Warning: Permanently added '2620:52:3:1:dead:beef:cafe:c1c8' (ED25519) to the list of known hosts. Running: /usr/bin/copr-rpmbuild --verbose --drop-resultdir --build-id 5361896 --chroot epel-8-x86_64 --detached Version: 0.64 PID: 5048 Logging PID: 5049 Task: {'appstream': False, 'background': False, 'build_id': 5361896, 'buildroot_pkgs': [], 'chroot': 'epel-8-x86_64', 'enable_net': False, 'fedora_review': False, 'git_hash': 'cc3c10fbd1fc46eab252000e197d0768480f6d64', 'git_repo': 'https://copr-dist-git.fedorainfracloud.org/git/wibi-sk/pymol/apbs', 'isolation': 'default', 'memory_reqs': 2048, 'package_name': 'apbs', 'package_version': '3.0.0-17.fc37', 'project_dirname': 'pymol', 'project_name': 'pymol', 'project_owner': 'wibi-sk', 'repos': [{'baseurl': 'https://download.copr.fedorainfracloud.org/results/wibi-sk/pymol/epel-8-x86_64/', 'id': 'copr_base', 'name': 'Copr repository'}], 'sandbox': 'wibi-sk/pymol--wibi-sk', 'source_json': {}, 'source_type': None, 'submitter': 'wibi-sk', 'tags': [], 'task_id': '5361896-epel-8-x86_64', 'timeout': 18000, 'uses_devel_repo': False, 'with_opts': [], 'without_opts': []} Running: git clone https://copr-dist-git.fedorainfracloud.org/git/wibi-sk/pymol/apbs /var/lib/copr-rpmbuild/workspace/workdir-lmv27hnw/apbs --depth 500 --no-single-branch --recursive cmd: ['git', 'clone', 'https://copr-dist-git.fedorainfracloud.org/git/wibi-sk/pymol/apbs', '/var/lib/copr-rpmbuild/workspace/workdir-lmv27hnw/apbs', '--depth', '500', '--no-single-branch', '--recursive'] cwd: . rc: 0 stdout: stderr: Cloning into '/var/lib/copr-rpmbuild/workspace/workdir-lmv27hnw/apbs'... Running: git checkout cc3c10fbd1fc46eab252000e197d0768480f6d64 cmd: ['git', 'checkout', 'cc3c10fbd1fc46eab252000e197d0768480f6d64'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-lmv27hnw/apbs rc: 0 stdout: stderr: Note: switching to 'cc3c10fbd1fc46eab252000e197d0768480f6d64'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by switching back to a branch. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -c with the switch command. Example: git switch -c Or undo this operation with: git switch - Turn off this advice by setting config variable advice.detachedHead to false HEAD is now at cc3c10f automatic import of apbs Running: copr-distgit-client sources /usr/bin/tail: /var/lib/copr-rpmbuild/main.log: file truncated cmd: ['copr-distgit-client', 'sources'] cwd: /var/lib/copr-rpmbuild/workspace/workdir-lmv27hnw/apbs rc: 0 stdout: stderr: INFO: Reading stdout from command: git rev-parse --abbrev-ref HEAD INFO: Reading stdout from command: git rev-parse HEAD INFO: Reading sources specification file: sources INFO: Downloading apbs-3.0.0.tar.gz INFO: Calling: curl -H Pragma: -o apbs-3.0.0.tar.gz --location --remote-time --show-error --fail https://copr-dist-git.fedorainfracloud.org/repo/pkgs/wibi-sk/pymol/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 25.9M 100 25.9M 0 0 27.7M 0 --:--:-- --:--:-- --:--:-- 27.7M INFO: Reading stdout from command: md5sum apbs-3.0.0.tar.gz Running (timeout=18000): unbuffer mock --buildsrpm --spec /var/lib/copr-rpmbuild/workspace/workdir-lmv27hnw/apbs/apbs.spec --sources /var/lib/copr-rpmbuild/workspace/workdir-lmv27hnw/apbs --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1675078509.656443 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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-lmv27hnw/apbs/apbs.spec) Config(rhel+epel-8-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-8-x86_64-bootstrap-1675078509.656443/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Start(bootstrap): dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity Copr repository 146 kB/s | 19 kB 00:00 Red Hat Enterprise Linux - BaseOS 43 MB/s | 56 MB 00:01 Red Hat Enterprise Linux - AppStream 22 MB/s | 52 MB 00:02 Red Hat Enterprise Linux - CodeReady Linux Buil 7.5 MB/s | 8.8 MB 00:01 Extra Packages for Enterprise Linux 8 - x86_64 32 MB/s | 13 MB 00:00 Dependencies resolved. =================================================================================================== Package Arch Version Repository Size =================================================================================================== Installing: dnf noarch 4.7.0-11.el8 rhel-baseos 541 k dnf-plugins-core noarch 4.0.21-14.1.el8 rhel-baseos 72 k subscription-manager x86_64 1.28.32-1.el8 rhel-baseos 1.2 M Installing dependencies: acl x86_64 2.2.53-1.el8 rhel-baseos 81 k audit-libs x86_64 3.0.7-4.el8 rhel-baseos 123 k basesystem noarch 11-5.el8 rhel-baseos 11 k bash x86_64 4.4.20-4.el8_6 rhel-baseos 1.5 M brotli x86_64 1.0.6-3.el8 rhel-baseos 323 k bzip2-libs x86_64 1.0.6-26.el8 rhel-baseos 48 k ca-certificates noarch 2022.2.54-80.2.el8_6 rhel-baseos 921 k chkconfig x86_64 1.19.1-1.el8 rhel-baseos 198 k coreutils x86_64 8.30-13.el8 rhel-baseos 1.2 M coreutils-common x86_64 8.30-13.el8 rhel-baseos 2.0 M cracklib x86_64 2.9.6-15.el8 rhel-baseos 93 k cracklib-dicts x86_64 2.9.6-15.el8 rhel-baseos 4.0 M crypto-policies noarch 20211116-1.gitae470d6.el8 rhel-baseos 64 k cryptsetup-libs x86_64 2.3.7-2.el8 rhel-baseos 488 k curl x86_64 7.61.1-25.el8_7.1 rhel-baseos 352 k cyrus-sasl-lib x86_64 2.1.27-6.el8_5 rhel-baseos 123 k dbus x86_64 1:1.12.8-23.el8_7.1 rhel-baseos 42 k dbus-common noarch 1:1.12.8-23.el8_7.1 rhel-baseos 47 k dbus-daemon x86_64 1:1.12.8-23.el8_7.1 rhel-baseos 241 k dbus-glib x86_64 0.110-2.el8 rhel-baseos 127 k dbus-libs x86_64 1:1.12.8-23.el8_7.1 rhel-baseos 185 k dbus-tools x86_64 1:1.12.8-23.el8_7.1 rhel-baseos 86 k device-mapper x86_64 8:1.02.181-6.el8 rhel-baseos 377 k device-mapper-libs x86_64 8:1.02.181-6.el8 rhel-baseos 410 k dmidecode x86_64 1:3.3-4.el8 rhel-baseos 92 k dnf-data noarch 4.7.0-11.el8 rhel-baseos 155 k dnf-plugin-subscription-manager x86_64 1.28.32-1.el8 rhel-baseos 314 k elfutils-default-yama-scope noarch 0.187-4.el8 rhel-baseos 52 k elfutils-libelf x86_64 0.187-4.el8 rhel-baseos 231 k elfutils-libs x86_64 0.187-4.el8 rhel-baseos 297 k expat x86_64 2.2.5-10.el8_7.1 rhel-baseos 113 k file-libs x86_64 5.33-21.el8 rhel-baseos 543 k filesystem x86_64 3.8-6.el8 rhel-baseos 1.1 M gawk x86_64 4.2.1-4.el8 rhel-baseos 1.1 M gdbm x86_64 1:1.18-2.el8 rhel-baseos 130 k gdbm-libs x86_64 1:1.18-2.el8 rhel-baseos 60 k glib2 x86_64 2.56.4-159.el8 rhel-baseos 2.5 M glibc x86_64 2.28-211.el8 rhel-baseos 2.2 M glibc-all-langpacks x86_64 2.28-211.el8 rhel-baseos 26 M glibc-common x86_64 2.28-211.el8 rhel-baseos 1.0 M gmp x86_64 1:6.1.2-10.el8 rhel-baseos 321 k gnupg2 x86_64 2.2.20-3.el8_6 rhel-baseos 2.4 M gnutls x86_64 3.6.16-5.el8_6 rhel-baseos 1.0 M gobject-introspection x86_64 1.56.1-1.el8 rhel-baseos 255 k gpgme x86_64 1.13.1-11.el8 rhel-baseos 336 k grep x86_64 3.1-6.el8 rhel-baseos 274 k gzip x86_64 1.9-13.el8_5 rhel-baseos 167 k ima-evm-utils x86_64 1.3.2-12.el8 rhel-baseos 64 k info x86_64 6.5-7.el8 rhel-baseos 198 k json-c x86_64 0.13.1-3.el8 rhel-baseos 41 k json-glib x86_64 1.4.4-1.el8 rhel-baseos 144 k keyutils-libs x86_64 1.5.10-9.el8 rhel-baseos 34 k kmod-libs x86_64 25-19.el8 rhel-baseos 68 k krb5-libs x86_64 1.18.2-22.el8_7 rhel-baseos 840 k libacl x86_64 2.2.53-1.el8 rhel-baseos 35 k libarchive x86_64 3.3.3-4.el8 rhel-baseos 360 k libassuan x86_64 2.5.1-3.el8 rhel-baseos 83 k libattr x86_64 2.4.48-3.el8 rhel-baseos 27 k libblkid x86_64 2.32.1-39.el8_7 rhel-baseos 220 k libcap x86_64 2.48-4.el8 rhel-baseos 74 k libcap-ng x86_64 0.7.11-1.el8 rhel-baseos 33 k libcom_err x86_64 1.45.6-5.el8 rhel-baseos 49 k libcomps x86_64 0.1.18-1.el8 rhel-baseos 82 k libcurl x86_64 7.61.1-25.el8_7.1 rhel-baseos 302 k libdb x86_64 5.3.28-42.el8_4 rhel-baseos 751 k libdb-utils x86_64 5.3.28-42.el8_4 rhel-baseos 150 k libdnf x86_64 0.63.0-11.1.el8 rhel-baseos 710 k libfdisk x86_64 2.32.1-39.el8_7 rhel-baseos 253 k libffi x86_64 3.1-23.el8 rhel-baseos 37 k libgcc x86_64 8.5.0-16.el8_7 rhel-baseos 81 k libgcrypt x86_64 1.8.5-7.el8_6 rhel-baseos 463 k libgpg-error x86_64 1.31-1.el8 rhel-baseos 242 k libidn2 x86_64 2.2.0-1.el8 rhel-baseos 94 k libksba x86_64 1.3.5-8.el8_6 rhel-baseos 134 k libmodulemd x86_64 2.13.0-1.el8 rhel-baseos 233 k libmount x86_64 2.32.1-39.el8_7 rhel-baseos 236 k libnghttp2 x86_64 1.33.0-3.el8_2.1 rhel-baseos 77 k libnl3 x86_64 3.7.0-1.el8 rhel-baseos 337 k libnsl2 x86_64 1.2.0-2.20180605git4a062cf.el8 rhel-baseos 58 k libpsl x86_64 0.20.2-6.el8 rhel-baseos 61 k libpwquality x86_64 1.4.4-5.el8 rhel-baseos 107 k librepo x86_64 1.14.2-3.el8 rhel-baseos 93 k libreport-filesystem x86_64 2.9.5-15.el8 rhel-baseos 21 k librhsm x86_64 0.0.3-4.el8 rhel-baseos 33 k libseccomp x86_64 2.5.2-1.el8 rhel-baseos 71 k libselinux x86_64 2.9-6.el8 rhel-baseos 165 k libsemanage x86_64 2.9-9.el8_6 rhel-baseos 168 k libsepol x86_64 2.9-3.el8 rhel-baseos 340 k libsigsegv x86_64 2.11-5.el8 rhel-baseos 30 k libsmartcols x86_64 2.32.1-39.el8_7 rhel-baseos 179 k libsolv x86_64 0.7.20-4.el8_7 rhel-baseos 376 k libssh x86_64 0.9.6-3.el8 rhel-baseos 216 k libssh-config noarch 0.9.6-3.el8 rhel-baseos 19 k libstdc++ x86_64 8.5.0-16.el8_7 rhel-baseos 454 k libtasn1 x86_64 4.13-4.el8_7 rhel-baseos 76 k libtirpc x86_64 1.1.4-8.el8 rhel-baseos 113 k libunistring x86_64 0.9.9-3.el8 rhel-baseos 422 k libusbx x86_64 1.0.23-4.el8 rhel-baseos 74 k libuser x86_64 0.62-24.el8 rhel-baseos 414 k libutempter x86_64 1.1.6-14.el8 rhel-baseos 32 k libuuid x86_64 2.32.1-39.el8_7 rhel-baseos 98 k libverto x86_64 0.3.2-2.el8 rhel-baseos 24 k libxcrypt x86_64 4.1.1-6.el8 rhel-baseos 73 k libxml2 x86_64 2.9.7-15.el8_7.1 rhel-baseos 697 k libyaml x86_64 0.1.7-5.el8 rhel-baseos 61 k libzstd x86_64 1.4.4-1.el8 rhel-baseos 266 k lua-libs x86_64 5.3.4-12.el8 rhel-baseos 118 k lz4-libs x86_64 1.8.3-3.el8_4 rhel-baseos 66 k mpfr x86_64 3.1.6-1.el8 rhel-baseos 221 k ncurses x86_64 6.1-9.20180224.el8 rhel-baseos 387 k ncurses-base noarch 6.1-9.20180224.el8 rhel-baseos 81 k ncurses-libs x86_64 6.1-9.20180224.el8 rhel-baseos 334 k nettle x86_64 3.4.1-7.el8 rhel-baseos 301 k npth x86_64 1.5-4.el8 rhel-baseos 26 k openldap x86_64 2.4.46-18.el8 rhel-baseos 352 k openssl-libs x86_64 1:1.1.1k-7.el8_6 rhel-baseos 1.5 M p11-kit x86_64 0.23.22-1.el8 rhel-baseos 324 k p11-kit-trust x86_64 0.23.22-1.el8 rhel-baseos 137 k pam x86_64 1.3.1-22.el8 rhel-baseos 743 k passwd x86_64 0.80-4.el8 rhel-baseos 115 k pcre x86_64 8.42-6.el8 rhel-baseos 211 k pcre2 x86_64 10.32-3.el8_6 rhel-baseos 247 k platform-python x86_64 3.6.8-48.el8_7 rhel-baseos 86 k platform-python-setuptools noarch 39.2.0-6.el8 rhel-baseos 632 k popt x86_64 1.18-1.el8 rhel-baseos 61 k publicsuffix-list-dafsa noarch 20180723-1.el8 rhel-baseos 56 k python3-chardet noarch 3.0.4-7.el8 rhel-baseos 195 k python3-cloud-what x86_64 1.28.32-1.el8 rhel-baseos 313 k python3-dateutil noarch 1:2.6.1-6.el8 rhel-baseos 251 k python3-dbus x86_64 1.2.4-15.el8 rhel-baseos 134 k python3-decorator noarch 4.2.1-2.el8 rhel-baseos 27 k python3-dmidecode x86_64 3.12.2-15.el8 rhel-baseos 94 k python3-dnf noarch 4.7.0-11.el8 rhel-baseos 548 k python3-dnf-plugins-core noarch 4.0.21-14.1.el8 rhel-baseos 243 k python3-ethtool x86_64 0.14-5.el8 rhel-baseos 45 k python3-gobject-base x86_64 3.28.3-2.el8 rhel-baseos 313 k python3-gpg x86_64 1.13.1-11.el8 rhel-baseos 244 k python3-hawkey x86_64 0.63.0-11.1.el8 rhel-baseos 117 k python3-idna noarch 2.5-5.el8 rhel-baseos 97 k python3-iniparse noarch 0.4-31.el8 rhel-baseos 49 k python3-inotify noarch 0.9.6-13.el8 rhel-baseos 57 k python3-libcomps x86_64 0.1.18-1.el8 rhel-baseos 52 k python3-libdnf x86_64 0.63.0-11.1.el8 rhel-baseos 779 k python3-librepo x86_64 1.14.2-3.el8 rhel-baseos 54 k python3-libs x86_64 3.6.8-48.el8_7 rhel-baseos 7.8 M python3-libxml2 x86_64 2.9.7-15.el8_7.1 rhel-baseos 238 k python3-pip-wheel noarch 9.0.3-22.el8 rhel-baseos 895 k python3-pysocks noarch 1.6.8-3.el8 rhel-baseos 34 k python3-requests noarch 2.20.0-2.1.el8_1 rhel-baseos 123 k python3-rpm x86_64 4.14.3-24.el8_7 rhel-baseos 155 k python3-setuptools-wheel noarch 39.2.0-6.el8 rhel-baseos 289 k python3-six noarch 1.11.0-8.el8 rhel-baseos 38 k python3-subscription-manager-rhsm x86_64 1.28.32-1.el8 rhel-baseos 391 k python3-syspurpose x86_64 1.28.32-1.el8 rhel-baseos 330 k python3-urllib3 noarch 1.24.2-5.el8 rhel-baseos 177 k readline x86_64 7.0-10.el8 rhel-baseos 199 k redhat-release x86_64 8.7-0.3.el8 rhel-baseos 44 k rpm x86_64 4.14.3-24.el8_7 rhel-baseos 543 k rpm-build-libs x86_64 4.14.3-24.el8_7 rhel-baseos 157 k rpm-libs x86_64 4.14.3-24.el8_7 rhel-baseos 346 k sed x86_64 4.5-5.el8 rhel-baseos 298 k setup noarch 2.12.2-7.el8 rhel-baseos 181 k shadow-utils x86_64 2:4.6-17.el8 rhel-baseos 1.2 M sqlite-libs x86_64 3.26.0-17.el8_7 rhel-baseos 581 k subscription-manager-rhsm-certificates x86_64 1.28.32-1.el8 rhel-baseos 288 k systemd x86_64 239-68.el8_7.2 rhel-baseos 3.6 M systemd-libs x86_64 239-68.el8_7.2 rhel-baseos 1.1 M systemd-pam x86_64 239-68.el8_7.2 rhel-baseos 492 k tpm2-tss x86_64 2.3.2-4.el8 rhel-baseos 275 k tzdata noarch 2022g-1.el8 rhel-baseos 470 k usermode x86_64 1.113-2.el8 rhel-baseos 202 k util-linux x86_64 2.32.1-39.el8_7 rhel-baseos 2.5 M virt-what x86_64 1.25-1.el8 rhel-baseos 38 k which x86_64 2.21-18.el8 rhel-baseos 50 k xz-libs x86_64 5.2.4-4.el8_6 rhel-baseos 94 k zlib x86_64 1.2.11-21.el8_7 rhel-baseos 103 k Transaction Summary =================================================================================================== Install 179 Packages Total download size: 98 M Installed size: 653 M Downloading Packages: (1/179): libassuan-2.5.1-3.el8.x86_64.rpm 187 kB/s | 83 kB 00:00 (2/179): cracklib-2.9.6-15.el8.x86_64.rpm 208 kB/s | 93 kB 00:00 (3/179): json-glib-1.4.4-1.el8.x86_64.rpm 298 kB/s | 144 kB 00:00 (4/179): libutempter-1.1.6-14.el8.x86_64.rpm 271 kB/s | 32 kB 00:00 (5/179): readline-7.0-10.el8.x86_64.rpm 1.4 MB/s | 199 kB 00:00 (6/179): grep-3.1-6.el8.x86_64.rpm 1.5 MB/s | 274 kB 00:00 (7/179): libyaml-0.1.7-5.el8.x86_64.rpm 521 kB/s | 61 kB 00:00 (8/179): npth-1.5-4.el8.x86_64.rpm 279 kB/s | 26 kB 00:00 (9/179): libsigsegv-2.11-5.el8.x86_64.rpm 299 kB/s | 30 kB 00:00 (10/179): bzip2-libs-1.0.6-26.el8.x86_64.rpm 450 kB/s | 48 kB 00:00 (11/179): libattr-2.4.48-3.el8.x86_64.rpm 186 kB/s | 27 kB 00:00 (12/179): mpfr-3.1.6-1.el8.x86_64.rpm 1.7 MB/s | 221 kB 00:00 (13/179): acl-2.2.53-1.el8.x86_64.rpm 787 kB/s | 81 kB 00:00 (14/179): cracklib-dicts-2.9.6-15.el8.x86_64.rp 10 MB/s | 4.0 MB 00:00 (15/179): python3-inotify-0.9.6-13.el8.noarch.r 569 kB/s | 57 kB 00:00 (16/179): libunistring-0.9.9-3.el8.x86_64.rpm 2.4 MB/s | 422 kB 00:00 (17/179): dbus-glib-0.110-2.el8.x86_64.rpm 1.4 MB/s | 127 kB 00:00 (18/179): python3-iniparse-0.4-31.el8.noarch.rp 417 kB/s | 49 kB 00:00 (19/179): libnsl2-1.2.0-2.20180605git4a062cf.el 506 kB/s | 58 kB 00:00 (20/179): publicsuffix-list-dafsa-20180723-1.el 484 kB/s | 56 kB 00:00 (21/179): python3-decorator-4.2.1-2.el8.noarch. 303 kB/s | 27 kB 00:00 (22/179): gobject-introspection-1.56.1-1.el8.x8 1.3 MB/s | 255 kB 00:00 (23/179): python3-idna-2.5-5.el8.noarch.rpm 887 kB/s | 97 kB 00:00 (24/179): python3-pysocks-1.6.8-3.el8.noarch.rp 345 kB/s | 34 kB 00:00 (25/179): python3-dateutil-2.6.1-6.el8.noarch.r 2.6 MB/s | 251 kB 00:00 (26/179): basesystem-11-5.el8.noarch.rpm 121 kB/s | 11 kB 00:00 (27/179): libacl-2.2.53-1.el8.x86_64.rpm 299 kB/s | 35 kB 00:00 (28/179): libgpg-error-1.31-1.el8.x86_64.rpm 2.4 MB/s | 242 kB 00:00 (29/179): python3-six-1.11.0-8.el8.noarch.rpm 397 kB/s | 38 kB 00:00 (30/179): python3-chardet-3.0.4-7.el8.noarch.rp 1.8 MB/s | 195 kB 00:00 (31/179): python3-dmidecode-3.12.2-15.el8.x86_6 629 kB/s | 94 kB 00:00 (32/179): python3-requests-2.20.0-2.1.el8_1.noa 1.1 MB/s | 123 kB 00:00 (33/179): gmp-6.1.2-10.el8.x86_64.rpm 2.2 MB/s | 321 kB 00:00 (34/179): libidn2-2.2.0-1.el8.x86_64.rpm 1.0 MB/s | 94 kB 00:00 (35/179): python3-dbus-1.2.4-15.el8.x86_64.rpm 1.2 MB/s | 134 kB 00:00 (36/179): libnghttp2-1.33.0-3.el8_2.1.x86_64.rp 834 kB/s | 77 kB 00:00 (37/179): libzstd-1.4.4-1.el8.x86_64.rpm 2.9 MB/s | 266 kB 00:00 (38/179): libreport-filesystem-2.9.5-15.el8.x86 178 kB/s | 21 kB 00:00 (39/179): libusbx-1.0.23-4.el8.x86_64.rpm 715 kB/s | 74 kB 00:00 (40/179): python3-setuptools-wheel-39.2.0-6.el8 2.4 MB/s | 289 kB 00:00 (41/179): p11-kit-trust-0.23.22-1.el8.x86_64.rp 1.5 MB/s | 137 kB 00:00 (42/179): platform-python-setuptools-39.2.0-6.e 5.3 MB/s | 632 kB 00:00 (43/179): python3-gobject-base-3.28.3-2.el8.x86 2.1 MB/s | 313 kB 00:00 (44/179): libpsl-0.20.2-6.el8.x86_64.rpm 653 kB/s | 61 kB 00:00 (45/179): python3-urllib3-1.24.2-5.el8.noarch.r 1.4 MB/s | 177 kB 00:00 (46/179): librhsm-0.0.3-4.el8.x86_64.rpm 324 kB/s | 33 kB 00:00 (47/179): popt-1.18-1.el8.x86_64.rpm 555 kB/s | 61 kB 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(release key 2) " Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat8-release Key imported successfully Importing GPG key 0x2FA658E0: Userid : "Red Hat, Inc. (auxiliary key) " Fingerprint: 43A6 E49C 4A38 F4BE 9ABF 2A53 4568 9C88 2FA6 58E0 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat8-release Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.8-6.el8.x86_64 1/1 Preparing : 1/1 Installing : libgcc-8.5.0-16.el8_7.x86_64 1/179 Running scriptlet: libgcc-8.5.0-16.el8_7.x86_64 1/179 Installing : crypto-policies-20211116-1.gitae470d6.el8.noarch 2/179 Running scriptlet: crypto-policies-20211116-1.gitae470d6.el8.noarch 2/179 Installing : tzdata-2022g-1.el8.noarch 3/179 Installing : python3-pip-wheel-9.0.3-22.el8.noarch 4/179 Installing : python3-setuptools-wheel-39.2.0-6.el8.noarch 5/179 Installing : redhat-release-8.7-0.3.el8.x86_64 6/179 Installing : setup-2.12.2-7.el8.noarch 7/179 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.12.2-7.el8.noarch 7/179 Installing : filesystem-3.8-6.el8.x86_64 8/179 Installing : basesystem-11-5.el8.noarch 9/179 Installing : subscription-manager-rhsm-certificates-1.28.32-1 10/179 Installing : libssh-config-0.9.6-3.el8.noarch 11/179 Installing : ncurses-base-6.1-9.20180224.el8.noarch 12/179 Installing : 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Verifying : python3-requests-2.20.0-2.1.el8_1.noarch 33/179 Verifying : libidn2-2.2.0-1.el8.x86_64 34/179 Verifying : python3-dbus-1.2.4-15.el8.x86_64 35/179 Verifying : libnghttp2-1.33.0-3.el8_2.1.x86_64 36/179 Verifying : libzstd-1.4.4-1.el8.x86_64 37/179 Verifying : libreport-filesystem-2.9.5-15.el8.x86_64 38/179 Verifying : python3-setuptools-wheel-39.2.0-6.el8.noarch 39/179 Verifying : libusbx-1.0.23-4.el8.x86_64 40/179 Verifying : python3-gobject-base-3.28.3-2.el8.x86_64 41/179 Verifying : platform-python-setuptools-39.2.0-6.el8.noarch 42/179 Verifying : p11-kit-trust-0.23.22-1.el8.x86_64 43/179 Verifying : python3-urllib3-1.24.2-5.el8.noarch 44/179 Verifying : libpsl-0.20.2-6.el8.x86_64 45/179 Verifying : librhsm-0.0.3-4.el8.x86_64 46/179 Verifying : popt-1.18-1.el8.x86_64 47/179 Verifying : brotli-1.0.6-3.el8.x86_64 