlive-alphalph-1 100% | 122.8 MiB/s | 377.1 KiB | 00m00s [285/860] Installing texlive-transparen 100% | 98.6 MiB/s | 302.8 KiB | 00m00s [286/860] Installing texlive-hopatch-12 100% | 113.0 MiB/s | 347.2 KiB | 00m00s [287/860] Installing texlive-hycolor-12 100% | 100.9 MiB/s | 413.1 KiB | 00m00s [288/860] Installing texlive-multirow-1 100% | 127.8 MiB/s | 654.2 KiB | 00m00s [289/860] Installing texlive-sectsty-12 100% | 87.5 MiB/s | 268.7 KiB | 00m00s [290/860] Installing texlive-appendix-1 100% | 83.0 MiB/s | 339.9 KiB | 00m00s [291/860] Installing texlive-bibtex-12: 100% | 23.2 MiB/s | 1.3 MiB | 00m00s [292/860] Installing texlive-epstopdf-1 100% | 1.1 MiB/s | 47.0 KiB | 00m00s [293/860] Installing texlive-makeindex- 100% | 11.1 MiB/s | 523.6 KiB | 00m00s [294/860] Installing texlive-pspicture- 100% | 29.1 MiB/s | 89.3 KiB | 00m00s [295/860] Installing texlive-anysize-12 100% | 25.4 MiB/s | 52.0 KiB | 00m00s [296/860] Installing texlive-euenc-12:s 100% | 46.7 MiB/s | 191.3 KiB | 00m00s [297/860] Installing texlive-euler-12:s 100% | 90.7 MiB/s | 278.8 KiB | 00m00s [298/860] Installing texlive-fancybox-1 100% | 89.9 MiB/s | 368.3 KiB | 00m00s [299/860] Installing texlive-index-12:s 100% | 31.7 MiB/s | 324.7 KiB | 00m00s [300/860] Installing texlive-cm-super-1 100% | 160.6 MiB/s | 65.2 MiB | 00m00s [301/860] Installing texlive-fpl-12:svn 100% | 97.2 MiB/s | 696.5 KiB | 00m00s [302/860] Installing texlive-lm-math-12 100% | 83.1 MiB/s | 851.3 KiB | 00m00s [303/860] Installing texlive-marvosym-1 100% | 66.0 MiB/s | 675.8 KiB | 00m00s [304/860] Installing texlive-palatino-1 100% | 45.0 MiB/s | 1.1 MiB | 00m00s [305/860] Installing texlive-symbol-12: 100% | 21.3 MiB/s | 87.3 KiB | 00m00s [306/860] Installing texlive-amscls-12: 100% | 120.3 MiB/s | 1.4 MiB | 00m00s [307/860] Installing texlive-graphics-c 100% | 2.6 MiB/s | 5.2 KiB | 00m00s [308/860] Installing texlive-extractbb- 100% | 1.0 MiB/s | 42.4 KiB | 00m00s [309/860] Installing texlive-glyphlist- 100% | 44.5 MiB/s | 91.1 KiB | 00m00s [310/860] Installing texlive-modes-12:s 100% | 93.4 MiB/s | 382.4 KiB | 00m00s [311/860] Installing texlive-placeins-1 100% | 84.7 MiB/s | 260.2 KiB | 00m00s [312/860] Installing texlive-paralist-1 100% | 82.4 MiB/s | 253.2 KiB | 00m00s [313/860] Installing texlive-dehyph-12: 100% | 78.5 MiB/s | 241.2 KiB | 00m00s [314/860] Installing tex-preview-0:14.1 100% | 97.4 MiB/s | 398.8 KiB | 00m00s [315/860] Installing texlive-xetexconfi 100% | 19.3 MiB/s | 19.7 KiB | 00m00s [316/860] Installing texlive-xesearch-1 100% | 101.5 MiB/s | 727.5 KiB | 00m00s [317/860] Installing texlive-adobemappi 100% | 122.0 MiB/s | 20.1 MiB | 00m00s [318/860] Installing texlive-ipaex-12:s 100% | 142.8 MiB/s | 40.6 MiB | 00m00s [319/860] Installing texlive-ptex-base- 100% | 14.5 MiB/s | 44.6 KiB | 00m00s [320/860] Installing texlive-l3backend- 100% | 135.6 MiB/s | 1.1 MiB | 00m00s [321/860] Installing texlive-l3kernel-d 100% | 167.0 MiB/s | 15.2 MiB | 00m00s [322/860] Installing texlive-ptex-fonts 100% | 133.4 MiB/s | 4.8 MiB | 00m00s [323/860] Installing texlive-mathpazo-1 100% | 66.6 MiB/s | 545.9 KiB | 00m00s [324/860] Installing texlive-ragged2e-1 100% | 130.4 MiB/s | 801.2 KiB | 00m00s [325/860] Installing texlive-wasy-type1 100% | 65.8 MiB/s | 336.7 KiB | 00m00s [326/860] Installing texlive-interchar- 100% | 47.5 MiB/s | 145.8 KiB | 00m00s [327/860] Installing texlive-regexpatch 100% | 139.3 MiB/s | 570.7 KiB | 00m00s [328/860] Installing texlive-l3experime 100% | 148.6 MiB/s | 1.6 MiB | 00m00s [329/860] Installing texlive-hypcap-12: 100% | 103.5 MiB/s | 318.1 KiB | 00m00s [330/860] Installing texlive-mfirstuc-1 100% | 138.3 MiB/s | 1.1 MiB | 00m00s [331/860] Installing texlive-euro-12:sv 100% | 85.7 MiB/s | 263.4 KiB | 00m00s [332/860] Installing texlive-pagesel-12 100% | 115.9 MiB/s | 356.1 KiB | 00m00s [333/860] Installing texlive-xurl-12:sv 100% | 37.8 MiB/s | 77.4 KiB | 00m00s [334/860] Installing texlive-catchfile- 100% | 104.2 MiB/s | 320.0 KiB | 00m00s [335/860] Installing texlive-ucharclass 100% | 66.1 MiB/s | 203.0 KiB | 00m00s [336/860] Installing texlive-unisugar-1 100% | 105.6 MiB/s | 540.6 KiB | 00m00s [337/860] Installing texlive-hanging-12 100% | 61.6 MiB/s | 189.3 KiB | 00m00s [338/860] Installing texlive-newunicode 100% | 98.9 MiB/s | 404.9 KiB | 00m00s [339/860] Installing texlive-tocloft-12 100% | 134.6 MiB/s | 551.5 KiB | 00m00s [340/860] Installing texlive-import-12: 100% | 81.8 MiB/s | 251.1 KiB | 00m00s [341/860] Installing texlive-xtab-12:sv 100% | 96.7 MiB/s | 396.1 KiB | 00m00s [342/860] Installing texlive-cite-12:sv 100% | 76.8 MiB/s | 314.7 KiB | 00m00s [343/860] Installing texlive-cmap-12:sv 100% | 17.3 MiB/s | 53.2 KiB | 00m00s [344/860] Installing texlive-extsizes-1 100% | 84.9 MiB/s | 347.6 KiB | 00m00s [345/860] Installing texlive-footnotehy 100% | 57.4 MiB/s | 117.6 KiB | 00m00s [346/860] Installing texlive-latexbug-1 100% | 93.5 MiB/s | 287.3 KiB | 00m00s [347/860] Installing texlive-ltx-talk-1 100% | 110.7 MiB/s | 1.2 MiB | 00m00s [348/860] Installing texlive-lua-unicod 100% | 19.5 MiB/s | 279.9 KiB | 00m00s [349/860] Installing texlive-lwarp-12:s 100% | 44.5 MiB/s | 4.9 MiB | 00m00s [350/860] Installing texlive-mdwtools-1 100% | 139.8 MiB/s | 2.1 MiB | 00m00s [351/860] Installing texlive-memoir-12: 100% | 151.6 MiB/s | 4.9 MiB | 00m00s [352/860] Installing texlive-ntgclass-1 100% | 148.7 MiB/s | 2.4 MiB | 00m00s [353/860] Installing texlive-rcs-12:svn 100% | 78.6 MiB/s | 241.4 KiB | 00m00s [354/860] Installing texlive-sansmath-1 100% | 96.6 MiB/s | 197.9 KiB | 00m00s [355/860] Installing texlive-section-12 100% | 100.6 MiB/s | 411.9 KiB | 00m00s [356/860] Installing texlive-sepnum-12: 100% | 121.4 MiB/s | 372.9 KiB | 00m00s [357/860] Installing texlive-textcase-1 100% | 81.4 MiB/s | 250.0 KiB | 00m00s [358/860] Installing texlive-ucharcat-1 100% | 86.4 MiB/s | 177.0 KiB | 00m00s [359/860] Installing texlive-collectbox 100% | 94.3 MiB/s | 193.2 KiB | 00m00s [360/860] Installing texlive-ifoddpage- 100% | 80.5 MiB/s | 164.8 KiB | 00m00s [361/860] Installing texlive-listofitem 100% | 84.8 MiB/s | 521.0 KiB | 00m00s [362/860] Installing texlive-avantgar-1 100% | 35.9 MiB/s | 1.0 MiB | 00m00s [363/860] Installing texlive-bookman-12 100% | 45.7 MiB/s | 982.9 KiB | 00m00s [364/860] Installing texlive-charter-12 100% | 45.3 MiB/s | 417.3 KiB | 00m00s [365/860] Installing texlive-cmextra-12 100% | 23.0 MiB/s | 141.6 KiB | 00m00s [366/860] Installing texlive-courier-12 100% | 50.2 MiB/s | 822.0 KiB | 00m00s [367/860] Installing texlive-euro-ce-12 100% | 11.5 MiB/s | 47.1 KiB | 00m00s [368/860] Installing texlive-eurosym-12 100% | 51.9 MiB/s | 531.0 KiB | 00m00s [369/860] Installing texlive-helvetic-1 100% | 55.5 MiB/s | 1.8 MiB | 00m00s [370/860] Installing texlive-manfnt-fon 100% | 21.6 MiB/s | 44.2 KiB | 00m00s [371/860] Installing texlive-mflogo-fon 100% | 10.6 MiB/s | 43.6 KiB | 00m00s [372/860] Installing texlive-ncntrsbk-1 100% | 47.0 MiB/s | 963.6 KiB | 00m00s [373/860] Installing texlive-pxfonts-12 100% | 64.6 MiB/s | 1.4 MiB | 00m00s [374/860] Installing texlive-rsfs-12:sv 100% | 21.0 MiB/s | 107.4 KiB | 00m00s [375/860] Installing texlive-tex-gyre-m 100% | 104.6 MiB/s | 3.2 MiB | 00m00s [376/860] Installing texlive-times-12:s 100% | 43.5 MiB/s | 1.0 MiB | 00m00s [377/860] Installing texlive-txfonts-12 100% | 63.9 MiB/s | 2.4 MiB | 00m00s [378/860] Installing texlive-utopia-12: 100% | 54.5 MiB/s | 557.8 KiB | 00m00s [379/860] Installing texlive-zapfchan-1 100% | 26.5 MiB/s | 190.3 KiB | 00m00s [380/860] Installing texlive-citeref-12 100% | 35.9 MiB/s | 73.5 KiB | 00m00s [381/860] Installing texlive-natbib-12: 100% | 101.8 MiB/s | 625.6 KiB | 00m00s [382/860] Installing texlive-pdfcolmk-1 100% | 20.2 MiB/s | 20.7 KiB | 00m00s [383/860] Installing texlive-fix2col-12 100% | 76.7 MiB/s | 235.7 KiB | 00m00s [384/860] Installing texlive-mfnfss-12: 100% | 99.2 MiB/s | 508.2 KiB | 00m00s [385/860] Installing texlive-pslatex-12 100% | 19.0 MiB/s | 39.0 KiB | 00m00s [386/860] Installing texlive-finstrut-1 100% | 75.9 MiB/s | 233.2 KiB | 00m00s [387/860] Installing texlive-luabidi-12 100% | 61.8 MiB/s | 189.8 KiB | 00m00s [388/860] Installing texlive-makecmds-1 100% | 75.3 MiB/s | 154.1 KiB | 00m00s [389/860] Installing texlive-unibidi-lu 100% | 127.4 MiB/s | 782.9 KiB | 00m00s [390/860] Installing texlive-chicago-12 100% | 23.7 MiB/s | 48.6 KiB | 00m00s [391/860] Installing texlive-colorprofi 100% | 54.1 MiB/s | 277.1 KiB | 00m00s [392/860] Installing texlive-enctex-12: 100% | 63.2 MiB/s | 582.0 KiB | 00m00s [393/860] Installing texlive-hyphenex-1 100% | 26.4 MiB/s | 27.1 KiB | 00m00s [394/860] Installing texlive-knuth-loca 100% | 22.0 MiB/s | 112.9 KiB | 00m00s [395/860] Installing texlive-luahbtex-1 100% | 75.4 MiB/s | 7.3 MiB | 00m00s [396/860] Installing texlive-mflogo-12: 100% | 54.7 MiB/s | 279.9 KiB | 00m00s [397/860] Installing texlive-mfware-12: 100% | 8.9 MiB/s | 426.8 KiB | 00m00s [398/860] Installing texlive-texlive-co 100% | 83.2 MiB/s | 681.5 KiB | 00m00s [399/860] Installing texlive-texlive-en 100% | 159.0 MiB/s | 6.2 MiB | 00m00s [400/860] Installing texlive-texlive-ms 100% | 131.7 MiB/s | 1.4 MiB | 00m00s [401/860] Installing texlive-notoccite- 100% | 45.5 MiB/s | 232.9 KiB | 00m00s [402/860] Installing texlive-latex-base 100% | 173.3 MiB/s | 51.5 MiB | 00m00s [403/860] Installing texlive-ntheorem-1 100% | 86.7 MiB/s | 532.6 KiB | 00m00s [404/860] Installing texlive-minitoc-12 100% | 128.0 MiB/s | 9.6 MiB | 00m00s [405/860] Installing texlive-hypdoc-12: 100% | 88.2 MiB/s | 361.1 KiB | 00m00s [406/860] Installing texlive-hyperref-1 100% | 149.0 MiB/s | 5.4 MiB | 00m00s [407/860] Installing texlive-graphics-1 100% | 148.4 MiB/s | 3.1 MiB | 00m00s [408/860] Installing texlive-tools-12:s 100% | 168.7 MiB/s | 8.4 MiB | 00m00s [409/860] Installing texlive-kvoptions- 100% | 107.7 MiB/s | 551.6 KiB | 00m00s [410/860] Installing texlive-gettitlest 100% | 110.7 MiB/s | 340.1 KiB | 00m00s [411/860] Installing texlive-rerunfilec 100% | 117.9 MiB/s | 362.1 KiB | 00m00s [412/860] Installing texlive-epstopdf-p 100% | 94.7 MiB/s | 388.0 KiB | 00m00s [413/860] Installing texlive-xkeyval-12 100% | 95.1 MiB/s | 681.6 KiB | 00m00s [414/860] Installing texlive-psnfss-12: 100% | 32.4 MiB/s | 431.1 KiB | 00m00s [415/860] Installing texlive-geometry-1 100% | 109.0 MiB/s | 1.0 MiB | 00m00s [416/860] Installing texlive-tipa-12:sv 100% | 120.9 MiB/s | 6.5 MiB | 00m00s [417/860] Installing texlive-xunicode-1 100% | 72.0 MiB/s | 221.1 KiB | 00m00s [418/860] Installing texlive-hologo-12: 100% | 131.7 MiB/s | 674.3 KiB | 00m00s [419/860] Installing texlive-mathtools- 100% | 157.9 MiB/s | 1.3 MiB | 00m00s [420/860] Installing texlive-colortbl-1 100% | 136.0 MiB/s | 696.1 KiB | 00m00s [421/860] Installing texlive-xcolor-12: 100% | 84.3 MiB/s | 1.1 MiB | 00m00s [422/860] Installing texlive-pgf-12:svn 100% | 121.2 MiB/s | 25.0 MiB | 00m00s [423/860] Installing texlive-filehook-1 100% | 89.7 MiB/s | 367.3 KiB | 00m00s [424/860] Installing texlive-currfile-1 100% | 70.1 MiB/s | 215.4 KiB | 00m00s [425/860] Installing texlive-jknapltx-1 100% | 19.6 MiB/s | 60.1 KiB | 00m00s [426/860] Installing texlive-lualatex-m 100% | 76.4 MiB/s | 234.7 KiB | 00m00s [427/860] Installing texlive-eso-pic-12 100% | 81.1 MiB/s | 332.1 KiB | 00m00s [428/860] Installing texlive-fmtcount-1 100% | 86.7 MiB/s | 888.1 KiB | 00m00s [429/860] Installing texlive-fonts-tlwg 100% | 105.3 MiB/s | 8.5 MiB | 00m00s [430/860] Installing texlive-grffile-12 100% | 41.3 MiB/s | 380.7 KiB | 00m00s [431/860] Installing texlive-tex-gyre-1 100% | 135.0 MiB/s | 37.8 MiB | 00m00s [432/860] Installing texlive-koma-scrip 100% | 140.7 MiB/s | 14.9 MiB | 00m00s [433/860] Installing texlive-carlisle-1 100% | 38.8 MiB/s | 119.1 KiB | 00m00s [434/860] Installing texlive-ifplatform 100% | 84.1 MiB/s | 172.3 KiB | 00m00s [435/860] Installing texlive-siunitx-12 100% | 150.9 MiB/s | 1.5 MiB | 00m00s [436/860] Installing texlive-pst-calcul 100% | 32.9 MiB/s | 67.4 KiB | 00m00s [437/860] Installing texlive-sttools-12 100% | 128.7 MiB/s | 791.0 KiB | 00m00s [438/860] Installing texlive-newfloat-1 100% | 77.1 MiB/s | 236.7 KiB | 00m00s [439/860] Installing texlive-caption-12 100% | 136.8 MiB/s | 1.9 MiB | 00m00s [440/860] Installing texlive-pdflscape- 100% | 83.8 MiB/s | 343.3 KiB | 00m00s [441/860] Installing texlive-translator 100% | 42.7 MiB/s | 525.1 KiB | 00m00s [442/860] Installing texlive-pdfcol-12: 100% | 112.9 MiB/s | 346.8 KiB | 00m00s [443/860] Installing texlive-sauerj-12: 100% | 60.2 MiB/s | 1.0 MiB | 00m00s [444/860] Installing texlive-japanese-o 100% | 161.5 MiB/s | 42.6 MiB | 00m00s [445/860] Installing texlive-bookmark-1 100% | 108.7 MiB/s | 556.3 KiB | 00m00s [446/860] Installing texlive-cqubeamer- 100% | 161.7 MiB/s | 3.1 MiB | 00m00s [447/860] Installing texlive-pdfcolfoot 100% | 109.7 MiB/s | 337.1 KiB | 00m00s [448/860] Installing texlive-subfig-12: 100% | 105.3 MiB/s | 754.5 KiB | 00m00s [449/860] Installing texlive-sansmathac 100% | 36.5 MiB/s | 224.4 KiB | 00m00s [450/860] Installing texlive-beamer-12: 100% | 110.8 MiB/s | 4.9 MiB | 00m00s [451/860] Installing texlive-garuda-c90 100% | 17.4 MiB/s | 35.6 KiB | 00m00s [452/860] Installing texlive-norasi-c90 100% | 15.1 MiB/s | 46.5 KiB | 00m00s [453/860] Installing texlive-datetime-1 100% | 72.7 MiB/s | 819.3 KiB | 00m00s [454/860] Installing texlive-adjustbox- 100% | 109.5 MiB/s | 896.7 KiB | 00m00s [455/860] Installing texlive-bidipagegr 100% | 29.4 MiB/s | 60.2 KiB | 00m00s [456/860] Installing texlive-tkz-tab-12 100% | 106.6 MiB/s | 545.6 KiB | 00m00s [457/860] Installing texlive-na-positio 100% | 57.7 MiB/s | 118.1 KiB | 00m00s [458/860] Installing texlive-tikz-cd-12 100% | 87.6 MiB/s | 358.8 KiB | 00m00s [459/860] Installing texlive-ctable-12: 100% | 133.6 MiB/s | 821.1 KiB | 00m00s [460/860] Installing texlive-microtype- 100% | 148.7 MiB/s | 3.1 MiB | 00m00s [461/860] Installing texlive-ninecolors 100% | 48.5 MiB/s | 99.4 KiB | 00m00s [462/860] Installing texlive-xespotcolo 100% | 59.5 MiB/s | 182.7 KiB | 00m00s [463/860] Installing texlive-passivetex 100% | 72.5 MiB/s | 296.8 KiB | 00m00s [464/860] Installing texlive-etoc-12:sv 100% | 124.3 MiB/s | 1.2 MiB | 00m00s [465/860] Installing texlive-attachfile 100% | 11.1 MiB/s | 522.1 KiB | 00m00s [466/860] Installing texlive-parskip-12 100% | 103.6 MiB/s | 424.3 KiB | 00m00s [467/860] Installing texlive-stackengin 100% | 92.2 MiB/s | 472.1 KiB | 00m00s [468/860] Installing texlive-breqn-12:s 100% | 139.2 MiB/s | 1.3 MiB | 00m00s [469/860] Installing texlive-fancyref-1 100% | 56.7 MiB/s | 174.0 KiB | 00m00s [470/860] Installing texlive-diagbox-12 100% | 89.0 MiB/s | 273.4 KiB | 00m00s [471/860] Installing texlive-tabularray 100% | 151.9 MiB/s | 1.8 MiB | 00m00s [472/860] Installing texlive-ltablex-12 100% | 83.2 MiB/s | 255.7 KiB | 00m00s [473/860] Installing texlive-xltabular- 100% | 42.1 MiB/s | 302.1 KiB | 00m00s [474/860] Installing texlive-latex-lab- 100% | 164.8 MiB/s | 16.5 MiB | 00m00s [475/860] Installing texlive-ltabptch-1 100% | 102.3 MiB/s | 314.4 KiB | 00m00s [476/860] Installing texlive-lineno-12: 100% | 113.8 MiB/s | 1.3 MiB | 00m00s [477/860] Installing texlive-t2-12:svn4 100% | 32.5 MiB/s | 466.6 KiB | 00m00s [478/860] Installing texlive-collcell-1 100% | 72.8 MiB/s | 223.6 KiB | 00m00s [479/860] Installing texlive-crop-12:sv 100% | 116.6 MiB/s | 358.3 KiB | 00m00s [480/860] Installing texlive-psfrag-12: 100% | 41.3 MiB/s | 126.9 KiB | 00m00s [481/860] Installing texlive-xfrac-12:s 100% | 132.7 MiB/s | 679.5 KiB | 00m00s [482/860] Installing texlive-algorithms 100% | 95.7 MiB/s | 391.9 KiB | 00m00s [483/860] Installing texlive-titlesec-1 100% | 120.4 MiB/s | 862.8 KiB | 00m00s [484/860] Installing texlive-bidicontou 100% | 31.0 MiB/s | 63.6 KiB | 00m00s [485/860] Installing texlive-bidishadow 100% | 69.7 MiB/s | 142.7 KiB | 00m00s [486/860] Installing texlive-logreq-12: 100% | 18.5 MiB/s | 56.8 KiB | 00m00s [487/860] Installing texlive-pdfmanagem 100% | 159.9 MiB/s | 6.6 MiB | 00m00s [488/860] Installing texlive-typehtml-1 100% | 73.4 MiB/s | 225.4 KiB | 00m00s [489/860] Installing texlive-underscore 100% | 70.5 MiB/s | 288.7 KiB | 00m00s [490/860] Installing texlive-ae-12:svn1 100% | 32.9 MiB/s | 505.1 KiB | 00m00s [491/860] Installing texlive-mnsymbol-1 100% | 100.8 MiB/s | 6.0 MiB | 00m00s [492/860] Installing texlive-bibtopic-1 100% | 74.3 MiB/s | 304.5 KiB | 00m00s [493/860] Installing texlive-bidi-atbeg 100% | 71.6 MiB/s | 220.0 KiB | 00m00s [494/860] Installing texlive-xeindex-12 100% | 56.2 MiB/s | 115.0 KiB | 00m00s [495/860] Installing texlive-tocvsec2-1 100% | 105.3 MiB/s | 323.6 KiB | 00m00s [496/860] Installing texlive-hyphen-eng 100% | 6.0 MiB/s | 179.2 KiB | 00m00s [497/860] Installing texlive-babel-engl 100% | 56.8 MiB/s | 174.6 KiB | 00m00s [498/860] Installing texlive-beton-12:s 100% | 62.0 MiB/s | 126.9 KiB | 00m00s [499/860] Installing texlive-ltxmisc-12 100% | 27.2 MiB/s | 83.7 KiB | 00m00s [500/860] Installing texlive-parallel-1 100% | 58.2 MiB/s | 178.7 KiB | 00m00s [501/860] Installing texlive-lualibs-12 100% | 87.3 MiB/s | 893.6 KiB | 00m00s [502/860] Installing texlive-changepage 100% | 91.2 MiB/s | 373.4 KiB | 00m00s [503/860] Installing texlive-texlive-sc 100% | 2.4 MiB/s | 115.7 KiB | 00m00s [504/860] Installing texlive-luatex85-1 100% | 62.7 MiB/s | 192.6 KiB | 00m00s [505/860] Installing texlive-makerobust 100% | 42.0 MiB/s | 86.0 KiB | 00m00s [506/860] Installing texlive-zref-12:sv 100% | 112.3 MiB/s | 804.9 KiB | 00m00s [507/860] Installing texlive-linegoal-1 100% | 68.9 MiB/s | 211.6 KiB | 00m00s [508/860] Installing texlive-tabu-12:sv 100% | 159.0 MiB/s | 2.5 MiB | 00m00s [509/860] Installing texlive-ctablestac 100% | 55.1 MiB/s | 169.3 KiB | 00m00s [510/860] Installing texlive-luatexbase 100% | 71.1 MiB/s | 291.3 KiB | 00m00s [511/860] Installing texlive-luaotfload 100% | 83.5 MiB/s | 8.3 MiB | 00m00s [512/860] Installing texlive-fontspec-1 100% | 81.6 MiB/s | 1.6 MiB | 00m00s [513/860] Installing texlive-babel-12:s 100% | 23.1 MiB/s | 3.9 MiB | 00m00s [514/860] Installing texlive-unicode-ma 100% | 159.8 MiB/s | 3.8 MiB | 00m00s [515/860] Installing texlive-metalogo-1 100% | 9.9 MiB/s | 122.0 KiB | 00m00s [516/860] Installing texlive-oberdiek-1 100% | 170.3 MiB/s | 11.2 MiB | 00m00s [517/860] Installing texlive-pdfpages-1 100% | 64.0 MiB/s | 327.8 KiB | 00m00s [518/860] Installing texlive-babelbib-1 100% | 135.7 MiB/s | 2.4 MiB | 00m00s [519/860] Installing texlive-mathspec-1 100% | 62.7 MiB/s | 256.8 KiB | 00m00s [520/860] Installing texlive-realscript 100% | 63.7 MiB/s | 130.5 KiB | 00m00s [521/860] Installing texlive-xltxtra-12 100% | 61.9 MiB/s | 126.7 KiB | 00m00s [522/860] Installing texlive-fontbook-1 100% | 146.3 MiB/s | 1.5 MiB | 00m00s [523/860] Installing texlive-xecolor-12 100% | 13.2 MiB/s | 27.1 KiB | 00m00s [524/860] Installing texlive-luacode-12 100% | 104.6 MiB/s | 428.3 KiB | 00m00s [525/860] Installing texlive-luatextra- 100% | 76.7 MiB/s | 314.0 KiB | 00m00s [526/860] Installing texlive-xecyr-12:s 100% | 67.1 MiB/s | 824.7 KiB | 00m00s [527/860] Installing texlive-ifmtarg-12 100% | 28.0 MiB/s | 57.3 KiB | 00m00s [528/860] Installing texlive-xifthen-12 100% | 124.3 MiB/s | 509.1 KiB | 00m00s [529/860] Installing texlive-trimspaces 100% | 62.6 MiB/s | 192.3 KiB | 00m00s [530/860] Installing texlive-environ-12 100% | 57.6 MiB/s | 177.0 KiB | 00m00s [531/860] Installing texlive-pst-pdf-12 100% | 24.7 MiB/s | 1.3 MiB | 00m00s [532/860] Installing texlive-pstricks-1 100% | 157.1 MiB/s | 13.8 MiB | 00m00s [533/860] Installing texlive-pst-3d-12: 100% | 47.6 MiB/s | 194.8 KiB | 00m00s [534/860] Installing texlive-pst-node-1 100% | 115.8 MiB/s | 1.0 MiB | 00m00s [535/860] Installing texlive-pst-plot-1 100% | 123.9 MiB/s | 2.4 MiB | 00m00s [536/860] Installing texlive-pst-coil-1 100% | 165.4 MiB/s | 3.6 MiB | 00m00s [537/860] Installing texlive-pst-eps-12 100% | 50.1 MiB/s | 153.8 KiB | 00m00s [538/860] Installing texlive-pst-fill-1 100% | 124.7 MiB/s | 1.0 MiB | 00m00s [539/860] Installing texlive-pst-grad-1 100% | 73.4 MiB/s | 300.8 KiB | 00m00s [540/860] Installing texlive-pst-text-1 100% | 50.0 MiB/s | 256.2 KiB | 00m00s [541/860] Installing texlive-pst-tree-1 100% | 68.8 MiB/s | 281.8 KiB | 00m00s [542/860] Installing texlive-pst-math-1 100% | 75.0 MiB/s | 307.4 KiB | 00m00s [543/860] Installing texlive-pstricks-a 100% | 149.0 MiB/s | 18.0 MiB | 00m00s [544/860] Installing texlive-fancyvrb-1 100% | 71.2 MiB/s | 291.7 KiB | 00m00s [545/860] Installing texlive-listings-1 100% | 167.9 MiB/s | 4.4 MiB | 00m00s [546/860] Installing texlive-pst-ovl-12 100% | 17.3 MiB/s | 70.9 KiB | 00m00s [547/860] Installing texlive-seminar-12 100% | 85.4 MiB/s | 786.6 KiB | 00m00s [548/860] Installing texlive-changebar- 100% | 136.7 MiB/s | 839.8 KiB | 00m00s [549/860] Installing texlive-subfigure- 100% | 87.0 MiB/s | 445.5 KiB | 00m00s [550/860] Installing texlive-bidipresen 100% | 71.3 MiB/s | 292.0 KiB | 00m00s [551/860] Installing texlive-businessca 100% | 88.0 MiB/s | 631.1 KiB | 00m00s [552/860] Installing texlive-ctex-faq-1 100% | 119.1 MiB/s | 731.5 KiB | 00m00s [553/860] Installing texlive-font-chang 100% | 112.8 MiB/s | 693.2 KiB | 00m00s [554/860] Installing texlive-simple-res 100% | 58.5 MiB/s | 119.7 KiB | 00m00s [555/860] Installing texlive-simple-the 100% | 66.3 MiB/s | 271.4 KiB | 00m00s [556/860] Installing texlive-tetragonos 100% | 123.1 MiB/s | 1.6 MiB | 00m00s [557/860] Installing texlive-unicode-bi 100% | 7.5 MiB/s | 23.1 KiB | 00m00s [558/860] Installing texlive-unimath-pl 100% | 59.4 MiB/s | 1.2 MiB | 00m00s [559/860] Installing texlive-xebaposter 100% | 113.8 MiB/s | 1.0 MiB | 00m00s [560/860] Installing texlive-xechangeba 100% | 21.6 MiB/s | 66.4 KiB | 00m00s [561/860] Installing texlive-xetex-deva 100% | 189.1 MiB/s | 1.1 MiB | 00m00s [562/860] Installing texlive-xetex-itra 100% | 55.1 MiB/s | 1.2 MiB | 00m00s [563/860] Installing texlive-xetex-pstr 100% | 1.1 MiB/s | 3.5 KiB | 00m00s [564/860] Installing texlive-xetex-tibe 100% | 227.1 MiB/s | 1.1 MiB | 00m00s [565/860] Installing texlive-xetexfonti 100% | 9.3 MiB/s | 19.0 KiB | 00m00s [566/860] Installing texlive-xetexref-1 100% | 75.3 MiB/s | 231.2 KiB | 00m00s [567/860] Installing texlive-xevlna-12: 100% | 47.1 MiB/s | 96.5 KiB | 00m00s [568/860] Installing texlive-eepic-12:s 100% | 48.4 MiB/s | 198.1 KiB | 00m00s [569/860] Installing texlive-overpic-12 100% | 103.1 MiB/s | 422.3 KiB | 00m00s [570/860] Installing texlive-cjkpunct-1 100% | 47.3 MiB/s | 193.7 KiB | 00m00s [571/860] Installing texlive-fandol-12: 100% | 110.8 MiB/s | 33.3 MiB | 00m00s [572/860] Installing texlive-ttfutils-1 100% | 24.0 MiB/s | 1.4 MiB | 00m00s [573/860] Installing texlive-xcjk2uni-1 100% | 54.9 MiB/s | 2.2 MiB | 00m00s [574/860] Installing texlive-xpinyin-12 100% | 31.8 MiB/s | 1.4 MiB | 00m00s [575/860] Installing texlive-zhmetrics- 100% | 18.1 MiB/s | 6.4 MiB | 00m00s [576/860] Installing texlive-zhmetrics- 100% | 178.6 MiB/s | 7.5 MiB | 00m00s [577/860] Installing texlive-zhnumber-1 100% | 89.9 MiB/s | 368.4 KiB | 00m00s [578/860] Installing texlive-was-12:svn 100% | 89.4 MiB/s | 366.0 KiB | 00m00s [579/860] Installing texlive-perltex-12 100% | 9.9 MiB/s | 468.0 KiB | 00m00s [580/860] Installing texlive-fontwrap-1 100% | 75.9 MiB/s | 388.6 KiB | 00m00s [581/860] Installing texlive-lastpage-1 100% | 103.5 MiB/s | 635.9 KiB | 00m00s [582/860] Installing texlive-undolabl-1 100% | 95.6 MiB/s | 391.5 KiB | 00m00s [583/860] Installing texlive-xits-12:sv 100% | 108.3 MiB/s | 1.4 MiB | 00m00s [584/860] Installing texlive-gensymb-12 100% | 84.3 MiB/s | 259.1 KiB | 00m00s [585/860] Installing texlive-zbmath-rev 100% | 19.9 MiB/s | 285.9 KiB | 00m00s [586/860] Installing texlive-arphic-12: 100% | 114.8 MiB/s | 31.1 MiB | 00m00s [587/860] Installing texlive-cns-12:svn 100% | 78.5 MiB/s | 9.7 MiB | 00m00s [588/860] Installing texlive-uhc-12:svn 100% | 30.2 MiB/s | 7.9 MiB | 00m00s [589/860] Installing texlive-wadalab-12 100% | 106.4 MiB/s | 21.3 MiB | 00m00s [590/860] Installing texlive-cjk-12:svn 100% | 60.1 MiB/s | 2.9 MiB | 00m00s [591/860] Installing texlive-ascmac-12: 100% | 40.4 MiB/s | 206.9 KiB | 00m00s [592/860] Installing texlive-luatexja-1 100% | 137.1 MiB/s | 5.6 MiB | 00m00s [593/860] Installing texlive-convbkmk-1 100% | 413.1 KiB/s | 17.4 KiB | 00m00s [594/860] Installing texlive-uptex-base 100% | 47.8 MiB/s | 685.3 KiB | 00m00s [595/860] Installing texlive-uptex-font 100% | 180.6 MiB/s | 15.7 MiB | 00m00s [596/860] Installing texlive-minifp-12: 100% | 100.8 MiB/s | 516.3 KiB | 00m00s [597/860] Installing texlive-lettrine-1 100% | 90.1 MiB/s | 646.1 KiB | 00m00s [598/860] Installing texlive-philokalia 100% | 59.1 MiB/s | 241.9 KiB | 00m00s [599/860] Installing texlive-latex-firs 100% | 82.6 MiB/s | 338.1 KiB | 00m00s [600/860] Installing texlive-fnpara-12: 100% | 66.5 MiB/s | 204.2 KiB | 00m00s [601/860] Installing texlive-kotex-utf- 100% | 173.2 MiB/s | 11.1 MiB | 00m00s [602/860] Installing texlive-cjk-ko-12: 100% | 63.6 MiB/s | 260.3 KiB | 00m00s [603/860] Installing texlive-xetexko-12 100% | 96.2 MiB/s | 591.1 KiB | 00m00s [604/860] Installing texlive-luatexko-1 100% | 99.9 MiB/s | 511.7 KiB | 00m00s [605/860] Installing texlive-arydshln-1 100% | 132.4 MiB/s | 948.8 KiB | 00m00s [606/860] Installing perl-XML-SAX-0:1.0 100% | 1.1 MiB/s | 126.0 KiB | 00m00s [607/860] Installing perl-XML-LibXML-1: 100% | 5.6 MiB/s | 1.1 MiB | 00m00s [608/860] Installing perl-XML-LibXML-Si 100% | 12.8 MiB/s | 52.3 KiB | 00m00s [609/860] Installing perl-Class-Accesso 100% | 14.0 MiB/s | 42.9 KiB | 00m00s [610/860] Installing perl-File-Slurper- 100% | 14.7 MiB/s | 30.0 KiB | 00m00s [611/860] Installing perl-FindBin-0:1.5 100% | 7.0 MiB/s | 7.2 KiB | 00m00s [612/860] Installing perl-IO-String-0:1 100% | 8.7 MiB/s | 17.8 KiB | 00m00s [613/860] Installing perl-IPC-Run3-0:0. 100% | 15.5 MiB/s | 63.3 KiB | 00m00s [614/860] Installing perl-Regexp-Common 100% | 38.6 MiB/s | 474.0 KiB | 00m00s [615/860] Installing perl-Sort-Key-0:1. 100% | 22.8 MiB/s | 116.8 KiB | 00m00s [616/860] Installing perl-Text-CSV-0:2. 100% | 71.7 MiB/s | 367.0 KiB | 00m00s [617/860] Installing perl-Text-Roman-0: 100% | 11.3 MiB/s | 34.7 KiB | 00m00s [618/860] Installing perl-XML-Writer-0: 100% | 16.8 MiB/s | 68.6 KiB | 00m00s [619/860] Installing perl-autovivificat 100% | 31.0 MiB/s | 95.4 KiB | 00m00s [620/860] Installing perl-lib-0:0.65-52 100% | 4.4 MiB/s | 8.9 KiB | 00m00s [621/860] Installing perl-Business-ISBN 100% | 50.9 MiB/s | 313.0 KiB | 00m00s [622/860] Installing perl-Business-ISBN 100% | 19.0 MiB/s | 58.2 KiB | 00m00s [623/860] Installing perl-Tie-Cycle-0:1 100% | 12.5 MiB/s | 25.5 KiB | 00m00s [624/860] Installing perl-Business-ISMN 100% | 18.8 MiB/s | 38.5 KiB | 00m00s [625/860] Installing perl-Class-Singlet 100% | 20.2 MiB/s | 41.4 KiB | 00m00s [626/860] Installing perl-File-Compare- 100% | 6.0 MiB/s | 6.2 KiB | 00m00s [627/860] Installing perl-ExtUtils-MM-U 100% | 3.6 MiB/s | 3.7 KiB | 00m00s [628/860] Installing perl-Mozilla-CA-0: 100% | 12.8 MiB/s | 13.1 KiB | 00m00s [629/860] Installing perl-LWP-Protocol- 100% | 15.7 MiB/s | 32.2 KiB | 00m00s [630/860] Installing perl-List-UtilsBy- 100% | 27.9 MiB/s | 57.2 KiB | 00m00s [631/860] Installing perl-List-AllUtils 100% | 66.4 MiB/s | 135.9 KiB | 00m00s [632/860] Installing perl-IPC-SysV-0:2. 100% | 37.9 MiB/s | 116.3 KiB | 00m00s [633/860] Installing perl-Getopt-Tabula 100% | 43.0 MiB/s | 88.1 KiB | 00m00s [634/860] Installing perl-Text-BibTeX-0 100% | 14.1 MiB/s | 750.4 KiB | 00m00s [635/860] Installing perl-MIME-Charset- 100% | 26.2 MiB/s | 107.3 KiB | 00m00s [636/860] Installing perl-meta-notation 100% | 2.2 MiB/s | 2.3 KiB | 00m00s [637/860] Installing perl-sigtrap-0:1.1 100% | 11.2 MiB/s | 11.5 KiB | 00m00s [638/860] Installing perl-Number-Compar 100% | 5.3 MiB/s | 5.4 KiB | 00m00s [639/860] Installing perl-Text-Glob-0:0 100% | 9.1 MiB/s | 9.3 KiB | 00m00s [640/860] Installing perl-File-Find-Rul 100% | 1.0 MiB/s | 44.5 KiB | 00m00s [641/860] Installing perl-Data-Compare- 100% | 18.9 MiB/s | 58.1 KiB | 00m00s [642/860] Installing perl-Math-Complex- 100% | 42.0 MiB/s | 86.0 KiB | 00m00s [643/860] Installing perl-Math-BigInt-1 100% | 106.4 MiB/s | 1.1 MiB | 00m00s [644/860] Installing perl-Data-Uniqid-0 100% | 2.8 MiB/s | 5.8 KiB | 00m00s [645/860] Installing perl-JSON-0:4.11-2 100% | 66.0 MiB/s | 270.4 KiB | 00m00s [646/860] Installing perl-JSON-PP-1:4.1 100% | 3.4 MiB/s | 144.5 KiB | 00m00s [647/860] Installing perl-Clone-PP-0:1. 100% | 6.8 MiB/s | 13.9 KiB | 00m00s [648/860] Installing perl-MRO-Compat-0: 100% | 21.9 MiB/s | 44.9 KiB | 00m00s [649/860] Installing perl-XString-0:0.0 100% | 29.4 MiB/s | 90.3 KiB | 00m00s [650/860] Installing perl-Convert-ASN1- 100% | 42.3 MiB/s | 173.4 KiB | 00m00s [651/860] Installing 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Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1785110400 Wrote: /builddir/build/SRPMS/apbs-3.0.0-38.fc45.src.rpm Updating and loading repositories: fedora 100% | 7.0 KiB/s | 2.9 KiB | 00m00s Copr repository 100% | 14.5 KiB/s | 1.5 KiB | 00m00s Repositories loaded. Package "chrpath-0.16-29.fc45.ppc64le" is already installed. Package "cmake-4.3.0-5.fc45.ppc64le" is already installed. Package "doxygen-2:1.17.0-3.fc45.ppc64le" is already installed. Package "doxygen-latex-2:1.17.0-3.fc45.noarch" is already installed. Package "gcc-c++-16.1.1-4.fc45.1.ppc64le" is already installed. Package "graphviz-15.1.0-5.fc45.ppc64le" is already installed. Package "make-1:4.4.1-13.fc45.ppc64le" is already installed. Package "maloc-devel-1.5-36.fc45.ppc64le" is already installed. Package "python3-devel-3.15.0~b4-1.fc45.ppc64le" is already installed. Package "python3-numpy-1:2.5.1-3.fc45.ppc64le" is already installed. Package "python3-sphinx-1:9.1.0-7.fc45.noarch" is already installed. Package "swig-4.5.0-1.fc45.ppc64le" is already installed. Package "texlive-collection-latexrecommended-12:svn78568-4.fc45.noarch" is already installed. Package "texlive-adjustbox-12:svn78101-7.fc45.noarch" is already installed. Package "texlive-etoc-12:svn78908-7.fc45.noarch" is already installed. Package "texlive-hanging-12:svn77682-7.fc45.noarch" is already installed. Package "texlive-multirow-12:svn77682-7.fc45.noarch" is already installed. Package "texlive-newunicodechar-12:svn77682-7.fc45.noarch" is already installed. Package "texlive-sectsty-12:svn77682-7.fc45.noarch" is already installed. Package "texlive-stackengine-12:svn75878-7.fc45.noarch" is already installed. Package "texlive-tocloft-12:svn77682-7.fc45.noarch" is already installed. Package "texlive-ulem-12:svn77682-5.fc45.noarch" is already installed. Package "texlive-wasy-12:svn53533-9.fc45.noarch" is already installed. Package "texlive-wasysym-12:svn77682-9.fc45.noarch" is already installed. Package "zlib-ng-compat-devel-2.3.3-6.fc45.ppc64le" is already installed. Nothing to do. Finish: build setup for apbs-3.0.0-38.fc45.src.rpm Start: rpmbuild apbs-3.0.0-38.fc45.src.rpm Building target platforms: ppc64le Building for target ppc64le setting SOURCE_DATE_EPOCH=1785110400 Executing(mkbuilddir): /bin/sh -e /var/tmp/rpm-tmp.1L1plZ Creating(rpmbuild.env): /builddir/build/BUILD/apbs-3.0.0-build/rpmbuild.env RPM_SOURCE_DIR="/builddir/build/SOURCES" RPM_BUILD_DIR="/builddir/build/BUILD/apbs-3.0.0-build" RPM_OPT_FLAGS="-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wno-complain-wrong-lang -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection" RPM_LD_FLAGS="-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes " RPM_ARCH="ppc64le" RPM_OS="linux" RPM_BUILD_NCPUS="5" RPM_SPECPARTS_DIR="/builddir/build/BUILD/apbs-3.0.0-build/SPECPARTS" export RPM_SOURCE_DIR RPM_BUILD_DIR RPM_OPT_FLAGS RPM_ARCH RPM_OS RPM_BUILD_NCPUS RPM_SPECPARTS_DIR RPM_LD_FLAGS RPM_DOC_DIR="/usr/share/doc" export RPM_DOC_DIR RPM_PACKAGE_NAME="apbs" RPM_PACKAGE_VERSION="3.0.0" RPM_PACKAGE_RELEASE="38.fc45" export RPM_PACKAGE_NAME RPM_PACKAGE_VERSION RPM_PACKAGE_RELEASE LANG=C.UTF-8 export LANG unset CDPATH DISPLAY ||: unset DEBUGINFOD_URLS ||: unset RPM_CONFIG_DIR ||: RPM_BUILD_ROOT="/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT" export RPM_BUILD_ROOT PKG_CONFIG_PATH="${PKG_CONFIG_PATH}:/usr/lib64/pkgconfig:/usr/share/pkgconfig" export PKG_CONFIG_PATH CONFIG_SITE=${CONFIG_SITE:-NONE} export CONFIG_SITE Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.CcKvOL + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + cd /builddir/build/BUILD/apbs-3.0.0-build + rm -rf apbs-3.0.0 + /usr/bin/rpmuncompress -x /builddir/build/SOURCES/apbs-3.0.0.tar.gz + STATUS=0 + '[' 0 -ne 0 ']' + cd apbs-3.0.0 + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w . Patch #0 (apbs-cmake.patch): + echo 'Patch #0 (apbs-cmake.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p2 -b --suffix .apbs-cmake --fuzz=0 patching file CMakeLists.txt patching file src/CMakeLists.txt patching file tools/manip/CMakeLists.txt patching file tools/mesh/CMakeLists.txt patching file tools/python/CMakeLists.txt Patch #1 (apbs-exclude_tests.patch): + echo 'Patch #1 (apbs-exclude_tests.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .exclude_tests --fuzz=0 patching file tests/test_cases.cfg Patch #2 (apbs-python311.patch): + echo 'Patch #2 (apbs-python311.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 -b --suffix .python311 --fuzz=0 patching file tools/manip/inputgen.py Patch #3 (apbs-c99.patch): + echo 'Patch #3 (apbs-c99.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file contrib/iapbs/src/apbs_driver.c Patch #4 (apbs-swig45.patch): + echo 'Patch #4 (apbs-swig45.patch):' + /usr/bin/patch --no-backup-if-mismatch -f -p1 --fuzz=0 patching file tools/python/apbslib.c patching file tools/python/apbslib.i patching file tools/python/vgrid/vgridlib.c + cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING + cp -p /builddir/build/SOURCES/apbs-LGPL_V2 contrib/iapbs/iapbs-LGPLv2 + RPM_EC=0 ++ jobs -p + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.6eW0a2 + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd apbs-3.0.0 + export 'CFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + export 'CXXFLAGS=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + /usr/bin/cmake -S . -B redhat-linux-build -G Ninja -DCMAKE_C_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_CXX_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_Fortran_FLAGS_RELEASE:STRING=-DNDEBUG -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON -DCMAKE_INSTALL_DO_STRIP:BOOL=OFF -DCMAKE_INSTALL_PREFIX:PATH=/usr -DCMAKE_INSTALL_FULL_SBINDIR:PATH=/usr/bin -DCMAKE_INSTALL_SBINDIR:PATH=bin -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSYSCONF_INSTALL_DIR:PATH=/etc -DSHARE_INSTALL_PREFIX:PATH=/usr/share -DLIB_SUFFIX=64 -DBUILD_SHARED_LIBS:BOOL=ON -DCMAKE_BUILD_TYPE:STRING=Release -DENABLE_iAPBS:BOOL=ON -DENABLE_OPENMP:BOOL=ON -DENABLE_VERBOSE_DEBUG:BOOL=OFF -DENABLE_FETK:BOOL=OFF '-DCMAKE_C_FLAGS:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG' '-DCMAKE_CXX_FLAGS:STRING=-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG' -DENABLE_PYTHON:BOOL=ON -DBUILD_DOC:BOOL=ON -DBUILD_TESTING:BOOL=ON -DENABLE_TESTS:BOOL=ON -DCMAKE_INSTALL_PREFIX:PATH=/usr -DINCLUDE_INSTALL_DIR:PATH=/usr/include -DLIB_INSTALL_DIR:PATH=/usr/lib64 -DSHARE_INSTALL_PREFIX:PATH=/usr/share -- The C compiler identification is GNU 16.1.1 -- The CXX compiler identification is GNU 16.1.1 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/gcc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/g++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Setting project paths -- Setting lookup paths for headers and libraries -- Computing machine epsilon values -- Floating point epsilon is 2.220446e-16 -- Double precision epsilon is 2.220446e-16 -- Looking for time -- Looking for time - found -- Looking for rand -- Looking for rand - found -- Looking for srand -- Looking for srand - found -- Inline functions enabled -- Checking for OpenMP -- Found OpenMP_C: -fopenmp (found version "5.2") -- Found OpenMP_CXX: -fopenmp (found version "5.2") -- Found OpenMP: TRUE (found version "5.2") -- OpenMP support enabled -- Adding apbs_generic -- With source files nosh.c;mgparm.c;femparm.c;pbamparm.c;pbsamparm.c;pbeparm.c;bemparm.c;geoflowparm.c;apolparm.c;vacc.c;valist.c;vatom.c;vpbe.c;vcap.c;vclist.c;vstring.c;vparam.c;vgreen.c -- With external header files nosh.h;mgparm.h;femparm.h;pbamparm.h;pbsamparm.h;pbeparm.h;bemparm.h;geoflowparm.h;apolparm.h;vacc.h;valist.h;vatom.h;vpbe.h;vcap.h;vclist.h;vstring.h;vparam.h;vgreen.h;vmatrix.h;vhal.h;vunit.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_generic -- Adding apbs_pmgc -- With source files buildAd.c;buildBd.c;buildGd.c;buildPd.c;cgd.c;gsd.c;matvecd.c;mgcsd.c;mgdrvd.c;mgsubd.c;mikpckd.c;mlinpckd.c;mypdec.c;newtond.c;newdrvd.c;powerd.c;smoothd.c;mgfasd.c -- With external header files buildAd.h;buildBd.h;buildGd.h;buildPd.h;cgd.h;gsd.h;matvecd.h;mgcsd.h;mgdrvd.h;mgsubd.h;mikpckd.h;mlinpckd.h;mypdec.h;newtond.h;newdrvd.h;powerd.h;smoothd.h;mgfasd.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_pmgc -- Adding apbs_mg -- With source files vgrid.c;vmgrid.c;vopot.c;vpmg.c;vpmgp.c -- With external header files vgrid.h;vmgrid.h;vopot.h;vpmg.h;vpmgp.h -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp;apbs_generic;apbs_pmgc -- Added apbs_mg -- Adding apbs_routines -- With source files routines.c -- With external header files -- With internal header files -- With library dependencies m;stdc++;maloc;-fopenmp -- Added apbs_routines -- External Headers: -- -- APBS Libraries: m;stdc++;maloc;-fopenmp -- Internal Libraries: apbs_generic;apbs_pmgc;apbs_mg;apbs_routines -- -- -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -- Building documentation enabled -- Found Doxygen: /usr/bin/doxygen (found version "1.17.0") found components: doxygen dot -- Supplemental tools enabled -- Building mesh -- libraries: apbs -- Building manip -- libraries: apbs CMake Deprecation Warning at tools/python/CMakeLists.txt:3 (CMAKE_POLICY): The OLD behavior for policy CMP0078 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. CMake Deprecation Warning at tools/python/CMakeLists.txt:4 (CMAKE_POLICY): The OLD behavior for policy CMP0086 will be removed from a future version of CMake. The cmake-policies(7) manual explains that the OLD behaviors of all policies are deprecated and that a policy should be set to OLD only under specific short-term circumstances. Projects should be ported to the NEW behavior and not rely on setting a policy to OLD. -- Found SWIG: /usr/bin/swig (found version "4.5.0") -- Found Python3: /usr/bin/python3.15 (found version "3.15.0") found components: Interpreter Development Development.Module Development.Embed -- ******* Python3 FOUND -- ***** Python3 include path is: /usr/include/python3.15 -- ***** Python3 library path is: /usr/lib64/libpython3.15.so -- ***** Python3 library dir is: /usr/lib64 -- Building of iAPBS interface enabled -- Found Python3: /usr/bin/python3.15 (found version "3.15.0") found components: Interpreter -- ******* Python3 FOUND /usr/bin/python3.15 -- TEST born_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t born -- TEST actin-dimer-auto_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t actin-dimer-auto -- TEST actin-dimer-parallel_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t actin-dimer-parallel -- TEST alkanes_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t alkanes -- TEST FKBP_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t FKBP -- TEST hca-bind_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t hca-bind -- TEST ionize_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t ionize -- TEST ion-pmf_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t ion-pmf -- TEST ion-protein_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t ion-protein -- TEST pka-lig_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t pka-lig -- TEST point-pmf_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t point-pmf -- TEST solv_test COMMAND /usr/bin/python3.15 /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/apbs -t solv -- Configuring done (2.9s) -- Generating done (0.1s) CMake Warning: Manually-specified variables were not used by the project: CMAKE_CXX_FLAGS_RELEASE CMAKE_Fortran_FLAGS_RELEASE CMAKE_INSTALL_DO_STRIP CMAKE_INSTALL_FULL_SBINDIR CMAKE_INSTALL_SBINDIR LIB_SUFFIX SYSCONF_INSTALL_DIR -- Build files have been written to: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build + /usr/bin/cmake --build redhat-linux-build -j5 --verbose Change Dir: '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build' Run Build Command(s): /usr/bin/ninja-build -v -j 5 [1/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c [2/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseRandorient’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:305:17: warning: unused variable ‘name’ [-Wunused-variable] 305 | const char* name = "randorient"; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parse3Dmap’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:373:10: warning: unused variable ‘tok’ [-Wunused-variable] 373 | char tok[VMAX_BUFSIZE]; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:372:17: warning: unused variable ‘name’ [-Wunused-variable] 372 | const char* name = "3dmap"; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseRunType’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:282:7: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 282 | strncpy(thee->runtype, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseRunName’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:297:7: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 297 | strncpy(thee->runname, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseUnits’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:344:7: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 344 | strncpy(thee->units, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseGrid2D’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:400:7: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 400 | strncpy(thee->grid2Dname[thee->grid2Dct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:408:7: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 408 | strncpy(thee->grid2Dax[thee->grid2Dct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseTermcombine’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:452:7: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 452 | strncpy(thee->termcombine, tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseXYZ’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:656:8: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 656 | strncpy(thee->xyzfil[mol][thee->xyzct[mol]], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseDiff’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:500:8: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 500 | strncpy(thee->moveType[molind], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c: In function ‘PBAMparm_parseTerm’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:563:12: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 563 | strncpy(thee->termnam[thee->termct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:573:11: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 573 | strncpy(thee->confil[thee->confilct], tok, CHR_MAXLEN); | ^ [3/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c [4/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_ctor2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c:79:9: warning: unused variable ‘i’ [-Wunused-variable] 79 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_parseMSMS’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c:183:13: warning: unused variable ‘td’ [-Wunused-variable] 183 | int td; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_parseSurf’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c:174:8: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 174 | strncpy(thee->surffil[thee->surfct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_parseImat’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c:211:8: warning: ‘__strncpy_chk’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 211 | strncpy(thee->imatfil[thee->imatct], tok, CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c: In function ‘PBSAMparm_parseExp’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.c:226:8: warning: ‘strncpy’ output may be truncated copying 1000 bytes from a string of length 8191 [-Wstringop-truncation] 226 | strncpy(thee->expfil[thee->expct], tok, CHR_MAXLEN); | ^ [5/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c: In function ‘BEMparm_ctor2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:79:9: warning: unused variable ‘i’ [-Wunused-variable] 79 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c: In function ‘BEMparm_check’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:127:36: warning: unused variable ‘nlev’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:127:26: warning: unused variable ‘tnlev’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:127:22: warning: unused variable ‘ti’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:127:12: warning: unused variable ‘tdime’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:127:9: warning: unused variable ‘i’ [-Wunused-variable] 127 | int i, tdime[3], ti, tnlev[3], nlev; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c: In function ‘BEMparm_copy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:176:9: warning: unused variable ‘i’ [-Wunused-variable] 176 | int i; | ^ [6/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.c: In function ‘GEOFLOWparm_ctor2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.c:79:9: warning: unused variable ‘i’ [-Wunused-variable] 79 | int i; | ^ [7/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c [8/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c: In function ‘PBEparm_parseWRITE’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:1163:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1163 | strncpy(thee->writestem[thee->numwrite], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c: In function ‘PBEparm_parseWRITEMAT’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:1204:5: warning: ‘strncpy’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1204 | strncpy(thee->writematstem, tok, VMAX_ARGLEN); | ^ [9/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vatom.c [10/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/valist.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/valist.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/valist.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c: In function ‘Valist_readPQR’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:618:10: warning: unused variable ‘chs’ [-Wunused-variable] 618 | char chs[VMAX_BUFSIZE]; | ^~~ [11/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vcap.c [12/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c: In function ‘NOsh_setupCalcGEOFLOWMANUAL’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2683:15: warning: variable ‘apolparm’ set but not used [-Wunused-but-set-variable=] 2683 | APOLparm *apolparm = VNULL; | ^~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:57: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c: In function ‘NOsh_parsePBAM’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:3139:17: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation] 3139 | strncpy(parm->dxname, pbeparm->writestem[pbeparm->numwrite -1], CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c: In function ‘NOsh_parsePBSAM’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:3268:17: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation] 3268 | strncpy(parm->dxname, pbeparm->writestem[pbeparm->numwrite - 1], CHR_MAXLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c: In function ‘NOsh_parseInput.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1348:13: warning: ‘strncpy’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1348 | strncpy(thee->apolname[thee->napol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1222:13: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 1222 | strncpy(thee->elecname[thee->nelec], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:953:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 953 | strncpy(thee->meshpath[thee->nmesh], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:918:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 918 | strncpy(thee->chargepath[thee->ncharge], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:872:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 872 | strncpy(thee->potpath[thee->npot], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:827:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 827 | strncpy(thee->kappapath[thee->nkappa], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:772:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 772 | strncpy(thee->dielXpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:776:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 776 | strncpy(thee->dielYpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:780:5: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 780 | strncpy(thee->dielZpath[thee->ndiel], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:723:13: warning: ‘strncpy’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 723 | strncpy(thee->parmpath, tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:701:13: warning: ‘strncpy’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 701 | strncpy(thee->parmpath, tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:659:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 659 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:640:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 640 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:621:9: warning: ‘__strncpy_chk’ output may be truncated copying 1024 bytes from a string of length 8191 [-Wstringop-truncation] 621 | strncpy(thee->molpath[thee->nmol], tok, VMAX_ARGLEN); | ^ [13/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vpbe.c [14/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vstring.c [15/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vclist.c [16/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c: In function ‘VaccSurf_dtor’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:841:11: warning: variable ‘mem’ set but not used [-Wunused-but-set-variable=] 841 | Vmem *mem; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_splineAccGradAtomNorm3’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1104:27: warning: variable ‘e5’ set but not used [-Wunused-but-set-variable=] 1104 | double e, e2, e3, e4, e5; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_atomdSASA’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1338:12: warning: variable ‘ts’ set but not used [-Wunused-but-set-variable=] 1338 | time_t ts; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1335:15: warning: variable ‘ref’ set but not used [-Wunused-but-set-variable=] 1335 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_totalAtomdSASA’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1395:15: warning: variable ‘ref’ set but not used [-Wunused-but-set-variable=] 1395 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1392:23: warning: variable ‘tRad’ set but not used [-Wunused-but-set-variable=] 1392 | double *temp_Pos, tRad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1391:9: warning: variable ‘iatom’ set but not used [-Wunused-but-set-variable=] 1391 | int iatom; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_totalAtomdSAV’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1454:15: warning: variable ‘ref’ set but not used [-Wunused-but-set-variable=] 1454 | VaccSurf *ref; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1451:23: warning: variable ‘tRad’ set but not used [-Wunused-but-set-variable=] 1451 | double *temp_Pos, tRad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1450:9: warning: variable ‘iatom’ set but not used [-Wunused-but-set-variable=] 1450 | int iatom; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_totalSAV’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1509:45: warning: variable ‘vol’ set but not used [-Wunused-but-set-variable=] 1509 | double w, wx, wy, wz, len, fn, x, y, z, vol; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_wcaEnergyAtom’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1593:45: warning: variable ‘vol’ set but not used [-Wunused-but-set-variable=] 1593 | double w, wx, wy, wz, len, fn, x, y, z, vol; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1584:9: warning: variable ‘npts’ set but not used [-Wunused-but-set-variable=] 1584 | int npts[3]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c: In function ‘Vacc_wcaForceAtom’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1807:12: warning: variable ‘ts’ set but not used [-Wunused-but-set-variable=] 1807 | time_t ts; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1787:12: warning: variable ‘vol’ set but not used [-Wunused-but-set-variable=] 1787 | vol, | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1764:9: warning: variable ‘npts’ set but not used [-Wunused-but-set-variable=] 1764 | npts[3], | ^~~~ [17/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c: In function ‘Vgreen_coulomb_direct’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:229:31: warning: unused variable ‘fz’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:229:27: warning: unused variable ‘fy’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:229:23: warning: unused variable ‘fx’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:229:16: warning: unused variable ‘qtemp’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:229:13: warning: unused variable ‘q’ [-Wunused-variable] 229 | double *q, qtemp, fx, fy, fz; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c: In function ‘Vgreen_coulomb’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:264:9: warning: unused variable ‘iatom’ [-Wunused-variable] 264 | int iatom, ipos; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:263:31: warning: unused variable ‘fz’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:263:27: warning: unused variable ‘fy’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:263:23: warning: unused variable ‘fx’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:263:16: warning: unused variable ‘qtemp’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:263:13: warning: unused variable ‘q’ [-Wunused-variable] 263 | double *q, qtemp, fx, fy, fz; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:262:45: warning: unused variable ‘scale’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:262:41: warning: unused variable ‘dz’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:262:37: warning: unused variable ‘dy’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:262:33: warning: unused variable ‘dx’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:262:27: warning: unused variable ‘dist’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:262:19: warning: unused variable ‘charge’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:262:13: warning: unused variable ‘apos’ [-Wunused-variable] 262 | double *apos, charge, dist, dx, dy, dz, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:261:12: warning: unused variable ‘atom’ [-Wunused-variable] 261 | Vatom *atom; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c: In function ‘Vgreen_coulombD_direct’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:316:16: warning: unused variable ‘qtemp’ [-Wunused-variable] 316 | double *q, qtemp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:316:13: warning: unused variable ‘q’ [-Wunused-variable] 316 | double *q, qtemp; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c: In function ‘Vgreen_coulombD’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:368:9: warning: unused variable ‘iatom’ [-Wunused-variable] 368 | int iatom, ipos; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:367:16: warning: unused variable ‘qtemp’ [-Wunused-variable] 367 | double *q, qtemp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:367:13: warning: unused variable ‘q’ [-Wunused-variable] 367 | double *q, qtemp; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:60: warning: unused variable ‘scale’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:56: warning: unused variable ‘dx’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:52: warning: unused variable ‘dz’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:48: warning: unused variable ‘dy’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:40: warning: unused variable ‘idist3’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:33: warning: unused variable ‘dist2’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:27: warning: unused variable ‘dist’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:19: warning: unused variable ‘charge’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:366:13: warning: unused variable ‘apos’ [-Wunused-variable] 366 | double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:365:12: warning: unused variable ‘atom’ [-Wunused-variable] 365 | Vatom *atom; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:525:14: warning: ‘treecalc’ defined but not used [-Wunused-function] 525 | VPRIVATE int treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:505:14: warning: ‘treecleanup’ defined but not used [-Wunused-function] 505 | VPRIVATE int treecleanup(Vgreen *thee) { | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:425:14: warning: ‘treesetup’ defined but not used [-Wunused-function] 425 | VPRIVATE int treesetup(Vgreen *thee) { | ^~~~~~~~~ [18/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c: In function ‘VbuildA’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:66:5: note: in expansion of macro ‘MAT2’ 66 | MAT2(ac, *nx * *ny * *nz, 14); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c: In function ‘VbuildA_fv’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gzcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:167:5: note: in expansion of macro ‘MAT3’ 167 | MAT3(gzcf, *nx, *ny, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gycf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:166:5: note: in expansion of macro ‘MAT3’ 166 | MAT3(gycf, *nx, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gxcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:165:5: note: in expansion of macro ‘MAT3’ 165 | MAT3(gxcf, *ny, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:164:5: note: in expansion of macro ‘MAT3’ 164 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:163:5: note: in expansion of macro ‘MAT3’ 163 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:162:5: note: in expansion of macro ‘MAT3’ 162 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a3cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:161:5: note: in expansion of macro ‘MAT3’ 161 | MAT3(a3cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a2cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:160:5: note: in expansion of macro ‘MAT3’ 160 | MAT3(a2cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a1cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:159:5: note: in expansion of macro ‘MAT3’ 159 | MAT3(a1cf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:158:5: note: in expansion of macro ‘MAT3’ 158 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_ccf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:157:5: note: in expansion of macro ‘MAT3’ 157 | MAT3( ccf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:156:5: note: in expansion of macro ‘MAT3’ 156 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:155:5: note: in expansion of macro ‘MAT3’ 155 | MAT3( fcf, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildAd.c:154:5: note: in expansion of macro ‘MAT3’ 154 | MAT3( fc, *nx, *ny, *nz); | ^~~~ [19/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c: In function ‘Vbuildband’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:65:5: note: in expansion of macro ‘MAT2’ 65 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c: In function ‘Vbuildband1_7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:133:5: note: in expansion of macro ‘MAT3’ 133 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:132:5: note: in expansion of macro ‘MAT3’ 132 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:131:5: note: in expansion of macro ‘MAT3’ 131 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:130:5: note: in expansion of macro ‘MAT3’ 130 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_acB’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:128:5: note: in expansion of macro ‘MAT2’ 128 | MAT2(acB, *lda, *ny-1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c: In function ‘Vbuildband1_27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:213:5: note: in expansion of macro ‘MAT3’ 213 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:212:5: note: in expansion of macro ‘MAT3’ 212 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:211:5: note: in expansion of macro ‘MAT3’ 211 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:210:5: note: in expansion of macro ‘MAT3’ 210 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:208:5: note: in expansion of macro ‘MAT3’ 208 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:207:5: note: in expansion of macro ‘MAT3’ 207 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:206:5: note: in expansion of macro ‘MAT3’ 206 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:205:5: note: in expansion of macro ‘MAT3’ 205 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:203:5: note: in expansion of macro ‘MAT3’ 203 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:202:5: note: in expansion of macro ‘MAT3’ 202 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:200:5: note: in expansion of macro ‘MAT3’ 200 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:199:5: note: in expansion of macro ‘MAT3’ 199 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:198:5: note: in expansion of macro ‘MAT3’ 198 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:197:5: note: in expansion of macro ‘MAT3’ 197 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_acB’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildBd.c:195:5: note: in expansion of macro ‘MAT2’ 195 | MAT2(acB, *lda, *ny-1); | ^~~~ [20/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o -MF src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o.d -o src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vparam.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vparam.c: In function ‘Vparam_readXMLFile’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vparam.c:412:22: warning: ‘natoms’ may be used uninitialized [-Wmaybe-uninitialized] 412 | for (i=0; ivmem, nalloc, sizeof(Vparam_AtomData), (void **)&(atoms)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vparam.c:309:26: note: ‘nalloc’ was declared here 309 | int i, ires, natoms, nalloc, ralloc; | ^~~~~~ [21/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/cgd.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/cgd.c: In function ‘Vcghs’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/cgd.c:99:24: warning: ‘rhok1’ may be used uninitialized [-Wmaybe-uninitialized] 99 | beta = rhok2 / rhok1; | ~~~~~~^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/cgd.c:66:12: note: ‘rhok1’ was declared here 66 | double rhok1, rhok2, alpha, beta; | ^~~~~ [22/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/CMakeFiles/apbs_routines.dir/routines.c.o -MF src/CMakeFiles/apbs_routines.dir/routines.c.o.d -o src/CMakeFiles/apbs_routines.dir/routines.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘loadDielMaps’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:296:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 296 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:298:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 298 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:331:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 331 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:333:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 333 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:420:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 420 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:422:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 422 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:454:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 454 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:456:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 456 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘initMG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1235:12: warning: variable ‘q’ set but not used [-Wunused-but-set-variable=] 1235 | q; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1234:12: warning: variable ‘iparm’ set but not used [-Wunused-but-set-variable=] 1234 | iparm, | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘energyMG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1584:13: warning: variable ‘mgparm’ set but not used [-Wunused-but-set-variable=] 1584 | MGparm *mgparm; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writematMG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1803:10: warning: variable ‘mxtype’ set but not used [-Wunused-but-set-variable=] 1803 | char mxtype[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘printApolForce’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:3485:12: warning: variable ‘scalar’ set but not used [-Wunused-but-set-variable=] 3485 | scalar, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:3484:12: warning: variable ‘temp’ set but not used [-Wunused-but-set-variable=] 3484 | double temp, | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘initAPOL’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4508:12: warning: variable ‘charge’ set but not used [-Wunused-but-set-variable=] 4508 | charge, /**< @todo document */ | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4496:12: warning: variable ‘sav’ set but not used [-Wunused-but-set-variable=] 4496 | sav, /**< @todo document */ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4495:12: warning: variable ‘sasa’ set but not used [-Wunused-but-set-variable=] 4495 | double sasa, /**< @todo document */ | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4489:12: warning: unused variable ‘ts’ [-Wunused-variable] 4489 | time_t ts; /**< Temporary timing variable for debugging (PCE) */ | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘forceAPOL’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4753:13: warning: unused variable ‘apos’ [-Wunused-variable] 4753 | *apos; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4737:46: warning: unused variable ‘ts_sub’ [-Wunused-variable] 4737 | time_t ts, ts_main, ts_sub; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘initAPOL’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4590:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4590:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type ‘char[1024]’ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.h:73, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:73: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4591:43: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4591:43: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writematMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1826:34: warning: ‘-PE’ directive writing 3 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1826 | sprintf(writematstem, "%s-PE%d", pbeparm->writematstem,nosh->proc_rank); | ^~~ In file included from /usr/include/stdio.h:974, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:67: In function ‘*__sprintfieee128’, inlined from ‘writematMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1826:9: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1038 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writematMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1840:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1840 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writematMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1840:9: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2676:30: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2676 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2676:9: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2720:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2720 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2720:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2711:38: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2711 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2711:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2694:38: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2694 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2694:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2687:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2687 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2687:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2701:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2701 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2701:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2666:38: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2666 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2666:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataFlat’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2105:33: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2105 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1906:44: note: ‘scalar’ was declared here 1906 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataXML’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2363:33: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2363 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2140:44: note: ‘scalar’ was declared here 2140 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘returnEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2778:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2778 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2762:12: note: ‘scalar’ was declared here 2762 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘printEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2839:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2839 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2795:12: note: ‘scalar’ was declared here 2795 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘printElecEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2904:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2904 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2863:12: note: ‘scalar’ was declared here 2863 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘printApolEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2970:18: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2970 | gtenergy += (scalar * ((apolparm->gamma*apolparm->sasa) + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2971 | (apolparm->press*apolparm->sav) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2972 | (apolparm->wcaEnergy))); | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2925:12: note: ‘scalar’ was declared here 2925 | scalar; | ^~~~~~ [23/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c: In function ‘Vgsrb’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:67:5: note: in expansion of macro ‘MAT2’ 67 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c: In function ‘Vgsrb7x’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:116:5: note: in expansion of macro ‘MAT3’ 116 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:115:5: note: in expansion of macro ‘MAT3’ 115 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:114:5: note: in expansion of macro ‘MAT3’ 114 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:113:5: note: in expansion of macro ‘MAT3’ 113 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro ‘MAT3’ 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_r’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro ‘MAT3’ 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_r’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro ‘MAT3’ 111 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w2’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro ‘MAT3’ 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_w2’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro ‘MAT3’ 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_w2’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro ‘MAT3’ 110 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro ‘MAT3’ 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_w1’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro ‘MAT3’ 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_w1’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro ‘MAT3’ 109 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:108:5: note: in expansion of macro ‘MAT3’ 108 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:107:5: note: in expansion of macro ‘MAT3’ 107 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:106:5: note: in expansion of macro ‘MAT3’ 106 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c: In function ‘Vgsrb27x’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:208:5: note: in expansion of macro ‘MAT3’ 208 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:207:5: note: in expansion of macro ‘MAT3’ 207 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:206:5: note: in expansion of macro ‘MAT3’ 206 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:205:5: note: in expansion of macro ‘MAT3’ 205 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:204:5: note: in expansion of macro ‘MAT3’ 204 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:203:5: note: in expansion of macro ‘MAT3’ 203 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:202:5: note: in expansion of macro ‘MAT3’ 202 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:201:5: note: in expansion of macro ‘MAT3’ 201 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:199:5: note: in expansion of macro ‘MAT3’ 199 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:198:5: note: in expansion of macro ‘MAT3’ 198 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:196:5: note: in expansion of macro ‘MAT3’ 196 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:195:5: note: in expansion of macro ‘MAT3’ 195 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:194:5: note: in expansion of macro ‘MAT3’ 194 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:193:5: note: in expansion of macro ‘MAT3’ 193 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro ‘MAT3’ 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_r’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro ‘MAT3’ 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_r’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro ‘MAT3’ 191 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w2’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro ‘MAT3’ 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_w2’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro ‘MAT3’ 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_w2’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro ‘MAT3’ 190 | MAT3(w2, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro ‘MAT3’ 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_w1’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro ‘MAT3’ 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_w1’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro ‘MAT3’ 189 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:188:5: note: in expansion of macro ‘MAT3’ 188 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:187:5: note: in expansion of macro ‘MAT3’ 187 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:186:5: note: in expansion of macro ‘MAT3’ 186 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:182:9: warning: variable ‘istep’ set but not used [-Wunused-but-set-variable=] 182 | int istep; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:180:17: warning: variable ‘k2’ set but not used [-Wunused-but-set-variable=] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:180:13: warning: variable ‘j2’ set but not used [-Wunused-but-set-variable=] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:180:9: warning: variable ‘i2’ set but not used [-Wunused-but-set-variable=] 180 | int i2, j2, k2; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:179:17: warning: variable ‘k1’ set but not used [-Wunused-but-set-variable=] 179 | int i1, j1, k1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:179:13: warning: variable ‘j1’ set but not used [-Wunused-but-set-variable=] 179 | int i1, j1, k1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/gsd.c:179:9: warning: variable ‘i1’ set but not used [-Wunused-but-set-variable=] 179 | int i1, j1, k1; | ^~ [24/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgcsd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgcsd.h:58, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgcsd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgcsd.c: In function ‘Vmvcs’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgcsd.c:99:5: note: in expansion of macro ‘MAT2’ 99 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgcsd.c:560:13: warning: ‘rsden’ may be used uninitialized [-Wmaybe-uninitialized] 560 | Vprtstp(*iok, *iters, rsnrm, rsden, orsnrm); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgcsd.c:88:12: note: ‘rsden’ was declared here 88 | double rsden; // @todo: doc | ^~~~~ [25/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c: In function ‘Vmgdriv’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:85:9: warning: unused variable ‘ierror’ [-Wunused-variable] 85 | int ierror = 0; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.h:62, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c: In function ‘Vmgdriv2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:267:5: note: in expansion of macro ‘MAT2’ 267 | MAT2(iz, 50, nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:234:12: warning: unused variable ‘tsolve’ [-Wunused-variable] 234 | double tsolve = 0.0; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:233:12: warning: unused variable ‘tsetupc’ [-Wunused-variable] 233 | double tsetupc = 0.0; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:232:12: warning: unused variable ‘tsetupf’ [-Wunused-variable] 232 | double tsetupf = 0.0; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:231:12: warning: unused variable ‘oh’ [-Wunused-variable] 231 | double oh = 0.0; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:230:12: warning: unused variable ‘bf’ [-Wunused-variable] 230 | double bf = 0.0; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:226:12: warning: unused variable ‘epsmac’ [-Wunused-variable] 226 | double epsmac = 0.0; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c: In function ‘Vmgsz’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:655:26: warning: ‘num_narrc_oper’ may be used uninitialized [-Wmaybe-uninitialized] 655 | + (num_narrc + num_narrc_oper) * *narrc | ~~~~~~~~~~~^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:580:22: note: ‘num_narrc_oper’ was declared here 580 | int num_nf_oper, num_narrc_oper; | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:654:41: warning: ‘num_nf_oper’ may be used uninitialized [-Wmaybe-uninitialized] 654 | + (num_nf + num_nf_oper) * *nf | ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:580:9: note: ‘num_nf_oper’ was declared here 580 | int num_nf_oper, num_narrc_oper; | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:656:13: warning: ‘n_band’ may be used uninitialized [-Wmaybe-uninitialized] 653 | *iretot = num_narr * *narr | ~~~~~~~~~~~~~~~~ 654 | + (num_nf + num_nf_oper) * *nf | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 655 | + (num_narrc + num_narrc_oper) * *narrc | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 656 | + n_band | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgdrvd.c:577:28: note: ‘n_band’ was declared here 577 | int nc_band, num_band, n_band; | ^~~~~~ [26/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.h:58, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c: In function ‘Vbuildops’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:83:5: note: in expansion of macro ‘MAT2’ 83 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c: In function ‘Vbuildstr’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:266:5: note: in expansion of macro ‘MAT2’ 266 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c: In function ‘Vbuildcopy0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:628:5: note: in expansion of macro ‘MAT3’ 628 | MAT3( fcf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_ccf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:627:5: note: in expansion of macro ‘MAT3’ 627 | MAT3( ccf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_tcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:626:5: note: in expansion of macro ‘MAT3’ 626 | MAT3( tcf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a3cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:625:5: note: in expansion of macro ‘MAT3’ 625 | MAT3(a3cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a2cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:624:5: note: in expansion of macro ‘MAT3’ 624 | MAT3(a2cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a1cf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:623:5: note: in expansion of macro ‘MAT3’ 623 | MAT3(a1cf, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gzcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:622:5: note: in expansion of macro ‘MAT3’ 622 | MAT3(gzcf, *nxf, *nyf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gycf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:621:5: note: in expansion of macro ‘MAT3’ 621 | MAT3(gycf, *nxf, *nzf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gxcf’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:620:5: note: in expansion of macro ‘MAT3’ 620 | MAT3(gxcf, *nyf, *nzf, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_tc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:619:5: note: in expansion of macro ‘MAT3’ 619 | MAT3( tc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:618:5: note: in expansion of macro ‘MAT3’ 618 | MAT3( fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:617:5: note: in expansion of macro ‘MAT3’ 617 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a3c’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:616:5: note: in expansion of macro ‘MAT3’ 616 | MAT3( a3c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a2c’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:615:5: note: in expansion of macro ‘MAT3’ 615 | MAT3( a2c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_a1c’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:614:5: note: in expansion of macro ‘MAT3’ 614 | MAT3( a1c, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gzc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:613:5: note: in expansion of macro ‘MAT3’ 613 | MAT3( gzc, *nx, *ny, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gyc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:612:5: note: in expansion of macro ‘MAT3’ 612 | MAT3( gyc, *nx, *nz, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gxc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:611:5: note: in expansion of macro ‘MAT3’ 611 | MAT3( gxc, *ny, *nz, 4); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c: In function ‘Vbuildalg’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgsubd.c:914:5: note: in expansion of macro ‘MAT2’ 914 | MAT2(iz, 50, *nlev); | ^~~~ [27/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.h:58, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildP’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:67:5: note: in expansion of macro ‘MAT2’ 67 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:66:5: note: in expansion of macro ‘MAT2’ 66 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildP_trilin’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:101:5: note: in expansion of macro ‘MAT2’ 101 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildPb_trilin’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:163:5: note: in expansion of macro ‘MAT3’ 163 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:162:5: note: in expansion of macro ‘MAT3’ 162 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:161:5: note: in expansion of macro ‘MAT3’ 161 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:160:5: note: in expansion of macro ‘MAT3’ 160 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:158:5: note: in expansion of macro ‘MAT3’ 158 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:157:5: note: in expansion of macro ‘MAT3’ 157 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:156:5: note: in expansion of macro ‘MAT3’ 156 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:155:5: note: in expansion of macro ‘MAT3’ 155 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:154:5: note: in expansion of macro ‘MAT3’ 154 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:152:5: note: in expansion of macro ‘MAT3’ 152 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:151:5: note: in expansion of macro ‘MAT3’ 151 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:150:5: note: in expansion of macro ‘MAT3’ 150 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:149:5: note: in expansion of macro ‘MAT3’ 149 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:147:5: note: in expansion of macro ‘MAT3’ 147 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:146:5: note: in expansion of macro ‘MAT3’ 146 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:145:5: note: in expansion of macro ‘MAT3’ 145 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:144:5: note: in expansion of macro ‘MAT3’ 144 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:143:5: note: in expansion of macro ‘MAT3’ 143 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:141:5: note: in expansion of macro ‘MAT3’ 141 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:140:5: note: in expansion of macro ‘MAT3’ 140 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:139:5: note: in expansion of macro ‘MAT3’ 139 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:138:5: note: in expansion of macro ‘MAT3’ 138 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:136:5: note: in expansion of macro ‘MAT3’ 136 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:135:5: note: in expansion of macro ‘MAT3’ 135 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:134:5: note: in expansion of macro ‘MAT3’ 134 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:133:5: note: in expansion of macro ‘MAT3’ 133 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:132:5: note: in expansion of macro ‘MAT3’ 132 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildP_op7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:212:5: note: in expansion of macro ‘MAT2’ 212 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:211:5: note: in expansion of macro ‘MAT2’ 211 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildPb_op7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:287:5: note: in expansion of macro ‘MAT3’ 287 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:286:5: note: in expansion of macro ‘MAT3’ 286 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:285:5: note: in expansion of macro ‘MAT3’ 285 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:284:5: note: in expansion of macro ‘MAT3’ 284 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:283:5: note: in expansion of macro ‘MAT3’ 283 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:282:5: note: in expansion of macro ‘MAT3’ 282 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:281:5: note: in expansion of macro ‘MAT3’ 281 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:280:5: note: in expansion of macro ‘MAT3’ 280 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:279:5: note: in expansion of macro ‘MAT3’ 279 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:278:5: note: in expansion of macro ‘MAT3’ 278 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:277:5: note: in expansion of macro ‘MAT3’ 277 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:276:5: note: in expansion of macro ‘MAT3’ 276 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:275:5: note: in expansion of macro ‘MAT3’ 275 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:274:5: note: in expansion of macro ‘MAT3’ 274 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:273:5: note: in expansion of macro ‘MAT3’ 273 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:272:5: note: in expansion of macro ‘MAT3’ 272 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:271:5: note: in expansion of macro ‘MAT3’ 271 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:270:5: note: in expansion of macro ‘MAT3’ 270 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:269:5: note: in expansion of macro ‘MAT3’ 269 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:268:5: note: in expansion of macro ‘MAT3’ 268 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:267:5: note: in expansion of macro ‘MAT3’ 267 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:266:5: note: in expansion of macro ‘MAT3’ 266 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:265:5: note: in expansion of macro ‘MAT3’ 265 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:264:5: note: in expansion of macro ‘MAT3’ 264 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:263:5: note: in expansion of macro ‘MAT3’ 263 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:262:5: note: in expansion of macro ‘MAT3’ 262 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:261:5: note: in expansion of macro ‘MAT3’ 261 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:260:5: note: in expansion of macro ‘MAT3’ 260 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:259:5: note: in expansion of macro ‘MAT3’ 259 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:258:5: note: in expansion of macro ‘MAT3’ 258 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:257:5: note: in expansion of macro ‘MAT3’ 257 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:255:32: warning: variable ‘eighth’ set but not used [-Wunused-but-set-variable=] 255 | double won, half, quarter, eighth; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:255:23: warning: variable ‘quarter’ set but not used [-Wunused-but-set-variable=] 255 | double won, half, quarter, eighth; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:255:17: warning: variable ‘half’ set but not used [-Wunused-but-set-variable=] 255 | double won, half, quarter, eighth; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:253:15: warning: variable ‘kkp1’ set but not used [-Wunused-but-set-variable=] 253 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:253:9: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable=] 253 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:252:15: warning: variable ‘jjp1’ set but not used [-Wunused-but-set-variable=] 252 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:252:9: warning: variable ‘jjm1’ set but not used [-Wunused-but-set-variable=] 252 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:251:15: warning: variable ‘iip1’ set but not used [-Wunused-but-set-variable=] 251 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:251:9: warning: variable ‘iim1’ set but not used [-Wunused-but-set-variable=] 251 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:250:16: warning: variable ‘kp2’ set but not used [-Wunused-but-set-variable=] 250 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:250:10: warning: variable ‘km2’ set but not used [-Wunused-but-set-variable=] 250 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:248:16: warning: variable ‘jp2’ set but not used [-Wunused-but-set-variable=] 248 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:248:10: warning: variable ‘jm2’ set but not used [-Wunused-but-set-variable=] 248 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:246:16: warning: variable ‘ip2’ set but not used [-Wunused-but-set-variable=] 246 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:246:10: warning: variable ‘im2’ set but not used [-Wunused-but-set-variable=] 246 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildP_op27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:728:5: note: in expansion of macro ‘MAT2’ 728 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:727:5: note: in expansion of macro ‘MAT2’ 727 | MAT2(ac, *nxf * *nyf * *nzf, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c: In function ‘VbuildPb_op27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:818:7: note: in expansion of macro ‘MAT3’ 818 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:817:7: note: in expansion of macro ‘MAT3’ 817 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:816:7: note: in expansion of macro ‘MAT3’ 816 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:815:7: note: in expansion of macro ‘MAT3’ 815 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:814:7: note: in expansion of macro ‘MAT3’ 814 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:813:7: note: in expansion of macro ‘MAT3’ 813 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:812:7: note: in expansion of macro ‘MAT3’ 812 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:811:7: note: in expansion of macro ‘MAT3’ 811 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:810:7: note: in expansion of macro ‘MAT3’ 810 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:809:7: note: in expansion of macro ‘MAT3’ 809 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:808:7: note: in expansion of macro ‘MAT3’ 808 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:807:7: note: in expansion of macro ‘MAT3’ 807 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:806:7: note: in expansion of macro ‘MAT3’ 806 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:805:7: note: in expansion of macro ‘MAT3’ 805 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:804:7: note: in expansion of macro ‘MAT3’ 804 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:803:7: note: in expansion of macro ‘MAT3’ 803 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:802:7: note: in expansion of macro ‘MAT3’ 802 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:801:7: note: in expansion of macro ‘MAT3’ 801 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:800:7: note: in expansion of macro ‘MAT3’ 800 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:799:7: note: in expansion of macro ‘MAT3’ 799 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:798:7: note: in expansion of macro ‘MAT3’ 798 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:797:7: note: in expansion of macro ‘MAT3’ 797 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:796:7: note: in expansion of macro ‘MAT3’ 796 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:795:7: note: in expansion of macro ‘MAT3’ 795 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:794:7: note: in expansion of macro ‘MAT3’ 794 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:793:7: note: in expansion of macro ‘MAT3’ 793 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:792:7: note: in expansion of macro ‘MAT3’ 792 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:791:7: note: in expansion of macro ‘MAT3’ 791 | MAT3( uSW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:790:7: note: in expansion of macro ‘MAT3’ 790 | MAT3( uSE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:789:7: note: in expansion of macro ‘MAT3’ 789 | MAT3( uNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:788:7: note: in expansion of macro ‘MAT3’ 788 | MAT3( uNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:787:7: note: in expansion of macro ‘MAT3’ 787 | MAT3( uS, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:786:7: note: in expansion of macro ‘MAT3’ 786 | MAT3( uN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:785:7: note: in expansion of macro ‘MAT3’ 785 | MAT3( uW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:784:7: note: in expansion of macro ‘MAT3’ 784 | MAT3( uE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:783:7: note: in expansion of macro ‘MAT3’ 783 | MAT3( oNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:782:7: note: in expansion of macro ‘MAT3’ 782 | MAT3( oNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:781:7: note: in expansion of macro ‘MAT3’ 781 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:780:7: note: in expansion of macro ‘MAT3’ 780 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:779:7: note: in expansion of macro ‘MAT3’ 779 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:778:7: note: in expansion of macro ‘MAT3’ 778 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:776:34: warning: variable ‘eighth’ set but not used [-Wunused-but-set-variable=] 776 | double won, half, quarter, eighth; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:776:25: warning: variable ‘quarter’ set but not used [-Wunused-but-set-variable=] 776 | double won, half, quarter, eighth; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:776:19: warning: variable ‘half’ set but not used [-Wunused-but-set-variable=] 776 | double won, half, quarter, eighth; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:774:17: warning: variable ‘kkp1’ set but not used [-Wunused-but-set-variable=] 774 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:774:11: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable=] 774 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:773:17: warning: variable ‘jjp1’ set but not used [-Wunused-but-set-variable=] 773 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:773:11: warning: variable ‘jjm1’ set but not used [-Wunused-but-set-variable=] 773 | int jjm1, jjp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:772:17: warning: variable ‘iip1’ set but not used [-Wunused-but-set-variable=] 772 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:772:11: warning: variable ‘iim1’ set but not used [-Wunused-but-set-variable=] 772 | int iim1, iip1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:771:18: warning: variable ‘kp2’ set but not used [-Wunused-but-set-variable=] 771 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:771:12: warning: variable ‘km2’ set but not used [-Wunused-but-set-variable=] 771 | int km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:769:18: warning: variable ‘jp2’ set but not used [-Wunused-but-set-variable=] 769 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:769:12: warning: variable ‘jm2’ set but not used [-Wunused-but-set-variable=] 769 | int jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:767:18: warning: variable ‘ip2’ set but not used [-Wunused-but-set-variable=] 767 | int im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildPd.c:767:12: warning: variable ‘im2’ set but not used [-Wunused-but-set-variable=] 767 | int im2, ip2; | ^~~ [28/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.h:58, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxcopy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:60:5: note: in expansion of macro ‘MAT3’ 60 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:59:5: note: in expansion of macro ‘MAT3’ 59 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxcopy_small’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:78:5: note: in expansion of macro ‘MAT3’ 78 | MAT3(y, *nx - 2, *ny - 2, *nz - 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:77:5: note: in expansion of macro ‘MAT3’ 77 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxcopy_large’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:99:5: note: in expansion of macro ‘MAT3’ 99 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:98:5: note: in expansion of macro ‘MAT3’ 98 | MAT3(x, *nx - 2, *ny - 2, *nz - 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxaxpy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:117:5: note: in expansion of macro ‘MAT3’ 117 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:116:5: note: in expansion of macro ‘MAT3’ 116 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxnrm1’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:136:5: note: in expansion of macro ‘MAT3’ 136 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxnrm2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:157:5: note: in expansion of macro ‘MAT3’ 157 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxdot’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:182:5: note: in expansion of macro ‘MAT3’ 182 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:181:5: note: in expansion of macro ‘MAT3’ 181 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vazeros’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:198:9: warning: unused variable ‘nproc’ [-Wunused-variable] 198 | int nproc = 1; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘VfboundPMG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gzc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:218:5: note: in expansion of macro ‘MAT3’ 218 | MAT3(gzc, *nx, *ny, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gyc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:217:5: note: in expansion of macro ‘MAT3’ 217 | MAT3(gyc, *nx, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_gxc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:216:5: note: in expansion of macro ‘MAT3’ 216 | MAT3(gxc, *ny, *nz, 2); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:215:5: note: in expansion of macro ‘MAT3’ 215 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘VfboundPMG00’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:262:5: note: in expansion of macro ‘MAT3’ 262 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vaxrand’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:295:12: warning: variable ‘xdum’ set but not used [-Wunused-but-set-variable=] 295 | double xdum; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:293:33: warning: variable ‘iflag’ set but not used [-Wunused-but-set-variable=] 293 | int n, i, ii, ipara, ivect, iflag; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:293:26: warning: variable ‘ivect’ set but not used [-Wunused-but-set-variable=] 293 | int n, i, ii, ipara, ivect, iflag; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vxscal’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:322:5: note: in expansion of macro ‘MAT3’ 322 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vprtmatd’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:337:5: note: in expansion of macro ‘MAT2’ 337 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vprtmatd7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:370:5: note: in expansion of macro ‘MAT3’ 370 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:369:5: note: in expansion of macro ‘MAT3’ 369 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:368:5: note: in expansion of macro ‘MAT3’ 368 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:367:5: note: in expansion of macro ‘MAT3’ 367 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c: In function ‘Vprtmatd27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:415:5: note: in expansion of macro ‘MAT3’ 415 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:414:5: note: in expansion of macro ‘MAT3’ 414 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:413:5: note: in expansion of macro ‘MAT3’ 413 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:412:5: note: in expansion of macro ‘MAT3’ 412 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:411:5: note: in expansion of macro ‘MAT3’ 411 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:410:5: note: in expansion of macro ‘MAT3’ 410 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:409:5: note: in expansion of macro ‘MAT3’ 409 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:408:5: note: in expansion of macro ‘MAT3’ 408 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:407:5: note: in expansion of macro ‘MAT3’ 407 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:406:5: note: in expansion of macro ‘MAT3’ 406 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:405:5: note: in expansion of macro ‘MAT3’ 405 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:404:5: note: in expansion of macro ‘MAT3’ 404 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:403:5: note: in expansion of macro ‘MAT3’ 403 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.c:402:5: note: in expansion of macro ‘MAT3’ 402 | MAT3( oC, *nx, *ny, *nz); | ^~~~ [29/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c: In function ‘Vdpbsl’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_abd’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c:62:5: note: in expansion of macro ‘MAT2’ 62 | MAT2(abd, *lda, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c: In function ‘Vddot’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c:141:16: warning: variable ‘iy’ set but not used [-Wunused-but-set-variable=] 141 | int i, ix, iy, m, mp1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c:141:12: warning: variable ‘ix’ set but not used [-Wunused-but-set-variable=] 141 | int i, ix, iy, m, mp1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c: In function ‘Vdpbfa’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_abd’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c:199:5: note: in expansion of macro ‘MAT2’ 199 | MAT2(abd, *lda, 1); | ^~~~ [30/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c: In function ‘Vnewdriv’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:86:9: warning: unused variable ‘maxlev’ [-Wunused-variable] 86 | int maxlev; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:85:9: warning: unused variable ‘ierror’ [-Wunused-variable] 85 | int ierror; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c: In function ‘Vnewdriv2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:223:9: warning: unused variable ‘i’ [-Wunused-variable] 223 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:221:12: warning: unused variable ‘orsnrm_t’ [-Wunused-variable] 221 | double orsnrm_t; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:220:12: warning: unused variable ‘rsden_t’ [-Wunused-variable] 220 | double rsden_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:219:12: warning: unused variable ‘rsnrm_t’ [-Wunused-variable] 219 | double rsnrm_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:218:9: warning: unused variable ‘iters_t’ [-Wunused-variable] 218 | int iters_t; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:217:9: warning: unused variable ‘iok_t’ [-Wunused-variable] 217 | int iok_t; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:215:9: warning: unused variable ‘numlev’ [-Wunused-variable] 215 | int numlev; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:210:12: warning: unused variable ‘tsolve’ [-Wunused-variable] 210 | double tsolve; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:209:12: warning: unused variable ‘tsetupc’ [-Wunused-variable] 209 | double tsetupc; /// @todo: Doc | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:208:12: warning: unused variable ‘tsetupf’ [-Wunused-variable] 208 | double tsetupf; /// @todo: Doc | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:207:12: warning: unused variable ‘oh’ [-Wunused-variable] 207 | double oh; /// @todo: Doc | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:206:12: warning: unused variable ‘bf’ [-Wunused-variable] 206 | double bf; /// @todo: Doc | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:204:12: warning: variable ‘omegal’ set but not used [-Wunused-but-set-variable=] 204 | double omegal; /// @todo: Doc | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c:202:12: warning: unused variable ‘epsmac’ [-Wunused-variable] 202 | double epsmac; /// @todo: Doc | ^~~~~~ [31/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vmypdefinitsmpbe’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:96:9: warning: unused variable ‘i’ [-Wunused-variable] 96 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vc_vecsmpbe’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:223:26: warning: variable ‘ivect’ set but not used [-Wunused-but-set-variable=] 223 | int n, i, ii, ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:223:19: warning: variable ‘ipara’ set but not used [-Wunused-but-set-variable=] 223 | int n, i, ii, ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:223:15: warning: unused variable ‘ii’ [-Wunused-variable] 223 | int n, i, ii, ipara, ivect; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:222:9: warning: unused variable ‘iion’ [-Wunused-variable] 222 | int iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:219:28: warning: unused variable ‘fact’ [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:219:22: warning: unused variable ‘poly’ [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:219:12: warning: unused variable ‘argument’ [-Wunused-variable] 219 | double argument, poly, fact; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:218:29: warning: unused variable ‘am_pos’ [-Wunused-variable] 218 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:218:21: warning: unused variable ‘am_neg’ [-Wunused-variable] 218 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:217:18: warning: unused variable ‘zu2’ [-Wunused-variable] 217 | double zcf2, zu2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:217:12: warning: unused variable ‘zcf2’ [-Wunused-variable] 217 | double zcf2, zu2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:216:9: warning: unused variable ‘ideg’ [-Wunused-variable] 216 | int ideg; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vdc_vec’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:345:9: warning: unused variable ‘n’ [-Wunused-variable] 345 | int n = *nx * *ny * *nz; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:344:9: warning: unused variable ‘i’ [-Wunused-variable] 344 | int i; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vdc_vecpmg’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:360:28: warning: unused variable ‘fact’ [-Wunused-variable] 360 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:360:22: warning: unused variable ‘poly’ [-Wunused-variable] 360 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:357:9: warning: unused variable ‘ideg’ [-Wunused-variable] 357 | int ideg, iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c: In function ‘Vdc_vecsmpbe’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:433:16: warning: variable ‘ivect’ set but not used [-Wunused-but-set-variable=] 433 | int ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:433:9: warning: variable ‘ipara’ set but not used [-Wunused-but-set-variable=] 433 | int ipara, ivect; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:432:15: warning: unused variable ‘ii’ [-Wunused-variable] 432 | int n, i, ii; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:429:28: warning: unused variable ‘fact’ [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:429:22: warning: unused variable ‘poly’ [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:429:12: warning: unused variable ‘argument’ [-Wunused-variable] 429 | double argument, poly, fact; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:428:29: warning: unused variable ‘am_pos’ [-Wunused-variable] 428 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:428:21: warning: unused variable ‘am_neg’ [-Wunused-variable] 428 | double am_zero, am_neg, am_pos; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:427:18: warning: unused variable ‘zu2’ [-Wunused-variable] 427 | double zcf2, zu2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:427:12: warning: unused variable ‘zcf2’ [-Wunused-variable] 427 | double zcf2, zu2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:426:15: warning: unused variable ‘iion’ [-Wunused-variable] 426 | int ideg, iion; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c:426:9: warning: unused variable ‘ideg’ [-Wunused-variable] 426 | int ideg, iion; | ^~~~ [32/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c:56: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c: In function ‘Vfnewton’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c:77:5: note: in expansion of macro ‘MAT2’ 77 | MAT2( iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c: In function ‘Vnewton’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c:187:5: note: in expansion of macro ‘MAT2’ 187 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c: In function ‘Vgetjac’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c:560:5: note: in expansion of macro ‘MAT2’ 560 | MAT2(iz, 50, 1); | ^~~~ [33/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c: In function ‘Vpower’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c:74:5: note: in expansion of macro ‘MAT2’ 74 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c:71:9: warning: unused variable ‘skipIters’ [-Wunused-variable] 71 | int skipIters = 0; | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c: In function ‘Vipower’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c:188:5: note: in expansion of macro ‘MAT2’ 188 | MAT2(iz, 50, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c: In function ‘Vmpower’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c:311:5: note: in expansion of macro ‘MAT2’ 311 | MAT2(iz, 50, 1); | ^~~~ [34/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/smoothd.c [35/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o -MF src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o.d -o src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vmgrid.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vmgrid.c: In function ‘Vmgrid_addGrid’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vmgrid.c:198:12: warning: unused variable ‘tgrad’ [-Wunused-variable] 198 | double tgrad[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vmgrid.c:197:15: warning: unused variable ‘rc’ [-Wunused-variable] 197 | int i, j, rc; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vmgrid.c:197:12: warning: unused variable ‘j’ [-Wunused-variable] 197 | int i, j, rc; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vmgrid.c:197:9: warning: unused variable ‘i’ [-Wunused-variable] 197 | int i, j, rc; | ^ [36/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.h:55, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmatvec7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:87:5: note: in expansion of macro ‘MAT2’ 87 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmatvec7_1s’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:112:5: note: in expansion of macro ‘MAT3’ 112 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:111:5: note: in expansion of macro ‘MAT3’ 111 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:110:5: note: in expansion of macro ‘MAT3’ 110 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:109:5: note: in expansion of macro ‘MAT3’ 109 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:108:5: note: in expansion of macro ‘MAT3’ 108 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:107:5: note: in expansion of macro ‘MAT3’ 107 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:106:5: note: in expansion of macro ‘MAT3’ 106 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmatvec27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:139:5: note: in expansion of macro ‘MAT2’ 139 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmatvec27_1s’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:184:5: note: in expansion of macro ‘MAT3’ 184 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:183:5: note: in expansion of macro ‘MAT3’ 183 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:182:5: note: in expansion of macro ‘MAT3’ 182 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:181:5: note: in expansion of macro ‘MAT3’ 181 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:180:5: note: in expansion of macro ‘MAT3’ 180 | MAT3(uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:179:5: note: in expansion of macro ‘MAT3’ 179 | MAT3(uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:178:5: note: in expansion of macro ‘MAT3’ 178 | MAT3(uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:177:5: note: in expansion of macro ‘MAT3’ 177 | MAT3(uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:176:5: note: in expansion of macro ‘MAT3’ 176 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:174:5: note: in expansion of macro ‘MAT3’ 174 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:173:5: note: in expansion of macro ‘MAT3’ 173 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:172:5: note: in expansion of macro ‘MAT3’ 172 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:171:5: note: in expansion of macro ‘MAT3’ 171 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:170:5: note: in expansion of macro ‘MAT3’ 170 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:168:5: note: in expansion of macro ‘MAT3’ 168 | MAT3(y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:167:5: note: in expansion of macro ‘MAT3’ 167 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:166:5: note: in expansion of macro ‘MAT3’ 166 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmatvec7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:263:5: note: in expansion of macro ‘MAT2’ 263 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmatvecd7_1s’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:292:5: note: in expansion of macro ‘MAT3’ 292 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:291:5: note: in expansion of macro ‘MAT3’ 291 | MAT3( y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:290:5: note: in expansion of macro ‘MAT3’ 290 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:289:5: note: in expansion of macro ‘MAT3’ 289 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro ‘MAT3’ 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_cc’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro ‘MAT3’ 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_cc’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro ‘MAT3’ 288 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:287:5: note: in expansion of macro ‘MAT3’ 287 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:286:5: note: in expansion of macro ‘MAT3’ 286 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:285:5: note: in expansion of macro ‘MAT3’ 285 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmatvec27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:322:5: note: in expansion of macro ‘MAT2’ 322 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmatvecd27_1s’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:370:5: note: in expansion of macro ‘MAT3’ 370 | MAT3( w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_y’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:369:5: note: in expansion of macro ‘MAT3’ 369 | MAT3( y, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:368:5: note: in expansion of macro ‘MAT3’ 368 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:367:5: note: in expansion of macro ‘MAT3’ 367 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro ‘MAT3’ 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_cc’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro ‘MAT3’ 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_cc’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro ‘MAT3’ 366 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:365:5: note: in expansion of macro ‘MAT3’ 365 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:364:5: note: in expansion of macro ‘MAT3’ 364 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:363:5: note: in expansion of macro ‘MAT3’ 363 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:362:5: note: in expansion of macro ‘MAT3’ 362 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:361:5: note: in expansion of macro ‘MAT3’ 361 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:360:5: note: in expansion of macro ‘MAT3’ 360 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:359:5: note: in expansion of macro ‘MAT3’ 359 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:358:5: note: in expansion of macro ‘MAT3’ 358 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:357:5: note: in expansion of macro ‘MAT3’ 357 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:356:5: note: in expansion of macro ‘MAT3’ 356 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:355:5: note: in expansion of macro ‘MAT3’ 355 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:354:5: note: in expansion of macro ‘MAT3’ 354 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:353:5: note: in expansion of macro ‘MAT3’ 353 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmresid7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:451:5: note: in expansion of macro ‘MAT2’ 451 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmresid7_1s’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:476:5: note: in expansion of macro ‘MAT3’ 476 | MAT3(r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:475:5: note: in expansion of macro ‘MAT3’ 475 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:474:5: note: in expansion of macro ‘MAT3’ 474 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:473:5: note: in expansion of macro ‘MAT3’ 473 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:472:5: note: in expansion of macro ‘MAT3’ 472 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:471:5: note: in expansion of macro ‘MAT3’ 471 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:470:5: note: in expansion of macro ‘MAT3’ 470 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:469:5: note: in expansion of macro ‘MAT3’ 469 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmresid27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:503:5: note: in expansion of macro ‘MAT2’ 503 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vmresid27_1s’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:550:5: note: in expansion of macro ‘MAT3’ 550 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:549:5: note: in expansion of macro ‘MAT3’ 549 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:548:5: note: in expansion of macro ‘MAT3’ 548 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:547:5: note: in expansion of macro ‘MAT3’ 547 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:546:5: note: in expansion of macro ‘MAT3’ 546 | MAT3(uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:545:5: note: in expansion of macro ‘MAT3’ 545 | MAT3(uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:544:5: note: in expansion of macro ‘MAT3’ 544 | MAT3(uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:543:5: note: in expansion of macro ‘MAT3’ 543 | MAT3(uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:542:5: note: in expansion of macro ‘MAT3’ 542 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:540:5: note: in expansion of macro ‘MAT3’ 540 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:539:5: note: in expansion of macro ‘MAT3’ 539 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:538:5: note: in expansion of macro ‘MAT3’ 538 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:537:5: note: in expansion of macro ‘MAT3’ 537 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:536:5: note: in expansion of macro ‘MAT3’ 536 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:534:5: note: in expansion of macro ‘MAT3’ 534 | MAT3(r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:533:5: note: in expansion of macro ‘MAT3’ 533 | MAT3(x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:532:5: note: in expansion of macro ‘MAT3’ 532 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:531:5: note: in expansion of macro ‘MAT3’ 531 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmresid7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:623:5: note: in expansion of macro ‘MAT2’ 623 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmresid7_1s’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:650:5: note: in expansion of macro ‘MAT3’ 650 | MAT3(w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:649:5: note: in expansion of macro ‘MAT3’ 649 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:648:5: note: in expansion of macro ‘MAT3’ 648 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:647:5: note: in expansion of macro ‘MAT3’ 647 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:646:5: note: in expansion of macro ‘MAT3’ 646 | MAT3(fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro ‘MAT3’ 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_cc’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro ‘MAT3’ 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_cc’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro ‘MAT3’ 645 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:644:5: note: in expansion of macro ‘MAT3’ 644 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:643:5: note: in expansion of macro ‘MAT3’ 643 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:642:5: note: in expansion of macro ‘MAT3’ 642 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmresid27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:681:5: note: in expansion of macro ‘MAT2’ 681 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vnmresid27_1s’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_w1’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:727:5: note: in expansion of macro ‘MAT3’ 727 | MAT3( w1, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_r’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:726:5: note: in expansion of macro ‘MAT3’ 726 | MAT3( r, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_x’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:725:5: note: in expansion of macro ‘MAT3’ 725 | MAT3( x, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:724:5: note: in expansion of macro ‘MAT3’ 724 | MAT3(uSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:723:5: note: in expansion of macro ‘MAT3’ 723 | MAT3(uSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:722:5: note: in expansion of macro ‘MAT3’ 722 | MAT3(uNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:721:5: note: in expansion of macro ‘MAT3’ 721 | MAT3(uNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:720:5: note: in expansion of macro ‘MAT3’ 720 | MAT3( uS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:719:5: note: in expansion of macro ‘MAT3’ 719 | MAT3( uN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:718:5: note: in expansion of macro ‘MAT3’ 718 | MAT3( uW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:717:5: note: in expansion of macro ‘MAT3’ 717 | MAT3( uE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:716:5: note: in expansion of macro ‘MAT3’ 716 | MAT3(oNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:715:5: note: in expansion of macro ‘MAT3’ 715 | MAT3(oNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:714:5: note: in expansion of macro ‘MAT3’ 714 | MAT3( uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:713:5: note: in expansion of macro ‘MAT3’ 713 | MAT3( oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:712:5: note: in expansion of macro ‘MAT3’ 712 | MAT3( oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_fc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:711:5: note: in expansion of macro ‘MAT3’ 711 | MAT3( fc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro ‘MAT3’ 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_cc’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro ‘MAT3’ 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_cc’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro ‘MAT3’ 710 | MAT3( cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:709:5: note: in expansion of macro ‘MAT3’ 709 | MAT3( oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vrestrc’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:786:5: note: in expansion of macro ‘MAT2’ 786 | MAT2(pc, *nxc * *nyc * *nzc, 1 ); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vrestrc2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:852:5: note: in expansion of macro ‘MAT3’ 852 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:851:5: note: in expansion of macro ‘MAT3’ 851 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:850:5: note: in expansion of macro ‘MAT3’ 850 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:849:5: note: in expansion of macro ‘MAT3’ 849 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:847:5: note: in expansion of macro ‘MAT3’ 847 | MAT3(dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:846:5: note: in expansion of macro ‘MAT3’ 846 | MAT3(dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:845:5: note: in expansion of macro ‘MAT3’ 845 | MAT3(dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:844:5: note: in expansion of macro ‘MAT3’ 844 | MAT3(dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:843:5: note: in expansion of macro ‘MAT3’ 843 | MAT3(dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:841:5: note: in expansion of macro ‘MAT3’ 841 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:840:5: note: in expansion of macro ‘MAT3’ 840 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:839:5: note: in expansion of macro ‘MAT3’ 839 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:838:5: note: in expansion of macro ‘MAT3’ 838 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:836:5: note: in expansion of macro ‘MAT3’ 836 | MAT3(uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:835:5: note: in expansion of macro ‘MAT3’ 835 | MAT3(uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:834:5: note: in expansion of macro ‘MAT3’ 834 | MAT3(uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:833:5: note: in expansion of macro ‘MAT3’ 833 | MAT3(uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:832:5: note: in expansion of macro ‘MAT3’ 832 | MAT3(uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:830:5: note: in expansion of macro ‘MAT3’ 830 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:829:5: note: in expansion of macro ‘MAT3’ 829 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:828:5: note: in expansion of macro ‘MAT3’ 828 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:827:5: note: in expansion of macro ‘MAT3’ 827 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:825:5: note: in expansion of macro ‘MAT3’ 825 | MAT3(oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:824:5: note: in expansion of macro ‘MAT3’ 824 | MAT3(oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:823:5: note: in expansion of macro ‘MAT3’ 823 | MAT3(oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:822:5: note: in expansion of macro ‘MAT3’ 822 | MAT3(oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:821:5: note: in expansion of macro ‘MAT3’ 821 | MAT3(oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xout’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:819:5: note: in expansion of macro ‘MAT3’ 819 | MAT3(xout, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xin’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:818:5: note: in expansion of macro ‘MAT3’ 818 | MAT3(xin, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:816:12: warning: variable ‘dimfac’ set but not used [-Wunused-but-set-variable=] 816 | double dimfac; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘VinterpPMG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pc’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:920:5: note: in expansion of macro ‘MAT2’ 920 | MAT2(pc, *nxc * *nyc * *nzc, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘VinterpPMG2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:982:5: note: in expansion of macro ‘MAT3’ 982 | MAT3(dPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:981:5: note: in expansion of macro ‘MAT3’ 981 | MAT3(dPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:980:5: note: in expansion of macro ‘MAT3’ 980 | MAT3(dPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:979:5: note: in expansion of macro ‘MAT3’ 979 | MAT3(dPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:977:5: note: in expansion of macro ‘MAT3’ 977 | MAT3( dPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:976:5: note: in expansion of macro ‘MAT3’ 976 | MAT3( dPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:975:5: note: in expansion of macro ‘MAT3’ 975 | MAT3( dPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:974:5: note: in expansion of macro ‘MAT3’ 974 | MAT3( dPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:973:5: note: in expansion of macro ‘MAT3’ 973 | MAT3( dPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:971:5: note: in expansion of macro ‘MAT3’ 971 | MAT3(uPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:970:5: note: in expansion of macro ‘MAT3’ 970 | MAT3(uPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:969:5: note: in expansion of macro ‘MAT3’ 969 | MAT3(uPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:968:5: note: in expansion of macro ‘MAT3’ 968 | MAT3(uPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:966:5: note: in expansion of macro ‘MAT3’ 966 | MAT3( uPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:965:5: note: in expansion of macro ‘MAT3’ 965 | MAT3( uPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:964:5: note: in expansion of macro ‘MAT3’ 964 | MAT3( uPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:963:5: note: in expansion of macro ‘MAT3’ 963 | MAT3( uPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:962:5: note: in expansion of macro ‘MAT3’ 962 | MAT3( uPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:960:5: note: in expansion of macro ‘MAT3’ 960 | MAT3(oPSW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:959:5: note: in expansion of macro ‘MAT3’ 959 | MAT3(oPSE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:958:5: note: in expansion of macro ‘MAT3’ 958 | MAT3(oPNW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:957:5: note: in expansion of macro ‘MAT3’ 957 | MAT3(oPNE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:955:5: note: in expansion of macro ‘MAT3’ 955 | MAT3( oPW, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:954:5: note: in expansion of macro ‘MAT3’ 954 | MAT3( oPE, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:953:5: note: in expansion of macro ‘MAT3’ 953 | MAT3( oPS, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:952:5: note: in expansion of macro ‘MAT3’ 952 | MAT3( oPN, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro ‘MAT3’ 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable ‘dy_oPC’ [-Wunused-variable] 78 | int dy_##mat = dy; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro ‘MAT3’ 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable ‘dx_oPC’ [-Wunused-variable] 77 | int dx_##mat = dx; \ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro ‘MAT3’ 951 | MAT3( oPC, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xout’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:949:5: note: in expansion of macro ‘MAT3’ 949 | MAT3(xout, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xin’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:948:5: note: in expansion of macro ‘MAT3’ 948 | MAT3( xin, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c: In function ‘Vextrac’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xout’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:1086:5: note: in expansion of macro ‘MAT3’ 1086 | MAT3(xout, *nxc, *nyc, *nzc); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_xin’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/matvecd.c:1085:5: note: in expansion of macro ‘MAT3’ 1085 | MAT3( xin, *nxf, *nyf, *nzf); | ^~~~ [37/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/smoothd.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c: In function ‘Vfmvfas’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c:79:5: note: in expansion of macro ‘MAT2’ 79 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c:74:12: warning: variable ‘errd’ set but not used [-Wunused-but-set-variable=] 74 | double errd; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c: In function ‘Vmvfas’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c:182:5: note: in expansion of macro ‘MAT2’ 182 | MAT2(iz, 50, *nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c:171:33: warning: unused variable ‘ivariv’ [-Wunused-variable] 171 | int itmax_s, iters_s, nuuu, ivariv, mgsmoo_s, iresid; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c:254:13: warning: ‘rsden’ may be used uninitialized [-Wmaybe-uninitialized] 254 | if (rsden == 0.0) { | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mgfasd.c:176:12: note: ‘rsden’ was declared here 176 | double rsden, rsnrm, orsnrm; | ^~~~~ [38/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o -MF src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o.d -o src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vopot.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vopot.c: In function ‘Vopot_curvature’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vopot.c:219:26: warning: variable ‘eps_w’ set but not used [-Wunused-but-set-variable=] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vopot.c:219:18: warning: variable ‘charge’ set but not used [-Wunused-but-set-variable=] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vopot.c:219:15: warning: variable ‘T’ set but not used [-Wunused-but-set-variable=] 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vopot.c:269:23: warning: ‘val’ may be used uninitialized [-Wmaybe-uninitialized] 269 | u = u + val; | ~~^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vopot.c:219:53: note: ‘val’ was declared here 219 | double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; | ^~~ [39/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -MF src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o.d -o src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmgp.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmgp.c: In function ‘Vpmgp_size’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmgp.c:204:87: warning: unused variable ‘iretot’ [-Wunused-variable] 204 | int nxf, nyf, nzf, level, num_nf_oper, num_narrc_oper, n_band, nc_band, num_band, iretot; | ^~~~~~ [40/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs-bin.dir/main.c.o -MF src/CMakeFiles/apbs-bin.dir/main.c.o.d -o src/CMakeFiles/apbs-bin.dir/main.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/main.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/main.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/main.c:117:11: warning: unused variable ‘gm’ [-Wunused-variable] 117 | void *gm[NOSH_MAXMOL]; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/main.c:116:11: warning: variable ‘fetk’ set but not used [-Wunused-but-set-variable=] 116 | void *fetk[NOSH_MAXCALC]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/main.c:96:18: warning: unused variable ‘geoflowparm’ [-Wunused-variable] 96 | GEOFLOWparm *geoflowparm = VNULL; | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/main.c:92:14: warning: unused variable ‘feparm’ [-Wunused-variable] 92 | FEMparm *feparm = VNULL; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/main.c:86:17: warning: unused variable ‘te’ [-Wunused-variable] 86 | clock_t ts, te; | ^~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/main.c:70: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [41/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -MF src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o.d -o src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:816:13: warning: variable ‘isBinary’ set but not used [-Wunused-but-set-variable=] 816 | int isBinary = 0; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:813:25: warning: unused variable ‘itmp’ [-Wunused-variable] 813 | size_t i, j, k, itmp, u; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c: In function ‘Vgrid_writeUHBD’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:1697:36: warning: variable ‘hy’ set but not used [-Wunused-but-set-variable=] 1697 | double xmin, ymin, zmin, hzed, hy, hx; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:1697:30: warning: variable ‘hzed’ set but not used [-Wunused-but-set-variable=] 1697 | double xmin, ymin, zmin, hzed, hy, hx; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c: In function ‘Vgrid_readDXBIN’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:853:17: warning: ignoring return value of ‘fgets’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 853 | fgets(tok, VMAX_BUFSIZE, fd); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:831:17: warning: argument 1 null where non-null expected [-Wnonnull] 831 | fclose(fd); | ^~~~~~~~~~ In file included from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.h:67, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:57: /usr/include/stdio.h:191:12: note: in a call to function ‘fclose’ declared ‘nonnull’ 191 | extern int fclose (FILE *__stream) __nonnull ((1)); | ^~~~~~ [42/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o -MF tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o.d -o tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mgmesh.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mgmesh.c:10: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [43/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/smooth.dir/smooth.c.o -MF tools/mesh/CMakeFiles/smooth.dir/smooth.c.o.d -o tools/mesh/CMakeFiles/smooth.dir/smooth.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/smooth.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/smooth.c:13: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [44/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o -MF tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o.d -o tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dxmath.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dxmath.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dxmath.c:41:10: warning: unused variable ‘format’ [-Wunused-variable] 41 | char format[VMAX_BUFSIZE]; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dxmath.c:13: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [45/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o -MF tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o.d -o tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c:8: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: ‘nz’ may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c:29:17: note: ‘nz’ was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: ‘ny’ may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c:29:13: note: ‘ny’ was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: ‘nx’ may be used uninitialized [-Wmaybe-uninitialized] 81 | mgrid = Vgrid_ctor(nx, ny, nz, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, VNULL); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx.c:29:9: note: ‘nx’ was declared here 29 | int nx, ny, nz, count, numfnams; | ^~ [46/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o -MF tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o.d -o tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx2.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/mergedx2.c:8: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [47/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/value.dir/value.c.o -MF tools/mesh/CMakeFiles/value.dir/value.c.o.d -o tools/mesh/CMakeFiles/value.dir/value.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/value.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/value.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/value.c:37:9: warning: unused variable ‘inorm’ [-Wunused-variable] 37 | int inorm; | ^~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/value.c:8: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [48/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT src/CMakeFiles/apbs-bin.dir/routines.c.o -MF src/CMakeFiles/apbs-bin.dir/routines.c.o.d -o src/CMakeFiles/apbs-bin.dir/routines.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘loadDielMaps’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:296:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 296 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:298:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 298 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:331:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 331 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:333:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 333 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:420:17: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 420 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:422:21: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 422 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:454:9: warning: this ‘for’ clause does not guard... [-Wmisleading-indentation] 454 | for (ii=0; ii<(nx*ny*nz); ii++) | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:456:11: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘for’ 456 | sum = sum*hx*hy*hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘initMG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1235:12: warning: variable ‘q’ set but not used [-Wunused-but-set-variable=] 1235 | q; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1234:12: warning: variable ‘iparm’ set but not used [-Wunused-but-set-variable=] 1234 | iparm, | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘energyMG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1584:13: warning: variable ‘mgparm’ set but not used [-Wunused-but-set-variable=] 1584 | MGparm *mgparm; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writematMG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1803:10: warning: variable ‘mxtype’ set but not used [-Wunused-but-set-variable=] 1803 | char mxtype[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘printApolForce’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:3485:12: warning: variable ‘scalar’ set but not used [-Wunused-but-set-variable=] 3485 | scalar, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:3484:12: warning: variable ‘temp’ set but not used [-Wunused-but-set-variable=] 3484 | double temp, | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘initAPOL’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4508:12: warning: variable ‘charge’ set but not used [-Wunused-but-set-variable=] 4508 | charge, /**< @todo document */ | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4496:12: warning: variable ‘sav’ set but not used [-Wunused-but-set-variable=] 4496 | sav, /**< @todo document */ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4495:12: warning: variable ‘sasa’ set but not used [-Wunused-but-set-variable=] 4495 | double sasa, /**< @todo document */ | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4489:12: warning: unused variable ‘ts’ [-Wunused-variable] 4489 | time_t ts; /**< Temporary timing variable for debugging (PCE) */ | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘forceAPOL’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4753:13: warning: unused variable ‘apos’ [-Wunused-variable] 4753 | *apos; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4737:46: warning: unused variable ‘ts_sub’ [-Wunused-variable] 4737 | time_t ts, ts_main, ts_sub; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘initAPOL’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4590:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4590 | atomData = Vparam_getAtomData(param, "WAT", "OW"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 2 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4590:20: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 3 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4590:20: note: referencing argument 3 of type ‘char[1024]’ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.h:73, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:73: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4591:43: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 4 [-Wstringop-overflow=] 4591 | if (atomData == VNULL) atomData = Vparam_getAtomData(param, "WAT", "O"); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 2 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4591:43: warning: ‘Vparam_getAtomData’ accessing 1024 bytes in a region of size 2 [-Wstringop-overflow=] /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4591:43: note: referencing argument 3 of type ‘char[1024]’ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vparam.h:304:27: note: in a call to function ‘Vparam_getAtomData’ 304 | VEXTERNC Vparam_AtomData* Vparam_getAtomData(Vparam *thee, | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writematMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1826:34: warning: ‘-PE’ directive writing 3 bytes into a region of size between 1 and 1024 [-Wformat-overflow=] 1826 | sprintf(writematstem, "%s-PE%d", pbeparm->writematstem,nosh->proc_rank); | ^~~ In file included from /usr/include/stdio.h:974, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:67: In function ‘*__sprintfieee128’, inlined from ‘writematMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1826:9: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1038 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writematMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1840:30: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 1840 | sprintf(outpath, "%s.%s", writematstem, "mat"); | ^~ ~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writematMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1840:9: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2676:30: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2676 | sprintf(outpath, "%s.%s", writestem, "dxbin"); | ^~ ~~~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2676:9: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2720:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2720 | sprintf(outpath, "%s.%s", writestem, "txt"); | ^~ ~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2720:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2711:38: warning: ‘%s’ directive writing 5 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2711 | sprintf(outpath, "%s.%s", writestem, "dx.gz"); | ^~ ~~~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2711:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 7 and 1030 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2694:38: warning: ‘%s’ directive writing 4 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2694 | sprintf(outpath, "%s.%s", writestem, "mcsf"); | ^~ ~~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2694:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 6 and 1029 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2687:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2687 | sprintf(outpath, "%s.%s", writestem, "ucd"); | ^~ ~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2687:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2701:38: warning: ‘%s’ directive writing 3 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2701 | sprintf(outpath, "%s.%s", writestem, "grd"); | ^~ ~~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2701:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 5 and 1028 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataMG.part.0’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2666:38: warning: ‘%s’ directive writing 2 bytes into a region of size between 0 and 1023 [-Wformat-overflow=] 2666 | sprintf(outpath, "%s.%s", writestem, "dx"); | ^~ ~~~~ In function ‘*__sprintfieee128’, inlined from ‘writedataMG.part.0’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2666:17: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 4 and 1027 bytes into a destination of size 1024 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataFlat’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2105:33: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2105 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:1906:44: note: ‘scalar’ was declared here 1906 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘writedataXML’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2363:33: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2363 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2140:44: note: ‘scalar’ was declared here 2140 | double conversion, ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘returnEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2778:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2778 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2762:12: note: ‘scalar’ was declared here 2762 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘printEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2839:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2839 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2795:12: note: ‘scalar’ was declared here 2795 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘printElecEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2904:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2904 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2863:12: note: ‘scalar’ was declared here 2863 | scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c: In function ‘printApolEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2970:18: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 2970 | gtenergy += (scalar * ((apolparm->gamma*apolparm->sasa) + | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2971 | (apolparm->press*apolparm->sav) + | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 2972 | (apolparm->wcaEnergy))); | ~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:2925:12: note: ‘scalar’ was declared here 2925 | scalar; | ^~~~~~ [49/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o -MF tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o.d -o tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/multivalue.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/multivalue.c:46: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [50/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o -MF tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o.d -o tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:28:12: warning: unused variable ‘grid’ [-Wunused-variable] 28 | Vgrid *grid; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:58: warning: unused variable ‘sum’ [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:51: warning: unused variable ‘value’ [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:44: warning: unused variable ‘pt’ [-Wunused-variable] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:38: warning: variable ‘zmin’ set but not used [-Wunused-but-set-variable=] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:32: warning: variable ‘ymin’ set but not used [-Wunused-but-set-variable=] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:26: warning: variable ‘xmin’ set but not used [-Wunused-but-set-variable=] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:20: warning: variable ‘hzed’ set but not used [-Wunused-but-set-variable=] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:16: warning: variable ‘hx’ set but not used [-Wunused-but-set-variable=] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:18:12: warning: variable ‘hy’ set but not used [-Wunused-but-set-variable=] 18 | double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:17:27: warning: unused variable ‘k’ [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:17:24: warning: unused variable ‘j’ [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:17:21: warning: unused variable ‘i’ [-Wunused-variable] 17 | int nx, ny, nz, i, j, k, itmp; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/benchmark.c:8: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [51/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/similarity.dir/similarity.c.o -MF tools/mesh/CMakeFiles/similarity.dir/similarity.c.o.d -o tools/mesh/CMakeFiles/similarity.dir/similarity.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/similarity.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/similarity.c:13: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/similarity.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/similarity.c:298:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 298 | strncpy(scalar1Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/similarity.c:305:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 305 | strncpy(scalar2Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/similarity.c:312:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 312 | strncpy(transformPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/similarity.c:322:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 322 | strncpy(mask1Path, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/similarity.c:329:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 329 | strncpy(mask2Path, tstr, VMAX_ARGLEN); | ^ [52/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/analysis.dir/analysis.c.o -MF tools/mesh/CMakeFiles/analysis.dir/analysis.c.o.d -o tools/mesh/CMakeFiles/analysis.dir/analysis.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:14: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:123:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 123 | strncpy(scalarPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:133:13: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation] 133 | strncpy(maskPath, tstr, VMAX_ARGLEN); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:268:15: warning: ‘minS’ may be used uninitialized [-Wmaybe-uninitialized] 268 | norm_Linf = VMAX2(VABS(maxS), VABS(minS)); | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:86:12: note: ‘minS’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:298:5: warning: ‘norm_Linf’ may be used uninitialized [-Wmaybe-uninitialized] 298 | Vnm_print(1, "Linf norm = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 299 | norm_Linf); | ~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:84:49: note: ‘norm_Linf’ was declared here 84 | double norm_L1, norm_L2, snorm_H1, norm_H1, norm_Linf; | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: ‘minSpt[2]’ may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: ‘minSpt[2]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:286:5: warning: ‘maxG2’ may be used uninitialized [-Wmaybe-uninitialized] 286 | Vnm_print(1, "Max gradient-squared value = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 287 | maxG2); | ~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:85:29: note: ‘maxG2’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:278:5: warning: ‘maxS’ may be used uninitialized [-Wmaybe-uninitialized] 278 | Vnm_print(1, "Max scalar value = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 279 | maxS); | ~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:85:12: note: ‘maxS’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:290:5: warning: ‘minG2’ may be used uninitialized [-Wmaybe-uninitialized] 290 | Vnm_print(1, "Min gradient-squared value = %1.12E\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 291 | minG2); | ~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:86:29: note: ‘minG2’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: ‘minSpt[1]’ may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: ‘minSpt[1]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: ‘minSpt[0]’ may be used uninitialized [-Wmaybe-uninitialized] 284 | Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 285 | minSpt[0], minSpt[1], minSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:86:18: note: ‘minSpt[0]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: ‘maxG2pt[2]’ may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: ‘maxG2pt[2]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: ‘maxG2pt[1]’ may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: ‘maxG2pt[1]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: ‘maxG2pt[0]’ may be used uninitialized [-Wmaybe-uninitialized] 288 | Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 289 | maxG2pt[0], maxG2pt[1], maxG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:85:36: note: ‘maxG2pt[0]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: ‘maxSpt[2]’ may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: ‘maxSpt[2]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: ‘maxSpt[1]’ may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: ‘maxSpt[1]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: ‘maxSpt[0]’ may be used uninitialized [-Wmaybe-uninitialized] 280 | Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 281 | maxSpt[0], maxSpt[1], maxSpt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:85:18: note: ‘maxSpt[0]’ was declared here 85 | double maxS, maxSpt[3], maxG2, maxG2pt[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: ‘minG2pt[0]’ may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: ‘minG2pt[0]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: ‘minG2pt[1]’ may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: ‘minG2pt[1]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: ‘minG2pt[2]’ may be used uninitialized [-Wmaybe-uninitialized] 292 | Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 293 | minG2pt[0], minG2pt[1], minG2pt[2]); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/analysis.c:86:36: note: ‘minG2pt[2]’ was declared here 86 | double minS, minSpt[3], minG2, minG2pt[3]; | ^~~~~~~ [53/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o -MF tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o.d -o tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2mol.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2mol.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2mol.c:28:12: warning: unused variable ‘avg’ [-Wunused-variable] 28 | double avg; | ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2mol.c:19: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [54/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -MF tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o.d -o tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2uhbd.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2uhbd.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2uhbd.c:25:10: warning: unused variable ‘avg’ [-Wunused-variable] 25 | double avg; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:19: warning: unused variable ‘k’ [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:16: warning: unused variable ‘j’ [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:13: warning: unused variable ‘i’ [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:10: warning: unused variable ‘u’ [-Wunused-variable] 24 | size_t u, i, j, k, nx, ny, nz; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/dx2uhbd.c:17: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [55/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o -MF tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o.d -o tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:42:19: warning: unused variable ‘index’ [-Wunused-variable] 42 | int i,j,k,index,icol; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:42:17: warning: unused variable ‘k’ [-Wunused-variable] 42 | int i,j,k,index,icol; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:42:15: warning: unused variable ‘j’ [-Wunused-variable] 42 | int i,j,k,index,icol; | ^ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:14: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:97:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:98:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 98 | fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:137:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 137 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:139:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 139 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:140:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 140 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:155:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 155 | fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:156:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 156 | fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:157:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 157 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/tensor2dx.c:158:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 158 | fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [56/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o -MF tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o.d -o tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:45:64: warning: variable ‘extent’ set but not used [-Wunused-but-set-variable=] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:45:50: warning: unused variable ‘xdata’ [-Wunused-variable] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:45:15: warning: unused variable ‘val’ [-Wunused-variable] 45 | float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; | ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:16: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:76:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 76 | fread(&igrid, 1, sizeof(int), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:89:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 89 | fread(buffer, 1, sizeof(char) * 10, pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:97:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 97 | fread(data, tot_grid, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:103:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 103 | fread(&scale, 1, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/del2dx.c:106:9: warning: ignoring return value of ‘fread’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 106 | fread(oldmid, 3, sizeof(float), pfile); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [57/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -MF tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o.d -o tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:93, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:3: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_grid’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:24:5: note: in expansion of macro ‘MAT3’ 24 | MAT3(grid, MXGRD, MXGRD, MXGRD); | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:30:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 30 | scanf("%s", flnm); | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:42:5: warning: ignoring return value of ‘scanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 42 | scanf("%s", newfile); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:54:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 54 | fscanf(inFile, "%s", title); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:57:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 57 | fscanf(inFile, "%lf", &scale); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:60:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 60 | fscanf(inFile, "%lf", &dum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:63:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 63 | fscanf(inFile, "%d", &grdflg); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:66:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 66 | fscanf(inFile, "%d", &idum2); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:69:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 69 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:72:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 72 | fscanf(inFile, "%d", &one); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:75:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 75 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:78:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 78 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:81:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 81 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:84:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 84 | fscanf(inFile, "%d", &km); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:87:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 87 | fscanf(inFile, "%lf", &h); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:90:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 90 | fscanf(inFile, "%lf", &ox); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:93:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 93 | fscanf(inFile, "%lf", &oy); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:96:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 96 | fscanf(inFile, "%lf", &oz); | ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:99:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 99 | fscanf(inFile, "%lf", &dum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:102:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 102 | fscanf(inFile, "%lf", &dum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:105:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 105 | fscanf(inFile, "%lf", &dum5); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:108:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 108 | fscanf(inFile, "%lf", &dum6); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:111:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 111 | fscanf(inFile, "%lf", &dum7); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:114:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 114 | fscanf(inFile, "%lf", &dum8); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:117:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 117 | fscanf(inFile, "%d", &idum3); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:120:5: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 120 | fscanf(inFile, "%d", &idum4); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:125:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 125 | fscanf(inFile, "%d", &kk); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:128:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 128 | fscanf(inFile, "%d", &im); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:131:9: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 131 | fscanf(inFile, "%d", &jm); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:138:17: warning: ignoring return value of ‘fscanf’ declared with attribute ‘warn_unused_result’ [-Wunused-result] 138 | fscanf(inFile, "%lf", RAT3(grid, i, j, k)); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [58/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o -MF tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o.d -o tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/manip/coulomb.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/manip/coulomb.c: In function ‘main’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/manip/coulomb.c:20:12: warning: unused variable ‘j’ [-Wunused-variable] 20 | int i, j; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/manip/coulomb.c:18:34: warning: unused variable ‘disp’ [-Wunused-variable] 18 | double *pos, energy, zmagic, disp[3], force[3]; | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/manip/coulomb.c:8: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [59/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIE -fopenmp -MD -MT tools/manip/CMakeFiles/born.dir/born.c.o -MF tools/manip/CMakeFiles/born.dir/born.c.o.d -o tools/manip/CMakeFiles/born.dir/born.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/manip/born.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/manip/born.c:8: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [60/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/. -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT contrib/iapbs/src/CMakeFiles/iapbs.dir/apbs_driver.c.o -MF contrib/iapbs/src/CMakeFiles/iapbs.dir/apbs_driver.c.o.d -o contrib/iapbs/src/CMakeFiles/iapbs.dir/apbs_driver.