48/179 Verifying : lz4-libs-1.8.3-3.el8_4.x86_64 49/179 Verifying : ima-evm-utils-1.3.2-12.el8.x86_64 50/179 Verifying : p11-kit-0.23.22-1.el8.x86_64 51/179 Verifying : tpm2-tss-2.3.2-4.el8.x86_64 52/179 Verifying : pcre-8.42-6.el8.x86_64 53/179 Verifying : openldap-2.4.46-18.el8.x86_64 54/179 Verifying : nettle-3.4.1-7.el8.x86_64 55/179 Verifying : ncurses-libs-6.1-9.20180224.el8.x86_64 56/179 Verifying : libmodulemd-2.13.0-1.el8.x86_64 57/179 Verifying : libdb-utils-5.3.28-42.el8_4.x86_64 58/179 Verifying : filesystem-3.8-6.el8.x86_64 59/179 Verifying : usermode-1.113-2.el8.x86_64 60/179 Verifying : libxcrypt-4.1.1-6.el8.x86_64 61/179 Verifying : chkconfig-1.19.1-1.el8.x86_64 62/179 Verifying : libcap-ng-0.7.11-1.el8.x86_64 63/179 Verifying : libdb-5.3.28-42.el8_4.x86_64 64/179 Verifying : ncurses-6.1-9.20180224.el8.x86_64 65/179 Verifying : libsepol-2.9-3.el8.x86_64 66/179 Verifying : gzip-1.9-13.el8_5.x86_64 67/179 Verifying : dmidecode-1:3.3-4.el8.x86_64 68/179 Verifying : passwd-0.80-4.el8.x86_64 69/179 Verifying : keyutils-libs-1.5.10-9.el8.x86_64 70/179 Verifying : ncurses-base-6.1-9.20180224.el8.noarch 71/179 Verifying : cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 72/179 Verifying : lua-libs-5.3.4-12.el8.x86_64 73/179 Verifying : gpgme-1.13.1-11.el8.x86_64 74/179 Verifying : sed-4.5-5.el8.x86_64 75/179 Verifying : kmod-libs-25-19.el8.x86_64 76/179 Verifying : python3-gpg-1.13.1-11.el8.x86_64 77/179 Verifying : python3-ethtool-0.14-5.el8.x86_64 78/179 Verifying : python3-libcomps-0.1.18-1.el8.x86_64 79/179 Verifying : libffi-3.1-23.el8.x86_64 80/179 Verifying : json-c-0.13.1-3.el8.x86_64 81/179 Verifying : python3-pip-wheel-9.0.3-22.el8.noarch 82/179 Verifying : libssh-0.9.6-3.el8.x86_64 83/179 Verifying : libseccomp-2.5.2-1.el8.x86_64 84/179 Verifying : libcomps-0.1.18-1.el8.x86_64 85/179 Verifying : libuser-0.62-24.el8.x86_64 86/179 Verifying : cryptsetup-libs-2.3.7-2.el8.x86_64 87/179 Verifying : gawk-4.2.1-4.el8.x86_64 88/179 Verifying : xz-libs-5.2.4-4.el8_6.x86_64 89/179 Verifying : crypto-policies-20211116-1.gitae470d6.el8.noarch 90/179 Verifying : info-6.5-7.el8.x86_64 91/179 Verifying : libssh-config-0.9.6-3.el8.noarch 92/179 Verifying : coreutils-8.30-13.el8.x86_64 93/179 Verifying : dnf-data-4.7.0-11.el8.noarch 94/179 Verifying : libpwquality-1.4.4-5.el8.x86_64 95/179 Verifying : glibc-all-langpacks-2.28-211.el8.x86_64 96/179 Verifying : subscription-manager-1.28.32-1.el8.x86_64 97/179 Verifying : libksba-1.3.5-8.el8_6.x86_64 98/179 Verifying : libverto-0.3.2-2.el8.x86_64 99/179 Verifying : gdbm-libs-1:1.18-2.el8.x86_64 100/179 Verifying : gnupg2-2.2.20-3.el8_6.x86_64 101/179 Verifying : coreutils-common-8.30-13.el8.x86_64 102/179 Verifying : libtirpc-1.1.4-8.el8.x86_64 103/179 Verifying : virt-what-1.25-1.el8.x86_64 104/179 Verifying : ca-certificates-2022.2.54-80.2.el8_6.noarch 105/179 Verifying : pcre2-10.32-3.el8_6.x86_64 106/179 Verifying : pam-1.3.1-22.el8.x86_64 107/179 Verifying : libgcrypt-1.8.5-7.el8_6.x86_64 108/179 Verifying : openssl-libs-1:1.1.1k-7.el8_6.x86_64 109/179 Verifying : python3-dnf-4.7.0-11.el8.noarch 110/179 Verifying : libcom_err-1.45.6-5.el8.x86_64 111/179 Verifying : libsemanage-2.9-9.el8_6.x86_64 112/179 Verifying : bash-4.4.20-4.el8_6.x86_64 113/179 Verifying : device-mapper-8:1.02.181-6.el8.x86_64 114/179 Verifying : gnutls-3.6.16-5.el8_6.x86_64 115/179 Verifying : libdnf-0.63.0-11.1.el8.x86_64 116/179 Verifying : elfutils-libelf-0.187-4.el8.x86_64 117/179 Verifying : file-libs-5.33-21.el8.x86_64 118/179 Verifying : dnf-plugins-core-4.0.21-14.1.el8.noarch 119/179 Verifying : python3-dnf-plugins-core-4.0.21-14.1.el8.noarch 120/179 Verifying : librepo-1.14.2-3.el8.x86_64 121/179 Verifying : python3-syspurpose-1.28.32-1.el8.x86_64 122/179 Verifying : python3-cloud-what-1.28.32-1.el8.x86_64 123/179 Verifying : which-2.21-18.el8.x86_64 124/179 Verifying : gdbm-1:1.18-2.el8.x86_64 125/179 Verifying : libnl3-3.7.0-1.el8.x86_64 126/179 Verifying : python3-hawkey-0.63.0-11.1.el8.x86_64 127/179 Verifying : glibc-2.28-211.el8.x86_64 128/179 Verifying : glibc-common-2.28-211.el8.x86_64 129/179 Verifying : setup-2.12.2-7.el8.noarch 130/179 Verifying : elfutils-libs-0.187-4.el8.x86_64 131/179 Verifying : libarchive-3.3.3-4.el8.x86_64 132/179 Verifying : dnf-plugin-subscription-manager-1.28.32-1.el8.x8 133/179 Verifying : dnf-4.7.0-11.el8.noarch 134/179 Verifying : audit-libs-3.0.7-4.el8.x86_64 135/179 Verifying : device-mapper-libs-8:1.02.181-6.el8.x86_64 136/179 Verifying : python3-librepo-1.14.2-3.el8.x86_64 137/179 Verifying : subscription-manager-rhsm-certificates-1.28.32-1 138/179 Verifying : python3-subscription-manager-rhsm-1.28.32-1.el8. 139/179 Verifying : python3-libdnf-0.63.0-11.1.el8.x86_64 140/179 Verifying : libcap-2.48-4.el8.x86_64 141/179 Verifying : elfutils-default-yama-scope-0.187-4.el8.noarch 142/179 Verifying : shadow-utils-2:4.6-17.el8.x86_64 143/179 Verifying : glib2-2.56.4-159.el8.x86_64 144/179 Verifying : libselinux-2.9-6.el8.x86_64 145/179 Verifying : redhat-release-8.7-0.3.el8.x86_64 146/179 Verifying : rpm-libs-4.14.3-24.el8_7.x86_64 147/179 Verifying : rpm-4.14.3-24.el8_7.x86_64 148/179 Verifying : python3-rpm-4.14.3-24.el8_7.x86_64 149/179 Verifying : python3-libs-3.6.8-48.el8_7.x86_64 150/179 Verifying : rpm-build-libs-4.14.3-24.el8_7.x86_64 151/179 Verifying : platform-python-3.6.8-48.el8_7.x86_64 152/179 Verifying : krb5-libs-1.18.2-22.el8_7.x86_64 153/179 Verifying : tzdata-2022g-1.el8.noarch 154/179 Verifying : libsolv-0.7.20-4.el8_7.x86_64 155/179 Verifying : dbus-tools-1:1.12.8-23.el8_7.1.x86_64 156/179 Verifying : curl-7.61.1-25.el8_7.1.x86_64 157/179 Verifying : libuuid-2.32.1-39.el8_7.x86_64 158/179 Verifying : libgcc-8.5.0-16.el8_7.x86_64 159/179 Verifying : util-linux-2.32.1-39.el8_7.x86_64 160/179 Verifying : expat-2.2.5-10.el8_7.1.x86_64 161/179 Verifying : systemd-pam-239-68.el8_7.2.x86_64 162/179 Verifying : libtasn1-4.13-4.el8_7.x86_64 163/179 Verifying : libblkid-2.32.1-39.el8_7.x86_64 164/179 Verifying : dbus-libs-1:1.12.8-23.el8_7.1.x86_64 165/179 Verifying : systemd-239-68.el8_7.2.x86_64 166/179 Verifying : libstdc++-8.5.0-16.el8_7.x86_64 167/179 Verifying : dbus-daemon-1:1.12.8-23.el8_7.1.x86_64 168/179 Verifying : libcurl-7.61.1-25.el8_7.1.x86_64 169/179 Verifying : libmount-2.32.1-39.el8_7.x86_64 170/179 Verifying : systemd-libs-239-68.el8_7.2.x86_64 171/179 Verifying : zlib-1.2.11-21.el8_7.x86_64 172/179 Verifying : dbus-1:1.12.8-23.el8_7.1.x86_64 173/179 Verifying : sqlite-libs-3.26.0-17.el8_7.x86_64 174/179 Verifying : dbus-common-1:1.12.8-23.el8_7.1.noarch 175/179 Verifying : libfdisk-2.32.1-39.el8_7.x86_64 176/179 Verifying : libsmartcols-2.32.1-39.el8_7.x86_64 177/179 Verifying : libxml2-2.9.7-15.el8_7.1.x86_64 178/179 Verifying : python3-libxml2-2.9.7-15.el8_7.1.x86_64 179/179 Installed products updated. Installed: acl-2.2.53-1.el8.x86_64 audit-libs-3.0.7-4.el8.x86_64 basesystem-11-5.el8.noarch bash-4.4.20-4.el8_6.x86_64 brotli-1.0.6-3.el8.x86_64 bzip2-libs-1.0.6-26.el8.x86_64 ca-certificates-2022.2.54-80.2.el8_6.noarch chkconfig-1.19.1-1.el8.x86_64 coreutils-8.30-13.el8.x86_64 coreutils-common-8.30-13.el8.x86_64 cracklib-2.9.6-15.el8.x86_64 cracklib-dicts-2.9.6-15.el8.x86_64 crypto-policies-20211116-1.gitae470d6.el8.noarch cryptsetup-libs-2.3.7-2.el8.x86_64 curl-7.61.1-25.el8_7.1.x86_64 cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 dbus-1:1.12.8-23.el8_7.1.x86_64 dbus-common-1:1.12.8-23.el8_7.1.noarch dbus-daemon-1:1.12.8-23.el8_7.1.x86_64 dbus-glib-0.110-2.el8.x86_64 dbus-libs-1:1.12.8-23.el8_7.1.x86_64 dbus-tools-1:1.12.8-23.el8_7.1.x86_64 device-mapper-8:1.02.181-6.el8.x86_64 device-mapper-libs-8:1.02.181-6.el8.x86_64 dmidecode-1:3.3-4.el8.x86_64 dnf-4.7.0-11.el8.noarch dnf-data-4.7.0-11.el8.noarch dnf-plugin-subscription-manager-1.28.32-1.el8.x86_64 dnf-plugins-core-4.0.21-14.1.el8.noarch elfutils-default-yama-scope-0.187-4.el8.noarch elfutils-libelf-0.187-4.el8.x86_64 elfutils-libs-0.187-4.el8.x86_64 expat-2.2.5-10.el8_7.1.x86_64 file-libs-5.33-21.el8.x86_64 filesystem-3.8-6.el8.x86_64 gawk-4.2.1-4.el8.x86_64 gdbm-1:1.18-2.el8.x86_64 gdbm-libs-1:1.18-2.el8.x86_64 glib2-2.56.4-159.el8.x86_64 glibc-2.28-211.el8.x86_64 glibc-all-langpacks-2.28-211.el8.x86_64 glibc-common-2.28-211.el8.x86_64 gmp-1:6.1.2-10.el8.x86_64 gnupg2-2.2.20-3.el8_6.x86_64 gnutls-3.6.16-5.el8_6.x86_64 gobject-introspection-1.56.1-1.el8.x86_64 gpgme-1.13.1-11.el8.x86_64 grep-3.1-6.el8.x86_64 gzip-1.9-13.el8_5.x86_64 ima-evm-utils-1.3.2-12.el8.x86_64 info-6.5-7.el8.x86_64 json-c-0.13.1-3.el8.x86_64 json-glib-1.4.4-1.el8.x86_64 keyutils-libs-1.5.10-9.el8.x86_64 kmod-libs-25-19.el8.x86_64 krb5-libs-1.18.2-22.el8_7.x86_64 libacl-2.2.53-1.el8.x86_64 libarchive-3.3.3-4.el8.x86_64 libassuan-2.5.1-3.el8.x86_64 libattr-2.4.48-3.el8.x86_64 libblkid-2.32.1-39.el8_7.x86_64 libcap-2.48-4.el8.x86_64 libcap-ng-0.7.11-1.el8.x86_64 libcom_err-1.45.6-5.el8.x86_64 libcomps-0.1.18-1.el8.x86_64 libcurl-7.61.1-25.el8_7.1.x86_64 libdb-5.3.28-42.el8_4.x86_64 libdb-utils-5.3.28-42.el8_4.x86_64 libdnf-0.63.0-11.1.el8.x86_64 libfdisk-2.32.1-39.el8_7.x86_64 libffi-3.1-23.el8.x86_64 libgcc-8.5.0-16.el8_7.x86_64 libgcrypt-1.8.5-7.el8_6.x86_64 libgpg-error-1.31-1.el8.x86_64 libidn2-2.2.0-1.el8.x86_64 libksba-1.3.5-8.el8_6.x86_64 libmodulemd-2.13.0-1.el8.x86_64 libmount-2.32.1-39.el8_7.x86_64 libnghttp2-1.33.0-3.el8_2.1.x86_64 libnl3-3.7.0-1.el8.x86_64 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libpsl-0.20.2-6.el8.x86_64 libpwquality-1.4.4-5.el8.x86_64 librepo-1.14.2-3.el8.x86_64 libreport-filesystem-2.9.5-15.el8.x86_64 librhsm-0.0.3-4.el8.x86_64 libseccomp-2.5.2-1.el8.x86_64 libselinux-2.9-6.el8.x86_64 libsemanage-2.9-9.el8_6.x86_64 libsepol-2.9-3.el8.x86_64 libsigsegv-2.11-5.el8.x86_64 libsmartcols-2.32.1-39.el8_7.x86_64 libsolv-0.7.20-4.el8_7.x86_64 libssh-0.9.6-3.el8.x86_64 libssh-config-0.9.6-3.el8.noarch libstdc++-8.5.0-16.el8_7.x86_64 libtasn1-4.13-4.el8_7.x86_64 libtirpc-1.1.4-8.el8.x86_64 libunistring-0.9.9-3.el8.x86_64 libusbx-1.0.23-4.el8.x86_64 libuser-0.62-24.el8.x86_64 libutempter-1.1.6-14.el8.x86_64 libuuid-2.32.1-39.el8_7.x86_64 libverto-0.3.2-2.el8.x86_64 libxcrypt-4.1.1-6.el8.x86_64 libxml2-2.9.7-15.el8_7.1.x86_64 libyaml-0.1.7-5.el8.x86_64 libzstd-1.4.4-1.el8.x86_64 lua-libs-5.3.4-12.el8.x86_64 lz4-libs-1.8.3-3.el8_4.x86_64 mpfr-3.1.6-1.el8.x86_64 ncurses-6.1-9.20180224.el8.x86_64 ncurses-base-6.1-9.20180224.el8.noarch ncurses-libs-6.1-9.20180224.el8.x86_64 nettle-3.4.1-7.el8.x86_64 npth-1.5-4.el8.x86_64 openldap-2.4.46-18.el8.x86_64 openssl-libs-1:1.1.1k-7.el8_6.x86_64 p11-kit-0.23.22-1.el8.x86_64 p11-kit-trust-0.23.22-1.el8.x86_64 pam-1.3.1-22.el8.x86_64 passwd-0.80-4.el8.x86_64 pcre-8.42-6.el8.x86_64 pcre2-10.32-3.el8_6.x86_64 platform-python-3.6.8-48.el8_7.x86_64 platform-python-setuptools-39.2.0-6.el8.noarch popt-1.18-1.el8.x86_64 publicsuffix-list-dafsa-20180723-1.el8.noarch python3-chardet-3.0.4-7.el8.noarch python3-cloud-what-1.28.32-1.el8.x86_64 python3-dateutil-1:2.6.1-6.el8.noarch python3-dbus-1.2.4-15.el8.x86_64 python3-decorator-4.2.1-2.el8.noarch python3-dmidecode-3.12.2-15.el8.x86_64 python3-dnf-4.7.0-11.el8.noarch python3-dnf-plugins-core-4.0.21-14.1.el8.noarch python3-ethtool-0.14-5.el8.x86_64 python3-gobject-base-3.28.3-2.el8.x86_64 python3-gpg-1.13.1-11.el8.x86_64 python3-hawkey-0.63.0-11.1.el8.x86_64 python3-idna-2.5-5.el8.noarch python3-iniparse-0.4-31.el8.noarch python3-inotify-0.9.6-13.el8.noarch python3-libcomps-0.1.18-1.el8.x86_64 python3-libdnf-0.63.0-11.1.el8.x86_64 python3-librepo-1.14.2-3.el8.x86_64 python3-libs-3.6.8-48.el8_7.x86_64 python3-libxml2-2.9.7-15.el8_7.1.x86_64 python3-pip-wheel-9.0.3-22.el8.noarch python3-pysocks-1.6.8-3.el8.noarch python3-requests-2.20.0-2.1.el8_1.noarch python3-rpm-4.14.3-24.el8_7.x86_64 python3-setuptools-wheel-39.2.0-6.el8.noarch python3-six-1.11.0-8.el8.noarch python3-subscription-manager-rhsm-1.28.32-1.el8.x86_64 python3-syspurpose-1.28.32-1.el8.x86_64 python3-urllib3-1.24.2-5.el8.noarch readline-7.0-10.el8.x86_64 redhat-release-8.7-0.3.el8.x86_64 rpm-4.14.3-24.el8_7.x86_64 rpm-build-libs-4.14.3-24.el8_7.x86_64 rpm-libs-4.14.3-24.el8_7.x86_64 sed-4.5-5.el8.x86_64 setup-2.12.2-7.el8.noarch shadow-utils-2:4.6-17.el8.x86_64 sqlite-libs-3.26.0-17.el8_7.x86_64 subscription-manager-1.28.32-1.el8.x86_64 subscription-manager-rhsm-certificates-1.28.32-1.el8.x86_64 systemd-239-68.el8_7.2.x86_64 systemd-libs-239-68.el8_7.2.x86_64 systemd-pam-239-68.el8_7.2.x86_64 tpm2-tss-2.3.2-4.el8.x86_64 tzdata-2022g-1.el8.noarch usermode-1.113-2.el8.x86_64 util-linux-2.32.1-39.el8_7.x86_64 virt-what-1.25-1.el8.x86_64 which-2.21-18.el8.x86_64 xz-libs-5.2.4-4.el8_6.x86_64 zlib-1.2.11-21.el8_7.x86_64 Complete! Finish(bootstrap): dnf install Start(bootstrap): creating root cache Finish(bootstrap): creating root cache Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf install No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 234 kB/s | 19 kB 00:00 Red Hat Enterprise Linux - BaseOS 36 MB/s | 56 MB 00:01 Red Hat Enterprise Linux - AppStream 35 MB/s | 52 MB 00:01 Red Hat Enterprise Linux - CodeReady Linux Buil 6.7 MB/s | 8.8 MB 00:01 Extra Packages for Enterprise Linux 8 - x86_64 13 MB/s | 13 MB 00:01 Dependencies resolved. =========================================================================================== Package Arch Version Repository Size =========================================================================================== Installing: bash x86_64 4.4.20-4.el8_6 rhel-baseos 1.5 M bzip2 x86_64 1.0.6-26.el8 rhel-baseos 60 k coreutils x86_64 8.30-13.el8 rhel-baseos 1.2 M cpio x86_64 2.12-11.el8 rhel-baseos 266 k diffutils x86_64 3.6-6.el8 rhel-baseos 359 k epel-rpm-macros noarch 8-35 epel 24 k findutils x86_64 1:4.6.0-20.el8 rhel-baseos 528 k gawk x86_64 4.2.1-4.el8 rhel-baseos 1.1 M gcc x86_64 8.5.0-16.el8_7 rhel-appstream 23 M gcc-c++ x86_64 8.5.0-16.el8_7 rhel-appstream 12 M grep x86_64 3.1-6.el8 rhel-baseos 274 k gzip x86_64 1.9-13.el8_5 rhel-baseos 167 k info x86_64 6.5-7.el8 rhel-baseos 198 k make x86_64 1:4.2.1-11.el8 rhel-baseos 498 k patch x86_64 2.7.6-11.el8 rhel-baseos 138 k redhat-release x86_64 8.7-0.3.el8 rhel-baseos 44 k redhat-rpm-config noarch 130-1.el8 rhel-appstream 90 k rpm-build x86_64 4.14.3-24.el8_7 rhel-appstream 174 k sed x86_64 4.5-5.el8 rhel-baseos 298 k shadow-utils x86_64 2:4.6-17.el8 rhel-baseos 1.2 M tar x86_64 2:1.30-6.el8 rhel-baseos 838 k unzip x86_64 6.0-46.el8 rhel-baseos 196 k util-linux x86_64 2.32.1-39.el8_7 rhel-baseos 2.5 M which x86_64 2.21-18.el8 rhel-baseos 50 k xz x86_64 5.2.4-4.el8_6 rhel-baseos 153 k Installing dependencies: annobin x86_64 10.67-3.el8 rhel-appstream 955 k ansible-srpm-macros noarch 1-8.1.el8 epel 8.5 k audit-libs x86_64 3.0.7-4.el8 rhel-baseos 123 k basesystem noarch 11-5.el8 rhel-baseos 11 k binutils x86_64 2.30-117.el8 rhel-baseos 5.8 M brotli x86_64 1.0.6-3.el8 rhel-baseos 323 k bzip2-libs x86_64 1.0.6-26.el8 rhel-baseos 48 k ca-certificates noarch 2022.2.54-80.2.el8_6 rhel-baseos 921 k chkconfig x86_64 1.19.1-1.el8 rhel-baseos 198 k coreutils-common x86_64 8.30-13.el8 rhel-baseos 2.0 M cpp x86_64 8.5.0-16.el8_7 rhel-appstream 10 M cracklib x86_64 2.9.6-15.el8 rhel-baseos 93 k cracklib-dicts x86_64 2.9.6-15.el8 rhel-baseos 4.0 M crypto-policies noarch 20211116-1.gitae470d6.el8 rhel-baseos 64 k curl x86_64 7.61.1-25.el8_7.1 rhel-baseos 352 k cyrus-sasl-lib x86_64 2.1.27-6.el8_5 rhel-baseos 123 k dwz x86_64 0.12-10.el8 rhel-appstream 109 k efi-srpm-macros noarch 3-3.el8 rhel-appstream 22 k elfutils x86_64 0.187-4.el8 rhel-baseos 543 k elfutils-default-yama-scope noarch 0.187-4.el8 rhel-baseos 52 k elfutils-libelf x86_64 0.187-4.el8 rhel-baseos 231 k elfutils-libs x86_64 0.187-4.el8 rhel-baseos 297 k expat x86_64 2.2.5-10.el8_7.1 rhel-baseos 113 k file x86_64 5.33-21.el8 rhel-baseos 77 k file-libs x86_64 5.33-21.el8 rhel-baseos 543 k filesystem x86_64 3.8-6.el8 rhel-baseos 1.1 M fpc-srpm-macros noarch 1.3-1.el8 epel 8.2 k gc x86_64 7.6.4-3.el8 rhel-appstream 109 k gcc-plugin-annobin x86_64 8.5.0-16.el8_7 rhel-appstream 35 k gdb-headless x86_64 8.2-19.el8 rhel-appstream 3.7 M gdbm x86_64 1:1.18-2.el8 rhel-baseos 130 k gdbm-libs x86_64 1:1.18-2.el8 rhel-baseos 60 k ghc-srpm-macros noarch 1.4.2-7.el8 rhel-appstream 9.4 k glib2 x86_64 2.56.4-159.el8 rhel-baseos 2.5 M glibc x86_64 2.28-211.el8 rhel-baseos 2.2 M glibc-all-langpacks x86_64 2.28-211.el8 rhel-baseos 26 M glibc-common x86_64 2.28-211.el8 rhel-baseos 1.0 M glibc-devel x86_64 2.28-211.el8 rhel-baseos 82 k glibc-gconv-extra x86_64 2.28-211.el8 rhel-baseos 1.5 M glibc-headers x86_64 2.28-211.el8 rhel-baseos 486 k gmp x86_64 1:6.1.2-10.el8 rhel-baseos 321 k gnupg2 x86_64 2.2.20-3.el8_6 rhel-baseos 2.4 M gnutls x86_64 3.6.16-5.el8_6 rhel-baseos 1.0 M go-srpm-macros noarch 2-17.el8 rhel-appstream 13 k guile x86_64 5:2.0.14-7.el8 rhel-appstream 3.5 M ima-evm-utils x86_64 1.3.2-12.el8 rhel-baseos 64 k isl x86_64 0.16.1-6.el8 rhel-appstream 841 k kernel-headers x86_64 4.18.0-425.10.1.el8_7 rhel-baseos 10 M keyutils-libs x86_64 1.5.10-9.el8 rhel-baseos 34 k krb5-libs x86_64 1.18.2-22.el8_7 rhel-baseos 840 k libacl x86_64 2.2.53-1.el8 rhel-baseos 35 k libarchive x86_64 3.3.3-4.el8 rhel-baseos 360 k libassuan x86_64 2.5.1-3.el8 rhel-baseos 83 k libatomic_ops x86_64 7.6.2-3.el8 rhel-appstream 38 k libattr x86_64 2.4.48-3.el8 rhel-baseos 27 k libbabeltrace x86_64 1.5.4-4.el8 rhel-baseos 200 k libblkid x86_64 2.32.1-39.el8_7 rhel-baseos 220 k libcap x86_64 2.48-4.el8 rhel-baseos 74 k libcap-ng x86_64 0.7.11-1.el8 rhel-baseos 33 k libcom_err x86_64 1.45.6-5.el8 rhel-baseos 49 k libcurl x86_64 7.61.1-25.el8_7.1 rhel-baseos 302 k libdb x86_64 5.3.28-42.el8_4 rhel-baseos 751 k libdb-utils x86_64 5.3.28-42.el8_4 rhel-baseos 150 k libfdisk x86_64 2.32.1-39.el8_7 rhel-baseos 253 k libffi x86_64 3.1-23.el8 rhel-baseos 37 k libgcc x86_64 8.5.0-16.el8_7 rhel-baseos 81 k libgcrypt x86_64 1.8.5-7.el8_6 rhel-baseos 463 k libgomp x86_64 8.5.0-16.el8_7 rhel-baseos 207 k libgpg-error x86_64 1.31-1.el8 rhel-baseos 242 k libidn2 x86_64 2.2.0-1.el8 rhel-baseos 94 k libipt x86_64 1.6.1-8.el8 rhel-appstream 50 k libksba x86_64 1.3.5-8.el8_6 rhel-baseos 134 k libmount x86_64 2.32.1-39.el8_7 rhel-baseos 236 k libmpc x86_64 1.1.0-9.1.el8 rhel-appstream 61 k libnghttp2 x86_64 1.33.0-3.el8_2.1 rhel-baseos 77 k libnsl2 x86_64 1.2.0-2.20180605git4a062cf.el8 rhel-baseos 58 k libpkgconf x86_64 1.4.2-1.el8 rhel-baseos 35 k libpsl x86_64 0.20.2-6.el8 rhel-baseos 61 k libpwquality x86_64 1.4.4-5.el8 rhel-baseos 107 k libselinux x86_64 2.9-6.el8 rhel-baseos 165 k libsemanage x86_64 2.9-9.el8_6 rhel-baseos 168 k libsepol x86_64 2.9-3.el8 rhel-baseos 340 k libsigsegv x86_64 2.11-5.el8 rhel-baseos 30 k libsmartcols x86_64 2.32.1-39.el8_7 rhel-baseos 179 k libssh x86_64 0.9.6-3.el8 