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:62:21: warning: argument 23 of type ‘double[1]’ with mismatched bound [-Warray-parameter=] 62 | double esenergy[1], | ~~~~~~~^~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:19: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.h:173:30: note: previously declared as ‘double[20]’ 173 | double esEnergy[NOSH_MAXCALC], | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:63:21: warning: argument 24 of type ‘double[1]’ with mismatched bound [-Warray-parameter=] 63 | double npenergy[1], | ~~~~~~~^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.h:174:30: note: previously declared as ‘double[20]’ 174 | double npEnergy[NOSH_MAXCALC], | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘apbsdrv_’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:283:5: warning: multi-line comment [-Wcomment] 283 | // Vnm_print(1,"\nError you must provide a parameter file if you\n" \ | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:115:21: warning: unused variable ‘isolve’ [-Wunused-variable] 115 | int rank, size, isolve, debug, natom; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:103:11: warning: unused variable ‘gm’ [-Wunused-variable] 103 | void *gm[NOSH_MAXMOL]; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:102:11: warning: variable ‘fetk’ set but not used [-Wunused-but-set-variable=] 102 | void *fetk[NOSH_MAXCALC]; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:90:14: warning: unused variable ‘feparm’ [-Wunused-variable] 90 | FEMparm *feparm = VNULL; | ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:11: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘setupString’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:943:26: warning: ‘write pot dx iapbs-pot-’ directive writing 23 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] 943 | sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:974, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:67: In function ‘*__sprintfieee128’, inlined from ‘setupString’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:943:7: /usr/include/bits/stdio2.h:30:10: note: ‘*__sprintf_chkieee128’ output between 26 and 4131 bytes into a destination of size 4096 30 | return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 32 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ /usr/include/bits/stdio2.h:30:10: warning: ‘*__sprintf_chkieee128’ argument 5 overlaps destination object ‘string.1’ [-Wrestrict] /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘setupString’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:803:17: note: destination object referenced by ‘restrict’-qualified argument 1 was declared here 803 | static char string[MAX_BUF_SIZE]; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘getElecEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:1060:29: warning: ‘scalar’ may be used uninitialized [-Wmaybe-uninitialized] 1060 | ltenergy += (scalar * Vunit_kb * (1e-3) * Vunit_Na * /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:1043:32: note: ‘scalar’ was declared here 1043 | double ltenergy, gtenergy, scalar; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function ‘apbsdrv_’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:554:56: warning: ‘outputformat’ may be used uninitialized [-Wmaybe-uninitialized] 554 | if ((pbeparm->calcenergy == PCE_COMPS) && (outputformat != OUTPUT_NULL)){ | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:118:20: note: ‘outputformat’ was declared here 118 | Voutput_Format outputformat; | ^~~~~~~~~~~~ [61/88] : && /usr/bin/cmake -E rm -f lib/libiapbs.a && /usr/bin/ar qc lib/libiapbs.a contrib/iapbs/src/CMakeFiles/iapbs.dir/apbs_driver.c.o && /usr/bin/ranlib lib/libiapbs.a && : [62/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o -MF src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o.d -o src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_ctor2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:157:61: warning: variable ‘zkappa2’ set but not used [-Wunused-but-set-variable=] 157 | double ionConc[MAXION], ionQ[MAXION], ionRadii[MAXION], zkappa2, zks2; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_qmEnergySMPBE’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1503:12: warning: variable ‘zks2’ set but not used [-Wunused-but-set-variable=] 1503 | zks2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_qfEnergyPoint’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1712:13: warning: variable ‘pvec’ set but not used [-Wunused-but-set-variable=] 1712 | double *pvec; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1709:24: warning: variable ‘zmax’ set but not used [-Wunused-but-set-variable=] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1709:18: warning: variable ‘ymax’ set but not used [-Wunused-but-set-variable=] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1709:12: warning: variable ‘xmax’ set but not used [-Wunused-but-set-variable=] 1709 | double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_qfAtomEnergy’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1794:36: warning: variable ‘zmax’ set but not used [-Wunused-but-set-variable=] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1794:24: warning: variable ‘ymax’ set but not used [-Wunused-but-set-variable=] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1794:12: warning: variable ‘xmax’ set but not used [-Wunused-but-set-variable=] 1794 | double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘focusFillBound’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1953:12: warning: variable ‘charge’ set but not used [-Wunused-but-set-variable=] 1953 | charge, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1952:13: warning: variable ‘apos’ set but not used [-Wunused-but-set-variable=] 1952 | *apos, | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1951:12: warning: variable ‘size’ set but not used [-Wunused-but-set-variable=] 1951 | size, | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1950:12: warning: variable ‘xkappa’ set but not used [-Wunused-but-set-variable=] 1950 | xkappa, | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2668:40: warning: variable ‘qzy’ set but not used [-Wunused-but-set-variable=] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2668:36: warning: variable ‘qzx’ set but not used [-Wunused-but-set-variable=] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2668:24: warning: variable ‘qyx’ set but not used [-Wunused-but-set-variable=] 2668 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcCalcOrig’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2832:34: warning: unused variable ‘debye’ [-Wunused-variable] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2832:22: warning: variable ‘quadrupole’ set but not used [-Wunused-but-set-variable=] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2832:13: warning: variable ‘dipole’ set but not used [-Wunused-but-set-variable=] 2832 | double *dipole, *quadrupole, debye, eps_p; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcflnew’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3415:31: warning: variable ‘eps_p’ set but not used [-Wunused-but-set-variable=] 3415 | double dist, pre1, eps_w, eps_p, T, xkappa; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3410:29: warning: unused variable ‘z1’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3410:25: warning: unused variable ‘z0’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3410:21: warning: unused variable ‘y1’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3410:17: warning: unused variable ‘y0’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3410:13: warning: unused variable ‘x1’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3410:9: warning: unused variable ‘x0’ [-Wunused-variable] 3410 | int x0, x1, y0, y1, z0, z1; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3409:13: warning: unused variable ‘k’ [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3409:11: warning: unused variable ‘j’ [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3409:9: warning: unused variable ‘i’ [-Wunused-variable] 3409 | int i,j,k, iatom, igrid; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘multipolebc’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3492:19: warning: variable ‘kr3’ set but not used [-Wunused-but-set-variable=] 3492 | double kr,kr2,kr3; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl_sdh’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3608:40: warning: variable ‘qzy’ set but not used [-Wunused-but-set-variable=] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3608:36: warning: variable ‘qzx’ set but not used [-Wunused-but-set-variable=] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3608:24: warning: variable ‘qyx’ set but not used [-Wunused-but-set-variable=] 3608 | double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3604:22: warning: unused variable ‘quadrupole’ [-Wunused-variable] 3604 | double *dipole, *quadrupole; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3604:13: warning: unused variable ‘dipole’ [-Wunused-variable] 3604 | double *dipole, *quadrupole; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl_mdh’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3875:41: warning: variable ‘eps_p’ set but not used [-Wunused-but-set-variable=] 3875 | double size, charge, xkappa, eps_w, eps_p, T, pre1, dist; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3874:22: warning: unused variable ‘quadrupole’ [-Wunused-variable] 3874 | double *dipole, *quadrupole; | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3874:13: warning: unused variable ‘dipole’ [-Wunused-variable] 3874 | double *dipole, *quadrupole; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl_mem’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4008:24: warning: unused variable ‘edge_L’ [-Wunused-variable] 4008 | double A, B, C, D, edge_L, l; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4007:38: warning: unused variable ‘z_shift’ [-Wunused-variable] 4007 | double dist, val, z_low, z_high, z_shift; | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4007:12: warning: unused variable ‘dist’ [-Wunused-variable] 4007 | double dist, val, z_low, z_high, z_shift; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcfl_map’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4177:38: warning: variable ‘hzed’ set but not used [-Wunused-but-set-variable=] 4177 | double position[3], pot, hx, hy, hzed; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4177:34: warning: variable ‘hy’ set but not used [-Wunused-but-set-variable=] 4177 | double position[3], pot, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4177:30: warning: variable ‘hx’ set but not used [-Wunused-but-set-variable=] 4177 | double position[3], pot, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4176:11: warning: unused variable ‘pbe’ [-Wunused-variable] 4176 | Vpbe *pbe; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefMap’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4492:46: warning: unused variable ‘pot’ [-Wunused-variable] 4492 | double ionstr, position[3], tkappa, eps, pot, hx, hy, hzed; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefMolIon’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4638:16: warning: variable ‘surfMeth’ set but not used [-Wunused-but-set-variable=] 4638 | Vsurf_Meth surfMeth; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4630:11: warning: variable ‘acc’ set but not used [-Wunused-but-set-variable=] 4630 | Vacc *acc; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefMolDielNoSmooth’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4746:30: warning: unused variable ‘deps’ [-Wunused-variable] 4746 | double srad, epsw, epsp, deps, area; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefSpline’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5031:47: warning: variable ‘rtot2’ set but not used [-Wunused-but-set-variable=] 5031 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin, w3i; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCharge’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5289:15: warning: unused variable ‘rc’ [-Wunused-variable] 5289 | Vrc_Codes rc; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoChargeMap’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5346:49: warning: variable ‘hzed’ set but not used [-Wunused-but-set-variable=] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5346:45: warning: variable ‘hy’ set but not used [-Wunused-but-set-variable=] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5346:41: warning: variable ‘hx’ set but not used [-Wunused-but-set-variable=] 5346 | double position[3], charge, zmagic, hx, hy, hzed; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_force’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5829:12: warning: unused variable ‘npF’ [-Wunused-variable] 5829 | double npF[3]; /* Non-polar boundary force */ | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_ibForce’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5860:16: warning: variable ‘nchop’ set but not used [-Wunused-but-set-variable=] 5860 | int ichop, nchop, nion, m; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5854:24: warning: variable ‘zlen’ set but not used [-Wunused-but-set-variable=] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5854:18: warning: variable ‘ylen’ set but not used [-Wunused-but-set-variable=] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5854:12: warning: variable ‘xlen’ set but not used [-Wunused-but-set-variable=] 5854 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:5848:13: warning: variable ‘alist’ set but not used [-Wunused-but-set-variable=] 5848 | Valist *alist; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_dbForce’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6019:55: warning: variable ‘kT’ set but not used [-Wunused-but-set-variable=] 6019 | double rtot, dx, gpos[3], tgrad[3], dbFmag, epsw, kT; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6019:18: warning: variable ‘dx’ set but not used [-Wunused-but-set-variable=] 6019 | double rtot, dx, gpos[3], tgrad[3], dbFmag, epsw, kT; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6018:66: warning: variable ‘rtot2’ set but not used [-Wunused-but-set-variable=] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6018:24: warning: variable ‘zlen’ set but not used [-Wunused-but-set-variable=] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6018:18: warning: variable ‘ylen’ set but not used [-Wunused-but-set-variable=] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6018:12: warning: variable ‘xlen’ set but not used [-Wunused-but-set-variable=] 6018 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘qfForceSpline2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6453:24: warning: variable ‘zlen’ set but not used [-Wunused-but-set-variable=] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6453:18: warning: variable ‘ylen’ set but not used [-Wunused-but-set-variable=] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6453:12: warning: variable ‘xlen’ set but not used [-Wunused-but-set-variable=] 6453 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘qfForceSpline4’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6576:15: warning: unused variable ‘k’ [-Wunused-variable] 6576 | int i, j, k, ii, jj, kk; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6576:12: warning: unused variable ‘j’ [-Wunused-variable] 6576 | int i, j, k, ii, jj, kk; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6568:24: warning: variable ‘zlen’ set but not used [-Wunused-but-set-variable=] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6568:18: warning: variable ‘ylen’ set but not used [-Wunused-but-set-variable=] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6568:12: warning: variable ‘xlen’ set but not used [-Wunused-but-set-variable=] 6568 | double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘markFrac’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6692:39: warning: variable ‘a000’ set but not used [-Wunused-but-set-variable=] 6692 | double dx, dx2, dy, dy2, dz, dz2, a000, a001, a010, a100, r2; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘zlapSolve’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6912:12: warning: unused variable ‘norm’ [-Wunused-variable] 6912 | double norm, coef, proj, eigx, eigy, eigz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_solveLaplace’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7044:35: warning: variable ‘n’ set but not used [-Wunused-but-set-variable=] 7044 | int i, j, k, ijk, nx, ny, nz, n, dilo, dihi, djlo, djhi, dklo, dkhi; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7044:18: warning: unused variable ‘ijk’ [-Wunused-variable] 7044 | int i, j, k, ijk, nx, ny, nz, n, dilo, dihi, djlo, djhi, dklo, dkhi; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoPermanentMultipole’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:58: warning: unused variable ‘mqzz’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:53: warning: unused variable ‘mqzy’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:48: warning: unused variable ‘mqzx’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:43: warning: unused variable ‘mqyy’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:38: warning: unused variable ‘mqyx’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:33: warning: unused variable ‘mqxx’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:29: warning: unused variable ‘muz’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:25: warning: unused variable ‘muy’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:21: warning: unused variable ‘mux’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:18: warning: unused variable ‘mc’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7263:12: warning: unused variable ‘debye’ [-Wunused-variable] 7263 | double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7262:24: warning: unused variable ‘mr2’ [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7262:20: warning: unused variable ‘mkr’ [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7262:16: warning: unused variable ‘mjr’ [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7262:12: warning: unused variable ‘mir’ [-Wunused-variable] 7262 | double mir,mjr,mkr,mr2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7258:9: warning: unused variable ‘i’ [-Wunused-variable] 7258 | int i, ii, jj, kk, nx, ny, nz, iatom; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7253:47: warning: unused variable ‘qave’ [-Wunused-variable] 7253 | double c,ux,uy,uz,qxx,qyx,qyy,qzx,qzy,qzz,qave; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7252:29: warning: unused variable ‘quad’ [-Wunused-variable] 7252 | double charge, *dipole,*quad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7252:21: warning: unused variable ‘dipole’ [-Wunused-variable] 7252 | double charge, *dipole,*quad; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefSpline4’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:9948:47: warning: variable ‘rtot2’ set but not used [-Wunused-but-set-variable=] 9948 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:9946:42: warning: unused variable ‘w2i’ [-Wunused-variable] 9946 | double irad, dx, dy, dz, epsw, epsp, w2i; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoPermanentInduced’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10278:9: warning: unused variable ‘i’ [-Wunused-variable] 10278 | int i, ii, jj, kk, nx, ny, nz, iatom; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10273:47: warning: unused variable ‘qave’ [-Wunused-variable] 10273 | double c,ux,uy,uz,qxx,qyx,qyy,qzx,qzy,qzz,qave; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10272:29: warning: unused variable ‘quad’ [-Wunused-variable] 10272 | double charge, *dipole,*quad; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10272:21: warning: unused variable ‘dipole’ [-Wunused-variable] 10272 | double charge, *dipole,*quad; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘fillcoCoefSpline3’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10441:27: warning: variable ‘e5’ set but not used [-Wunused-but-set-variable=] 10441 | double e, e2, e3, e4, e5; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10439:47: warning: variable ‘rtot2’ set but not used [-Wunused-but-set-variable=] 10439 | double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin; | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10437:42: warning: unused variable ‘w2i’ [-Wunused-variable] 10437 | double irad, dx, dy, dz, epsw, epsp, w2i; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcolcomp’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10746:55: warning: variable ‘mxlv’ set but not used [-Wunused-but-set-variable=] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10746:47: warning: unused variable ‘maxlev’ [-Wunused-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10746:39: warning: unused variable ‘ierror’ [-Wunused-variable] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10746:15: warning: variable ‘niwk’ set but not used [-Wunused-but-set-variable=] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10746:9: warning: variable ‘nrwk’ set but not used [-Wunused-but-set-variable=] 10746 | int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10743:29: warning: unused variable ‘i’ [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10743:21: warning: unused variable ‘nnzero’ [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10743:15: warning: unused variable ‘ncol’ [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10743:9: warning: unused variable ‘nrow’ [-Wunused-variable] 10743 | int nrow, ncol, nnzero, i; | ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:93, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:73: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcolcomp2’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_iz’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10804:5: note: in expansion of macro ‘MAT2’ 10804 | MAT2(iz, 50, nlev); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcolcomp3’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10836:5: note: in expansion of macro ‘MAT2’ 10836 | MAT2(ac, *nx * *ny * *nz, 1); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘bcolcomp4’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10874:5: note: in expansion of macro ‘MAT3’ 10874 | MAT3(oC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_cc’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10873:5: note: in expansion of macro ‘MAT3’ 10873 | MAT3(cc, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10872:5: note: in expansion of macro ‘MAT3’ 10872 | MAT3(uC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10871:5: note: in expansion of macro ‘MAT3’ 10871 | MAT3(oN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10870:5: note: in expansion of macro ‘MAT3’ 10870 | MAT3(oE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10866:27: warning: variable ‘nrow’ set but not used [-Wunused-but-set-variable=] 10866 | int inonz, iirow, nn, nrow, ncol, nonz, irow, n; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7229:16: warning: ‘d3bspline4’ defined but not used [-Wunused-function] 7229 | VPUBLIC double d3bspline4(double x) { | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6684:15: warning: ‘markFrac’ defined but not used [-Wunused-function] 6684 | VPRIVATE void markFrac( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3868:15: warning: ‘bcfl_mdh’ defined but not used [-Wunused-function] 3868 | VPRIVATE void bcfl_mdh(Vpmg *thee){ | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2828:15: warning: ‘bcCalcOrig’ defined but not used [-Wunused-function] 2828 | VPRIVATE void bcCalcOrig(Vpmg *thee) { | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2547:17: warning: ‘bcfl1sp’ defined but not used [-Wunused-function] 2547 | VPRIVATE double bcfl1sp(double size, double *apos, double charge, | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1148:17: warning: ‘Vpmg_polarizEnergy’ defined but not used [-Wunused-function] 1148 | VPRIVATE double Vpmg_polarizEnergy(Vpmg *thee, | ^~~~~~~~~~~~~~~~~~ In function ‘zlapSolve’, inlined from ‘Vpmg_solveLaplace’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7103:5: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6989:40: warning: ‘phiz’ may be used uninitialized [-Wmaybe-uninitialized] 6989 | phizp1 = (2.0-hzed*hzed*eigz)*phiz - phizm1; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_solveLaplace’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6911:56: note: ‘phiz’ was declared here 6911 | double phix, phixp1, phixm1, phiy, phiym1, phiyp1, phiz, phizm1, phizp1; | ^~~~ In function ‘zlapSolve’, inlined from ‘Vpmg_solveLaplace’ at /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:7103:5: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6989:40: warning: ‘phizm1’ may be used uninitialized [-Wmaybe-uninitialized] 6989 | phizp1 = (2.0-hzed*hzed*eigz)*phiz - phizm1; | ~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c: In function ‘Vpmg_solveLaplace’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6911:62: note: ‘phizm1’ was declared here 6911 | double phix, phixp1, phixm1, phiy, phiym1, phiyp1, phiz, phizm1, phizp1; | ^~~~~~ [63/88] /usr/bin/gcc -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o -MF src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o.d -o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.h:57, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:55: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c: In function ‘VbuildG’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_ac’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:64:5: note: in expansion of macro ‘MAT2’ 64 | MAT2( ac, *nxc * *nyc * *nzc, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_acFF’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:63:5: note: in expansion of macro ‘MAT2’ 63 | MAT2(acFF, *nxf * *nyf * *nzf, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable ‘dy_pcFF’ [-Wunused-variable] 66 | int dy_##mat = dy | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:62:5: note: in expansion of macro ‘MAT2’ 62 | MAT2(pcFF, *nxc * *nyc * *nzc, 27); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c: In function ‘VbuildG_1’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:216:5: note: in expansion of macro ‘MAT3’ 216 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:215:5: note: in expansion of macro ‘MAT3’ 215 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:214:5: note: in expansion of macro ‘MAT3’ 214 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:213:5: note: in expansion of macro ‘MAT3’ 213 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:212:5: note: in expansion of macro ‘MAT3’ 212 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:211:5: note: in expansion of macro ‘MAT3’ 211 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:210:5: note: in expansion of macro ‘MAT3’ 210 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:209:5: note: in expansion of macro ‘MAT3’ 209 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:208:5: note: in expansion of macro ‘MAT3’ 208 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:206:5: note: in expansion of macro ‘MAT3’ 206 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:205:5: note: in expansion of macro ‘MAT3’ 205 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:204:5: note: in expansion of macro ‘MAT3’ 204 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:203:5: note: in expansion of macro ‘MAT3’ 203 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:202:5: note: in expansion of macro ‘MAT3’ 202 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:201:5: note: in expansion of macro ‘MAT3’ 201 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:200:5: note: in expansion of macro ‘MAT3’ 200 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:199:5: note: in expansion of macro ‘MAT3’ 199 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:198:5: note: in expansion of macro ‘MAT3’ 198 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:196:5: note: in expansion of macro ‘MAT3’ 196 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:195:5: note: in expansion of macro ‘MAT3’ 195 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:194:5: note: in expansion of macro ‘MAT3’ 194 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:193:5: note: in expansion of macro ‘MAT3’ 193 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:192:5: note: in expansion of macro ‘MAT3’ 192 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:191:5: note: in expansion of macro ‘MAT3’ 191 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:190:5: note: in expansion of macro ‘MAT3’ 190 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:189:5: note: in expansion of macro ‘MAT3’ 189 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:188:5: note: in expansion of macro ‘MAT3’ 188 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:186:5: note: in expansion of macro ‘MAT3’ 186 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:185:5: note: in expansion of macro ‘MAT3’ 185 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:184:5: note: in expansion of macro ‘MAT3’ 184 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:183:5: note: in expansion of macro ‘MAT3’ 183 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:182:5: note: in expansion of macro ‘MAT3’ 182 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:181:5: note: in expansion of macro ‘MAT3’ 181 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:180:5: note: in expansion of macro ‘MAT3’ 180 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:179:5: note: in expansion of macro ‘MAT3’ 179 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:177:5: note: in expansion of macro ‘MAT3’ 177 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:176:5: note: in expansion of macro ‘MAT3’ 176 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:174:5: note: in expansion of macro ‘MAT3’ 174 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:172:5: note: in expansion of macro ‘MAT3’ 172 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:171:5: note: in expansion of macro ‘MAT3’ 171 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:170:5: note: in expansion of macro ‘MAT3’ 170 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:168:5: note: in expansion of macro ‘MAT3’ 168 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:164:21: warning: variable ‘nzm1’ set but not used [-Wunused-but-set-variable=] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:164:15: warning: variable ‘nym1’ set but not used [-Wunused-but-set-variable=] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:164:9: warning: variable ‘nxm1’ set but not used [-Wunused-but-set-variable=] 164 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:163:33: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable=] 163 | int iim1, iip1, jjm1, jjp1, kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c: In function ‘VbuildG_7’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:532:5: note: in expansion of macro ‘MAT3’ 532 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:531:5: note: in expansion of macro ‘MAT3’ 531 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:530:5: note: in expansion of macro ‘MAT3’ 530 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:529:5: note: in expansion of macro ‘MAT3’ 529 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:528:5: note: in expansion of macro ‘MAT3’ 528 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:527:5: note: in expansion of macro ‘MAT3’ 527 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:526:5: note: in expansion of macro ‘MAT3’ 526 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:525:5: note: in expansion of macro ‘MAT3’ 525 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:524:5: note: in expansion of macro ‘MAT3’ 524 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:522:5: note: in expansion of macro ‘MAT3’ 522 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:521:5: note: in expansion of macro ‘MAT3’ 521 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:520:5: note: in expansion of macro ‘MAT3’ 520 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:519:5: note: in expansion of macro ‘MAT3’ 519 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:518:5: note: in expansion of macro ‘MAT3’ 518 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:517:5: note: in expansion of macro ‘MAT3’ 517 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:516:5: note: in expansion of macro ‘MAT3’ 516 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:515:5: note: in expansion of macro ‘MAT3’ 515 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:514:5: note: in expansion of macro ‘MAT3’ 514 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:512:5: note: in expansion of macro ‘MAT3’ 512 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:511:5: note: in expansion of macro ‘MAT3’ 511 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:510:5: note: in expansion of macro ‘MAT3’ 510 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:509:5: note: in expansion of macro ‘MAT3’ 509 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:508:5: note: in expansion of macro ‘MAT3’ 508 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:507:5: note: in expansion of macro ‘MAT3’ 507 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:506:5: note: in expansion of macro ‘MAT3’ 506 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:505:5: note: in expansion of macro ‘MAT3’ 505 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:504:5: note: in expansion of macro ‘MAT3’ 504 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:502:5: note: in expansion of macro ‘MAT3’ 502 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:501:5: note: in expansion of macro ‘MAT3’ 501 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:500:5: note: in expansion of macro ‘MAT3’ 500 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:499:5: note: in expansion of macro ‘MAT3’ 499 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:498:5: note: in expansion of macro ‘MAT3’ 498 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:497:5: note: in expansion of macro ‘MAT3’ 497 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:496:5: note: in expansion of macro ‘MAT3’ 496 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:495:5: note: in expansion of macro ‘MAT3’ 495 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:494:5: note: in expansion of macro ‘MAT3’ 494 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:492:5: note: in expansion of macro ‘MAT3’ 492 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:491:5: note: in expansion of macro ‘MAT3’ 491 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:490:5: note: in expansion of macro ‘MAT3’ 490 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:489:5: note: in expansion of macro ‘MAT3’ 489 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:488:5: note: in expansion of macro ‘MAT3’ 488 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:486:5: note: in expansion of macro ‘MAT3’ 486 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:484:5: note: in expansion of macro ‘MAT3’ 484 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:483:5: note: in expansion of macro ‘MAT3’ 483 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:482:5: note: in expansion of macro ‘MAT3’ 482 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:473:21: warning: variable ‘nzm1’ set but not used [-Wunused-but-set-variable=] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:473:15: warning: variable ‘nym1’ set but not used [-Wunused-but-set-variable=] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:473:9: warning: variable ‘nxm1’ set but not used [-Wunused-but-set-variable=] 473 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:472:9: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable=] 472 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:469:28: warning: variable ‘kp2’ set but not used [-Wunused-but-set-variable=] 469 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:469:22: warning: variable ‘km2’ set but not used [-Wunused-but-set-variable=] 469 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:468:28: warning: variable ‘jp2’ set but not used [-Wunused-but-set-variable=] 468 | int jm1, jp1, jm2, jp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:467:28: warning: variable ‘ip2’ set but not used [-Wunused-but-set-variable=] 467 | int im1, ip1, im2, ip2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c: In function ‘VbuildG_27’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1380:5: note: in expansion of macro ‘MAT3’ 1380 | MAT3(dPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1379:5: note: in expansion of macro ‘MAT3’ 1379 | MAT3(dPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1378:5: note: in expansion of macro ‘MAT3’ 1378 | MAT3(dPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1377:5: note: in expansion of macro ‘MAT3’ 1377 | MAT3(dPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1376:5: note: in expansion of macro ‘MAT3’ 1376 | MAT3( dPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1375:5: note: in expansion of macro ‘MAT3’ 1375 | MAT3( dPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1374:5: note: in expansion of macro ‘MAT3’ 1374 | MAT3( dPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1373:5: note: in expansion of macro ‘MAT3’ 1373 | MAT3( dPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_dPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1372:5: note: in expansion of macro ‘MAT3’ 1372 | MAT3( dPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1370:5: note: in expansion of macro ‘MAT3’ 1370 | MAT3(uPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1369:5: note: in expansion of macro ‘MAT3’ 1369 | MAT3(uPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1368:5: note: in expansion of macro ‘MAT3’ 1368 | MAT3(uPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1367:5: note: in expansion of macro ‘MAT3’ 1367 | MAT3(uPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1366:5: note: in expansion of macro ‘MAT3’ 1366 | MAT3( uPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1365:5: note: in expansion of macro ‘MAT3’ 1365 | MAT3( uPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1364:5: note: in expansion of macro ‘MAT3’ 1364 | MAT3( uPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1363:5: note: in expansion of macro ‘MAT3’ 1363 | MAT3( uPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1362:5: note: in expansion of macro ‘MAT3’ 1362 | MAT3( uPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1360:5: note: in expansion of macro ‘MAT3’ 1360 | MAT3(oPSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1359:5: note: in expansion of macro ‘MAT3’ 1359 | MAT3(oPSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1358:5: note: in expansion of macro ‘MAT3’ 1358 | MAT3(oPNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1357:5: note: in expansion of macro ‘MAT3’ 1357 | MAT3(oPNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1356:5: note: in expansion of macro ‘MAT3’ 1356 | MAT3( oPW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1355:5: note: in expansion of macro ‘MAT3’ 1355 | MAT3( oPE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1354:5: note: in expansion of macro ‘MAT3’ 1354 | MAT3( oPS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1353:5: note: in expansion of macro ‘MAT3’ 1353 | MAT3( oPN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oPC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1352:5: note: in expansion of macro ‘MAT3’ 1352 | MAT3( oPC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1350:5: note: in expansion of macro ‘MAT3’ 1350 | MAT3(XuSW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1349:5: note: in expansion of macro ‘MAT3’ 1349 | MAT3(XuSE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1348:5: note: in expansion of macro ‘MAT3’ 1348 | MAT3(XuNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1347:5: note: in expansion of macro ‘MAT3’ 1347 | MAT3(XuNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1346:5: note: in expansion of macro ‘MAT3’ 1346 | MAT3( XuS, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1345:5: note: in expansion of macro ‘MAT3’ 1345 | MAT3( XuN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1344:5: note: in expansion of macro ‘MAT3’ 1344 | MAT3( XuW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1343:5: note: in expansion of macro ‘MAT3’ 1343 | MAT3( XuE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XuC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1342:5: note: in expansion of macro ‘MAT3’ 1342 | MAT3( XuC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1340:5: note: in expansion of macro ‘MAT3’ 1340 | MAT3(XoNW, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1339:5: note: in expansion of macro ‘MAT3’ 1339 | MAT3(XoNE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1338:5: note: in expansion of macro ‘MAT3’ 1338 | MAT3( XoN, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1337:5: note: in expansion of macro ‘MAT3’ 1337 | MAT3( XoE, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_XoC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1336:5: note: in expansion of macro ‘MAT3’ 1336 | MAT3( XoC, *nx, *ny, *nz); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1334:5: note: in expansion of macro ‘MAT3’ 1334 | MAT3( uSW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uSE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1333:5: note: in expansion of macro ‘MAT3’ 1333 | MAT3( uSE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1332:5: note: in expansion of macro ‘MAT3’ 1332 | MAT3( uNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1331:5: note: in expansion of macro ‘MAT3’ 1331 | MAT3( uNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uS’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1330:5: note: in expansion of macro ‘MAT3’ 1330 | MAT3( uS, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1329:5: note: in expansion of macro ‘MAT3’ 1329 | MAT3( uN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1328:5: note: in expansion of macro ‘MAT3’ 1328 | MAT3( uW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1327:5: note: in expansion of macro ‘MAT3’ 1327 | MAT3( uE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_uC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1326:5: note: in expansion of macro ‘MAT3’ 1326 | MAT3( uC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNW’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1324:5: note: in expansion of macro ‘MAT3’ 1324 | MAT3( oNW, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oNE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1323:5: note: in expansion of macro ‘MAT3’ 1323 | MAT3( oNE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oN’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1322:5: note: in expansion of macro ‘MAT3’ 1322 | MAT3( oN, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oE’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1321:5: note: in expansion of macro ‘MAT3’ 1321 | MAT3( oE, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable ‘dz_oC’ [-Wunused-variable] 79 | int dz_##mat = dz | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1320:5: note: in expansion of macro ‘MAT3’ 1320 | MAT3( oC, *nxf, *nyf, *nzf); | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1277:21: warning: variable ‘nzm1’ set but not used [-Wunused-but-set-variable=] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1277:15: warning: variable ‘nym1’ set but not used [-Wunused-but-set-variable=] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1277:9: warning: variable ‘nxm1’ set but not used [-Wunused-but-set-variable=] 1277 | int nxm1, nym1, nzm1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1276:9: warning: variable ‘kkm1’ set but not used [-Wunused-but-set-variable=] 1276 | int kkm1, kkp1; | ^~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1273:28: warning: variable ‘kp2’ set but not used [-Wunused-but-set-variable=] 1273 | int km1, kp1, km2, kp2; | ^~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/buildGd.c:1273:22: warning: variable ‘km2’ set but not used [-Wunused-but-set-variable=] 1273 | int km1, kp1, km2, kp2; | ^~~ [64/88] cd /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python && /usr/bin/cmake -E make_directory /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir && /usr/bin/cmake -E env SWIG_LIB=/usr/share/swig/4.5.0 /usr/bin/swig -python -outdir /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python -interface _apbslib -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -I/usr/include/python3.15 -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/python -o /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/python/apbslib.i [65/88] /usr/bin/gcc -D_apbslib_EXPORTS -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/src -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/include -I/usr/include/python3.15 -I/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tools/python -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -fPIC -fopenmp -MD -MT tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -MF tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o.d -o tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o -c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: In function ‘getPotentials’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3754:12: warning: unused variable ‘rc’ [-Wunused-variable] 3754 | int i, rc, nx, ny, nz; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: In function ‘getForces’: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3808:31: warning: unused variable ‘npholder’ [-Wunused-variable] 3808 | PyObject *npvalues, *np, *npholder; | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3808:26: warning: unused variable ‘np’ [-Wunused-variable] 3808 | PyObject *npvalues, *np, *npholder; | ^~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3808:15: warning: unused variable ‘npvalues’ [-Wunused-variable] 3808 | PyObject *npvalues, *np, *npholder; | ^~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3260: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h: At top level: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: ‘GEOFLOWparm_parseVDW’ declared ‘static’ but never defined [-Wunused-function] 169 | VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: ‘GEOFLOWparm_parseETOL’ declared ‘static’ but never defined [-Wunused-function] 171 | VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:78: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: ‘PBAMparm_parseSalt’ declared ‘static’ but never defined [-Wunused-function] 251 | VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: ‘PBAMparm_parseRunType’ declared ‘static’ but never defined [-Wunused-function] 260 | VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: ‘PBAMparm_parseRunName’ declared ‘static’ but never defined [-Wunused-function] 269 | VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: ‘PBAMparm_parseRandorient’ declared ‘static’ but never defined [-Wunused-function] 278 | VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: ‘PBAMparm_parsePBCS’ declared ‘static’ but never defined [-Wunused-function] 287 | VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: ‘PBAMparm_parseUnits’ declared ‘static’ but never defined [-Wunused-function] 296 | VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: ‘PBAMparm_parse3Dmap’ declared ‘static’ but never defined [-Wunused-function] 305 | VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: ‘PBAMparm_parseGrid2D’ declared ‘static’ but never defined [-Wunused-function] 314 | VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: ‘PBAMparm_parseDX’ declared ‘static’ but never defined [-Wunused-function] 323 | VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: ‘PBAMparm_parseGridPts’ declared ‘static’ but never defined [-Wunused-function] 332 | VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: ‘PBAMparm_parseTermcombine’ declared ‘static’ but never defined [-Wunused-function] 341 | VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: ‘PBAMparm_parseDiff’ declared ‘static’ but never defined [-Wunused-function] 350 | VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: ‘PBAMparm_parseXYZ’ declared ‘static’ but never defined [-Wunused-function] 359 | VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.h:79: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: ‘PBSAMparm_parseTolsp’ declared ‘static’ but never defined [-Wunused-function] 199 | VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: ‘PBSAMparm_parseSurf’ declared ‘static’ but never defined [-Wunused-function] 208 | VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: ‘PBSAMparm_parseImat’ declared ‘static’ but never defined [-Wunused-function] 217 | VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: ‘PBSAMparm_parseExp’ declared ‘static’ but never defined [-Wunused-function] 226 | VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: ‘PBSAMparm_parseMSMS’ declared ‘static’ but never defined [-Wunused-function] 235 | VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); | ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h:93: /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: ‘bcolcomp’ declared ‘static’ but never defined [-Wunused-function] 811 | VPRIVATE void bcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: ‘bcolcomp2’ declared ‘static’ but never defined [-Wunused-function] 834 | VPRIVATE void bcolcomp2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: ‘bcolcomp3’ declared ‘static’ but never defined [-Wunused-function] 863 | VPRIVATE void bcolcomp3( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: ‘bcolcomp4’ declared ‘static’ but never defined [-Wunused-function] 885 | VPRIVATE void bcolcomp4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: ‘pcolcomp’ declared ‘static’ but never defined [-Wunused-function] 910 | VPRIVATE void pcolcomp( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: ‘bspline2’ declared ‘static’ but never defined [-Wunused-function] 933 | VPRIVATE double bspline2( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: ‘dbspline2’ declared ‘static’ but never defined [-Wunused-function] 942 | VPRIVATE double dbspline2( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: ‘VFCHI4’ declared ‘static’ but never defined [-Wunused-function] 951 | VPRIVATE double VFCHI4( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: ‘bspline4’ declared ‘static’ but never defined [-Wunused-function] 961 | VPRIVATE double bspline4( | ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: ‘dbspline4’ declared ‘static’ but never defined [-Wunused-function] 970 | VPRIVATE double dbspline4( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: ‘d2bspline4’ declared ‘static’ but never defined [-Wunused-function] 979 | VPRIVATE double d2bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: ‘d3bspline4’ declared ‘static’ but never defined [-Wunused-function] 988 | VPRIVATE double d3bspline4( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: ‘Vpmg_polarizEnergy’ declared ‘static’ but never defined [-Wunused-function] 998 | VPRIVATE double Vpmg_polarizEnergy( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: ‘Vpmg_qfEnergyPoint’ declared ‘static’ but never defined [-Wunused-function] 1009 | VPRIVATE double Vpmg_qfEnergyPoint( | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: ‘Vpmg_qfEnergyVolume’ declared ‘static’ but never defined [-Wunused-function] 1020 | VPRIVATE double Vpmg_qfEnergyVolume( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: ‘Vpmg_splineSelect’ declared ‘static’ but never defined [-Wunused-function] 1031 | VPRIVATE void Vpmg_splineSelect( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: ‘focusFillBound’ declared ‘static’ but never defined [-Wunused-function] 1047 | VPRIVATE void focusFillBound( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: ‘bcfl1’ declared ‘static’ but never defined [-Wunused-function] 1058 | VPRIVATE void bcfl1( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: ‘bcfl2’ declared ‘static’ but never defined [-Wunused-function] 1080 | VPRIVATE void bcfl2( | ^~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: ‘multipolebc’ declared ‘static’ but never defined [-Wunused-function] 1109 | VPRIVATE void multipolebc( | ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: ‘bcfl1sp’ declared ‘static’ but never defined [-Wunused-function] 1126 | VPRIVATE double bcfl1sp( | ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: ‘bcCalc’ declared ‘static’ but never defined [-Wunused-function] 1139 | VPRIVATE void bcCalc( | ^~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: ‘fillcoCoef’ declared ‘static’ but never defined [-Wunused-function] 1147 | VPRIVATE void fillcoCoef( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: ‘fillcoCoefMap’ declared ‘static’ but never defined [-Wunused-function] 1155 | VPRIVATE void fillcoCoefMap( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: ‘fillcoCoefMol’ declared ‘static’ but never defined [-Wunused-function] 1164 | VPRIVATE void fillcoCoefMol( | ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: ‘fillcoCoefMolIon’ declared ‘static’ but never defined [-Wunused-function] 1173 | VPRIVATE void fillcoCoefMolIon( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: ‘fillcoCoefMolDiel’ declared ‘static’ but never defined [-Wunused-function] 1182 | VPRIVATE void fillcoCoefMolDiel( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: ‘fillcoCoefMolDielNoSmooth’ declared ‘static’ but never defined [-Wunused-function] 1191 | VPRIVATE void fillcoCoefMolDielNoSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: ‘fillcoCoefMolDielSmooth’ declared ‘static’ but never defined [-Wunused-function] 1208 | VPRIVATE void fillcoCoefMolDielSmooth( | ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: ‘fillcoCoefSpline’ declared ‘static’ but never defined [-Wunused-function] 1217 | VPRIVATE void fillcoCoefSpline( | ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: ‘fillcoCoefSpline3’ declared ‘static’ but never defined [-Wunused-function] 1226 | VPRIVATE void fillcoCoefSpline3( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: ‘fillcoCoefSpline4’ declared ‘static’ but never defined [-Wunused-function] 1235 | VPRIVATE void fillcoCoefSpline4( | ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: ‘fillcoCharge’ declared ‘static’ but never defined [-Wunused-function] 1244 | VPRIVATE Vrc_Codes fillcoCharge( | ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: ‘fillcoChargeMap’ declared ‘static’ but never defined [-Wunused-function] 1253 | VPRIVATE Vrc_Codes fillcoChargeMap( | ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: ‘fillcoChargeSpline1’ declared ‘static’ but never defined [-Wunused-function] 1261 | VPRIVATE void fillcoChargeSpline1( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: ‘fillcoChargeSpline2’ declared ‘static’ but never defined [-Wunused-function] 1269 | VPRIVATE void fillcoChargeSpline2( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: ‘fillcoPermanentMultipole’ declared ‘static’ but never defined [-Wunused-function] 1277 | VPRIVATE void fillcoPermanentMultipole( | ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: ‘fillcoInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1285 | VPRIVATE void fillcoInducedDipole( | ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: ‘fillcoNLInducedDipole’ declared ‘static’ but never defined [-Wunused-function] 1294 | VPRIVATE void fillcoNLInducedDipole( | ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: ‘extEnergy’ declared ‘static’ but never defined [-Wunused-function] 1304 | VPRIVATE void extEnergy( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: ‘qfForceSpline1’ declared ‘static’ but never defined [-Wunused-function] 1317 | VPRIVATE void qfForceSpline1( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: ‘qfForceSpline2’ declared ‘static’ but never defined [-Wunused-function] 1327 | VPRIVATE void qfForceSpline2( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: ‘qfForceSpline4’ declared ‘static’ but never defined [-Wunused-function] 1337 | VPRIVATE void qfForceSpline4( | ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: ‘zlapSolve’ declared ‘static’ but never defined [-Wunused-function] 1351 | VPRIVATE void zlapSolve( | ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: ‘markSphere’ declared ‘static’ but never defined [-Wunused-function] 1364 | VPRIVATE void markSphere( | ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: ‘Vpmg_qmEnergySMPBE’ declared ‘static’ but never defined [-Wunused-function] 1384 | VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: ‘Vpmg_qmEnergyNONLIN’ declared ‘static’ but never defined [-Wunused-function] 1385 | VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); | ^~~~~~~~~~~~~~~~~~~ [66/88] cd /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer && doxygen /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile warning: Tag 'TCL_SUBST' at line 213 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'COLS_IN_ALPHA_INDEX' at line 857 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'HTML_TIMESTAMP' at line 953 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'FORMULA_TRANSPARENT' at line 1175 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'LATEX_SOURCE_CODE' at line 1313 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'PERL_PATH' at line 1565 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'CLASS_DIAGRAMS' at line 1577 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'MSCGEN_PATH' at line 1586 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTNAME' at line 1616 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_FONTSIZE' at line 1621 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_TRANSPARENT' at line 1770 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: Tag 'DOT_MULTI_TARGETS' at line 1777 of file '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/Doxyfile' has become obsolete. To avoid this warning please remove this line from your configuration file or upgrade it using "doxygen -u" warning: tag INPUT: input source '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/doc/license/LICENSE.txt' does not exist warning: source '/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/doc/license/LICENSE.txt' is not a readable file or directory... skipping. Doxygen version used: 1.17.0 Searching for include files... Searching for example files... Searching for images... Searching for dot files... Searching for msc files... Searching for dia files... Searching for plantuml files... Searching for mermaid files... Searching for files to exclude Searching INPUT for files to process... Searching for files in directory /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src Searching for files in directory /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc Searching for files in directory /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg Searching for files in directory /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic Searching for files in directory /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem Reading and parsing tag files Parsing files Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/apbs.h... 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Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mikpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mlinpckd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/mypdec.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newdrvd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/newtond.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/powerd.h... Preprocessing /builddir/bu/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.h:7: warning: the name 'beparm.h' supplied as the argument in the \file statement is not an input file ild/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/smoothd.c... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/smoothd.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/smoothd.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/pmgc/smoothd.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h... Preprocessing /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/mainpage.h... Parsing file /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc/programmer/mainpage.h... Building macro definition list... Building group list... Building directory list... Building namespace list... Building file list... Building class list... Building concept list... Computing nesting relations for classes... Associating documentation with classes... Associating documentation with concepts... Associating documentation with modules... Building example list... Searching for enumerations... Searching for documented typedefs... Searching for members imported via using declarations... Searching for included using directives... Searching for documented variables... Building interface member list... Building member list... Searching for friends... Searching for documented defines... Computing class inheritance relations... Computing class usage relations... Flushing cached template relations that have become invalid... Warn for undocumented namespaces... Computing class relations... Add enum values to enums... Searching for member function documentation... Creating members for template instances... Building page list... Building requirements list... Search for main page... Computing page relations... Determining the scope of groups... Computing module relations... Sorting lists... Determining which enums are documented Computing member relations... Building full member lists recursively... Adding members to member groups. Computing member references... Inheriting documentation... Generating disk names... Adding source references... Adding xrefitems... Adding requirements... Sorting member lists... Setting anonymous enum type... Computing dependencies between directories... Generating citations page... Counting members... Counting data structures... Resolving user defined references... Finding anchors and sections in the documentation... Transferring function references... Combining using relations... Adding members to index pages... Correcting members for VHDL... Computing tooltip texts... Generating style sheet... Generating search indices... Generating images for formulas in HTML... Generating image form_0.png for formula Generating image form_1.png for formula Generating image form_2.png for formula Generating image form_3.png for formula Generating image form_4.png for formula Generating image form_5.png for formula Generating image form_6.png for formula Generating image form_7.png for formula Generating image form_8.png for formula Generating image form_9.png for formula Generating image form_10.png for formula Generating image form_11.png for formula Generating image form_12.png for formula Generating image form_13.png for formula Generating image form_14.png for formula Generating image form_15.png for formula Generating image form_16.png for formula Generating image form_17.png for formula Generating image form_18.png for formula Generating image form_19.png for formula Generating image form_20.png for formula Generating image form_21.png for formula Generating image form_22.png for formula Generating image form_23.png for formula Generating image form_24.png for formula Generating image form_25.png for formula Generating image form_26.png for formula Generating image form_27.png for formula Generating image form_28.png for formula Generating image form_29.png for formula Generating image form_30.png for formula Generating image form_31.png for formula Generating image form_32.png for formula Generating image form_33.png for formula Generating image form_34.png for formula Generating image form_35.png for formula Generating image form_36.png for formula Generating image form_37.png for formula Generating image form_38.png for formula Generating image form_39.png for formula Generating image form_40.png for formula Generating image form_41.png for formula Generating image form_42.png for formula Generating image form_43.png for formula Generating image form_44.png for formula Generating image form_45.png for formula Generating image form_46.png for formula Generating image form_47.png for formula Generating image form_48.png for formula Generating image form_49.png for formula Generating image form_50.png for formula Generating image form_51.png for formula Generating image form_52.png for formula Generating image form_53.png for formula Generating image form_54.png for formula Generating image form_55.png for formula Generating image form_56.png for formula Generating image form_57.png for formula Generating image form_58.png for formula Generating image form_59.png for formula Generating image form_60.png for formula Generating image form_61.png for formula Generating image form_62.png for formula Generating image form_63.png for formula Generating image form_64.png for formula Generating image form_0_dark.png for formula Generating image form_1_dark.png for formula Generating image form_2_dark.png for formula Generating image form_3_dark.png for formula Generating image form_4_dark.png for formula Generating image form_5_dark.png for formula Generating image form_6_dark.png for formula Generating image form_7_dark.png for formula Generating image form_8_dark.png for formula Generating image form_9_dark.png for formula Generating image form_10_dark.png for formula Generating image form_11_dark.png for formula Generating image form_12_dark.png for formula Generating image form_13_dark.png for formula Generating image form_14_dark.png for formula Generating image form_15_dark.png for formula Generating image form_16_dark.png for formula Generating image form_17_dark.png for formula Generating image form_18_dark.png for formula Generating image form_19_dark.png for formula Generating image form_20_dark.png for formula Generating image form_21_dark.png for formula Generating image form_22_dark.png for formula Generating image form_23_dark.png for formula Generating image form_24_dark.png for formula Generating image form_25_dark.png for formula Generating image form_26_dark.png for formula Generating image form_27_dark.png for formula Generating image form_28_dark.png for formula Generating image form_29_dark.png for formula Generating image form_30_dark.png for formula Generating image form_31_dark.png for formula Generating image form_32_dark.png for formula Generating image form_33_dark.png for formula Generating image form_34_dark.png for formula Generating image form_35_dark.png for formula Generating image form_36_dark.png for formula Generating image form_37_dark.png for formula Generating image form_38_dark.png for formula Generating image form_39_dark.png for formula Generating image form_40_dark.png for formula Generating image form_41_dark.png for formula Generating image form_42_dark.png for formula Generating image form_43_dark.png for formula Generating image form_44_dark.png for formula Generating image form_45_dark.png for formula Generating image form_46_dark.png for formula Generating image form_47_dark.png for formula Generating image form_48_dark.png for formula Generating image form_49_dark.png for formula Generating image form_50_dark.png for formula Generating image form_51_dark.png for formula Generating image form_52_dark.png for formula Generating image form_53_dark.png for formula Generating image form_54_dark.png for formula Generating image form_55_dark.png for formula Generating image form_56_dark.png for formula Generating image form_57_dark.pn/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:2095: warning: Member polyEval(int numP, double p[], double c[][VMAXP], double xv[]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:1528: warning: Member Vfetk_PDE_initElement(PDE *thee, int elementType, int chart, double tvx[][3], void *data) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:1571: warning: Member Vfetk_PDE_initPoint(PDE *thee, int pointType, int chart, double txq[], double tU[], double tdU[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:1741: warning: Member Vfetk_PDE_DFu_wv(PDE *thee, int key, double W[], double dW[][VAPBS_DIM], double V[], double dV[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:1902: warning: Member Vfetk_PDE_bisectEdge(int dim, int dimII, int edgeType, int chart[], double vx[][3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:1912: warning: Member Vfetk_PDE_mapBoundary(int dim, int dimII, int vertexType, int chart, double vx[3]) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:1917: warning: Member Vfetk_PDE_markSimplex(int dim, int dimII, int simplexType, int faceType[VAPBS_NVS], int vertexType[VAPBS_NVS], int chart[], double vx[][3], void *simplex) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:1998: warning: Member Vfetk_PDE_oneChart(int dim, int dimII, int objType, int chart[], double vx[][3], int dimV) (function) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:86: warning: Member var (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:93: warning: Member diriCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:130: warning: Member neumCubeString (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:366: warning: Member dim_2DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:386: warning: Member lgr_2DP1[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:395: warning: Member lgr_2DP1x[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:402: warning: Member lgr_2DP1y[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:409: warning: Member lgr_2DP1z[3][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:437: warning: Member dim_3DP1 (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:438: warning: Member lgr_3DP1[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:446: warning: Member lgr_3DP1x[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:454: warning: Member lgr_3DP1y[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:462: warning: Member lgr_3DP1z[VAPBS_NVS][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:476: warning: Member P_DEG (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:482: warning: Member numP (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:483: warning: Member c[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:484: warning: Member cx[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:485: warning: Member cy[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vfetk.c:486: warning: Member cz[VMAXP][VMAXP] (variable) of file vfetk.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vpee.c:498: warning: Member Vpee_userDefined(Vpee *thee, SS *sm) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vpee.c:532: warning: Member Vpee_ourSimp(Vpee *thee, SS *sm, int rcol) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vpee.c:66: warning: Member Aprx_estNonlinResid(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vpee.c:72: warning: Member Aprx_estLocalProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/fem/vpee.c:77: warning: Member Aprx_estDualProblem(Aprx *thee, SS *sm, Bvec *u, Bvec *ud, Bvec *f) (function) of file vpee.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:237: warning: Member APOLparm_parseGRID(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:268: warning: Member APOLparm_parseMOL(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:287: warning: Member APOLparm_parseSRFM(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:309: warning: Member APOLparm_parseSRAD(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:328: warning: Member APOLparm_parseSWIN(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:347: warning: Member APOLparm_parseTEMP(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:366: warning: Member APOLparm_parseGAMMA(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:385: warning: Member APOLparm_parseCALCENERGY(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:438: warning: Member APOLparm_parseCALCFORCE(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:491: warning: Member APOLparm_parseBCONC(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:510: warning: Member APOLparm_parseSDENS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:529: warning: Member APOLparm_parseDPOS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/apolparm.c:558: warning: Member APOLparm_parsePRESS(APOLparm *thee, Vio *sock) (function) of file apolparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:210: warning: Member BEMparm_parseTREE_ORDER(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:233: warning: Member BEMparm_parseTREE_N0(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:256: warning: Member BEMparm_parseMAC(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:279: warning: Member BEMparm_parseMESH(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/bemparm.c:308: warning: Member BEMparm_parseOUTDATA(BEMparm *thee, Vio *sock) (function) of file bemparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:196: warning: Member FEMparm_parseDOMAINLENGTH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:221: warning: Member FEMparm_parseETOL(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:244: warning: Member FEMparm_parseEKEY(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:276: warning: Member FEMparm_parseAKEYPRE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:303: warning: Member FEMparm_parseAKEYSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:333: warning: Member FEMparm_parseTARGETNUM(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:352: warning: Member FEMparm_parseTARGETRES(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:372: warning: Member FEMparm_parseMAXSOLVE(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:391: warning: Member FEMparm_parseMAXVERT(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/femparm.c:411: warning: Member FEMparm_parseUSEMESH(FEMparm *thee, Vio *sock) (function) of file femparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.c:138: warning: Member FUBAR(const char *name) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.c:143: warning: Member parseNonNeg(double *tf, double def, int *set, char *name, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.c:164: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.c:186: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:169: warning: Member GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:171: warning: Member GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock) (function) of file geoflowparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:415: warning: Member MGparm_parseDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:446: warning: Member MGparm_parseCHGM(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:497: warning: Member MGparm_parseNLEV(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:516: warning: Member MGparm_parseETOL(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:539: warning: Member MGparm_parseGRID(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:570: warning: Member MGparm_parseGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:601: warning: Member MGparm_parseGAMMA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:616: warning: Member MGparm_parseGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:668: warning: Member MGparm_parseCGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:699: warning: Member MGparm_parseFGLEN(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:730: warning: Member MGparm_parseCGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:782: warning: Member MGparm_parseFGCENT(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:834: warning: Member MGparm_parsePDIME(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:872: warning: Member MGparm_parseOFRAC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:892: warning: Member MGparm_parseASYNC(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/mgparm.c:912: warning: Member MGparm_parseUSEAQUA(MGparm *thee, Vio *sock) (function) of file mgparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:970: warning: Member NOsh_parseREAD(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1021: warning: Member NOsh_parsePRINT(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1187: warning: Member NOsh_parseELEC(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1313: warning: Member NOsh_parseAPOLAR(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2385: warning: Member NOsh_parseFEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1510: warning: Member NOsh_parseMG(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2845: warning: Member NOsh_parseBEM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2934: warning: Member NOsh_parseGEOFLOW(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:3048: warning: Member NOsh_parsePBAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:3166: warning: Member NOsh_parsePBSAM(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2508: warning: Member NOsh_parseAPOL(NOsh *thee, Vio *sock, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1603: warning: Member NOsh_setupCalcMG(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1815: warning: Member NOsh_setupCalcMGAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1747: warning: Member NOsh_setupCalcMGMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2090: warning: Member NOsh_setupCalcMGPARA(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1722: warning: Member NOsh_setupCalcFEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2471: warning: Member NOsh_setupCalcFEMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1638: warning: Member NOsh_setupCalcBEM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1666: warning: Member NOsh_setupCalcGEOFLOW(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1686: warning: Member NOsh_setupCalcPBAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:1704: warning: Member NOsh_setupCalcPBSAM(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2612: warning: Member NOsh_setupCalcBEMMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2677: warning: Member NOsh_setupCalcGEOFLOWMANUAL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2735: warning: Member NOsh_setupCalcPBAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2786: warning: Member NOsh_setupCalcPBSAMAUTO(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:2581: warning: Member NOsh_setupCalcAPOL(NOsh *thee, NOsh_calc *elec) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:598: warning: Member NOsh_parseREAD_MOL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:675: warning: Member NOsh_parseREAD_PARM(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:739: warning: Member NOsh_parseREAD_DIEL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:793: warning: Member NOsh_parseREAD_KAPPA(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:839: warning: Member NOsh_parseREAD_POTENTIAL(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:884: warning: Member NOsh_parseREAD_CHARGE(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/nosh.c:930: warning: Member NOsh_parseREAD_MESH(NOsh *thee, Vio *sock) (function) of file nosh.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:458: warning: Member PBAMparm_parseNtraj(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.c:549: warning: Member PBAMparm_parseTerm(PBAMparm *thee, Vio *sock) (function) of file pbamparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:77: warning: Member PBAMPARM_MAXWRITE (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:78: warning: Member PBAMPARM_MAXMOL (macro definition) of file pbamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:87: warning: Member PBEparm_getzmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:91: warning: Member PBEparm_getLmem(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:95: warning: Member PBEparm_getmembraneDiel(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:99: warning: Member PBEparm_getmemv(PBEparm *thee) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:368: warning: Member PBEparm_parseLPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:375: warning: Member PBEparm_parseNPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:382: warning: Member PBEparm_parseMOL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:401: warning: Member PBEparm_parseLRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:408: warning: Member PBEparm_parseNRPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:415: warning: Member PBEparm_parseSMPBE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:474: warning: Member PBEparm_parseBCFL(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:555: warning: Member PBEparm_parseION(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:652: warning: Member PBEparm_parsePDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:671: warning: Member PBEparm_parseSDENS(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:690: warning: Member PBEparm_parseSDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:709: warning: Member PBEparm_parseSRFM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:780: warning: Member PBEparm_parseSRAD(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:799: warning: Member PBEparm_parseSWIN(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:818: warning: Member PBEparm_parseTEMP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:837: warning: Member PBEparm_parseUSEMAP(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:895: warning: Member PBEparm_parseCALCENERGY(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:948: warning: Member PBEparm_parseCALCFORCE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:1005: warning: Member PBEparm_parseZMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:1025: warning: Member PBEparm_parseLMEM(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:1044: warning: Member PBEparm_parseMDIE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:1063: warning: Member PBEparm_parseMEMV(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:1084: warning: Member PBEparm_parseWRITE(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.c:1178: warning: Member PBEparm_parseWRITEMAT(PBEparm *thee, Vio *sock) (function) of file pbeparm.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:77: warning: Member PBSAMPARM_MAXWRITE (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:78: warning: Member PBSAMPARM_MAXMOL (macro definition) of file pbsamparm.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:277: warning: Member Vacc_vdwAcc(Vacc *thee, double center[3]) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:307: warning: Member Vacc_ivdwAcc(Vacc *thee, double center[3], double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:679: warning: Member Vacc_writeGMV(Vacc *thee, double radius, int meth, Gem *gm, char *iodev, char *iofmt, char *iohost, char *iofile) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1252: warning: Member Vacc_SASAPos(Vacc *thee, double radius) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:1277: warning: Member Vacc_atomSASAPos(Vacc *thee, double radius, Vatom *atom, int mode) (function) of file vacc.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:76: warning: The following parameter of ivdwAccExclus(Vacc *thee, double center[3], double radius, int atomID) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vacc.c:490: warning: The following parameter of splineAcc(Vacc *thee, double center[VAPBS_DIM], double win, double infrad, VclistCell *cell) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:186: warning: Member Valist_readPDBSerial(Valist *thee, Vio *sock, int *serial) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:206: warning: Member Valist_readPDBAtomName(Valist *thee, Vio *sock, char atomName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:224: warning: Member Valist_readPDBResidueName(Valist *thee, Vio *sock, char resName[VMAX_ARGLEN]) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:242: warning: Member Valist_readPDBResidueNumber(Valist *thee, Vio *sock, int *resSeq) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:298: warning: Member Valist_readPDBAtomCoord(Valist *thee, Vio *sock, double *coord) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:316: warning: Member Valist_readPDBChargeRadius(Valist *thee, Vio *sock, double *charge, double *radius) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:344: warning: Member Valist_readPDB_throughXYZ(Valist *thee, Vio *sock, int *serial, char atomName[VMAX_ARGLEN], char resName[VMAX_ARGLEN], int *resSeq, double *x, double *y, double *z) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:424: warning: Member Valist_getAtomStorage(Valist *thee, Vatom **plist, int *pnlist, int *pnatoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:480: warning: Member Valist_setAtomArray(Valist *thee, Vatom **plist, int nlist, int natoms) (function) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:60: warning: Member Valist_whiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:61: warning: Member Valist_commChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/valist.c:62: warning: Member Valist_xmlwhiteChars (variable) of file valist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vclist.c:128: warning: Member VCLIST_INFLATE (macro definition) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vclist.c:90: warning: Member Vclist_getMolDims(Vclist *thee, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM], double *r_max) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vclist.c:125: warning: Member Vclist_setupGrid(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vclist.c:174: warning: Member Vclist_storeParms(Vclist *thee, Valist *alist, double max_radius, int npts[VAPBS_DIM], Vclist_DomainMode mode, double lower_corner[VAPBS_DIM], double upper_corner[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vclist.c:231: warning: Member Vclist_gridSpan(Vclist *thee, Vatom *atom, int imin[VAPBS_DIM], int imax[VAPBS_DIM]) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vclist.c:262: warning: Member Vclist_arrayIndex(Vclist *thee, int i, int j, int k) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vclist.c:270: warning: Member Vclist_assignAtoms(Vclist *thee) (function) of file vclist.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:425: warning: Member treesetup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:505: warning: Member treecleanup(Vgreen *thee) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vgreen.c:525: warning: Member treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, double *qtar, int numtars, double *tpengtar, double *x, double *y, double *z, double *q, int numpars, double *fx, double *fy, double *fz, int iflag, int farrdim, int arrdim) (function) of file vgreen.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:458: warning: Member MAX_HASH_DIM (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:572: warning: Member OS_SEP_STR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:573: warning: Member OS_SEP_CHAR (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:600: warning: Member ANNOUNCE_FUNCTION (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:601: warning: Member WARN_UNTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:602: warning: Member WARN_PARTTESTED (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:653: warning: Member VCHANNELEDMESSAGE0(channel, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:658: warning: Member VCHANNELEDMESSAGE1(channel, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:665: warning: Member VCHANNELEDMESSAGE2(channel, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:672: warning: Member VCHANNELEDMESSAGE3(channel, msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:679: warning: Member VMESSAGE0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:680: warning: Member VMESSAGE1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:681: warning: Member VMESSAGE2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:682: warning: Member VMESSAGE3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:684: warning: Member VERRMSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:685: warning: Member VERRMSG1(msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:686: warning: Member VERRMSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:687: warning: Member VERRMSG3(msg, arg0, arg1, arg2) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:731: warning: Member VASSERT_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:741: warning: Member VASSERT_MSG1(cnd, msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:753: warning: Member VASSERT_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:825: warning: Member VWARN_MSG0(cnd, msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:838: warning: Member VWARN_MSG1(cnd, msg, arg0) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:853: warning: Member VWARN_MSG2(cnd, msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:899: warning: Member VABORT_MSG0(msg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:907: warning: Member VABORT_MSG1(msg, arg) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:917: warning: Member VABORT_MSG2(msg, arg0, arg1) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:944: warning: Member PRINT_INT(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:945: warning: Member PRINT_DBL(expr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:948: warning: Member VMALLOC(vmem, n, type) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:950: warning: Member VFREE(vmem, n, type, ptr) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:952: warning: Member VFILL(vec, n, val) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:959: warning: Member VCOPY(srcvec, dstvec, i, n) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:968: warning: Member VAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:969: warning: Member RAT(array, i) (macro definition) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:73: warning: Member Vrc_Codes (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:95: warning: Member Vsol_Meth (typedef) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vhal.h:966: warning: Member wrap_text(char *str, int right_margin, int left_padding) (function) of file vhal.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:64: warning: Member MAT2(mat, dx, dy) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:68: warning: Member RAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:71: warning: Member VAT2(mat, x, y) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:76: warning: Member MAT3(mat, dx, dy, dz) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:81: warning: Member RAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vmatrix.h:84: warning: Member VAT3(mat, x, y, z) (macro definition) of file vmatrix.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/vpbe.c:62: warning: Member MAX_SPLINE_WINDOW (macro definition) of file vpbe.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:67: warning: Member IJK(i, j, k) (macro definition) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:77: warning: Member MCwhiteChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:78: warning: Member MCcommChars (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:79: warning: Member Vcompare (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vgrid.c:80: warning: Member Vprecision[26] (variable) of file vgrid.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vopot.c:113: warning: Member IJK(i, j, k) (macro definition) of file vopot.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:1401: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:2828: warning: Member bcCalcOrig(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3130: warning: Member gridPointIsValid(int i, int j, int k, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3313: warning: Member packAtoms(double *ax, double *ay, double *az, double *charge, double *size, Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3338: warning: Member packUnpack(int nx, int ny, int nz, int ngrid, double *gx, double *gy, double *gz, double *value, Vpmg *thee, int pack) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3407: warning: Member bcflnew(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3597: warning: Member bcfl_sdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3868: warning: Member bcfl_mdh(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:3995: warning: Member bcfl_mem(double zmem, double L, double eps_m, double eps_w, double V, double xkappa, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:4174: warning: Member bcfl_map(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:6684: warning: Member markFrac(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *xarray, double *yarray, double *zarray) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.c:10260: warning: Member fillcoPermanentInduced(Vpmg *thee) (function) of file vpmg.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1056: warning: The following parameter of bcfl1(double size, double *apos, double charge, double xkappa, double pre1, double *gxcf, double *gycf, double *gzcf, double *xf, double *yf, double *zf, int nx, int ny, int nz) is not documented: parameter 'size' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1362: warning: argument 'hz' of command @param is not found in the argument list of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1362: warning: The following parameter of markSphere(double rtot, double *tpos, int nx, int ny, int nz, double hx, double hy, double hzed, double xmin, double ymin, double zmin, double *array, double markVal) is not documented: parameter 'rtot' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1107: warning: The following parameter of multipolebc(double r, double kappa, double eps_p, double eps_w, double rad, double tsr[3]) is not documented: parameter 'r' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1315: warning: The following parameters of qfForceSpline1(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1325: warning: The following parameters of qfForceSpline2(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1335: warning: The following parameters of qfForceSpline4(Vpmg *thee, double *force, int atomID) are not documented: parameter 'thee' parameter 'force' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:995: warning: The following parameter of Vpmg_polarizEnergy(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1006: warning: The following parameter of Vpmg_qfEnergyPoint(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1017: warning: The following parameter of Vpmg_qfEnergyVolume(Vpmg *thee, int extFlag) is not documented: parameter 'thee' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1029: warning: The following parameter of Vpmg_splineSelect(int srfm, Vacc *acc, double *gpos, double win, double infrad, Vatom *atom, double *force) is not documented: parameter 'srfm' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1348: warning: The following parameters of zlapSolve(Vpmg *thee, double **solution, double **source, double **work1) are not documented: parameter 'thee' parameter 'solution' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:105: warning: Member VPMGMAXPART (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1392: warning: Member VCUB(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1393: warning: Member VLOG(x) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1395: warning: Member IJK(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1396: warning: Member IJKx(j, k, i) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1397: warning: Member IJKy(i, k, j) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1398: warning: Member IJKz(i, j, k) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1399: warning: Member VFCHI(iint, iflt) (macro definition) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmg.h:1385: warning: Member Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag) (function) of file vpmg.h is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/mg/vpmgp.c:294: warning: Member coarsenThis(int nOld) (function) of file vpmgp.c is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:247: warning: argument 'parm' of command @param is not found in the argument list of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:247: warning: The following parameter of PBAMparm_parseSalt(PBAMparm *thee, Vio *sock) is not documented: parameter 'sock' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:513: warning: The following parameter of energyAPOL(APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms) is not documented: parameter 'apolparm' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:610: warning: The following parameter of killFE(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:262: warning: The following parameter of killMG(NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) is not documented: parameter 'nosh' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:882: warning: argument 'charge' of command @param is not found in the argument list of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:882: warning: The following parameter of loadChargeMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:662: warning: argument 'kappa' of command @param is not found in the argument list of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:662: warning: The following parameter of loadKappaMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:791: warning: argument 'pot' of command @param is not found in the argument list of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:791: warning: The following parameter of loadPotMaps(NOsh *nosh, Vgrid *map[NOSH_MAXMOL]) is not documented: parameter 'map' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:622: warning: argument 'nosh' of command @param is not found in the argument list of preRefineFE(int i, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:622: warning: too many @param commands for function preRefineFE. Found 4 while function has 3 parameters /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:494: warning: The following parameter of printApolForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:445: warning: The following parameter of printElecEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:481: warning: The following parameter of printElecForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:432: warning: The following parameter of printEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.h:468: warning: The following parameter of printForce(Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) is not documented: parameter 'com' /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/routines.c:4125: warning: argument 'i' of command @param is not found in the argument list of solveFE(int icalc, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:104: warning: Member vdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/geoflowparm.h:105: warning: Member setvdw (variable) of struct sGEOFLOWparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:111: warning: Member salt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:112: warning: Member setsalt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:115: warning: Member runtype[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:116: warning: Member setruntype (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:119: warning: Member runname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:120: warning: Member setrunname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:123: warning: Member setrandorient (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:126: warning: Member pbcboxlen (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:127: warning: Member setpbcs (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:130: warning: Member units[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:131: warning: Member setunits (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:137: warning: Member gridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:138: warning: Member setgridpt (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:141: warning: Member map3dname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:142: warning: Member set3dmap (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:145: warning: Member grid2Dname[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:146: warning: Member grid2Dax[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:147: warning: Member grid2Dloc[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:148: warning: Member grid2Dct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:149: warning: Member setgrid2Dname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:152: warning: Member dxname[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:153: warning: Member setdxname (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:158: warning: Member ntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:159: warning: Member setntraj (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:161: warning: Member termcombine[CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:162: warning: Member settermcombine (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:164: warning: Member diffct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:165: warning: Member moveType[PBAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:166: warning: Member transDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:167: warning: Member rotDiff[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:169: warning: Member termct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:170: warning: Member setterm (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:172: warning: Member termnam[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:173: warning: Member termnu[PBAMPARM_MAXWRITE][1] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:174: warning: Member termVal[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:175: warning: Member confil[PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:176: warning: Member conpad[PBAMPARM_MAXWRITE] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:177: warning: Member confilct (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:179: warning: Member setxyz (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:180: warning: Member xyzct[PBAMPARM_MAXMOL] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbamparm.h:181: warning: Member xyzfil[PBAMPARM_MAXMOL][PBAMPARM_MAXWRITE][CHR_MAXLEN] (variable) of struct sPBAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.h:202: warning: Member pbam_3dmapstem[VMAX_ARGLEN] (variable) of struct sPBEparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbeparm.h:203: warning: Member pbam_3dmapflag (variable) of struct sPBEparm is not documented. g for formula Generating image form_58_dark.png for formula Generating image form_59_dark.png for formula Generating image form_60_dark.png for formula Generating image form_61_dark.png for formula Generating image form_62_dark.png for formula Generating image form_63_dark.png for formula Generating image form_64_dark.png for formula Generating example documentation... Generating file sources... Generating code for file doc/programmer/mainpage.h... Generating code for file src/apbs.h... Generating code for file src/fem/vcsm.c... Generating code for file src/fem/vcsm.h... Generating code for file src/fem/vfetk.c... Generating code for file src/fem/vfetk.h... Generating code for file src/fem/vpee.c... Generating code for file src/fem/vpee.h... Generating code for file src/generic/apolparm.c... Generating code for file src/generic/apolparm.h... Generating code for file src/generic/bemparm.c... Generating code for file src/generic/bemparm.h... Generating code for file src/generic/femparm.c... Generating code for file src/generic/femparm.h... Generating code for file src/generic/geoflowparm.c... Generating code for file src/generic/geoflowparm.h... Generating code for file src/generic/mgparm.c... Generating code for file src/generic/mgparm.h... Generating code for file src/generic/nosh.c... Generating code for file src/generic/nosh.h... Generating code for file src/generic/pbamparm.c... Generating code for file src/generic/pbamparm.h... Generating code for file src/generic/pbeparm.c... Generating code for file src/generic/pbeparm.h... Generating code for file src/generic/pbsamparm.c... Generating code for file src/generic/pbsamparm.h... Generating code for file src/generic/vacc.c... Generating code for file src/generic/vacc.h... Generating code for file src/generic/valist.c... Generating code for file src/generic/valist.h... Generating code for file src/generic/vatom.c... Generating code for file src/generic/vatom.h... Generating code for file src/generic/vcap.c... Generating code for file src/generic/vcap.h... Generating code for file src/generic/vclist.c... Generating code for file src/generic/vclist.h... Generating code for file src/generic/vgreen.c... Generating code for file src/generic/vgreen.h... Generating code for file src/generic/vhal.h... Generating code for file src/generic/vmatrix.h... Generating code for file src/generic/vparam.c... Generating code for file src/generic/vparam.h... Generating code for file src/generic/vpbe.c... Generating code for file src/generic/vpbe.h... Generating code for file src/generic/vstring.c... Generating code for file src/generic/vstring.h... Generating code for file src/generic/vunit.h... Generating code for file src/main.c... Generating code for file src/mg/vgrid.c... Generating code for file src/mg/vgrid.h... Generating code for file src/mg/vmgrid.c... Generating code for file src/mg/vmgrid.h... Generating code for file src/mg/vopot.c... Generating code for file src/mg/vopot.h... Generating code for file src/mg/vpmg.c... Generating code for file src/mg/vpmg.h... Generating code for file src/mg/vpmgp.c... Generating code for file src/mg/vpmgp.h... Generating code for file src/pmgc/buildAd.c... Generating code for file src/pmgc/buildAd.h... Generating code for file src/pmgc/buildBd.c... Generating code for file src/pmgc/buildBd.h... Generating code for file src/pmgc/buildGd.c... Generating code for file src/pmgc/buildGd.h... Generating code for file src/pmgc/buildPd.c... Generating code for file src/pmgc/buildPd.h... Generating code for file src/pmgc/cgd.c... Generating code for file src/pmgc/cgd.h... Generating code for file src/pmgc/gsd.c... Generating code for file src/pmgc/gsd.h... Generating code for file src/pmgc/matvecd.c... Generating code for file src/pmgc/matvecd.h... Generating code for file src/pmgc/mgcsd.c... Generating code for file src/pmgc/mgcsd.h... Generating code for file src/pmgc/mgdrvd.c... Generating code for file src/pmgc/mgdrvd.h... Generating code for file src/pmgc/mgfasd.c... Generating code for file src/pmgc/mgfasd.h... Generating code for file src/pmgc/mgsubd.c... Generating code for file src/pmgc/mgsubd.h... Generating code for file src/pmgc/mikpckd.c... Generating code for file src/pmgc/mikpckd.h... Generating code for file src/pmgc/mlinpckd.c... Generating code for file src/pmgc/mlinpckd.h... Generating code for file src/pmgc/mypdec.c... Generating code for file src/pmgc/mypdec.h... Generating code for file src/pmgc/newdrvd.c... Generating code for file src/pmgc/newdrvd.h... Generating code for file src/pmgc/newtond.c... Generating code for file src/pmgc/newtond.h... Generating code for file src/pmgc/powerd.c... Generating code for file src/pmgc/powerd.h... Generating code for file src/pmgc/smoothd.c... Generating code for file src/pmgc/smoothd.h... Generating code for file src/routines.c... Generating code for file src/routines.h... Generating file documentation... Generating docs for file src/apbs.h... Generating docs for file src/fem/vcsm.c... Generating docs for file src/fem/vcsm.h... Generating docs for file src/fem/vfetk.c... Generating docs for file src/fem/vfetk.h... Generating docs for file src/fem/vpee.c... Generating docs for file src/fem/vpee.h... Generating docs for file src/generic/apolparm.c... Generating docs for file src/generic/bemparm.c... Generating docs for file src/generic/femparm.c... Generating docs for file src/generic/femparm.h... Generating docs for file src/generic/geoflowparm.c... Generating docs for file src/generic/geoflowparm.h... Generating docs for file src/generic/mgparm.c... Generating docs for file src/generic/mgparm.h... Generating docs for file src/generic/nosh.c... Generating docs for file src/generic/nosh.h... Generating docs for file src/generic/pbamparm.c... Generating docs for file src/generic/pbamparm.h... Generating docs for file src/generic/pbeparm.c... Generating docs for file src/generic/pbeparm.h... Generating docs for file src/generic/pbsamparm.c... Generating docs for file src/generic/pbsamparm.h... Generating docs for file src/generic/vacc.c... Generating docs for file src/generic/vacc.h... Generating docs for file src/generic/valist.c... Generating docs for file src/generic/valist.h... Generating docs for file src/generic/vatom.c... Generating docs for file src/generic/vatom.h... Generating docs for file src/generic/vcap.c... Generating docs for file src/generic/vcap.h... Generating docs for file src/generic/vclist.c... Generating docs for file src/generic/vclist.h... Generating docs for file src/generic/vgreen.c... Generating docs for file src/generic/vgreen.h... Generating docs for file src/generic/vhal.h... Generating docs for file src/generic/vmatrix.h... Generating docs for file src/generic/vparam.c... Generating docs for file src/generic/vparam.h... Generating docs for file src/generic/vpbe.c... Generating docs for file src/generic/vpbe.h... Generating docs for file src/generic/vstring.c... Generating docs for file src/generic/vstring.h... Generating docs for file src/generic/vunit.h... Generating docs for file src/main.c... Generating docs for file src/mg/vgrid.c... Generating docs for file src/mg/vgrid.h... Generating docs for file src/mg/vmgrid.c... Generating docs for file src/mg/vmgrid.h... Generating docs for file src/mg/vopot.c... Generating docs for file src/mg/vopot.h... Generating docs for file src/mg/vpmg.c... Generating docs for file src/mg/vpmg.h... Generating docs for file src/mg/vpmgp.c... Generating docs for file src/mg/vpmgp.h... Generating docs for file src/routines.c... Generating docs for file src/routines.h... Generating page documentation... Generating docs for page bug... Generating docs for page deprecated... Generating group documentation... Generating class documentation... Generating docs for compound AtomForce... Generating docs for compound sAPOLparm... Generating docs for compound sBEMparm... Generating docs for compound sFEMparm... Generating docs for compound sGEOFLOWparm... Generating docs for compound sMGparm... Generating docs for compound sNOsh... Generating docs for compound sNOsh_calc... Generating docs for compound sPBAMparm... Generating docs for compound sPBEparm... Ge/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:112: warning: Member settolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:113: warning: Member tolsp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:115: warning: Member setmsms (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:116: warning: Member probe_radius (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:117: warning: Member density (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:119: warning: Member setsurf (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:120: warning: Member surfct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:121: warning: Member surffil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:123: warning: Member setimat (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:124: warning: Member imatct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:125: warning: Member imatfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:127: warning: Member setexp (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:128: warning: Member expct (variable) of struct sPBSAMparm is not documented. /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/src/generic/pbsamparm.h:129: warning: Member expfil[PBSAMPARM_MAXMOL][CHR_MAXLEN] (variable) of struct sPBSAMparm is not documented. nerating docs for compound sPBSAMparm... Generating docs for compound sVacc... Generating docs for compound sVaccSurf... Generating docs for compound sValist... Generating docs for compound sVatom... Generating docs for compound sVclist... Generating docs for compound sVclistCell... Generating docs for compound sVcsm... Generating docs for compound sVfetk... Generating docs for compound sVfetk_LocalVar... Generating docs for compound sVgreen... Generating docs for compound sVgrid... Generating docs for compound sVmgrid... Generating docs for compound sVopot... Generating docs for compound sVparam_AtomData... Generating docs for compound sVpbe... Generating docs for compound sVpee... Generating docs for compound sVpmg... Generating docs for compound sVpmgp... Generating docs for compound Vparam... Generating docs for compound Vparam_ResData... Generating concept documentation... Generating module documentation... Generating namespace documentation... Generating graph info page... Generating directory documentation... Generating dependency graph for directory src/fem Generating dependency graph for directory src/generic Generating dependency graph for directory src/mg Generating dependency graph for directory src/pmgc Generating dependency graph for directory doc/programmer Generating dependency graph for directory src Generating index page... Generating main page... Generating page index... Generating topic index... Generating module index... Generating module member index... Generating namespace index... Generating namespace member index... Generating concept index... Generating annotated compound index... Generating alphabetical compound index... Generating hierarchical class index... Generating graphical class hierarchy... Generating member index... Generating file index... Generating file member index... Generating example index... finalizing index lists... writing tag file... Running plantuml with JAVA... Running mermaid (mmdc)... Running dot... Generating 175 dot graphs using 6 parallel threads with batch size 50... Finished running dot for graphs 1-14/175 Finished running dot for graphs 15-28/175 Finished running dot for graphs 29-42/175 Finished running dot for graphs 43-56/175 Finished running dot for graphs 57-70/175 Finished running dot for graphs 71-84/175 Finished running dot for graphs 85-100/175 Finished running dot for graphs 101-115/175 Finished running dot for graphs 116-130/175 Finished running dot for graphs 131-145/175 Finished running dot for graphs 146-160/175 Finished running dot for graphs 161-175/175 Patching output file 1/120 Patching output file 2/120 Patching output file 3/120 Patching output file 4/120 Patching output file 5/120 Patching output file 6/120 Patching output file 7/120 Patching output file 8/120 Patching output file 9/120 Patching output file 10/120 Patching output file 11/120 Patching output file 12/120 Patching output file 13/120 Patching output file 14/120 Patching output file 15/120 Patching output file 16/120 Patching output file 17/120 Patching output file 18/120 Patching output file 19/120 Patching output file 20/120 Patching output file 21/120 Patching output file 22/120 Patching output file 23/120 Patching output file 24/120 Patching output file 25/120 Patching output file 26/120 Patching output file 27/120 Patching output file 28/120 Patching output file 29/120 Patching output file 30/120 Patching output file 31/120 Patching output file 32/120 Patching output file 33/120 Patching output file 34/120 Patching output file 35/120 Patching output file 36/120 Patching output file 37/120 Patching output file 38/120 Patching output file 39/120 Patching output file 40/120 Patching output file 41/120 Patching output file 42/120 Patching output file 43/120 Patching output file 44/120 Patching output file 45/120 Patching output file 46/120 Patching output file 47/120 Patching output file 48/120 Patching output file 49/120 Patching output file 50/120 Patching output file 51/120 Patching output file 52/120 Patching output file 53/120 Patching output file 54/120 Patching output file 55/120 Patching output file 56/120 Patching output file 57/120 Patching output file 58/120 Patching output file 59/120 Patching output file 60/120 Patching output file 61/120 Patching output file 62/120 Patching output file 63/120 Patching output file 64/120 Patching output file 65/120 Patching output file 66/120 Patching output file 67/120 Patching output file 68/120 Patching output file 69/120 Patching output file 70/120 Patching output file 71/120 Patching output file 72/120 Patching output file 73/120 Patching output file 74/120 Patching output file 75/120 Patching output file 76/120 Patching output file 77/120 Patching output file 78/120 Patching output file 79/120 Patching output file 80/120 Patching output file 81/120 Patching output file 82/120 Patching output file 83/120 Patching output file 84/120 Patching output file 85/120 Patching output file 86/120 Patching output file 87/120 Patching output file 88/120 Patching output file 89/120 Patching output file 90/120 Patching output file 91/120 Patching output file 92/120 Patching output file 93/120 Patching output file 94/120 Patching output file 95/120 Patching output file 96/120 Patching output file 97/120 Patching output file 98/120 Patching output file 99/120 Patching output file 100/120 Patching output file 101/120 Patching output file 102/120 Patching output file 103/120 Patching output file 104/120 Patching output file 105/120 Patching output file 106/120 Patching output file 107/120 Patching output file 108/120 Patching output file 109/120 Patching output file 110/120 Patching output file 111/120 Patching output file 112/120 Patching output file 113/120 Patching output file 114/120 Patching output file 115/120 Patching output file 116/120 Patching output file 117/120 Patching output file 118/120 Patching output file 119/120 Patching output file 120/120 type lookup cache used 1911/65536 hits=12270 misses=2045 symbol lookup cache used 6559/65536 hits=63502 misses=6559 finished... [67/88] : && /usr/bin/gcc -fPIC -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -shared -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--dependency-file=src/CMakeFiles/apbs.dir/link.d -Wl,-soname,libapbs.so.1 -o lib/libapbs.so.1 src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o src/generic/CMakeFiles/apbs_generic.dir/valist.c.o src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o -Wl,-rpath,:::::::: && : [68/88] /usr/bin/cmake -E cmake_symlink_library lib/libapbs.so.1 lib/libapbs.so.1 lib/libapbs.so && : [69/88] : && /usr/bin/gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--dependency-file=tools/mesh/CMakeFiles/mgmesh.dir/link.d tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o -o tools/bin/mgmesh -Wl,-rpath,/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/lib: lib/libapbs.so.1 -lm -lstdc++ -lmaloc -fopenmp && : [70/88] : && /usr/bin/gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--dependency-file=tools/mesh/CMakeFiles/smooth.dir/link.d tools/mesh/CMakeFiles/smooth.dir/smooth.c.o -o tools/bin/smooth -Wl,-rpath,/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/lib: lib/libapbs.so.1 -lm -lstdc++ -lmaloc -fopenmp && : [71/88] : && /usr/bin/gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -fopenmp -lm -DNDEBUG -fPIC -DNDEBUG -Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes -Wl,--dependency-file=tools/mesh/CMakeFiles/dxmath.dir/link.d tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o -o tools/bin/dxmath -Wl,-rpath,/builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/lib: lib/libapbs.so.1 -lm -lstdc++ -lmaloc -fopenmp && : [72/88] : && /usr/bin/gcc -O2 -flto=auto -ffat-lto-objects -fexceptions -g 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LaTeX Warning: Reference `build_pd_8h_source' on page 17 undefined on input lin e 70. LaTeX Warning: Reference `cgd_8c_source' on page 17 undefined on input line 71. LaTeX Warning: Reference `cgd_8h_source' on page 17 undefined on input line 72. LaTeX Warning: Reference `gsd_8c_source' on page 17 undefined on input line 73. LaTeX Warning: Reference `gsd_8h_source' on page 17 undefined on input line 74. LaTeX Warning: Reference `matvecd_8c_source' on page 17 undefined on input line 75. LaTeX Warning: Reference `matvecd_8h_source' on page 17 undefined on input line 76. LaTeX Warning: Reference `mgcsd_8c_source' on page 17 undefined on input line 7 7. LaTeX Warning: Reference `mgcsd_8h_source' on page 17 undefined on input line 7 8. LaTeX Warning: Reference `mgdrvd_8c_source' on page 17 undefined on input line 79. LaTeX Warning: Reference `mgdrvd_8h_source' on page 17 undefined on input line 80. LaTeX Warning: Reference `mgfasd_8c_source' on page 17 undefined on input line 81. LaTeX Warning: Reference `mgfasd_8h_source' on page 17 undefined on input line 82. LaTeX Warning: Reference `mgsubd_8c_source' on page 17 undefined on input line 83. LaTeX Warning: Reference `mgsubd_8h_source' on page 17 undefined on input line 84. LaTeX Warning: Reference `mikpckd_8c_source' on page 17 undefined on input line 85. LaTeX Warning: Reference `mikpckd_8h_source' on page 17 undefined on input line 86. LaTeX Warning: Reference `mlinpckd_8c_source' on page 17 undefined on input lin e 87. LaTeX Warning: Reference `mlinpckd_8h_source' on page 17 undefined on input lin e 88. LaTeX Warning: Reference `mypdec_8c_source' on page 17 undefined on input line 89. [17] LaTeX Warning: Reference `mypdec_8h_source' on page 18 undefined on input line 90. LaTeX Warning: Reference `newdrvd_8c_source' on page 18 undefined on input line 91. LaTeX Warning: Reference `newdrvd_8h_source' on page 18 undefined on input line 92. LaTeX Warning: Reference `newtond_8c_source' on page 18 undefined on input line 93. LaTeX Warning: Reference `newtond_8h_source' on page 18 undefined on input line 94. LaTeX Warning: Reference `powerd_8c_source' on page 18 undefined on input line 95. LaTeX Warning: Reference `powerd_8h_source' on page 18 undefined on input line 96. LaTeX Warning: Reference `smoothd_8c_source' on page 18 undefined on input line 97. LaTeX Warning: Reference `smoothd_8h_source' on page 18 undefined on input line 98. ) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 97 [][][] [20] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [21] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] [22] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] [23] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 368 [][][] Underfull \hbox (badness 10000) detected at line 371 [][][] [24] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Underfull \hbox (badness 10000) detected at line 425 [][][] [25] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [31] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] [32] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 578 [][][] [33] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] [34] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 693 [][][] [35] Underfull \hbox (badness 10000) detected at line 714 [][][] Underfull \hbox (badness 10000) detected at line 717 [][][] Underfull \hbox (badness 10000) detected at line 747 [][][] [36] Underfull \hbox (badness 10000) detected at line 773 [][][] Underfull \hbox (badness 10000) detected at line 776 [][][] Underfull \hbox (badness 10000) detected at line 781 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] [37] Underfull \hbox (badness 10000) detected at line 835 [][][] Underfull \hbox (badness 10000) detected at line 838 [][][] Underfull \hbox (badness 10000) detected at line 860 [][][] Underfull \hbox (badness 10000) detected at line 863 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 890 [][][] Underfull \hbox (badness 10000) detected at line 893 [][][] [38] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [39] Underfull \hbox (badness 10000) detected at line 970 [][][] Underfull \hbox (badness 10000) detected at line 973 [][][] Underfull \hbox (badness 10000) detected at line 995 [][][] Underfull \hbox (badness 10000) detected at line 1015 [][][] [40] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1088--1088 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1088--1088 []\T1/phv/m/sl/10 dim[] [41] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] [42] Underfull \hbox (badness 10000) detected at line 1155 [][][] Underfull \hbox (badness 10000) detected at line 1192 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] [43] Underfull \hbox (badness 10000) detected at line 1225 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1250 [][][] Underfull \hbox (badness 10000) detected at line 1253 [][][] [44] Underfull \hbox (badness 10000) detected at line 1278 [][][] Underfull \hbox (badness 10000) detected at line 1311 [][][] Underfull \hbox (badness 10000) detected at line 1314 [][][] [45] Underfull \hbox (badness 10000) detected at line 1344 [][][] Underfull \hbox (badness 10000) detected at line 1347 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [46] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1431 [][][] [47] Underfull \hbox (badness 10000) detected at line 1465 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1494 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1512--1512 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1512--1512 []\T1/phv/m/sl/10 dim[] [48] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1526 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1549--1549 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1549--1549 []\T1/phv/m/sl/10 dim[] [49] Underfull \hbox (badness 10000) detected at line 1560 [][][] Underfull \hbox (badness 10000) detected at line 1563 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1580--1580 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1580--1580 []\T1/phv/m/sl/10 dim[] Underfull \hbox (badness 10000) detected at line 1591 [][][] [50] Underfull \hbox (badness 10000) detected at line 1625 [][][] Underfull \hbox (badness 10000) detected at line 1628 [][][] [51] Underfull \hbox (badness 10000) detected at line 1711 [][][] [52] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1748 [][][] [53] Underfull \hbox (badness 10000) detected at line 1791 [][][] Underfull \hbox (badness 10000) detected at line 1801 [][][] Underfull \hbox (badness 10000) detected at line 1825 [][][] Underfull \hbox (badness 10000) detected at line 1828 [][][] Underfull \hbox (badness 10000) detected at line 1831 [][][] [54] Underfull \hbox (badness 10000) detected at line 1853 [][][] Underfull \hbox (badness 10000) detected at line 1856 [][][] Underfull \hbox (badness 10000) detected at line 1859 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] [55] Underfull \hbox (badness 10000) detected at line 1907 [][][] Underfull \hbox (badness 10000) detected at line 1927 [][][] Underfull \hbox (badness 10000) detected at line 1932 [][][] [56]) (./group___vpee.tex Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 leads to the need for a few final overlapping Schwarz solves to smooth out the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 errors near partition boundaries. Supposedly, if the region in w hich we allow [57] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [58] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 118 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [59] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 199 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] [60] Underfull \hbox (badness 10000) detected at line 245 [][][] Underfull \hbox (badness 10000) detected at line 248 [][][] ) (./group___a_p_o_lparm.tex [61] [62] [63] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [64] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 368 [][][] [65]) (./group___b_e_mparm.tex [66] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] [67] Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [68] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] ) (./group___f_e_mparm.tex [69] [70] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [71] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [72] Underfull \hbox (badness 10000) detected at line 298 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] Underfull \hbox (badness 10000) detected at line 330 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [73] Underfull \hbox (badness 10000) detected at line 357 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [74] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] [75] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [76] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] [77] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] ) (./group___m_gparm.tex [78] [79] [80] Underfull \hbox (badness 10000) detected at line 243 [][][] [81] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] [82] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] [83] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] [84] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 496 [][][] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 521 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] [85] Underfull \hbox (badness 10000) detected at line 546 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 571 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 596 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] [86] Underfull \hbox (badness 10000) detected at line 621 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 654 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] [87] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [88] Underfull \hbox (badness 10000) detected at line 748 [][][] ) (./group___n_osh.tex [89] [90] [91] [92] [93] Underfull \hbox (badness 10000) detected at line 491 [][][] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [94] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 589 [][][] [95] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 645 [][][] [96] Underfull \hbox (badness 10000) detected at line 667 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 719 [][][] [97] Underfull \hbox (badness 10000) detected at line 729 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Underfull \hbox (badness 10000) detected at line 776 [][][] [98] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 803 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 830 [][][] [99] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 857 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [100] Underfull \hbox (badness 10000) detected at line 911 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 938 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] Underfull \hbox (badness 10000) detected at line 965 [][][] [101] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 992 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1029 [][][] [102] Underfull \hbox (badness 10000) detected at line 1046 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1103 [][][] Underfull \hbox (badness 10000) detected at line 1108 [][][] [103] Underfull \hbox (badness 10000) detected at line 1118 [][][] Underfull \hbox (badness 10000) detected at line 1135 [][][] Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] Underfull \hbox (badness 10000) detected at line 1153 [][][] Underfull \hbox (badness 10000) detected at line 1170 [][][] [104] Underfull \hbox (badness 10000) detected at line 1173 [][][] Underfull \hbox (badness 10000) detected at line 1183 [][][] Underfull \hbox (badness 10000) detected at line 1186 [][][] Underfull \hbox (badness 10000) detected at line 1203 [][][] Underfull \hbox (badness 10000) detected at line 1206 [][][] Underfull \hbox (badness 10000) detected at line 1218 [][][] Underfull \hbox (badness 10000) detected at line 1221 [][][] [105] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1241 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1254 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] Underfull \hbox (badness 10000) detected at line 1284 [][][] [106] Underfull \hbox (badness 10000) detected at line 1308 [][][] Underfull \hbox (badness 10000) detected at line 1311 [][][] Underfull \hbox (badness 10000) detected at line 1321 [][][] ) (./group___p_b_a_mparm.tex [107] [108] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [109] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 190 [][][] Underfull \hbox (badness 10000) detected at line 207 [][][] [110] Underfull \hbox (badness 10000) detected at line 231 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 266 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] [111] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [112] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 399 [][][] [113] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] [114] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 543 [][][] [115] Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] [116] Underfull \hbox (badness 10000) detected at line 644 [][][] ) (./group___p_b_eparm.tex [117] [118] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] [119] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 298 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 323 [][][] [120] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [121] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] [122]) (./group___p_b_s_a_mparm.tex [123] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [124] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 191 [][][] [125] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [126] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [127] Underfull \hbox (badness 10000) detected at line 359 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [128] Underfull \hbox (badness 10000) detected at line 407 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] ) (./group___vacc.tex [129] [130] [131] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [132] Underfull \hbox (badness 10000) detected at line 211 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [133] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] [134] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] [135] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [136] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] [137] Underfull \hbox (badness 10000) detected at line 534 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 540 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [138] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [139] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] [140] Underfull \hbox (badness 10000) detected at line 696 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] [141] Underfull \hbox (badness 10000) detected at line 762 [][][] Underfull \hbox (badness 10000) detected at line 794 [][][] [142] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 862 [][][] [143] Underfull \hbox (badness 10000) detected at line 886 [][][] Underfull \hbox (badness 10000) detected at line 889 [][][] Underfull \hbox (badness 10000) detected at line 892 [][][] Underfull \hbox (badness 10000) detected at line 922 [][][] Underfull \hbox (badness 10000) detected at line 925 [][][] [144] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] Underfull \hbox (badness 10000) detected at line 976 [][][] Underfull \hbox (badness 10000) detected at line 979 [][][] [145] Underfull \hbox (badness 10000) detected at line 1011 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1047 [][][] [146] Underfull \hbox (badness 10000) detected at line 1073 [][][] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1104 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] [147] Underfull \hbox (badness 10000) detected at line 1150 [][][] Underfull \hbox (badness 10000) detected at line 1153 [][][] Underfull \hbox (badness 10000) detected at line 1156 [][][] ) (./group___valist.tex [148] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [149] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 118 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] [150] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 187 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [151] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] [152] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] Underfull \hbox (badness 10000) detected at line 359 [][][] [153] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] [154] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] ) (./group___vatom.tex [155] [156] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] [157] Underfull \hbox (badness 10000) detected at line 188 [][][] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] Underfull \hbox (badness 10000) detected at line 233 [][][] [158] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [159] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 359 [][][] [160] Underfull \hbox (badness 10000) detected at line 376 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] Underfull \hbox (badness 10000) detected at line 434 [][][] [161] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [162] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 572 [][][] [163] Underfull \hbox (badness 10000) detected at line 596 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] Underfull \hbox (badness 10000) detected at line 644 [][][] [164] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./group___vcap.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [165] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [166] Underfull \hbox (badness 10000) detected at line 127 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] ) (./group___vclist.tex [167] [168] Underfull \hbox (badness 10000) detected at line 130 [][][] [169] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 169 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 204 [][][] [170] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [171] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] [172] Underfull \hbox (badness 10000) detected at line 359 [][][] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [173] Underfull \hbox (badness 10000) detected at line 433 [][][] ) (./group___vgreen.tex [174] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [175] Underfull \hbox (badness 10000) detected at line 145 [][][] [176] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] [177] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 219 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [178] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] [179] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [180] Underfull \hbox (badness 10000) detected at line 399 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 433 [][][] [181] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] [182] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 521 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] ) (./group___vhal.tex [183] [184] [185] [186] Underfull \hbox (badness 10000) detected at line 392 [][][] [187] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 505 [][][] [188] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [189] [190] Underfull \hbox (badness 10000) detected at line 778 [][][] Underfull \hbox (badness 10000) detected at line 839 [][][] [191] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 919 [][][] Underfull \hbox (badness 10000) detected at line 980 [][][] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) in paragraph at lines 1074--1074 []\T1/phv/m/n/10 Potential (k[] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! [192] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! [193] Underfull \hbox (badness 10000) detected at line 1205 [][][] Underfull \hbox (badness 10000) detected at line 1208 [][][] Underfull \hbox (badness 10000) detected at line 1239 [][][] Underfull \hbox (badness 10000) detected at line 1242 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] [194]) (./group___vmatrix.tex) (./group___vparam.tex [195] [196] [197] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [198] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] [199] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [200] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] [201] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] [202] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] [203] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] [204] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 640 [][][] Underfull \hbox (badness 10000) detected at line 657 [][][] [205] Underfull \hbox (badness 10000) detected at line 667 [][][] Underfull \hbox (badness 10000) detected at line 684 [][][] Underfull \hbox (badness 10000) detected at line 706 [][][] ) (./group___vpbe.tex [206] [207] [208] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] LaTeX Warning: Command \r invalid in math mode on input line 137. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 137. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 140 [][][] [209] Underfull \hbox (badness 10000) detected at line 190 [][][] [210] Underfull \hbox (badness 10000) detected at line 193 [][][] LaTeX Warning: Command \r invalid in math mode on input line 194. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 194. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 199 [][][] [211] Underfull \hbox (badness 10000) detected at line 251 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 322--322 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] [212] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [213] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] [214] Underfull \hbox (badness 10000) detected at line 465 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] [215] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 587 [][][] [216] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] Underfull \hbox (badness 10000) detected at line 654 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] [217] Underfull \hbox (badness 10000) detected at line 679 [][][] Underfull \hbox (badness 10000) detected at line 687 [][][] Underfull \hbox (badness 10000) detected at line 704 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] Underfull \hbox (badness 10000) detected at line 737 [][][] [218] Underfull \hbox (badness 10000) detected at line 754 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] Underfull \hbox (badness 10000) detected at line 779 [][][] Underfull \hbox (badness 10000) detected at line 787 [][][] Underfull \hbox (badness 10000) detected at line 804 [][][] Underfull \hbox (badness 10000) detected at line 812 [][][] [219] Underfull \hbox (badness 10000) detected at line 829 [][][] Underfull \hbox (badness 10000) detected at line 837 [][][] Underfull \hbox (badness 10000) detected at line 854 [][][] Underfull \hbox (badness 10000) detected at line 862 [][][] LaTeX Warning: Command \r invalid in math mode on input line 863. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 879 [][][] Underfull \hbox (badness 10000) detected at line 887 [][][] [220] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 937 [][][] ) (./group___vstring.tex [221] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] [222] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] ) (./group___vunit.tex [223] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Šin font cmr9! [224] LaTeX Warning: Command \r invalid in math mode on input line 144. Missing character: There is no Šin font cmr10! [225]) (./group___vgrid.tex [226] [227] Underfull \hbox (badness 10000) detected at line 131 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [228] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 219 [][][] [229] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] [230] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [231] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] [232] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 459 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] [233] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 515 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 534 [][][] [234] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 589 [][][] [235] Underfull \hbox (badness 10000) detected at line 606 [][][] Underfull \hbox (badness 10000) detected at line 618 [][][] Underfull \hbox (badness 10000) detected at line 635 [][][] [236] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 703 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [237]) (./group___vmgrid.tex [238] Underfull \hbox (badness 10000) detected at line 111 [][][] [239] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 138 [][][] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [240] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 199 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] [241] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] Underfull \hbox (badness 10000) detected at line 270 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 293 [][][] [242] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 318 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] ) (./group___vopot.tex [243] [244] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] [245] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [246] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [247] Underfull \hbox (badness 10000) detected at line 259 [][][] ) (./group___vpmg.tex [248] [249] [250] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] [251] Underfull \hbox (badness 10000) detected at line 190 [][][] [252] Underfull \hbox (badness 10000) detected at line 238 [][][] [253] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [254] Underfull \hbox (badness 10000) detected at line 366 [][][] [255] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] [256] Underfull \hbox (badness 10000) detected at line 462 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [257] Underfull \hbox (badness 10000) detected at line 496 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] [258] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 576 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] [259] Underfull \hbox (badness 10000) detected at line 611 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] [260] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [261] Underfull \hbox (badness 10000) detected at line 746 [][][] Underfull \hbox (badness 10000) detected at line 768 [][][] Underfull \hbox (badness 10000) detected at line 771 [][][] [262] Underfull \hbox (badness 10000) detected at line 803 [][][] Underfull \hbox (badness 10000) detected at line 806 [][][] [263] Underfull \hbox (badness 10000) detected at line 860 [][][] Underfull \hbox (badness 10000) detected at line 863 [][][] Underfull \hbox (badness 10000) detected at line 868 [][][] Underfull \hbox (badness 10000) detected at line 898 [][][] [264] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] [265] Underfull \hbox (badness 10000) detected at line 960 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] [266] Underfull \hbox (badness 10000) detected at line 1012 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] Underfull \hbox (badness 10000) detected at line 1037 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] [267] Underfull \hbox (badness 10000) detected at line 1097 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1103 [][][] [268] Underfull \hbox (badness 10000) detected at line 1127 [][][] Underfull \hbox (badness 10000) detected at line 1164 [][][] Underfull \hbox (badness 10000) detected at line 1167 [][][] Underfull \hbox (badness 10000) detected at line 1170 [][][] [269] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] Underfull \hbox (badness 10000) detected at line 1202 [][][] [270] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1256 [][][] Underfull \hbox (badness 10000) detected at line 1284 [][][] [271] Underfull \hbox (badness 10000) detected at line 1287 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1347 [][][] [272] Underfull \hbox (badness 10000) detected at line 1350 [][][] Underfull \hbox (badness 10000) detected at line 1353 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1405 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [273] Underfull \hbox (badness 10000) detected at line 1430 [][][] Underfull \hbox (badness 10000) detected at line 1433 [][][] Underfull \hbox (badness 10000) detected at line 1436 [][][] Underfull \hbox (badness 10000) detected at line 1458 [][][] ) (./group___vpmgp.tex [274] Underfull \hbox (badness 10000) detected at line 45 [][][] [275] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 134 [][][] [276] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [277] Underfull \hbox (badness 10000) detected at line 212 [][][] ) (./group___p_m_g_c.tex [278] [279] [280] [281] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 172--172 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [282] Underfull \hbox (badness 10000) detected at line 219 [][][] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 234--234 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [283] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [284] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] [285] Overfull \hbox (304.08286pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 413--413 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [286] Underfull \hbox (badness 10000) detected at line 448 [][][] [287] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 515 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 527--527 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [288] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [289] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] [290] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] [291] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 731 [][][] [292] Underfull \hbox (badness 10000) detected at line 781 [][][] Underfull \hbox (badness 10000) detected at line 784 [][][] Underfull \hbox (badness 10000) detected at line 787 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 797--797 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 834 [][][] [293] Underfull \hbox (badness 10000) detected at line 837 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 846--846 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] [295] Underfull \hbox (badness 10000) detected at line 916 [][][] Underfull \hbox (badness 10000) detected at line 919 [][][] [296] [297] [298] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] [299] [300] [301] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1241 [][][] [302] [303] Underfull \hbox (badness 10000) detected at line 1391 [][][] Underfull \hbox (badness 10000) detected at line 1394 [][][] Underfull \hbox (badness 10000) detected at line 1397 [][][] [304] [305] Underfull \hbox (badness 10000) detected at line 1455 [][][] Underfull \hbox (badness 10000) detected at line 1458 [][][] Underfull \hbox (badness 10000) detected at line 1461 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1471--1471 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [306] Underfull \hbox (badness 10000) detected at line 1508 [][][] Underfull \hbox (badness 10000) detected at line 1511 [][][] [307] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1594 [][][] Underfull \hbox (badness 10000) detected at line 1597 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1607--1607 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 1644 [][][] Underfull \hbox (badness 10000) detected at line 1647 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1659--1659 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 1737 [][][] Underfull \hbox (badness 10000) detected at line 1742 [][][] Underfull \hbox (badness 10000) detected at line 1745 [][][] [310] Underfull \hbox (badness 10000) detected at line 1775 [][][] Underfull \hbox (badness 10000) detected at line 1778 [][][] [311] Underfull \hbox (badness 10000) detected at line 1812 [][][] Underfull \hbox (badness 10000) detected at line 1815 [][][] Underfull \hbox (badness 10000) detected at line 1849 [][][] Underfull \hbox (badness 10000) detected at line 1852 [][][] [312] Underfull \hbox (badness 10000) detected at line 1886 [][][] Underfull \hbox (badness 10000) detected at line 1889 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1902--1902 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1939 [][][] Underfull \hbox (badness 10000) detected at line 1942 [][][] Underfull \hbox (badness 10000) detected at line 1945 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1954--1954 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [314] [315] Underfull \hbox (badness 10000) detected at line 2040 [][][] Underfull \hbox (badness 10000) detected at line 2043 [][][] Underfull \hbox (badness 10000) detected at line 2077 [][][] Underfull \hbox (badness 10000) detected at line 2080 [][][] Underfull \hbox (badness 10000) detected at line 2083 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2093--2093 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [316] Underfull \hbox (badness 10000) detected at line 2130 [][][] Underfull \hbox (badness 10000) detected at line 2133 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2142--2142 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2177 [][][] Underfull \hbox (badness 10000) detected at line 2180 [][][] Underfull \hbox (badness 10000) detected at line 2212 [][][] Underfull \hbox (badness 10000) detected at line 2215 [][][] [318] Underfull \hbox (badness 10000) detected at line 2251 [][][] Underfull \hbox (badness 10000) detected at line 2254 [][][] [319] Underfull \hbox (badness 10000) detected at line 2290 [][][] Underfull \hbox (badness 10000) detected at line 2293 [][][] [320] Underfull \hbox (badness 10000) detected at line 2321 [][][] Underfull \hbox (badness 10000) detected at line 2324 [][][] Underfull \hbox (badness 10000) detected at line 2327 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2337--2337 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [321] Underfull \hbox (badness 10000) detected at line 2374 [][][] Underfull \hbox (badness 10000) detected at line 2377 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2386--2386 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2421 [][][] Underfull \hbox (badness 10000) detected at line 2424 [][][] [322] [323] Underfull \hbox (badness 10000) detected at line 2510 [][][] Underfull \hbox (badness 10000) detected at line 2513 [][][] Underfull \hbox (badness 10000) detected at line 2516 [][][] [324] Underfull \hbox (badness 10000) detected at line 2564 [][][] Underfull \hbox (badness 10000) detected at line 2567 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2576--2576 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [325] Underfull \hbox (badness 10000) detected at line 2611 [][][] Underfull \hbox (badness 10000) detected at line 2614 [][][] [326] Underfull \hbox (badness 10000) detected at line 2704 [][][] Underfull \hbox (badness 10000) detected at line 2707 [][][] [327] Underfull \hbox (badness 10000) detected at line 2753 [][][] Underfull \hbox (badness 10000) detected at line 2756 [][][] Underfull \hbox (badness 10000) detected at line 2759 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2769--2769 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [328] Underfull \hbox (badness 10000) detected at line 2806 [][][] Underfull \hbox (badness 10000) detected at line 2809 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2818--2818 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [329] Underfull \hbox (badness 10000) detected at line 2853 [][][] Underfull \hbox (badness 10000) detected at line 2856 [][][] [330] Underfull \hbox (badness 10000) detected at line 2912 [][][] Underfull \hbox (badness 10000) detected at line 2915 [][][] [331] Underfull \hbox (badness 10000) detected at line 2953 [][][] Underfull \hbox (badness 10000) detected at line 2964 [][][] Underfull \hbox (badness 10000) detected at line 2967 [][][] [332] Underfull \hbox (badness 10000) detected at line 3053 [][][] Underfull \hbox (badness 10000) detected at line 3056 [][][] Underfull \hbox (badness 10000) detected at line 3059 [][][] [333] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3069--3069 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3106 [][][] Underfull \hbox (badness 10000) detected at line 3109 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3118--3118 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [334] Underfull \hbox (badness 10000) detected at line 3153 [][][] Underfull \hbox (badness 10000) detected at line 3156 [][][] [335] Underfull \hbox (badness 10000) detected at line 3194 [][][] Underfull \hbox (badness 10000) detected at line 3197 [][][] Underfull \hbox (badness 10000) detected at line 3200 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3210--3210 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [336] Underfull \hbox (badness 10000) detected at line 3247 [][][] Underfull \hbox (badness 10000) detected at line 3250 [][][] Underfull \hbox (badness 10000) detected at line 3253 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3262--3262 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3295 [][][] [337] [338] Underfull \hbox (badness 10000) detected at line 3349 [][][] [339] [340] Underfull \hbox (badness 10000) detected at line 3505 [][][] [341] Underfull \hbox (badness 10000) detected at line 3563 [][][] Underfull \hbox (badness 10000) detected at line 3566 [][][] [342] Underfull \hbox (badness 10000) detected at line 3606 [][][] [343] Underfull \hbox (badness 10000) detected at line 3609 [][][] Underfull \hbox (badness 10000) detected at line 3612 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3622--3622 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3659 [][][] Underfull \hbox (badness 10000) detected at line 3662 [][][] Underfull \hbox (badness 10000) detected at line 3665 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3674--3674 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [344] Underfull \hbox (badness 10000) detected at line 3723 [][][] [345] Underfull \hbox (badness 10000) detected at line 3726 [][][] [346] Underfull \hbox (badness 10000) detected at line 3810 [][][] Underfull \hbox (badness 10000) detected at line 3813 [][][] [347] [348] Underfull \hbox (badness 10000) detected at line 3911 [][][] Underfull \hbox (badness 10000) detected at line 3914 [][][] Underfull \hbox (badness 10000) detected at line 3917 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3927--3927 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3964 [][][] [349] Underfull \hbox (badness 10000) detected at line 3967 [][][] Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 3993 [][][] Underfull \hbox (badness 10000) detected at line 3996 [][][] Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 4022 [][][] [350] Underfull \hbox (badness 10000) detected at line 4025 [][][] Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 4055 [][][] Underfull \hbox (badness 10000) detected at line 4058 [][][] Underfull \hbox (badness 10000) detected at line 4061 [][][] [351] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4071--4071 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4108 [][][] Underfull \hbox (badness 10000) detected at line 4111 [][][] Underfull \hbox (badness 10000) detected at line 4114 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4123--4123 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [352] Underfull \hbox (badness 10000) detected at line 4158 [][][] Underfull \hbox (badness 10000) detected at line 4161 [][][] [353] Underfull \hbox (badness 10000) detected at line 4215 [][][] [354] Underfull \hbox (badness 10000) detected at line 4243 [][][] [355] Underfull \hbox (badness 10000) detected at line 4317 [][][] Underfull \hbox (badness 10000) detected at line 4320 [][][] [356] [357] Underfull \hbox (badness 10000) detected at line 4410 [][][] Underfull \hbox (badness 10000) detected at line 4413 [][][] [358] Underfull \hbox (badness 10000) detected at line 4453 [][][] Underfull \hbox (badness 10000) detected at line 4456 [][][] [359] Underfull \hbox (badness 10000) detected at line 4498 [][][] Underfull \hbox (badness 10000) detected at line 4501 [][][] [360] Underfull \hbox (badness 10000) detected at line 4559 [][][] Underfull \hbox (badness 10000) detected at line 4562 [][][] Underfull \hbox (badness 10000) detected at line 4565 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4575--4575 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4612 [][][] [361] Underfull \hbox (badness 10000) detected at line 4615 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4624--4624 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4657 [][][] Underfull \hbox (badness 10000) detected at line 4660 [][][] Underfull \hbox (badness 10000) detected at line 4663 [][][] [362] Underfull \hbox (badness 10000) detected at line 4719 [][][] Underfull \hbox (badness 10000) detected at line 4722 [][][] [363] Underfull \hbox (badness 10000) detected at line 4754 [][][] Underfull \hbox (badness 10000) detected at line 4757 [][][] [364] Underfull \hbox (badness 10000) detected at line 4795 [][][] Underfull \hbox (badness 10000) detected at line 4798 [][][] Underfull \hbox (badness 10000) detected at line 4801 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4811--4811 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [365] Underfull \hbox (badness 10000) detected at line 4849 [][][] Underfull \hbox (badness 10000) detected at line 4852 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4896 [][][] Underfull \hbox (badness 10000) detected at line 4899 [][][] Underfull \hbox (badness 10000) detected at line 4957 [][][] [367] Underfull \hbox (badness 10000) detected at line 4960 [][][] Underfull \hbox (badness 10000) detected at line 4992 [][][] Underfull \hbox (badness 10000) detected at line 4995 [][][] Underfull \hbox (badness 10000) detected at line 4998 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 5008--5008 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [368] Underfull \hbox (badness 10000) detected at line 5045 [][][] Underfull \hbox (badness 10000) detected at line 5048 [][][] Underfull \hbox (badness 10000) detected at line 5051 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5060--5060 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [369] Underfull \hbox (badness 10000) detected at line 5095 [][][] Underfull \hbox (badness 10000) detected at line 5098 [][][] Underfull \hbox (badness 10000) detected at line 5128 [][][] Underfull \hbox (badness 10000) detected at line 5131 [][][] Underfull \hbox (badness 10000) detected at line 5134 [][][] [370] Underfull \hbox (badness 10000) detected at line 5164 [][][] Underfull \hbox (badness 10000) detected at line 5167 [][][] Underfull \hbox (badness 10000) detected at line 5197 [][][] Underfull \hbox (badness 10000) detected at line 5200 [][][] [371] Underfull \hbox (badness 10000) detected at line 5230 [][][] Underfull \hbox (badness 10000) detected at line 5233 [][][] Underfull \hbox (badness 10000) detected at line 5261 [][][] [372] Underfull \hbox (badness 10000) detected at line 5264 [][][] Underfull \hbox (badness 10000) detected at line 5292 [][][] Underfull \hbox (badness 10000) detected at line 5295 [][][] ) (./group___frontend.tex [373] Underfull \hbox (badness 5175) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 5091) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n /10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][[]][], [] $\OMS/cmsy/m/n/10 ^ ^C$\T1/phv/m/n/10 pmgp[][[]][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][[ ]][], [] [374] Underfull \hbox (badness 4634) in paragraph at lines 78--79 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 78--79 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble Underfull \hbox (badness 3907) in paragraph at lines 80--81 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 80--81 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble [375] [376] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 187 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [377] Underfull \hbox (badness 10000) detected at line 241 [][][] [378] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 323 [][][] [379] Underfull \hbox (badness 10000) detected at line 357 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] [380] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 399 [][][] [381] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] [382] Underfull \hbox (badness 10000) detected at line 578 [][][] Underfull \hbox (badness 10000) detected at line 581 [][][] [383] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [384] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] [385] Underfull \hbox (badness 10000) detected at line 754 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] [386] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 848 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] [387] Underfull \hbox (badness 10000) detected at line 901 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 935 [][][] Underfull \hbox (badness 10000) detected at line 945 [][][] [388] Underfull \hbox (badness 10000) detected at line 964 [][][] Underfull \hbox (badness 10000) detected at line 967 [][][] Underfull \hbox (badness 10000) detected at line 987 [][][] Underfull \hbox (badness 10000) detected at line 990 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [389] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1051 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] [390] Underfull \hbox (badness 10000) detected at line 1097 [][][] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1128 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] [391] Underfull \hbox (badness 10000) detected at line 1171 [][][] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1206 [][][] [392] Underfull \hbox (badness 10000) detected at line 1209 [][][] Underfull \hbox (badness 10000) detected at line 1233 [][][] Underfull \hbox (badness 10000) detected at line 1236 [][][] Underfull \hbox (badness 10000) detected at line 1264 [][][] [393] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1293 [][][] Underfull \hbox (badness 10000) detected at line 1296 [][][] Underfull \hbox (badness 10000) detected at line 1324 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [394] Underfull \hbox (badness 10000) detected at line 1353 [][][] Underfull \hbox (badness 10000) detected at line 1381 [][][] Underfull \hbox (badness 10000) detected at line 1384 [][][] [395] Underfull \hbox (badness 10000) detected at line 1412 [][][] Underfull \hbox (badness 10000) detected at line 1436 [][][] [396] Underfull \hbox (badness 10000) detected at line 1458 [][][] Underfull \hbox (badness 10000) detected at line 1472 [][][] Underfull \hbox (badness 10000) detected at line 1489 [][][] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1518 [][][] [397] Underfull \hbox (badness 10000) detected at line 1532 [][][] Underfull \hbox (badness 10000) detected at line 1566 [][][] Underfull \hbox (badness 10000) detected at line 1578 [][][] [398] Underfull \hbox (badness 10000) detected at line 1595 [][][] Underfull \hbox (badness 10000) detected at line 1612 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [399] Underfull \hbox (badness 10000) detected at line 1654 [][][] Underfull \hbox (badness 10000) detected at line 1692 [][][] [400] Underfull \hbox (badness 10000) detected at line 1720 [][][] Underfull \hbox (badness 10000) detected at line 1737 [][][] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] [401] Underfull \hbox (badness 10000) detected at line 1796 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1827 [][][] ) [402] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [403]) (./structs_a_p_o_lparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [404] Underfull \hbox (badness 10000) detected at line 88 [][][] [405] Underfull \hbox (badness 10000) detected at line 226 [][][] [406] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 265 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] [407] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 330 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 382 [][][] [408]) (./structs_b_e_mparm.tex [409] Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [410] Underfull \hbox (badness 10000) detected at line 131 [][][] Underfull \hbox (badness 10000) detected at line 144 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [411] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] ) (./structs_f_e_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [412] Underfull \hbox (badness 10000) detected at line 68 [][][] [413] [414] [415]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [416]) (./structs_m_gparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [417] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [418] [419] [420] [421] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] [422] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 513 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 552 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [423] Underfull \hbox (badness 10000) detected at line 578 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 617 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 643 [][][] [424] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] ) (./structs_n_osh.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [425] Underfull \hbox (badness 10000) detected at line 108 [][][] [426] [427] [428] [429] [430]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [431] Underfull \hbox (badness 10000) detected at line 38 [][][] [432]) (./structs_p_b_a_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [433] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [434] [435] [436] [437]) (./structs_p_b_eparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [438] [439] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [440] [441] [442] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 432 [][][] [443] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 527 [][][] Underfull \hbox (badness 10000) detected at line 540 [][][] [444] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 592 [][][] Underfull \hbox (badness 10000) detected at line 605 [][][] Underfull \hbox (badness 10000) detected at line 618 [][][] [445] Underfull \hbox (badness 10000) detected at line 631 [][][] [446] [447]) (./structs_p_b_s_a_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [448] [449]) (./structs_vacc.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [450]) (./structs_vacc_surf.tex [451] Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [452]) (./structs_valist.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [453]) (./structs_vatom.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [454] Underfull \hbox (badness 10000) detected at line 36 [][][] [455]) (./structs_vclist.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 40 [][][] [456] [457]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [458] Underfull \hbox (badness 10000) detected at line 42 [][][] [459]) (./structs_vfetk.tex [460] Underfull \hbox (badness 10000) detected at line 60 [][][] [461] [462]) (./structs_vfetk___local_var.tex [463] Underfull \hbox (badness 10000) detected at line 86 [][][] [464] [465] [466] [467]) (./structs_vgreen.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 34 [][][] [468]) (./structs_vgrid.tex [469] Underfull \hbox (badness 10000) detected at line 52 [][][] [470] [471]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [472] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [473] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [474] Underfull \hbox (badness 10000) detected at line 86 [][][] [475] [476] [477] [478]) (./structs_vpee.tex [479] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [480] [481] Underfull \hbox (badness 10000) detected at line 116 [][][] [482] [483] [484] [485] [486]) (./structs_vpmgp.tex [487] Underfull \hbox (badness 10000) detected at line 126 [][][] [488] [489] [490] [491] [492] [493] [494] [495]) (./struct_vparam.