rhel-baseos 216 k libssh-config noarch 0.9.6-3.el8 rhel-baseos 19 k libstdc++ x86_64 8.5.0-16.el8_7 rhel-baseos 454 k libstdc++-devel x86_64 8.5.0-16.el8_7 rhel-appstream 2.1 M libtasn1 x86_64 4.13-4.el8_7 rhel-baseos 76 k libtirpc x86_64 1.1.4-8.el8 rhel-baseos 113 k libtool-ltdl x86_64 2.4.6-25.el8 rhel-baseos 58 k libunistring x86_64 0.9.9-3.el8 rhel-baseos 422 k libusbx x86_64 1.0.23-4.el8 rhel-baseos 74 k libutempter x86_64 1.1.6-14.el8 rhel-baseos 32 k libuuid x86_64 2.32.1-39.el8_7 rhel-baseos 98 k libverto x86_64 0.3.2-2.el8 rhel-baseos 24 k libxcrypt x86_64 4.1.1-6.el8 rhel-baseos 73 k libxcrypt-devel x86_64 4.1.1-6.el8 rhel-baseos 25 k libxml2 x86_64 2.9.7-15.el8_7.1 rhel-baseos 697 k libzstd x86_64 1.4.4-1.el8 rhel-baseos 266 k lua-libs x86_64 5.3.4-12.el8 rhel-baseos 118 k lua-srpm-macros noarch 1-3.el8 epel 8.1 k lz4-libs x86_64 1.8.3-3.el8_4 rhel-baseos 66 k mpfr x86_64 3.1.6-1.el8 rhel-baseos 221 k ncurses x86_64 6.1-9.20180224.el8 rhel-baseos 387 k ncurses-base noarch 6.1-9.20180224.el8 rhel-baseos 81 k ncurses-libs x86_64 6.1-9.20180224.el8 rhel-baseos 334 k nettle x86_64 3.4.1-7.el8 rhel-baseos 301 k npth x86_64 1.5-4.el8 rhel-baseos 26 k ocaml-srpm-macros noarch 5-4.el8 rhel-appstream 9.5 k openblas-srpm-macros noarch 2-2.el8 rhel-appstream 8.0 k openldap x86_64 2.4.46-18.el8 rhel-baseos 352 k openssl-libs x86_64 1:1.1.1k-7.el8_6 rhel-baseos 1.5 M p11-kit x86_64 0.23.22-1.el8 rhel-baseos 324 k p11-kit-trust x86_64 0.23.22-1.el8 rhel-baseos 137 k pam x86_64 1.3.1-22.el8 rhel-baseos 743 k pcre x86_64 8.42-6.el8 rhel-baseos 211 k pcre2 x86_64 10.32-3.el8_6 rhel-baseos 247 k perl-srpm-macros noarch 1-25.el8 rhel-appstream 11 k pkgconf x86_64 1.4.2-1.el8 rhel-baseos 38 k pkgconf-m4 noarch 1.4.2-1.el8 rhel-baseos 17 k pkgconf-pkg-config x86_64 1.4.2-1.el8 rhel-baseos 15 k platform-python x86_64 3.6.8-48.el8_7 rhel-baseos 86 k platform-python-setuptools noarch 39.2.0-6.el8 rhel-baseos 632 k popt x86_64 1.18-1.el8 rhel-baseos 61 k publicsuffix-list-dafsa noarch 20180723-1.el8 rhel-baseos 56 k python-rpm-macros noarch 3-43.el8 rhel-appstream 16 k python-srpm-macros noarch 3-43.el8 rhel-appstream 15 k python3-libs x86_64 3.6.8-48.el8_7 rhel-baseos 7.8 M python3-pip-wheel noarch 9.0.3-22.el8 rhel-baseos 895 k python3-rpm-macros noarch 3-43.el8 rhel-appstream 15 k python3-setuptools-wheel noarch 39.2.0-6.el8 rhel-baseos 289 k qt5-srpm-macros noarch 5.15.3-1.el8 rhel-appstream 11 k readline x86_64 7.0-10.el8 rhel-baseos 199 k rpm x86_64 4.14.3-24.el8_7 rhel-baseos 543 k rpm-build-libs x86_64 4.14.3-24.el8_7 rhel-baseos 157 k rpm-libs x86_64 4.14.3-24.el8_7 rhel-baseos 346 k rust-srpm-macros noarch 5-2.el8 rhel-appstream 9.3 k setup noarch 2.12.2-7.el8 rhel-baseos 181 k sqlite-libs x86_64 3.26.0-17.el8_7 rhel-baseos 581 k systemd-libs x86_64 239-68.el8_7.2 rhel-baseos 1.1 M tpm2-tss x86_64 2.3.2-4.el8 rhel-baseos 275 k tzdata noarch 2022g-1.el8 rhel-baseos 470 k xz-libs x86_64 5.2.4-4.el8_6 rhel-baseos 94 k zip x86_64 3.0-23.el8 rhel-baseos 270 k zlib x86_64 1.2.11-21.el8_7 rhel-baseos 103 k zstd x86_64 1.4.4-1.el8 rhel-appstream 393 k Transaction Summary =========================================================================================== Install 172 Packages Total download size: 162 M Installed size: 813 M Downloading Packages: (1/172): libutempter-1.1.6-14.el8.x86_64.rpm 86 kB/s | 32 kB 00:00 (2/172): libassuan-2.5.1-3.el8.x86_64.rpm 204 kB/s | 83 kB 00:00 (3/172): cracklib-2.9.6-15.el8.x86_64.rpm 192 kB/s | 93 kB 00:00 (4/172): grep-3.1-6.el8.x86_64.rpm 1.2 MB/s | 274 kB 00:00 (5/172): pkgconf-1.4.2-1.el8.x86_64.rpm 289 kB/s | 38 kB 00:00 (6/172): readline-7.0-10.el8.x86_64.rpm 767 kB/s | 199 kB 00:00 (7/172): libsigsegv-2.11-5.el8.x86_64.rpm 232 kB/s | 30 kB 00:00 (8/172): npth-1.5-4.el8.x86_64.rpm 135 kB/s | 26 kB 00:00 (9/172): libattr-2.4.48-3.el8.x86_64.rpm 215 kB/s | 27 kB 00:00 (10/172): cracklib-dicts-2.9.6-15.el8.x86_64.rp 13 MB/s | 4.0 MB 00:00 (11/172): bzip2-libs-1.0.6-26.el8.x86_64.rpm 326 kB/s | 48 kB 00:00 (12/172): pkgconf-pkg-config-1.4.2-1.el8.x86_64 69 kB/s | 15 kB 00:00 (13/172): mpfr-3.1.6-1.el8.x86_64.rpm 1.4 MB/s | 221 kB 00:00 (14/172): zip-3.0-23.el8.x86_64.rpm 1.6 MB/s | 270 kB 00:00 (15/172): libunistring-0.9.9-3.el8.x86_64.rpm 1.9 MB/s | 422 kB 00:00 (16/172): bzip2-1.0.6-26.el8.x86_64.rpm 440 kB/s | 60 kB 00:00 (17/172): libnsl2-1.2.0-2.20180605git4a062cf.el 461 kB/s | 58 kB 00:00 (18/172): publicsuffix-list-dafsa-20180723-1.el 424 kB/s | 56 kB 00:00 (19/172): pkgconf-m4-1.4.2-1.el8.noarch.rpm 139 kB/s | 17 kB 00:00 (20/172): libpkgconf-1.4.2-1.el8.x86_64.rpm 213 kB/s | 35 kB 00:00 (21/172): findutils-4.6.0-20.el8.x86_64.rpm 4.2 MB/s | 528 kB 00:00 (22/172): basesystem-11-5.el8.noarch.rpm 80 kB/s | 11 kB 00:00 (23/172): libacl-2.2.53-1.el8.x86_64.rpm 216 kB/s | 35 kB 00:00 (24/172): libtool-ltdl-2.4.6-25.el8.x86_64.rpm 456 kB/s | 58 kB 00:00 (25/172): libgpg-error-1.31-1.el8.x86_64.rpm 1.7 MB/s | 242 kB 00:00 (26/172): gmp-6.1.2-10.el8.x86_64.rpm 1.7 MB/s | 321 kB 00:00 (27/172): diffutils-3.6-6.el8.x86_64.rpm 2.8 MB/s | 359 kB 00:00 (28/172): libidn2-2.2.0-1.el8.x86_64.rpm 737 kB/s | 94 kB 00:00 (29/172): patch-2.7.6-11.el8.x86_64.rpm 936 kB/s | 138 kB 00:00 (30/172): libnghttp2-1.33.0-3.el8_2.1.x86_64.rp 569 kB/s | 77 kB 00:00 (31/172): libzstd-1.4.4-1.el8.x86_64.rpm 1.6 MB/s | 266 kB 00:00 (32/172): python3-setuptools-wheel-39.2.0-6.el8 1.7 MB/s | 289 kB 00:00 (33/172): libusbx-1.0.23-4.el8.x86_64.rpm 479 kB/s | 74 kB 00:00 (34/172): platform-python-setuptools-39.2.0-6.e 3.5 MB/s | 632 kB 00:00 (35/172): libpsl-0.20.2-6.el8.x86_64.rpm 489 kB/s | 61 kB 00:00 (36/172): p11-kit-trust-0.23.22-1.el8.x86_64.rp 981 kB/s | 137 kB 00:00 (37/172): popt-1.18-1.el8.x86_64.rpm 501 kB/s | 61 kB 00:00 (38/172): lz4-libs-1.8.3-3.el8_4.x86_64.rpm 533 kB/s | 66 kB 00:00 (39/172): brotli-1.0.6-3.el8.x86_64.rpm 2.3 MB/s | 323 kB 00:00 (40/172): ima-evm-utils-1.3.2-12.el8.x86_64.rpm 469 kB/s | 64 kB 00:00 (41/172): libxcrypt-devel-4.1.1-6.el8.x86_64.rp 216 kB/s | 25 kB 00:00 (42/172): p11-kit-0.23.22-1.el8.x86_64.rpm 1.6 MB/s | 324 kB 00:00 (43/172): tpm2-tss-2.3.2-4.el8.x86_64.rpm 2.1 MB/s | 275 kB 00:00 (44/172): pcre-8.42-6.el8.x86_64.rpm 1.5 MB/s | 211 kB 00:00 (45/172): nettle-3.4.1-7.el8.x86_64.rpm 2.2 MB/s | 301 kB 00:00 (46/172): openldap-2.4.46-18.el8.x86_64.rpm 2.3 MB/s | 352 kB 00:00 (47/172): ncurses-libs-6.1-9.20180224.el8.x86_6 2.5 MB/s | 334 kB 00:00 (48/172): libdb-utils-5.3.28-42.el8_4.x86_64.rp 1.2 MB/s | 150 kB 00:00 (49/172): filesystem-3.8-6.el8.x86_64.rpm 6.4 MB/s | 1.1 MB 00:00 (50/172): libxcrypt-4.1.1-6.el8.x86_64.rpm 515 kB/s | 73 kB 00:00 (51/172): chkconfig-1.19.1-1.el8.x86_64.rpm 1.5 MB/s | 198 kB 00:00 (52/172): libcap-ng-0.7.11-1.el8.x86_64.rpm 267 kB/s | 33 kB 00:00 (53/172): libdb-5.3.28-42.el8_4.x86_64.rpm 3.5 MB/s | 751 kB 00:00 (54/172): ncurses-6.1-9.20180224.el8.x86_64.rpm 2.3 MB/s | 387 kB 00:00 (55/172): libsepol-2.9-3.el8.x86_64.rpm 2.5 MB/s | 340 kB 00:00 (56/172): gzip-1.9-13.el8_5.x86_64.rpm 1.1 MB/s | 167 kB 00:00 (57/172): keyutils-libs-1.5.10-9.el8.x86_64.rpm 265 kB/s | 34 kB 00:00 (58/172): ncurses-base-6.1-9.20180224.el8.noarc 658 kB/s | 81 kB 00:00 (59/172): cpio-2.12-11.el8.x86_64.rpm 1.9 MB/s | 266 kB 00:00 (60/172): lua-libs-5.3.4-12.el8.x86_64.rpm 770 kB/s | 118 kB 00:00 (61/172): cyrus-sasl-lib-2.1.27-6.el8_5.x86_64. 567 kB/s | 123 kB 00:00 (62/172): sed-4.5-5.el8.x86_64.rpm 2.2 MB/s | 298 kB 00:00 (63/172): make-4.2.1-11.el8.x86_64.rpm 3.1 MB/s | 498 kB 00:00 (64/172): libffi-3.1-23.el8.x86_64.rpm 215 kB/s | 37 kB 00:00 (65/172): python3-pip-wheel-9.0.3-22.el8.noarch 5.9 MB/s | 895 kB 00:00 (66/172): libssh-0.9.6-3.el8.x86_64.rpm 1.4 MB/s | 216 kB 00:00 (67/172): xz-libs-5.2.4-4.el8_6.x86_64.rpm 638 kB/s | 94 kB 00:00 (68/172): xz-5.2.4-4.el8_6.x86_64.rpm 1.1 MB/s | 153 kB 00:00 (69/172): crypto-policies-20211116-1.gitae470d6 438 kB/s | 64 kB 00:00 (70/172): info-6.5-7.el8.x86_64.rpm 1.4 MB/s | 198 kB 00:00 (71/172): gawk-4.2.1-4.el8.x86_64.rpm 3.0 MB/s | 1.1 MB 00:00 (72/172): libssh-config-0.9.6-3.el8.noarch.rpm 137 kB/s | 19 kB 00:00 (73/172): unzip-6.0-46.el8.x86_64.rpm 1.5 MB/s | 196 kB 00:00 (74/172): coreutils-8.30-13.el8.x86_64.rpm 6.3 MB/s | 1.2 MB 00:00 (75/172): glibc-headers-2.28-211.el8.x86_64.rpm 3.0 MB/s | 486 kB 00:00 (76/172): libpwquality-1.4.4-5.el8.x86_64.rpm 626 kB/s | 107 kB 00:00 (77/172): tar-1.30-6.el8.x86_64.rpm 6.2 MB/s | 838 kB 00:00 (78/172): libbabeltrace-1.5.4-4.el8.x86_64.rpm 1.3 MB/s | 200 kB 00:00 (79/172): libksba-1.3.5-8.el8_6.x86_64.rpm 918 kB/s | 134 kB 00:00 (80/172): libverto-0.3.2-2.el8.x86_64.rpm 119 kB/s | 24 kB 00:00 (81/172): gdbm-libs-1.18-2.el8.x86_64.rpm 396 kB/s | 60 kB 00:00 (82/172): coreutils-common-8.30-13.el8.x86_64.r 12 MB/s | 2.0 MB 00:00 (83/172): glibc-all-langpacks-2.28-211.el8.x86_ 45 MB/s | 26 MB 00:00 (84/172): gnupg2-2.2.20-3.el8_6.x86_64.rpm 9.6 MB/s | 2.4 MB 00:00 (85/172): libtirpc-1.1.4-8.el8.x86_64.rpm 950 kB/s | 113 kB 00:00 (86/172): ca-certificates-2022.2.54-80.2.el8_6. 5.4 MB/s | 921 kB 00:00 (87/172): pam-1.3.1-22.el8.x86_64.rpm 5.2 MB/s | 743 kB 00:00 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00:09 Red Hat Enterprise Linux - BaseOS 3.1 MB/s | 3.1 kB 00:00 Importing GPG key 0xFD431D51: Userid : "Red Hat, Inc. (release key 2) " Fingerprint: 567E 347A D004 4ADE 55BA 8A5F 199E 2F91 FD43 1D51 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat8-release Key imported successfully Importing GPG key 0x2FA658E0: Userid : "Red Hat, Inc. (auxiliary key) " Fingerprint: 43A6 E49C 4A38 F4BE 9ABF 2A53 4568 9C88 2FA6 58E0 From : /usr/share/distribution-gpg-keys/redhat/RPM-GPG-KEY-redhat8-release Key imported successfully Extra Packages for Enterprise Linux 8 - x86_64 1.6 MB/s | 1.6 kB 00:00 Importing GPG key 0x2F86D6A1: Userid : "Fedora EPEL (8) " Fingerprint: 94E2 79EB 8D8F 25B2 1810 ADF1 21EA 45AB 2F86 D6A1 From : /usr/share/distribution-gpg-keys/epel/RPM-GPG-KEY-EPEL-8 Key imported successfully Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. Running transaction Running scriptlet: filesystem-3.8-6.el8.x86_64 1/1 Preparing : 1/1 Installing : libgcc-8.5.0-16.el8_7.x86_64 1/172 Running scriptlet: libgcc-8.5.0-16.el8_7.x86_64 1/172 Installing : python-srpm-macros-3-43.el8.noarch 2/172 Installing : crypto-policies-20211116-1.gitae470d6.el8.noarch 3/172 Running scriptlet: crypto-policies-20211116-1.gitae470d6.el8.noarch 3/172 Installing : python-rpm-macros-3-43.el8.noarch 4/172 Installing : redhat-release-8.7-0.3.el8.x86_64 5/172 Installing : setup-2.12.2-7.el8.noarch 6/172 warning: /etc/hosts created as /etc/hosts.rpmnew Running scriptlet: setup-2.12.2-7.el8.noarch 6/172 Installing : filesystem-3.8-6.el8.x86_64 7/172 Installing : python3-pip-wheel-9.0.3-22.el8.noarch 8/172 Installing : python3-setuptools-wheel-39.2.0-6.el8.noarch 9/172 Installing : basesystem-11-5.el8.noarch 10/172 Installing : python3-rpm-macros-3-43.el8.noarch 11/172 Installing : fpc-srpm-macros-1.3-1.el8.noarch 12/172 Installing : 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dwz-0.12-10.el8.x86_64 89/172 Installing : zstd-1.4.4-1.el8.x86_64 90/172 Installing : libstdc++-devel-8.5.0-16.el8_7.x86_64 91/172 Installing : libxml2-2.9.7-15.el8_7.1.x86_64 92/172 Installing : nettle-3.4.1-7.el8.x86_64 93/172 Running scriptlet: nettle-3.4.1-7.el8.x86_64 93/172 Installing : gnutls-3.6.16-5.el8_6.x86_64 94/172 Installing : isl-0.16.1-6.el8.x86_64 95/172 Running scriptlet: isl-0.16.1-6.el8.x86_64 95/172 Installing : bzip2-1.0.6-26.el8.x86_64 96/172 Installing : diffutils-3.6-6.el8.x86_64 97/172 Running scriptlet: diffutils-3.6-6.el8.x86_64 97/172 Installing : coreutils-common-8.30-13.el8.x86_64 98/172 Running scriptlet: coreutils-common-8.30-13.el8.x86_64 98/172 Installing : libgomp-8.5.0-16.el8_7.x86_64 99/172 Running scriptlet: libgomp-8.5.0-16.el8_7.x86_64 99/172 Installing : libsigsegv-2.11-5.el8.x86_64 100/172 Installing : gawk-4.2.1-4.el8.x86_64 101/172 Installing : npth-1.5-4.el8.x86_64 102/172 Installing : libpkgconf-1.4.2-1.el8.x86_64 103/172 Installing : pkgconf-1.4.2-1.el8.x86_64 104/172 Installing : libtool-ltdl-2.4.6-25.el8.x86_64 105/172 Running scriptlet: libtool-ltdl-2.4.6-25.el8.x86_64 105/172 Installing : libnghttp2-1.33.0-3.el8_2.1.x86_64 106/172 Installing : brotli-1.0.6-3.el8.x86_64 107/172 Installing : ncurses-6.1-9.20180224.el8.x86_64 108/172 Installing : openssl-libs-1:1.1.1k-7.el8_6.x86_64 109/172 Running scriptlet: openssl-libs-1:1.1.1k-7.el8_6.x86_64 109/172 Installing : coreutils-8.30-13.el8.x86_64 110/172 Running scriptlet: ca-certificates-2022.2.54-80.2.el8_6.noarch 111/172 Installing : ca-certificates-2022.2.54-80.2.el8_6.noarch 111/172 Running scriptlet: ca-certificates-2022.2.54-80.2.el8_6.noarch 111/172 Installing : libdb-5.3.28-42.el8_4.x86_64 112/172 Running scriptlet: libdb-5.3.28-42.el8_4.x86_64 112/172 Installing : libblkid-2.32.1-39.el8_7.x86_64 113/172 Running scriptlet: libblkid-2.32.1-39.el8_7.x86_64 113/172 Installing : libmount-2.32.1-39.el8_7.x86_64 114/172 Running scriptlet: libmount-2.32.1-39.el8_7.x86_64 114/172 Installing : systemd-libs-239-68.el8_7.2.x86_64 115/172 Running scriptlet: systemd-libs-239-68.el8_7.2.x86_64 115/172 Installing : gzip-1.9-13.el8_5.x86_64 116/172 Running scriptlet: gzip-1.9-13.el8_5.x86_64 116/172 Installing : cracklib-2.9.6-15.el8.x86_64 117/172 Installing : cracklib-dicts-2.9.6-15.el8.x86_64 118/172 Installing : binutils-2.30-117.el8.x86_64 119/172 Running scriptlet: binutils-2.30-117.el8.x86_64 119/172 Installing : shadow-utils-2:4.6-17.el8.x86_64 120/172 Running scriptlet: libutempter-1.1.6-14.el8.x86_64 121/172 Installing : libutempter-1.1.6-14.el8.x86_64 121/172 Running scriptlet: tpm2-tss-2.3.2-4.el8.x86_64 122/172 Installing : tpm2-tss-2.3.2-4.el8.x86_64 122/172 Running scriptlet: tpm2-tss-2.3.2-4.el8.x86_64 122/172 Installing : ima-evm-utils-1.3.2-12.el8.x86_64 123/172 Installing : libusbx-1.0.23-4.el8.x86_64 124/172 Installing : glib2-2.56.4-159.el8.x86_64 125/172 Installing : libbabeltrace-1.5.4-4.el8.x86_64 126/172 Running scriptlet: libbabeltrace-1.5.4-4.el8.x86_64 126/172 Installing : libfdisk-2.32.1-39.el8_7.x86_64 127/172 Running scriptlet: libfdisk-2.32.1-39.el8_7.x86_64 127/172 Installing : libdb-utils-5.3.28-42.el8_4.x86_64 128/172 Installing : libarchive-3.3.3-4.el8.x86_64 129/172 Installing : cpio-2.12-11.el8.x86_64 130/172 Installing : libverto-0.3.2-2.el8.x86_64 131/172 Installing : krb5-libs-1.18.2-22.el8_7.x86_64 132/172 Installing : libtirpc-1.1.4-8.el8.x86_64 133/172 Running scriptlet: libtirpc-1.1.4-8.el8.x86_64 133/172 Installing : libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 134/172 Running scriptlet: libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 134/172 Installing : libpwquality-1.4.4-5.el8.x86_64 135/172 Installing : pam-1.3.1-22.el8.x86_64 136/172 Running scriptlet: pam-1.3.1-22.el8.x86_64 136/172 Installing : platform-python-setuptools-39.2.0-6.el8.noarch 137/172 Installing : platform-python-3.6.8-48.el8_7.x86_64 138/172 Running scriptlet: platform-python-3.6.8-48.el8_7.x86_64 138/172 Installing : python3-libs-3.6.8-48.el8_7.x86_64 139/172 Installing : cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 140/172 Running scriptlet: cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 140/172 Installing : openldap-2.4.46-18.el8.x86_64 141/172 Installing : gnupg2-2.2.20-3.el8_6.x86_64 142/172 Installing : libssh-0.9.6-3.el8.x86_64 143/172 Installing : libsmartcols-2.32.1-39.el8_7.x86_64 144/172 Running scriptlet: libsmartcols-2.32.1-39.el8_7.x86_64 144/172 Installing : libatomic_ops-7.6.2-3.el8.x86_64 145/172 Installing : gc-7.6.4-3.el8.x86_64 146/172 Installing : guile-5:2.0.14-7.el8.x86_64 147/172 Running scriptlet: guile-5:2.0.14-7.el8.x86_64 147/172 Installing : libipt-1.6.1-8.el8.x86_64 148/172 Installing : pkgconf-m4-1.4.2-1.el8.noarch 149/172 Installing : pkgconf-pkg-config-1.4.2-1.el8.x86_64 150/172 Installing : glibc-devel-2.28-211.el8.x86_64 151/172 Running scriptlet: glibc-devel-2.28-211.el8.x86_64 151/172 Installing : libxcrypt-devel-4.1.1-6.el8.x86_64 152/172 Installing : gcc-8.5.0-16.el8_7.x86_64 153/172 Running scriptlet: gcc-8.5.0-16.el8_7.x86_64 153/172 Installing : annobin-10.67-3.el8.x86_64 154/172 Installing : gcc-plugin-annobin-8.5.0-16.el8_7.x86_64 155/172 Installing : publicsuffix-list-dafsa-20180723-1.el8.noarch 156/172 Installing : libpsl-0.20.2-6.el8.x86_64 157/172 Installing : libcurl-7.61.1-25.el8_7.1.x86_64 158/172 Installing : curl-7.61.1-25.el8_7.1.x86_64 159/172 Installing : rpm-libs-4.14.3-24.el8_7.x86_64 160/172 Running scriptlet: rpm-libs-4.14.3-24.el8_7.x86_64 160/172 Installing : rpm-4.14.3-24.el8_7.x86_64 161/172 Installing : efi-srpm-macros-3-3.el8.noarch 162/172 Installing : redhat-rpm-config-130-1.el8.noarch 163/172 Running scriptlet: redhat-rpm-config-130-1.el8.noarch 163/172 Installing : lua-srpm-macros-1-3.el8.noarch 164/172 Installing : rpm-build-libs-4.14.3-24.el8_7.x86_64 165/172 Running scriptlet: rpm-build-libs-4.14.3-24.el8_7.x86_64 165/172 Installing : gdb-headless-8.2-19.el8.x86_64 166/172 Installing : rpm-build-4.14.3-24.el8_7.x86_64 167/172 Installing : epel-rpm-macros-8-35.noarch 168/172 Installing : gcc-c++-8.5.0-16.el8_7.x86_64 169/172 Installing : util-linux-2.32.1-39.el8_7.x86_64 170/172 Running scriptlet: util-linux-2.32.1-39.el8_7.x86_64 170/172 Installing : which-2.21-18.el8.x86_64 171/172 Installing : make-1:4.2.1-11.el8.x86_64 172/172 Running scriptlet: make-1:4.2.1-11.el8.x86_64 172/172 Running scriptlet: filesystem-3.8-6.el8.x86_64 172/172 Running scriptlet: glibc-all-langpacks-2.28-211.el8.x86_64 172/172 Running scriptlet: ca-certificates-2022.2.54-80.2.el8_6.noarch 172/172 Running scriptlet: guile-5:2.0.14-7.el8.x86_64 172/172 Running scriptlet: glibc-common-2.28-211.el8.x86_64 172/172 Running scriptlet: info-6.5-7.el8.x86_64 172/172 Running scriptlet: glib2-2.56.4-159.el8.x86_64 172/172 Verifying : libassuan-2.5.1-3.el8.x86_64 1/172 Verifying : cracklib-2.9.6-15.el8.x86_64 2/172 Verifying : libutempter-1.1.6-14.el8.x86_64 3/172 Verifying : grep-3.1-6.el8.x86_64 4/172 Verifying : readline-7.0-10.el8.x86_64 5/172 Verifying : pkgconf-1.4.2-1.el8.x86_64 6/172 Verifying : libsigsegv-2.11-5.el8.x86_64 7/172 Verifying : npth-1.5-4.el8.x86_64 8/172 Verifying : cracklib-dicts-2.9.6-15.el8.x86_64 9/172 Verifying : libattr-2.4.48-3.el8.x86_64 10/172 Verifying : pkgconf-pkg-config-1.4.2-1.el8.x86_64 11/172 Verifying : bzip2-libs-1.0.6-26.el8.x86_64 12/172 Verifying : mpfr-3.1.6-1.el8.x86_64 13/172 Verifying : zip-3.0-23.el8.x86_64 14/172 Verifying : libunistring-0.9.9-3.el8.x86_64 15/172 Verifying : bzip2-1.0.6-26.el8.x86_64 16/172 Verifying : libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 17/172 Verifying : libpkgconf-1.4.2-1.el8.x86_64 18/172 Verifying : publicsuffix-list-dafsa-20180723-1.el8.noarch 19/172 Verifying : pkgconf-m4-1.4.2-1.el8.noarch 20/172 Verifying : findutils-1:4.6.0-20.el8.x86_64 21/172 Verifying : libacl-2.2.53-1.el8.x86_64 22/172 Verifying : basesystem-11-5.el8.noarch 23/172 Verifying : libtool-ltdl-2.4.6-25.el8.x86_64 24/172 Verifying : libgpg-error-1.31-1.el8.x86_64 25/172 Verifying : gmp-1:6.1.2-10.el8.x86_64 26/172 Verifying : diffutils-3.6-6.el8.x86_64 27/172 Verifying : libidn2-2.2.0-1.el8.x86_64 28/172 Verifying : patch-2.7.6-11.el8.x86_64 29/172 Verifying : libnghttp2-1.33.0-3.el8_2.1.x86_64 30/172 Verifying : libzstd-1.4.4-1.el8.x86_64 31/172 Verifying : python3-setuptools-wheel-39.2.0-6.el8.noarch 32/172 Verifying : libusbx-1.0.23-4.el8.x86_64 33/172 Verifying : platform-python-setuptools-39.2.0-6.el8.noarch 34/172 Verifying : p11-kit-trust-0.23.22-1.el8.x86_64 35/172 Verifying : libpsl-0.20.2-6.el8.x86_64 36/172 Verifying : popt-1.18-1.el8.x86_64 37/172 Verifying : brotli-1.0.6-3.el8.x86_64 38/172 Verifying : lz4-libs-1.8.3-3.el8_4.x86_64 39/172 Verifying : ima-evm-utils-1.3.2-12.el8.x86_64 40/172 Verifying : p11-kit-0.23.22-1.el8.x86_64 41/172 Verifying : libxcrypt-devel-4.1.1-6.el8.x86_64 42/172 Verifying : tpm2-tss-2.3.2-4.el8.x86_64 43/172 Verifying : pcre-8.42-6.el8.x86_64 44/172 Verifying : openldap-2.4.46-18.el8.x86_64 45/172 Verifying : nettle-3.4.1-7.el8.x86_64 46/172 Verifying : ncurses-libs-6.1-9.20180224.el8.x86_64 47/172 Verifying : libdb-utils-5.3.28-42.el8_4.x86_64 48/172 Verifying : filesystem-3.8-6.el8.x86_64 49/172 Verifying : libxcrypt-4.1.1-6.el8.x86_64 50/172 Verifying : chkconfig-1.19.1-1.el8.x86_64 51/172 Verifying : libcap-ng-0.7.11-1.el8.x86_64 52/172 Verifying : libdb-5.3.28-42.el8_4.x86_64 53/172 Verifying : ncurses-6.1-9.20180224.el8.x86_64 54/172 Verifying : libsepol-2.9-3.el8.x86_64 55/172 Verifying : gzip-1.9-13.el8_5.x86_64 56/172 Verifying : keyutils-libs-1.5.10-9.el8.x86_64 57/172 Verifying : ncurses-base-6.1-9.20180224.el8.noarch 58/172 Verifying : cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 59/172 Verifying : lua-libs-5.3.4-12.el8.x86_64 60/172 Verifying : cpio-2.12-11.el8.x86_64 61/172 Verifying : sed-4.5-5.el8.x86_64 62/172 Verifying : make-1:4.2.1-11.el8.x86_64 63/172 Verifying : libffi-3.1-23.el8.x86_64 64/172 Verifying : python3-pip-wheel-9.0.3-22.el8.noarch 65/172 Verifying : libssh-0.9.6-3.el8.x86_64 66/172 Verifying : gawk-4.2.1-4.el8.x86_64 67/172 Verifying : xz-libs-5.2.4-4.el8_6.x86_64 68/172 Verifying : xz-5.2.4-4.el8_6.x86_64 69/172 Verifying : crypto-policies-20211116-1.gitae470d6.el8.noarch 70/172 Verifying : info-6.5-7.el8.x86_64 71/172 Verifying : libssh-config-0.9.6-3.el8.noarch 72/172 Verifying : unzip-6.0-46.el8.x86_64 73/172 Verifying : coreutils-8.30-13.el8.x86_64 74/172 Verifying : libpwquality-1.4.4-5.el8.x86_64 75/172 Verifying : glibc-headers-2.28-211.el8.x86_64 76/172 Verifying : tar-2:1.30-6.el8.x86_64 77/172 Verifying : glibc-all-langpacks-2.28-211.el8.x86_64 78/172 Verifying : libbabeltrace-1.5.4-4.el8.x86_64 79/172 Verifying : libksba-1.3.5-8.el8_6.x86_64 80/172 Verifying : libverto-0.3.2-2.el8.x86_64 81/172 Verifying : gdbm-libs-1:1.18-2.el8.x86_64 82/172 Verifying : gnupg2-2.2.20-3.el8_6.x86_64 83/172 Verifying : coreutils-common-8.30-13.el8.x86_64 84/172 Verifying : libtirpc-1.1.4-8.el8.x86_64 85/172 Verifying : ca-certificates-2022.2.54-80.2.el8_6.noarch 86/172 Verifying : pcre2-10.32-3.el8_6.x86_64 87/172 Verifying : pam-1.3.1-22.el8.x86_64 88/172 Verifying : libgcrypt-1.8.5-7.el8_6.x86_64 89/172 Verifying : binutils-2.30-117.el8.x86_64 90/172 Verifying : glibc-devel-2.28-211.el8.x86_64 91/172 Verifying : openssl-libs-1:1.1.1k-7.el8_6.x86_64 92/172 Verifying : libcom_err-1.45.6-5.el8.x86_64 93/172 Verifying : libsemanage-2.9-9.el8_6.x86_64 94/172 Verifying : bash-4.4.20-4.el8_6.x86_64 95/172 Verifying : gnutls-3.6.16-5.el8_6.x86_64 96/172 Verifying : glibc-gconv-extra-2.28-211.el8.x86_64 97/172 Verifying : elfutils-libelf-0.187-4.el8.x86_64 98/172 Verifying : file-libs-5.33-21.el8.x86_64 99/172 Verifying : file-5.33-21.el8.x86_64 100/172 Verifying : which-2.21-18.el8.x86_64 101/172 Verifying : gdbm-1:1.18-2.el8.x86_64 102/172 Verifying : glibc-2.28-211.el8.x86_64 103/172 Verifying : elfutils-0.187-4.el8.x86_64 104/172 Verifying : glibc-common-2.28-211.el8.x86_64 105/172 Verifying : setup-2.12.2-7.el8.noarch 106/172 Verifying : elfutils-libs-0.187-4.el8.x86_64 107/172 Verifying : libarchive-3.3.3-4.el8.x86_64 108/172 Verifying : audit-libs-3.0.7-4.el8.x86_64 109/172 Verifying : libcap-2.48-4.el8.x86_64 110/172 Verifying : elfutils-default-yama-scope-0.187-4.el8.noarch 111/172 Verifying : shadow-utils-2:4.6-17.el8.x86_64 112/172 Verifying : glib2-2.56.4-159.el8.x86_64 113/172 Verifying : libselinux-2.9-6.el8.x86_64 114/172 Verifying : redhat-release-8.7-0.3.el8.x86_64 115/172 Verifying : rpm-libs-4.14.3-24.el8_7.x86_64 116/172 Verifying : rpm-4.14.3-24.el8_7.x86_64 117/172 Verifying : python3-libs-3.6.8-48.el8_7.x86_64 118/172 Verifying : rpm-build-libs-4.14.3-24.el8_7.x86_64 119/172 Verifying : platform-python-3.6.8-48.el8_7.x86_64 120/172 Verifying : krb5-libs-1.18.2-22.el8_7.x86_64 121/172 Verifying : tzdata-2022g-1.el8.noarch 122/172 Verifying : curl-7.61.1-25.el8_7.1.x86_64 123/172 Verifying : libuuid-2.32.1-39.el8_7.x86_64 124/172 Verifying : libgcc-8.5.0-16.el8_7.x86_64 125/172 Verifying : util-linux-2.32.1-39.el8_7.x86_64 126/172 Verifying : expat-2.2.5-10.el8_7.1.x86_64 127/172 Verifying : libtasn1-4.13-4.el8_7.x86_64 128/172 Verifying : libblkid-2.32.1-39.el8_7.x86_64 129/172 Verifying : kernel-headers-4.18.0-425.10.1.el8_7.x86_64 130/172 Verifying : libstdc++-8.5.0-16.el8_7.x86_64 131/172 Verifying : libcurl-7.61.1-25.el8_7.1.x86_64 132/172 Verifying : libmount-2.32.1-39.el8_7.x86_64 133/172 Verifying : systemd-libs-239-68.el8_7.2.x86_64 134/172 Verifying : zlib-1.2.11-21.el8_7.x86_64 135/172 Verifying : libgomp-8.5.0-16.el8_7.x86_64 136/172 Verifying : sqlite-libs-3.26.0-17.el8_7.x86_64 137/172 Verifying : libfdisk-2.32.1-39.el8_7.x86_64 138/172 Verifying : libsmartcols-2.32.1-39.el8_7.x86_64 139/172 Verifying : libxml2-2.9.7-15.el8_7.1.x86_64 140/172 Verifying : rust-srpm-macros-5-2.el8.noarch 141/172 Verifying : ocaml-srpm-macros-5-4.el8.noarch 142/172 Verifying : ghc-srpm-macros-1.4.2-7.el8.noarch 143/172 Verifying : openblas-srpm-macros-2-2.el8.noarch 144/172 Verifying : perl-srpm-macros-1-25.el8.noarch 145/172 Verifying : libatomic_ops-7.6.2-3.el8.x86_64 146/172 Verifying : gc-7.6.4-3.el8.x86_64 147/172 Verifying : guile-5:2.0.14-7.el8.x86_64 148/172 Verifying : isl-0.16.1-6.el8.x86_64 149/172 Verifying : libipt-1.6.1-8.el8.x86_64 150/172 Verifying : zstd-1.4.4-1.el8.x86_64 151/172 Verifying : libmpc-1.1.0-9.1.el8.x86_64 152/172 Verifying : efi-srpm-macros-3-3.el8.noarch 153/172 Verifying : go-srpm-macros-2-17.el8.noarch 154/172 Verifying : dwz-0.12-10.el8.x86_64 155/172 Verifying : qt5-srpm-macros-5.15.3-1.el8.noarch 156/172 Verifying : python3-rpm-macros-3-43.el8.noarch 157/172 Verifying : redhat-rpm-config-130-1.el8.noarch 158/172 Verifying : gdb-headless-8.2-19.el8.x86_64 159/172 Verifying : python-rpm-macros-3-43.el8.noarch 160/172 Verifying : python-srpm-macros-3-43.el8.noarch 161/172 Verifying : annobin-10.67-3.el8.x86_64 162/172 Verifying : rpm-build-4.14.3-24.el8_7.x86_64 163/172 Verifying : cpp-8.5.0-16.el8_7.x86_64 164/172 Verifying : gcc-8.5.0-16.el8_7.x86_64 165/172 Verifying : libstdc++-devel-8.5.0-16.el8_7.x86_64 166/172 Verifying : gcc-plugin-annobin-8.5.0-16.el8_7.x86_64 167/172 Verifying : gcc-c++-8.5.0-16.el8_7.x86_64 168/172 Verifying : ansible-srpm-macros-1-8.1.el8.noarch 169/172 Verifying : epel-rpm-macros-8-35.noarch 170/172 Verifying : fpc-srpm-macros-1.3-1.el8.noarch 171/172 Verifying : lua-srpm-macros-1-3.el8.noarch 172/172 Installed products updated. Installed: annobin-10.67-3.el8.x86_64 ansible-srpm-macros-1-8.1.el8.noarch audit-libs-3.0.7-4.el8.x86_64 basesystem-11-5.el8.noarch bash-4.4.20-4.el8_6.x86_64 binutils-2.30-117.el8.x86_64 brotli-1.0.6-3.el8.x86_64 bzip2-1.0.6-26.el8.x86_64 bzip2-libs-1.0.6-26.el8.x86_64 ca-certificates-2022.2.54-80.2.el8_6.noarch chkconfig-1.19.1-1.el8.x86_64 coreutils-8.30-13.el8.x86_64 coreutils-common-8.30-13.el8.x86_64 cpio-2.12-11.el8.x86_64 cpp-8.5.0-16.el8_7.x86_64 cracklib-2.9.6-15.el8.x86_64 cracklib-dicts-2.9.6-15.el8.x86_64 crypto-policies-20211116-1.gitae470d6.el8.noarch curl-7.61.1-25.el8_7.1.x86_64 cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 diffutils-3.6-6.el8.x86_64 dwz-0.12-10.el8.x86_64 efi-srpm-macros-3-3.el8.noarch elfutils-0.187-4.el8.x86_64 elfutils-default-yama-scope-0.187-4.el8.noarch elfutils-libelf-0.187-4.el8.x86_64 elfutils-libs-0.187-4.el8.x86_64 epel-rpm-macros-8-35.noarch expat-2.2.5-10.el8_7.1.x86_64 file-5.33-21.el8.x86_64 file-libs-5.33-21.el8.x86_64 filesystem-3.8-6.el8.x86_64 findutils-1:4.6.0-20.el8.x86_64 fpc-srpm-macros-1.3-1.el8.noarch gawk-4.2.1-4.el8.x86_64 gc-7.6.4-3.el8.x86_64 gcc-8.5.0-16.el8_7.x86_64 gcc-c++-8.5.0-16.el8_7.x86_64 gcc-plugin-annobin-8.5.0-16.el8_7.x86_64 gdb-headless-8.2-19.el8.x86_64 gdbm-1:1.18-2.el8.x86_64 gdbm-libs-1:1.18-2.el8.x86_64 ghc-srpm-macros-1.4.2-7.el8.noarch glib2-2.56.4-159.el8.x86_64 glibc-2.28-211.el8.x86_64 glibc-all-langpacks-2.28-211.el8.x86_64 glibc-common-2.28-211.el8.x86_64 glibc-devel-2.28-211.el8.x86_64 glibc-gconv-extra-2.28-211.el8.x86_64 glibc-headers-2.28-211.el8.x86_64 gmp-1:6.1.2-10.el8.x86_64 gnupg2-2.2.20-3.el8_6.x86_64 gnutls-3.6.16-5.el8_6.x86_64 go-srpm-macros-2-17.el8.noarch grep-3.1-6.el8.x86_64 guile-5:2.0.14-7.el8.x86_64 gzip-1.9-13.el8_5.x86_64 ima-evm-utils-1.3.2-12.el8.x86_64 info-6.5-7.el8.x86_64 isl-0.16.1-6.el8.x86_64 kernel-headers-4.18.0-425.10.1.el8_7.x86_64 keyutils-libs-1.5.10-9.el8.x86_64 krb5-libs-1.18.2-22.el8_7.x86_64 libacl-2.2.53-1.el8.x86_64 libarchive-3.3.3-4.el8.x86_64 libassuan-2.5.1-3.el8.x86_64 libatomic_ops-7.6.2-3.el8.x86_64 libattr-2.4.48-3.el8.x86_64 libbabeltrace-1.5.4-4.el8.x86_64 libblkid-2.32.1-39.el8_7.x86_64 libcap-2.48-4.el8.x86_64 libcap-ng-0.7.11-1.el8.x86_64 libcom_err-1.45.6-5.el8.x86_64 libcurl-7.61.1-25.el8_7.1.x86_64 libdb-5.3.28-42.el8_4.x86_64 libdb-utils-5.3.28-42.el8_4.x86_64 libfdisk-2.32.1-39.el8_7.x86_64 libffi-3.1-23.el8.x86_64 libgcc-8.5.0-16.el8_7.x86_64 libgcrypt-1.8.5-7.el8_6.x86_64 libgomp-8.5.0-16.el8_7.x86_64 libgpg-error-1.31-1.el8.x86_64 libidn2-2.2.0-1.el8.x86_64 libipt-1.6.1-8.el8.x86_64 libksba-1.3.5-8.el8_6.x86_64 libmount-2.32.1-39.el8_7.x86_64 libmpc-1.1.0-9.1.el8.x86_64 libnghttp2-1.33.0-3.el8_2.1.x86_64 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libpkgconf-1.4.2-1.el8.x86_64 libpsl-0.20.2-6.el8.x86_64 libpwquality-1.4.4-5.el8.x86_64 libselinux-2.9-6.el8.x86_64 libsemanage-2.9-9.el8_6.x86_64 libsepol-2.9-3.el8.x86_64 libsigsegv-2.11-5.el8.x86_64 libsmartcols-2.32.1-39.el8_7.x86_64 libssh-0.9.6-3.el8.x86_64 libssh-config-0.9.6-3.el8.noarch libstdc++-8.5.0-16.el8_7.x86_64 libstdc++-devel-8.5.0-16.el8_7.x86_64 libtasn1-4.13-4.el8_7.x86_64 libtirpc-1.1.4-8.el8.x86_64 libtool-ltdl-2.4.6-25.el8.x86_64 libunistring-0.9.9-3.el8.x86_64 libusbx-1.0.23-4.el8.x86_64 libutempter-1.1.6-14.el8.x86_64 libuuid-2.32.1-39.el8_7.x86_64 libverto-0.3.2-2.el8.x86_64 libxcrypt-4.1.1-6.el8.x86_64 libxcrypt-devel-4.1.1-6.el8.x86_64 libxml2-2.9.7-15.el8_7.1.x86_64 libzstd-1.4.4-1.el8.x86_64 lua-libs-5.3.4-12.el8.x86_64 lua-srpm-macros-1-3.el8.noarch lz4-libs-1.8.3-3.el8_4.x86_64 make-1:4.2.1-11.el8.x86_64 mpfr-3.1.6-1.el8.x86_64 ncurses-6.1-9.20180224.el8.x86_64 ncurses-base-6.1-9.20180224.el8.noarch ncurses-libs-6.1-9.20180224.el8.x86_64 nettle-3.4.1-7.el8.x86_64 npth-1.5-4.el8.x86_64 ocaml-srpm-macros-5-4.el8.noarch openblas-srpm-macros-2-2.el8.noarch openldap-2.4.46-18.el8.x86_64 openssl-libs-1:1.1.1k-7.el8_6.x86_64 p11-kit-0.23.22-1.el8.x86_64 p11-kit-trust-0.23.22-1.el8.x86_64 pam-1.3.1-22.el8.x86_64 patch-2.7.6-11.el8.x86_64 pcre-8.42-6.el8.x86_64 pcre2-10.32-3.el8_6.x86_64 perl-srpm-macros-1-25.el8.noarch pkgconf-1.4.2-1.el8.x86_64 pkgconf-m4-1.4.2-1.el8.noarch pkgconf-pkg-config-1.4.2-1.el8.x86_64 platform-python-3.6.8-48.el8_7.x86_64 platform-python-setuptools-39.2.0-6.el8.noarch popt-1.18-1.el8.x86_64 publicsuffix-list-dafsa-20180723-1.el8.noarch python-rpm-macros-3-43.el8.noarch python-srpm-macros-3-43.el8.noarch python3-libs-3.6.8-48.el8_7.x86_64 python3-pip-wheel-9.0.3-22.el8.noarch python3-rpm-macros-3-43.el8.noarch python3-setuptools-wheel-39.2.0-6.el8.noarch qt5-srpm-macros-5.15.3-1.el8.noarch readline-7.0-10.el8.x86_64 redhat-release-8.7-0.3.el8.x86_64 redhat-rpm-config-130-1.el8.noarch rpm-4.14.3-24.el8_7.x86_64 rpm-build-4.14.3-24.el8_7.x86_64 rpm-build-libs-4.14.3-24.el8_7.x86_64 rpm-libs-4.14.3-24.el8_7.x86_64 rust-srpm-macros-5-2.el8.noarch sed-4.5-5.el8.x86_64 setup-2.12.2-7.el8.noarch shadow-utils-2:4.6-17.el8.x86_64 sqlite-libs-3.26.0-17.el8_7.x86_64 systemd-libs-239-68.el8_7.2.x86_64 tar-2:1.30-6.el8.x86_64 tpm2-tss-2.3.2-4.el8.x86_64 tzdata-2022g-1.el8.noarch unzip-6.0-46.el8.x86_64 util-linux-2.32.1-39.el8_7.x86_64 which-2.21-18.el8.x86_64 xz-5.2.4-4.el8_6.x86_64 xz-libs-5.2.4-4.el8_6.x86_64 zip-3.0-23.el8.x86_64 zlib-1.2.11-21.el8_7.x86_64 zstd-1.4.4-1.el8.x86_64 Complete! Finish: dnf install Start: creating root cache Finish: creating root cache Finish: chroot init INFO: Installed packages: INFO: python3-rpm-macros-3-43.el8.noarch binutils-2.30-117.el8.x86_64 glibc-2.28-211.el8.x86_64 libtool-ltdl-2.4.6-25.el8.x86_64 zstd-1.4.4-1.el8.x86_64 chkconfig-1.19.1-1.el8.x86_64 p11-kit-0.23.22-1.el8.x86_64 redhat-release-8.7-0.3.el8.x86_64 libverto-0.3.2-2.el8.x86_64 gcc-plugin-annobin-8.5.0-16.el8_7.x86_64 rpm-build-libs-4.14.3-24.el8_7.x86_64 tzdata-2022g-1.el8.noarch openssl-libs-1.1.1k-7.el8_6.x86_64 kernel-headers-4.18.0-425.10.1.el8_7.x86_64 redhat-rpm-config-130-1.el8.noarch gdbm-1.18-2.el8.x86_64 gnutls-3.6.16-5.el8_6.x86_64 gpg-pubkey-2fa658e0-45700c69 libuuid-2.32.1-39.el8_7.x86_64 bzip2-libs-1.0.6-26.el8.x86_64 file-libs-5.33-21.el8.x86_64 libssh-0.9.6-3.el8.x86_64 cracklib-dicts-2.9.6-15.el8.x86_64 glib2-2.56.4-159.el8.x86_64 glibc-all-langpacks-2.28-211.el8.x86_64 guile-2.0.14-7.el8.x86_64 dwz-0.12-10.el8.x86_64 libcap-ng-0.7.11-1.el8.x86_64 rpm-4.14.3-24.el8_7.x86_64 expat-2.2.5-10.el8_7.1.x86_64 shadow-utils-4.6-17.el8.x86_64 annobin-10.67-3.el8.x86_64 zip-3.0-23.el8.x86_64 gawk-4.2.1-4.el8.x86_64 libselinux-2.9-6.el8.x86_64 libgomp-8.5.0-16.el8_7.x86_64 libmount-2.32.1-39.el8_7.x86_64 elfutils-libs-0.187-4.el8.x86_64 libfdisk-2.32.1-39.el8_7.x86_64 libpwquality-1.4.4-5.el8.x86_64 pam-1.3.1-22.el8.x86_64 ima-evm-utils-1.3.2-12.el8.x86_64 xz-5.2.4-4.el8_6.x86_64 pkgconf-pkg-config-1.4.2-1.el8.x86_64 file-5.33-21.el8.x86_64 pcre2-10.32-3.el8_6.x86_64 gpg-pubkey-fd431d51-4ae0493b pkgconf-1.4.2-1.el8.x86_64 cpp-8.5.0-16.el8_7.x86_64 bash-4.4.20-4.el8_6.x86_64 libzstd-1.4.4-1.el8.x86_64 crypto-policies-20211116-1.gitae470d6.el8.noarch python-srpm-macros-3-43.el8.noarch lz4-libs-1.8.3-3.el8_4.x86_64 popt-1.18-1.el8.x86_64 diffutils-3.6-6.el8.x86_64 keyutils-libs-1.5.10-9.el8.x86_64 sed-4.5-5.el8.x86_64 isl-0.16.1-6.el8.x86_64 publicsuffix-list-dafsa-20180723-1.el8.noarch ncurses-libs-6.1-9.20180224.el8.x86_64 libgpg-error-1.31-1.el8.x86_64 sqlite-libs-3.26.0-17.el8_7.x86_64 ansible-srpm-macros-1-8.1.el8.noarch cyrus-sasl-lib-2.1.27-6.el8_5.x86_64 rpm-build-4.14.3-24.el8_7.x86_64 gdbm-libs-1.18-2.el8.x86_64 grep-3.1-6.el8.x86_64 libipt-1.6.1-8.el8.x86_64 libgcrypt-1.8.5-7.el8_6.x86_64 bzip2-1.0.6-26.el8.x86_64 libcurl-7.61.1-25.el8_7.1.x86_64 go-srpm-macros-2-17.el8.noarch pcre-8.42-6.el8.x86_64 platform-python-3.6.8-48.el8_7.x86_64 unzip-6.0-46.el8.x86_64 rpm-libs-4.14.3-24.el8_7.x86_64 filesystem-3.8-6.el8.x86_64 libarchive-3.3.3-4.el8.x86_64 libnghttp2-1.33.0-3.el8_2.1.x86_64 glibc-headers-2.28-211.el8.x86_64 util-linux-2.32.1-39.el8_7.x86_64 libsepol-2.9-3.el8.x86_64 elfutils-libelf-0.187-4.el8.x86_64 elfutils-default-yama-scope-0.187-4.el8.noarch libusbx-1.0.23-4.el8.x86_64 python-rpm-macros-3-43.el8.noarch libcom_err-1.45.6-5.el8.x86_64 gzip-1.9-13.el8_5.x86_64 libtasn1-4.13-4.el8_7.x86_64 openldap-2.4.46-18.el8.x86_64 libsemanage-2.9-9.el8_6.x86_64 glibc-gconv-extra-2.28-211.el8.x86_64 zlib-1.2.11-21.el8_7.x86_64 libidn2-2.2.0-1.el8.x86_64 nettle-3.4.1-7.el8.x86_64 libsmartcols-2.32.1-39.el8_7.x86_64 gc-7.6.4-3.el8.x86_64 libtirpc-1.1.4-8.el8.x86_64 libcap-2.48-4.el8.x86_64 systemd-libs-239-68.el8_7.2.x86_64 coreutils-8.30-13.el8.x86_64 python3-setuptools-wheel-39.2.0-6.el8.noarch ca-certificates-2022.2.54-80.2.el8_6.noarch libmpc-1.1.0-9.1.el8.x86_64 tar-1.30-6.el8.x86_64 libstdc++-8.5.0-16.el8_7.x86_64 setup-2.12.2-7.el8.noarch libffi-3.1-23.el8.x86_64 p11-kit-trust-0.23.22-1.el8.x86_64 make-4.2.1-11.el8.x86_64 glibc-devel-2.28-211.el8.x86_64 ncurses-6.1-9.20180224.el8.x86_64 glibc-common-2.28-211.el8.x86_64 audit-libs-3.0.7-4.el8.x86_64 which-2.21-18.el8.x86_64 ghc-srpm-macros-1.4.2-7.el8.noarch rust-srpm-macros-5-2.el8.noarch libdb-utils-5.3.28-42.el8_4.x86_64 lua-srpm-macros-1-3.el8.noarch epel-rpm-macros-8-35.noarch xz-libs-5.2.4-4.el8_6.x86_64 libnsl2-1.2.0-2.20180605git4a062cf.el8.x86_64 libutempter-1.1.6-14.el8.x86_64 ncurses-base-6.1-9.20180224.el8.noarch gcc-c++-8.5.0-16.el8_7.x86_64 libblkid-2.32.1-39.el8_7.x86_64 python3-pip-wheel-9.0.3-22.el8.noarch efi-srpm-macros-3-3.el8.noarch basesystem-11-5.el8.noarch libpkgconf-1.4.2-1.el8.x86_64 libxcrypt-4.1.1-6.el8.x86_64 readline-7.0-10.el8.x86_64 gnupg2-2.2.20-3.el8_6.x86_64 libunistring-0.9.9-3.el8.x86_64 curl-7.61.1-25.el8_7.1.x86_64 cracklib-2.9.6-15.el8.x86_64 libdb-5.3.28-42.el8_4.x86_64 libstdc++-devel-8.5.0-16.el8_7.x86_64 libacl-2.2.53-1.el8.x86_64 qt5-srpm-macros-5.15.3-1.el8.noarch libxcrypt-devel-4.1.1-6.el8.x86_64 libksba-1.3.5-8.el8_6.x86_64 libassuan-2.5.1-3.el8.x86_64 libpsl-0.20.2-6.el8.x86_64 python3-libs-3.6.8-48.el8_7.x86_64 findutils-4.6.0-20.el8.x86_64 libattr-2.4.48-3.el8.x86_64 gmp-6.1.2-10.el8.x86_64 patch-2.7.6-11.el8.x86_64 brotli-1.0.6-3.el8.x86_64 libatomic_ops-7.6.2-3.el8.x86_64 coreutils-common-8.30-13.el8.x86_64 krb5-libs-1.18.2-22.el8_7.x86_64 tpm2-tss-2.3.2-4.el8.x86_64 perl-srpm-macros-1-25.el8.noarch mpfr-3.1.6-1.el8.x86_64 openblas-srpm-macros-2-2.el8.noarch elfutils-0.187-4.el8.x86_64 libxml2-2.9.7-15.el8_7.1.x86_64 gpg-pubkey-2f86d6a1-5cf7cefb info-6.5-7.el8.x86_64 gcc-8.5.0-16.el8_7.x86_64 lua-libs-5.3.4-12.el8.x86_64 pkgconf-m4-1.4.2-1.el8.noarch libsigsegv-2.11-5.el8.x86_64 libbabeltrace-1.5.4-4.el8.x86_64 libssh-config-0.9.6-3.el8.noarch cpio-2.12-11.el8.x86_64 gdb-headless-8.2-19.el8.x86_64 ocaml-srpm-macros-5-4.el8.noarch platform-python-setuptools-39.2.0-6.el8.noarch libgcc-8.5.0-16.el8_7.x86_64 fpc-srpm-macros-1.3-1.el8.noarch npth-1.5-4.el8.x86_64 Start: buildsrpm Start: rpmbuild -bs sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory warning: bogus date in %changelog: Thu Nov 04 2009 Tim Fenn - 1.2.0-1 Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/apbs-3.0.0-17.el8.src.rpm Finish: rpmbuild -bs cp: ‘var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/root/var/log’: No such file or directory INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/root/var/log/dnf.log Finish: buildsrpm INFO: Done(/var/lib/copr-rpmbuild/workspace/workdir-lmv27hnw/apbs/apbs.spec) Config(child) 2 minutes 39 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 (timeout=18000): unbuffer mock --rebuild /var/lib/copr-rpmbuild/results/apbs-3.0.0-17.el8.src.rpm --resultdir /var/lib/copr-rpmbuild/results --uniqueext 1675078509.656443 -r /var/lib/copr-rpmbuild/results/configs/child.cfg INFO: mock.py version 3.5 starting (python version = 3.11.0, NVR = mock-3.5-1.fc37)... 