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [496] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 28 [][][] [497]) [498] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [499] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [500]) (./apbs_8h_source.tex) (./vcsm_8c.tex [501] <./vcsm_8c__incl.pdf> [502] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [503]) (./vcsm_8c_source.tex [504] [505] [506] [507] [508] [509]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [510] [511] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [512]) (./vcsm_8h_source.tex [513]) (./vfetk_8c.tex [514] <./vfetk_8c__incl.pdf > [515] [516] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [517] Underfull \hbox (badness 10000) detected at line 169 [][][] [518] [519] [520] [521]) (./vfetk_8c_source.tex [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551]) (./vfetk_8h.tex [552] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [553] [554] [555] Underfull \hbox (badness 10000) detected at line 189 [][][] [556] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./vfetk_8h_source.tex [557] [558] [559] [560] [561] [562]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [563] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [564]) (./vpee_8c_source.tex [565] [566] [567] [568] [569] [570]) (./vpee_8h.tex <./vpee_8h__incl.pdf> [571] <./vpee_8h__dep__incl.pdf> [572] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] [573]) (./vpee_8h_source.tex [574]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [575] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [576] [577]) (./apolparm_8c_source.tex [578] [579] [580] [581] [582] [583] [584] [585]) (./apolparm_8h_source.tex [586]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [587] [588] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [589] Underfull \hbox (badness 10000) detected at line 123 [][][] ) (./bemparm_8c_source.tex [590] [591] [592] [593]) (./bemparm_8h_source.tex [594]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [595] [596] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [597] [598]) (./femparm_8c_source.tex [599] [600] [601] [602] [603]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [604] <./femparm_8h__dep__incl.pdf> [605] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [606] Underfull \hbox (badness 10000) detected at line 95 [][][] ) (./femparm_8h_source.tex [607]) (./geoflowparm_8c.tex [608] <./geoflowparm_8c __incl.pdf> [609] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [610]) (./geoflowparm_8c_source.tex [611] [612]) (./geoflowparm_8h.tex [613] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [614] [615] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [616]) (./geoflowparm_8h_source.tex [617]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [618] [619] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [620] [621] [622]) (./mgparm_8c_source.tex [623] [624] [625] [626] [627] [628] [629] [630] [631] [632] [633]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [634] <./mgparm_8h__dep__incl.pdf> [635] [636] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] [637]) (./mgparm_8h_source.tex [638]) (./nosh_8c.tex [639] <./nosh_8c__incl.pdf > [640] [641] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [642] [643] [644] [645] [646]) (./nosh_8c_source.tex [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [687] <./nosh_8h__dep__incl.pdf> [688] [689] [690] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] ) (./nosh_8h_source.tex [691] [692] [693]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [694] [695] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [696]) (./pbamparm_8c_source.tex [697] [698] [699] [700] [701] [702] [703] [704] [705]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [706] [707] Underfull \hbox (badness 10000) detected at line 102 [][][] [708] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [709]) (./pbamparm_8h_source.tex [710] [711]) (./pbeparm_8c.tex <./pbeparm_8c__ incl.pdf> [712] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [713] [714] [715] [716] [717]) (./pbeparm_8c_source.tex [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [733] <./pbeparm_8h__dep__incl.pdf> [734] Underfull \hbox (badness 10000) detected at line 88 [][][] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [735]) (./pbeparm_8h_source.tex [736] [737]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [738] [739] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [740]) (./pbsamparm_8c_source.tex [741] [742] [743]) (./pbsamparm_8h.tex <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [744] [745] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [746]) (./pbsamparm_8h_source.tex [747]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [748] [749] [750] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] [751] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [752] [753]) (./vacc_8c_source.tex [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [777] [778] [779] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 129 [][][] [780]) (./vacc_8h_source.tex [781] [782] [783]) (./valist_8c.tex [784] <./valis t_8c__incl.pdf> [785] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [786] [787] [788]) (./valist_8c_source.tex [789] [790] [791] [792] [793] [794] [795] [796] [797] [798]) (./valist_8h.tex [799] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [800] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [801]) (./valist_8h_source.tex [802] [803]) (./vatom_8c.tex <./vatom_8c__incl.p df> [804] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [805]) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [809] <./vatom_8h__dep__incl.pdf> [810] [811] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] ) (./vatom_8h_source.tex [812] [813]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [814] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [815]) (./vcap_8c_source.tex [816]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [817] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [818] Underfull \hbox (badness 10000) detected at line 53 [][][] ) (./vcap_8h_source.tex [819]) (./vclist_8c.tex <./vclist_8c__incl.pdf> [820] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [821] [822]) (./vclist_8c_source.tex [823] [824] [825] [826] [827] [828]) (./vclist_8h.tex <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [829] [830] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [831]) (./vclist_8h_source.tex [832]) (./vgreen_8c.tex [833] <./vgreen_8c__incl .pdf> [834] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [835]) (./vgreen_8c_source.tex [836] [837] [838] [839] [840] [841]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [842] <./vgreen_8h__dep__incl.pdf> [843] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] ) (./vgreen_8h_source.tex [844]) (./vhal_8h.tex [845] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [846] [847] [848] [849] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 318--318 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [850] [851] [852] [853] [854] [855] [856]) (./vhal_8h_source.tex [857] [858] [859] [860] [861] [862] [863] [864] [865]) (./vmatrix_8h.tex <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] [866] [867]) (./vmatrix_8h_source.tex [868]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [869] [870] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [871]) (./vparam_8c_source.tex [872] [873] [874] [875] [876] [877] [878] [879]) (./vparam_8h.tex <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [880] [881] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] [882]) (./vparam_8h_source.tex [883] [884]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf > [885] [886] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] ) (./vpbe_8c_source.tex [887] [888] [889] [890] [891] [892] [893]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [894] [895] [896] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] ) (./vpbe_8h_source.tex [897] [898] [899]) (./vstring_8c.tex <./vstring_8c__inc l.pdf> [900] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [901]) (./vstring_8c_source.tex [902] [903]) (./vstring_8h.tex <./vstring_8h__i ncl.pdf> [904] <./vstring_8h__dep__incl.pdf> Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [905] Underfull \hbox (badness 10000) detected at line 47 [][][] ) (./vstring_8h_source.tex [906]) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [907] LaTeX Warning: Command \r invalid in math mode on input line 42. Missing character: There is no Šin font cmr9! Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [908]) (./vunit_8h_source.tex) (./main_8c.tex <./main_8c__incl.pdf> [909] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [910]) (./main_8c_source.tex [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [922] [923] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [924] Underfull \hbox (badness 10000) detected at line 178 [][][] [925]) (./vgrid_8c_source.tex [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948]) (./vgrid_8h.tex [949] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [950] [951] Underfull \hbox (badness 10000) detected at line 93 [][][] [952] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] [953] Underfull \hbox (badness 10000) detected at line 167 [][][] ) (./vgrid_8h_source.tex [954]) (./vmgrid_8c.tex [955] <./vmgrid_8c__incl.pdf> [956] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 59--59 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [957] [958] [959]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [960] [961] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [962]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [963] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [964]) (./vopot_8c_source.tex [965] [966] [967] [968] [969]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [970] [971] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vopot_8h_source.tex [972]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [973] [974] [975] [976] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [977] Underfull \hbox (badness 10000) detected at line 263 [][][] [978] Underfull \hbox (badness 10000) detected at line 290 [][][] [979] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] [980] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 439 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 464 [][][] [981] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [982] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 576 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Underfull \hbox (badness 10000) detected at line 627 [][][] [983] Underfull \hbox (badness 10000) detected at line 644 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [984] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] [985] Underfull \hbox (badness 10000) detected at line 834 [][][] [986] Underfull \hbox (badness 10000) detected at line 878 [][][] [987] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 950 [][][] [988] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 994 [][][] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] Underfull \hbox (badness 10000) detected at line 1017 [][][] [989] Underfull \hbox (badness 10000) detected at line 1039 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] [990] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1116 [][][] Underfull \hbox (badness 10000) detected at line 1148 [][][] [991] Underfull \hbox (badness 10000) detected at line 1151 [][][] ) (./vpmg_8c_source.tex [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 241 [][][] [1134] [1135] Underfull \hbox (badness 10000) detected at line 445 [][][] [1136] Underfull \hbox (badness 10000) detected at line 462 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] [1137] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 561 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 586 [][][] [1138] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 611 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [1139] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] [1140] Underfull \hbox (badness 10000) detected at line 766 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 821 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [1141] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 892 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] [1142] Underfull \hbox (badness 10000) detected at line 922 [][][] Underfull \hbox (badness 10000) detected at line 935 [][][] Underfull \hbox (badness 10000) detected at line 952 [][][] [1143] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [1144] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1092 [][][] [1145] Underfull \hbox (badness 10000) detected at line 1095 [][][] Underfull \hbox (badness 10000) detected at line 1112 [][][] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1137 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] [1146] Underfull \hbox (badness 10000) detected at line 1165 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] Underfull \hbox (badness 10000) detected at line 1214 [][][] [1147] Underfull \hbox (badness 10000) detected at line 1246 [][][] Underfull \hbox (badness 10000) detected at line 1249 [][][] ) (./vpmg_8h_source.tex [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1157] [1158] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [1159]) (./vpmgp_8c_source.tex [1160] [1161] [1162]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1163] <./vpmgp_8h__dep__incl.pdf> [1164] [1165] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] [1166]) (./vpmgp_8h_source.tex [1167]) (./build_ad_8c_source.tex [1168] [1169] [1170]) (./build_ad_8h_source.tex [1171] [1172]) (./build_bd_8c_source.tex [1173] [1174] [1175]) (./build_bd_8h_source.tex [1176]) (./build_gd_8c_source.tex [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214]) (./build_gd_8h_source.tex [1215] [1216]) (./build_pd_8c_source.tex [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]) (./build_pd_8h_source.tex [1236] [1237] [1238]) (./cgd_8c_source.tex [1239]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1240] [1241] [1242] [1243]) (./gsd_8h_source.tex [1244]) (./matvecd_8c_source.tex [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]) (./matvecd_8h_source.tex [1258] [1259] [1260] [1261] [1262] [1263]) (./mgcsd_8c_source.tex [1264] [1265] [1266] [1267] [1268] [1269]) (./mgcsd_8h_source.tex [1270]) (./mgdrvd_8c_source.tex [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278]) (./mgdrvd_8h_source.tex [1279]) (./mgfasd_8c_source.tex [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgfasd_8h_source.tex [1287]) (./mgsubd_8c_source.tex [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]) (./mgsubd_8h_source.tex [1300] [1301] [1302]) (./mikpckd_8c_source.tex [1303] [1304] [1305] [1306] [1307]) (./mikpckd_8h_source.tex [1308] [1309]) (./mlinpckd_8c_source.tex [1310] [1311]) (./mlinpckd_8h_source.tex [1312]) (./mypdec_8c_source.tex [1313] [1314] [1315] [1316] [1317] [1318]) (./mypdec_8h_source.tex [1319] [1320]) (./newdrvd_8c_source.tex [1321] [1322] [1323]) (./newdrvd_8h_source.tex [1324]) (./newtond_8c_source.tex [1325] [1326] [1327] [1328] [1329] [1330] [1331]) (./newtond_8h_source.tex [1332] [1333]) (./powerd_8c_source.tex [1334] [1335] [1336] [1337]) (./powerd_8h_source.tex [1338] [1339]) (./smoothd_8c_source.tex [1340]) (./smoothd_8h_source.tex) (./routines_8c.tex [1341] <./routines_8c__incl.pdf> Underfull \hbox (badness 1237) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][[]][], [] $\OMS/cmsy/m/n/10 ^ ^C$\T1/phv/m/n/10 pmgp[][[]][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][[ ]][], [] [1342] Overfull \hbox (15.32974pt too wide) in paragraph at lines 68--69 \T1/phv/m/n/10 dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble diel[]Energy[][[]][] Underfull \hbox (badness 824) in paragraph at lines 68--69 \T1/phv/m/n/10 , int nenergy[][[]][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n /10 atom[]Energy[][[]][], int nforce[][[]][] Overfull \hbox (19.8584pt too wide) in paragraph at lines 70--71 \T1/phv/m/n/10 , dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-bl e diel[]Energy[][[]][] Underfull \hbox (badness 824) in paragraph at lines 70--71 \T1/phv/m/n/10 , int nenergy[][[]][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n /10 atom[]Energy[][[]][], int nforce[][[]][] [1343] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] [1344] Underfull \hbox (badness 10000) detected at line 123 [][][] ) (./routines_8c_source.tex [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]) (./routines_8h.tex [1413] <./routine s_8h__incl.pdf> <./routines_8h__dep__incl.pdf> [1414] Underfull \hbox (badness 5175) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 5091) in paragraph at lines 54--55 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n /10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 1237) in paragraph at lines 72--73 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][[]][], [] $\OMS/cmsy/m/n/10 ^ ^C$\T1/phv/m/n/10 pmgp[][[]][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][[ ]][], [] Underfull \hbox (badness 4634) in paragraph at lines 90--91 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 90--91 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble [1415] Underfull \hbox (badness 3907) in paragraph at lines 92--93 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 92--93 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble [1416] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [1417]) (./routines_8h_source.tex [1418] [1419] [1420] [1421]) [1422] No file refman.ind. (./refman.aux) LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. Package rerunfilecheck Warning: File `refman.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1424 pages, 6030279 bytes). Transcript written on refman.log. makeindex refman.idx This is makeindex, version 2.18 [TeX Live 2026] (kpathsea + Thai support). Scanning input file refman.idx.......done (3689 entries accepted, 0 rejected). Sorting entries......................................done (51309 comparisons). Generating output file refman.ind.......done (5314 lines written, 0 warnings). Output written in refman.ind. Transcript written in refman.ilg. pdflatex refman || \ if [ $? != 0 ] ; then \ \echo "Please consult refman.log to see the error messages" ; \ false; \ fi This is pdfTeX, Version 3.141592653-2.6-1.40.29 (TeX Live 2026) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./refman.tex LaTeX2e <2025-11-01> L3 programming layer <2026-03-20> (/usr/share/texlive/texmf-dist/tex/generic/iftex/iftex.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/book.cls Document Class: book 2025/01/22 v1.4n Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/bk10.clo)) (/usr/share/texlive/texmf-dist/tex/generic/infwarerr/infwarerr.sty) (./doxygen.sty (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/array.sty LaTeX Warning: You have requested release `2026/06/01' of LaTeX, but only release `2025-11-01' is available. ) (/usr/share/texlive/texmf-dist/tex/latex/tools/calc.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/ifthen.sty) (/usr/share/texlive/texmf-dist/tex/latex/tools/verbatim.sty) (/usr/share/texlive/texmf-dist/tex/latex/varwidth/varwidth.sty) ==> First Aid for varwidth.sty applied! 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(./refman.out) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) (/usr/share/texlive/texmf-dist/tex/latex/wasysym/uwasy.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}{/usr/share/texlive/texmf-dist/fonts/enc/dvips /base/8r.enc}] [2] [1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11] [12] [13] [14] [15] [16] [17] [18] [19] [20] [21] [22] [23] [24] [25] [26] [27] [28] [29] [30] [31] [32] [33] [34] [35] [36] [37] [38] [39] [40] [41] [42] [43] [44] [45] [46] [47] [48] [49] [50] [51] [52] [53] [54] [55] [56] (./index.tex Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1phv.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1pcr.fd) [1] (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1pcr.fd) [2]) (./bug.tex [3] [4] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 5--9 Underfull \hbox (badness 10000) in paragraph at lines 9--13 Underfull \hbox (badness 10000) in paragraph at lines 13--17 Underfull \hbox (badness 10000) in paragraph at lines 25--29 Underfull \hbox (badness 10000) in paragraph at lines 29--33 Underfull \hbox (badness 10000) in paragraph at lines 33--37 Underfull \hbox (badness 10000) in paragraph at lines 37--41 Underfull \hbox (badness 10000) in paragraph at lines 41--45 Underfull \hbox (badness 10000) in paragraph at lines 45--49 Underfull \hbox (badness 10000) in paragraph at lines 49--53 Underfull \hbox (badness 10000) in paragraph at lines 53--57 [5] Underfull \hbox (badness 10000) in paragraph at lines 57--61 Underfull \hbox (badness 10000) in paragraph at lines 61--65 Underfull \hbox (badness 10000) in paragraph at lines 65--69 Underfull \hbox (badness 10000) in paragraph at lines 73--77 Underfull \hbox (badness 10000) in paragraph at lines 77--81 Underfull \hbox (badness 10000) in paragraph at lines 81--85 Underfull \hbox (badness 10000) in paragraph at lines 85--89 Underfull \hbox (badness 10000) in paragraph at lines 93--97 Underfull \hbox (badness 10000) in paragraph at lines 97--101 Underfull \hbox (badness 10000) in paragraph at lines 101--105 Underfull \hbox (badness 10000) in paragraph at lines 109--113 Underfull \hbox (badness 10000) in paragraph at lines 113--117 Underfull \hbox (badness 10000) in paragraph at lines 117--121 Underfull \hbox (badness 10000) in paragraph at lines 121--125 [6] Underfull \hbox (badness 10000) in paragraph at lines 125--129 Underfull \hbox (badness 10000) in paragraph at lines 129--133 Underfull \hbox (badness 10000) in paragraph at lines 133--137 Underfull \hbox (badness 10000) in paragraph at lines 137--141 Underfull \hbox (badness 10000) in paragraph at lines 141--145 Underfull \hbox (badness 10000) in paragraph at lines 145--149 ) (./deprecated.tex [7] [8] Chapter 3. Underfull \hbox (badness 10000) in paragraph at lines 5--9 ) [9] [10] Chapter 4. (./topics.tex) [11] [12] Chapter 5. (./annotated.tex [13]) [14] Chapter 6. (./files.tex [15] [16] [17]) [18] Chapter 7. (./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 97 [][][] [20] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [21] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] [22] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] [23] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 368 [][][] Underfull \hbox (badness 10000) detected at line 371 [][][] [24] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Underfull \hbox (badness 10000) detected at line 425 [][][] [25] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [31] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] [32] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 578 [][][] [33] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] [34] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 693 [][][] [35] Underfull \hbox (badness 10000) detected at line 714 [][][] Underfull \hbox (badness 10000) detected at line 717 [][][] Underfull \hbox (badness 10000) detected at line 747 [][][] [36] Underfull \hbox (badness 10000) detected at line 773 [][][] Underfull \hbox (badness 10000) detected at line 776 [][][] Underfull \hbox (badness 10000) detected at line 781 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] [37] Underfull \hbox (badness 10000) detected at line 835 [][][] Underfull \hbox (badness 10000) detected at line 838 [][][] Underfull \hbox (badness 10000) detected at line 860 [][][] Underfull \hbox (badness 10000) detected at line 863 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 890 [][][] Underfull \hbox (badness 10000) detected at line 893 [][][] [38] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [39] Underfull \hbox (badness 10000) detected at line 970 [][][] Underfull \hbox (badness 10000) detected at line 973 [][][] Underfull \hbox (badness 10000) detected at line 995 [][][] Underfull \hbox (badness 10000) detected at line 1015 [][][] [40] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1088--1088 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1088--1088 []\T1/phv/m/sl/10 dim[] [41] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] [42] Underfull \hbox (badness 10000) detected at line 1155 [][][] Underfull \hbox (badness 10000) detected at line 1192 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] [43] Underfull \hbox (badness 10000) detected at line 1225 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1250 [][][] Underfull \hbox (badness 10000) detected at line 1253 [][][] [44] Underfull \hbox (badness 10000) detected at line 1278 [][][] Underfull \hbox (badness 10000) detected at line 1311 [][][] Underfull \hbox (badness 10000) detected at line 1314 [][][] [45] Underfull \hbox (badness 10000) detected at line 1344 [][][] Underfull \hbox (badness 10000) detected at line 1347 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [46] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1431 [][][] [47] Underfull \hbox (badness 10000) detected at line 1465 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1494 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1512--1512 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1512--1512 []\T1/phv/m/sl/10 dim[] [48] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1526 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1549--1549 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1549--1549 []\T1/phv/m/sl/10 dim[] [49] Underfull \hbox (badness 10000) detected at line 1560 [][][] Underfull \hbox (badness 10000) detected at line 1563 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1580--1580 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1580--1580 []\T1/phv/m/sl/10 dim[] Underfull \hbox (badness 10000) detected at line 1591 [][][] [50] Underfull \hbox (badness 10000) detected at line 1625 [][][] Underfull \hbox (badness 10000) detected at line 1628 [][][] [51] Underfull \hbox (badness 10000) detected at line 1711 [][][] [52] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1748 [][][] [53] Underfull \hbox (badness 10000) detected at line 1791 [][][] Underfull \hbox (badness 10000) detected at line 1801 [][][] Underfull \hbox (badness 10000) detected at line 1825 [][][] Underfull \hbox (badness 10000) detected at line 1828 [][][] Underfull \hbox (badness 10000) detected at line 1831 [][][] [54] Underfull \hbox (badness 10000) detected at line 1853 [][][] Underfull \hbox (badness 10000) detected at line 1856 [][][] Underfull \hbox (badness 10000) detected at line 1859 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] [55] Underfull \hbox (badness 10000) detected at line 1907 [][][] Underfull \hbox (badness 10000) detected at line 1927 [][][] Underfull \hbox (badness 10000) detected at line 1932 [][][] [56]) (./group___vpee.tex Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 leads to the need for a few final overlapping Schwarz solves to smooth out the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 errors near partition boundaries. Supposedly, if the region in w hich we allow [57] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [58] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 118 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [59] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 199 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] [60] Underfull \hbox (badness 10000) detected at line 245 [][][] Underfull \hbox (badness 10000) detected at line 248 [][][] ) (./group___a_p_o_lparm.tex [61] [62] [63] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [64] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 368 [][][] [65]) (./group___b_e_mparm.tex [66] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] [67] Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [68] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] ) (./group___f_e_mparm.tex [69] [70] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [71] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [72] Underfull \hbox (badness 10000) detected at line 298 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] Underfull \hbox (badness 10000) detected at line 330 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [73] Underfull \hbox (badness 10000) detected at line 357 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [74] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] [75] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [76] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] [77] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] ) (./group___m_gparm.tex [78] [79] [80] Underfull \hbox (badness 10000) detected at line 243 [][][] [81] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] [82] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] [83] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] [84] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 496 [][][] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 521 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] [85] Underfull \hbox (badness 10000) detected at line 546 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 571 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 596 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] [86] Underfull \hbox (badness 10000) detected at line 621 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 654 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] [87] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [88] Underfull \hbox (badness 10000) detected at line 748 [][][] ) (./group___n_osh.tex [89] [90] [91] [92] [93] Underfull \hbox (badness 10000) detected at line 491 [][][] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [94] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 589 [][][] [95] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 645 [][][] [96] Underfull \hbox (badness 10000) detected at line 667 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 719 [][][] [97] Underfull \hbox (badness 10000) detected at line 729 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Underfull \hbox (badness 10000) detected at line 776 [][][] [98] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 803 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 830 [][][] [99] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 857 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [100] Underfull \hbox (badness 10000) detected at line 911 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 938 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] Underfull \hbox (badness 10000) detected at line 965 [][][] [101] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 992 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1029 [][][] [102] Underfull \hbox (badness 10000) detected at line 1046 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1103 [][][] Underfull \hbox (badness 10000) detected at line 1108 [][][] [103] Underfull \hbox (badness 10000) detected at line 1118 [][][] Underfull \hbox (badness 10000) detected at line 1135 [][][] Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] Underfull \hbox (badness 10000) detected at line 1153 [][][] Underfull \hbox (badness 10000) detected at line 1170 [][][] [104] Underfull \hbox (badness 10000) detected at line 1173 [][][] Underfull \hbox (badness 10000) detected at line 1183 [][][] Underfull \hbox (badness 10000) detected at line 1186 [][][] Underfull \hbox (badness 10000) detected at line 1203 [][][] Underfull \hbox (badness 10000) detected at line 1206 [][][] Underfull \hbox (badness 10000) detected at line 1218 [][][] Underfull \hbox (badness 10000) detected at line 1221 [][][] [105] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1241 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1254 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] Underfull \hbox (badness 10000) detected at line 1284 [][][] [106] Underfull \hbox (badness 10000) detected at line 1308 [][][] Underfull \hbox (badness 10000) detected at line 1311 [][][] Underfull \hbox (badness 10000) detected at line 1321 [][][] ) (./group___p_b_a_mparm.tex [107] [108] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [109] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 190 [][][] Underfull \hbox (badness 10000) detected at line 207 [][][] [110] Underfull \hbox (badness 10000) detected at line 231 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 266 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] [111] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [112] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 399 [][][] [113] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] [114] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 543 [][][] [115] Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] [116] Underfull \hbox (badness 10000) detected at line 644 [][][] ) (./group___p_b_eparm.tex [117] [118] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] [119] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 298 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 323 [][][] [120] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [121] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] [122]) (./group___p_b_s_a_mparm.tex [123] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [124] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 191 [][][] [125] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [126] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [127] Underfull \hbox (badness 10000) detected at line 359 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [128] Underfull \hbox (badness 10000) detected at line 407 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] ) (./group___vacc.tex [129] [130] [131] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [132] Underfull \hbox (badness 10000) detected at line 211 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [133] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] [134] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] [135] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [136] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] [137] Underfull \hbox (badness 10000) detected at line 534 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 540 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [138] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [139] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] [140] Underfull \hbox (badness 10000) detected at line 696 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] [141] Underfull \hbox (badness 10000) detected at line 762 [][][] Underfull \hbox (badness 10000) detected at line 794 [][][] [142] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 862 [][][] [143] Underfull \hbox (badness 10000) detected at line 886 [][][] Underfull \hbox (badness 10000) detected at line 889 [][][] Underfull \hbox (badness 10000) detected at line 892 [][][] Underfull \hbox (badness 10000) detected at line 922 [][][] Underfull \hbox (badness 10000) detected at line 925 [][][] [144] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] Underfull \hbox (badness 10000) detected at line 976 [][][] Underfull \hbox (badness 10000) detected at line 979 [][][] [145] Underfull \hbox (badness 10000) detected at line 1011 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1047 [][][] [146] Underfull \hbox (badness 10000) detected at line 1073 [][][] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1104 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] [147] Underfull \hbox (badness 10000) detected at line 1150 [][][] Underfull \hbox (badness 10000) detected at line 1153 [][][] Underfull \hbox (badness 10000) detected at line 1156 [][][] ) (./group___valist.tex [148] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [149] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 118 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] [150] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 187 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [151] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] [152] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] Underfull \hbox (badness 10000) detected at line 359 [][][] [153] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] [154] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] ) (./group___vatom.tex [155] [156] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] [157] Underfull \hbox (badness 10000) detected at line 188 [][][] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] Underfull \hbox (badness 10000) detected at line 233 [][][] [158] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [159] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 359 [][][] [160] Underfull \hbox (badness 10000) detected at line 376 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] Underfull \hbox (badness 10000) detected at line 434 [][][] [161] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [162] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 572 [][][] [163] Underfull \hbox (badness 10000) detected at line 596 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] Underfull \hbox (badness 10000) detected at line 644 [][][] [164] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./group___vcap.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [165] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [166] Underfull \hbox (badness 10000) detected at line 127 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] ) (./group___vclist.tex [167] [168] Underfull \hbox (badness 10000) detected at line 130 [][][] [169] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 169 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 204 [][][] [170] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [171] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] [172] Underfull \hbox (badness 10000) detected at line 359 [][][] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [173] Underfull \hbox (badness 10000) detected at line 433 [][][] ) (./group___vgreen.tex [174] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [175] Underfull \hbox (badness 10000) detected at line 145 [][][] [176] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] [177] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 219 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [178] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] [179] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [180] Underfull \hbox (badness 10000) detected at line 399 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 433 [][][] [181] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] [182] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 521 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] ) (./group___vhal.tex [183] [184] [185] [186] Underfull \hbox (badness 10000) detected at line 392 [][][] [187] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 505 [][][] [188] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [189] [190] Underfull \hbox (badness 10000) detected at line 778 [][][] Underfull \hbox (badness 10000) detected at line 839 [][][] [191] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 919 [][][] Underfull \hbox (badness 10000) detected at line 980 [][][] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) in paragraph at lines 1074--1074 []\T1/phv/m/n/10 Potential (k[] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! [192] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! [193] Underfull \hbox (badness 10000) detected at line 1205 [][][] Underfull \hbox (badness 10000) detected at line 1208 [][][] Underfull \hbox (badness 10000) detected at line 1239 [][][] Underfull \hbox (badness 10000) detected at line 1242 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] [194]) (./group___vmatrix.tex) (./group___vparam.tex [195] [196] [197] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [198] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] [199] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [200] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] [201] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] [202] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] [203] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] [204] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 640 [][][] Underfull \hbox (badness 10000) detected at line 657 [][][] [205] Underfull \hbox (badness 10000) detected at line 667 [][][] Underfull \hbox (badness 10000) detected at line 684 [][][] Underfull \hbox (badness 10000) detected at line 706 [][][] ) (./group___vpbe.tex [206] [207] [208] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] LaTeX Warning: Command \r invalid in math mode on input line 137. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 137. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 140 [][][] [209] Underfull \hbox (badness 10000) detected at line 190 [][][] [210] Underfull \hbox (badness 10000) detected at line 193 [][][] LaTeX Warning: Command \r invalid in math mode on input line 194. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 194. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 199 [][][] [211] Underfull \hbox (badness 10000) detected at line 251 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 322--322 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] [212] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [213] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] [214] Underfull \hbox (badness 10000) detected at line 465 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] [215] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 587 [][][] [216] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] Underfull \hbox (badness 10000) detected at line 654 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] [217] Underfull \hbox (badness 10000) detected at line 679 [][][] Underfull \hbox (badness 10000) detected at line 687 [][][] Underfull \hbox (badness 10000) detected at line 704 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] Underfull \hbox (badness 10000) detected at line 737 [][][] [218] Underfull \hbox (badness 10000) detected at line 754 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] Underfull \hbox (badness 10000) detected at line 779 [][][] Underfull \hbox (badness 10000) detected at line 787 [][][] Underfull \hbox (badness 10000) detected at line 804 [][][] Underfull \hbox (badness 10000) detected at line 812 [][][] [219] Underfull \hbox (badness 10000) detected at line 829 [][][] Underfull \hbox (badness 10000) detected at line 837 [][][] Underfull \hbox (badness 10000) detected at line 854 [][][] Underfull \hbox (badness 10000) detected at line 862 [][][] LaTeX Warning: Command \r invalid in math mode on input line 863. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 879 [][][] Underfull \hbox (badness 10000) detected at line 887 [][][] [220] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 937 [][][] ) (./group___vstring.tex [221] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] [222] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] ) (./group___vunit.tex [223] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Šin font cmr9! [224] LaTeX Warning: Command \r invalid in math mode on input line 144. Missing character: There is no Šin font cmr10! [225]) (./group___vgrid.tex [226] [227] Underfull \hbox (badness 10000) detected at line 131 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [228] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 219 [][][] [229] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] [230] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [231] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] [232] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 459 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] [233] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 515 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 534 [][][] [234] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 589 [][][] [235] Underfull \hbox (badness 10000) detected at line 606 [][][] Underfull \hbox (badness 10000) detected at line 618 [][][] Underfull \hbox (badness 10000) detected at line 635 [][][] [236] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 703 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [237]) (./group___vmgrid.tex [238] Underfull \hbox (badness 10000) detected at line 111 [][][] [239] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 138 [][][] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [240] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 199 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] [241] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] Underfull \hbox (badness 10000) detected at line 270 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 293 [][][] [242] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 318 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] ) (./group___vopot.tex [243] [244] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] [245] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [246] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [247] Underfull \hbox (badness 10000) detected at line 259 [][][] ) (./group___vpmg.tex [248] [249] [250] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] [251] Underfull \hbox (badness 10000) detected at line 190 [][][] [252] Underfull \hbox (badness 10000) detected at line 238 [][][] [253] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [254] Underfull \hbox (badness 10000) detected at line 366 [][][] [255] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] [256] Underfull \hbox (badness 10000) detected at line 462 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [257] Underfull \hbox (badness 10000) detected at line 496 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] [258] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 576 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] [259] Underfull \hbox (badness 10000) detected at line 611 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] [260] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [261] Underfull \hbox (badness 10000) detected at line 746 [][][] Underfull \hbox (badness 10000) detected at line 768 [][][] Underfull \hbox (badness 10000) detected at line 771 [][][] [262] Underfull \hbox (badness 10000) detected at line 803 [][][] Underfull \hbox (badness 10000) detected at line 806 [][][] [263] Underfull \hbox (badness 10000) detected at line 860 [][][] Underfull \hbox (badness 10000) detected at line 863 [][][] Underfull \hbox (badness 10000) detected at line 868 [][][] Underfull \hbox (badness 10000) detected at line 898 [][][] [264] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] [265] Underfull \hbox (badness 10000) detected at line 960 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] [266] Underfull \hbox (badness 10000) detected at line 1012 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] Underfull \hbox (badness 10000) detected at line 1037 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] [267] Underfull \hbox (badness 10000) detected at line 1097 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1103 [][][] [268] Underfull \hbox (badness 10000) detected at line 1127 [][][] Underfull \hbox (badness 10000) detected at line 1164 [][][] Underfull \hbox (badness 10000) detected at line 1167 [][][] Underfull \hbox (badness 10000) detected at line 1170 [][][] [269] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] Underfull \hbox (badness 10000) detected at line 1202 [][][] [270] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1256 [][][] Underfull \hbox (badness 10000) detected at line 1284 [][][] [271] Underfull \hbox (badness 10000) detected at line 1287 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1347 [][][] [272] Underfull \hbox (badness 10000) detected at line 1350 [][][] Underfull \hbox (badness 10000) detected at line 1353 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1405 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [273] Underfull \hbox (badness 10000) detected at line 1430 [][][] Underfull \hbox (badness 10000) detected at line 1433 [][][] Underfull \hbox (badness 10000) detected at line 1436 [][][] Underfull \hbox (badness 10000) detected at line 1458 [][][] ) (./group___vpmgp.tex [274] Underfull \hbox (badness 10000) detected at line 45 [][][] [275] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 134 [][][] [276] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [277] Underfull \hbox (badness 10000) detected at line 212 [][][] ) (./group___p_m_g_c.tex [278] [279] [280] [281] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 172--172 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [282] Underfull \hbox (badness 10000) detected at line 219 [][][] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 234--234 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [283] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [284] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] [285] Overfull \hbox (304.08286pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 413--413 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [286] Underfull \hbox (badness 10000) detected at line 448 [][][] [287] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 515 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 527--527 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [288] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [289] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] [290] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] [291] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 731 [][][] [292] Underfull \hbox (badness 10000) detected at line 781 [][][] Underfull \hbox (badness 10000) detected at line 784 [][][] Underfull \hbox (badness 10000) detected at line 787 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 797--797 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 834 [][][] [293] Underfull \hbox (badness 10000) detected at line 837 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 846--846 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] [295] Underfull \hbox (badness 10000) detected at line 916 [][][] Underfull \hbox (badness 10000) detected at line 919 [][][] [296] [297] [298] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] [299] [300] [301] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1241 [][][] [302] [303] Underfull \hbox (badness 10000) detected at line 1391 [][][] Underfull \hbox (badness 10000) detected at line 1394 [][][] Underfull \hbox (badness 10000) detected at line 1397 [][][] [304] [305] Underfull \hbox (badness 10000) detected at line 1455 [][][] Underfull \hbox (badness 10000) detected at line 1458 [][][] Underfull \hbox (badness 10000) detected at line 1461 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1471--1471 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [306] Underfull \hbox (badness 10000) detected at line 1508 [][][] Underfull \hbox (badness 10000) detected at line 1511 [][][] [307] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1594 [][][] Underfull \hbox (badness 10000) detected at line 1597 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1607--1607 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 1644 [][][] Underfull \hbox (badness 10000) detected at line 1647 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1659--1659 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 1737 [][][] Underfull \hbox (badness 10000) detected at line 1742 [][][] Underfull \hbox (badness 10000) detected at line 1745 [][][] [310] Underfull \hbox (badness 10000) detected at line 1775 [][][] Underfull \hbox (badness 10000) detected at line 1778 [][][] [311] Underfull \hbox (badness 10000) detected at line 1812 [][][] Underfull \hbox (badness 10000) detected at line 1815 [][][] Underfull \hbox (badness 10000) detected at line 1849 [][][] Underfull \hbox (badness 10000) detected at line 1852 [][][] [312] Underfull \hbox (badness 10000) detected at line 1886 [][][] Underfull \hbox (badness 10000) detected at line 1889 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1902--1902 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1939 [][][] Underfull \hbox (badness 10000) detected at line 1942 [][][] Underfull \hbox (badness 10000) detected at line 1945 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1954--1954 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [314] [315] Underfull \hbox (badness 10000) detected at line 2040 [][][] Underfull \hbox (badness 10000) detected at line 2043 [][][] Underfull \hbox (badness 10000) detected at line 2077 [][][] Underfull \hbox (badness 10000) detected at line 2080 [][][] Underfull \hbox (badness 10000) detected at line 2083 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2093--2093 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [316] Underfull \hbox (badness 10000) detected at line 2130 [][][] Underfull \hbox (badness 10000) detected at line 2133 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2142--2142 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2177 [][][] Underfull \hbox (badness 10000) detected at line 2180 [][][] Underfull \hbox (badness 10000) detected at line 2212 [][][] Underfull \hbox (badness 10000) detected at line 2215 [][][] [318] Underfull \hbox (badness 10000) detected at line 2251 [][][] Underfull \hbox (badness 10000) detected at line 2254 [][][] [319] Underfull \hbox (badness 10000) detected at line 2290 [][][] Underfull \hbox (badness 10000) detected at line 2293 [][][] [320] Underfull \hbox (badness 10000) detected at line 2321 [][][] Underfull \hbox (badness 10000) detected at line 2324 [][][] Underfull \hbox (badness 10000) detected at line 2327 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2337--2337 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [321] Underfull \hbox (badness 10000) detected at line 2374 [][][] Underfull \hbox (badness 10000) detected at line 2377 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2386--2386 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2421 [][][] Underfull \hbox (badness 10000) detected at line 2424 [][][] [322] [323] Underfull \hbox (badness 10000) detected at line 2510 [][][] Underfull \hbox (badness 10000) detected at line 2513 [][][] Underfull \hbox (badness 10000) detected at line 2516 [][][] [324] Underfull \hbox (badness 10000) detected at line 2564 [][][] Underfull \hbox (badness 10000) detected at line 2567 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2576--2576 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [325] Underfull \hbox (badness 10000) detected at line 2611 [][][] Underfull \hbox (badness 10000) detected at line 2614 [][][] [326] Underfull \hbox (badness 10000) detected at line 2704 [][][] Underfull \hbox (badness 10000) detected at line 2707 [][][] [327] Underfull \hbox (badness 10000) detected at line 2753 [][][] Underfull \hbox (badness 10000) detected at line 2756 [][][] Underfull \hbox (badness 10000) detected at line 2759 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2769--2769 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [328] Underfull \hbox (badness 10000) detected at line 2806 [][][] Underfull \hbox (badness 10000) detected at line 2809 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2818--2818 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [329] Underfull \hbox (badness 10000) detected at line 2853 [][][] Underfull \hbox (badness 10000) detected at line 2856 [][][] [330] Underfull \hbox (badness 10000) detected at line 2912 [][][] Underfull \hbox (badness 10000) detected at line 2915 [][][] [331] Underfull \hbox (badness 10000) detected at line 2953 [][][] Underfull \hbox (badness 10000) detected at line 2964 [][][] Underfull \hbox (badness 10000) detected at line 2967 [][][] [332] Underfull \hbox (badness 10000) detected at line 3053 [][][] Underfull \hbox (badness 10000) detected at line 3056 [][][] Underfull \hbox (badness 10000) detected at line 3059 [][][] [333] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3069--3069 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3106 [][][] Underfull \hbox (badness 10000) detected at line 3109 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3118--3118 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [334] Underfull \hbox (badness 10000) detected at line 3153 [][][] Underfull \hbox (badness 10000) detected at line 3156 [][][] [335] Underfull \hbox (badness 10000) detected at line 3194 [][][] Underfull \hbox (badness 10000) detected at line 3197 [][][] Underfull \hbox (badness 10000) detected at line 3200 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3210--3210 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [336] Underfull \hbox (badness 10000) detected at line 3247 [][][] Underfull \hbox (badness 10000) detected at line 3250 [][][] Underfull \hbox (badness 10000) detected at line 3253 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3262--3262 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3295 [][][] [337] [338] Underfull \hbox (badness 10000) detected at line 3349 [][][] [339] [340] Underfull \hbox (badness 10000) detected at line 3505 [][][] [341] Underfull \hbox (badness 10000) detected at line 3563 [][][] Underfull \hbox (badness 10000) detected at line 3566 [][][] [342] Underfull \hbox (badness 10000) detected at line 3606 [][][] [343] Underfull \hbox (badness 10000) detected at line 3609 [][][] Underfull \hbox (badness 10000) detected at line 3612 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3622--3622 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3659 [][][] Underfull \hbox (badness 10000) detected at line 3662 [][][] Underfull \hbox (badness 10000) detected at line 3665 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3674--3674 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [344] Underfull \hbox (badness 10000) detected at line 3723 [][][] [345] Underfull \hbox (badness 10000) detected at line 3726 [][][] [346] Underfull \hbox (badness 10000) detected at line 3810 [][][] Underfull \hbox (badness 10000) detected at line 3813 [][][] [347] [348] Underfull \hbox (badness 10000) detected at line 3911 [][][] Underfull \hbox (badness 10000) detected at line 3914 [][][] Underfull \hbox (badness 10000) detected at line 3917 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3927--3927 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3964 [][][] [349] Underfull \hbox (badness 10000) detected at line 3967 [][][] Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 3993 [][][] Underfull \hbox (badness 10000) detected at line 3996 [][][] Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 4022 [][][] [350] Underfull \hbox (badness 10000) detected at line 4025 [][][] Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 4055 [][][] Underfull \hbox (badness 10000) detected at line 4058 [][][] Underfull \hbox (badness 10000) detected at line 4061 [][][] [351] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4071--4071 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4108 [][][] Underfull \hbox (badness 10000) detected at line 4111 [][][] Underfull \hbox (badness 10000) detected at line 4114 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4123--4123 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [352] Underfull \hbox (badness 10000) detected at line 4158 [][][] Underfull \hbox (badness 10000) detected at line 4161 [][][] [353] Underfull \hbox (badness 10000) detected at line 4215 [][][] [354] Underfull \hbox (badness 10000) detected at line 4243 [][][] [355] Underfull \hbox (badness 10000) detected at line 4317 [][][] Underfull \hbox (badness 10000) detected at line 4320 [][][] [356] [357] Underfull \hbox (badness 10000) detected at line 4410 [][][] Underfull \hbox (badness 10000) detected at line 4413 [][][] [358] Underfull \hbox (badness 10000) detected at line 4453 [][][] Underfull \hbox (badness 10000) detected at line 4456 [][][] [359] Underfull \hbox (badness 10000) detected at line 4498 [][][] Underfull \hbox (badness 10000) detected at line 4501 [][][] [360] Underfull \hbox (badness 10000) detected at line 4559 [][][] Underfull \hbox (badness 10000) detected at line 4562 [][][] Underfull \hbox (badness 10000) detected at line 4565 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4575--4575 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4612 [][][] [361] Underfull \hbox (badness 10000) detected at line 4615 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4624--4624 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4657 [][][] Underfull \hbox (badness 10000) detected at line 4660 [][][] Underfull \hbox (badness 10000) detected at line 4663 [][][] [362] Underfull \hbox (badness 10000) detected at line 4719 [][][] Underfull \hbox (badness 10000) detected at line 4722 [][][] [363] Underfull \hbox (badness 10000) detected at line 4754 [][][] Underfull \hbox (badness 10000) detected at line 4757 [][][] [364] Underfull \hbox (badness 10000) detected at line 4795 [][][] Underfull \hbox (badness 10000) detected at line 4798 [][][] Underfull \hbox (badness 10000) detected at line 4801 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4811--4811 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [365] Underfull \hbox (badness 10000) detected at line 4849 [][][] Underfull \hbox (badness 10000) detected at line 4852 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4896 [][][] Underfull \hbox (badness 10000) detected at line 4899 [][][] Underfull \hbox (badness 10000) detected at line 4957 [][][] [367] Underfull \hbox (badness 10000) detected at line 4960 [][][] Underfull \hbox (badness 10000) detected at line 4992 [][][] Underfull \hbox (badness 10000) detected at line 4995 [][][] Underfull \hbox (badness 10000) detected at line 4998 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 5008--5008 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [368] Underfull \hbox (badness 10000) detected at line 5045 [][][] Underfull \hbox (badness 10000) detected at line 5048 [][][] Underfull \hbox (badness 10000) detected at line 5051 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5060--5060 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [369] Underfull \hbox (badness 10000) detected at line 5095 [][][] Underfull \hbox (badness 10000) detected at line 5098 [][][] Underfull \hbox (badness 10000) detected at line 5128 [][][] Underfull \hbox (badness 10000) detected at line 5131 [][][] Underfull \hbox (badness 10000) detected at line 5134 [][][] [370] Underfull \hbox (badness 10000) detected at line 5164 [][][] Underfull \hbox (badness 10000) detected at line 5167 [][][] Underfull \hbox (badness 10000) detected at line 5197 [][][] Underfull \hbox (badness 10000) detected at line 5200 [][][] [371] Underfull \hbox (badness 10000) detected at line 5230 [][][] Underfull \hbox (badness 10000) detected at line 5233 [][][] Underfull \hbox (badness 10000) detected at line 5261 [][][] [372] Underfull \hbox (badness 10000) detected at line 5264 [][][] Underfull \hbox (badness 10000) detected at line 5292 [][][] Underfull \hbox (badness 10000) detected at line 5295 [][][] ) (./group___frontend.tex [373] Underfull \hbox (badness 5175) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 5091) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n /10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][[]][], [] $\OMS/cmsy/m/n/10 ^ ^C$\T1/phv/m/n/10 pmgp[][[]][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][[ ]][], [] [374] Underfull \hbox (badness 4634) in paragraph at lines 78--79 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 78--79 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble Underfull \hbox (badness 3907) in paragraph at lines 80--81 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 80--81 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble [375] [376] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 187 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [377] Underfull \hbox (badness 10000) detected at line 241 [][][] [378] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 323 [][][] [379] Underfull \hbox (badness 10000) detected at line 357 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] [380] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 399 [][][] [381] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] [382] Underfull \hbox (badness 10000) detected at line 578 [][][] Underfull \hbox (badness 10000) detected at line 581 [][][] [383] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [384] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] [385] Underfull \hbox (badness 10000) detected at line 754 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] [386] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 848 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] [387] Underfull \hbox (badness 10000) detected at line 901 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 935 [][][] Underfull \hbox (badness 10000) detected at line 945 [][][] [388] Underfull \hbox (badness 10000) detected at line 964 [][][] Underfull \hbox (badness 10000) detected at line 967 [][][] Underfull \hbox (badness 10000) detected at line 987 [][][] Underfull \hbox (badness 10000) detected at line 990 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [389] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1051 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] [390] Underfull \hbox (badness 10000) detected at line 1097 [][][] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1128 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] [391] Underfull \hbox (badness 10000) detected at line 1171 [][][] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1206 [][][] [392] Underfull \hbox (badness 10000) detected at line 1209 [][][] Underfull \hbox (badness 10000) detected at line 1233 [][][] Underfull \hbox (badness 10000) detected at line 1236 [][][] Underfull \hbox (badness 10000) detected at line 1264 [][][] [393] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1293 [][][] Underfull \hbox (badness 10000) detected at line 1296 [][][] Underfull \hbox (badness 10000) detected at line 1324 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [394] Underfull \hbox (badness 10000) detected at line 1353 [][][] Underfull \hbox (badness 10000) detected at line 1381 [][][] Underfull \hbox (badness 10000) detected at line 1384 [][][] [395] Underfull \hbox (badness 10000) detected at line 1412 [][][] Underfull \hbox (badness 10000) detected at line 1436 [][][] [396] Underfull \hbox (badness 10000) detected at line 1458 [][][] Underfull \hbox (badness 10000) detected at line 1472 [][][] Underfull \hbox (badness 10000) detected at line 1489 [][][] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1518 [][][] [397] Underfull \hbox (badness 10000) detected at line 1532 [][][] Underfull \hbox (badness 10000) detected at line 1566 [][][] Underfull \hbox (badness 10000) detected at line 1578 [][][] [398] Underfull \hbox (badness 10000) detected at line 1595 [][][] Underfull \hbox (badness 10000) detected at line 1612 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [399] Underfull \hbox (badness 10000) detected at line 1654 [][][] Underfull \hbox (badness 10000) detected at line 1692 [][][] [400] Underfull \hbox (badness 10000) detected at line 1720 [][][] Underfull \hbox (badness 10000) detected at line 1737 [][][] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] [401] Underfull \hbox (badness 10000) detected at line 1796 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1827 [][][] ) [402] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [403]) (./structs_a_p_o_lparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [404] Underfull \hbox (badness 10000) detected at line 88 [][][] [405] Underfull \hbox (badness 10000) detected at line 226 [][][] [406] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 265 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] [407] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 330 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 382 [][][] [408]) (./structs_b_e_mparm.tex [409] Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [410] Underfull \hbox (badness 10000) detected at line 131 [][][] Underfull \hbox (badness 10000) detected at line 144 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [411] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] ) (./structs_f_e_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [412] Underfull \hbox (badness 10000) detected at line 68 [][][] [413] [414] [415]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [416]) (./structs_m_gparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [417] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [418] [419] [420] [421] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] [422] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 513 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 552 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [423] Underfull \hbox (badness 10000) detected at line 578 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 617 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 643 [][][] [424] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] ) (./structs_n_osh.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [425] Underfull \hbox (badness 10000) detected at line 108 [][][] [426] [427] [428] [429] [430]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [431] Underfull \hbox (badness 10000) detected at line 38 [][][] [432]) (./structs_p_b_a_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [433] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [434] [435] [436] [437]) (./structs_p_b_eparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [438] [439] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [440] [441] [442] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 432 [][][] [443] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 527 [][][] Underfull \hbox (badness 10000) detected at line 540 [][][] [444] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 592 [][][] Underfull \hbox (badness 10000) detected at line 605 [][][] Underfull \hbox (badness 10000) detected at line 618 [][][] [445] Underfull \hbox (badness 10000) detected at line 631 [][][] [446] [447]) (./structs_p_b_s_a_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [448] [449]) (./structs_vacc.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [450]) (./structs_vacc_surf.tex [451] Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [452]) (./structs_valist.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [453]) (./structs_vatom.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [454] Underfull \hbox (badness 10000) detected at line 36 [][][] [455]) (./structs_vclist.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 40 [][][] [456] [457]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [458] Underfull \hbox (badness 10000) detected at line 42 [][][] [459]) (./structs_vfetk.tex [460] Underfull \hbox (badness 10000) detected at line 60 [][][] [461] [462]) (./structs_vfetk___local_var.tex [463] Underfull \hbox (badness 10000) detected at line 86 [][][] [464] [465] [466] [467]) (./structs_vgreen.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 34 [][][] [468]) (./structs_vgrid.tex [469] Underfull \hbox (badness 10000) detected at line 52 [][][] [470] [471]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [472] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [473] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [474] Underfull \hbox (badness 10000) detected at line 86 [][][] [475] [476] [477] [478]) (./structs_vpee.tex [479] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [480] [481] Underfull \hbox (badness 10000) detected at line 116 [][][] [482] [483] [484] [485] [486]) (./structs_vpmgp.tex [487] Underfull \hbox (badness 10000) detected at line 126 [][][] [488] [489] [490] [491] [492] [493] [494] [495]) (./struct_vparam.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [496] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 28 [][][] [497]) [498] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [499] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [500]) (./apbs_8h_source.tex) (./vcsm_8c.tex [501] <./vcsm_8c__incl.pdf> [502] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [503]) (./vcsm_8c_source.tex [504] [505] [506] [507] [508] [509]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [510] [511] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [512]) (./vcsm_8h_source.tex [513]) (./vfetk_8c.tex [514] <./vfetk_8c__incl.pdf > [515] [516] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [517] Underfull \hbox (badness 10000) detected at line 169 [][][] [518] [519] [520] [521]) (./vfetk_8c_source.tex [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551]) (./vfetk_8h.tex [552] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [553] [554] [555] Underfull \hbox (badness 10000) detected at line 189 [][][] [556] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./vfetk_8h_source.tex [557] [558] [559] [560] [561] [562]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [563] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [564]) (./vpee_8c_source.tex [565] [566] [567] [568] [569] [570]) (./vpee_8h.tex <./vpee_8h__incl.pdf> [571] <./vpee_8h__dep__incl.pdf> [572] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] [573]) (./vpee_8h_source.tex [574]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [575] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [576] [577]) (./apolparm_8c_source.tex [578] [579] [580] [581] [582] [583] [584] [585]) (./apolparm_8h_source.tex [586]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [587] [588] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [589] Underfull \hbox (badness 10000) detected at line 123 [][][] ) (./bemparm_8c_source.tex [590] [591] [592] [593]) (./bemparm_8h_source.tex [594]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [595] [596] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [597] [598]) (./femparm_8c_source.tex [599] [600] [601] [602] [603]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [604] <./femparm_8h__dep__incl.pdf> [605] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [606] Underfull \hbox (badness 10000) detected at line 95 [][][] ) (./femparm_8h_source.tex [607]) (./geoflowparm_8c.tex [608] <./geoflowparm_8c __incl.pdf> [609] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [610]) (./geoflowparm_8c_source.tex [611] [612]) (./geoflowparm_8h.tex [613] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [614] [615] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [616]) (./geoflowparm_8h_source.tex [617]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [618] [619] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [620] [621] [622]) (./mgparm_8c_source.tex [623] [624] [625] [626] [627] [628] [629] [630] [631] [632] [633]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [634] <./mgparm_8h__dep__incl.pdf> [635] [636] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] [637]) (./mgparm_8h_source.tex [638]) (./nosh_8c.tex [639] <./nosh_8c__incl.pdf > [640] [641] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [642] [643] [644] [645] [646]) (./nosh_8c_source.tex [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [687] <./nosh_8h__dep__incl.pdf> [688] [689] [690] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] ) (./nosh_8h_source.tex [691] [692] [693]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [694] [695] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [696]) (./pbamparm_8c_source.tex [697] [698] [699] [700] [701] [702] [703] [704] [705]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [706] [707] Underfull \hbox (badness 10000) detected at line 102 [][][] [708] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [709]) (./pbamparm_8h_source.tex [710] [711]) (./pbeparm_8c.tex <./pbeparm_8c__ incl.pdf> [712] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [713] [714] [715] [716] [717]) (./pbeparm_8c_source.tex [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [733] <./pbeparm_8h__dep__incl.pdf> [734] Underfull \hbox (badness 10000) detected at line 88 [][][] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [735]) (./pbeparm_8h_source.tex [736] [737]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [738] [739] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [740]) (./pbsamparm_8c_source.tex [741] [742] [743]) (./pbsamparm_8h.tex <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [744] [745] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [746]) (./pbsamparm_8h_source.tex [747]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [748] [749] [750] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] [751] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [752] [753]) (./vacc_8c_source.tex [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [777] [778] [779] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 129 [][][] [780]) (./vacc_8h_source.tex [781] [782] [783]) (./valist_8c.tex [784] <./valis t_8c__incl.pdf> [785] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [786] [787] [788]) (./valist_8c_source.tex [789] [790] [791] [792] [793] [794] [795] [796] [797] [798]) (./valist_8h.tex [799] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [800] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [801]) (./valist_8h_source.tex [802] [803]) (./vatom_8c.tex <./vatom_8c__incl.p df> [804] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [805]) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [809] <./vatom_8h__dep__incl.pdf> [810] [811] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] ) (./vatom_8h_source.tex [812] [813]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [814] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [815]) (./vcap_8c_source.tex [816]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [817] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [818] Underfull \hbox (badness 10000) detected at line 53 [][][] ) (./vcap_8h_source.tex [819]) (./vclist_8c.tex <./vclist_8c__incl.pdf> [820] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [821] [822]) (./vclist_8c_source.tex [823] [824] [825] [826] [827] [828]) (./vclist_8h.tex <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [829] [830] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [831]) (./vclist_8h_source.tex [832]) (./vgreen_8c.tex [833] <./vgreen_8c__incl .pdf> [834] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [835]) (./vgreen_8c_source.tex [836] [837] [838] [839] [840] [841]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [842] <./vgreen_8h__dep__incl.pdf> [843] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] ) (./vgreen_8h_source.tex [844]) (./vhal_8h.tex [845] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [846] [847] [848] [849] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 318--318 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [850] [851] [852] [853] [854] [855] [856]) (./vhal_8h_source.tex [857] [858] [859] [860] [861] [862] [863] [864] [865]) (./vmatrix_8h.tex <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] [866] [867]) (./vmatrix_8h_source.tex [868]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [869] [870] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [871]) (./vparam_8c_source.tex [872] [873] [874] [875] [876] [877] [878] [879]) (./vparam_8h.tex <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [880] [881] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] [882]) (./vparam_8h_source.tex [883] [884]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf > [885] [886] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] ) (./vpbe_8c_source.tex [887] [888] [889] [890] [891] [892] [893]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [894] [895] [896] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] ) (./vpbe_8h_source.tex [897] [898] [899]) (./vstring_8c.tex <./vstring_8c__inc l.pdf> [900] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [901]) (./vstring_8c_source.tex [902] [903]) (./vstring_8h.tex <./vstring_8h__i ncl.pdf> [904] <./vstring_8h__dep__incl.pdf> Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [905] Underfull \hbox (badness 10000) detected at line 47 [][][] ) (./vstring_8h_source.tex [906]) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [907] LaTeX Warning: Command \r invalid in math mode on input line 42. Missing character: There is no Šin font cmr9! Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [908]) (./vunit_8h_source.tex) (./main_8c.tex <./main_8c__incl.pdf> [909] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [910]) (./main_8c_source.tex [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [922] [923] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [924] Underfull \hbox (badness 10000) detected at line 178 [][][] [925]) (./vgrid_8c_source.tex [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948]) (./vgrid_8h.tex [949] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [950] [951] Underfull \hbox (badness 10000) detected at line 93 [][][] [952] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] [953] Underfull \hbox (badness 10000) detected at line 167 [][][] ) (./vgrid_8h_source.tex [954]) (./vmgrid_8c.tex [955] <./vmgrid_8c__incl.pdf> [956] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 59--59 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [957] [958] [959]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [960] [961] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [962]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [963] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [964]) (./vopot_8c_source.tex [965] [966] [967] [968] [969]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [970] [971] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vopot_8h_source.tex [972]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [973] [974] [975] [976] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [977] Underfull \hbox (badness 10000) detected at line 263 [][][] [978] Underfull \hbox (badness 10000) detected at line 290 [][][] [979] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] [980] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 439 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 464 [][][] [981] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [982] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 576 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Underfull \hbox (badness 10000) detected at line 627 [][][] [983] Underfull \hbox (badness 10000) detected at line 644 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [984] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] [985] Underfull \hbox (badness 10000) detected at line 834 [][][] [986] Underfull \hbox (badness 10000) detected at line 878 [][][] [987] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 950 [][][] [988] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 994 [][][] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] Underfull \hbox (badness 10000) detected at line 1017 [][][] [989] Underfull \hbox (badness 10000) detected at line 1039 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] [990] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1116 [][][] Underfull \hbox (badness 10000) detected at line 1148 [][][] [991] Underfull \hbox (badness 10000) detected at line 1151 [][][] ) (./vpmg_8c_source.tex [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 241 [][][] [1134] [1135] Underfull \hbox (badness 10000) detected at line 445 [][][] [1136] Underfull \hbox (badness 10000) detected at line 462 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] [1137] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 561 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 586 [][][] [1138] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 611 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [1139] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] [1140] Underfull \hbox (badness 10000) detected at line 766 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 821 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [1141] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 892 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] [1142] Underfull \hbox (badness 10000) detected at line 922 [][][] Underfull \hbox (badness 10000) detected at line 935 [][][] Underfull \hbox (badness 10000) detected at line 952 [][][] [1143] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [1144] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1092 [][][] [1145] Underfull \hbox (badness 10000) detected at line 1095 [][][] Underfull \hbox (badness 10000) detected at line 1112 [][][] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1137 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] [1146] Underfull \hbox (badness 10000) detected at line 1165 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] Underfull \hbox (badness 10000) detected at line 1214 [][][] [1147] Underfull \hbox (badness 10000) detected at line 1246 [][][] Underfull \hbox (badness 10000) detected at line 1249 [][][] ) (./vpmg_8h_source.tex [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1157] [1158] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [1159]) (./vpmgp_8c_source.tex [1160] [1161] [1162]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1163] <./vpmgp_8h__dep__incl.pdf> [1164] [1165] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] [1166]) (./vpmgp_8h_source.tex [1167]) (./build_ad_8c_source.tex [1168] [1169] [1170]) (./build_ad_8h_source.tex [1171] [1172]) (./build_bd_8c_source.tex [1173] [1174] [1175]) (./build_bd_8h_source.tex [1176]) (./build_gd_8c_source.tex [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214]) (./build_gd_8h_source.tex [1215] [1216]) (./build_pd_8c_source.tex [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]) (./build_pd_8h_source.tex [1236] [1237] [1238]) (./cgd_8c_source.tex [1239]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1240] [1241] [1242] [1243]) (./gsd_8h_source.tex [1244]) (./matvecd_8c_source.tex [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]) (./matvecd_8h_source.tex [1258] [1259] [1260] [1261] [1262] [1263]) (./mgcsd_8c_source.tex [1264] [1265] [1266] [1267] [1268] [1269]) (./mgcsd_8h_source.tex [1270]) (./mgdrvd_8c_source.tex [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278]) (./mgdrvd_8h_source.tex [1279]) (./mgfasd_8c_source.tex [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgfasd_8h_source.tex [1287]) (./mgsubd_8c_source.tex [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]) (./mgsubd_8h_source.tex [1300] [1301] [1302]) (./mikpckd_8c_source.tex [1303] [1304] [1305] [1306] [1307]) (./mikpckd_8h_source.tex 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1529 pages, 6459030 bytes). Transcript written on refman.log. latex_count=8 ; \ while grep -E -s 'Rerun (LaTeX|to get cross-references right|to get bibliographical references right)' refman.log && [ $latex_count -gt 0 ] ;\ do \ echo "Rerunning latex...." ;\ pdflatex refman || \ if [ $? != 0 ] ; then \ \echo "Please consult refman.log to see the error messages" ; \ false; \ fi; \ latex_count=`expr $latex_count - 1` ;\ done makeindex refman.idx This is makeindex, version 2.18 [TeX Live 2026] (kpathsea + Thai support). Scanning input file refman.idx.......done (3689 entries accepted, 0 rejected). Sorting entries......................................done (51309 comparisons). 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(./group___header.tex) (./group___vcsm.tex [19] Underfull \hbox (badness 10000) detected at line 97 [][][] [20] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 125 [][][] Underfull \hbox (badness 10000) detected at line 149 [][][] Underfull \hbox (badness 10000) detected at line 152 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [21] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] Underfull \hbox (badness 10000) detected at line 227 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] [22] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 259 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 288 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] [23] Underfull \hbox (badness 10000) detected at line 315 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 342 [][][] Underfull \hbox (badness 10000) detected at line 368 [][][] Underfull \hbox (badness 10000) detected at line 371 [][][] [24] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 422 [][][] Underfull \hbox (badness 10000) detected at line 425 [][][] [25] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 472 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] ) (./group___vfetk.tex [26] [27] [28] [29] [30] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 363 [][][] [31] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 477 [][][] [32] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 522 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 551 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 578 [][][] [33] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 584 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] Underfull \hbox (badness 10000) detected at line 625 [][][] [34] Underfull \hbox (badness 10000) detected at line 649 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] Underfull \hbox (badness 10000) detected at line 693 [][][] [35] Underfull \hbox (badness 10000) detected at line 714 [][][] Underfull \hbox (badness 10000) detected at line 717 [][][] Underfull \hbox (badness 10000) detected at line 747 [][][] [36] Underfull \hbox (badness 10000) detected at line 773 [][][] Underfull \hbox (badness 10000) detected at line 776 [][][] Underfull \hbox (badness 10000) detected at line 781 [][][] Underfull \hbox (badness 10000) detected at line 807 [][][] [37] Underfull \hbox (badness 10000) detected at line 835 [][][] Underfull \hbox (badness 10000) detected at line 838 [][][] Underfull \hbox (badness 10000) detected at line 860 [][][] Underfull \hbox (badness 10000) detected at line 863 [][][] Underfull \hbox (badness 10000) detected at line 866 [][][] Underfull \hbox (badness 10000) detected at line 890 [][][] Underfull \hbox (badness 10000) detected at line 893 [][][] [38] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] [39] Underfull \hbox (badness 10000) detected at line 970 [][][] Underfull \hbox (badness 10000) detected at line 973 [][][] Underfull \hbox (badness 10000) detected at line 995 [][][] Underfull \hbox (badness 10000) detected at line 1015 [][][] [40] Underfull \hbox (badness 10000) detected at line 1045 [][][] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1088--1088 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1088--1088 []\T1/phv/m/sl/10 dim[] [41] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1102 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] Underfull \hbox (badness 10000) detected at line 1129 [][][] [42] Underfull \hbox (badness 10000) detected at line 1155 [][][] Underfull \hbox (badness 10000) detected at line 1192 [][][] Underfull \hbox (badness 10000) detected at line 1195 [][][] [43] Underfull \hbox (badness 10000) detected at line 1225 [][][] Underfull \hbox (badness 10000) detected at line 1228 [][][] Underfull \hbox (badness 10000) detected at line 1250 [][][] Underfull \hbox (badness 10000) detected at line 1253 [][][] [44] Underfull \hbox (badness 10000) detected at line 1278 [][][] Underfull \hbox (badness 10000) detected at line 1311 [][][] Underfull \hbox (badness 10000) detected at line 1314 [][][] [45] Underfull \hbox (badness 10000) detected at line 1344 [][][] Underfull \hbox (badness 10000) detected at line 1347 [][][] Underfull \hbox (badness 10000) detected at line 1373 [][][] [46] Underfull \hbox (badness 10000) detected at line 1401 [][][] Underfull \hbox (badness 10000) detected at line 1431 [][][] [47] Underfull \hbox (badness 10000) detected at line 1465 [][][] Underfull \hbox (badness 10000) detected at line 1468 [][][] Underfull \hbox (badness 10000) detected at line 1494 [][][] Underfull \hbox (badness 10000) detected at line 1497 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1512--1512 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1512--1512 []\T1/phv/m/sl/10 dim[] [48] Underfull \hbox (badness 10000) detected at line 1523 [][][] Underfull \hbox (badness 10000) detected at line 1526 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1549--1549 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1549--1549 []\T1/phv/m/sl/10 dim[] [49] Underfull \hbox (badness 10000) detected at line 1560 [][][] Underfull \hbox (badness 10000) detected at line 1563 [][][] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1580--1580 []\T1/phv/m/sl/10 dim[] Overfull \hbox (3.97772pt too wide) in paragraph at lines 1580--1580 []\T1/phv/m/sl/10 dim[] Underfull \hbox (badness 10000) detected at line 1591 [][][] [50] Underfull \hbox (badness 10000) detected at line 1625 [][][] Underfull \hbox (badness 10000) detected at line 1628 [][][] [51] Underfull \hbox (badness 10000) detected at line 1711 [][][] [52] Underfull \hbox (badness 10000) detected at line 1745 [][][] Underfull \hbox (badness 10000) detected at line 1748 [][][] [53] Underfull \hbox (badness 10000) detected at line 1791 [][][] Underfull \hbox (badness 10000) detected at line 1801 [][][] Underfull \hbox (badness 10000) detected at line 1825 [][][] Underfull \hbox (badness 10000) detected at line 1828 [][][] Underfull \hbox (badness 10000) detected at line 1831 [][][] [54] Underfull \hbox (badness 10000) detected at line 1853 [][][] Underfull \hbox (badness 10000) detected at line 1856 [][][] Underfull \hbox (badness 10000) detected at line 1859 [][][] Underfull \hbox (badness 10000) detected at line 1881 [][][] [55] Underfull \hbox (badness 10000) detected at line 1907 [][][] Underfull \hbox (badness 10000) detected at line 1927 [][][] Underfull \hbox (badness 10000) detected at line 1932 [][][] [56]) (./group___vpee.tex Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 leads to the need for a few final overlapping Schwarz solves to smooth out the Underfull \hbox (badness 10000) in paragraph at lines 45--46 \T1/pcr/m/n/10 errors near partition boundaries. Supposedly, if the region in w hich we allow [57] Underfull \hbox (badness 10000) detected at line 79 [][][] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [58] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 118 [][][] Underfull \hbox (badness 10000) detected at line 136 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [59] Underfull \hbox (badness 10000) detected at line 175 [][][] Underfull \hbox (badness 10000) detected at line 199 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 205 [][][] [60] Underfull \hbox (badness 10000) detected at line 245 [][][] Underfull \hbox (badness 10000) detected at line 248 [][][] ) (./group___a_p_o_lparm.tex [61] [62] [63] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] [64] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] Underfull \hbox (badness 10000) detected at line 321 [][][] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 346 [][][] Underfull \hbox (badness 10000) detected at line 368 [][][] [65]) (./group___b_e_mparm.tex [66] Underfull \hbox (badness 10000) detected at line 67 [][][] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] [67] Underfull \hbox (badness 10000) detected at line 143 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] Underfull \hbox (badness 10000) detected at line 185 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] Underfull \hbox (badness 10000) detected at line 212 [][][] [68] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 268 [][][] ) (./group___f_e_mparm.tex [69] [70] Underfull \hbox (badness 10000) detected at line 129 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [71] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 231 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] [72] Underfull \hbox (badness 10000) detected at line 298 [][][] Underfull \hbox (badness 10000) detected at line 322 [][][] Underfull \hbox (badness 10000) detected at line 330 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] [73] Underfull \hbox (badness 10000) detected at line 357 [][][] Underfull \hbox (badness 10000) detected at line 374 [][][] Underfull \hbox (badness 10000) detected at line 396 [][][] ) (./group___g_e_o_f_l_o_wparm.tex [74] Underfull \hbox (badness 10000) detected at line 70 [][][] Underfull \hbox (badness 10000) detected at line 73 [][][] [75] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [76] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 189 [][][] Underfull \hbox (badness 10000) detected at line 206 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] [77] Underfull \hbox (badness 10000) detected at line 233 [][][] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] ) (./group___m_gparm.tex [78] [79] [80] Underfull \hbox (badness 10000) detected at line 243 [][][] [81] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 284 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] [82] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] [83] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 402 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 446 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] [84] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 496 [][][] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 521 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] [85] Underfull \hbox (badness 10000) detected at line 546 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 571 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 596 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] [86] Underfull \hbox (badness 10000) detected at line 621 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 646 [][][] Underfull \hbox (badness 10000) detected at line 654 [][][] Underfull \hbox (badness 10000) detected at line 671 [][][] [87] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 724 [][][] [88] Underfull \hbox (badness 10000) detected at line 748 [][][] ) (./group___n_osh.tex [89] [90] [91] [92] [93] Underfull \hbox (badness 10000) detected at line 491 [][][] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] [94] Underfull \hbox (badness 10000) detected at line 542 [][][] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 589 [][][] [95] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 616 [][][] Underfull \hbox (badness 10000) detected at line 628 [][][] Underfull \hbox (badness 10000) detected at line 645 [][][] [96] Underfull \hbox (badness 10000) detected at line 667 [][][] Underfull \hbox (badness 10000) detected at line 689 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 719 [][][] [97] Underfull \hbox (badness 10000) detected at line 729 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] Underfull \hbox (badness 10000) detected at line 759 [][][] Underfull \hbox (badness 10000) detected at line 776 [][][] [98] Underfull \hbox (badness 10000) detected at line 786 [][][] Underfull \hbox (badness 10000) detected at line 803 [][][] Underfull \hbox (badness 10000) detected at line 813 [][][] Underfull \hbox (badness 10000) detected at line 830 [][][] [99] Underfull \hbox (badness 10000) detected at line 840 [][][] Underfull \hbox (badness 10000) detected at line 857 [][][] Underfull \hbox (badness 10000) detected at line 867 [][][] Underfull \hbox (badness 10000) detected at line 884 [][][] Underfull \hbox (badness 10000) detected at line 894 [][][] [100] Underfull \hbox (badness 10000) detected at line 911 [][][] Underfull \hbox (badness 10000) detected at line 921 [][][] Underfull \hbox (badness 10000) detected at line 938 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] Underfull \hbox (badness 10000) detected at line 965 [][][] [101] Underfull \hbox (badness 10000) detected at line 975 [][][] Underfull \hbox (badness 10000) detected at line 992 [][][] Underfull \hbox (badness 10000) detected at line 1002 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] Underfull \hbox (badness 10000) detected at line 1029 [][][] [102] Underfull \hbox (badness 10000) detected at line 1046 [][][] Underfull \hbox (badness 10000) detected at line 1056 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1086 [][][] Underfull \hbox (badness 10000) detected at line 1103 [][][] Underfull \hbox (badness 10000) detected at line 1108 [][][] [103] Underfull \hbox (badness 10000) detected at line 1118 [][][] Underfull \hbox (badness 10000) detected at line 1135 [][][] Underfull \hbox (badness 10000) detected at line 1138 [][][] Underfull \hbox (badness 10000) detected at line 1150 [][][] Underfull \hbox (badness 10000) detected at line 1153 [][][] Underfull \hbox (badness 10000) detected at line 1170 [][][] [104] Underfull \hbox (badness 10000) detected at line 1173 [][][] Underfull \hbox (badness 10000) detected at line 1183 [][][] Underfull \hbox (badness 10000) detected at line 1186 [][][] Underfull \hbox (badness 10000) detected at line 1203 [][][] Underfull \hbox (badness 10000) detected at line 1206 [][][] Underfull \hbox (badness 10000) detected at line 1218 [][][] Underfull \hbox (badness 10000) detected at line 1221 [][][] [105] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1241 [][][] Underfull \hbox (badness 10000) detected at line 1251 [][][] Underfull \hbox (badness 10000) detected at line 1254 [][][] Underfull \hbox (badness 10000) detected at line 1271 [][][] Underfull \hbox (badness 10000) detected at line 1274 [][][] Underfull \hbox (badness 10000) detected at line 1284 [][][] [106] Underfull \hbox (badness 10000) detected at line 1308 [][][] Underfull \hbox (badness 10000) detected at line 1311 [][][] Underfull \hbox (badness 10000) detected at line 1321 [][][] ) (./group___p_b_a_mparm.tex [107] [108] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [109] Underfull \hbox (badness 10000) detected at line 182 [][][] Underfull \hbox (badness 10000) detected at line 190 [][][] Underfull \hbox (badness 10000) detected at line 207 [][][] [110] Underfull \hbox (badness 10000) detected at line 231 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 256 [][][] Underfull \hbox (badness 10000) detected at line 266 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] [111] Underfull \hbox (badness 10000) detected at line 305 [][][] Underfull \hbox (badness 10000) detected at line 327 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] [112] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 399 [][][] [113] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] [114] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 519 [][][] Underfull \hbox (badness 10000) detected at line 543 [][][] [115] Underfull \hbox (badness 10000) detected at line 567 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 603 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] [116] Underfull \hbox (badness 10000) detected at line 644 [][][] ) (./group___p_b_eparm.tex [117] [118] Underfull \hbox (badness 10000) detected at line 229 [][][] Underfull \hbox (badness 10000) detected at line 232 [][][] [119] Underfull \hbox (badness 10000) detected at line 254 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 298 [][][] Underfull \hbox (badness 10000) detected at line 301 [][][] Underfull \hbox (badness 10000) detected at line 323 [][][] [120] Underfull \hbox (badness 10000) detected at line 345 [][][] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 370 [][][] [121] Underfull \hbox (badness 10000) detected at line 394 [][][] Underfull \hbox (badness 10000) detected at line 397 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] Underfull \hbox (badness 10000) detected at line 424 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] [122]) (./group___p_b_s_a_mparm.tex [123] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [124] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 191 [][][] [125] Underfull \hbox (badness 10000) detected at line 215 [][][] Underfull \hbox (badness 10000) detected at line 223 [][][] Underfull \hbox (badness 10000) detected at line 240 [][][] Underfull \hbox (badness 10000) detected at line 250 [][][] Underfull \hbox (badness 10000) detected at line 267 [][][] [126] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] [127] Underfull \hbox (badness 10000) detected at line 359 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] [128] Underfull \hbox (badness 10000) detected at line 407 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 436 [][][] ) (./group___vacc.tex [129] [130] [131] Underfull \hbox (badness 10000) detected at line 153 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] [132] Underfull \hbox (badness 10000) detected at line 211 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] Underfull \hbox (badness 10000) detected at line 246 [][][] [133] Underfull \hbox (badness 10000) detected at line 272 [][][] Underfull \hbox (badness 10000) detected at line 275 [][][] Underfull \hbox (badness 10000) detected at line 287 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] [134] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 341 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] [135] Underfull \hbox (badness 10000) detected at line 391 [][][] Underfull \hbox (badness 10000) detected at line 415 [][][] Underfull \hbox (badness 10000) detected at line 418 [][][] Underfull \hbox (badness 10000) detected at line 421 [][][] [136] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] Underfull \hbox (badness 10000) detected at line 503 [][][] Underfull \hbox (badness 10000) detected at line 506 [][][] [137] Underfull \hbox (badness 10000) detected at line 534 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 540 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [138] Underfull \hbox (badness 10000) detected at line 599 [][][] Underfull \hbox (badness 10000) detected at line 602 [][][] [139] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 664 [][][] [140] Underfull \hbox (badness 10000) detected at line 696 [][][] Underfull \hbox (badness 10000) detected at line 728 [][][] [141] Underfull \hbox (badness 10000) detected at line 762 [][][] Underfull \hbox (badness 10000) detected at line 794 [][][] [142] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 856 [][][] Underfull \hbox (badness 10000) detected at line 859 [][][] Underfull \hbox (badness 10000) detected at line 862 [][][] [143] Underfull \hbox (badness 10000) detected at line 886 [][][] Underfull \hbox (badness 10000) detected at line 889 [][][] Underfull \hbox (badness 10000) detected at line 892 [][][] Underfull \hbox (badness 10000) detected at line 922 [][][] Underfull \hbox (badness 10000) detected at line 925 [][][] [144] Underfull \hbox (badness 10000) detected at line 945 [][][] Underfull \hbox (badness 10000) detected at line 948 [][][] Underfull \hbox (badness 10000) detected at line 976 [][][] Underfull \hbox (badness 10000) detected at line 979 [][][] [145] Underfull \hbox (badness 10000) detected at line 1011 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] Underfull \hbox (badness 10000) detected at line 1044 [][][] Underfull \hbox (badness 10000) detected at line 1047 [][][] [146] Underfull \hbox (badness 10000) detected at line 1073 [][][] Underfull \hbox (badness 10000) detected at line 1076 [][][] Underfull \hbox (badness 10000) detected at line 1104 [][][] Underfull \hbox (badness 10000) detected at line 1126 [][][] [147] Underfull \hbox (badness 10000) detected at line 1150 [][][] Underfull \hbox (badness 10000) detected at line 1153 [][][] Underfull \hbox (badness 10000) detected at line 1156 [][][] ) (./group___valist.tex [148] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [149] Underfull \hbox (badness 10000) detected at line 115 [][][] Underfull \hbox (badness 10000) detected at line 118 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] [150] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 187 [][][] Underfull \hbox (badness 10000) detected at line 211 [][][] Underfull \hbox (badness 10000) detected at line 214 [][][] Underfull \hbox (badness 10000) detected at line 236 [][][] Underfull \hbox (badness 10000) detected at line 239 [][][] [151] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 264 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] Underfull \hbox (badness 10000) detected at line 311 [][][] [152] Underfull \hbox (badness 10000) detected at line 314 [][][] Underfull \hbox (badness 10000) detected at line 336 [][][] Underfull \hbox (badness 10000) detected at line 339 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] Underfull \hbox (badness 10000) detected at line 359 [][][] [153] Underfull \hbox (badness 10000) detected at line 381 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 413 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] [154] Underfull \hbox (badness 10000) detected at line 447 [][][] Underfull \hbox (badness 10000) detected at line 450 [][][] Underfull \hbox (badness 10000) detected at line 453 [][][] ) (./group___vatom.tex [155] [156] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 140 [][][] Underfull \hbox (badness 10000) detected at line 164 [][][] [157] Underfull \hbox (badness 10000) detected at line 188 [][][] Underfull \hbox (badness 10000) detected at line 191 [][][] Underfull \hbox (badness 10000) detected at line 208 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] Underfull \hbox (badness 10000) detected at line 233 [][][] [158] Underfull \hbox (badness 10000) detected at line 255 [][][] Underfull \hbox (badness 10000) detected at line 277 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 302 [][][] [159] Underfull \hbox (badness 10000) detected at line 326 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 359 [][][] [160] Underfull \hbox (badness 10000) detected at line 376 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] Underfull \hbox (badness 10000) detected at line 434 [][][] [161] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 483 [][][] Underfull \hbox (badness 10000) detected at line 500 [][][] [162] Underfull \hbox (badness 10000) detected at line 524 [][][] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 572 [][][] [163] Underfull \hbox (badness 10000) detected at line 596 [][][] Underfull \hbox (badness 10000) detected at line 620 [][][] Underfull \hbox (badness 10000) detected at line 644 [][][] [164] Underfull \hbox (badness 10000) detected at line 668 [][][] ) (./group___vcap.tex Underfull \hbox (badness 10000) detected at line 36 [][][] [165] Underfull \hbox (badness 10000) detected at line 92 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] [166] Underfull \hbox (badness 10000) detected at line 127 [][][] Underfull \hbox (badness 10000) detected at line 130 [][][] Underfull \hbox (badness 10000) detected at line 133 [][][] Underfull \hbox (badness 10000) detected at line 162 [][][] Underfull \hbox (badness 10000) detected at line 165 [][][] Underfull \hbox (badness 10000) detected at line 168 [][][] ) (./group___vclist.tex [167] [168] Underfull \hbox (badness 10000) detected at line 130 [][][] [169] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 169 [][][] Underfull \hbox (badness 10000) detected at line 201 [][][] Underfull \hbox (badness 10000) detected at line 204 [][][] [170] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] [171] Underfull \hbox (badness 10000) detected at line 282 [][][] Underfull \hbox (badness 10000) detected at line 285 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Underfull \hbox (badness 10000) detected at line 312 [][][] Underfull \hbox (badness 10000) detected at line 334 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] [172] Underfull \hbox (badness 10000) detected at line 359 [][][] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 384 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] [173] Underfull \hbox (badness 10000) detected at line 433 [][][] ) (./group___vgreen.tex [174] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] [175] Underfull \hbox (badness 10000) detected at line 145 [][][] [176] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 182 [][][] [177] Underfull \hbox (badness 10000) detected at line 200 [][][] Underfull \hbox (badness 10000) detected at line 219 [][][] Underfull \hbox (badness 10000) detected at line 243 [][][] [178] Underfull \hbox (badness 10000) detected at line 262 [][][] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] [179] Underfull \hbox (badness 10000) detected at line 311 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] Underfull \hbox (badness 10000) detected at line 338 [][][] Underfull \hbox (badness 10000) detected at line 355 [][][] Underfull \hbox (badness 10000) detected at line 377 [][][] [180] Underfull \hbox (badness 10000) detected at line 399 [][][] Underfull \hbox (badness 10000) detected at line 407 [][][] Underfull \hbox (badness 10000) detected at line 428 [][][] Underfull \hbox (badness 10000) detected at line 433 [][][] [181] Underfull \hbox (badness 10000) detected at line 453 [][][] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 480 [][][] [182] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 521 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] ) (./group___vhal.tex [183] [184] [185] [186] Underfull \hbox (badness 10000) detected at line 392 [][][] [187] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 505 [][][] [188] Underfull \hbox (badness 10000) detected at line 528 [][][] Underfull \hbox (badness 10000) detected at line 569 [][][] [189] [190] Underfull \hbox (badness 10000) detected at line 778 [][][] Underfull \hbox (badness 10000) detected at line 839 [][][] [191] Underfull \hbox (badness 10000) detected at line 876 [][][] Underfull \hbox (badness 10000) detected at line 919 [][][] Underfull \hbox (badness 10000) detected at line 980 [][][] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) in paragraph at lines 1074--1074 []\T1/phv/m/n/10 Potential (k[] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! [192] LaTeX Warning: Command \r invalid in math mode on input line 1074. Missing character: There is no Šin font cmr10! [193] Underfull \hbox (badness 10000) detected at line 1205 [][][] Underfull \hbox (badness 10000) detected at line 1208 [][][] Underfull \hbox (badness 10000) detected at line 1239 [][][] Underfull \hbox (badness 10000) detected at line 1242 [][][] Underfull \hbox (badness 10000) detected at line 1259 [][][] [194]) (./group___vmatrix.tex) (./group___vparam.tex [195] [196] [197] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 193 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] [198] Underfull \hbox (badness 10000) detected at line 234 [][][] Underfull \hbox (badness 10000) detected at line 258 [][][] Underfull \hbox (badness 10000) detected at line 261 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] [199] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] [200] Underfull \hbox (badness 10000) detected at line 367 [][][] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 392 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] [201] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 454 [][][] Underfull \hbox (badness 10000) detected at line 471 [][][] Underfull \hbox (badness 10000) detected at line 481 [][][] Underfull \hbox (badness 10000) detected at line 484 [][][] [202] Underfull \hbox (badness 10000) detected at line 487 [][][] Underfull \hbox (badness 10000) detected at line 504 [][][] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 545 [][][] [203] Underfull \hbox (badness 10000) detected at line 548 [][][] Underfull \hbox (badness 10000) detected at line 575 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] [204] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 632 [][][] Underfull \hbox (badness 10000) detected at line 640 [][][] Underfull \hbox (badness 10000) detected at line 657 [][][] [205] Underfull \hbox (badness 10000) detected at line 667 [][][] Underfull \hbox (badness 10000) detected at line 684 [][][] Underfull \hbox (badness 10000) detected at line 706 [][][] ) (./group___vpbe.tex [206] [207] [208] Underfull \hbox (badness 10000) detected at line 132 [][][] Underfull \hbox (badness 10000) detected at line 135 [][][] LaTeX Warning: Command \r invalid in math mode on input line 137. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 137. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 140 [][][] [209] Underfull \hbox (badness 10000) detected at line 190 [][][] [210] Underfull \hbox (badness 10000) detected at line 193 [][][] LaTeX Warning: Command \r invalid in math mode on input line 194. Missing character: There is no Šin font cmr10! LaTeX Warning: Command \r invalid in math mode on input line 194. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 199 [][][] [211] Underfull \hbox (badness 10000) detected at line 251 [][][] Underfull \hbox (badness 10000) detected at line 273 [][][] Underfull \hbox (badness 10000) detected at line 295 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Overfull \hbox (151.96916pt too wide) in paragraph at lines 322--322 [] \T1/p cr/m/n/8 permittivity equal to the protein interior) and zero ionic[] [212] Underfull \hbox (badness 10000) detected at line 329 [][][] Underfull \hbox (badness 10000) detected at line 337 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] Underfull \hbox (badness 10000) detected at line 362 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] Underfull \hbox (badness 10000) detected at line 387 [][][] [213] Underfull \hbox (badness 10000) detected at line 400 [][][] Underfull \hbox (badness 10000) detected at line 416 [][][] Underfull \hbox (badness 10000) detected at line 440 [][][] Underfull \hbox (badness 10000) detected at line 457 [][][] [214] Underfull \hbox (badness 10000) detected at line 465 [][][] Underfull \hbox (badness 10000) detected at line 482 [][][] Underfull \hbox (badness 10000) detected at line 490 [][][] Underfull \hbox (badness 10000) detected at line 507 [][][] [215] Underfull \hbox (badness 10000) detected at line 529 [][][] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 562 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 587 [][][] [216] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 629 [][][] Underfull \hbox (badness 10000) detected at line 637 [][][] Underfull \hbox (badness 10000) detected at line 654 [][][] Underfull \hbox (badness 10000) detected at line 662 [][][] [217] Underfull \hbox (badness 10000) detected at line 679 [][][] Underfull \hbox (badness 10000) detected at line 687 [][][] Underfull \hbox (badness 10000) detected at line 704 [][][] Underfull \hbox (badness 10000) detected at line 712 [][][] Underfull \hbox (badness 10000) detected at line 729 [][][] Underfull \hbox (badness 10000) detected at line 737 [][][] [218] Underfull \hbox (badness 10000) detected at line 754 [][][] Underfull \hbox (badness 10000) detected at line 762 [][][] Underfull \hbox (badness 10000) detected at line 779 [][][] Underfull \hbox (badness 10000) detected at line 787 [][][] Underfull \hbox (badness 10000) detected at line 804 [][][] Underfull \hbox (badness 10000) detected at line 812 [][][] [219] Underfull \hbox (badness 10000) detected at line 829 [][][] Underfull \hbox (badness 10000) detected at line 837 [][][] Underfull \hbox (badness 10000) detected at line 854 [][][] Underfull \hbox (badness 10000) detected at line 862 [][][] LaTeX Warning: Command \r invalid in math mode on input line 863. Missing character: There is no Šin font cmr10! Underfull \hbox (badness 10000) detected at line 879 [][][] Underfull \hbox (badness 10000) detected at line 887 [][][] [220] Underfull \hbox (badness 10000) detected at line 904 [][][] Underfull \hbox (badness 10000) detected at line 912 [][][] Underfull \hbox (badness 10000) detected at line 929 [][][] Underfull \hbox (badness 10000) detected at line 937 [][][] ) (./group___vstring.tex [221] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] [222] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] ) (./group___vunit.tex [223] LaTeX Warning: Command \r invalid in math mode on input line 39. Missing character: There is no Šin font cmr9! [224] LaTeX Warning: Command \r invalid in math mode on input line 144. Missing character: There is no Šin font cmr10! [225]) (./group___vgrid.tex [226] [227] Underfull \hbox (badness 10000) detected at line 131 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [228] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 202 [][][] Underfull \hbox (badness 10000) detected at line 219 [][][] [229] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 274 [][][] [230] Underfull \hbox (badness 10000) detected at line 296 [][][] Underfull \hbox (badness 10000) detected at line 308 [][][] Underfull \hbox (badness 10000) detected at line 325 [][][] Underfull \hbox (badness 10000) detected at line 333 [][][] Underfull \hbox (badness 10000) detected at line 350 [][][] Underfull \hbox (badness 10000) detected at line 358 [][][] [231] Underfull \hbox (badness 10000) detected at line 375 [][][] Underfull \hbox (badness 10000) detected at line 383 [][][] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 409 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] [232] Underfull \hbox (badness 10000) detected at line 434 [][][] Underfull \hbox (badness 10000) detected at line 451 [][][] Underfull \hbox (badness 10000) detected at line 459 [][][] Underfull \hbox (badness 10000) detected at line 476 [][][] Underfull \hbox (badness 10000) detected at line 479 [][][] [233] Underfull \hbox (badness 10000) detected at line 495 [][][] Underfull \hbox (badness 10000) detected at line 498 [][][] Underfull \hbox (badness 10000) detected at line 515 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] Underfull \hbox (badness 10000) detected at line 534 [][][] [234] Underfull \hbox (badness 10000) detected at line 537 [][][] Underfull \hbox (badness 10000) detected at line 554 [][][] Underfull \hbox (badness 10000) detected at line 557 [][][] Underfull \hbox (badness 10000) detected at line 581 [][][] Underfull \hbox (badness 10000) detected at line 589 [][][] [235] Underfull \hbox (badness 10000) detected at line 606 [][][] Underfull \hbox (badness 10000) detected at line 618 [][][] Underfull \hbox (badness 10000) detected at line 635 [][][] [236] Underfull \hbox (badness 10000) detected at line 669 [][][] Underfull \hbox (badness 10000) detected at line 703 [][][] Underfull \hbox (badness 10000) detected at line 708 [][][] [237]) (./group___vmgrid.tex [238] Underfull \hbox (badness 10000) detected at line 111 [][][] [239] Underfull \hbox (badness 10000) detected at line 121 [][][] Underfull \hbox (badness 10000) detected at line 138 [][][] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 158 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [240] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 199 [][][] Underfull \hbox (badness 10000) detected at line 216 [][][] [241] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 260 [][][] Underfull \hbox (badness 10000) detected at line 270 [][][] Underfull \hbox (badness 10000) detected at line 283 [][][] Underfull \hbox (badness 10000) detected at line 293 [][][] [242] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 318 [][][] Underfull \hbox (badness 10000) detected at line 335 [][][] Underfull \hbox (badness 10000) detected at line 347 [][][] ) (./group___vopot.tex [243] [244] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 124 [][][] [245] Underfull \hbox (badness 10000) detected at line 141 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] [246] Underfull \hbox (badness 10000) detected at line 196 [][][] Underfull \hbox (badness 10000) detected at line 218 [][][] Underfull \hbox (badness 10000) detected at line 230 [][][] Underfull \hbox (badness 10000) detected at line 247 [][][] [247] Underfull \hbox (badness 10000) detected at line 259 [][][] ) (./group___vpmg.tex [248] [249] [250] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] [251] Underfull \hbox (badness 10000) detected at line 190 [][][] [252] Underfull \hbox (badness 10000) detected at line 238 [][][] [253] Underfull \hbox (badness 10000) detected at line 280 [][][] Underfull \hbox (badness 10000) detected at line 328 [][][] [254] Underfull \hbox (badness 10000) detected at line 366 [][][] [255] Underfull \hbox (badness 10000) detected at line 385 [][][] Underfull \hbox (badness 10000) detected at line 388 [][][] Underfull \hbox (badness 10000) detected at line 420 [][][] Underfull \hbox (badness 10000) detected at line 423 [][][] Underfull \hbox (badness 10000) detected at line 426 [][][] [256] Underfull \hbox (badness 10000) detected at line 462 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 491 [][][] [257] Underfull \hbox (badness 10000) detected at line 496 [][][] Underfull \hbox (badness 10000) detected at line 524 [][][] [258] Underfull \hbox (badness 10000) detected at line 550 [][][] Underfull \hbox (badness 10000) detected at line 576 [][][] Underfull \hbox (badness 10000) detected at line 608 [][][] [259] Underfull \hbox (badness 10000) detected at line 611 [][][] Underfull \hbox (badness 10000) detected at line 614 [][][] Underfull \hbox (badness 10000) detected at line 647 [][][] Underfull \hbox (badness 10000) detected at line 650 [][][] Underfull \hbox (badness 10000) detected at line 672 [][][] [260] Underfull \hbox (badness 10000) detected at line 694 [][][] Underfull \hbox (badness 10000) detected at line 716 [][][] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 722 [][][] [261] Underfull \hbox (badness 10000) detected at line 746 [][][] Underfull \hbox (badness 10000) detected at line 768 [][][] Underfull \hbox (badness 10000) detected at line 771 [][][] [262] Underfull \hbox (badness 10000) detected at line 803 [][][] Underfull \hbox (badness 10000) detected at line 806 [][][] [263] Underfull \hbox (badness 10000) detected at line 860 [][][] Underfull \hbox (badness 10000) detected at line 863 [][][] Underfull \hbox (badness 10000) detected at line 868 [][][] Underfull \hbox (badness 10000) detected at line 898 [][][] [264] Underfull \hbox (badness 10000) detected at line 924 [][][] Underfull \hbox (badness 10000) detected at line 927 [][][] Underfull \hbox (badness 10000) detected at line 932 [][][] [265] Underfull \hbox (badness 10000) detected at line 960 [][][] Underfull \hbox (badness 10000) detected at line 986 [][][] [266] Underfull \hbox (badness 10000) detected at line 1012 [][][] Underfull \hbox (badness 10000) detected at line 1034 [][][] Underfull \hbox (badness 10000) detected at line 1037 [][][] Underfull \hbox (badness 10000) detected at line 1059 [][][] [267] Underfull \hbox (badness 10000) detected at line 1097 [][][] Underfull \hbox (badness 10000) detected at line 1100 [][][] Underfull \hbox (badness 10000) detected at line 1103 [][][] [268] Underfull \hbox (badness 10000) detected at line 1127 [][][] Underfull \hbox (badness 10000) detected at line 1164 [][][] Underfull \hbox (badness 10000) detected at line 1167 [][][] Underfull \hbox (badness 10000) detected at line 1170 [][][] [269] Underfull \hbox (badness 10000) detected at line 1194 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] Underfull \hbox (badness 10000) detected at line 1202 [][][] [270] Underfull \hbox (badness 10000) detected at line 1230 [][][] Underfull \hbox (badness 10000) detected at line 1256 [][][] Underfull \hbox (badness 10000) detected at line 1284 [][][] [271] Underfull \hbox (badness 10000) detected at line 1287 [][][] Underfull \hbox (badness 10000) detected at line 1307 [][][] Underfull \hbox (badness 10000) detected at line 1347 [][][] [272] Underfull \hbox (badness 10000) detected at line 1350 [][][] Underfull \hbox (badness 10000) detected at line 1353 [][][] Underfull \hbox (badness 10000) detected at line 1377 [][][] Underfull \hbox (badness 10000) detected at line 1405 [][][] Underfull \hbox (badness 10000) detected at line 1408 [][][] [273] Underfull \hbox (badness 10000) detected at line 1430 [][][] Underfull \hbox (badness 10000) detected at line 1433 [][][] Underfull \hbox (badness 10000) detected at line 1436 [][][] Underfull \hbox (badness 10000) detected at line 1458 [][][] ) (./group___vpmgp.tex [274] Underfull \hbox (badness 10000) detected at line 45 [][][] [275] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 134 [][][] [276] Underfull \hbox (badness 10000) detected at line 156 [][][] Underfull \hbox (badness 10000) detected at line 178 [][][] [277] Underfull \hbox (badness 10000) detected at line 212 [][][] ) (./group___p_m_g_c.tex [278] [279] [280] [281] Underfull \hbox (badness 10000) detected at line 157 [][][] Underfull \hbox (badness 10000) detected at line 160 [][][] Underfull \hbox (badness 10000) detected at line 163 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 172--172 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [282] Underfull \hbox (badness 10000) detected at line 219 [][][] Underfull \hbox (badness 10000) detected at line 222 [][][] Underfull \hbox (badness 10000) detected at line 225 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 234--234 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [283] Underfull \hbox (badness 10000) detected at line 286 [][][] Underfull \hbox (badness 10000) detected at line 289 [][][] [284] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 348 [][][] Underfull \hbox (badness 10000) detected at line 351 [][][] Underfull \hbox (badness 10000) detected at line 354 [][][] [285] Overfull \hbox (304.08286pt too wide) in paragraph at lines 364--364 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 401 [][][] Underfull \hbox (badness 10000) detected at line 404 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 413--413 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [286] Underfull \hbox (badness 10000) detected at line 448 [][][] [287] Underfull \hbox (badness 10000) detected at line 512 [][][] Underfull \hbox (badness 10000) detected at line 515 [][][] Underfull \hbox (badness 10000) detected at line 518 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 527--527 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [288] Underfull \hbox (badness 10000) detected at line 565 [][][] Underfull \hbox (badness 10000) detected at line 568 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 577--577 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [289] Underfull \hbox (badness 10000) detected at line 612 [][][] Underfull \hbox (badness 10000) detected at line 615 [][][] [290] Underfull \hbox (badness 10000) detected at line 655 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] [291] Underfull \hbox (badness 10000) detected at line 728 [][][] Underfull \hbox (badness 10000) detected at line 731 [][][] [292] Underfull \hbox (badness 10000) detected at line 781 [][][] Underfull \hbox (badness 10000) detected at line 784 [][][] Underfull \hbox (badness 10000) detected at line 787 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 797--797 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 834 [][][] [293] Underfull \hbox (badness 10000) detected at line 837 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 846--846 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [294] [295] Underfull \hbox (badness 10000) detected at line 916 [][][] Underfull \hbox (badness 10000) detected at line 919 [][][] [296] [297] [298] Underfull \hbox (badness 10000) detected at line 1059 [][][] Underfull \hbox (badness 10000) detected at line 1062 [][][] [299] [300] [301] Underfull \hbox (badness 10000) detected at line 1238 [][][] Underfull \hbox (badness 10000) detected at line 1241 [][][] [302] [303] Underfull \hbox (badness 10000) detected at line 1391 [][][] Underfull \hbox (badness 10000) detected at line 1394 [][][] Underfull \hbox (badness 10000) detected at line 1397 [][][] [304] [305] Underfull \hbox (badness 10000) detected at line 1455 [][][] Underfull \hbox (badness 10000) detected at line 1458 [][][] Underfull \hbox (badness 10000) detected at line 1461 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1471--1471 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [306] Underfull \hbox (badness 10000) detected at line 1508 [][][] Underfull \hbox (badness 10000) detected at line 1511 [][][] [307] Underfull \hbox (badness 10000) detected at line 1591 [][][] Underfull \hbox (badness 10000) detected at line 1594 [][][] Underfull \hbox (badness 10000) detected at line 1597 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1607--1607 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [308] Underfull \hbox (badness 10000) detected at line 1644 [][][] Underfull \hbox (badness 10000) detected at line 1647 [][][] Underfull \hbox (badness 10000) detected at line 1650 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1659--1659 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [309] Underfull \hbox (badness 10000) detected at line 1737 [][][] Underfull \hbox (badness 10000) detected at line 1742 [][][] Underfull \hbox (badness 10000) detected at line 1745 [][][] [310] Underfull \hbox (badness 10000) detected at line 1775 [][][] Underfull \hbox (badness 10000) detected at line 1778 [][][] [311] Underfull \hbox (badness 10000) detected at line 1812 [][][] Underfull \hbox (badness 10000) detected at line 1815 [][][] Underfull \hbox (badness 10000) detected at line 1849 [][][] Underfull \hbox (badness 10000) detected at line 1852 [][][] [312] Underfull \hbox (badness 10000) detected at line 1886 [][][] Underfull \hbox (badness 10000) detected at line 1889 [][][] Underfull \hbox (badness 10000) detected at line 1892 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 1902--1902 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [313] Underfull \hbox (badness 10000) detected at line 1939 [][][] Underfull \hbox (badness 10000) detected at line 1942 [][][] Underfull \hbox (badness 10000) detected at line 1945 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 1954--1954 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [314] [315] Underfull \hbox (badness 10000) detected at line 2040 [][][] Underfull \hbox (badness 10000) detected at line 2043 [][][] Underfull \hbox (badness 10000) detected at line 2077 [][][] Underfull \hbox (badness 10000) detected at line 2080 [][][] Underfull \hbox (badness 10000) detected at line 2083 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2093--2093 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [316] Underfull \hbox (badness 10000) detected at line 2130 [][][] Underfull \hbox (badness 10000) detected at line 2133 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2142--2142 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [317] Underfull \hbox (badness 10000) detected at line 2177 [][][] Underfull \hbox (badness 10000) detected at line 2180 [][][] Underfull \hbox (badness 10000) detected at line 2212 [][][] Underfull \hbox (badness 10000) detected at line 2215 [][][] [318] Underfull \hbox (badness 10000) detected at line 2251 [][][] Underfull \hbox (badness 10000) detected at line 2254 [][][] [319] Underfull \hbox (badness 10000) detected at line 2290 [][][] Underfull \hbox (badness 10000) detected at line 2293 [][][] [320] Underfull \hbox (badness 10000) detected at line 2321 [][][] Underfull \hbox (badness 10000) detected at line 2324 [][][] Underfull \hbox (badness 10000) detected at line 2327 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2337--2337 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [321] Underfull \hbox (badness 10000) detected at line 2374 [][][] Underfull \hbox (badness 10000) detected at line 2377 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2386--2386 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 2421 [][][] Underfull \hbox (badness 10000) detected at line 2424 [][][] [322] [323] Underfull \hbox (badness 10000) detected at line 2510 [][][] Underfull \hbox (badness 10000) detected at line 2513 [][][] Underfull \hbox (badness 10000) detected at line 2516 [][][] [324] Underfull \hbox (badness 10000) detected at line 2564 [][][] Underfull \hbox (badness 10000) detected at line 2567 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2576--2576 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [325] Underfull \hbox (badness 10000) detected at line 2611 [][][] Underfull \hbox (badness 10000) detected at line 2614 [][][] [326] Underfull \hbox (badness 10000) detected at line 2704 [][][] Underfull \hbox (badness 10000) detected at line 2707 [][][] [327] Underfull \hbox (badness 10000) detected at line 2753 [][][] Underfull \hbox (badness 10000) detected at line 2756 [][][] Underfull \hbox (badness 10000) detected at line 2759 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 2769--2769 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [328] Underfull \hbox (badness 10000) detected at line 2806 [][][] Underfull \hbox (badness 10000) detected at line 2809 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 2818--2818 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [329] Underfull \hbox (badness 10000) detected at line 2853 [][][] Underfull \hbox (badness 10000) detected at line 2856 [][][] [330] Underfull \hbox (badness 10000) detected at line 2912 [][][] Underfull \hbox (badness 10000) detected at line 2915 [][][] [331] Underfull \hbox (badness 10000) detected at line 2953 [][][] Underfull \hbox (badness 10000) detected at line 2964 [][][] Underfull \hbox (badness 10000) detected at line 2967 [][][] [332] Underfull \hbox (badness 10000) detected at line 3053 [][][] Underfull \hbox (badness 10000) detected at line 3056 [][][] Underfull \hbox (badness 10000) detected at line 3059 [][][] [333] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3069--3069 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3106 [][][] Underfull \hbox (badness 10000) detected at line 3109 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3118--3118 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [334] Underfull \hbox (badness 10000) detected at line 3153 [][][] Underfull \hbox (badness 10000) detected at line 3156 [][][] [335] Underfull \hbox (badness 10000) detected at line 3194 [][][] Underfull \hbox (badness 10000) detected at line 3197 [][][] Underfull \hbox (badness 10000) detected at line 3200 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3210--3210 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [336] Underfull \hbox (badness 10000) detected at line 3247 [][][] Underfull \hbox (badness 10000) detected at line 3250 [][][] Underfull \hbox (badness 10000) detected at line 3253 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3262--3262 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 3295 [][][] [337] [338] Underfull \hbox (badness 10000) detected at line 3349 [][][] [339] [340] Underfull \hbox (badness 10000) detected at line 3505 [][][] [341] Underfull \hbox (badness 10000) detected at line 3563 [][][] Underfull \hbox (badness 10000) detected at line 3566 [][][] [342] Underfull \hbox (badness 10000) detected at line 3606 [][][] [343] Underfull \hbox (badness 10000) detected at line 3609 [][][] Underfull \hbox (badness 10000) detected at line 3612 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3622--3622 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3659 [][][] Underfull \hbox (badness 10000) detected at line 3662 [][][] Underfull \hbox (badness 10000) detected at line 3665 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 3674--3674 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [344] Underfull \hbox (badness 10000) detected at line 3723 [][][] [345] Underfull \hbox (badness 10000) detected at line 3726 [][][] [346] Underfull \hbox (badness 10000) detected at line 3810 [][][] Underfull \hbox (badness 10000) detected at line 3813 [][][] [347] [348] Underfull \hbox (badness 10000) detected at line 3911 [][][] Underfull \hbox (badness 10000) detected at line 3914 [][][] Underfull \hbox (badness 10000) detected at line 3917 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 3927--3927 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 3964 [][][] [349] Underfull \hbox (badness 10000) detected at line 3967 [][][] Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 3978--3978 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 3993 [][][] Underfull \hbox (badness 10000) detected at line 3996 [][][] Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 3849) in paragraph at lines 4007--4007 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 4022 [][][] [350] Underfull \hbox (badness 10000) detected at line 4025 [][][] Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 2134) in paragraph at lines 4040--4040 []\T1/phv/m/n/10 Prefactor for con-te-rion Bolz-mann dis-tri-bu-tion terms. Ba- si-cally a scaled con-cen-tra-tion -(ion Underfull \hbox (badness 10000) detected at line 4055 [][][] Underfull \hbox (badness 10000) detected at line 4058 [][][] Underfull \hbox (badness 10000) detected at line 4061 [][][] [351] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4071--4071 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4108 [][][] Underfull \hbox (badness 10000) detected at line 4111 [][][] Underfull \hbox (badness 10000) detected at line 4114 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4123--4123 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [352] Underfull \hbox (badness 10000) detected at line 4158 [][][] Underfull \hbox (badness 10000) detected at line 4161 [][][] [353] Underfull \hbox (badness 10000) detected at line 4215 [][][] [354] Underfull \hbox (badness 10000) detected at line 4243 [][][] [355] Underfull \hbox (badness 10000) detected at line 4317 [][][] Underfull \hbox (badness 10000) detected at line 4320 [][][] [356] [357] Underfull \hbox (badness 10000) detected at line 4410 [][][] Underfull \hbox (badness 10000) detected at line 4413 [][][] [358] Underfull \hbox (badness 10000) detected at line 4453 [][][] Underfull \hbox (badness 10000) detected at line 4456 [][][] [359] Underfull \hbox (badness 10000) detected at line 4498 [][][] Underfull \hbox (badness 10000) detected at line 4501 [][][] [360] Underfull \hbox (badness 10000) detected at line 4559 [][][] Underfull \hbox (badness 10000) detected at line 4562 [][][] Underfull \hbox (badness 10000) detected at line 4565 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 4575--4575 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] Underfull \hbox (badness 10000) detected at line 4612 [][][] [361] Underfull \hbox (badness 10000) detected at line 4615 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4624--4624 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] Underfull \hbox (badness 10000) detected at line 4657 [][][] Underfull \hbox (badness 10000) detected at line 4660 [][][] Underfull \hbox (badness 10000) detected at line 4663 [][][] [362] Underfull \hbox (badness 10000) detected at line 4719 [][][] Underfull \hbox (badness 10000) detected at line 4722 [][][] [363] Underfull \hbox (badness 10000) detected at line 4754 [][][] Underfull \hbox (badness 10000) detected at line 4757 [][][] [364] Underfull \hbox (badness 10000) detected at line 4795 [][][] Underfull \hbox (badness 10000) detected at line 4798 [][][] Underfull \hbox (badness 10000) detected at line 4801 [][][] Overfull \hbox (20.88268pt too wide) in paragraph at lines 4811--4811 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute,[] [365] Underfull \hbox (badness 10000) detected at line 4849 [][][] Underfull \hbox (badness 10000) detected at line 4852 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 4861--4861 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [366] Underfull \hbox (badness 10000) detected at line 4896 [][][] Underfull \hbox (badness 10000) detected at line 4899 [][][] Underfull \hbox (badness 10000) detected at line 4957 [][][] [367] Underfull \hbox (badness 10000) detected at line 4960 [][][] Underfull \hbox (badness 10000) detected at line 4992 [][][] Underfull \hbox (badness 10000) detected at line 4995 [][][] Underfull \hbox (badness 10000) detected at line 4998 [][][] Overfull \hbox (304.08286pt too wide) in paragraph at lines 5008--5008 []\T1/pcr/m/n/8 * Developed at the Pacific Northwest National Laboratory, oper ated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. De partment Energy.[] [368] Underfull \hbox (badness 10000) detected at line 5045 [][][] Underfull \hbox (badness 10000) detected at line 5048 [][][] Underfull \hbox (badness 10000) detected at line 5051 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 5060--5060 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [369] Underfull \hbox (badness 10000) detected at line 5095 [][][] Underfull \hbox (badness 10000) detected at line 5098 [][][] Underfull \hbox (badness 10000) detected at line 5128 [][][] Underfull \hbox (badness 10000) detected at line 5131 [][][] Underfull \hbox (badness 10000) detected at line 5134 [][][] [370] Underfull \hbox (badness 10000) detected at line 5164 [][][] Underfull \hbox (badness 10000) detected at line 5167 [][][] Underfull \hbox (badness 10000) detected at line 5197 [][][] Underfull \hbox (badness 10000) detected at line 5200 [][][] [371] Underfull \hbox (badness 10000) detected at line 5230 [][][] Underfull \hbox (badness 10000) detected at line 5233 [][][] Underfull \hbox (badness 10000) detected at line 5261 [][][] [372] Underfull \hbox (badness 10000) detected at line 5264 [][][] Underfull \hbox (badness 10000) detected at line 5292 [][][] Underfull \hbox (badness 10000) detected at line 5295 [][][] ) (./group___frontend.tex [373] Underfull \hbox (badness 5175) in paragraph at lines 40--41 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 5091) in paragraph at lines 42--43 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n /10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 1237) in paragraph at lines 60--61 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][[]][], [] $\OMS/cmsy/m/n/10 ^ ^C$\T1/phv/m/n/10 pmgp[][[]][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][[ ]][], [] [374] Underfull \hbox (badness 4634) in paragraph at lines 78--79 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 78--79 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble Underfull \hbox (badness 3907) in paragraph at lines 80--81 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 80--81 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble [375] [376] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 187 [][][] Underfull \hbox (badness 10000) detected at line 217 [][][] [377] Underfull \hbox (badness 10000) detected at line 241 [][][] [378] Underfull \hbox (badness 10000) detected at line 281 [][][] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 320 [][][] Underfull \hbox (badness 10000) detected at line 323 [][][] [379] Underfull \hbox (badness 10000) detected at line 357 [][][] Underfull \hbox (badness 10000) detected at line 379 [][][] [380] Underfull \hbox (badness 10000) detected at line 396 [][][] Underfull \hbox (badness 10000) detected at line 399 [][][] [381] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] [382] Underfull \hbox (badness 10000) detected at line 578 [][][] Underfull \hbox (badness 10000) detected at line 581 [][][] [383] Underfull \hbox (badness 10000) detected at line 631 [][][] Underfull \hbox (badness 10000) detected at line 655 [][][] [384] Underfull \hbox (badness 10000) detected at line 683 [][][] Underfull \hbox (badness 10000) detected at line 700 [][][] Underfull \hbox (badness 10000) detected at line 726 [][][] [385] Underfull \hbox (badness 10000) detected at line 754 [][][] Underfull \hbox (badness 10000) detected at line 778 [][][] Underfull \hbox (badness 10000) detected at line 798 [][][] [386] Underfull \hbox (badness 10000) detected at line 824 [][][] Underfull \hbox (badness 10000) detected at line 848 [][][] Underfull \hbox (badness 10000) detected at line 872 [][][] Underfull \hbox (badness 10000) detected at line 882 [][][] [387] Underfull \hbox (badness 10000) detected at line 901 [][][] Underfull \hbox (badness 10000) detected at line 915 [][][] Underfull \hbox (badness 10000) detected at line 918 [][][] Underfull \hbox (badness 10000) detected at line 935 [][][] Underfull \hbox (badness 10000) detected at line 945 [][][] [388] Underfull \hbox (badness 10000) detected at line 964 [][][] Underfull \hbox (badness 10000) detected at line 967 [][][] Underfull \hbox (badness 10000) detected at line 987 [][][] Underfull \hbox (badness 10000) detected at line 990 [][][] Underfull \hbox (badness 10000) detected at line 1016 [][][] Underfull \hbox (badness 10000) detected at line 1019 [][][] [389] Underfull \hbox (badness 10000) detected at line 1041 [][][] Underfull \hbox (badness 10000) detected at line 1051 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1073 [][][] [390] Underfull \hbox (badness 10000) detected at line 1097 [][][] Underfull \hbox (badness 10000) detected at line 1111 [][][] Underfull \hbox (badness 10000) detected at line 1128 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1143 [][][] [391] Underfull \hbox (badness 10000) detected at line 1171 [][][] Underfull \hbox (badness 10000) detected at line 1185 [][][] Underfull \hbox (badness 10000) detected at line 1206 [][][] [392] Underfull \hbox (badness 10000) detected at line 1209 [][][] Underfull \hbox (badness 10000) detected at line 1233 [][][] Underfull \hbox (badness 10000) detected at line 1236 [][][] Underfull \hbox (badness 10000) detected at line 1264 [][][] [393] Underfull \hbox (badness 10000) detected at line 1267 [][][] Underfull \hbox (badness 10000) detected at line 1293 [][][] Underfull \hbox (badness 10000) detected at line 1296 [][][] Underfull \hbox (badness 10000) detected at line 1324 [][][] Underfull \hbox (badness 10000) detected at line 1327 [][][] [394] Underfull \hbox (badness 10000) detected at line 1353 [][][] Underfull \hbox (badness 10000) detected at line 1381 [][][] Underfull \hbox (badness 10000) detected at line 1384 [][][] [395] Underfull \hbox (badness 10000) detected at line 1412 [][][] Underfull \hbox (badness 10000) detected at line 1436 [][][] [396] Underfull \hbox (badness 10000) detected at line 1458 [][][] Underfull \hbox (badness 10000) detected at line 1472 [][][] Underfull \hbox (badness 10000) detected at line 1489 [][][] Underfull \hbox (badness 10000) detected at line 1501 [][][] Underfull \hbox (badness 10000) detected at line 1518 [][][] [397] Underfull \hbox (badness 10000) detected at line 1532 [][][] Underfull \hbox (badness 10000) detected at line 1566 [][][] Underfull \hbox (badness 10000) detected at line 1578 [][][] [398] Underfull \hbox (badness 10000) detected at line 1595 [][][] Underfull \hbox (badness 10000) detected at line 1612 [][][] Underfull \hbox (badness 10000) detected at line 1640 [][][] [399] Underfull \hbox (badness 10000) detected at line 1654 [][][] Underfull \hbox (badness 10000) detected at line 1692 [][][] [400] Underfull \hbox (badness 10000) detected at line 1720 [][][] Underfull \hbox (badness 10000) detected at line 1737 [][][] Underfull \hbox (badness 10000) detected at line 1751 [][][] Underfull \hbox (badness 10000) detected at line 1768 [][][] [401] Underfull \hbox (badness 10000) detected at line 1796 [][][] Underfull \hbox (badness 10000) detected at line 1813 [][][] Underfull \hbox (badness 10000) detected at line 1827 [][][] ) [402] Chapter 8. (./struct_atom_force.tex Underfull \hbox (badness 10000) detected at line 32 [][][] [403]) (./structs_a_p_o_lparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [404] Underfull \hbox (badness 10000) detected at line 88 [][][] [405] Underfull \hbox (badness 10000) detected at line 226 [][][] [406] Underfull \hbox (badness 10000) detected at line 239 [][][] Underfull \hbox (badness 10000) detected at line 252 [][][] Underfull \hbox (badness 10000) detected at line 265 [][][] Underfull \hbox (badness 10000) detected at line 278 [][][] Underfull \hbox (badness 10000) detected at line 291 [][][] Underfull \hbox (badness 10000) detected at line 304 [][][] [407] Underfull \hbox (badness 10000) detected at line 317 [][][] Underfull \hbox (badness 10000) detected at line 330 [][][] Underfull \hbox (badness 10000) detected at line 343 [][][] Underfull \hbox (badness 10000) detected at line 356 [][][] Underfull \hbox (badness 10000) detected at line 369 [][][] Underfull \hbox (badness 10000) detected at line 382 [][][] [408]) (./structs_b_e_mparm.tex [409] Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [410] Underfull \hbox (badness 10000) detected at line 131 [][][] Underfull \hbox (badness 10000) detected at line 144 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [411] Underfull \hbox (badness 10000) detected at line 170 [][][] Underfull \hbox (badness 10000) detected at line 183 [][][] Underfull \hbox (badness 10000) detected at line 196 [][][] ) (./structs_f_e_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [412] Underfull \hbox (badness 10000) detected at line 68 [][][] [413] [414] [415]) (./structs_g_e_o_f_l_o_wparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] [416]) (./structs_m_gparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [417] Underfull \hbox (badness 10000) detected at line 120 [][][] Underfull \hbox (badness 10000) detected at line 123 [][][] [418] [419] [420] [421] Underfull \hbox (badness 10000) detected at line 435 [][][] Underfull \hbox (badness 10000) detected at line 448 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 474 [][][] Underfull \hbox (badness 10000) detected at line 487 [][][] [422] Underfull \hbox (badness 10000) detected at line 500 [][][] Underfull \hbox (badness 10000) detected at line 513 [][][] Underfull \hbox (badness 10000) detected at line 526 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 552 [][][] Underfull \hbox (badness 10000) detected at line 565 [][][] [423] Underfull \hbox (badness 10000) detected at line 578 [][][] Underfull \hbox (badness 10000) detected at line 591 [][][] Underfull \hbox (badness 10000) detected at line 604 [][][] Underfull \hbox (badness 10000) detected at line 617 [][][] Underfull \hbox (badness 10000) detected at line 630 [][][] Underfull \hbox (badness 10000) detected at line 643 [][][] [424] Underfull \hbox (badness 10000) detected at line 656 [][][] Underfull \hbox (badness 10000) detected at line 669 [][][] ) (./structs_n_osh.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [425] Underfull \hbox (badness 10000) detected at line 108 [][][] [426] [427] [428] [429] [430]) (./structs_n_osh__calc.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [431] Underfull \hbox (badness 10000) detected at line 38 [][][] [432]) (./structs_p_b_a_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [433] Underfull \hbox (badness 10000) detected at line 106 [][][] Underfull \hbox (badness 10000) detected at line 109 [][][] [434] [435] [436] [437]) (./structs_p_b_eparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [438] [439] Underfull \hbox (badness 10000) detected at line 142 [][][] Underfull \hbox (badness 10000) detected at line 145 [][][] [440] [441] [442] Underfull \hbox (badness 10000) detected at line 393 [][][] Underfull \hbox (badness 10000) detected at line 406 [][][] Underfull \hbox (badness 10000) detected at line 419 [][][] Underfull \hbox (badness 10000) detected at line 432 [][][] [443] Underfull \hbox (badness 10000) detected at line 475 [][][] Underfull \hbox (badness 10000) detected at line 488 [][][] Underfull \hbox (badness 10000) detected at line 501 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 527 [][][] Underfull \hbox (badness 10000) detected at line 540 [][][] [444] Underfull \hbox (badness 10000) detected at line 553 [][][] Underfull \hbox (badness 10000) detected at line 566 [][][] Underfull \hbox (badness 10000) detected at line 579 [][][] Underfull \hbox (badness 10000) detected at line 592 [][][] Underfull \hbox (badness 10000) detected at line 605 [][][] Underfull \hbox (badness 10000) detected at line 618 [][][] [445] Underfull \hbox (badness 10000) detected at line 631 [][][] [446] [447]) (./structs_p_b_s_a_mparm.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [448] [449]) (./structs_vacc.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [450]) (./structs_vacc_surf.tex [451] Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [452]) (./structs_valist.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 36 [][][] [453]) (./structs_vatom.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [454] Underfull \hbox (badness 10000) detected at line 36 [][][] [455]) (./structs_vclist.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 40 [][][] [456] [457]) (./structs_vclist_cell.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vcsm.tex [458] Underfull \hbox (badness 10000) detected at line 42 [][][] [459]) (./structs_vfetk.tex [460] Underfull \hbox (badness 10000) detected at line 60 [][][] [461] [462]) (./structs_vfetk___local_var.tex [463] Underfull \hbox (badness 10000) detected at line 86 [][][] [464] [465] [466] [467]) (./structs_vgreen.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 34 [][][] [468]) (./structs_vgrid.tex [469] Underfull \hbox (badness 10000) detected at line 52 [][][] [470] [471]) (./structs_vmgrid.tex Underfull \hbox (badness 10000) detected at line 24 [][][] ) (./structs_vopot.tex [472] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./structs_vparam___atom_data.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [473] Underfull \hbox (badness 10000) detected at line 30 [][][] Underfull \hbox (badness 10000) detected at line 33 [][][] ) (./structs_vpbe.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [474] Underfull \hbox (badness 10000) detected at line 86 [][][] [475] [476] [477] [478]) (./structs_vpee.tex [479] Underfull \hbox (badness 10000) detected at line 34 [][][] ) (./structs_vpmg.tex [480] [481] Underfull \hbox (badness 10000) detected at line 116 [][][] [482] [483] [484] [485] [486]) (./structs_vpmgp.tex [487] Underfull \hbox (badness 10000) detected at line 126 [][][] [488] [489] [490] [491] [492] [493] [494] [495]) (./struct_vparam.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] [496] Underfull \hbox (badness 10000) detected at line 26 [][][] ) (./struct_vparam___res_data.tex Underfull \hbox (badness 10000) in paragraph at lines 10--11 [][]\T1/pcr/m/n/10 #include $\OML/cmm/m/it/10 <$\T1/pcr/m/n/10 /[]builddir/[]bu ild/[][]BUILD/[]apbs-3.[]0.[]0-build/[]apbs-3.[]0.[]0/[]src/[]generic/[] Underfull \hbox (badness 10000) detected at line 28 [][][] [497]) [498] Chapter 9. (./mainpage_8h_source.tex) (./apbs_8h.tex <./apbs_8h__incl.pdf> <./apbs_8h__dep __incl.pdf> [499] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [500]) (./apbs_8h_source.tex) (./vcsm_8c.tex [501] <./vcsm_8c__incl.pdf> [502] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] Underfull \hbox (badness 10000) detected at line 59 [][][] [503]) (./vcsm_8c_source.tex [504] [505] [506] [507] [508] [509]) (./vcsm_8h.tex <./vcsm_8h__incl.pdf> <./vcsm_8h__dep__incl.pdf> [510] [511] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [512]) (./vcsm_8h_source.tex [513]) (./vfetk_8c.tex [514] <./vfetk_8c__incl.pdf > [515] [516] Underfull \hbox (badness 10000) detected at line 163 [][][] Underfull \hbox (badness 10000) detected at line 166 [][][] [517] Underfull \hbox (badness 10000) detected at line 169 [][][] [518] [519] [520] [521]) (./vfetk_8c_source.tex [522] [523] [524] [525] [526] [527] [528] [529] [530] [531] [532] [533] [534] [535] [536] [537] [538] [539] [540] [541] [542] [543] [544] [545] [546] [547] [548] [549] [550] [551]) (./vfetk_8h.tex [552] <./vfetk_8h__incl.pdf> <./vfetk_8h__dep__inc l.pdf> [553] [554] [555] Underfull \hbox (badness 10000) detected at line 189 [][][] [556] Underfull \hbox (badness 10000) detected at line 192 [][][] Underfull \hbox (badness 10000) detected at line 195 [][][] ) (./vfetk_8h_source.tex [557] [558] [559] [560] [561] [562]) (./vpee_8c.tex <. /vpee_8c__incl.pdf> [563] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] Underfull \hbox (badness 10000) detected at line 56 [][][] [564]) (./vpee_8c_source.tex [565] [566] [567] [568] [569] [570]) (./vpee_8h.tex <./vpee_8h__incl.pdf> [571] <./vpee_8h__dep__incl.pdf> [572] Underfull \hbox (badness 10000) detected at line 57 [][][] Underfull \hbox (badness 10000) detected at line 60 [][][] Underfull \hbox (badness 10000) detected at line 63 [][][] [573]) (./vpee_8h_source.tex [574]) (./apolparm_8c.tex <./apolparm_8c__incl.pdf > [575] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [576] [577]) (./apolparm_8c_source.tex [578] [579] [580] [581] [582] [583] [584] [585]) (./apolparm_8h_source.tex [586]) (./bemparm_8c.tex <./bemparm_8c__ incl.pdf> [587] [588] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [589] Underfull \hbox (badness 10000) detected at line 123 [][][] ) (./bemparm_8c_source.tex [590] [591] [592] [593]) (./bemparm_8h_source.tex [594]) (./femparm_8c.tex <./femparm_8c__incl.pdf> [595] [596] Underfull \hbox (badness 10000) detected at line 59 [][][] Underfull \hbox (badness 10000) detected at line 62 [][][] Underfull \hbox (badness 10000) detected at line 65 [][][] [597] [598]) (./femparm_8c_source.tex [599] [600] [601] [602] [603]) (./femparm_8h.tex <./femparm_8h__incl.pdf> [604] <./femparm_8h__dep__incl.pdf> [605] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [606] Underfull \hbox (badness 10000) detected at line 95 [][][] ) (./femparm_8h_source.tex [607]) (./geoflowparm_8c.tex [608] <./geoflowparm_8c __incl.pdf> [609] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 53 [][][] [610]) (./geoflowparm_8c_source.tex [611] [612]) (./geoflowparm_8h.tex [613] <. /geoflowparm_8h__incl.pdf> <./geoflowparm_8h__dep__incl.pdf> [614] [615] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [616]) (./geoflowparm_8h_source.tex [617]) (./mgparm_8c.tex <./mgparm_8c__incl. pdf> [618] [619] Underfull \hbox (badness 10000) detected at line 95 [][][] Underfull \hbox (badness 10000) detected at line 98 [][][] Underfull \hbox (badness 10000) detected at line 101 [][][] [620] [621] [622]) (./mgparm_8c_source.tex [623] [624] [625] [626] [627] [628] [629] [630] [631] [632] [633]) (./mgparm_8h.tex <./mgparm_8h__incl.pdf> [634] <./mgparm_8h__dep__incl.pdf> [635] [636] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] [637]) (./mgparm_8h_source.tex [638]) (./nosh_8c.tex [639] <./nosh_8c__incl.pdf > [640] [641] Underfull \hbox (badness 10000) detected at line 151 [][][] Underfull \hbox (badness 10000) detected at line 154 [][][] Underfull \hbox (badness 10000) detected at line 157 [][][] [642] [643] [644] [645] [646]) (./nosh_8c_source.tex [647] [648] [649] [650] [651] [652] [653] [654] [655] [656] [657] [658] [659] [660] [661] [662] [663] [664] [665] [666] [667] [668] [669] [670] [671] [672] [673] [674] [675] [676] [677] [678] [679] [680] [681] [682] [683] [684] [685] [686]) (./nosh_8h.tex <./nosh_8h__incl.pdf> [687] <./nosh_8h__dep__incl.pdf> [688] [689] [690] Underfull \hbox (badness 10000) detected at line 171 [][][] Underfull \hbox (badness 10000) detected at line 174 [][][] Underfull \hbox (badness 10000) detected at line 177 [][][] ) (./nosh_8h_source.tex [691] [692] [693]) (./pbamparm_8c.tex <./pbamparm_8c__i ncl.pdf> [694] [695] Underfull \hbox (badness 10000) detected at line 69 [][][] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] [696]) (./pbamparm_8c_source.tex [697] [698] [699] [700] [701] [702] [703] [704] [705]) (./pbamparm_8h.tex <./pbamparm_8h__incl.pdf> <./pbamparm_8h__dep__ incl.pdf> [706] [707] Underfull \hbox (badness 10000) detected at line 102 [][][] [708] Underfull \hbox (badness 10000) detected at line 105 [][][] Underfull \hbox (badness 10000) detected at line 108 [][][] [709]) (./pbamparm_8h_source.tex [710] [711]) (./pbeparm_8c.tex <./pbeparm_8c__ incl.pdf> [712] Underfull \hbox (badness 10000) detected at line 101 [][][] Underfull \hbox (badness 10000) detected at line 104 [][][] Underfull \hbox (badness 10000) detected at line 107 [][][] [713] [714] [715] [716] [717]) (./pbeparm_8c_source.tex [718] [719] [720] [721] [722] [723] [724] [725] [726] [727] [728] [729] [730] [731] [732]) (./pbeparm_8h.tex <./pbeparm_8h__incl.pdf> [733] <./pbeparm_8h__dep__incl.pdf> [734] Underfull \hbox (badness 10000) detected at line 88 [][][] Underfull \hbox (badness 10000) detected at line 91 [][][] Underfull \hbox (badness 10000) detected at line 94 [][][] [735]) (./pbeparm_8h_source.tex [736] [737]) (./pbsamparm_8c.tex <./pbsamparm_8 c__incl.pdf> [738] [739] Underfull \hbox (badness 10000) detected at line 49 [][][] Underfull \hbox (badness 10000) detected at line 52 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] [740]) (./pbsamparm_8c_source.tex [741] [742] [743]) (./pbsamparm_8h.tex <./pbs amparm_8h__incl.pdf> <./pbsamparm_8h__dep__incl.pdf> [744] [745] Underfull \hbox (badness 10000) detected at line 86 [][][] Underfull \hbox (badness 10000) detected at line 89 [][][] Underfull \hbox (badness 10000) detected at line 92 [][][] [746]) (./pbsamparm_8h_source.tex [747]) (./vacc_8c.tex <./vacc_8c__incl.pdf> [748] [749] [750] Underfull \hbox (badness 10000) detected at line 107 [][][] Underfull \hbox (badness 10000) detected at line 110 [][][] Underfull \hbox (badness 10000) detected at line 113 [][][] [751] Underfull \hbox (badness 10000) detected at line 181 [][][] Underfull \hbox (badness 10000) detected at line 184 [][][] Underfull \hbox (badness 10000) detected at line 210 [][][] Underfull \hbox (badness 10000) detected at line 213 [][][] [752] [753]) (./vacc_8c_source.tex [754] [755] [756] [757] [758] [759] [760] [761] [762] [763] [764] [765] [766] [767] [768] [769] [770] [771] [772] [773] [774] [775] [776]) (./vacc_8h.tex <./vacc_8h__incl.pdf> <./vacc_8h__dep__ incl.pdf> [777] [778] [779] Underfull \hbox (badness 10000) detected at line 123 [][][] Underfull \hbox (badness 10000) detected at line 126 [][][] Underfull \hbox (badness 10000) detected at line 129 [][][] [780]) (./vacc_8h_source.tex [781] [782] [783]) (./valist_8c.tex [784] <./valis t_8c__incl.pdf> [785] Underfull \hbox (badness 10000) detected at line 82 [][][] Underfull \hbox (badness 10000) detected at line 85 [][][] Underfull \hbox (badness 10000) detected at line 88 [][][] [786] [787] [788]) (./valist_8c_source.tex [789] [790] [791] [792] [793] [794] [795] [796] [797] [798]) (./valist_8h.tex [799] <./valist_8h__incl.pdf> < ./valist_8h__dep__incl.pdf> [800] Underfull \hbox (badness 10000) detected at line 77 [][][] Underfull \hbox (badness 10000) detected at line 80 [][][] Underfull \hbox (badness 10000) detected at line 83 [][][] [801]) (./valist_8h_source.tex [802] [803]) (./vatom_8c.tex <./vatom_8c__incl.p df> [804] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [805]) (./vatom_8c_source.tex [806] [807] [808]) (./vatom_8h.tex <./vatom_8h__i ncl.pdf> [809] <./vatom_8h__dep__incl.pdf> [810] [811] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] ) (./vatom_8h_source.tex [812] [813]) (./vcap_8c.tex <./vcap_8c__incl.pdf> [814] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [815]) (./vcap_8c_source.tex [816]) (./vcap_8h.tex <./vcap_8h__incl.pdf> <./vca p_8h__dep__incl.pdf> [817] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [818] Underfull \hbox (badness 10000) detected at line 53 [][][] ) (./vcap_8h_source.tex [819]) (./vclist_8c.tex <./vclist_8c__incl.pdf> [820] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] [821] [822]) (./vclist_8c_source.tex [823] [824] [825] [826] [827] [828]) (./vclist_8h.tex <./vclist_8h__incl.pdf> <./vclist_8h__dep__incl.pdf> [829] [830] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [831]) (./vclist_8h_source.tex [832]) (./vgreen_8c.tex [833] <./vgreen_8c__incl .pdf> [834] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] [835]) (./vgreen_8c_source.tex [836] [837] [838] [839] [840] [841]) (./vgreen_8h.tex <./vgreen_8h__incl.pdf> [842] <./vgreen_8h__dep__incl.pdf> [843] Underfull \hbox (badness 10000) detected at line 72 [][][] Underfull \hbox (badness 10000) detected at line 75 [][][] ) (./vgreen_8h_source.tex [844]) (./vhal_8h.tex [845] <./vhal_8h__incl.pdf> <./ vhal_8h__dep__incl.pdf> [846] [847] [848] [849] Underfull \hbox (badness 10000) detected at line 303 [][][] Underfull \hbox (badness 10000) detected at line 306 [][][] Underfull \hbox (badness 10000) detected at line 309 [][][] Overfull \hbox (1744.08377pt too wide) in paragraph at lines 318--318 []\T1/pcr/m/n/8 * Copyright (c) 2010-2020 Battelle Memorial Institute. Develop ed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyrig ht (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regen ts of the University of California. Portions Copyright (c) 1995, Michael Holst. [] [850] [851] [852] [853] [854] [855] [856]) (./vhal_8h_source.tex [857] [858] [859] [860] [861] [862] [863] [864] [865]) (./vmatrix_8h.tex <./vmatrix_8h__dep __incl.pdf> Underfull \hbox (badness 10000) detected at line 36 [][][] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] [866] [867]) (./vmatrix_8h_source.tex [868]) (./vparam_8c.tex <./vparam_8c__inc l.pdf> [869] [870] Underfull \hbox (badness 10000) detected at line 78 [][][] Underfull \hbox (badness 10000) detected at line 81 [][][] Underfull \hbox (badness 10000) detected at line 84 [][][] [871]) (./vparam_8c_source.tex [872] [873] [874] [875] [876] [877] [878] [879]) (./vparam_8h.tex <./vparam_8h__incl.pdf> <./vparam_8h__dep__incl.pdf> [880] [881] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] Underfull \hbox (badness 10000) detected at line 102 [][][] [882]) (./vparam_8h_source.tex [883] [884]) (./vpbe_8c.tex <./vpbe_8c__incl.pdf > [885] [886] Underfull \hbox (badness 10000) detected at line 90 [][][] Underfull \hbox (badness 10000) detected at line 93 [][][] Underfull \hbox (badness 10000) detected at line 96 [][][] ) (./vpbe_8c_source.tex [887] [888] [889] [890] [891] [892] [893]) (./vpbe_8h.tex <./vpbe_8h__incl.pdf> <./vpbe_8h__dep__incl.pdf> [894] [895] [896] Underfull \hbox (badness 10000) detected at line 111 [][][] Underfull \hbox (badness 10000) detected at line 114 [][][] Underfull \hbox (badness 10000) detected at line 117 [][][] ) (./vpbe_8h_source.tex [897] [898] [899]) (./vstring_8c.tex <./vstring_8c__inc l.pdf> [900] Underfull \hbox (badness 10000) detected at line 31 [][][] Underfull \hbox (badness 10000) detected at line 34 [][][] Underfull \hbox (badness 10000) detected at line 37 [][][] [901]) (./vstring_8c_source.tex [902] [903]) (./vstring_8h.tex <./vstring_8h__i ncl.pdf> [904] <./vstring_8h__dep__incl.pdf> Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [905] Underfull \hbox (badness 10000) detected at line 47 [][][] ) (./vstring_8h_source.tex [906]) (./vunit_8h.tex <./vunit_8h__dep__incl.pdf> [907] LaTeX Warning: Command \r invalid in math mode on input line 42. Missing character: There is no Šin font cmr9! Underfull \hbox (badness 10000) detected at line 50 [][][] Underfull \hbox (badness 10000) detected at line 55 [][][] Underfull \hbox (badness 10000) detected at line 58 [][][] [908]) (./vunit_8h_source.tex) (./main_8c.tex <./main_8c__incl.pdf> [909] Underfull \hbox (badness 10000) detected at line 28 [][][] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] [910]) (./main_8c_source.tex [911] [912] [913] [914] [915] [916] [917] [918] [919] [920] [921]) (./vgrid_8c.tex <./vgrid_8c__incl.pdf> [922] [923] Underfull \hbox (badness 10000) detected at line 84 [][][] Underfull \hbox (badness 10000) detected at line 87 [][][] Underfull \hbox (badness 10000) detected at line 90 [][][] [924] Underfull \hbox (badness 10000) detected at line 178 [][][] [925]) (./vgrid_8c_source.tex [926] [927] [928] [929] [930] [931] [932] [933] [934] [935] [936] [937] [938] [939] [940] [941] [942] [943] [944] [945] [946] [947] [948]) (./vgrid_8h.tex [949] <./vgrid_8h__incl.pdf> <./vgrid_ 8h__dep__incl.pdf> [950] [951] Underfull \hbox (badness 10000) detected at line 93 [][][] [952] Underfull \hbox (badness 10000) detected at line 96 [][][] Underfull \hbox (badness 10000) detected at line 99 [][][] [953] Underfull \hbox (badness 10000) detected at line 167 [][][] ) (./vgrid_8h_source.tex [954]) (./vmgrid_8c.tex [955] <./vmgrid_8c__incl.pdf> [956] Underfull \hbox (badness 10000) detected at line 41 [][][] Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] Overfull \hbox (1024.08331pt too wide) in paragraph at lines 59--59 []\T1/pcr/m/n/8 * Copyright (c) 2010, Pacific Northwest National Laboratory. Portions Copyright (c) 2002-2020, Washington University in St. Louis. Portions Copyright (c) 2002-2010, Nathan A. Baker. Portions Copyright (c) 1999-2020, T he Regents of the University of California. Portions Copyright (c) 1995, Michae l Holst.