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/results/apbs-3.0.0-17.el8.src.rpm) Config(rhel+epel-8-x86_64) Start: clean chroot Finish: clean chroot Start(bootstrap): chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-8-x86_64-bootstrap-1675078509.656443/root. INFO: reusing tmpfs at /var/lib/mock/rhel+epel-8-x86_64-bootstrap-1675078509.656443/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: enabled HW Info plugin Mock Version: 3.5 INFO: Mock Version: 3.5 Finish(bootstrap): chroot init Start: chroot init INFO: mounting tmpfs at /var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/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 Mock Version: 3.5 INFO: Mock Version: 3.5 Start: dnf update No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 21 kB/s | 3.0 kB 00:00 Red Hat Enterprise Linux - BaseOS 12 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 12 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 20 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 408 kB/s | 24 kB 00:00 Dependencies resolved. Nothing to do. Complete! Finish: dnf update Finish: chroot init Start: build phase for apbs-3.0.0-17.el8.src.rpm Start: build setup for apbs-3.0.0-17.el8.src.rpm sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory sh: /usr/bin/python3.6: No such file or directory warning: bogus date in %changelog: Thu Nov 04 2009 Tim Fenn - 1.2.0-1 Building target platforms: x86_64 Building for target x86_64 Wrote: /builddir/build/SRPMS/apbs-3.0.0-17.el8.src.rpm No matches found for the following disable plugin patterns: local, spacewalk, versionlock Updating Subscription Management repositories. Unable to read consumer identity This system is not registered with an entitlement server. You can use subscription-manager to register. Copr repository 84 kB/s | 3.0 kB 00:00 Red Hat Enterprise Linux - BaseOS 18 kB/s | 4.1 kB 00:00 Red Hat Enterprise Linux - AppStream 15 kB/s | 4.5 kB 00:00 Red Hat Enterprise Linux - CodeReady Linux Buil 8.5 kB/s | 4.5 kB 00:00 Extra Packages for Enterprise Linux 8 - x86_64 727 kB/s | 24 kB 00:00 Package gcc-c++-8.5.0-16.el8_7.x86_64 is already installed. Package make-1:4.2.1-11.el8.x86_64 is already installed. Dependencies resolved. =============================================================================================================== Package Arch Version Repository Size =============================================================================================================== Installing: chrpath x86_64 0.16-7.el8 rhel-baseos 33 k cmake x86_64 3.20.2-4.el8 rhel-appstream 12 M doxygen x86_64 1:1.8.14-12.el8 codeready-builder 3.9 M graphviz x86_64 2.40.1-43.el8 rhel-appstream 1.7 M maloc-devel x86_64 1.5-27.el8 copr_base 194 k python3-numpy x86_64 1:1.14.3-10.el8 rhel-appstream 3.7 M python3-sphinx noarch 1:1.7.6-3.el8 codeready-builder 1.7 M python36-devel x86_64 3.6.8-38.module+el8.5.0+12207+5c5719bc rhel-appstream 17 k swig x86_64 3.0.12-19.module+el8.3.0+6248+838326ab rhel-appstream 1.5 M zlib-devel x86_64 1.2.11-21.el8_7 rhel-baseos 58 k Installing dependencies: Lmod x86_64 8.7.7-1.el8 epel 261 k adobe-mappings-cmap noarch 20171205-3.el8 rhel-appstream 2.1 M adobe-mappings-cmap-deprecated noarch 20171205-3.el8 rhel-appstream 119 k adobe-mappings-pdf noarch 20180407-1.el8 rhel-appstream 707 k atk x86_64 2.28.1-1.el8 rhel-appstream 272 k avahi-libs x86_64 0.7-20.el8 rhel-baseos 62 k cairo x86_64 1.15.12-6.el8 rhel-appstream 719 k cmake-data noarch 3.20.2-4.el8 rhel-appstream 1.7 M cmake-filesystem x86_64 3.20.2-4.el8 rhel-appstream 45 k cmake-rpm-macros noarch 3.20.2-4.el8 rhel-appstream 44 k cups-libs x86_64 1:2.2.6-50.el8 rhel-baseos 435 k dbus-libs x86_64 1:1.12.8-23.el8_7.1 rhel-baseos 185 k emacs-filesystem noarch 1:26.1-7.el8 rhel-baseos 70 k fontawesome-fonts noarch 4.7.0-4.el8 rhel-appstream 203 k fontawesome-fonts-web noarch 4.7.0-4.el8 codeready-builder 429 k fontconfig x86_64 2.13.1-4.el8 rhel-baseos 274 k fontpackages-filesystem noarch 1.44-22.el8 rhel-baseos 16 k freetype x86_64 2.9.1-9.el8 rhel-baseos 394 k fribidi x86_64 1.0.4-9.el8 rhel-appstream 89 k gd x86_64 2.2.5-7.el8 rhel-appstream 144 k gdk-pixbuf2 x86_64 2.36.12-5.el8 rhel-baseos 467 k gdk-pixbuf2-modules x86_64 2.36.12-5.el8 rhel-appstream 109 k google-droid-sans-fonts noarch 20120715-13.el8 rhel-appstream 2.5 M google-roboto-slab-fonts noarch 1.100263-0.7.20150923git.el8 codeready-builder 238 k graphite2 x86_64 1.3.10-10.el8 rhel-appstream 122 k groff-base x86_64 1.22.3-18.el8 rhel-baseos 1.0 M gtk-update-icon-cache x86_64 3.22.30-11.el8 rhel-appstream 33 k gtk2 x86_64 2.24.32-5.el8 rhel-appstream 3.4 M harfbuzz x86_64 1.7.5-3.el8 rhel-appstream 294 k hicolor-icon-theme noarch 0.17-2.el8 rhel-appstream 48 k jasper-libs x86_64 2.0.14-5.el8 rhel-appstream 167 k jbig2dec-libs x86_64 0.16-1.el8 rhel-appstream 72 k jbigkit-libs x86_64 2.1-14.el8 rhel-appstream 55 k lato-fonts noarch 2.015-5.el8 rhel-appstream 3.3 M lcms2 x86_64 2.9-2.el8 rhel-appstream 165 k libICE x86_64 1.0.9-15.el8 rhel-appstream 74 k libSM x86_64 1.2.3-1.el8 rhel-appstream 48 k libX11 x86_64 1.6.8-5.el8 rhel-appstream 611 k libX11-common noarch 1.6.8-5.el8 rhel-appstream 158 k libXau x86_64 1.0.9-3.el8 rhel-appstream 37 k libXaw x86_64 1.0.13-10.el8 rhel-appstream 194 k libXcomposite x86_64 0.4.4-14.el8 rhel-appstream 29 k libXcursor x86_64 1.1.15-3.el8 rhel-appstream 36 k libXdamage x86_64 1.1.4-14.el8 rhel-appstream 27 k libXext x86_64 1.3.4-1.el8 rhel-appstream 45 k libXfixes x86_64 5.0.3-7.el8 rhel-appstream 25 k libXft x86_64 2.3.3-1.el8 rhel-appstream 67 k libXi x86_64 1.7.10-1.el8 rhel-appstream 49 k libXinerama x86_64 1.1.4-1.el8 rhel-appstream 16 k libXmu x86_64 1.1.3-1.el8 rhel-appstream 75 k libXpm x86_64 3.5.12-9.el8_7 rhel-appstream 58 k libXrandr x86_64 1.5.2-1.el8 rhel-appstream 34 k libXrender x86_64 0.9.10-7.el8 rhel-appstream 33 k libXt x86_64 1.1.5-12.el8 rhel-appstream 185 k libXxf86misc x86_64 1.0.4-1.el8 rhel-appstream 23 k libXxf86vm x86_64 1.1.4-9.el8 rhel-appstream 19 k libcroco x86_64 0.6.12-4.el8_2.1 rhel-baseos 113 k libdatrie x86_64 0.2.9-7.el8 rhel-appstream 33 k libfontenc x86_64 1.1.3-8.el8 rhel-appstream 37 k libgfortran x86_64 8.5.0-16.el8_7 rhel-baseos 644 k libgs x86_64 9.27-4.el8 rhel-appstream 3.1 M libidn x86_64 1.34-5.el8 rhel-appstream 239 k libijs x86_64 0.35-5.el8 rhel-appstream 30 k libjpeg-turbo x86_64 1.5.3-12.el8 rhel-appstream 157 k libmcpp x86_64 2.7.2-20.el8 rhel-appstream 81 k libpaper x86_64 1.1.24-22.el8 rhel-appstream 45 k libpng x86_64 2:1.6.34-5.el8 rhel-baseos 126 k libquadmath x86_64 8.5.0-16.el8_7 rhel-baseos 172 k librsvg2 x86_64 2.42.7-4.el8 rhel-appstream 555 k libthai x86_64 0.1.27-2.el8 rhel-appstream 203 k libtiff x86_64 4.0.9-26.el8_7 rhel-appstream 189 k libuv x86_64 1:1.41.1-1.el8_4 rhel-appstream 156 k libwebp x86_64 1.0.0-5.el8 rhel-appstream 273 k libxcb x86_64 1.13.1-1.el8 rhel-appstream 229 k lua x86_64 5.3.4-12.el8 rhel-appstream 192 k lua-filesystem x86_64 1.6.3-7.el8 codeready-builder 36 k lua-json noarch 1.3.2-9.el8 rhel-appstream 29 k lua-lpeg x86_64 1.0.1-6.el8 rhel-appstream 67 k lua-posix x86_64 33.3.1-9.el8 codeready-builder 176 k lua-term x86_64 0.07-9.el8 epel 16 k maloc x86_64 1.5-27.el8 copr_base 98 k mcpp x86_64 2.7.2-20.el8 rhel-appstream 31 k openblas x86_64 0.3.15-4.el8 rhel-appstream 4.7 M openblas-threads x86_64 0.3.15-4.el8 rhel-appstream 4.9 M openjpeg2 x86_64 2.4.0-5.el8 rhel-appstream 165 k pango x86_64 1.42.4-8.el8 rhel-appstream 297 k perl-Carp noarch 1.42-396.el8 rhel-baseos 30 k perl-Encode x86_64 4:2.97-3.el8 rhel-baseos 1.5 M perl-Errno x86_64 1.28-421.el8 rhel-baseos 76 k perl-Exporter noarch 5.72-396.el8 rhel-baseos 34 k perl-File-Path noarch 2.15-2.el8 rhel-baseos 38 k perl-File-Temp noarch 0.230.600-1.el8 rhel-baseos 63 k perl-Getopt-Long noarch 1:2.50-4.el8 rhel-baseos 63 k perl-HTTP-Tiny noarch 0.074-1.el8 rhel-baseos 58 k perl-IO x86_64 1.38-421.el8 rhel-baseos 142 k perl-MIME-Base64 x86_64 3.15-396.el8 rhel-baseos 31 k perl-PathTools x86_64 3.74-1.el8 rhel-baseos 90 k perl-Pod-Escapes noarch 1:1.07-395.el8 rhel-baseos 20 k perl-Pod-Perldoc noarch 3.28-396.el8 rhel-baseos 88 k perl-Pod-Simple noarch 1:3.35-395.el8 rhel-baseos 213 k perl-Pod-Usage noarch 4:1.69-395.el8 rhel-baseos 34 k perl-Scalar-List-Utils x86_64 3:1.49-2.el8 rhel-baseos 68 k perl-Socket x86_64 4:2.027-3.el8 rhel-baseos 59 k perl-Storable x86_64 1:3.11-3.el8 rhel-baseos 98 k perl-Term-ANSIColor noarch 4.06-396.el8 rhel-baseos 46 k perl-Term-Cap noarch 1.17-395.el8 rhel-baseos 23 k perl-Text-ParseWords noarch 3.30-395.el8 rhel-baseos 18 k perl-Text-Tabs+Wrap noarch 2013.0523-395.el8 rhel-baseos 24 k perl-Time-Local noarch 1:1.280-1.el8 rhel-baseos 34 k perl-Unicode-Normalize x86_64 1.25-396.el8 rhel-baseos 82 k perl-constant noarch 1.33-396.el8 rhel-baseos 25 k perl-interpreter x86_64 4:5.26.3-421.el8 rhel-baseos 6.3 M perl-libs x86_64 4:5.26.3-421.el8 rhel-baseos 1.6 M perl-macros x86_64 4:5.26.3-421.el8 rhel-baseos 72 k perl-parent noarch 1:0.237-1.el8 rhel-baseos 20 k perl-podlators noarch 4.11-1.el8 rhel-baseos 118 k perl-threads x86_64 1:2.21-2.el8 rhel-baseos 61 k perl-threads-shared x86_64 1.58-2.el8 rhel-baseos 48 k pixman x86_64 0.38.4-2.el8 rhel-appstream 257 k platform-python-devel x86_64 3.6.8-48.el8_7 rhel-appstream 250 k platform-python-pip noarch 9.0.3-22.el8 rhel-baseos 1.6 M procps-ng x86_64 3.3.15-9.el8 rhel-baseos 329 k python-sphinx-locale noarch 1:1.7.6-3.el8 codeready-builder 171 k python3-babel noarch 2.5.1-7.el8 rhel-appstream 4.8 M python3-chardet noarch 3.0.4-7.el8 rhel-baseos 195 k python3-docutils noarch 0.14-12.module+el8.1.0+3334+5cb623d7 rhel-appstream 1.6 M python3-idna noarch 2.5-5.el8 rhel-baseos 97 k python3-imagesize noarch 1.0.0-2.el8 codeready-builder 16 k python3-jinja2 noarch 2.10.1-3.el8 rhel-appstream 538 k python3-markupsafe x86_64 0.23-19.el8 rhel-appstream 39 k python3-mock noarch 2.0.0-11.el8 codeready-builder 59 k python3-packaging noarch 16.8-9.el8 codeready-builder 48 k python3-pip noarch 9.0.3-22.el8 rhel-appstream 20 k python3-pygments noarch 2.2.0-22.module+el8.5.0+10789+e4939b94 rhel-appstream 1.9 M python3-pyparsing noarch 2.1.10-7.el8 rhel-baseos 142 k python3-pysocks noarch 1.6.8-3.el8 rhel-baseos 34 k python3-pytz noarch 2017.2-9.el8 rhel-appstream 54 k python3-requests noarch 2.20.0-2.1.el8_1 rhel-baseos 123 k python3-rpm-generators noarch 5-7.el8 rhel-appstream 25 k python3-setuptools noarch 39.2.0-6.el8 rhel-baseos 163 k python3-six noarch 1.11.0-8.el8 rhel-baseos 38 k python3-snowballstemmer noarch 1.2.1-6.el8 codeready-builder 108 k python3-sphinx-theme-alabaster noarch 0.7.9-7.el8 codeready-builder 24 k python3-sphinx_rtd_theme noarch 0.3.1-3.el8 codeready-builder 128 k python3-sphinxcontrib-websupport noarch 1.0.1-10.20180316git.el8 codeready-builder 50 k python3-sqlalchemy x86_64 1.3.2-2.module+el8.3.0+6646+6b4b10ec rhel-appstream 1.9 M python3-urllib3 noarch 1.24.2-5.el8 rhel-baseos 177 k python3-whoosh noarch 2.7.4-9.el8 codeready-builder 1.1 M python36 x86_64 3.6.8-38.module+el8.5.0+12207+5c5719bc rhel-appstream 19 k python36-rpm-macros noarch 3.6.8-38.module+el8.5.0+12207+5c5719bc rhel-appstream 16 k shared-mime-info x86_64 1.9-3.el8 rhel-baseos 329 k tcl x86_64 1:8.6.8-2.el8 rhel-baseos 1.1 M urw-base35-bookman-fonts noarch 20170801-10.el8 rhel-appstream 857 k urw-base35-c059-fonts noarch 20170801-10.el8 rhel-appstream 884 k urw-base35-d050000l-fonts noarch 20170801-10.el8 rhel-appstream 79 k urw-base35-fonts noarch 20170801-10.el8 rhel-appstream 12 k urw-base35-fonts-common noarch 20170801-10.el8 rhel-appstream 23 k urw-base35-gothic-fonts noarch 20170801-10.el8 rhel-appstream 654 k urw-base35-nimbus-mono-ps-fonts noarch 20170801-10.el8 rhel-appstream 801 k urw-base35-nimbus-roman-fonts noarch 20170801-10.el8 rhel-appstream 865 k urw-base35-nimbus-sans-fonts noarch 20170801-10.el8 rhel-appstream 1.3 M urw-base35-p052-fonts noarch 20170801-10.el8 rhel-appstream 982 k urw-base35-standard-symbols-ps-fonts noarch 20170801-10.el8 rhel-appstream 44 k urw-base35-z003-fonts noarch 20170801-10.el8 rhel-appstream 279 k vim-filesystem noarch 2:8.0.1763-19.el8_6.4 rhel-appstream 50 k xorg-x11-font-utils x86_64 1:7.5-41.el8 rhel-appstream 104 k xorg-x11-fonts-ISO8859-1-100dpi noarch 7.5-19.el8 rhel-appstream 1.1 M xorg-x11-server-utils x86_64 7.7-27.el8 rhel-appstream 197 k Enabling module streams: python36 3.6 swig 3.0 Transaction Summary =============================================================================================================== Install 178 Packages Total download size: 100 M Installed size: 391 M Downloading Packages: (1/178): maloc-1.5-27.el8.x86_64.rpm 1.9 MB/s | 98 kB 00:00 (2/178): maloc-devel-1.5-27.el8.x86_64.rpm 3.1 MB/s | 194 kB 00:00 (3/178): perl-Scalar-List-Utils-1.49-2.el8.x86_ 265 kB/s | 68 kB 00:00 (4/178): perl-PathTools-3.74-1.el8.x86_64.rpm 301 kB/s | 90 kB 00:00 (5/178): perl-threads-shared-1.58-2.el8.x86_64. 428 kB/s | 48 kB 00:00 (6/178): tcl-8.6.8-2.el8.x86_64.rpm 2.6 MB/s | 1.1 MB 00:00 (7/178): shared-mime-info-1.9-3.el8.x86_64.rpm 1.9 MB/s | 329 kB 00:00 (8/178): libpng-1.6.34-5.el8.x86_64.rpm 1.3 MB/s | 126 kB 00:00 (9/178): perl-Encode-2.97-3.el8.x86_64.rpm 5.6 MB/s | 1.5 MB 00:00 (10/178): perl-Unicode-Normalize-1.25-396.el8.x 827 kB/s | 82 kB 00:00 (11/178): groff-base-1.22.3-18.el8.x86_64.rpm 5.5 MB/s | 1.0 MB 00:00 (12/178): perl-MIME-Base64-3.15-396.el8.x86_64. 313 kB/s | 31 kB 00:00 (13/178): fontpackages-filesystem-1.44-22.el8.n 119 kB/s | 16 kB 00:00 (14/178): perl-threads-2.21-2.el8.x86_64.rpm 585 kB/s | 61 kB 00:00 (15/178): perl-Pod-Simple-3.35-395.el8.noarch.r 2.2 MB/s | 213 kB 00:00 (16/178): perl-HTTP-Tiny-0.074-1.el8.noarch.rpm 587 kB/s | 58 kB 00:00 (17/178): perl-Term-ANSIColor-4.06-396.el8.noar 453 kB/s | 46 kB 00:00 (18/178): perl-Pod-Escapes-1.07-395.el8.noarch. 215 kB/s | 20 kB 00:00 (19/178): perl-File-Path-2.15-2.el8.noarch.rpm 424 kB/s | 38 kB 00:00 (20/178): perl-Pod-Perldoc-3.28-396.el8.noarch. 690 kB/s | 88 kB 00:00 (21/178): chrpath-0.16-7.el8.x86_64.rpm 242 kB/s | 33 kB 00:00 (22/178): perl-parent-0.237-1.el8.noarch.rpm 198 kB/s | 20 kB 00:00 (23/178): python3-pysocks-1.6.8-3.el8.noarch.rp 339 kB/s | 34 kB 00:00 (24/178): python3-idna-2.5-5.el8.noarch.rpm 534 kB/s | 97 kB 00:00 (25/178): perl-Text-Tabs+Wrap-2013.0523-395.el8 270 kB/s | 24 kB 00:00 (26/178): perl-Getopt-Long-2.50-4.el8.noarch.rp 646 kB/s | 63 kB 00:00 (27/178): perl-podlators-4.11-1.el8.noarch.rpm 1.3 MB/s | 118 kB 00:00 (28/178): perl-Time-Local-1.280-1.el8.noarch.rp 355 kB/s | 34 kB 00:00 (29/178): perl-Carp-1.42-396.el8.noarch.rpm 314 kB/s | 30 kB 00:00 (30/178): perl-Storable-3.11-3.el8.x86_64.rpm 1.0 MB/s | 98 kB 00:00 (31/178): perl-Text-ParseWords-3.30-395.el8.noa 177 kB/s | 18 kB 00:00 (32/178): perl-Exporter-5.72-396.el8.noarch.rpm 206 kB/s | 34 kB 00:00 (33/178): perl-File-Temp-0.230.600-1.el8.noarch 623 kB/s | 63 kB 00:00 (34/178): perl-Term-Cap-1.17-395.el8.noarch.rpm 249 kB/s | 23 kB 00:00 (35/178): perl-constant-1.33-396.el8.noarch.rpm 273 kB/s | 25 kB 00:00 (36/178): python3-chardet-3.0.4-7.el8.noarch.rp 2.0 MB/s | 195 kB 00:00 (37/178): python3-pyparsing-2.1.10-7.el8.noarch 1.6 MB/s | 142 kB 00:00 (38/178): perl-Pod-Usage-1.69-395.el8.noarch.rp 301 kB/s | 34 kB 00:00 (39/178): python3-six-1.11.0-8.el8.noarch.rpm 336 kB/s | 38 kB 00:00 (40/178): gdk-pixbuf2-2.36.12-5.el8.x86_64.rpm 3.5 MB/s | 467 kB 00:00 (41/178): python3-requests-2.20.0-2.1.el8_1.noa 1.1 MB/s | 123 kB 00:00 (42/178): perl-Socket-2.027-3.el8.x86_64.rpm 537 kB/s | 59 kB 00:00 (43/178): libcroco-0.6.12-4.el8_2.1.x86_64.rpm 1.2 MB/s | 113 kB 00:00 (44/178): python3-urllib3-1.24.2-5.el8.noarch.r 1.5 MB/s | 177 kB 00:00 (45/178): python3-setuptools-39.2.0-6.el8.noarc 1.6 MB/s | 163 kB 00:00 (46/178): avahi-libs-0.7-20.el8.x86_64.rpm 562 kB/s | 62 kB 00:00 (47/178): emacs-filesystem-26.1-7.el8.noarch.rp 595 kB/s | 70 kB 00:00 (48/178): fontconfig-2.13.1-4.el8.x86_64.rpm 3.0 MB/s | 274 kB 00:00 (49/178): perl-libs-5.26.3-421.el8.x86_64.rpm 12 MB/s | 1.6 MB 00:00 (50/178): perl-IO-1.38-421.el8.x86_64.rpm 1.4 MB/s | 142 kB 00:00 (51/178): platform-python-pip-9.0.3-22.el8.noar 8.9 MB/s | 1.6 MB 00:00 (52/178): perl-macros-5.26.3-421.el8.x86_64.rpm 797 kB/s | 72 kB 00:00 (53/178): perl-Errno-1.28-421.el8.x86_64.rpm 718 kB/s | 76 kB 00:00 (54/178): freetype-2.9.1-9.el8.x86_64.rpm 3.5 MB/s | 394 kB 00:00 (55/178): perl-interpreter-5.26.3-421.el8.x86_6 27 MB/s | 6.3 MB 00:00 (56/178): cups-libs-2.2.6-50.el8.x86_64.rpm 2.3 MB/s | 435 kB 00:00 (57/178): libquadmath-8.5.0-16.el8_7.x86_64.rpm 1.6 MB/s | 172 kB 00:00 (58/178): dbus-libs-1.12.8-23.el8_7.1.x86_64.rp 1.9 MB/s | 185 kB 00:00 (59/178): libgfortran-8.5.0-16.el8_7.x86_64.rpm 4.5 MB/s | 644 kB 00:00 (60/178): xorg-x11-fonts-ISO8859-1-100dpi-7.5-1 9.8 MB/s | 1.1 MB 00:00 (61/178): fontawesome-fonts-4.7.0-4.el8.noarch. 1.9 MB/s | 203 kB 00:00 (62/178): urw-base35-p052-fonts-20170801-10.el8 7.7 MB/s | 982 kB 00:00 (63/178): procps-ng-3.3.15-9.el8.x86_64.rpm 359 kB/s | 329 kB 00:00 (64/178): zlib-devel-1.2.11-21.el8_7.x86_64.rpm 78 kB/s | 58 kB 00:00 (65/178): urw-base35-gothic-fonts-20170801-10.e 1.3 MB/s | 654 kB 00:00 (66/178): urw-base35-fonts-20170801-10.el8.noar 88 kB/s | 12 kB 00:00 (67/178): lua-json-1.3.2-9.el8.noarch.rpm 342 kB/s | 29 kB 00:00 (68/178): python3-pytz-2017.2-9.el8.noarch.rpm 602 kB/s | 54 kB 00:00 (69/178): google-droid-sans-fonts-20120715-13.e 15 MB/s | 2.5 MB 00:00 (70/178): lato-fonts-2.015-5.el8.noarch.rpm 19 MB/s | 3.3 MB 00:00 (71/178): urw-base35-bookman-fonts-20170801-10. 6.9 MB/s | 857 kB 00:00 (72/178): urw-base35-fonts-common-20170801-10.e 246 kB/s | 23 kB 00:00 (73/178): urw-base35-d050000l-fonts-20170801-10 770 kB/s | 79 kB 00:00 (74/178): urw-base35-c059-fonts-20170801-10.el8 7.7 MB/s | 884 kB 00:00 (75/178): urw-base35-nimbus-mono-ps-fonts-20170 7.0 MB/s | 801 kB 00:00 (76/178): adobe-mappings-cmap-deprecated-201712 1.3 MB/s | 119 kB 00:00 (77/178): adobe-mappings-pdf-20180407-1.el8.noa 6.0 MB/s | 707 kB 00:00 (78/178): hicolor-icon-theme-0.17-2.el8.noarch. 