[] ) (./vmgrid_8c_source.tex [957] [958] [959]) (./vmgrid_8h.tex <./vmgrid_8h__inc l.pdf> <./vmgrid_8h__dep__incl.pdf> [960] [961] Underfull \hbox (badness 10000) detected at line 71 [][][] Underfull \hbox (badness 10000) detected at line 74 [][][] Underfull \hbox (badness 10000) detected at line 77 [][][] [962]) (./vmgrid_8h_source.tex) (./vopot_8c.tex [963] <./vopot_8c__incl.pdf> Underfull \hbox (badness 10000) detected at line 44 [][][] Underfull \hbox (badness 10000) detected at line 47 [][][] Underfull \hbox (badness 10000) detected at line 50 [][][] [964]) (./vopot_8c_source.tex [965] [966] [967] [968] [969]) (./vopot_8h.tex <. /vopot_8h__incl.pdf> <./vopot_8h__dep__incl.pdf> [970] [971] Underfull \hbox (badness 10000) detected at line 65 [][][] Underfull \hbox (badness 10000) detected at line 68 [][][] Underfull \hbox (badness 10000) detected at line 71 [][][] ) (./vopot_8h_source.tex [972]) (./vpmg_8c.tex <./vpmg_8c__incl.pdf> [973] [974] [975] [976] Underfull \hbox (badness 10000) detected at line 173 [][][] Underfull \hbox (badness 10000) detected at line 176 [][][] Underfull \hbox (badness 10000) detected at line 179 [][][] [977] Underfull \hbox (badness 10000) detected at line 263 [][][] [978] Underfull \hbox (badness 10000) detected at line 290 [][][] [979] Underfull \hbox (badness 10000) detected at line 386 [][][] Underfull \hbox (badness 10000) detected at line 389 [][][] Underfull \hbox (badness 10000) detected at line 411 [][][] Underfull \hbox (badness 10000) detected at line 414 [][][] [980] Underfull \hbox (badness 10000) detected at line 436 [][][] Underfull \hbox (badness 10000) detected at line 439 [][][] Underfull \hbox (badness 10000) detected at line 461 [][][] Underfull \hbox (badness 10000) detected at line 464 [][][] [981] Underfull \hbox (badness 10000) detected at line 486 [][][] Underfull \hbox (badness 10000) detected at line 489 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] Underfull \hbox (badness 10000) detected at line 514 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 539 [][][] Underfull \hbox (badness 10000) detected at line 556 [][][] [982] Underfull \hbox (badness 10000) detected at line 559 [][][] Underfull \hbox (badness 10000) detected at line 576 [][][] Underfull \hbox (badness 10000) detected at line 593 [][][] Underfull \hbox (badness 10000) detected at line 610 [][][] Underfull \hbox (badness 10000) detected at line 627 [][][] [983] Underfull \hbox (badness 10000) detected at line 644 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 699 [][][] Underfull \hbox (badness 10000) detected at line 702 [][][] [984] Underfull \hbox (badness 10000) detected at line 719 [][][] Underfull \hbox (badness 10000) detected at line 736 [][][] Underfull \hbox (badness 10000) detected at line 753 [][][] Underfull \hbox (badness 10000) detected at line 770 [][][] Underfull \hbox (badness 10000) detected at line 797 [][][] [985] Underfull \hbox (badness 10000) detected at line 834 [][][] [986] Underfull \hbox (badness 10000) detected at line 878 [][][] [987] Underfull \hbox (badness 10000) detected at line 928 [][][] Underfull \hbox (badness 10000) detected at line 950 [][][] [988] Underfull \hbox (badness 10000) detected at line 972 [][][] Underfull \hbox (badness 10000) detected at line 994 [][][] Underfull \hbox (badness 10000) detected at line 997 [][][] Underfull \hbox (badness 10000) detected at line 1014 [][][] Underfull \hbox (badness 10000) detected at line 1017 [][][] [989] Underfull \hbox (badness 10000) detected at line 1039 [][][] Underfull \hbox (badness 10000) detected at line 1042 [][][] Underfull \hbox (badness 10000) detected at line 1064 [][][] Underfull \hbox (badness 10000) detected at line 1067 [][][] [990] Underfull \hbox (badness 10000) detected at line 1099 [][][] Underfull \hbox (badness 10000) detected at line 1116 [][][] Underfull \hbox (badness 10000) detected at line 1148 [][][] [991] Underfull \hbox (badness 10000) detected at line 1151 [][][] ) (./vpmg_8c_source.tex [992] [993] [994] [995] [996] [997] [998] [999] [1000] [1001] [1002] [1003] [1004] [1005] [1006] [1007] [1008] [1009] [1010] [1011] [1012] [1013] [1014] [1015] [1016] [1017] [1018] [1019] [1020] [1021] [1022] [1023] [1024] [1025] [1026] [1027] [1028] [1029] [1030] [1031] [1032] [1033] [1034] [1035] [1036] [1037] [1038] [1039] [1040] [1041] [1042] [1043] [1044] [1045] [1046] [1047] [1048] [1049] [1050] [1051] [1052] [1053] [1054] [1055] [1056] [1057] [1058] [1059] [1060] [1061] [1062] [1063] [1064] [1065] [1066] [1067] [1068] [1069] [1070] [1071] [1072] [1073] [1074] [1075] [1076] [1077] [1078] [1079] [1080] [1081] [1082] [1083] [1084] [1085] [1086] [1087] [1088] [1089] [1090] [1091] [1092] [1093] [1094] [1095] [1096] [1097] [1098] [1099] [1100] [1101] [1102] [1103] [1104] [1105] [1106] [1107] [1108] [1109] [1110] [1111] [1112] [1113] [1114] [1115] [1116] [1117] [1118] [1119] [1120] [1121] [1122] [1123] [1124] [1125] [1126] [1127]) (./vpmg_8h.tex <./vpmg_8h__in cl.pdf> <./vpmg_8h__dep__incl.pdf> [1128] [1129] [1130] [1131] [1132] [1133] Underfull \hbox (badness 10000) detected at line 235 [][][] Underfull \hbox (badness 10000) detected at line 238 [][][] Underfull \hbox (badness 10000) detected at line 241 [][][] [1134] [1135] Underfull \hbox (badness 10000) detected at line 445 [][][] [1136] Underfull \hbox (badness 10000) detected at line 462 [][][] Underfull \hbox (badness 10000) detected at line 508 [][][] Underfull \hbox (badness 10000) detected at line 511 [][][] [1137] Underfull \hbox (badness 10000) detected at line 533 [][][] Underfull \hbox (badness 10000) detected at line 536 [][][] Underfull \hbox (badness 10000) detected at line 558 [][][] Underfull \hbox (badness 10000) detected at line 561 [][][] Underfull \hbox (badness 10000) detected at line 583 [][][] Underfull \hbox (badness 10000) detected at line 586 [][][] [1138] Underfull \hbox (badness 10000) detected at line 608 [][][] Underfull \hbox (badness 10000) detected at line 611 [][][] Underfull \hbox (badness 10000) detected at line 633 [][][] Underfull \hbox (badness 10000) detected at line 636 [][][] Underfull \hbox (badness 10000) detected at line 658 [][][] Underfull \hbox (badness 10000) detected at line 661 [][][] [1139] Underfull \hbox (badness 10000) detected at line 678 [][][] Underfull \hbox (badness 10000) detected at line 681 [][][] Underfull \hbox (badness 10000) detected at line 698 [][][] Underfull \hbox (badness 10000) detected at line 715 [][][] Underfull \hbox (badness 10000) detected at line 732 [][][] Underfull \hbox (badness 10000) detected at line 749 [][][] [1140] Underfull \hbox (badness 10000) detected at line 766 [][][] Underfull \hbox (badness 10000) detected at line 783 [][][] Underfull \hbox (badness 10000) detected at line 800 [][][] Underfull \hbox (badness 10000) detected at line 821 [][][] Underfull \hbox (badness 10000) detected at line 824 [][][] [1141] Underfull \hbox (badness 10000) detected at line 841 [][][] Underfull \hbox (badness 10000) detected at line 858 [][][] Underfull \hbox (badness 10000) detected at line 875 [][][] Underfull \hbox (badness 10000) detected at line 892 [][][] Underfull \hbox (badness 10000) detected at line 909 [][][] [1142] Underfull \hbox (badness 10000) detected at line 922 [][][] Underfull \hbox (badness 10000) detected at line 935 [][][] Underfull \hbox (badness 10000) detected at line 952 [][][] [1143] Underfull \hbox (badness 10000) detected at line 996 [][][] Underfull \hbox (badness 10000) detected at line 1026 [][][] [1144] Underfull \hbox (badness 10000) detected at line 1048 [][][] Underfull \hbox (badness 10000) detected at line 1070 [][][] Underfull \hbox (badness 10000) detected at line 1092 [][][] [1145] Underfull \hbox (badness 10000) detected at line 1095 [][][] Underfull \hbox (badness 10000) detected at line 1112 [][][] Underfull \hbox (badness 10000) detected at line 1115 [][][] Underfull \hbox (badness 10000) detected at line 1137 [][][] Underfull \hbox (badness 10000) detected at line 1140 [][][] Underfull \hbox (badness 10000) detected at line 1162 [][][] [1146] Underfull \hbox (badness 10000) detected at line 1165 [][][] Underfull \hbox (badness 10000) detected at line 1197 [][][] Underfull \hbox (badness 10000) detected at line 1214 [][][] [1147] Underfull \hbox (badness 10000) detected at line 1246 [][][] Underfull \hbox (badness 10000) detected at line 1249 [][][] ) (./vpmg_8h_source.tex [1148] [1149] [1150] [1151] [1152] [1153] [1154] [1155] [1156]) (./vpmgp_8c.tex <./vpmgp_8c__incl.pdf> [1157] [1158] Underfull \hbox (badness 10000) detected at line 39 [][][] Underfull \hbox (badness 10000) detected at line 42 [][][] Underfull \hbox (badness 10000) detected at line 45 [][][] [1159]) (./vpmgp_8c_source.tex [1160] [1161] [1162]) (./vpmgp_8h.tex <./vpmgp_8 h__incl.pdf> [1163] <./vpmgp_8h__dep__incl.pdf> [1164] [1165] Underfull \hbox (badness 10000) detected at line 58 [][][] Underfull \hbox (badness 10000) detected at line 61 [][][] Underfull \hbox (badness 10000) detected at line 64 [][][] Underfull \hbox (badness 10000) detected at line 67 [][][] [1166]) (./vpmgp_8h_source.tex [1167]) (./build_ad_8c_source.tex [1168] [1169] [1170]) (./build_ad_8h_source.tex [1171] [1172]) (./build_bd_8c_source.tex [1173] [1174] [1175]) (./build_bd_8h_source.tex [1176]) (./build_gd_8c_source.tex [1177] [1178] [1179] [1180] [1181] [1182] [1183] [1184] [1185] [1186] [1187] [1188] [1189] [1190] [1191] [1192] [1193] [1194] [1195] [1196] [1197] [1198] [1199] [1200] [1201] [1202] [1203] [1204] [1205] [1206] [1207] [1208] [1209] [1210] [1211] [1212] [1213] [1214]) (./build_gd_8h_source.tex [1215] [1216]) (./build_pd_8c_source.tex [1217] [1218] [1219] [1220] [1221] [1222] [1223] [1224] [1225] [1226] [1227] [1228] [1229] [1230] [1231] [1232] [1233] [1234] [1235]) (./build_pd_8h_source.tex [1236] [1237] [1238]) (./cgd_8c_source.tex [1239]) (./cgd_8h_source.tex) (./gsd_8c_source.tex [1240] [1241] [1242] [1243]) (./gsd_8h_source.tex [1244]) (./matvecd_8c_source.tex [1245] [1246] [1247] [1248] [1249] [1250] [1251] [1252] [1253] [1254] [1255] [1256] [1257]) (./matvecd_8h_source.tex [1258] [1259] [1260] [1261] [1262] [1263]) (./mgcsd_8c_source.tex [1264] [1265] [1266] [1267] [1268] [1269]) (./mgcsd_8h_source.tex [1270]) (./mgdrvd_8c_source.tex [1271] [1272] [1273] [1274] [1275] [1276] [1277] [1278]) (./mgdrvd_8h_source.tex [1279]) (./mgfasd_8c_source.tex [1280] [1281] [1282] [1283] [1284] [1285] [1286]) (./mgfasd_8h_source.tex [1287]) (./mgsubd_8c_source.tex [1288] [1289] [1290] [1291] [1292] [1293] [1294] [1295] [1296] [1297] [1298] [1299]) (./mgsubd_8h_source.tex [1300] [1301] [1302]) (./mikpckd_8c_source.tex [1303] [1304] [1305] [1306] [1307]) (./mikpckd_8h_source.tex [1308] [1309]) (./mlinpckd_8c_source.tex [1310] [1311]) (./mlinpckd_8h_source.tex [1312]) (./mypdec_8c_source.tex [1313] [1314] [1315] [1316] [1317] [1318]) (./mypdec_8h_source.tex [1319] [1320]) (./newdrvd_8c_source.tex [1321] [1322] [1323]) (./newdrvd_8h_source.tex [1324]) (./newtond_8c_source.tex [1325] [1326] [1327] [1328] [1329] [1330] [1331]) (./newtond_8h_source.tex [1332] [1333]) (./powerd_8c_source.tex [1334] [1335] [1336] [1337]) (./powerd_8h_source.tex [1338] [1339]) (./smoothd_8c_source.tex [1340]) (./smoothd_8h_source.tex) (./routines_8c.tex [1341] <./routines_8c__incl.pdf> Underfull \hbox (badness 1237) in paragraph at lines 48--49 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][[]][], [] $\OMS/cmsy/m/n/10 ^ ^C$\T1/phv/m/n/10 pmgp[][[]][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][[ ]][], [] [1342] Overfull \hbox (15.32974pt too wide) in paragraph at lines 68--69 \T1/phv/m/n/10 dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble diel[]Energy[][[]][] Underfull \hbox (badness 824) in paragraph at lines 68--69 \T1/phv/m/n/10 , int nenergy[][[]][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n /10 atom[]Energy[][[]][], int nforce[][[]][] Overfull \hbox (19.8584pt too wide) in paragraph at lines 70--71 \T1/phv/m/n/10 , dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-bl e diel[]Energy[][[]][] Underfull \hbox (badness 824) in paragraph at lines 70--71 \T1/phv/m/n/10 , int nenergy[][[]][], dou-ble $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n /10 atom[]Energy[][[]][], int nforce[][[]][] [1343] Underfull \hbox (badness 10000) detected at line 117 [][][] Underfull \hbox (badness 10000) detected at line 120 [][][] [1344] Underfull \hbox (badness 10000) detected at line 123 [][][] ) (./routines_8c_source.tex [1345] [1346] [1347] [1348] [1349] [1350] [1351] [1352] [1353] [1354] [1355] [1356] [1357] [1358] [1359] [1360] [1361] [1362] [1363] [1364] [1365] [1366] [1367] [1368] [1369] [1370] [1371] [1372] [1373] [1374] [1375] [1376] [1377] [1378] [1379] [1380] [1381] [1382] [1383] [1384] [1385] [1386] [1387] [1388] [1389] [1390] [1391] [1392] [1393] [1394] [1395] [1396] [1397] [1398] [1399] [1400] [1401] [1402] [1403] [1404] [1405] [1406] [1407] [1408] [1409] [1410] [1411] [1412]) (./routines_8h.tex [1413] <./routine s_8h__incl.pdf> <./routines_8h__dep__incl.pdf> [1414] Underfull \hbox (badness 5175) in paragraph at lines 52--53 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n/ 10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 5091) in paragraph at lines 54--55 []\T1/phv/m/n/10 VEXTERNC void [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh , [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 diel[]XMap[][[]][], [] $\OMS/cmsy/m/n /10 ^^C$\T1/phv/m/n/10 diel[]YMap[] Underfull \hbox (badness 1237) in paragraph at lines 72--73 \OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 charge[]Map[][[]][], [] $\OMS/cmsy/m/n/10 ^ ^C$\T1/phv/m/n/10 pmgp[][[]][], [] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 pmg[][[ ]][], [] Underfull \hbox (badness 4634) in paragraph at lines 90--91 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 90--91 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble [1415] Underfull \hbox (badness 3907) in paragraph at lines 92--93 []\T1/phv/m/n/10 VEXTERNC int [] ([] $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 nosh, Vcom $\OMS/cmsy/m/n/10 ^^C$\T1/phv/m/n/10 com, const char $\OMS/cmsy/m/n/10 ^^ C$\T1/phv/m/n/10 fname, dou-ble tot[]Energy[] Underfull \hbox (badness 4660) in paragraph at lines 92--93 \T1/phv/m/n/10 [[]][], dou-ble qf[]Energy[][[]][], dou-ble qm[]Energy[][[]][], dou-ble [1416] Underfull \hbox (badness 10000) detected at line 147 [][][] Underfull \hbox (badness 10000) detected at line 150 [][][] Underfull \hbox (badness 10000) detected at line 153 [][][] [1417]) (./routines_8h_source.tex [1418] [1419] [1420] [1421]) [1422] (./refman.ind [1423] [1424] [1425] [1426] [1427] [1428] [1429] [1430] [1431] [1432] [1433] [1434] [1435] [1436] [1437] [1438] [1439] [1440] [1441] [1442] [1443] [1444] [1445] [1446] [1447] [1448] [1449] [1450] [1451] [1452] [1453] [1454] [1455] [1456] [1457] [1458] [1459] [1460] [1461] [1462] [1463] [1464] [1465] [1466] [1467] [1468] [1469] [1470] [1471]) (./refman.aux) ) (see the transcript file for additional information)< /usr/share/texlive/texmf-dist/fonts/type1/urw/courier/ucrro8a.pfb> Output written on refman.pdf (1529 pages, 6459098 bytes). Transcript written on refman.log. + RPM_EC=0 ++ jobs -p + exit 0 + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + '[' /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT '!=' / ']' + rm -rf /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT ++ dirname /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT + mkdir -p /builddir/build/BUILD/apbs-3.0.0-build + mkdir /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd apbs-3.0.0 + DESTDIR=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT + /usr/bin/cmake --install redhat-linux-build + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/coulomb + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/coulomb /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-coulomb + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/coulomb + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/born + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/born /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-born + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/born + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mgmesh + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mgmesh /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-mgmesh + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mgmesh + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dxmath + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dxmath /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-dxmath + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dxmath + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx2 + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx2 /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-mergedx2 + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx2 + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-mergedx + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/value + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/value /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-value + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/value + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/uhbd_asc2bin + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/uhbd_asc2bin /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-uhbd_asc2bin + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/uhbd_asc2bin + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/smooth + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/smooth /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-smooth + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/smooth + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2mol + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2mol /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-dx2mol + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2mol + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2uhbd + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2uhbd /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-dx2uhbd + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2uhbd + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/similarity + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/similarity /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-similarity + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/similarity + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/multivalue + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/multivalue /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-multivalue + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/multivalue + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/benchmark + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/benchmark /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-benchmark + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/benchmark + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/analysis + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/analysis /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-analysis + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/analysis + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/del2dx + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/del2dx /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-del2dx + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/del2dx + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/tensor2dx + cp -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/tensor2dx /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-tensor2dx + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/tensor2dx + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-coulomb + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-born + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-mgmesh + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-dxmath + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-mergedx2 + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-mergedx + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-value + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-uhbd_asc2bin + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-smooth + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-dx2mol + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-dx2uhbd + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-similarity + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-multivalue + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-benchmark + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-analysis + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-del2dx + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + for bin in /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-tensor2dx + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs + chrpath -d /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/libapbs.so.1 + mkdir -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/python3.15/site-packages/apbs + install -pm 755 tools/manip/psize.py /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/python3.15/site-packages/apbs/ Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.tjaLIc -- Install configuration: "Release" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/nosh.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/mgparm.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/femparm.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/pbamparm.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/pbsamparm.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/pbeparm.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/bemparm.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/geoflowparm.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/apolparm.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vacc.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/valist.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vatom.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vpbe.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vcap.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vclist.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vstring.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vparam.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vgreen.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vmatrix.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vhal.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/generic/vunit.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/buildAd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/buildBd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/buildGd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/buildPd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/cgd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/gsd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/matvecd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/mgcsd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/mgdrvd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/mgsubd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/mikpckd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/mlinpckd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/mypdec.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/newtond.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/newdrvd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/powerd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/smoothd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/pmgc/mgfasd.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/mg/vgrid.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/mg/vmgrid.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/mg/vopot.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/mg/vpmg.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/mg/vpmgp.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/libapbs.so.1 -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/libapbs.so.1" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/libapbs.so -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/apbscfg.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/apbs.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/apbs/routines.h -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mgmesh -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mgmesh" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/smooth -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/smooth" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dxmath -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dxmath" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx2 -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/mergedx2" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/value -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/value" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/multivalue -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/multivalue" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/benchmark -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/benchmark" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/similarity -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/similarity" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/analysis -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/analysis" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2mol -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2mol" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2uhbd -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/dx2uhbd" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/del2dx -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/del2dx" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/tensor2dx -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/tensor2dx" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/uhbd_asc2bin -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/uhbd_asc2bin" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/coulomb -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/coulomb" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/born -- Set non-toolchain portion of runtime path of "/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/born" to "/usr/lib" -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/programmer.pdf -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vunit_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vstring_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vstring_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vpmgp_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vpmgp_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vpmg_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vpmg_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vpee_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vpee_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vpbe_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vpbe_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vparam_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vparam_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vopot_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vopot_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vmgrid_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vmgrid_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vmatrix_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vhal_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vgrid_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vgrid_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vgreen_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vgreen_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vfetk_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vfetk_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vcsm_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vcsm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vclist_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vclist_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vcap_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vcap_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vatom_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vatom_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/valist_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/valist_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vacc_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/vacc_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/routines_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/routines_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/pbsamparm_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/pbsamparm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/pbeparm_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/pbeparm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/pbamparm_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/pbamparm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/nosh_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/nosh_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/mgparm_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/mgparm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/main_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/geoflowparm_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/geoflowparm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/femparm_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/femparm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_e7eac49c1a1228b34aea87d37b387ddc.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_68267d1309a1af8e8297ef4c3efbcdba.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_5c54498a5f003097a138165fef7dee16.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_4075b182e53a3873a42d885f4e1e98c4.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_325c623946aaadef5114ca9e069898d6.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_1d197ef0d9947f4cc1ac44e7f59e2b57.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/bemparm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/apolparm_8c.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/apbs_8h.html -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_68267d1309a1af8e8297ef4c3efbcdba_dep.md5 -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_5c54498a5f003097a138165fef7dee16_dep.md5 -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_e7eac49c1a1228b34aea87d37b387ddc_dep.md5 -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs/doc/programmer/html/dir_1d197ef0d9947f4cc1ac44e7f59e2b57_dep.md5 -- Installing: 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/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib/libiapbs.a -- Installing: /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/include/iapbs/apbs_driver.h + /usr/bin/python3 /usr/lib/rpm/redhat/pathfix.py -pn -i /usr/bin/python3 /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/python3.15/site-packages/apbs/psize.py + ln -s /usr/lib64/python3.15/site-packages/apbs/psize.py /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin/apbs-psize.py + install -pm 755 redhat-linux-build/lib/_apbslib.so /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/python3.15/site-packages/apbs/ + rm -rf /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/apbs ++ find /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT -type f '(' -name '*.a' ')' + for i in `find /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT -type f \( -name "*.a" \)` + rm -f /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib/libiapbs.a + /usr/bin/find-debuginfo -j5 --strict-build-id -m -i --build-id-seed 3.0.0-38.fc45 --unique-debug-suffix -3.0.0-38.fc45.ppc64le --unique-debug-src-base apbs-3.0.0-38.fc45.ppc64le --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 --remove-section .gnu.build.attributes -S debugsourcefiles.list /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0 /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/python3.15/site-packages/apbs/psize.py: updating find-debuginfo: starting Extracting debug info from 20 files DWARF-compressing 20 files sepdebugcrcfix: Updated 20 CRC32s, 0 CRC32s did match. Creating .debug symlinks for symlinks to ELF files Copying sources found by 'debugedit -l' to /usr/src/debug/apbs-3.0.0-38.fc45.ppc64le find-debuginfo: done + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig + COMPRESS='gzip -9 -n' + COMPRESS_EXT=.gz + /usr/lib/rpm/brp-compress + /usr/lib/rpm/redhat/brp-strip-lto /usr/bin/strip + /usr/lib/rpm/check-rpaths + /usr/lib/rpm/redhat/brp-mangle-shebangs + /usr/lib/rpm/brp-remove-la-files + /usr/lib/rpm/redhat/brp-python-rpm-in-distinfo + env /usr/lib/rpm/redhat/brp-python-bytecompile '' 1 0 -j5 Bytecompiling .py files below /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib/debug/usr/lib64/python3.15 using python3.15 Bytecompiling .py files below /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/python3.15 using python3.15 + /usr/lib/rpm/redhat/brp-python-hardlink + /usr/bin/add-det --brp -j5 /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64/python3.15/site-packages/apbs/__pycache__/psize.cpython-315.opt-1.pyc: rewriting with normalized contents Scanned 39 directories and 198 files, processed 1 inodes, 1 modified (0 replaced + 1 rewritten), 0 unsupported format, 0 errors + /usr/bin/linkdupes --brp /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr Scanned 38 directories and 198 files, considered 196 files, read 98 files, linked 43 files, 0 errors sum of sizes of linked files: 526479 bytes Reading /builddir/build/BUILD/apbs-3.0.0-build/SPECPARTS/rpm-debuginfo.specpart Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.41qeoR + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + CFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CFLAGS + CXXFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection ' + export CXXFLAGS ~/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/tests ~/build/BUILD/apbs-3.0.0-build/apbs-3.0.0 + FFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FFLAGS + FCFLAGS='-O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Wp,-U_FORTIFY_SOURCE,-D_FORTIFY_SOURCE=3 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -fcommon -m64 -mcpu=power8 -mtune=power8 -fasynchronous-unwind-tables -fstack-clash-protection -I/usr/lib64/gfortran/modules ' + export FCFLAGS + VALAFLAGS=-g + export VALAFLAGS + RUSTFLAGS='-Copt-level=3 -Cdebuginfo=2 -Ccodegen-units=1 -Cstrip=none -Clink-arg=-specs=/usr/lib/rpm/redhat/redhat-package-notes --cap-lints=warn' + export RUSTFLAGS + LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,pack-relative-relocs -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-hardened-ld-errors -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -Wl,--build-id=sha1 -specs=/usr/lib/rpm/redhat/redhat-package-notes ' + export LDFLAGS + LT_SYS_LIBRARY_PATH=/usr/lib64: + export LT_SYS_LIBRARY_PATH + CC=gcc + export CC + CXX=g++ + export CXX + cd apbs-3.0.0 + pushd tests + export LD_LIBRARY_PATH=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64 + LD_LIBRARY_PATH=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/lib64 + export PATH=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin + PATH=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/bin + /usr/bin/python3 ./apbs_tester.py Testing all sections The following sections will be tested: born, actin-dimer-auto, actin-dimer-parallel, alkanes, FKBP, hca-bind, ionize, ion-pmf, ion-protein, pka-lig, point-pmf, solv ================================================================================ Running tests for born section -------------------------------------------------------------------------------- Testing forces from apbs-forces.in Checking forces for input file apbs-forces.inChecking Polar ForcesChecking Apolar ForcesElapsed time: 0.001285 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: apbs INPUT: apbs-mol-auto.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.607073836227E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200266567971E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to potential.dx.gz Total electrostatic energy = 4.732245131587E+03 kJ/mol Calculating forces... Writing potential to potential.dx.gz ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.297735526282E+02 kJ/mol Global net ELEC energy = -2.297735526282E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-auto.out RESULT 960.7073836227 RESULT 2200.266567971 RESULT 4732.245131587 RESULT 1190.871482831 RESULT 2430.874049735 RESULT 4962.018684215 RESULT -229.7735526282 Testing computed result 9.607073836227E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 2.200266567971E+03 against expected result 2.200267E+03 *** PASSED *** Testing computed result 4.732245131587E+03 against expected result 4.732245E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.297735526282E+02 against expected result -2.297735E+02 *** PASSED *** Elapsed time: 1.289663 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: apbs INPUT: apbs-smol-auto.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.532928767450E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.201243880085E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.733006258977E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.190871482831E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.383 x 0.383 x 0.383 Grid lengths: 24.495 x 24.495 x 24.495 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.430874049735E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.962018684215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -2.290124252387E+02 kJ/mol Global net ELEC energy = -2.290124252387E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-auto.out RESULT 953.292876745 RESULT 2201.243880085 RESULT 4733.006258977 RESULT 1190.871482831 RESULT 2430.874049735 RESULT 4962.018684215 RESULT -229.0124252387 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 2.201243880085E+03 against expected result 2.201244E+03 *** PASSED *** Testing computed result 4.733006258977E+03 against expected result 4.733006E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 2.430874049735E+03 against expected result 2.430874E+03 *** PASSED *** Testing computed result 4.962018684215E+03 against expected result 4.962019E+03 *** PASSED *** Testing computed result -2.290124252387E+02 against expected result -2.290124E+02 *** PASSED *** Elapsed time: 1.105730 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: apbs INPUT: apbs-mol-parallel-PE0.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935592471E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255308186E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864094552E+01 kJ/mol Global net ELEC energy = -5.761864094552E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 2.401768459022E+02 8.142935592471E+02 1.485255308186E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.761864094552E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE1.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459022E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778312125E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246667424E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728170718E+01 kJ/mol Global net ELEC energy = -5.762728170718E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 2.401768459022E+02 8.142778312125E+02 1.485246667424E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.762728170718E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE2.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142935605695E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485255306569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.761864257239E+01 kJ/mol Global net ELEC energy = -5.761864257239E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 2.401768459091E+02 8.142935605695E+02 1.485255306569E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.761864257239E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE3.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.401768459091E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.142778325440E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485246665692E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.762728344953E+01 kJ/mol Global net ELEC energy = -5.762728344953E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 2.401768459091E+02 8.142778325440E+02 1.485246665692E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.762728344953E+01 RESULT 960.7073836226 RESULT 3257.1427835730997 RESULT 5941.0039478710005 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -230.49184867462003 Testing computed result 9.607073836226E+02 against expected result 9.607074E+02 *** PASSED *** Testing computed result 3.257142783573E+03 against expected result 3.257143E+03 *** PASSED *** Testing computed result 5.941003947871E+03 against expected result 5.941004E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.304918486746E+02 against expected result -2.304918E+02 *** PASSED *** Elapsed time: 6.006150 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: apbs INPUT: apbs-smol-parallel-PE0.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369591602E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524998001E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895113069E+01 kJ/mol Global net ELEC energy = -5.734895113069E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 2.383232191816E+02 8.145369591602E+02 1.485524998001E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734895113069E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE1.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191816E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419898332E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328612E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707009E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557588E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, -2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949131E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462051928E+01 kJ/mol Global net ELEC energy = -5.734462051928E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 2.383232191816E+02 8.145419898332E+02 1.485529328612E+03 2.977178707009E+02 8.799304557588E+02 1.542873949131E+03 -5.734462051928E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE2.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145369593489E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485524997676E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (-2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734895146550E+01 kJ/mol Global net ELEC energy = -5.734895146550E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 2.383232191909E+02 8.145369593489E+02 1.485524997676E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734895146550E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE3.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 1 molecules Reading XML-format atom data from ion.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 61.280 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.383232191909E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.145419900310E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #3 (solvated): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.280 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.485529328301E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.781 x 0.781 x 0.781 Grid lengths: 50.000 x 50.000 x 50.000 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977178707146E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.296 x 0.296 x 0.383 Grid lengths: 18.944 x 18.944 x 24.495 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.799304557596E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (reference): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.207 MB total, 122.102 MB high water Using cubic spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 1 Grid dimensions: 65 x 65 x 65 Grid spacings: 0.112 x 0.112 x 0.188 Grid lengths: 7.178 x 7.178 x 12.000 Grid center: (2.411, 2.411, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.542873949141E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (solvated) - 2 (reference) end Local net energy (PE 0) = -5.734462084052E+01 kJ/mol Global net ELEC energy = -5.734462084052E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 0.001 MB total, 122.102 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 2.383232191909E+02 8.145419900310E+02 1.485529328301E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.734462084052E+01 RESULT 953.292876745 RESULT 3258.1578983732998 RESULT 5942.108652589999 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -229.38714395599 Testing computed result 9.532928767450E+02 against expected result 9.532929E+02 *** PASSED *** Testing computed result 3.258157898373E+03 against expected result 3.258158E+03 *** PASSED *** Testing computed result 5.942108652590E+03 against expected result 5.942109E+03 *** PASSED *** Testing computed result 1.190871482831E+03 against expected result 1.190871E+03 *** PASSED *** Testing computed result 3.519721823037E+03 against expected result 3.519722E+03 *** PASSED *** Testing computed result 6.171495796544E+03 against expected result 6.171496E+03 *** PASSED *** Testing computed result -2.293871439560E+02 against expected result -2.293871E+02 *** PASSED *** Elapsed time: 5.998020 seconds -------------------------------------------------------------------------------- Total elapsed time: 14.400848 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-auto section -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: apbs INPUT: apbs-mol-auto.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527617850342E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.919510754196E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.527671844880E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.915468859278E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.056317807611E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.836028296532E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.048683058621E+02 kJ/mol Global net ELEC energy = 1.048683058621E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-auto.out RESULT 152761.7850342 RESULT 291951.0754196 RESULT 152767.184488 RESULT 291546.8859278 RESULT 305631.7807611 RESULT 583602.8296532 RESULT 104.8683058621 Testing computed result 1.527617850342E+05 against expected result 1.527618E+05 *** PASSED *** Testing computed result 2.919510754196E+05 against expected result 2.919511E+05 *** PASSED *** Testing computed result 1.527671844880E+05 against expected result 1.527672E+05 *** PASSED *** Testing computed result 2.915468859278E+05 against expected result 2.915469E+05 *** PASSED *** Testing computed result 3.056317807611E+05 against expected result 3.056318E+05 *** PASSED *** Testing computed result 5.836028296532E+05 against expected result 5.836028E+05 *** PASSED *** Testing computed result 1.048683058621E+02 against expected result 1.048683E+02 *** PASSED *** Elapsed time: 75.930361 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: apbs INPUT: apbs-smol-auto.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-auto.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 1028.322 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.528632421825E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1028.322 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.920618662320E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2042.113 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.529297900572E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1030.291 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.916592202835E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2046.048 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.975 x 0.756 x 1.012 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.059244262535E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 1046.446 MB total, 2069.492 MB high water Using linear spline charge discretization. Grid dimensions: 161 x 161 x 161 Grid spacings: 0.700 x 0.569 x 0.725 Grid lengths: 112.000 x 91.000 x 116.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.838306706232E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 2 (mol2) - 1 (mol1) end Local net energy (PE 0) = 1.095841077688E+02 kJ/mol Global net ELEC energy = 1.095841077688E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 2069.492 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-auto.out RESULT 152863.2421825 RESULT 292061.866232 RESULT 152929.7900572 RESULT 291659.2202835 RESULT 305924.4262535 RESULT 583830.6706232 RESULT 109.5841077688 Testing computed result 1.528632421825E+05 against expected result 1.528632E+05 *** PASSED *** Testing computed result 2.920618662320E+05 against expected result 2.920619E+05 *** PASSED *** Testing computed result 1.529297900572E+05 against expected result 1.529298E+05 *** PASSED *** Testing computed result 2.916592202835E+05 against expected result 2.916592E+05 *** PASSED *** Testing computed result 3.059244262535E+05 against expected result 3.059244E+05 *** PASSED *** Testing computed result 5.838306706232E+05 against expected result 5.838307E+05 *** PASSED *** Testing computed result 1.095841077688E+02 against expected result 1.095841E+02 *** PASSED *** Elapsed time: 63.122982 seconds -------------------------------------------------------------------------------- Total elapsed time: 139.053343 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-parallel section -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: apbs INPUT: apbs-mol-parallel-PE0.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.335181353180E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.307364296734E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.892640552270E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.287358143371E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.237489755360E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595556932858E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.344927525614E+00 kJ/mol Global net ELEC energy = 8.344927525614E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE0.out Processor 0 results: 1.335181353180E+03 1.307364296734E+04 2.892640552270E+03 2.287358143371E+04 4.237489755360E+03 3.595556932858E+04 8.344927525614E+00 BINARY: apbs INPUT: apbs-mol-parallel-PE1.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161150884899E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.271350510933E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.084559511557E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.159029781186E-02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.161009682231E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.271251267660E+04 kJ/mol Calculating forces... Writing potential to pot-PE1.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -9.008424333884E-01 kJ/mol Global net ELEC energy = -9.008424333884E-01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE1.out Processor 1 results: 1.161150884899E+04 9.271350510933E+04 1.084559511557E-01 9.159029781186E-02 1.161009682231E+04 9.271251267660E+04 -9.008424333884E-01 BINARY: apbs INPUT: apbs-mol-parallel-PE2.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.533327920982E+01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.349327483109E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.753646268927E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.716901575464E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.760706267384E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.753396861378E+04 kJ/mol Calculating forces... Writing potential to pot-PE2.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.002011083294E+01 kJ/mol Global net ELEC energy = 3.002011083294E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE2.out Processor 2 results: 1.533327920982E+01 3.349327483109E+02 4.753646268927E+03 3.716901575464E+04 4.760706267384E+03 3.753396861378E+04 3.002011083294E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE3.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.803290534287E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.400275505449E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.150603559111E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.573366340513E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.804039178218E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.400354034488E+05 kJ/mol Calculating forces... Writing potential to pot-PE3.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.710240552064E+00 kJ/mol Global net ELEC energy = 8.710240552064E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE3.out Processor 3 results: 1.803290534287E+04 1.400275505449E+05 8.150603559111E-01 8.573366340513E-01 1.804039178218E+04 1.400354034488E+05 8.710240552064E+00 BINARY: apbs INPUT: apbs-mol-parallel-PE4.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.015087619451E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.216054444942E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.620207421716E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.273875108812E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.666622027749E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306246500367E+05 kJ/mol Calculating forces... Writing potential to pot-PE4.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.108471049009E+01 kJ/mol Global net ELEC energy = 2.108471049009E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE4.out Processor 4 results: 4.015087619451E+02 3.216054444942E+03 1.620207421716E+04 1.273875108812E+05 1.666622027749E+04 1.306246500367E+05 2.108471049009E+01 BINARY: apbs INPUT: apbs-mol-parallel-PE5.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE5.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.100112513614E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.662571945373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.370921758038E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.012777153962E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.115105077953E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.662769018146E+04 kJ/mol Calculating forces... Writing potential to pot-PE5.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 2.372005444809E+00 kJ/mol Global net ELEC energy = 2.372005444809E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE5.out Processor 5 results: 2.100112513614E+03 1.662571945373E+04 4.370921758038E-01 4.012777153962E-01 2.115105077953E+03 1.662769018146E+04 2.372005444809E+00 BINARY: apbs INPUT: apbs-mol-parallel-PE6.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE6.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.817378781616E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.959534462269E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176793266728E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.643533578081E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.176229449467E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.643148330287E+04 kJ/mol Calculating forces... Writing potential to pot-PE6.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.892943480303E+00 kJ/mol Global net ELEC energy = -1.892943480303E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE6.out Processor 6 results: 2.817378781616E+00 1.959534462269E+00 1.176793266728E+04 9.643533578081E+04 1.176229449467E+04 9.643148330287E+04 -1.892943480303E+00 BINARY: apbs INPUT: apbs-mol-parallel-PE7.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-parallel-PE7.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.428230292158E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.199832997920E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.881300088062E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.152799174875E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.847712854852E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618156668929E+04 kJ/mol Calculating forces... Writing potential to pot-PE7.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.043753521021E+01 kJ/mol Global net ELEC energy = 3.043753521021E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-parallel-PE7.out Processor 7 results: 2.428230292158E+03 2.199832997920E+04 3.881300088062E+02 4.152799174875E+03 2.847712854852E+03 2.618156668929E+04 3.043753521021E+01 RESULT 35927.59777074854 RESULT 287991.6947822151 RESULT 36005.78432292607 RESULT 288019.59322988224 RESULT 72040.017332199 RESULT 576102.84427808 RESULT 98.1757441420356 Testing computed result 3.592759777075E+04 against expected result 3.592760E+04 *** PASSED *** Testing computed result 2.879916947822E+05 against expected result 2.879917E+05 *** PASSED *** Testing computed result 3.600578432293E+04 against expected result 3.600578E+04 *** PASSED *** Testing computed result 2.880195932299E+05 against expected result 2.880196E+05 *** PASSED *** Testing computed result 7.204001733220E+04 against expected result 7.204002E+04 *** PASSED *** Testing computed result 5.761028442781E+05 against expected result 5.761028E+05 *** PASSED *** Testing computed result 9.817574414204E+01 against expected result 9.817456E+01 *** PASSED (with rounding error - see log) *** Elapsed time: 280.726848 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: apbs INPUT: apbs-smol-parallel-PE0.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE0.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.371266245949E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.306912290219E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.977036667733E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.288057507497E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.356039288708E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.595843060209E+04 kJ/mol Calculating forces... Writing potential to pot-PE0.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 8.732624922090E+00 kJ/mol Global net ELEC energy = 8.732624922090E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE0.out Processor 0 results: 1.371266245949E+03 1.306912290219E+04 2.977036667733E+03 2.288057507497E+04 4.356039288708E+03 3.595843060209E+04 8.732624922090E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE1.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183935033618E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.276169789420E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.420924995464E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -1.129030298944E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.183791435221E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.276043001853E+04 kJ/mol Calculating forces... Writing potential to pot-PE1.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.154972633314E+00 kJ/mol Global net ELEC energy = -1.154972633314E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE1.out Processor 1 results: 1.183935033618E+04 9.276169789420E+04 1.420924995464E-01 1.129030298944E-01 1.183791435221E+04 9.276043001853E+04 -1.154972633314E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE2.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.992726432058E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.375960934473E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.863608503641E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.720602537782E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.896854387650E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 3.757590620855E+04 kJ/mol Calculating forces... Writing potential to pot-PE2.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.228473728522E+01 kJ/mol Global net ELEC energy = 3.228473728522E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE2.out Processor 2 results: 9.992726432058E+00 3.375960934473E+02 4.863608503641E+03 3.720602537782E+04 4.896854387650E+03 3.757590620855E+04 3.228473728522E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE3.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.826846317904E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.401007397614E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -9.966525690477E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -8.961424692860E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827933209233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, -6.674) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.401092487740E+05 kJ/mol Calculating forces... Writing potential to pot-PE3.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 9.405155088186E+00 kJ/mol Global net ELEC energy = 9.405155088186E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE3.out Processor 3 results: 1.826846317904E+04 1.401007397614E+05 9.966525690477E-01 8.961424692860E-01 1.827933209233E+04 1.401092487740E+05 9.405155088186E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE4.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.021998204986E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.215581391535E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.644646339930E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.274227987774E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.689865332202E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.306747563963E+05 kJ/mol Calculating forces... Writing potential to pot-PE4.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.637622734662E+01 kJ/mol Global net ELEC energy = 3.637622734662E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE4.out Processor 4 results: 4.021998204986E+02 3.215581391535E+03 1.644646339930E+04 1.274227987774E+05 1.689865332202E+04 1.306747563963E+05 3.637622734662E+01 BINARY: apbs INPUT: apbs-smol-parallel-PE5.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE5.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.187673595319E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.663590090053E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.710032885061E-01 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.848912615891E-01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189033693728E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, -20.834, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 1.663642086377E+04 kJ/mol Calculating forces... Writing potential to pot-PE5.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 1.004854500183E+00 kJ/mol Global net ELEC energy = 1.004854500183E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE5.out Processor 5 results: 2.187673595319E+03 1.663590090053E+04 4.710032885061E-01 4.848912615891E-01 2.189033693728E+03 1.663642086377E+04 1.004854500183E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE6.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE6.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -4.897659240526E+00 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = -2.552765434658E+00 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.200266111088E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.646358551314E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.199560371894E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (-20.091, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 9.645933328248E+04 kJ/mol Calculating forces... Writing potential to pot-PE6.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = -1.699465221137E+00 kJ/mol Global net ELEC energy = -1.699465221137E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE6.out Processor 6 results: 4.897659240526E+00 2.552765434658E+00 1.200266111088E+04 9.646358551314E+04 1.199560371894E+04 9.645933328248E+04 -1.699465221137E+00 BINARY: apbs INPUT: apbs-smol-parallel-PE7.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-parallel-PE7.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (1.535e+01, -3.100e-02, 2.993e+00) Net charge -1.20e+01 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5877 atoms Centered at (-1.404e+01, -3.356e+00, 3.049e+01) Net charge -1.20e+01 e Reading PQR-format atom data from complex.pqr. 11754 atoms Centered at (2.518e+00, -2.465e+00, 1.674e+01) Net charge -2.40e+01 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 274.673 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.521894873214E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (mol1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 274.673 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 1 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.200161660501E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 534.816 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.033680106430E+02 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (mol2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 276.642 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 2 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 4.154432431334E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 538.751 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 1.625 x 1.260 x 1.688 Grid lengths: 156.000 x 121.000 x 162.000 Grid center: (2.518, -2.465, 16.742) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.960165191413E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------- CALCULATION #6 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.608 A Current memory usage: 292.797 MB total, 562.195 MB high water Using linear spline charge discretization. Partition overlap fraction = 0.1 Processor array = 2 x 2 x 2 Grid dimensions: 97 x 97 x 97 Grid spacings: 0.696 x 0.565 x 0.720 Grid lengths: 66.783 x 54.261 x 69.168 Grid center: (25.127, 15.905, 40.159) Multigrid levels: 4 Molecule ID: 3 Nonlinear traditional PBE Boundary conditions from focusing 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Potential to be written to pot.dx Total electrostatic energy = 2.618664307349E+04 kJ/mol Calculating forces... Writing potential to pot-PE7.dx ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (mol1) - 2 (mol2) end Local net energy (PE 0) = 3.059403714563E+01 kJ/mol Global net ELEC energy = 3.059403714563E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 562.195 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-parallel-PE7.out Processor 7 results: 2.521894873214E+03 2.200161660501E+04 4.033680106430E+02 4.154432431334E+03 2.960165191413E+03 2.618664307349E+04 3.059403714563E+01 RESULT 36605.73843587318 RESULT 288124.808313747 RESULT 36694.74744055409 RESULT 288128.91111142474 RESULT 73413.59604699901 RESULT 576361.16921921 RESULT 115.54319843347798 Testing computed result 3.660573843587E+04 against expected result 3.660574E+04 *** PASSED *** Testing computed result 2.881248083137E+05 against expected result 2.881248E+05 *** PASSED *** Testing computed result 3.669474744055E+04 against expected result 3.669475E+04 *** PASSED *** Testing computed result 2.881289111114E+05 against expected result 2.881289E+05 *** PASSED *** Testing computed result 7.341359604700E+04 against expected result 7.341360E+04 *** PASSED *** Testing computed result 5.763611692192E+05 against expected result 5.763611E+05 *** PASSED *** Testing computed result 1.155431984335E+02 against expected result 1.155421E+02 *** PASSED (with rounding error - see log) *** Elapsed time: 264.505875 seconds -------------------------------------------------------------------------------- Total elapsed time: 545.232723 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for alkanes section -------------------------------------------------------------------------------- Testing input file alkanes.in BINARY: apbs INPUT: alkanes.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file alkanes.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 11 molecules Reading PDB-format atom data from 2-methylbutane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 4.33e+00 e Reading PDB-format atom data from butane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (3.917e+00, 7.025e-01, -8.575e+00) Net charge 3.51e+00 e Reading PDB-format atom data from cyclohexane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (1.123e+00, 5.880e-01, 7.680e-01) Net charge 4.93e+00 e Reading PDB-format atom data from cyclopentane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 13 atoms Centered at (1.320e+00, 5.255e-01, 1.289e+00) Net charge 3.88e+00 e Reading PDB-format atom data from ethane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 8 atoms Centered at (2.210e-01, -2.100e-02, 7.650e-01) Net charge 1.87e+00 e Reading PDB-format atom data from hexane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 20 atoms Centered at (4.951e+00, -9.500e-03, -8.406e+00) Net charge 5.16e+00 e Reading PDB-format atom data from isobutane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.859e+01, 1.864e+01, 1.921e+01) Net charge 3.51e+00 e Reading PDB-format atom data from methane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 5 atoms Centered at (1.803e+01, 1.779e+01, 1.782e+01) Net charge 1.05e+00 e Reading PDB-format atom data from neopentane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (1.867e+01, 1.894e+01, 1.920e+01) Net charge 4.33e+00 e Reading PDB-format atom data from pentane.pdb. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 17 atoms Centered at (4.460e+00, 1.615e-01, -8.566e+00) Net charge 4.33e+00 e Reading PDB-format atom data from propane.pdb. 11 atoms Centered at (1.836e+01, 1.896e+01, 1.861e+01) Net charge 2.69e+00 e Preparing to run 11 PBE calculations. ---------------------------------------- CALCULATION #1 (solvated-2-methylbutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.815624614267E+00 SASA for atom 1: 0.000000000000E+00 SASA for atom 2: 6.122920124655E-01 SASA for atom 3: 3.957497153740E+00 SASA for atom 4: 4.308445014544E+00 SASA for atom 5: 1.843264951960E+01 SASA for atom 6: 1.837011296483E+01 SASA for atom 7: 1.666599184724E+01 SASA for atom 8: 1.480031796315E+01 SASA for atom 9: 1.603020354037E+01 SASA for atom 10: 1.473778140838E+01 SASA for atom 11: 1.611879699297E+01 SASA for atom 12: 1.810954398660E+01 SASA for atom 13: 1.420100931324E+01 SASA for atom 14: 1.437298483886E+01 SASA for atom 15: 1.814081226399E+01 SASA for atom 16: 2.152820898091E+01 Total solvent accessible surface area: 214.202 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.243280922127E-02 Surface tension*area energy for atom 1: 0.000000000000E+00 Surface tension*area energy for atom 2: 5.204482105957E-03 Surface tension*area energy for atom 3: 3.363872580679E-02 Surface tension*area energy for atom 4: 3.662178262362E-02 Surface tension*area energy for atom 5: 1.566775209166E-01 Surface tension*area energy for atom 6: 1.561459602010E-01 Surface tension*area energy for atom 7: 1.416609307015E-01 Surface tension*area energy for atom 8: 1.258027026868E-01 Surface tension*area energy for atom 9: 1.362567300932E-01 Surface tension*area energy for atom 10: 1.252711419712E-01 Surface tension*area energy for atom 11: 1.370097744402E-01 Surface tension*area energy for atom 12: 1.539311238861E-01 Surface tension*area energy for atom 13: 1.207085791625E-01 Surface tension*area energy for atom 14: 1.221703711303E-01 Surface tension*area energy for atom 15: 1.541969042439E-01 Surface tension*area energy for atom 16: 1.829897763377E-01 Total surface tension energy: 1.82072 kJ/mol Total solvent accessible volume: 253.665 A^3 Total pressure*volume energy: 60.7274 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.271287875274E+00 WCA energy for atom 1: -5.600872869478E+00 WCA energy for atom 2: -5.773775123943E+00 WCA energy for atom 3: -6.072801488986E+00 WCA energy for atom 4: -6.378470721845E+00 WCA energy for atom 5: -1.573474558351E+00 WCA energy for atom 6: -1.582338715648E+00 WCA energy for atom 7: -1.504044838266E+00 WCA energy for atom 8: -1.351002262819E+00 WCA energy for atom 9: -1.437367175239E+00 WCA energy for atom 10: -1.384626257493E+00 WCA energy for atom 11: -1.468867560891E+00 WCA energy for atom 12: -1.557005662832E+00 WCA energy for atom 13: -1.473759654043E+00 WCA energy for atom 14: -1.502261431335E+00 WCA energy for atom 15: -1.550940901474E+00 WCA energy for atom 16: -1.667828659696E+00 Total WCA energy: -48.1507 kJ/mol Total non-polar energy = 1.439739455792E+01 kJ/mol ---------------------------------------- CALCULATION #2 (solvated-butane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 8.064333822716E-01 SASA for atom 3: 4.375647796400E+00 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.660345529247E+01 SASA for atom 8: 1.658782115377E+01 SASA for atom 9: 1.658260977421E+01 SASA for atom 10: 1.658260977421E+01 SASA for atom 11: 2.145003828744E+01 SASA for atom 12: 1.852124297220E+01 SASA for atom 13: 1.856293400871E+01 Total solvent accessible surface area: 193.855 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 6.854683749309E-03 Surface tension*area energy for atom 3: 3.719300626940E-02 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.411293699860E-01 Surface tension*area energy for atom 8: 1.409964798071E-01 Surface tension*area energy for atom 9: 1.409521830808E-01 Surface tension*area energy for atom 10: 1.409521830808E-01 Surface tension*area energy for atom 11: 1.823253254433E-01 Surface tension*area energy for atom 12: 1.574305652637E-01 Surface tension*area energy for atom 13: 1.577849390741E-01 Total surface tension energy: 1.64777 kJ/mol Total solvent accessible volume: 217.863 A^3 Total pressure*volume energy: 52.1564 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.728858147814E+00 WCA energy for atom 1: -6.204037472587E+00 WCA energy for atom 2: -6.202937735018E+00 WCA energy for atom 3: -6.728762249931E+00 WCA energy for atom 4: -1.623549989062E+00 WCA energy for atom 5: -1.709092300778E+00 WCA energy for atom 6: -1.625196457114E+00 WCA energy for atom 7: -1.484289341167E+00 WCA energy for atom 8: -1.485410538626E+00 WCA energy for atom 9: -1.485593139015E+00 WCA energy for atom 10: -1.484878734279E+00 WCA energy for atom 11: -1.708585062695E+00 WCA energy for atom 12: -1.625094916482E+00 WCA energy for atom 13: -1.624416805392E+00 Total WCA energy: -41.7207 kJ/mol Total non-polar energy = 1.208346456826E+01 kJ/mol ---------------------------------------- CALCULATION #3 (solvated-cyclohexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 7.840324549863E-01 SASA for atom 1: 8.064333822716E-01 SASA for atom 2: 8.288343095569E-01 SASA for atom 3: 7.840324549863E-01 SASA for atom 4: 7.989664065098E-01 SASA for atom 5: 8.363012853187E-01 SASA for atom 6: 2.001169752764E+01 SASA for atom 7: 1.616048802948E+01 SASA for atom 8: 2.001169752764E+01 SASA for atom 9: 1.619175630687E+01 SASA for atom 10: 1.616048802948E+01 SASA for atom 11: 1.993352683418E+01 SASA for atom 12: 2.001169752764E+01 SASA for atom 13: 1.618133354774E+01 SASA for atom 14: 1.617091078861E+01 SASA for atom 15: 2.001690890721E+01 SASA for atom 16: 1.993873821374E+01 SASA for atom 17: 1.617091078861E+01 Total solvent accessible surface area: 221.799 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 6.664275867383E-03 Surface tension*area energy for atom 1: 6.854683749309E-03 Surface tension*area energy for atom 2: 7.045091631234E-03 Surface tension*area energy for atom 3: 6.664275867383E-03 Surface tension*area energy for atom 4: 6.791214455333E-03 Surface tension*area energy for atom 5: 7.108560925209E-03 Surface tension*area energy for atom 6: 1.700994289850E-01 Surface tension*area energy for atom 7: 1.373641482506E-01 Surface tension*area energy for atom 8: 1.700994289850E-01 Surface tension*area energy for atom 9: 1.376299286084E-01 Surface tension*area energy for atom 10: 1.373641482506E-01 Surface tension*area energy for atom 11: 1.694349780905E-01 Surface tension*area energy for atom 12: 1.700994289850E-01 Surface tension*area energy for atom 13: 1.375413351558E-01 Surface tension*area energy for atom 14: 1.374527417032E-01 Surface tension*area energy for atom 15: 1.701437257113E-01 Surface tension*area energy for atom 16: 1.694792748168E-01 Surface tension*area energy for atom 17: 1.374527417032E-01 Total surface tension energy: 1.88529 kJ/mol Total solvent accessible volume: 267.435 A^3 Total pressure*volume energy: 64.0239 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -5.793234697241E+00 WCA energy for atom 1: -5.784370526583E+00 WCA energy for atom 2: -5.791799130412E+00 WCA energy for atom 3: -5.788504399087E+00 WCA energy for atom 4: -5.797319672490E+00 WCA energy for atom 5: -5.787358035342E+00 WCA energy for atom 6: -1.523887929614E+00 WCA energy for atom 7: -1.413678912317E+00 WCA energy for atom 8: -1.521751604392E+00 WCA energy for atom 9: -1.414741802525E+00 WCA energy for atom 10: -1.413367854344E+00 WCA energy for atom 11: -1.523407238081E+00 WCA energy for atom 12: -1.523000623583E+00 WCA energy for atom 13: -1.413922068538E+00 WCA energy for atom 14: -1.416316744211E+00 WCA energy for atom 15: -1.524577474659E+00 WCA energy for atom 16: -1.523300410052E+00 WCA energy for atom 17: -1.414522566061E+00 Total WCA energy: -52.3691 kJ/mol Total non-polar energy = 1.354016672221E+01 kJ/mol ---------------------------------------- CALCULATION #4 (solvated-cyclopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 9.490526193215E+00 SASA for atom 1: 9.512927120500E+00 SASA for atom 2: 2.299828534626E+00 SASA for atom 3: 1.919012770776E+00 SASA for atom 4: 2.307295510388E+00 SASA for atom 5: 2.325838699632E+01 SASA for atom 6: 2.325838699632E+01 SASA for atom 7: 2.045987617019E+01 SASA for atom 8: 2.067875411190E+01 SASA for atom 9: 2.028790064456E+01 SASA for atom 10: 1.897463299431E+01 SASA for atom 11: 2.048593306801E+01 SASA for atom 12: 2.070481100972E+01 Total solvent accessible surface area: 193.638 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.066947264233E-02 Surface tension*area energy for atom 1: 8.085988052425E-02 Surface tension*area energy for atom 2: 1.954854254432E-02 Surface tension*area energy for atom 3: 1.631160855160E-02 Surface tension*area energy for atom 4: 1.961201183830E-02 Surface tension*area energy for atom 5: 1.976962894687E-01 Surface tension*area energy for atom 6: 1.976962894687E-01 Surface tension*area energy for atom 7: 1.739089474466E-01 Surface tension*area energy for atom 8: 1.757694099511E-01 Surface tension*area energy for atom 9: 1.724471554788E-01 Surface tension*area energy for atom 10: 1.612843804516E-01 Surface tension*area energy for atom 11: 1.741304310781E-01 Surface tension*area energy for atom 12: 1.759908935826E-01 Total surface tension energy: 1.64593 kJ/mol Total solvent accessible volume: 217.998 A^3 Total pressure*volume energy: 52.1887 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.343496616804E+00 WCA energy for atom 1: -6.327869601807E+00 WCA energy for atom 2: -6.334858040579E+00 WCA energy for atom 3: -6.296075406417E+00 WCA energy for atom 4: -6.345600816761E+00 WCA energy for atom 5: -1.663697465126E+00 WCA energy for atom 6: -1.662444032853E+00 WCA energy for atom 7: -1.572325104493E+00 WCA energy for atom 8: -1.604626551065E+00 WCA energy for atom 9: -1.586431484963E+00 WCA energy for atom 10: -1.554291291374E+00 WCA energy for atom 11: -1.574315220751E+00 WCA energy for atom 12: -1.604941679892E+00 Total WCA energy: -44.471 kJ/mol Total non-polar energy = 9.363673200142E+00 kJ/mol ---------------------------------------- CALCULATION #5 (solvated-ethane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 5.995981536705E+00 SASA for atom 1: 5.966113633657E+00 SASA for atom 2: 2.121552620704E+01 SASA for atom 3: 2.124158310486E+01 SASA for atom 4: 2.125200586399E+01 SASA for atom 5: 2.123116034573E+01 SASA for atom 6: 2.125200586399E+01 SASA for atom 7: 2.127285138225E+01 Total solvent accessible surface area: 139.427 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 5.096584306199E-02 Surface tension*area energy for atom 1: 5.071196588609E-02 Surface tension*area energy for atom 2: 1.803319727598E-01 Surface tension*area energy for atom 3: 1.805534563913E-01 Surface tension*area energy for atom 4: 1.806420498439E-01 Surface tension*area energy for atom 5: 1.804648629387E-01 Surface tension*area energy for atom 6: 1.806420498439E-01 Surface tension*area energy for atom 7: 1.808192367491E-01 Total surface tension energy: 1.18513 kJ/mol Total solvent accessible volume: 140.346 A^3 Total pressure*volume energy: 33.5988 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -7.360066353115E+00 WCA energy for atom 1: -7.355483516201E+00 WCA energy for atom 2: -1.776106201066E+00 WCA energy for atom 3: -1.773973940651E+00 WCA energy for atom 4: -1.775401936843E+00 WCA energy for atom 5: -1.773464835521E+00 WCA energy for atom 6: -1.774382856097E+00 WCA energy for atom 7: -1.772366599434E+00 Total WCA energy: -25.3612 kJ/mol Total non-polar energy = 9.422717598546E+00 kJ/mol ---------------------------------------- CALCULATION #6 (solvated-hexane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 2.986790304710E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.381536722546E+01 SASA for atom 12: 1.384142412329E+01 SASA for atom 13: 7.765654792245E-01 SASA for atom 14: 1.684839013200E+01 SASA for atom 15: 1.682233323417E+01 SASA for atom 16: 4.166572475070E+00 SASA for atom 17: 2.179398933870E+01 SASA for atom 18: 1.877660057086E+01 SASA for atom 19: 1.876096643216E+01 Total solvent accessible surface area: 250.291 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 2.538771759003E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.174306214164E-01 Surface tension*area energy for atom 12: 1.176521050479E-01 Surface tension*area energy for atom 13: 6.600806573408E-03 Surface tension*area energy for atom 14: 1.432113161220E-01 Surface tension*area energy for atom 15: 1.429898324905E-01 Surface tension*area energy for atom 16: 3.541586603809E-02 Surface tension*area energy for atom 17: 1.852489093789E-01 Surface tension*area energy for atom 18: 1.596011048523E-01 Surface tension*area energy for atom 19: 1.594682146734E-01 Total surface tension energy: 2.12748 kJ/mol Total solvent accessible volume: 298.053 A^3 Total pressure*volume energy: 71.3539 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.635406071935E+00 WCA energy for atom 1: -5.957247427848E+00 WCA energy for atom 2: -5.524801144538E+00 WCA energy for atom 3: -5.522294168859E+00 WCA energy for atom 4: -1.605314409440E+00 WCA energy for atom 5: -1.701051761776E+00 WCA energy for atom 6: -1.606669162773E+00 WCA energy for atom 7: -1.442505934938E+00 WCA energy for atom 8: -1.443059002759E+00 WCA energy for atom 9: -1.328947132810E+00 WCA energy for atom 10: -1.328906972440E+00 WCA energy for atom 11: -1.331566344214E+00 WCA energy for atom 12: -1.328041776815E+00 WCA energy for atom 13: -5.937562025661E+00 WCA energy for atom 14: -1.442277774427E+00 WCA energy for atom 15: -1.442777091510E+00 WCA energy for atom 16: -6.602262542378E+00 WCA energy for atom 17: -1.698172146664E+00 WCA energy for atom 18: -1.600970858835E+00 WCA energy for atom 19: -1.600841970217E+00 Total WCA energy: -57.0807 kJ/mol Total non-polar energy = 1.640068943201E+01 kJ/mol ---------------------------------------- CALCULATION #7 (solvated-isobutane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.464676753463E+00 SASA for atom 1: 1.984493338158E+01 SASA for atom 2: 1.778643845361E+01 SASA for atom 3: 1.671289426332E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 3.531879535319E+00 SASA for atom 6: 1.673895116114E+01 SASA for atom 7: 1.793756846098E+01 SASA for atom 8: 1.973549441072E+01 SASA for atom 9: 1.710895911022E+01 SASA for atom 10: 4.599657069253E+00 SASA for atom 11: 1.937069784121E+01 SASA for atom 12: 1.654613011726E+01 SASA for atom 13: 1.936548646165E+01 Total solvent accessible surface area: 192.744 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.944975240444E-02 Surface tension*area energy for atom 1: 1.686819337434E-01 Surface tension*area energy for atom 2: 1.511847268556E-01 Surface tension*area energy for atom 3: 1.420596012382E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 3.002097605021E-02 Surface tension*area energy for atom 6: 1.422810848697E-01 Surface tension*area energy for atom 7: 1.524693319183E-01 Surface tension*area energy for atom 8: 1.677517024912E-01 Surface tension*area energy for atom 9: 1.454261524369E-01 Surface tension*area energy for atom 10: 3.909708508865E-02 Surface tension*area energy for atom 11: 1.646509316503E-01 Surface tension*area energy for atom 12: 1.406421059967E-01 Surface tension*area energy for atom 13: 1.646066349240E-01 Total surface tension energy: 1.63832 kJ/mol Total solvent accessible volume: 218.943 A^3 Total pressure*volume energy: 52.415 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.381016335247E+00 WCA energy for atom 1: -1.612317964554E+00 WCA energy for atom 2: -1.588013719598E+00 WCA energy for atom 3: -1.532162371190E+00 WCA energy for atom 4: -5.987950445279E+00 WCA energy for atom 5: -6.393089030861E+00 WCA energy for atom 6: -1.533454887042E+00 WCA energy for atom 7: -1.587650918485E+00 WCA energy for atom 8: -1.614083521570E+00 WCA energy for atom 9: -1.442402031577E+00 WCA energy for atom 10: -6.408813541353E+00 WCA energy for atom 11: -1.605830214390E+00 WCA energy for atom 12: -1.529385873788E+00 WCA energy for atom 13: -1.605662490385E+00 Total WCA energy: -40.8218 kJ/mol Total non-polar energy = 1.323144287435E+01 kJ/mol ---------------------------------------- CALCULATION #8 (solvated-methane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.231304303117E+01 SASA for atom 1: 2.323233009850E+01 SASA for atom 2: 2.345641941977E+01 SASA for atom 3: 2.377431357320E+01 SASA for atom 4: 2.264344420771E+01 Total solvent accessible surface area: 105.42 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 1.046608657649E-01 Surface tension*area energy for atom 1: 1.974748058372E-01 Surface tension*area energy for atom 2: 1.993795650680E-01 Surface tension*area energy for atom 3: 2.020816653722E-01 Surface tension*area energy for atom 4: 1.924692757655E-01 Total surface tension energy: 0.896066 kJ/mol Total solvent accessible volume: 95.985 A^3 Total pressure*volume energy: 22.9788 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -8.133807570805E+00 WCA energy for atom 1: -1.962181541765E+00 WCA energy for atom 2: -1.964078319162E+00 WCA energy for atom 3: -1.963015006647E+00 WCA energy for atom 4: -1.957425549100E+00 Total WCA energy: -15.9805 kJ/mol Total non-polar energy = 7.894367190329E+00 kJ/mol ---------------------------------------- CALCULATION #9 (solvated-neopentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 2.441701074100E+00 SASA for atom 1: 1.663993494942E+01 SASA for atom 2: 1.715586152630E+01 SASA for atom 3: 1.645753666466E+01 SASA for atom 4: 0.000000000000E+00 SASA for atom 5: 2.389432243768E+00 SASA for atom 6: 1.638457735076E+01 SASA for atom 7: 1.667641460637E+01 SASA for atom 8: 1.721839808108E+01 SASA for atom 9: 2.419300146815E+00 SASA for atom 10: 1.640021148945E+01 SASA for atom 11: 1.666599184724E+01 SASA for atom 12: 1.719234118325E+01 SASA for atom 13: 2.449168049862E+00 SASA for atom 14: 1.723403221977E+01 SASA for atom 15: 1.639500010989E+01 SASA for atom 16: 1.663472356985E+01 Total solvent accessible surface area: 210.755 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.075445912985E-02 Surface tension*area energy for atom 1: 1.414394470700E-01 Surface tension*area energy for atom 2: 1.458248229736E-01 Surface tension*area energy for atom 3: 1.398890616496E-01 Surface tension*area energy for atom 4: 0.000000000000E+00 Surface tension*area energy for atom 5: 2.031017407203E-02 Surface tension*area energy for atom 6: 1.392689074814E-01 Surface tension*area energy for atom 7: 1.417495241541E-01 Surface tension*area energy for atom 8: 1.463563836891E-01 Surface tension*area energy for atom 9: 2.056405124793E-02 Surface tension*area energy for atom 10: 1.394017976603E-01 Surface tension*area energy for atom 11: 1.416609307015E-01 Surface tension*area energy for atom 12: 1.461349000577E-01 Surface tension*area energy for atom 13: 2.081792842383E-02 Surface tension*area energy for atom 14: 1.464892738680E-01 Surface tension*area energy for atom 15: 1.393575009340E-01 Surface tension*area energy for atom 16: 1.413951503437E-01 Total surface tension energy: 1.79141 kJ/mol Total solvent accessible volume: 251.127 A^3 Total pressure*volume energy: 60.1198 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.011082520236E+00 WCA energy for atom 1: -1.497367782613E+00 WCA energy for atom 2: -1.498546483218E+00 WCA energy for atom 3: -1.492562171495E+00 WCA energy for atom 4: -5.447325863939E+00 WCA energy for atom 5: -6.004516149175E+00 WCA energy for atom 6: -1.492776531092E+00 WCA energy for atom 7: -1.496078170066E+00 WCA energy for atom 8: -1.501529655270E+00 WCA energy for atom 9: -5.996267554365E+00 WCA energy for atom 10: -1.492194267752E+00 WCA energy for atom 11: -1.496027211216E+00 WCA energy for atom 12: -1.500561393960E+00 WCA energy for atom 13: -6.000218612907E+00 WCA energy for atom 14: -1.500859921426E+00 WCA energy for atom 15: -1.492908499790E+00 WCA energy for atom 16: -1.494057174414E+00 Total WCA energy: -47.4149 kJ/mol Total non-polar energy = 1.449633815052E+01 kJ/mol ---------------------------------------- CALCULATION #10 (solvated-pentane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 4.405515699447E+00 SASA for atom 1: 8.213673337951E-01 SASA for atom 2: 3.285469335181E-01 SASA for atom 3: 7.466975761774E-01 SASA for atom 4: 1.855251124959E+01 SASA for atom 5: 2.147609518526E+01 SASA for atom 6: 1.852645435176E+01 SASA for atom 7: 1.655655287639E+01 SASA for atom 8: 1.655134149682E+01 SASA for atom 9: 1.360170066332E+01 SASA for atom 10: 1.357043238593E+01 SASA for atom 11: 1.685881289113E+01 SASA for atom 12: 1.687444702982E+01 SASA for atom 13: 4.196440378117E+00 SASA for atom 14: 1.881308022781E+01 SASA for atom 15: 1.882350298694E+01 SASA for atom 16: 2.182004623652E+01 Total solvent accessible surface area: 222.524 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 3.744688344530E-02 Surface tension*area energy for atom 1: 6.981622337259E-03 Surface tension*area energy for atom 2: 2.792648934903E-03 Surface tension*area energy for atom 3: 6.346929397508E-03 Surface tension*area energy for atom 4: 1.576963456215E-01 Surface tension*area energy for atom 5: 1.825468090747E-01 Surface tension*area energy for atom 6: 1.574748619900E-01 Surface tension*area energy for atom 7: 1.407306994493E-01 Surface tension*area energy for atom 8: 1.406864027230E-01 Surface tension*area energy for atom 9: 1.156144556382E-01 Surface tension*area energy for atom 10: 1.153486752804E-01 Surface tension*area energy for atom 11: 1.432999095746E-01 Surface tension*area energy for atom 12: 1.434327997535E-01 Surface tension*area energy for atom 13: 3.566974321399E-02 Surface tension*area energy for atom 14: 1.599111819364E-01 Surface tension*area energy for atom 15: 1.599997753890E-01 Surface tension*area energy for atom 16: 1.854703930104E-01 Total surface tension energy: 1.89145 kJ/mol Total solvent accessible volume: 258.93 A^3 Total pressure*volume energy: 61.9878 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.655804319869E+00 WCA energy for atom 1: -6.027315962813E+00 WCA energy for atom 2: -5.696430965386E+00 WCA energy for atom 3: -6.016749084714E+00 WCA energy for atom 4: -1.608595384643E+00 WCA energy for atom 5: -1.703300955380E+00 WCA energy for atom 6: -1.609931495887E+00 WCA energy for atom 7: -1.457107525189E+00 WCA energy for atom 8: -1.457741620594E+00 WCA energy for atom 9: -1.354235498709E+00 WCA energy for atom 10: -1.354106470090E+00 WCA energy for atom 11: -1.456736412636E+00 WCA energy for atom 12: -1.455995435596E+00 WCA energy for atom 13: -6.633650611186E+00 WCA energy for atom 14: -1.605996088477E+00 WCA energy for atom 15: -1.606549890103E+00 WCA energy for atom 16: -1.700042300035E+00 Total WCA energy: -49.4003 kJ/mol Total non-polar energy = 1.447900211546E+01 kJ/mol ---------------------------------------- CALCULATION #11 (solvated-propane): APOLAR Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 3.173464698754E+00 SASA for atom 1: 1.931858404557E+01 SASA for atom 2: 2.014198201675E+01 SASA for atom 3: 2.149694070352E+01 SASA for atom 4: 1.904078819252E+00 SASA for atom 5: 2.067354273233E+01 SASA for atom 6: 1.937590922077E+01 SASA for atom 7: 3.098794941136E+00 SASA for atom 8: 1.942802301642E+01 SASA for atom 9: 1.973028303116E+01 SASA for atom 10: 2.204934693736E+01 Total solvent accessible surface area: 170.391 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 2.697444993941E-02 Surface tension*area energy for atom 1: 1.642079643873E-01 Surface tension*area energy for atom 2: 1.712068471424E-01 Surface tension*area energy for atom 3: 1.827239959799E-01 Surface tension*area energy for atom 4: 1.618466996365E-02 Surface tension*area energy for atom 5: 1.757251132248E-01 Surface tension*area energy for atom 6: 1.646952283766E-01 Surface tension*area energy for atom 7: 2.633975699966E-02 Surface tension*area energy for atom 8: 1.651381956396E-01 Surface tension*area energy for atom 9: 1.677074057649E-01 Surface tension*area energy for atom 10: 1.874194489675E-01 Total surface tension energy: 1.44832 kJ/mol Total solvent accessible volume: 183.573 A^3 Total pressure*volume energy: 43.9474 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.818670105515E+00 WCA energy for atom 1: -1.641297645338E+00 WCA energy for atom 2: -1.649584120441E+00 WCA energy for atom 3: -1.711408141255E+00 WCA energy for atom 4: -6.624720142882E+00 WCA energy for atom 5: -1.610117050515E+00 WCA energy for atom 6: -1.596858009746E+00 WCA energy for atom 7: -6.816460624835E+00 WCA energy for atom 8: -1.642782751806E+00 WCA energy for atom 9: -1.645779566650E+00 WCA energy for atom 10: -1.714436154542E+00 Total WCA energy: -33.4721 kJ/mol Total non-polar energy = 1.192358496286E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print APOL energy 1 (solvated-2-methylbutane) end Global net APOL energy = 1.439739455792E+01 kJ/mol print APOL energy 2 (solvated-butane) end Global net APOL energy = 1.208346456826E+01 kJ/mol print APOL energy 3 (solvated-cyclohexane) end Global net APOL energy = 1.354016672221E+01 kJ/mol print APOL energy 4 (solvated-cyclopentane) end Global net APOL energy = 9.363673200142E+00 kJ/mol print APOL energy 5 (solvated-ethane) end Global net APOL energy = 9.422717598546E+00 kJ/mol print APOL energy 6 (solvated-hexane) end Global net APOL energy = 1.640068943201E+01 kJ/mol print APOL energy 7 (solvated-isobutane) end Global net APOL energy = 1.323144287435E+01 kJ/mol print APOL energy 8 (solvated-methane) end Global net APOL energy = 7.894367190329E+00 kJ/mol print APOL energy 9 (solvated-neopentane) end Global net APOL energy = 1.449633815052E+01 kJ/mol print APOL energy 10 (solvated-pentane) end Global net APOL energy = 1.447900211546E+01 kJ/mol print APOL energy 11 (solvated-propane) end Global net APOL energy = 1.192358496286E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 11 molecules Final memory usage: 0.001 MB total, 2.267 MB high water Thanks for using APBS! Checking for intermidiate energies in input file alkanes.out RESULT 14.39739455792 RESULT 12.08346456826 RESULT 13.54016672221 RESULT 9.363673200142 RESULT 9.422717598546 RESULT 16.40068943201 RESULT 13.23144287435 RESULT 7.894367190329 RESULT 14.49633815052 RESULT 14.47900211546 RESULT 11.92358496286 Testing computed result 1.439739455792E+01 against expected result 1.439739E+01 *** PASSED *** Testing computed result 1.208346456826E+01 against expected result 1.208346E+01 *** PASSED *** Testing computed result 1.354016672221E+01 against expected result 1.354017E+01 *** PASSED *** Testing computed result 9.363673200142E+00 against expected result 9.363673E+00 *** PASSED *** Testing computed result 9.422717598546E+00 against expected result 9.422718E+00 *** PASSED *** Testing computed result 1.640068943201E+01 against expected result 1.640069E+01 *** PASSED *** Testing computed result 1.323144287435E+01 against expected result 1.323144E+01 *** PASSED *** Testing computed result 7.894367190329E+00 against expected result 7.894367E+00 *** PASSED *** Testing computed result 1.449633815052E+01 against expected result 1.449634E+01 *** PASSED *** Testing computed result 1.447900211546E+01 against expected result 1.447900E+01 *** PASSED *** Testing computed result 1.192358496286E+01 against expected result 1.192358E+01 *** PASSED *** Elapsed time: 19.385191 seconds -------------------------------------------------------------------------------- Total elapsed time: 19.385191 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for FKBP section -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in BINARY: apbs INPUT: 1d7h-dmso-mol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file 1d7h-dmso-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.060899690259E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.276523673491E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.961107503213E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.121048606059E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.058410584089E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.205385249581E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.335429017008E+03 kJ/mol Global net ELEC energy = -3.335429017008E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.180527370616E+01 kJ/mol Global net ELEC energy = -2.180527370616E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.328631844166E+03 kJ/mol Global net ELEC energy = -3.328631844166E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.500810086373E+01 kJ/mol Global net ELEC energy = 1.500810086373E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7h-dmso-mol.out RESULT 10608.99690259 RESULT 42765.23673491 RESULT 13992.34956777 RESULT 46100.66575192 RESULT 39.61107503213 RESULT 712.1048606059 RESULT 67.51571424823 RESULT 733.9101343121 RESULT 10584.10584089 RESULT 42053.85249581 RESULT 13959.61902233 RESULT 45382.48433997 RESULT -3335.429017008 RESULT -21.80527370616 RESULT -3328.631844166 RESULT 15.00810086373 Testing computed result 1.060899690259E+04 against expected result 1.060900E+04 *** PASSED *** Testing computed result 4.276523673491E+04 against expected result 4.276524E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.961107503213E+01 against expected result 3.961108E+01 *** PASSED *** Testing computed result 7.121048606059E+02 against expected result 7.121049E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.058410584089E+04 against expected result 1.058411E+04 *** PASSED *** Testing computed result 4.205385249581E+04 against expected result 4.205385E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.500810086373E+01 against expected result 1.500810E+01 *** PASSED *** Elapsed time: 14.338821 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in BINARY: apbs INPUT: 1d7h-dmso-smol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file 1d7h-dmso-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7h-dmso-complex.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1673 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dmso-min.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 10 atoms Centered at (1.775e+01, 1.777e+01, 2.049e+01) Net charge 2.78e-17 e Reading PQR-format atom data from 1d7h-min.pqr. 1663 atoms Centered at (2.587e+01, 1.835e+01, 1.911e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 122.059 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.074948704824E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.289487256481E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.399234956777E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.059 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.610066575192E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dmso-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.719709905887E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dmso-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.125747080979E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dmso-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.751571424823E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dmso-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.428 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.339101343121E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7h-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.071654753674E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7h-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.218178203716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7h-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.875, 18.349, 19.112) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.395961902233E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7h-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.736 MB total, 221.696 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.751, 17.770, 20.492) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.538248433997E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.205793187109E+03 kJ/mol Global net ELEC energy = -3.205793187109E+03 kJ/mol print energy 6 (dmso-solv-fine) - 8 (dmso-ref-fine) end Local net energy (PE 0) = -2.133542621421E+01 kJ/mol Global net ELEC energy = -2.133542621421E+01 kJ/mol print energy 10 (1d7h-solv-fine) - 12 (1d7h-ref-fine) end Local net energy (PE 0) = -3.200702302816E+03 kJ/mol Global net ELEC energy = -3.200702302816E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dmso-solv-fine) + 8 (dmso-ref-fine) - 10 (1d7h-solv-fine) + 12 (1d7h-ref-fine) end Local net energy (PE 0) = 1.624454192074E+01 kJ/mol Global net ELEC energy = 1.624454192074E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 221.696 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7h-dmso-smol.out RESULT 10749.48704824 RESULT 42894.87256481 RESULT 13992.34956777 RESULT 46100.66575192 RESULT 37.19709905887 RESULT 712.5747080979 RESULT 67.51571424823 RESULT 733.9101343121 RESULT 10716.54753674 RESULT 42181.78203716 RESULT 13959.61902233 RESULT 45382.48433997 RESULT -3205.793187109 RESULT -21.33542621421 RESULT -3200.702302816 RESULT 16.24454192074 Testing computed result 1.074948704824E+04 against expected result 1.074949E+04 *** PASSED *** Testing computed result 4.289487256481E+04 against expected result 4.289487E+04 *** PASSED *** Testing computed result 1.399234956777E+04 against expected result 1.399235E+04 *** PASSED *** Testing computed result 4.610066575192E+04 against expected result 4.610067E+04 *** PASSED *** Testing computed result 3.719709905887E+01 against expected result 3.719710E+01 *** PASSED *** Testing computed result 7.125747080979E+02 against expected result 7.125747E+02 *** PASSED *** Testing computed result 6.751571424823E+01 against expected result 6.751571E+01 *** PASSED *** Testing computed result 7.339101343121E+02 against expected result 7.339101E+02 *** PASSED *** Testing computed result 1.071654753674E+04 against expected result 1.071655E+04 *** PASSED *** Testing computed result 4.218178203716E+04 against expected result 4.218178E+04 *** PASSED *** Testing computed result 1.395961902233E+04 against expected result 1.395962E+04 *** PASSED *** Testing computed result 4.538248433997E+04 against expected result 4.538248E+04 *** PASSED *** Testing computed result 1.624454192074E+01 against expected result 1.624454E+01 *** PASSED *** Elapsed time: 12.399601 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in BINARY: apbs INPUT: 1d7i-dss-mol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file 1d7i-dss-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.160578033846E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.955701871716E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.431133325426E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677348113184E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.040108332204E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.787747796627E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -3.460997931137E+03 kJ/mol Global net ELEC energy = -3.460997931137E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.052167100108E+01 kJ/mol Global net ELEC energy = -2.052167100108E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -3.454901259473E+03 kJ/mol Global net ELEC energy = -3.454901259473E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.442499933664E+01 kJ/mol Global net ELEC energy = 1.442499933664E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7i-dss-mol.out RESULT 9160.578033846 RESULT 39557.01871716 RESULT 12649.65939588 RESULT 43018.01664829 RESULT 94.31133325426 RESULT 1677.348113184 RESULT 117.1079106781 RESULT 1697.869784185 RESULT 9040.108332204 RESULT 37877.47796627 RESULT 12524.95566243 RESULT 41332.37922574 RESULT -3460.997931137 RESULT -20.52167100108 RESULT -3454.901259473 RESULT 14.42499933664 Testing computed result 9.160578033846E+03 against expected result 9.160578E+03 *** PASSED *** Testing computed result 3.955701871716E+04 against expected result 3.955702E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 9.431133325426E+01 against expected result 9.431133E+01 *** PASSED *** Testing computed result 1.677348113184E+03 against expected result 1.677348E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.040108332204E+03 against expected result 9.040108E+03 *** PASSED *** Testing computed result 3.787747796627E+04 against expected result 3.787748E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.442499933664E+01 against expected result 1.442501E+01 *** PASSED *** Elapsed time: 14.467083 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in BINARY: apbs INPUT: 1d7i-dss-smol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file 1d7i-dss-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from 1d7i-dss-complex.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1677 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Reading PQR-format atom data from dss-min.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 14 atoms Centered at (1.734e+01, 1.921e+01, 2.050e+01) Net charge -8.33e-17 e Reading PQR-format atom data from 1d7i-min.pqr. 1663 atoms Centered at (2.526e+01, 1.899e+01, 1.912e+01) Net charge 9.91e-01 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (complex-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 122.425 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.634884642408E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #2 (complex-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.003177540425E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.264965939588E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (complex-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 122.425 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.301801664829E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (dss-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 7.942232645345E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (dss-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.677798535473E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (dss-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.171079106781E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #8 (dss-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 62.528 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.697869784185E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (1d7i-solv-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.507068451372E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #10 (1d7i-solv-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 30.4176 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.835075772299E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (1d7i-ref-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (25.264, 18.988, 19.122) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.252495566243E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (1d7i-ref-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 4.87072 A Current memory usage: 121.977 MB total, 222.305 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (17.340, 19.211, 20.503) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.010 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.010 M concentration 2.000 A-radius, -1.000 e-charge, 0.010 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.133237922574E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) end Local net energy (PE 0) = -2.986241244040E+03 kJ/mol Global net ELEC energy = -2.986241244040E+03 kJ/mol print energy 6 (dss-solv-fine) - 8 (dss-ref-fine) end Local net energy (PE 0) = -2.007124871262E+01 kJ/mol Global net ELEC energy = -2.007124871262E+01 kJ/mol print energy 10 (1d7i-solv-fine) - 12 (1d7i-ref-fine) end Local net energy (PE 0) = -2.981621502756E+03 kJ/mol Global net ELEC energy = -2.981621502756E+03 kJ/mol print energy 2 (complex-solv-fine) - 4 (complex-ref-fine) - 6 (dss-solv-fine) + 8 (dss-ref-fine) - 10 (1d7i-solv-fine) + 12 (1d7i-ref-fine) end Local net energy (PE 0) = 1.545150742843E+01 kJ/mol Global net ELEC energy = 1.545150742843E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 222.305 MB high water Thanks for using APBS! Checking for intermidiate energies in input file 1d7i-dss-smol.out RESULT 9634.884642408 RESULT 40031.77540425 RESULT 12649.65939588 RESULT 43018.01664829 RESULT 79.42232645345 RESULT 1677.798535473 RESULT 117.1079106781 RESULT 1697.869784185 RESULT 9507.068451372 RESULT 38350.75772299 RESULT 12524.95566243 RESULT 41332.37922574 RESULT -2986.24124404 RESULT -20.07124871262 RESULT -2981.621502756 RESULT 15.45150742843 Testing computed result 9.634884642408E+03 against expected result 9.634885E+03 *** PASSED *** Testing computed result 4.003177540425E+04 against expected result 4.003178E+04 *** PASSED *** Testing computed result 1.264965939588E+04 against expected result 1.264966E+04 *** PASSED *** Testing computed result 4.301801664829E+04 against expected result 4.301802E+04 *** PASSED *** Testing computed result 7.942232645345E+01 against expected result 7.942233E+01 *** PASSED *** Testing computed result 1.677798535473E+03 against expected result 1.677799E+03 *** PASSED *** Testing computed result 1.171079106781E+02 against expected result 1.171079E+02 *** PASSED *** Testing computed result 1.697869784185E+03 against expected result 1.697870E+03 *** PASSED *** Testing computed result 9.507068451372E+03 against expected result 9.507068E+03 *** PASSED *** Testing computed result 3.835075772299E+04 against expected result 3.835076E+04 *** PASSED *** Testing computed result 1.252495566243E+04 against expected result 1.252496E+04 *** PASSED *** Testing computed result 4.133237922574E+04 against expected result 4.133238E+04 *** PASSED *** Testing computed result 1.545150742843E+01 against expected result 1.545150E+01 *** PASSED *** Elapsed time: 12.186330 seconds -------------------------------------------------------------------------------- Total elapsed time: 53.391835 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for hca-bind section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: apbs INPUT: apbs-mol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.213600726771E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.825764811255E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.458471211905E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.093606095527E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.515433544464E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.786369323561E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.105322784838E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.533304996252E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850429388099E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.246475812684E+01 kJ/mol Global net ELEC energy = -5.246475812684E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 221.3600726771 RESULT 1825.764811255 RESULT 6458.471211905 RESULT 20936.06095527 RESULT 151543.3544464 RESULT 178636.9323561 RESULT 21053.22784838 RESULT 153330.4996252 RESULT 185042.9388099 RESULT -52.46475812684 Testing computed result 2.213600726771E+02 against expected result 2.213601E+02 *** PASSED *** Testing computed result 1.825764811255E+03 against expected result 1.825765E+03 *** PASSED *** Testing computed result 6.458471211905E+03 against expected result 6.458471E+03 *** PASSED *** Testing computed result 2.093606095527E+04 against expected result 2.093606E+04 *** PASSED *** Testing computed result 1.515433544464E+05 against expected result 1.515434E+05 *** PASSED *** Testing computed result 1.786369323561E+05 against expected result 1.786369E+05 *** PASSED *** Testing computed result 2.105322784838E+04 against expected result 2.105323E+04 *** PASSED *** Testing computed result 1.533304996252E+05 against expected result 1.533305E+05 *** PASSED *** Testing computed result 1.850429388099E+05 against expected result 1.850429E+05 *** PASSED *** Testing computed result -5.246475812684E+01 against expected result -5.246476E+01 *** PASSED *** Elapsed time: 14.812334 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: apbs INPUT: apbs-smol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from acet.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 18 atoms Centered at (-6.028e+00, 3.898e+00, 1.518e+01) Net charge -1.00e+00 e Reading PQR-format atom data from hca.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 2482 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge 1.00e+00 e Reading PQR-format atom data from complex.pqr. 2500 atoms Centered at (-7.196e+00, 4.070e-01, 1.704e+01) Net charge -1.02e-14 e Preparing to run 9 PBE calculations. ---------------------------------------- CALCULATION #1 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 62.727 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.884888131017E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.820045922544E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acet): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 62.727 MB total, 123.701 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 6.460002606908E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 146.516 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.189161497021E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #5 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.520000494925E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (hca): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.516 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.790436191580E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.092 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 1.500 x 1.500 x 1.500 Grid lengths: 96.000 x 96.000 x 96.000 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.195842512312E+04 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.581 x 0.581 x 0.581 Grid lengths: 37.181 x 37.181 x 37.181 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.537771604355E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #9 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 146.926 MB total, 245.725 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.225 x 0.225 x 0.225 Grid lengths: 14.400 x 14.400 x 14.400 Grid center: (-6.028, 3.898, 15.179) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.540 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.854495619747E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (acet) - 2 (hca) end Local net energy (PE 0) = -5.405979017059E+01 kJ/mol Global net ELEC energy = -5.405979017059E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 245.725 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 188.4888131017 RESULT 1820.045922544 RESULT 6460.002606908 RESULT 21891.61497021 RESULT 152000.0494925 RESULT 179043.619158 RESULT 21958.42512312 RESULT 153777.1604355 RESULT 185449.5619747 RESULT -54.05979017059 Testing computed result 1.884888131017E+02 against expected result 1.884888E+02 *** PASSED *** Testing computed result 1.820045922544E+03 against expected result 1.820046E+03 *** PASSED *** Testing computed result 6.460002606908E+03 against expected result 6.460003E+03 *** PASSED *** Testing computed result 2.189161497021E+04 against expected result 2.189161E+04 *** PASSED *** Testing computed result 1.520000494925E+05 against expected result 1.520000E+05 *** PASSED *** Testing computed result 1.790436191580E+05 against expected result 1.790436E+05 *** PASSED *** Testing computed result 2.195842512312E+04 against expected result 2.195843E+04 *** PASSED *** Testing computed result 1.537771604355E+05 against expected result 1.537772E+05 *** PASSED *** Testing computed result 1.854495619747E+05 against expected result 1.854496E+05 *** PASSED *** Testing computed result -5.405979017059E+01 against expected result -5.405978E+01 *** PASSED *** Elapsed time: 11.431532 seconds -------------------------------------------------------------------------------- Total elapsed time: 26.243866 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ionize section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: apbs INPUT: apbs-mol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning Vio_ctor2: Gethostbyname fail INET sock <> dueto 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning Vio_ctor2: Gethostbyname fail INET sock <> dueto 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.823898055191E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793274462353E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.219846763777E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392741988698E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.862359524598E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.288156251610E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.267882018629E+01 kJ/mol Global net ELEC energy = -2.267882018629E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.997462636633E+02 kJ/mol Global net ELEC energy = -1.997462636633E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.974598403628E+02 kJ/mol Global net ELEC energy = -2.974598403628E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.745272838398E+02 kJ/mol Global net ELEC energy = -4.745272838398E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 5823.898055191 RESULT 9793.274462353 RESULT 5846.917564309 RESULT 9815.953282539 RESULT 8219.846763777 RESULT 13927.41988698 RESULT 8420.373979905 RESULT 14127.16615065 RESULT 3862.359524598 RESULT 6288.15625161 RESULT 4162.533113906 RESULT 6585.616091973 RESULT -22.67882018629 RESULT -199.7462636633 RESULT -297.4598403628 RESULT -474.5272838398 Testing computed result 5.823898055191E+03 against expected result 5.823898E+03 *** PASSED *** Testing computed result 9.793274462353E+03 against expected result 9.793274E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.219846763777E+03 against expected result 8.219847E+03 *** PASSED *** Testing computed result 1.392741988698E+04 against expected result 1.392742E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.862359524598E+03 against expected result 3.862360E+03 *** PASSED *** Testing computed result 6.288156251610E+03 against expected result 6.288156E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.267882018629E+01 against expected result -2.267882E+01 *** PASSED *** Testing computed result -1.997462636633E+02 against expected result -1.997463E+02 *** PASSED *** Testing computed result -2.974598403628E+02 against expected result -2.974598E+02 *** PASSED *** Testing computed result -4.745272838398E+02 against expected result -4.745273E+02 *** PASSED *** Elapsed time: 2.615668 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: apbs INPUT: apbs-smol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading XML-format atom data from acetic-acid.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning Vio_ctor2: Gethostbyname fail INET sock <> dueto 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.67e-16 e Reading XML-format atom data from acetate.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning Vio_ctor2: Gethostbyname fail INET sock <> dueto 8 atoms Centered at (0.000e+00, -1.535e-01, 1.287e+00) Net charge -1.00e+00 e Reading XML-format atom data from proton.xml. Valist_readXML: Warning Warning Warning Warning Warning Valist_readXML: The use of XML input files with parameter Valist_readXML: files is currently not supported. Valist_readXML: Warning Warning Warning Warning Warning 1 atoms Centered at (1.780e-01, -1.286e+00, 2.937e+00) Net charge 1.00e+00 e Preparing to run 12 PBE calculations. ---------------------------------------- CALCULATION #1 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 61.598 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.824172730822E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (acetic-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.793622759239E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 5.846917564309E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (acetic-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 9.815953282539E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.221328580569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #6 (acetate-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.598 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.392867783119E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #7 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 8.420373979905E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #8 (acetate-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.422 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.412716615065E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #9 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.863066835285E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #10 (proton-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 7.76163 A Current memory usage: 61.412 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.150 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.150 M concentration 2.000 A-radius, -1.000 e-charge, 0.150 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.289649216644E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #11 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.188 x 0.188 x 0.188 Grid lengths: 12.000 x 12.000 x 12.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 4.162533113906E+03 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #12 (proton-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.373 MB total, 122.404 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.094 x 0.094 x 0.094 Grid lengths: 6.000 x 6.000 x 6.000 Grid center: (0.000, -0.154, 1.287) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 2.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 293.000 K Electrostatic energies will be calculated Total electrostatic energy = 6.585616091973E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (acetic-solv) - 2 (acetic-ref) end Local net energy (PE 0) = -2.233052329981E+01 kJ/mol Global net ELEC energy = -2.233052329981E+01 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) end Local net energy (PE 0) = -1.984883194538E+02 kJ/mol Global net ELEC energy = -1.984883194538E+02 kJ/mol print energy 5 (proton-solv) - 6 (proton-ref) end Local net energy (PE 0) = -2.959668753288E+02 kJ/mol Global net ELEC energy = -2.959668753288E+02 kJ/mol print energy 3 (acetate-solv) - 4 (acetate-ref) + 5 (proton-solv) - 6 (proton-ref) - 1 (acetic-solv) + 2 (acetic-ref) end Local net energy (PE 0) = -4.721246714828E+02 kJ/mol Global net ELEC energy = -4.721246714828E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 122.404 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 5824.172730822 RESULT 9793.622759239 RESULT 5846.917564309 RESULT 9815.953282539 RESULT 8221.328580569 RESULT 13928.67783119 RESULT 8420.373979905 RESULT 14127.16615065 RESULT 3863.066835285 RESULT 6289.649216644 RESULT 4162.533113906 RESULT 6585.616091973 RESULT -22.33052329981 RESULT -198.4883194538 RESULT -295.9668753288 RESULT -472.1246714828 Testing computed result 5.824172730822E+03 against expected result 5.824173E+03 *** PASSED *** Testing computed result 9.793622759239E+03 against expected result 9.793623E+03 *** PASSED *** Testing computed result 5.846917564309E+03 against expected result 5.846918E+03 *** PASSED *** Testing computed result 9.815953282539E+03 against expected result 9.815953E+03 *** PASSED *** Testing computed result 8.221328580569E+03 against expected result 8.221329E+03 *** PASSED *** Testing computed result 1.392867783119E+04 against expected result 1.392868E+04 *** PASSED *** Testing computed result 8.420373979905E+03 against expected result 8.420374E+03 *** PASSED *** Testing computed result 1.412716615065E+04 against expected result 1.412717E+04 *** PASSED *** Testing computed result 3.863066835285E+03 against expected result 3.863067E+03 *** PASSED *** Testing computed result 6.289649216644E+03 against expected result 6.289649E+03 *** PASSED *** Testing computed result 4.162533113906E+03 against expected result 4.162533E+03 *** PASSED *** Testing computed result 6.585616091973E+03 against expected result 6.585616E+03 *** PASSED *** Testing computed result -2.233052329981E+01 against expected result -2.233050E+01 *** PASSED *** Testing computed result -1.984883194538E+02 against expected result -1.984883E+02 *** PASSED *** Testing computed result -2.959668753288E+02 against expected result -2.959669E+02 *** PASSED *** Testing computed result -4.721246714828E+02 against expected result -4.721247E+02 *** PASSED *** Elapsed time: 2.748578 seconds -------------------------------------------------------------------------------- Total elapsed time: 5.364246 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-pmf section -------------------------------------------------------------------------------- Testing input file ion-pmf.in BINARY: apbs INPUT: ion-pmf.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file ion-pmf.in... rank 0 size 1... Parsed input file. Reading parameter data from parm.dat. Got paths for 1 molecules Reading PDB-format atom data from ion-pmf.pdb. Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.106 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 7.839535983197E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.760e+03 -4.398e-05 -7.763e-05 mgF qf 0 -3.767e+03 -1.730e-05 -2.384e-05 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 6.148e+00 -2.668e-05 -5.379e-05 mgF tot 1 -3.596e+03 -5.403e-05 -1.012e-04 mgF qf 1 -3.598e+03 -2.253e-05 -3.831e-05 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 2.883e+00 -3.150e-05 -6.291e-05 Vpmg_ibForce: No force for zero ionic strength! Vpmg_ibForce: No force for zero ionic strength! ---------------------------------------- CALCULATION #2 (ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.106 MB total, 61.155 MB high water Using cubic spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 1.000 Solvent dielectric: 1.000 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated All-atom solvent forces will be calculated Total electrostatic energy = 8.964727588811E+03 kJ/mol Calculating forces... Printing per-atom forces for molecule 1 (kJ/mol/A) Legend: tot n -- total force for atom n qf n -- fixed charge force for atom n db n -- dielectric boundary force for atom n ib n -- ionic boundary force for atom n mgF tot 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF qf 0 -3.850e+03 -4.055e-06 -7.703e-06 mgF ib 0 0.000e+00 0.000e+00 0.000e+00 mgF db 0 0.000e+00 0.000e+00 0.000e+00 mgF tot 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF qf 1 -3.514e+03 -4.163e-06 -7.690e-06 mgF ib 1 0.000e+00 0.000e+00 0.000e+00 mgF db 1 0.000e+00 0.000e+00 0.000e+00 ---------------------------------------- CALCULATION #3 (asolv): APOLAR Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n gamma 0.000720 pressure 0.000000 bconc 0.033000 tot 0 2.715e-02 9.130e-07 9.128e-07 sasa 0 -1.100e+01 0.000e+00 0.000e+00 sav 0 0.000e+00 0.000e+00 0.000e+00 wca 0 -5.827e-01 -2.767e-05 -2.766e-05 tot 1 -2.723e-02 9.131e-07 9.134e-07 sasa 1 1.112e+01 0.000e+00 0.000e+00 sav 1 0.000e+00 0.000e+00 0.000e+00 wca 1 5.827e-01 -2.767e-05 -2.768e-05 Solvent Accessible Surface Area (SASA) for each atom: SASA for atom 0: 1.153275282828E+02 SASA for atom 1: 1.153114143344E+02 Total solvent accessible surface area: 230.639 A^2 Surface tension*area energies (gamma * SASA) for each atom: Surface tension*area energy for atom 0: 8.303582036361E-02 Surface tension*area energy for atom 1: 8.302421832080E-02 Total surface tension energy: 0.16606 kJ/mol Total solvent accessible volume: 0 A^3 Total pressure*volume energy: 0 kJ/mol WCA dispersion Energies for each atom: WCA energy for atom 0: -6.909718345777E+00 WCA energy for atom 1: -6.909411348230E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365306965532E+01 kJ/mol ---------------------------------------- PRINT STATEMENTS print energy 1 (solv) - 2 (ref) end Local net energy (PE 0) = -1.125191605614E+03 kJ/mol Global net ELEC energy = -1.125191605614E+03 kJ/mol print force 1 (solv) - 2 (ref) end Printing per-atom forces (kJ/mol/A). Legend: tot n -- Total force for atom n qf n -- Fixed charge force for atom n db n -- Dielectric boundary force for atom n ib n -- Ionic boundary force for atom n tot all -- Total force for system qf 0 8.398642197664E+01 -1.324564203755E-05 -1.613436083011E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517416421E-05 -5.378919663831E-05 tot 0 9.013477903582E+01 -3.992081620176E-05 -6.992355746842E-05 qf 1 -8.466423642736E+01 -1.836748085161E-05 -3.062224261564E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230549E+00 -3.149946352664E-05 -6.291495498709E-05 tot 1 -8.178149719681E+01 -4.986694437825E-05 -9.353719760273E-05 tot all 8.353281839012E+00 -8.978776058001E-05 -1.634607550711E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365306965532E+01 kJ/mol print APOL force 1 (asolv) end Printing per atom forces (kJ/mol/A) Legend: tot n -- Total force for atom n sasa n -- SASA force for atom n sav n -- SAV force for atom n wca n -- WCA force for atom n tot all -- Total force for system sasa 0 -1.099776974333E+01 0.000000000000E+00 0.000000000000E+00 sav 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 0 -5.826577103767E-01 -2.766566538180E-05 -2.766098638935E-05 tot 0 -1.158042745371E+01 -2.766566538180E-05 -2.766098638935E-05 sasa 1 1.111862435589E+01 0.000000000000E+00 0.000000000000E+00 sav 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 wca 1 5.826650307914E-01 -2.767034437463E-05 -2.767796940038E-05 tot 1 1.170128938668E+01 -2.767034437463E-05 -2.767796940038E-05 tot all 1.208619329787E-01 -5.533600975643E-05 -5.533895578973E-05 ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 1 molecules Final memory usage: 60.711 MB total, 62.250 MB high water Thanks for using APBS! Checking for intermidiate energies in input file ion-pmf.out RESULT 7839.535983197 RESULT 8964.727588811 RESULT -1125.191605614 RESULT -13.65306965532 Testing computed result 7.839535983197E+03 against expected result 7.839536E+03 *** PASSED *** Testing computed result 8.964727588811E+03 against expected result 8.964728E+03 *** PASSED *** Testing computed result -1.125191605614E+03 against expected result -1.125192E+03 *** PASSED *** Elapsed time: 10.712109 seconds -------------------------------------------------------------------------------- Total elapsed time: 10.712109 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-protein section -------------------------------------------------------------------------------- Testing input file apbs-mol-pdiel2.in BINARY: apbs INPUT: apbs-mol-pdiel2.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-pdiel2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 7.525554553704E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.967613272771E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050875942181E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.559159533658E+01 kJ/mol Global net ELEC energy = 1.559159533658E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-pdiel2.out RESULT 7525.554553704 RESULT 2967.613272771 RESULT 10508.75942181 RESULT 15.59159533658 Testing computed result 7.525554553704E+03 against expected result 7.525555E+03 *** PASSED *** Testing computed result 2.967613272771E+03 against expected result 2.967613E+03 *** PASSED *** Testing computed result 1.050875942181E+04 against expected result 1.050876E+04 *** PASSED *** Testing computed result 1.559159533658E+01 against expected result 1.559160E+01 *** PASSED *** Elapsed time: 14.046691 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-pdiel2.in BINARY: apbs INPUT: apbs-smol-pdiel2.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-pdiel2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 7.561237446444E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.974076897757E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.055886976547E+04 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 2.355542126539E+01 kJ/mol Global net ELEC energy = 2.355542126539E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-pdiel2.out RESULT 7561.237446444 RESULT 2974.076897757 RESULT 10558.86976547 RESULT 23.55542126539 Testing computed result 7.561237446444E+03 against expected result 7.561237E+03 *** PASSED *** Testing computed result 2.974076897757E+03 against expected result 2.974077E+03 *** PASSED *** Testing computed result 1.055886976547E+04 against expected result 1.055887E+04 *** PASSED *** Testing computed result 2.355542126539E+01 against expected result 2.355542E+01 *** PASSED *** Elapsed time: 12.120784 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-pdiel12.in BINARY: apbs INPUT: apbs-mol-pdiel12.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-pdiel12.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.363584355927E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.110802147229E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.892691797082E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.802722643145E+01 kJ/mol Global net ELEC energy = 1.802722643145E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-pdiel12.out RESULT 1363.584355927 RESULT 511.0802147229 RESULT 1892.691797082 RESULT 18.02722643145 Testing computed result 1.363584355927E+03 against expected result 1.363584E+03 *** PASSED *** Testing computed result 5.110802147229E+02 against expected result 5.110802E+02 *** PASSED *** Testing computed result 1.892691797082E+03 against expected result 1.892692E+03 *** PASSED *** Testing computed result 1.802722643145E+01 against expected result 1.802723E+01 *** PASSED *** Elapsed time: 12.159696 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-pdiel12.in BINARY: apbs INPUT: apbs-smol-pdiel12.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-pdiel12.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from small491.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 259 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 1.97e+01 e Reading PQR-format atom data from 491.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (2.998e+02, 1.629e+02, 8.934e+01) Net charge 2.00e+00 e Reading PQR-format atom data from complex.pqr. 260 atoms Centered at (2.898e+02, 1.679e+02, 8.192e+01) Net charge 2.17e+01 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (protein): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.491 MB total, 518.491 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 1 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.366571366426E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (ion): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 499.862 MB total, 518.560 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 2 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 5.108315415905E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 13.5959 A Current memory usage: 518.565 MB total, 518.565 MB high water Using linear spline charge discretization. Grid dimensions: 129 x 129 x 129 Grid spacings: 0.523 x 0.523 x 0.586 Grid lengths: 67.000 x 67.000 x 75.000 Grid center: (289.756, 167.946, 81.925) Multigrid levels: 6 Molecule ID: 3 Nonlinear traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.050 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.050 M concentration 2.000 A-radius, -1.000 e-charge, 0.050 M concentration Solute dielectric: 12.000 Solvent dielectric: 78.400 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.896685358215E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (protein) - 2 (ion) end Local net energy (PE 0) = 1.928245019843E+01 kJ/mol Global net ELEC energy = 1.928245019843E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 518.565 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-pdiel12.out RESULT 1366.571366426 RESULT 510.8315415905 RESULT 1896.685358215 RESULT 19.28245019843 Testing computed result 1.366571366426E+03 against expected result 1.366571E+03 *** PASSED *** Testing computed result 5.108315415905E+02 against expected result 5.108315E+02 *** PASSED *** Testing computed result 1.896685358215E+03 against expected result 1.896685E+03 *** PASSED *** Testing computed result 1.928245019843E+01 against expected result 1.928245E+01 *** PASSED *** Elapsed time: 12.987010 seconds -------------------------------------------------------------------------------- Total elapsed time: 51.314181 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for pka-lig section -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in BINARY: apbs INPUT: apbs-mol-vdw.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.224988750664E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.049695084686E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.818450789522E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.008254338259E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.840918409896E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.113304681884E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 8.083515648803E+00 kJ/mol Global net ELEC energy = 8.083515648803E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-vdw.out RESULT 2224.988750664 RESULT 10496.95084686 RESULT 181845.0789522 RESULT 300825.4338259 RESULT 184091.8409896 RESULT 311330.4681884 RESULT 8.083515648803 Testing computed result 2.224988750664E+03 against expected result 2.224989E+03 *** PASSED *** Testing computed result 1.049695084686E+04 against expected result 1.049695E+04 *** PASSED *** Testing computed result 1.818450789522E+05 against expected result 1.818451E+05 *** PASSED *** Testing computed result 3.008254338259E+05 against expected result 3.008254E+05 *** PASSED *** Testing computed result 1.840918409896E+05 against expected result 1.840918E+05 *** PASSED *** Testing computed result 3.113304681884E+05 against expected result 3.113305E+05 *** PASSED *** Testing computed result 8.083515648803E+00 against expected result 8.083516E+00 *** PASSED *** Elapsed time: 17.883394 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in BINARY: apbs INPUT: apbs-smol-vdw.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-vdw.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 204.292 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.226793167046E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 204.292 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.050504485887E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 406.001 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.827976621645E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 291.151 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.017228546773E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 533.426 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.850819075387E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 292.063 MB total, 534.806 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.122488625388E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 2.096300255720E+01 kJ/mol Global net ELEC energy = 2.096300255720E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 534.806 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-vdw.out RESULT 2226.793167046 RESULT 10505.04485887 RESULT 182797.6621645 RESULT 301722.8546773 RESULT 185081.9075387 RESULT 312248.8625388 RESULT 20.9630025572 Testing computed result 2.226793167046E+03 against expected result 2.226793E+03 *** PASSED *** Testing computed result 1.050504485887E+04 against expected result 1.050504E+04 *** PASSED *** Testing computed result 1.827976621645E+05 against expected result 1.827977E+05 *** PASSED *** Testing computed result 3.017228546773E+05 against expected result 3.017229E+05 *** PASSED *** Testing computed result 1.850819075387E+05 against expected result 1.850819E+05 *** PASSED *** Testing computed result 3.122488625388E+05 against expected result 3.122489E+05 *** PASSED *** Testing computed result 2.096300255720E+01 against expected result 2.096296E+01 *** PASSED *** Elapsed time: 16.094578 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in BINARY: apbs INPUT: apbs-mol-surf.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.244350164274E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052149475373E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.862615690066E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.051810884053E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.886625455219E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.158218439277E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.192607686582E+02 kJ/mol Global net ELEC energy = 1.192607686582E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol-surf.out RESULT 2244.350164274 RESULT 10521.49475373 RESULT 186261.5690066 RESULT 305181.0884053 RESULT 188662.5455219 RESULT 315821.8439277 RESULT 119.2607686582 Testing computed result 2.244350164274E+03 against expected result 2.244350E+03 *** PASSED *** Testing computed result 1.052149475373E+04 against expected result 1.052149E+04 *** PASSED *** Testing computed result 1.862615690066E+05 against expected result 1.862616E+05 *** PASSED *** Testing computed result 3.051810884053E+05 against expected result 3.051811E+05 *** PASSED *** Testing computed result 1.886625455219E+05 against expected result 1.886625E+05 *** PASSED *** Testing computed result 3.158218439277E+05 against expected result 3.158218E+05 *** PASSED *** Testing computed result 1.192607686582E+02 against expected result 1.192608E+02 *** PASSED *** Elapsed time: 12.593155 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in BINARY: apbs INPUT: apbs-smol-surf.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol-surf.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from bx6_7_lig_apbs.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 47 atoms Centered at (2.482e+01, -3.315e+01, 2.154e+01) Net charge 1.11e-16 e Reading PQR-format atom data from bx6_7_apo_apbs.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3423 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Reading PQR-format atom data from bx6_7_bin_apbs.pqr. 3470 atoms Centered at (2.897e+01, -3.251e+01, 2.702e+01) Net charge 1.00e+00 e Preparing to run 6 PBE calculations. ---------------------------------------- CALCULATION #1 (lig-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 203.877 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.251466789420E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (lig-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 203.877 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 1 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.052814502873E+04 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (pka-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 405.586 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.864071689626E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #4 (pka-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.521 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 2 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.053319953673E+05 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #5 (complex-coarse): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 493.795 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.729 x 0.729 x 0.729 Grid lengths: 70.000 x 70.000 x 70.000 Grid center: (28.969, -32.507, 27.022) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Single Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.888027142979E+05 kJ/mol Calculating forces... [focusFillBound()]: WARNING: Unusually large potential values detected on the focusing boundary! Convergence not guaranteed for NPBE/NRPBE calculations! ---------------------------------------- CALCULATION #6 (complex-fine): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 251.858 MB total, 494.601 MB high water Using linear spline charge discretization. Grid dimensions: 97 x 97 x 97 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 24.000 x 24.000 x 24.000 Grid center: (24.822, -33.153, 21.545) Multigrid levels: 4 Molecule ID: 3 Linearized traditional PBE Boundary conditions from focusing 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 1.400 A Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 3.159690177241E+05 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 6 (complex-fine) - 2 (lig-fine) - 4 (pka-fine) end Local net energy (PE 0) = 1.088773280806E+02 kJ/mol Global net ELEC energy = 1.088773280806E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 494.601 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol-surf.out RESULT 2251.46678942 RESULT 10528.14502873 RESULT 186407.1689626 RESULT 305331.9953673 RESULT 188802.7142979 RESULT 315969.0177241 RESULT 108.8773280806 Testing computed result 2.251466789420E+03 against expected result 2.251467E+03 *** PASSED *** Testing computed result 1.052814502873E+04 against expected result 1.052815E+04 *** PASSED *** Testing computed result 1.864071689626E+05 against expected result 1.864072E+05 *** PASSED *** Testing computed result 3.053319953673E+05 against expected result 3.053320E+05 *** PASSED *** Testing computed result 1.888027142979E+05 against expected result 1.888027E+05 *** PASSED *** Testing computed result 3.159690177241E+05 against expected result 3.159690E+05 *** PASSED *** Testing computed result 1.088773280806E+02 against expected result 1.088773E+02 *** PASSED *** Elapsed time: 12.857568 seconds -------------------------------------------------------------------------------- Total elapsed time: 59.428695 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for point-pmf section -------------------------------------------------------------------------------- Testing input file complex-0_1.in BINARY: apbs INPUT: complex-0_1.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file complex-0_1.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol1.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_1.pqr. 2 atoms Centered at (-2.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 8.975920687031E+01 kJ/mol Fixed charge energy = 89.7592 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 88.6151 kJ/mol Per-atom energies: Atom 0: 8.975920687031E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.058277719334E+02 kJ/mol Fixed charge energy = 205.828 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 201.106 kJ/mol Per-atom energies: Atom 0: 1.069144350786E+02 kJ/mol Atom 1: 9.891333685475E+01 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 1.830820799027E+01 kJ/mol Global net ELEC energy = 1.830820799027E+01 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.067 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_1.out RESULT 97.76035707281 RESULT 89.75920687031 RESULT 205.8277719334 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 89.7592 RESULT 205.828 RESULT 96.5336 RESULT 88.6151 RESULT 201.106 RESULT 18.30820799027 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 8.975920687031E+01 against expected result 8.975921E+01 *** PASSED *** Testing computed result 2.058277719334E+02 against expected result 2.058278E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 8.975920000000E+01 against expected result 8.975920E+01 *** PASSED *** Testing computed result 2.058280000000E+02 against expected result 2.058280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 8.861510000000E+01 against expected result 8.861510E+01 *** PASSED *** Testing computed result 2.011060000000E+02 against expected result 2.011060E+02 *** PASSED *** Testing computed result 1.830820799027E+01 against expected result 1.830821E+01 *** PASSED *** Elapsed time: 0.766273 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in BINARY: apbs INPUT: complex-0_2.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file complex-0_2.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol2.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_2.pqr. 2 atoms Centered at (-2.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.656 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.084282010393E+02 kJ/mol Fixed charge energy = 208.428 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 203.83 kJ/mol Per-atom energies: Atom 0: 1.022136878480E+02 kJ/mol Atom 1: 1.062145131913E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 8.906694086751E+00 kJ/mol Global net ELEC energy = 8.906694086751E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_2.out RESULT 97.76035707281 RESULT 101.7611498797 RESULT 208.4282010393 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 101.761 RESULT 208.428 RESULT 96.5336 RESULT 100.656 RESULT 203.83 RESULT 8.906694086751 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.084282010393E+02 against expected result 2.084282E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.084280000000E+02 against expected result 2.084280E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006560000000E+02 against expected result 1.006560E+02 *** PASSED *** Testing computed result 2.038300000000E+02 against expected result 2.038300E+02 *** PASSED *** Testing computed result 8.906694086751E+00 against expected result 8.906694E+00 *** PASSED *** Elapsed time: 0.442427 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in BINARY: apbs INPUT: complex-0_3.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file complex-0_3.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol3.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (0.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_3.pqr. 2 atoms Centered at (-1.500e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.337661883222E+02 kJ/mol Fixed charge energy = 133.766 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 132.672 kJ/mol Per-atom energies: Atom 0: 1.337661883222E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.374361452120E+02 kJ/mol Fixed charge energy = 237.436 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 232.924 kJ/mol Per-atom energies: Atom 0: 1.007151570480E+02 kJ/mol Atom 1: 1.367209881640E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 5.909599816984E+00 kJ/mol Global net ELEC energy = 5.909599816984E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_3.out RESULT 97.76035707281 RESULT 133.7661883222 RESULT 237.436145212 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 133.766 RESULT 237.436 RESULT 96.5336 RESULT 132.672 RESULT 232.924 RESULT 5.909599816984 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.337661883222E+02 against expected result 1.337662E+02 *** PASSED *** Testing computed result 2.374361452120E+02 against expected result 2.374361E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.337660000000E+02 against expected result 1.337660E+02 *** PASSED *** Testing computed result 2.374360000000E+02 against expected result 2.374360E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.326720000000E+02 against expected result 1.326720E+02 *** PASSED *** Testing computed result 2.329240000000E+02 against expected result 2.329240E+02 *** PASSED *** Testing computed result 5.909599816984E+00 against expected result 5.909600E+00 *** PASSED *** Elapsed time: 0.629441 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in BINARY: apbs INPUT: complex-0_4.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file complex-0_4.in... rank 0 size 1... Parsed input file. Got paths for 3 molecules Reading PQR-format atom data from mol0.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (-3.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from mol4.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 1 atoms Centered at (1.000e+00, 0.000e+00, 0.000e+00) Net charge 1.00e+00 e Reading PQR-format atom data from complex-0_4.pqr. 2 atoms Centered at (-1.000e+00, 0.000e+00, 0.000e+00) Net charge 2.00e+00 e Preparing to run 3 PBE calculations. ---------------------------------------- CALCULATION #1 (point1): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.060 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 9.776035707281E+01 kJ/mol Fixed charge energy = 97.7604 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 96.5336 kJ/mol Per-atom energies: Atom 0: 9.776035707281E+01 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (point2): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.060 MB total, 61.067 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 1.017611498797E+02 kJ/mol Fixed charge energy = 101.761 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 100.654 kJ/mol Per-atom energies: Atom 0: 1.017611498797E+02 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (complex): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (0 A) for exclusion function Debye length: 0 A Current memory usage: 61.061 MB total, 61.068 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.210 x 0.210 x 0.210 Grid lengths: 13.440 x 13.440 x 13.440 Grid center: (0.000, 0.000, 0.000) Multigrid levels: 5 Molecule ID: 3 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 0 ion species (0.000 M ionic strength): Solute dielectric: 78.540 Solvent dielectric: 78.540 Using spline-based surface definition;window = 0.300 Temperature: 298.150 K Electrostatic energies will be calculated Total electrostatic energy = 2.039516519000E+02 kJ/mol Fixed charge energy = 203.952 kJ/mol Mobile charge energy = 0 kJ/mol Dielectric energy = 199.493 kJ/mol Per-atom energies: Atom 0: 9.997541697022E+01 kJ/mol Atom 1: 1.039762349297E+02 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 3 (complex) - 1 (point1) - 2 (point2) end Local net energy (PE 0) = 4.430144947418E+00 kJ/mol Global net ELEC energy = 4.430144947418E+00 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 3 molecules Final memory usage: 0.001 MB total, 61.068 MB high water Thanks for using APBS! Checking for intermidiate energies in input file complex-0_4.out RESULT 97.76035707281 RESULT 101.7611498797 RESULT 203.9516519 RESULT 0.0 RESULT 0.0 RESULT 0.0 RESULT 97.7604 RESULT 101.761 RESULT 203.952 RESULT 96.5336 RESULT 100.654 RESULT 199.493 RESULT 4.430144947418 Testing computed result 9.776035707281E+01 against expected result 9.776036E+01 *** PASSED *** Testing computed result 1.017611498797E+02 against expected result 1.017611E+02 *** PASSED *** Testing computed result 2.039516519000E+02 against expected result 2.039517E+02 *** PASSED *** Testing computed result 9.776040000000E+01 against expected result 9.776040E+01 *** PASSED *** Testing computed result 1.017610000000E+02 against expected result 1.017610E+02 *** PASSED *** Testing computed result 2.039520000000E+02 against expected result 2.039520E+02 *** PASSED *** Testing computed result 9.653360000000E+01 against expected result 9.653360E+01 *** PASSED *** Testing computed result 1.006540000000E+02 against expected result 1.006540E+02 *** PASSED *** Testing computed result 1.994930000000E+02 against expected result 1.994930E+02 *** PASSED *** Testing computed result 4.430144947418E+00 against expected result 4.430145E+00 *** PASSED *** Elapsed time: 0.583211 seconds -------------------------------------------------------------------------------- Total elapsed time: 2.421352 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for solv section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: apbs INPUT: apbs-mol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-mol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847663548071E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.883912182952E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.732623683321E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition; no smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.123035854133E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.624863488075E+01 kJ/mol Global net ELEC energy = -3.624863488075E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.904121708125E+02 kJ/mol Global net ELEC energy = -3.904121708125E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.541635359318E+02 kJ/mol Global net ELEC energy = -3.541635359318E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-mol.out RESULT 1847.663548071 RESULT 1883.912182952 RESULT 2732.623683321 RESULT 3123.035854133 RESULT -36.24863488075 RESULT -390.4121708125 RESULT -354.1635359318 Testing computed result 1.847663548071E+03 against expected result 1.847664E+03 *** PASSED *** Testing computed result 1.883912182952E+03 against expected result 1.883912E+03 *** PASSED *** Testing computed result 2.732623683321E+03 against expected result 2.732624E+03 *** PASSED *** Testing computed result 3.123035854133E+03 against expected result 3.123036E+03 *** PASSED *** Testing computed result -3.624863488075E+01 against expected result -3.624863E+01 *** PASSED *** Testing computed result -3.904121708125E+02 against expected result -3.904121E+02 *** PASSED *** Testing computed result -3.541635359318E+02 against expected result -3.541635E+02 *** PASSED *** Elapsed time: 0.965420 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: apbs INPUT: apbs-smol.in Vio_ctor2: Gethostbyname fail INET sock <> dueto Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. ---------------------------------------------------------------------- APBS -- Adaptive Poisson-Boltzmann Solver Version 3.0 Nathan A. Baker (nathan.baker@pnnl.gov) Pacific Northwest National Laboratory Additional contributing authors listed in the code documentation. Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department of Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2020, Nathan A. Baker. Portions Copyright (c) 1999-2002, The Regents of the University of California. Portions Copyright (c) 1995, Michael Holst. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * Neither the name of the developer nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. ---------------------------------------------------------------------- APBS uses FETK (the Finite Element ToolKit) to solve the Poisson-Boltzmann equation numerically. FETK is a portable collection of finite element modeling class libraries developed by the Michael Holst research group and written in an object-oriented form of C. FEtk is designed to solve general coupled systems of nonlinear partial differential equations using adaptive finite element methods, inexact Newton methods, and algebraic multilevel methods. More information about FEtk may be found at . ---------------------------------------------------------------------- APBS also uses Aqua to solve the Poisson-Boltzmann equation numerically. Aqua is a modified form of the Holst group PMG library which has been modified by Patrice Koehl for improved efficiency and memory usage when solving the Poisson-Boltzmann equation. ---------------------------------------------------------------------- Please cite your use of APBS as: Baker NA, Sept D, Joseph S, Holst MJ, McCammon JA. Electrostatics of nanosystems: application to microtubules and the ribosome. Proc. Natl. Acad. Sci. USA 98, 10037-10041 2001. This executable compiled on Jul 27 2026 at 00:00:00 Parsing input file apbs-smol.in... rank 0 size 1... Parsed input file. Got paths for 2 molecules Reading PQR-format atom data from methanol.pqr. Vio_ctor2: Gethostbyname fail INET sock <> dueto asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 3 atoms Centered at (3.086e-01, 0.000e+00, -2.417e-01) Net charge 5.55e-17 e Reading PQR-format atom data from methoxide.pqr. 2 atoms Centered at (0.000e+00, 0.000e+00, -1.279e-01) Net charge -1.00e+00 e Preparing to run 4 PBE calculations. ---------------------------------------- CALCULATION #1 (methanol-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.253 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.847860440020E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #2 (methanol-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.253 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.309, 0.000, -0.242) Multigrid levels: 5 Molecule ID: 1 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 1.885436377745E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #3 (methoxide-solv): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 78.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 2.734040568569E+03 kJ/mol Calculating forces... ---------------------------------------- CALCULATION #4 (methoxide-ref): MULTIGRID Setting up problem... Vpbe_ctor: Using max ion radius (2 A) for exclusion function Debye length: 0 A Current memory usage: 61.250 MB total, 61.328 MB high water Using linear spline charge discretization. Grid dimensions: 65 x 65 x 65 Grid spacings: 0.250 x 0.250 x 0.250 Grid lengths: 16.000 x 16.000 x 16.000 Grid center: (0.000, 0.000, -0.128) Multigrid levels: 5 Molecule ID: 2 Linearized traditional PBE Multiple Debye-Huckel sphere boundary conditions 2 ion species (0.000 M ionic strength): 2.000 A-radius, 1.000 e-charge, 0.000 M concentration 2.000 A-radius, -1.000 e-charge, 0.000 M concentration Solute dielectric: 2.000 Solvent dielectric: 1.000 Using "molecular" surface definition;harmonic average smoothing Solvent probe radius: 0.000 A Temperature: 300.000 K Electrostatic energies will be calculated Total electrostatic energy = 3.125279428954E+03 kJ/mol Calculating forces... ---------------------------------------- PRINT STATEMENTS print energy 1 (methanol-solv) - 2 (methanol-ref) end Local net energy (PE 0) = -3.757593772492E+01 kJ/mol Global net ELEC energy = -3.757593772492E+01 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) end Local net energy (PE 0) = -3.912388603848E+02 kJ/mol Global net ELEC energy = -3.912388603848E+02 kJ/mol print energy 3 (methoxide-solv) - 4 (methoxide-ref) - 1 (methanol-solv) + 2 (methanol-ref) end Local net energy (PE 0) = -3.536629226599E+02 kJ/mol Global net ELEC energy = -3.536629226599E+02 kJ/mol ---------------------------------------- CLEANING UP AND SHUTTING DOWN... Destroying force arrays. No energy arrays to destroy. Destroying multigrid structures. Destroying 2 molecules Final memory usage: 0.001 MB total, 61.328 MB high water Thanks for using APBS! Checking for intermidiate energies in input file apbs-smol.out RESULT 1847.86044002 RESULT 1885.436377745 RESULT 2734.040568569 RESULT 3125.279428954 RESULT -37.57593772492 RESULT -391.2388603848 RESULT -353.6629226599 Testing computed result 1.847860440020E+03 against expected result 1.847860E+03 *** PASSED *** Testing computed result 1.885436377745E+03 against expected result 1.885436E+03 *** PASSED *** Testing computed result 2.734040568569E+03 against expected result 2.734041E+03 *** PASSED *** Testing computed result 3.125279428954E+03 against expected result 3.125279E+03 *** PASSED *** Testing computed result -3.757593772492E+01 against expected result -3.757594E+01 *** PASSED *** Testing computed result -3.912388603848E+02 against expected result -3.912388E+02 *** PASSED *** Testing computed result -3.536629226599E+02 against expected result -3.536629E+02 *** PASSED *** Elapsed time: 0.877370 seconds -------------------------------------------------------------------------------- Total elapsed time: 1.842790 seconds Test results have been logged -------------------------------------------------------------------------------- Processing files: apbs-3.0.0-38.fc45.ppc64le Provides: apbs = 3.0.0-38.fc45 apbs(ppc-64) = 3.0.0-38.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libapbs.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libm.so.6()(64bit) libmaloc.so.1()(64bit) rtld(GNU_HASH) Processing files: apbs-tools-3.0.0-38.fc45.ppc64le + RPM_EC=0 ++ jobs -p + exit 0 warning: absolute symlink: /usr/bin/apbs-psize.py -> /usr/lib64/python3.15/site-packages/apbs/psize.py Provides: apbs-tools = 3.0.0-38.fc45 apbs-tools(ppc-64) = 3.0.0-38.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libapbs.so.1()(64bit) libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.34)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libmaloc.so.1()(64bit) rtld(GNU_HASH) Processing files: apbs-libs-3.0.0-38.fc45.ppc64le Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.2DKxiP + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + cd apbs-3.0.0 + DOCDIR=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/doc/apbs-libs + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/doc/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/README.md /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/doc/apbs-libs + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.tAbmhp + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + cd apbs-3.0.0 + LICENSEDIR=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-libs + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/LICENSE.md /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/COPYING /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/iapbs-COPYING /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-libs + cp -pr /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/contrib/iapbs/iapbs-LGPLv2 /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-libs + RPM_EC=0 ++ jobs -p + exit 0 Provides: apbs-libs = 3.0.0-38.fc45 apbs-libs(ppc-64) = 3.0.0-38.fc45 libapbs.so.1()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.44)(64bit) rtld(GNU_HASH) Processing files: apbs-devel-3.0.0-38.fc45.ppc64le Provides: apbs-devel = 3.0.0-38.fc45 apbs-devel(ppc-64) = 3.0.0-38.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: libapbs.so.1()(64bit) Processing files: apbs-doc-3.0.0-38.fc45.noarch Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.f1eFC9 + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + cd apbs-3.0.0 + DOCDIR=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/doc/apbs-doc + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/doc/apbs-doc + cp -pr /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/redhat-linux-build/doc /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/doc/apbs-doc + RPM_EC=0 ++ jobs -p + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.KWINvs + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + cd apbs-3.0.0 + LICENSEDIR=/builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-doc + export LC_ALL=C.UTF-8 + LC_ALL=C.UTF-8 + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-doc + cp -pr /builddir/build/BUILD/apbs-3.0.0-build/apbs-3.0.0/LICENSE.md /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT/usr/share/licenses/apbs-doc + RPM_EC=0 ++ jobs -p + exit 0 Provides: apbs-doc = 3.0.0-38.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: python3-apbs-3.0.0-38.fc45.ppc64le Provides: python-apbs = 3.0.0-38.fc45 python3-apbs = 3.0.0-38.fc45 python3-apbs(ppc-64) = 3.0.0-38.fc45 python3.15-apbs = 3.0.0-38.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PartialHardlinkSets) <= 4.0.4-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Requires: /usr/bin/python3 libc.so.6()(64bit) libc.so.6(GLIBC_2.17)(64bit) libc.so.6(GLIBC_2.32)(64bit) libc.so.6(GLIBC_2.38)(64bit) libc.so.6(GLIBC_ABI_DT_RELR)(64bit) libgcc_s.so.1()(64bit) libgcc_s.so.1(GCC_3.3.1)(64bit) libgomp.so.1()(64bit) libgomp.so.1(GOMP_4.0)(64bit) libgomp.so.1(OMP_1.0)(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.17)(64bit) libm.so.6(GLIBC_2.29)(64bit) libm.so.6(GLIBC_2.44)(64bit) libmaloc.so.1()(64bit) libpython3.15.so.1.0()(64bit) python(abi) = 3.15 rtld(GNU_HASH) Obsoletes: apbs-libs < 0:3.0.0-11 python-apbs < 3.0.0-38.fc45 Processing files: apbs-debugsource-3.0.0-38.fc45.ppc64le Provides: apbs-debugsource = 3.0.0-38.fc45 apbs-debugsource(ppc-64) = 3.0.0-38.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: apbs-debuginfo-3.0.0-38.fc45.ppc64le Provides: apbs-debuginfo = 3.0.0-38.fc45 apbs-debuginfo(ppc-64) = 3.0.0-38.fc45 debuginfo(build-id) = 566f088fd8715fe4f33718c1503f1d7f9daebadf Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(ppc-64) = 3.0.0-38.fc45 Processing files: apbs-tools-debuginfo-3.0.0-38.fc45.ppc64le Provides: apbs-tools-debuginfo = 3.0.0-38.fc45 apbs-tools-debuginfo(ppc-64) = 3.0.0-38.fc45 debuginfo(build-id) = 0ada85076f776312244e7563e51f1aeb6e5df800 debuginfo(build-id) = 0fe2569c42a25f6a61eab4e193717f1cc3da5bf2 debuginfo(build-id) = 140da94e7090bb61f704831d760e73ad6ef44d9e debuginfo(build-id) = 2675fbdb0ad43d9133c5763a74d4ef9c69484298 debuginfo(build-id) = 3dc2dfe27a7e87564887abea8e95dbb0f49f5ff1 debuginfo(build-id) = 60c49947ea0f78bbe6c502818e1ca8df1dbef0be debuginfo(build-id) = 68ac770bfd37b158e5c0848e280c728619eda3dc debuginfo(build-id) = 8ab74f807a2b8baebe63e159118ce9b2fcfed231 debuginfo(build-id) = 937389fe7cff52ec78b78aec1b05b152cca52c95 debuginfo(build-id) = 9d6149f881077bbde95910f78d1e6149618c7ff3 debuginfo(build-id) = 9feb4df1e9b5c82640686205983f17f215093001 debuginfo(build-id) = a456ff93a8591bf416226b97a8d75ffc0aed7572 debuginfo(build-id) = a8a2447c4cb9b9f877c316459c9ed1f14ed7044a debuginfo(build-id) = d1747f80dfdfa5be934c9a212b6490c3390a0d93 debuginfo(build-id) = dd3737f2824c450cf49ba43fbc5ab724d1f54147 debuginfo(build-id) = dff8cc382b2041a1e92cdee424c0df3a05b05907 debuginfo(build-id) = f521152d26a7c4e68192a32ff539b921bd4cfa96 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(ppc-64) = 3.0.0-38.fc45 Processing files: apbs-libs-debuginfo-3.0.0-38.fc45.ppc64le Provides: apbs-libs-debuginfo = 3.0.0-38.fc45 apbs-libs-debuginfo(ppc-64) = 3.0.0-38.fc45 debuginfo(build-id) = da7c081cf26d1c056db2884c6e041c570e6365be libapbs.so.1-3.0.0-38.fc45.ppc64le.debug()(64bit) Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(ppc-64) = 3.0.0-38.fc45 Processing files: python3-apbs-debuginfo-3.0.0-38.fc45.ppc64le Provides: debuginfo(build-id) = 33ff0d4a41e9367ec9be0f7b8de676bd58e0751b python-apbs-debuginfo = 3.0.0-38.fc45 python3-apbs-debuginfo = 3.0.0-38.fc45 python3-apbs-debuginfo(ppc-64) = 3.0.0-38.fc45 python3.15-apbs-debuginfo = 3.0.0-38.fc45 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(ppc-64) = 3.0.0-38.fc45 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILD/apbs-3.0.0-build/BUILDROOT Wrote: /builddir/build/RPMS/apbs-tools-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/apbs-libs-debuginfo-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/python3-apbs-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/python3-apbs-debuginfo-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/apbs-libs-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/apbs-devel-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/apbs-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/apbs-debuginfo-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/apbs-tools-debuginfo-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/apbs-debugsource-3.0.0-38.fc45.ppc64le.rpm Wrote: /builddir/build/RPMS/apbs-doc-3.0.0-38.fc45.noarch.rpm Executing(rmbuild): /bin/sh -e /var/tmp/rpm-tmp.ylNOSW + umask 022 + cd /builddir/build/BUILD/apbs-3.0.0-build + test -d /builddir/build/BUILD/apbs-3.0.0-build + /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w /builddir/build/BUILD/apbs-3.0.0-build + rm -rf /builddir/build/BUILD/apbs-3.0.0-build + RPM_EC=0 ++ jobs -p + exit 0 RPM build warnings: absolute symlink: /usr/bin/apbs-psize.py -> /usr/lib64/python3.15/site-packages/apbs/psize.py Finish: rpmbuild apbs-3.0.0-38.fc45.src.rpm Finish: build phase for apbs-3.0.0-38.fc45.src.rpm INFO: chroot_scan: 1 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/fedora-rawhide-ppc64le-1785937922.137901/root/var/log/dnf5.log INFO: chroot_scan: creating tarball /var/lib/copr-rpmbuild/results/chroot_scan.tar.gz /bin/tar: Removing leading `/' from member names INFO: Done(/var/lib/copr-rpmbuild/results/apbs-3.0.0-38.fc45.src.rpm) Config(child) 30 minutes 11 seconds INFO: Results and/or logs in: /var/lib/copr-rpmbuild/results INFO: Cleaning up build root ('cleanup_on_success=True') Start: clean chroot INFO: unmounting tmpfs. Finish: clean chroot Finish: run Running RPMResults tool Package info: { "packages": [ { "name": "apbs-debuginfo", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "apbs-doc", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "noarch" }, { "name": "apbs-tools", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "python3-apbs-debuginfo", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "apbs-libs-debuginfo", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "apbs-tools-debuginfo", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "apbs-libs", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "apbs-debugsource", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "python3-apbs", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "apbs", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "src" }, { "name": "apbs-devel", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" }, { "name": "apbs", "epoch": null, "version": "3.0.0", "release": "38.fc45", "arch": "ppc64le" } ] } RPMResults finished