504 kB/s | 48 kB 00:00 (79/178): adobe-mappings-cmap-20171205-3.el8.no 18 MB/s | 2.1 MB 00:00 (80/178): urw-base35-nimbus-sans-fonts-20170801 11 MB/s | 1.3 MB 00:00 (81/178): urw-base35-standard-symbols-ps-fonts- 467 kB/s | 44 kB 00:00 (82/178): urw-base35-nimbus-roman-fonts-2017080 7.6 MB/s | 865 kB 00:00 (83/178): lcms2-2.9-2.el8.x86_64.rpm 1.7 MB/s | 165 kB 00:00 (84/178): urw-base35-z003-fonts-20170801-10.el8 2.7 MB/s | 279 kB 00:00 (85/178): jbigkit-libs-2.1-14.el8.x86_64.rpm 582 kB/s | 55 kB 00:00 (86/178): libXxf86misc-1.0.4-1.el8.x86_64.rpm 247 kB/s | 23 kB 00:00 (87/178): libmcpp-2.7.2-20.el8.x86_64.rpm 945 kB/s | 81 kB 00:00 (88/178): xorg-x11-server-utils-7.7-27.el8.x86_ 1.9 MB/s | 197 kB 00:00 (89/178): libXinerama-1.1.4-1.el8.x86_64.rpm 181 kB/s | 16 kB 00:00 (90/178): graphite2-1.3.10-10.el8.x86_64.rpm 1.2 MB/s | 122 kB 00:00 (91/178): libXcursor-1.1.15-3.el8.x86_64.rpm 438 kB/s | 36 kB 00:00 (92/178): mcpp-2.7.2-20.el8.x86_64.rpm 311 kB/s | 31 kB 00:00 (93/178): libidn-1.34-5.el8.x86_64.rpm 2.8 MB/s | 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kB 00:00 (109/178): python3-markupsafe-0.23-19.el8.x86_6 402 kB/s | 39 kB 00:00 (110/178): libXt-1.1.5-12.el8.x86_64.rpm 1.7 MB/s | 185 kB 00:00 (111/178): python3-docutils-0.14-12.module+el8. 12 MB/s | 1.6 MB 00:00 (112/178): libICE-1.0.9-15.el8.x86_64.rpm 666 kB/s | 74 kB 00:00 (113/178): gdk-pixbuf2-modules-2.36.12-5.el8.x8 683 kB/s | 109 kB 00:00 (114/178): libxcb-1.13.1-1.el8.x86_64.rpm 2.1 MB/s | 229 kB 00:00 (115/178): swig-3.0.12-19.module+el8.3.0+6248+8 12 MB/s | 1.5 MB 00:00 (116/178): libXext-1.3.4-1.el8.x86_64.rpm 399 kB/s | 45 kB 00:00 (117/178): python3-sqlalchemy-1.3.2-2.module+el 9.9 MB/s | 1.9 MB 00:00 (118/178): libXi-1.7.10-1.el8.x86_64.rpm 424 kB/s | 49 kB 00:00 (119/178): librsvg2-2.42.7-4.el8.x86_64.rpm 5.1 MB/s | 555 kB 00:00 (120/178): libXrandr-1.5.2-1.el8.x86_64.rpm 323 kB/s | 34 kB 00:00 (121/178): libXft-2.3.3-1.el8.x86_64.rpm 762 kB/s | 67 kB 00:00 (122/178): libXau-1.0.9-3.el8.x86_64.rpm 374 kB/s | 37 kB 00:00 (123/178): gd-2.2.5-7.el8.x86_64.rpm 1.5 MB/s | 144 kB 00:00 (124/178): libXmu-1.1.3-1.el8.x86_64.rpm 781 kB/s | 75 kB 00:00 (125/178): jbig2dec-libs-0.16-1.el8.x86_64.rpm 808 kB/s | 72 kB 00:00 (126/178): libuv-1.41.1-1.el8_4.x86_64.rpm 1.7 MB/s | 156 kB 00:00 (127/178): gtk2-2.24.32-5.el8.x86_64.rpm 19 MB/s | 3.4 MB 00:00 (128/178): python36-devel-3.6.8-38.module+el8.5 145 kB/s | 17 kB 00:00 (129/178): python36-rpm-macros-3.6.8-38.module+ 163 kB/s | 16 kB 00:00 (130/178): python3-pygments-2.2.0-22.module+el8 15 MB/s | 1.9 MB 00:00 (131/178): python36-3.6.8-38.module+el8.5.0+122 68 kB/s | 19 kB 00:00 (132/178): libjpeg-turbo-1.5.3-12.el8.x86_64.rp 1.3 MB/s | 157 kB 00:00 (133/178): lua-5.3.4-12.el8.x86_64.rpm 1.9 MB/s | 192 kB 00:00 (134/178): python3-numpy-1.14.3-10.el8.x86_64.r 20 MB/s | 3.7 MB 00:00 (135/178): cmake-filesystem-3.20.2-4.el8.x86_64 330 kB/s | 45 kB 00:00 (136/178): xorg-x11-font-utils-7.5-41.el8.x86_6 376 kB/s | 104 kB 00:00 (137/178): graphviz-2.40.1-43.el8.x86_64.rpm 14 MB/s | 1.7 MB 00:00 (138/178): python3-rpm-generators-5-7.el8.noarc 192 kB/s | 25 kB 00:00 (139/178): pango-1.42.4-8.el8.x86_64.rpm 2.6 MB/s | 297 kB 00:00 (140/178): python3-jinja2-2.10.1-3.el8.noarch.r 5.6 MB/s | 538 kB 00:00 (141/178): python3-babel-2.5.1-7.el8.noarch.rpm 23 MB/s | 4.8 MB 00:00 (142/178): cmake-data-3.20.2-4.el8.noarch.rpm 12 MB/s | 1.7 MB 00:00 (143/178): libX11-1.6.8-5.el8.x86_64.rpm 3.4 MB/s | 611 kB 00:00 (144/178): libX11-common-1.6.8-5.el8.noarch.rpm 1.4 MB/s | 158 kB 00:00 (145/178): libwebp-1.0.0-5.el8.x86_64.rpm 2.2 MB/s | 273 kB 00:00 (146/178): cmake-3.20.2-4.el8.x86_64.rpm 31 MB/s | 12 MB 00:00 (147/178): cmake-rpm-macros-3.20.2-4.el8.noarch 329 kB/s | 44 kB 00:00 (148/178): pixman-0.38.4-2.el8.x86_64.rpm 2.2 MB/s | 257 kB 00:00 (149/178): python3-pip-9.0.3-22.el8.noarch.rpm 156 kB/s | 20 kB 00:00 (150/178): jasper-libs-2.0.14-5.el8.x86_64.rpm 175 kB/s | 167 kB 00:00 (151/178): vim-filesystem-8.0.1763-19.el8_6.4.n 124 kB/s | 50 kB 00:00 (152/178): cairo-1.15.12-6.el8.x86_64.rpm 1.0 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google-roboto-slab-fonts-1.100263-0. 1.8 MB/s | 238 kB 00:00 (168/178): python3-snowballstemmer-1.2.1-6.el8. 799 kB/s | 108 kB 00:00 (169/178): python3-imagesize-1.0.0-2.el8.noarch 131 kB/s | 16 kB 00:00 (170/178): python3-packaging-16.8-9.el8.noarch. 464 kB/s | 48 kB 00:00 (171/178): fontawesome-fonts-web-4.7.0-4.el8.no 3.1 MB/s | 429 kB 00:00 (172/178): python3-sphinx-theme-alabaster-0.7.9 209 kB/s | 24 kB 00:00 (173/178): python3-whoosh-2.7.4-9.el8.noarch.rp 8.5 MB/s | 1.1 MB 00:00 (174/178): python-sphinx-locale-1.7.6-3.el8.noa 1.5 MB/s | 171 kB 00:00 (175/178): python3-sphinx-1.7.6-3.el8.noarch.rp 6.5 MB/s | 1.7 MB 00:00 (176/178): lua-term-0.07-9.el8.x86_64.rpm 66 kB/s | 16 kB 00:00 (177/178): Lmod-8.7.7-1.el8.x86_64.rpm 373 kB/s | 261 kB 00:00 (178/178): doxygen-1.8.14-12.el8.x86_64.rpm 3.8 MB/s | 3.9 MB 00:01 -------------------------------------------------------------------------------- Total 10 MB/s | 100 MB 00:09 Running transaction check Transaction check succeeded. Running transaction test Transaction test succeeded. 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fontpackages-filesystem-1.44-22.el8.noarch 13/178 Verifying : perl-threads-1:2.21-2.el8.x86_64 14/178 Verifying : perl-Pod-Simple-1:3.35-395.el8.noarch 15/178 Verifying : perl-Term-ANSIColor-4.06-396.el8.noarch 16/178 Verifying : perl-HTTP-Tiny-0.074-1.el8.noarch 17/178 Verifying : perl-Pod-Escapes-1:1.07-395.el8.noarch 18/178 Verifying : chrpath-0.16-7.el8.x86_64 19/178 Verifying : perl-Pod-Perldoc-3.28-396.el8.noarch 20/178 Verifying : perl-File-Path-2.15-2.el8.noarch 21/178 Verifying : python3-idna-2.5-5.el8.noarch 22/178 Verifying : perl-parent-1:0.237-1.el8.noarch 23/178 Verifying : python3-pysocks-1.6.8-3.el8.noarch 24/178 Verifying : perl-Text-Tabs+Wrap-2013.0523-395.el8.noarch 25/178 Verifying : perl-Getopt-Long-1:2.50-4.el8.noarch 26/178 Verifying : perl-podlators-4.11-1.el8.noarch 27/178 Verifying : perl-Time-Local-1:1.280-1.el8.noarch 28/178 Verifying : perl-Carp-1.42-396.el8.noarch 29/178 Verifying : perl-Exporter-5.72-396.el8.noarch 30/178 Verifying : perl-Storable-1:3.11-3.el8.x86_64 31/178 Verifying : perl-Text-ParseWords-3.30-395.el8.noarch 32/178 Verifying : perl-File-Temp-0.230.600-1.el8.noarch 33/178 Verifying : perl-constant-1.33-396.el8.noarch 34/178 Verifying : perl-Term-Cap-1.17-395.el8.noarch 35/178 Verifying : python3-chardet-3.0.4-7.el8.noarch 36/178 Verifying : perl-Pod-Usage-4:1.69-395.el8.noarch 37/178 Verifying : python3-pyparsing-2.1.10-7.el8.noarch 38/178 Verifying : python3-six-1.11.0-8.el8.noarch 39/178 Verifying : gdk-pixbuf2-2.36.12-5.el8.x86_64 40/178 Verifying : python3-requests-2.20.0-2.1.el8_1.noarch 41/178 Verifying : perl-Socket-4:2.027-3.el8.x86_64 42/178 Verifying : libcroco-0.6.12-4.el8_2.1.x86_64 43/178 Verifying : python3-urllib3-1.24.2-5.el8.noarch 44/178 Verifying : python3-setuptools-39.2.0-6.el8.noarch 45/178 Verifying : avahi-libs-0.7-20.el8.x86_64 46/178 Verifying : emacs-filesystem-1:26.1-7.el8.noarch 47/178 Verifying : fontconfig-2.13.1-4.el8.x86_64 48/178 Verifying : platform-python-pip-9.0.3-22.el8.noarch 49/178 Verifying : perl-libs-4:5.26.3-421.el8.x86_64 50/178 Verifying : perl-IO-1.38-421.el8.x86_64 51/178 Verifying : perl-interpreter-4:5.26.3-421.el8.x86_64 52/178 Verifying : perl-macros-4:5.26.3-421.el8.x86_64 53/178 Verifying : perl-Errno-1.28-421.el8.x86_64 54/178 Verifying : freetype-2.9.1-9.el8.x86_64 55/178 Verifying : cups-libs-1:2.2.6-50.el8.x86_64 56/178 Verifying : procps-ng-3.3.15-9.el8.x86_64 57/178 Verifying : libquadmath-8.5.0-16.el8_7.x86_64 58/178 Verifying : libgfortran-8.5.0-16.el8_7.x86_64 59/178 Verifying : dbus-libs-1:1.12.8-23.el8_7.1.x86_64 60/178 Verifying : zlib-devel-1.2.11-21.el8_7.x86_64 61/178 Verifying : xorg-x11-fonts-ISO8859-1-100dpi-7.5-19.el8.noarc 62/178 Verifying : fontawesome-fonts-4.7.0-4.el8.noarch 63/178 Verifying : urw-base35-p052-fonts-20170801-10.el8.noarch 64/178 Verifying : urw-base35-gothic-fonts-20170801-10.el8.noarch 65/178 Verifying : urw-base35-fonts-20170801-10.el8.noarch 66/178 Verifying : lua-json-1.3.2-9.el8.noarch 67/178 Verifying : google-droid-sans-fonts-20120715-13.el8.noarch 68/178 Verifying : python3-pytz-2017.2-9.el8.noarch 69/178 Verifying : lato-fonts-2.015-5.el8.noarch 70/178 Verifying : urw-base35-bookman-fonts-20170801-10.el8.noarch 71/178 Verifying : urw-base35-fonts-common-20170801-10.el8.noarch 72/178 Verifying : urw-base35-d050000l-fonts-20170801-10.el8.noarch 73/178 Verifying : urw-base35-c059-fonts-20170801-10.el8.noarch 74/178 Verifying : urw-base35-nimbus-mono-ps-fonts-20170801-10.el8. 75/178 Verifying : adobe-mappings-cmap-deprecated-20171205-3.el8.no 76/178 Verifying : adobe-mappings-pdf-20180407-1.el8.noarch 77/178 Verifying : hicolor-icon-theme-0.17-2.el8.noarch 78/178 Verifying : adobe-mappings-cmap-20171205-3.el8.noarch 79/178 Verifying : urw-base35-nimbus-sans-fonts-20170801-10.el8.noa 80/178 Verifying : urw-base35-standard-symbols-ps-fonts-20170801-10 81/178 Verifying : urw-base35-nimbus-roman-fonts-20170801-10.el8.no 82/178 Verifying : lcms2-2.9-2.el8.x86_64 83/178 Verifying : urw-base35-z003-fonts-20170801-10.el8.noarch 84/178 Verifying : jbigkit-libs-2.1-14.el8.x86_64 85/178 Verifying : libXxf86misc-1.0.4-1.el8.x86_64 86/178 Verifying : libmcpp-2.7.2-20.el8.x86_64 87/178 Verifying : xorg-x11-server-utils-7.7-27.el8.x86_64 88/178 Verifying : libXinerama-1.1.4-1.el8.x86_64 89/178 Verifying : graphite2-1.3.10-10.el8.x86_64 90/178 Verifying : libXcursor-1.1.15-3.el8.x86_64 91/178 Verifying : mcpp-2.7.2-20.el8.x86_64 92/178 Verifying : libidn-1.34-5.el8.x86_64 93/178 Verifying : libSM-1.2.3-1.el8.x86_64 94/178 Verifying : libXfixes-5.0.3-7.el8.x86_64 95/178 Verifying : lua-lpeg-1.0.1-6.el8.x86_64 96/178 Verifying : libXaw-1.0.13-10.el8.x86_64 97/178 Verifying : libXxf86vm-1.1.4-9.el8.x86_64 98/178 Verifying : libthai-0.1.27-2.el8.x86_64 99/178 Verifying : libijs-0.35-5.el8.x86_64 100/178 Verifying : libXdamage-1.1.4-14.el8.x86_64 101/178 Verifying : harfbuzz-1.7.5-3.el8.x86_64 102/178 Verifying : libpaper-1.1.24-22.el8.x86_64 103/178 Verifying : libXcomposite-0.4.4-14.el8.x86_64 104/178 Verifying : libfontenc-1.1.3-8.el8.x86_64 105/178 Verifying : libXrender-0.9.10-7.el8.x86_64 106/178 Verifying : atk-2.28.1-1.el8.x86_64 107/178 Verifying : libdatrie-0.2.9-7.el8.x86_64 108/178 Verifying : python3-markupsafe-0.23-19.el8.x86_64 109/178 Verifying : libXt-1.1.5-12.el8.x86_64 110/178 Verifying : python3-docutils-0.14-12.module+el8.1.0+3334+5cb 111/178 Verifying : gdk-pixbuf2-modules-2.36.12-5.el8.x86_64 112/178 Verifying : libICE-1.0.9-15.el8.x86_64 113/178 Verifying : libxcb-1.13.1-1.el8.x86_64 114/178 Verifying : swig-3.0.12-19.module+el8.3.0+6248+838326ab.x86_ 115/178 Verifying : python3-sqlalchemy-1.3.2-2.module+el8.3.0+6646+6 116/178 Verifying : libXext-1.3.4-1.el8.x86_64 117/178 Verifying : libXi-1.7.10-1.el8.x86_64 118/178 Verifying : librsvg2-2.42.7-4.el8.x86_64 119/178 Verifying : libXrandr-1.5.2-1.el8.x86_64 120/178 Verifying : libXft-2.3.3-1.el8.x86_64 121/178 Verifying : libXau-1.0.9-3.el8.x86_64 122/178 Verifying : gd-2.2.5-7.el8.x86_64 123/178 Verifying : libXmu-1.1.3-1.el8.x86_64 124/178 Verifying : gtk2-2.24.32-5.el8.x86_64 125/178 Verifying : jbig2dec-libs-0.16-1.el8.x86_64 126/178 Verifying : libuv-1:1.41.1-1.el8_4.x86_64 127/178 Verifying : python36-3.6.8-38.module+el8.5.0+12207+5c5719bc. 128/178 Verifying : python36-devel-3.6.8-38.module+el8.5.0+12207+5c5 129/178 Verifying : python36-rpm-macros-3.6.8-38.module+el8.5.0+1220 130/178 Verifying : python3-pygments-2.2.0-22.module+el8.5.0+10789+e 131/178 Verifying : libjpeg-turbo-1.5.3-12.el8.x86_64 132/178 Verifying : lua-5.3.4-12.el8.x86_64 133/178 Verifying : xorg-x11-font-utils-1:7.5-41.el8.x86_64 134/178 Verifying : python3-numpy-1:1.14.3-10.el8.x86_64 135/178 Verifying : cmake-filesystem-3.20.2-4.el8.x86_64 136/178 Verifying : graphviz-2.40.1-43.el8.x86_64 137/178 Verifying : python3-rpm-generators-5-7.el8.noarch 138/178 Verifying : pango-1.42.4-8.el8.x86_64 139/178 Verifying : python3-babel-2.5.1-7.el8.noarch 140/178 Verifying : python3-jinja2-2.10.1-3.el8.noarch 141/178 Verifying : libX11-1.6.8-5.el8.x86_64 142/178 Verifying : cmake-data-3.20.2-4.el8.noarch 143/178 Verifying : cmake-3.20.2-4.el8.x86_64 144/178 Verifying : jasper-libs-2.0.14-5.el8.x86_64 145/178 Verifying : libX11-common-1.6.8-5.el8.noarch 146/178 Verifying : libwebp-1.0.0-5.el8.x86_64 147/178 Verifying : cmake-rpm-macros-3.20.2-4.el8.noarch 148/178 Verifying : pixman-0.38.4-2.el8.x86_64 149/178 Verifying : cairo-1.15.12-6.el8.x86_64 150/178 Verifying : python3-pip-9.0.3-22.el8.noarch 151/178 Verifying : vim-filesystem-2:8.0.1763-19.el8_6.4.noarch 152/178 Verifying : openjpeg2-2.4.0-5.el8.x86_64 153/178 Verifying : fribidi-1.0.4-9.el8.x86_64 154/178 Verifying : gtk-update-icon-cache-3.22.30-11.el8.x86_64 155/178 Verifying : libgs-9.27-4.el8.x86_64 156/178 Verifying : openblas-threads-0.3.15-4.el8.x86_64 157/178 Verifying : openblas-0.3.15-4.el8.x86_64 158/178 Verifying : platform-python-devel-3.6.8-48.el8_7.x86_64 159/178 Verifying : libtiff-4.0.9-26.el8_7.x86_64 160/178 Verifying : libXpm-3.5.12-9.el8_7.x86_64 161/178 Verifying : lua-posix-33.3.1-9.el8.x86_64 162/178 Verifying : lua-filesystem-1.6.3-7.el8.x86_64 163/178 Verifying : python3-sphinx_rtd_theme-0.3.1-3.el8.noarch 164/178 Verifying : python3-mock-2.0.0-11.el8.noarch 165/178 Verifying : python3-sphinxcontrib-websupport-1.0.1-10.201803 166/178 Verifying : google-roboto-slab-fonts-1.100263-0.7.20150923gi 167/178 Verifying : python3-snowballstemmer-1.2.1-6.el8.noarch 168/178 Verifying : python3-imagesize-1.0.0-2.el8.noarch 169/178 Verifying : fontawesome-fonts-web-4.7.0-4.el8.noarch 170/178 Verifying : python3-packaging-16.8-9.el8.noarch 171/178 Verifying : python3-sphinx-theme-alabaster-0.7.9-7.el8.noarc 172/178 Verifying : python3-whoosh-2.7.4-9.el8.noarch 173/178 Verifying : doxygen-1:1.8.14-12.el8.x86_64 174/178 Verifying : python-sphinx-locale-1:1.7.6-3.el8.noarch 175/178 Verifying : python3-sphinx-1:1.7.6-3.el8.noarch 176/178 Verifying : Lmod-8.7.7-1.el8.x86_64 177/178 Verifying : lua-term-0.07-9.el8.x86_64 178/178 Installed products updated. Installed: Lmod-8.7.7-1.el8.x86_64 adobe-mappings-cmap-20171205-3.el8.noarch adobe-mappings-cmap-deprecated-20171205-3.el8.noarch adobe-mappings-pdf-20180407-1.el8.noarch atk-2.28.1-1.el8.x86_64 avahi-libs-0.7-20.el8.x86_64 cairo-1.15.12-6.el8.x86_64 chrpath-0.16-7.el8.x86_64 cmake-3.20.2-4.el8.x86_64 cmake-data-3.20.2-4.el8.noarch cmake-filesystem-3.20.2-4.el8.x86_64 cmake-rpm-macros-3.20.2-4.el8.noarch cups-libs-1:2.2.6-50.el8.x86_64 dbus-libs-1:1.12.8-23.el8_7.1.x86_64 doxygen-1:1.8.14-12.el8.x86_64 emacs-filesystem-1:26.1-7.el8.noarch fontawesome-fonts-4.7.0-4.el8.noarch fontawesome-fonts-web-4.7.0-4.el8.noarch fontconfig-2.13.1-4.el8.x86_64 fontpackages-filesystem-1.44-22.el8.noarch freetype-2.9.1-9.el8.x86_64 fribidi-1.0.4-9.el8.x86_64 gd-2.2.5-7.el8.x86_64 gdk-pixbuf2-2.36.12-5.el8.x86_64 gdk-pixbuf2-modules-2.36.12-5.el8.x86_64 google-droid-sans-fonts-20120715-13.el8.noarch google-roboto-slab-fonts-1.100263-0.7.20150923git.el8.noarch graphite2-1.3.10-10.el8.x86_64 graphviz-2.40.1-43.el8.x86_64 groff-base-1.22.3-18.el8.x86_64 gtk-update-icon-cache-3.22.30-11.el8.x86_64 gtk2-2.24.32-5.el8.x86_64 harfbuzz-1.7.5-3.el8.x86_64 hicolor-icon-theme-0.17-2.el8.noarch jasper-libs-2.0.14-5.el8.x86_64 jbig2dec-libs-0.16-1.el8.x86_64 jbigkit-libs-2.1-14.el8.x86_64 lato-fonts-2.015-5.el8.noarch lcms2-2.9-2.el8.x86_64 libICE-1.0.9-15.el8.x86_64 libSM-1.2.3-1.el8.x86_64 libX11-1.6.8-5.el8.x86_64 libX11-common-1.6.8-5.el8.noarch libXau-1.0.9-3.el8.x86_64 libXaw-1.0.13-10.el8.x86_64 libXcomposite-0.4.4-14.el8.x86_64 libXcursor-1.1.15-3.el8.x86_64 libXdamage-1.1.4-14.el8.x86_64 libXext-1.3.4-1.el8.x86_64 libXfixes-5.0.3-7.el8.x86_64 libXft-2.3.3-1.el8.x86_64 libXi-1.7.10-1.el8.x86_64 libXinerama-1.1.4-1.el8.x86_64 libXmu-1.1.3-1.el8.x86_64 libXpm-3.5.12-9.el8_7.x86_64 libXrandr-1.5.2-1.el8.x86_64 libXrender-0.9.10-7.el8.x86_64 libXt-1.1.5-12.el8.x86_64 libXxf86misc-1.0.4-1.el8.x86_64 libXxf86vm-1.1.4-9.el8.x86_64 libcroco-0.6.12-4.el8_2.1.x86_64 libdatrie-0.2.9-7.el8.x86_64 libfontenc-1.1.3-8.el8.x86_64 libgfortran-8.5.0-16.el8_7.x86_64 libgs-9.27-4.el8.x86_64 libidn-1.34-5.el8.x86_64 libijs-0.35-5.el8.x86_64 libjpeg-turbo-1.5.3-12.el8.x86_64 libmcpp-2.7.2-20.el8.x86_64 libpaper-1.1.24-22.el8.x86_64 libpng-2:1.6.34-5.el8.x86_64 libquadmath-8.5.0-16.el8_7.x86_64 librsvg2-2.42.7-4.el8.x86_64 libthai-0.1.27-2.el8.x86_64 libtiff-4.0.9-26.el8_7.x86_64 libuv-1:1.41.1-1.el8_4.x86_64 libwebp-1.0.0-5.el8.x86_64 libxcb-1.13.1-1.el8.x86_64 lua-5.3.4-12.el8.x86_64 lua-filesystem-1.6.3-7.el8.x86_64 lua-json-1.3.2-9.el8.noarch lua-lpeg-1.0.1-6.el8.x86_64 lua-posix-33.3.1-9.el8.x86_64 lua-term-0.07-9.el8.x86_64 maloc-1.5-27.el8.x86_64 maloc-devel-1.5-27.el8.x86_64 mcpp-2.7.2-20.el8.x86_64 openblas-0.3.15-4.el8.x86_64 openblas-threads-0.3.15-4.el8.x86_64 openjpeg2-2.4.0-5.el8.x86_64 pango-1.42.4-8.el8.x86_64 perl-Carp-1.42-396.el8.noarch perl-Encode-4:2.97-3.el8.x86_64 perl-Errno-1.28-421.el8.x86_64 perl-Exporter-5.72-396.el8.noarch perl-File-Path-2.15-2.el8.noarch perl-File-Temp-0.230.600-1.el8.noarch perl-Getopt-Long-1:2.50-4.el8.noarch perl-HTTP-Tiny-0.074-1.el8.noarch perl-IO-1.38-421.el8.x86_64 perl-MIME-Base64-3.15-396.el8.x86_64 perl-PathTools-3.74-1.el8.x86_64 perl-Pod-Escapes-1:1.07-395.el8.noarch perl-Pod-Perldoc-3.28-396.el8.noarch perl-Pod-Simple-1:3.35-395.el8.noarch perl-Pod-Usage-4:1.69-395.el8.noarch perl-Scalar-List-Utils-3:1.49-2.el8.x86_64 perl-Socket-4:2.027-3.el8.x86_64 perl-Storable-1:3.11-3.el8.x86_64 perl-Term-ANSIColor-4.06-396.el8.noarch perl-Term-Cap-1.17-395.el8.noarch perl-Text-ParseWords-3.30-395.el8.noarch perl-Text-Tabs+Wrap-2013.0523-395.el8.noarch perl-Time-Local-1:1.280-1.el8.noarch perl-Unicode-Normalize-1.25-396.el8.x86_64 perl-constant-1.33-396.el8.noarch perl-interpreter-4:5.26.3-421.el8.x86_64 perl-libs-4:5.26.3-421.el8.x86_64 perl-macros-4:5.26.3-421.el8.x86_64 perl-parent-1:0.237-1.el8.noarch perl-podlators-4.11-1.el8.noarch perl-threads-1:2.21-2.el8.x86_64 perl-threads-shared-1.58-2.el8.x86_64 pixman-0.38.4-2.el8.x86_64 platform-python-devel-3.6.8-48.el8_7.x86_64 platform-python-pip-9.0.3-22.el8.noarch procps-ng-3.3.15-9.el8.x86_64 python-sphinx-locale-1:1.7.6-3.el8.noarch python3-babel-2.5.1-7.el8.noarch python3-chardet-3.0.4-7.el8.noarch python3-docutils-0.14-12.module+el8.1.0+3334+5cb623d7.noarch python3-idna-2.5-5.el8.noarch python3-imagesize-1.0.0-2.el8.noarch python3-jinja2-2.10.1-3.el8.noarch python3-markupsafe-0.23-19.el8.x86_64 python3-mock-2.0.0-11.el8.noarch python3-numpy-1:1.14.3-10.el8.x86_64 python3-packaging-16.8-9.el8.noarch python3-pip-9.0.3-22.el8.noarch python3-pygments-2.2.0-22.module+el8.5.0+10789+e4939b94.noarch python3-pyparsing-2.1.10-7.el8.noarch python3-pysocks-1.6.8-3.el8.noarch python3-pytz-2017.2-9.el8.noarch python3-requests-2.20.0-2.1.el8_1.noarch python3-rpm-generators-5-7.el8.noarch python3-setuptools-39.2.0-6.el8.noarch python3-six-1.11.0-8.el8.noarch python3-snowballstemmer-1.2.1-6.el8.noarch python3-sphinx-1:1.7.6-3.el8.noarch python3-sphinx-theme-alabaster-0.7.9-7.el8.noarch python3-sphinx_rtd_theme-0.3.1-3.el8.noarch python3-sphinxcontrib-websupport-1.0.1-10.20180316git.el8.noarch python3-sqlalchemy-1.3.2-2.module+el8.3.0+6646+6b4b10ec.x86_64 python3-urllib3-1.24.2-5.el8.noarch python3-whoosh-2.7.4-9.el8.noarch python36-3.6.8-38.module+el8.5.0+12207+5c5719bc.x86_64 python36-devel-3.6.8-38.module+el8.5.0+12207+5c5719bc.x86_64 python36-rpm-macros-3.6.8-38.module+el8.5.0+12207+5c5719bc.noarch shared-mime-info-1.9-3.el8.x86_64 swig-3.0.12-19.module+el8.3.0+6248+838326ab.x86_64 tcl-1:8.6.8-2.el8.x86_64 urw-base35-bookman-fonts-20170801-10.el8.noarch urw-base35-c059-fonts-20170801-10.el8.noarch urw-base35-d050000l-fonts-20170801-10.el8.noarch urw-base35-fonts-20170801-10.el8.noarch urw-base35-fonts-common-20170801-10.el8.noarch urw-base35-gothic-fonts-20170801-10.el8.noarch urw-base35-nimbus-mono-ps-fonts-20170801-10.el8.noarch urw-base35-nimbus-roman-fonts-20170801-10.el8.noarch urw-base35-nimbus-sans-fonts-20170801-10.el8.noarch urw-base35-p052-fonts-20170801-10.el8.noarch urw-base35-standard-symbols-ps-fonts-20170801-10.el8.noarch urw-base35-z003-fonts-20170801-10.el8.noarch vim-filesystem-2:8.0.1763-19.el8_6.4.noarch xorg-x11-font-utils-1:7.5-41.el8.x86_64 xorg-x11-fonts-ISO8859-1-100dpi-7.5-19.el8.noarch xorg-x11-server-utils-7.7-27.el8.x86_64 zlib-devel-1.2.11-21.el8_7.x86_64 Complete! Finish: build setup for apbs-3.0.0-17.el8.src.rpm Start: rpmbuild apbs-3.0.0-17.el8.src.rpm warning: bogus date in %changelog: Thu Nov 04 2009 Tim Fenn - 1.2.0-1 Building target platforms: x86_64 Building for target x86_64 Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.yzT3Yv + umask 022 + cd /builddir/build/BUILD + cd /builddir/build/BUILD + rm -rf apbs-3.0.0 + /usr/bin/gzip -dc /builddir/build/SOURCES/apbs-3.0.0.tar.gz + /usr/bin/tar -xof - + 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 -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 Patch #1 (apbs-exclude_tests.patch): + echo 'Patch #1 (apbs-exclude_tests.patch):' + /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .exclude_tests --fuzz=0 patching file tests/test_cases.cfg + cp -p contrib/iapbs/COPYING contrib/iapbs/iapbs-COPYING + cp -p /builddir/build/SOURCES/apbs-LGPL_V2 contrib/iapbs/iapbs-LGPLv2 + exit 0 Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.EApiV8 + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + export 'CFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -lm' + CFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -lm' + export 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -lm' + CXXFLAGS='-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -lm' + mkdir -p build + cmake -S . -B build -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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -lm -DNDEBUG' '-DCMAKE_CXX_FLAGS:STRING=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -lm -DNDEBUG' -DBUILD_SHARED_LIBS:BOOL=OFF -DENABLE_PYTHON: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 CMake Deprecation Warning at CMakeLists.txt:11 (cmake_policy): The OLD behavior for policy CMP0054 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. -- The C compiler identification is GNU 8.5.0 -- The CXX compiler identification is GNU 8.5.0 -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - 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/c++ - 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 "4.5") -- Found OpenMP_CXX: -fopenmp (found version "4.5") -- Found OpenMP: TRUE (found version "4.5") -- OpenMP support enabled CMake Deprecation Warning at src/CMakeLists.txt:1 (cmake_minimum_required): Compatibility with CMake < 2.8.12 will be removed from a future version of CMake. Update the VERSION argument value or use a ... suffix to tell CMake that the project does not need compatibility with older versions. -- 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 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -lm -DNDEBUG -fPIC -- Supplemental tools enabled -- Building mesh -- libraries: apbs -- Building manip -- libraries: apbs -- Found SWIG: /usr/bin/swig (found version "3.0.12") -- Found Python3: /usr/bin/python3.6 (found version "3.6.8") found components: Interpreter Development Development.Module Development.Embed -- ******* Python3 FOUND -- ***** Python3 include path is: /usr/include/python3.6m -- ***** Python3 library path is: /usr/lib64/libpython3.6m.so -- ***** Python3 library dir is: /usr/lib64 -- Building of iAPBS interface enabled -- Found Python3: /usr/bin/python3.6 (found version "3.6.8") found components: Interpreter -- ******* Python3 FOUND /usr/bin/python3.6 -- TEST born_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t born -- TEST actin-dimer-auto_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t actin-dimer-auto -- TEST actin-dimer-parallel_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t actin-dimer-parallel -- TEST alkanes_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t alkanes -- TEST FKBP_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t FKBP -- TEST hca-bind_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t hca-bind -- TEST ionize_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ionize -- TEST ion-pmf_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ion-pmf -- TEST ion-protein_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t ion-protein -- TEST pka-lig_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t pka-lig -- TEST point-pmf_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t point-pmf -- TEST solv_test COMMAND /usr/bin/python3.6 /builddir/build/BUILD/apbs-3.0.0/tests/apbs_tester.py -c /builddir/build/BUILD/apbs-3.0.0/tests/test_cases.cfg -e /builddir/build/BUILD/apbs-3.0.0/build/apbs -t solv -- Configuring done -- Generating done -- Build files have been written to: /builddir/build/BUILD/apbs-3.0.0/build + make -O -j1 V=1 -C build make: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[1]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 1%] Building C object src/CMakeFiles/apbs_routines.dir/routines.c.o /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'loadDielMaps': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:296:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (ii=0; ii<(nx*ny*nz); ii++) ^~~ /builddir/build/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' sum = sum*hx*hy*hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:331:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (ii=0; ii<(nx*ny*nz); ii++) ^~~ /builddir/build/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' sum = sum*hx*hy*hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:420:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (ii=0; ii<(nx*ny*nz); ii++) ^~~ /builddir/build/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' sum = sum*hx*hy*hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:454:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (ii=0; ii<(nx*ny*nz); ii++) ^~~ /builddir/build/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' sum = sum*hx*hy*hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1234:12: warning: variable 'iparm' set but not used [-Wunused-but-set-variable] iparm, ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'energyMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1584:13: warning: variable 'mgparm' set but not used [-Wunused-but-set-variable] MGparm *mgparm; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1803:10: warning: variable 'mxtype' set but not used [-Wunused-but-set-variable] char mxtype[3]; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printApolForce': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3485:12: warning: variable 'scalar' set but not used [-Wunused-but-set-variable] scalar, ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3484:12: warning: variable 'temp' set but not used [-Wunused-but-set-variable] double temp, ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4496:12: warning: variable 'sav' set but not used [-Wunused-but-set-variable] sav, /**< @todo document */ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4495:12: warning: variable 'sasa' set but not used [-Wunused-but-set-variable] double sasa, /**< @todo document */ ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4489:12: warning: unused variable 'ts' [-Wunused-variable] time_t ts; /**< Temporary timing variable for debugging (PCE) */ ^~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'forceAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4753:13: warning: unused variable 'apos' [-Wunused-variable] *apos; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4737:46: warning: unused variable 'ts_sub' [-Wunused-variable] time_t ts, ts_main, ts_sub; ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/routines.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/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=] sprintf(writematstem, "%s-PE%d", pbeparm->writematstem,nosh->proc_rank); ^~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1038 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writematstem, "mat"); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataFlat': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1906:44: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] double conversion, ltenergy, gtenergy, scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataXML': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2140:44: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] double conversion, ltenergy, gtenergy, scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "dxbin"); ^~ ~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "txt"); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "dx.gz"); ^~ ~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "mcsf"); ^~ ~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 1029 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "ucd"); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "grd"); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "dx"); ^~ ~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'returnEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2762:12: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2795:12: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printElecEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2863:12: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printApolEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2970:29: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] gtenergy += (scalar * ((apolparm->gamma*apolparm->sasa) + ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (apolparm->press*apolparm->sav) + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (apolparm->wcaEnergy))); ~~~~~~~~~~~~~~~~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 1%] Built target apbs_routines make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 2%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vgrid.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function 'Vgrid_readDXBIN': /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:816:6: warning: variable 'isBinary' set but not used [-Wunused-but-set-variable] int isBinary = 0; ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:813:18: warning: unused variable 'itmp' [-Wunused-variable] size_t i, j, k, itmp, u; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function 'Vgrid_writeUHBD': /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:1697:36: warning: variable 'hy' set but not used [-Wunused-but-set-variable] double xmin, ymin, zmin, hzed, hy, hx; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:1697:30: warning: variable 'hzed' set but not used [-Wunused-but-set-variable] double xmin, ymin, zmin, hzed, hy, hx; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c: In function 'Vgrid_readDXBIN': /builddir/build/BUILD/apbs-3.0.0/src/mg/vgrid.c:853:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result] fgets(tok, VMAX_BUFSIZE, fd); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 3%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vmgrid.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c: In function 'Vmgrid_addGrid': /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:198:12: warning: unused variable 'tgrad' [-Wunused-variable] double tgrad[3]; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:15: warning: unused variable 'rc' [-Wunused-variable] int i, j, rc; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:12: warning: unused variable 'j' [-Wunused-variable] int i, j, rc; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vmgrid.c:197:9: warning: unused variable 'i' [-Wunused-variable] int i, j, rc; ^ [ 4%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vopot.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c: In function 'Vopot_curvature': /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:26: warning: variable 'eps_w' set but not used [-Wunused-but-set-variable] double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:18: warning: variable 'charge' set but not used [-Wunused-but-set-variable] double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:219:15: warning: variable 'T' set but not used [-Wunused-but-set-variable] double u, T, charge, eps_w, xkappa, dist, size, val, *position, zkappa2; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vopot.c:269:23: warning: 'val' may be used uninitialized in this function [-Wmaybe-uninitialized] u = u + val; ~~^~~~~~~~~ [ 5%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmg.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_ctor2': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:157:61: warning: variable 'zkappa2' set but not used [-Wunused-but-set-variable] double ionConc[MAXION], ionQ[MAXION], ionRadii[MAXION], zkappa2, zks2; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_qmEnergySMPBE': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1503:12: warning: variable 'zks2' set but not used [-Wunused-but-set-variable] zks2; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_qfEnergyPoint': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1712:13: warning: variable 'pvec' set but not used [-Wunused-but-set-variable] double *pvec; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:24: warning: variable 'zmax' set but not used [-Wunused-but-set-variable] double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:18: warning: variable 'ymax' set but not used [-Wunused-but-set-variable] double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1709:12: warning: variable 'xmax' set but not used [-Wunused-but-set-variable] double xmax, ymax, zmax, xmin, ymin, zmin, hx, hy, hzed, ifloat, jfloat; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_qfAtomEnergy': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:36: warning: variable 'zmax' set but not used [-Wunused-but-set-variable] double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:24: warning: variable 'ymax' set but not used [-Wunused-but-set-variable] double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1794:12: warning: variable 'xmax' set but not used [-Wunused-but-set-variable] double xmax, xmin, ymax, ymin, zmax, zmin, hx, hy, hzed, ifloat, jfloat; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'focusFillBound': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1953:12: warning: variable 'charge' set but not used [-Wunused-but-set-variable] charge, ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1952:13: warning: variable 'apos' set but not used [-Wunused-but-set-variable] *apos, ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1951:12: warning: variable 'size' set but not used [-Wunused-but-set-variable] size, ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1950:12: warning: variable 'xkappa' set but not used [-Wunused-but-set-variable] xkappa, ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl2': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:40: warning: variable 'qzy' set but not used [-Wunused-but-set-variable] double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:36: warning: variable 'qzx' set but not used [-Wunused-but-set-variable] double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2668:24: warning: variable 'qyx' set but not used [-Wunused-but-set-variable] double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcCalcOrig': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:34: warning: unused variable 'debye' [-Wunused-variable] double *dipole, *quadrupole, debye, eps_p; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:22: warning: variable 'quadrupole' set but not used [-Wunused-but-set-variable] double *dipole, *quadrupole, debye, eps_p; ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2832:13: warning: variable 'dipole' set but not used [-Wunused-but-set-variable] double *dipole, *quadrupole, debye, eps_p; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcflnew': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3415:31: warning: variable 'eps_p' set but not used [-Wunused-but-set-variable] double dist, pre1, eps_w, eps_p, T, xkappa; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:29: warning: unused variable 'z1' [-Wunused-variable] int x0, x1, y0, y1, z0, z1; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:25: warning: unused variable 'z0' [-Wunused-variable] int x0, x1, y0, y1, z0, z1; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:21: warning: unused variable 'y1' [-Wunused-variable] int x0, x1, y0, y1, z0, z1; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:17: warning: unused variable 'y0' [-Wunused-variable] int x0, x1, y0, y1, z0, z1; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:13: warning: unused variable 'x1' [-Wunused-variable] int x0, x1, y0, y1, z0, z1; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3410:9: warning: unused variable 'x0' [-Wunused-variable] int x0, x1, y0, y1, z0, z1; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:13: warning: unused variable 'k' [-Wunused-variable] int i,j,k, iatom, igrid; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:11: warning: unused variable 'j' [-Wunused-variable] int i,j,k, iatom, igrid; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3409:9: warning: unused variable 'i' [-Wunused-variable] int i,j,k, iatom, igrid; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'multipolebc': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3492:19: warning: variable 'kr3' set but not used [-Wunused-but-set-variable] double kr,kr2,kr3; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl_sdh': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:40: warning: variable 'qzy' set but not used [-Wunused-but-set-variable] double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:36: warning: variable 'qzx' set but not used [-Wunused-but-set-variable] double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3608:24: warning: variable 'qyx' set but not used [-Wunused-but-set-variable] double qxx,qxy,qxz,qyx,qyy,qyz,qzx,qzy,qzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3604:22: warning: unused variable 'quadrupole' [-Wunused-variable] double *dipole, *quadrupole; ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3604:13: warning: unused variable 'dipole' [-Wunused-variable] double *dipole, *quadrupole; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl_mdh': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3875:41: warning: variable 'eps_p' set but not used [-Wunused-but-set-variable] double size, charge, xkappa, eps_w, eps_p, T, pre1, dist; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3874:22: warning: unused variable 'quadrupole' [-Wunused-variable] double *dipole, *quadrupole; ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3874:13: warning: unused variable 'dipole' [-Wunused-variable] double *dipole, *quadrupole; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl_mem': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4008:24: warning: unused variable 'edge_L' [-Wunused-variable] double A, B, C, D, edge_L, l; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4007:38: warning: unused variable 'z_shift' [-Wunused-variable] double dist, val, z_low, z_high, z_shift; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4007:12: warning: unused variable 'dist' [-Wunused-variable] double dist, val, z_low, z_high, z_shift; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcfl_map': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:38: warning: variable 'hzed' set but not used [-Wunused-but-set-variable] double position[3], pot, hx, hy, hzed; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:34: warning: variable 'hy' set but not used [-Wunused-but-set-variable] double position[3], pot, hx, hy, hzed; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4177:30: warning: variable 'hx' set but not used [-Wunused-but-set-variable] double position[3], pot, hx, hy, hzed; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4176:11: warning: unused variable 'pbe' [-Wunused-variable] Vpbe *pbe; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefMap': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4492:46: warning: unused variable 'pot' [-Wunused-variable] double ionstr, position[3], tkappa, eps, pot, hx, hy, hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefMolIon': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4638:16: warning: variable 'surfMeth' set but not used [-Wunused-but-set-variable] Vsurf_Meth surfMeth; ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4630:11: warning: variable 'acc' set but not used [-Wunused-but-set-variable] Vacc *acc; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefMolDielNoSmooth': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:4746:30: warning: unused variable 'deps' [-Wunused-variable] double srad, epsw, epsp, deps, area; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefSpline': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5031:47: warning: variable 'rtot2' set but not used [-Wunused-but-set-variable] double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin, w3i; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCharge': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5289:15: warning: unused variable 'rc' [-Wunused-variable] Vrc_Codes rc; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoChargeMap': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:49: warning: variable 'hzed' set but not used [-Wunused-but-set-variable] double position[3], charge, zmagic, hx, hy, hzed; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:45: warning: variable 'hy' set but not used [-Wunused-but-set-variable] double position[3], charge, zmagic, hx, hy, hzed; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5346:41: warning: variable 'hx' set but not used [-Wunused-but-set-variable] double position[3], charge, zmagic, hx, hy, hzed; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_force': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5829:12: warning: unused variable 'npF' [-Wunused-variable] double npF[3]; /* Non-polar boundary force */ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_ibForce': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:24: warning: variable 'zlen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:18: warning: variable 'ylen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5854:12: warning: variable 'xlen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:5848:13: warning: variable 'alist' set but not used [-Wunused-but-set-variable] Valist *alist; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_dbForce': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6019:55: warning: variable 'kT' set but not used [-Wunused-but-set-variable] double rtot, dx, gpos[3], tgrad[3], dbFmag, epsw, kT; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6019:18: warning: variable 'dx' set but not used [-Wunused-but-set-variable] double rtot, dx, gpos[3], tgrad[3], dbFmag, epsw, kT; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:66: warning: variable 'rtot2' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:24: warning: variable 'zlen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:18: warning: variable 'ylen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6018:12: warning: variable 'xlen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax, rtot2, epsp; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'qfForceSpline2': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:24: warning: variable 'zlen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:18: warning: variable 'ylen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6453:12: warning: variable 'xlen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'qfForceSpline4': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6576:15: warning: unused variable 'k' [-Wunused-variable] int i, j, k, ii, jj, kk; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6576:12: warning: unused variable 'j' [-Wunused-variable] int i, j, k, ii, jj, kk; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:24: warning: variable 'zlen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:18: warning: variable 'ylen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6568:12: warning: variable 'xlen' set but not used [-Wunused-but-set-variable] double xlen, ylen, zlen, xmin, ymin, zmin, xmax, ymax, zmax; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'markFrac': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6692:39: warning: variable 'a000' set but not used [-Wunused-but-set-variable] double dx, dx2, dy, dy2, dz, dz2, a000, a001, a010, a100, r2; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'zlapSolve': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6912:12: warning: unused variable 'norm' [-Wunused-variable] double norm, coef, proj, eigx, eigy, eigz; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'Vpmg_solveLaplace': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7044:35: warning: variable 'n' set but not used [-Wunused-but-set-variable] int i, j, k, ijk, nx, ny, nz, n, dilo, dihi, djlo, djhi, dklo, dkhi; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7044:18: warning: unused variable 'ijk' [-Wunused-variable] int i, j, k, ijk, nx, ny, nz, n, dilo, dihi, djlo, djhi, dklo, dkhi; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoPermanentMultipole': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:58: warning: unused variable 'mqzz' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:53: warning: unused variable 'mqzy' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:48: warning: unused variable 'mqzx' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:43: warning: unused variable 'mqyy' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:38: warning: unused variable 'mqyx' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:33: warning: unused variable 'mqxx' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:29: warning: unused variable 'muz' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:25: warning: unused variable 'muy' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:21: warning: unused variable 'mux' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:18: warning: unused variable 'mc' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7263:12: warning: unused variable 'debye' [-Wunused-variable] double debye,mc,mux,muy,muz,mqxx,mqyx,mqyy,mqzx,mqzy,mqzz; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:24: warning: unused variable 'mr2' [-Wunused-variable] double mir,mjr,mkr,mr2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:20: warning: unused variable 'mkr' [-Wunused-variable] double mir,mjr,mkr,mr2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:16: warning: unused variable 'mjr' [-Wunused-variable] double mir,mjr,mkr,mr2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7262:12: warning: unused variable 'mir' [-Wunused-variable] double mir,mjr,mkr,mr2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7258:9: warning: unused variable 'i' [-Wunused-variable] int i, ii, jj, kk, nx, ny, nz, iatom; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7253:47: warning: unused variable 'qave' [-Wunused-variable] double c,ux,uy,uz,qxx,qyx,qyy,qzx,qzy,qzz,qave; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7252:29: warning: unused variable 'quad' [-Wunused-variable] double charge, *dipole,*quad; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7252:21: warning: unused variable 'dipole' [-Wunused-variable] double charge, *dipole,*quad; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefSpline4': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:9948:47: warning: variable 'rtot2' set but not used [-Wunused-but-set-variable] double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:9946:42: warning: unused variable 'w2i' [-Wunused-variable] double irad, dx, dy, dz, epsw, epsp, w2i; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoPermanentInduced': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10278:9: warning: unused variable 'i' [-Wunused-variable] int i, ii, jj, kk, nx, ny, nz, iatom; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10273:47: warning: unused variable 'qave' [-Wunused-variable] double c,ux,uy,uz,qxx,qyx,qyy,qzx,qzy,qzz,qave; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10272:29: warning: unused variable 'quad' [-Wunused-variable] double charge, *dipole,*quad; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10272:21: warning: unused variable 'dipole' [-Wunused-variable] double charge, *dipole,*quad; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'fillcoCoefSpline3': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10441:27: warning: variable 'e5' set but not used [-Wunused-but-set-variable] double e, e2, e3, e4, e5; ^~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10439:47: warning: variable 'rtot2' set but not used [-Wunused-but-set-variable] double dx2, dy2, dz2, stot2, itot2, rtot, rtot2, splineWin; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10437:42: warning: unused variable 'w2i' [-Wunused-variable] double irad, dx, dy, dz, epsw, epsp, w2i; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcolcomp': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:55: warning: variable 'mxlv' set but not used [-Wunused-but-set-variable] int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:47: warning: unused variable 'maxlev' [-Wunused-variable] int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:39: warning: unused variable 'ierror' [-Wunused-variable] int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:15: warning: variable 'niwk' set but not used [-Wunused-but-set-variable] int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10746:9: warning: variable 'nrwk' set but not used [-Wunused-but-set-variable] int nrwk, niwk, nx, ny, nz, nlev, ierror, maxlev, mxlv; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:29: warning: unused variable 'i' [-Wunused-variable] int nrow, ncol, nnzero, i; ^ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:21: warning: unused variable 'nnzero' [-Wunused-variable] int nrow, ncol, nnzero, i; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:15: warning: unused variable 'ncol' [-Wunused-variable] int nrow, ncol, nnzero, i; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10743:9: warning: unused variable 'nrow' [-Wunused-variable] int nrow, ncol, nnzero, i; ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:73: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcolcomp2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10804:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, nlev); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcolcomp3': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10836:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: In function 'bcolcomp4': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10874:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10873:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10872:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10871:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10870:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:10866:27: warning: variable 'nrow' set but not used [-Wunused-but-set-variable] int inonz, iirow, nn, nrow, ncol, nonz, irow, n; ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:73: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:7229:16: warning: 'd3bspline4' defined but not used [-Wunused-function] VPUBLIC double d3bspline4(double x) { ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:6684:15: warning: 'markFrac' defined but not used [-Wunused-function] VPRIVATE void markFrac( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:3868:15: warning: 'bcfl_mdh' defined but not used [-Wunused-function] VPRIVATE void bcfl_mdh(Vpmg *thee){ ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2828:15: warning: 'bcCalcOrig' defined but not used [-Wunused-function] VPRIVATE void bcCalcOrig(Vpmg *thee) { ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:2547:17: warning: 'bcfl1sp' defined but not used [-Wunused-function] VPRIVATE double bcfl1sp(double size, double *apos, double charge, ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.c:1148:17: warning: 'Vpmg_polarizEnergy' defined but not used [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy(Vpmg *thee, ^~~~~~~~~~~~~~~~~~ [ 7%] Building C object src/mg/CMakeFiles/apbs_mg.dir/vpmgp.c.o /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c: In function 'Vpmgp_size': /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmgp.c:204:87: warning: unused variable 'iretot' [-Wunused-variable] int nxf, nyf, nzf, level, num_nf_oper, num_narrc_oper, n_band, nc_band, num_band, iretot; ^~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 7%] Built target apbs_mg make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 8%] Building C object src/generic/CMakeFiles/apbs_generic.dir/nosh.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: In function 'NOsh_setupCalcGEOFLOWMANUAL': /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:2683:15: warning: variable 'apolparm' set but not used [-Wunused-but-set-variable] APOLparm *apolparm = VNULL; ^~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:57: /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:57: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.c:57: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ [ 9%] Building C object src/generic/CMakeFiles/apbs_generic.dir/mgparm.c.o [ 10%] Building C object src/generic/CMakeFiles/apbs_generic.dir/femparm.c.o [ 11%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbamparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parseRandorient': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:305:17: warning: unused variable 'name' [-Wunused-variable] const char* name = "randorient"; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c: In function 'PBAMparm_parse3Dmap': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:373:10: warning: unused variable 'tok' [-Wunused-variable] char tok[VMAX_BUFSIZE]; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.c:372:17: warning: unused variable 'name' [-Wunused-variable] const char* name = "3dmap"; ^~~~ [ 12%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbsamparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function 'PBSAMparm_ctor2': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:79:9: warning: unused variable 'i' [-Wunused-variable] int i; ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c: In function 'PBSAMparm_parseMSMS': /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.c:183:6: warning: unused variable 'td' [-Wunused-variable] int td; ^~ [ 14%] Building C object src/generic/CMakeFiles/apbs_generic.dir/pbeparm.c.o [ 15%] Building C object src/generic/CMakeFiles/apbs_generic.dir/bemparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function 'BEMparm_ctor2': /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:79:9: warning: unused variable 'i' [-Wunused-variable] int i; ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function 'BEMparm_check': /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:36: warning: unused variable 'nlev' [-Wunused-variable] int i, tdime[3], ti, tnlev[3], nlev; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:26: warning: unused variable 'tnlev' [-Wunused-variable] int i, tdime[3], ti, tnlev[3], nlev; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:22: warning: unused variable 'ti' [-Wunused-variable] int i, tdime[3], ti, tnlev[3], nlev; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:12: warning: unused variable 'tdime' [-Wunused-variable] int i, tdime[3], ti, tnlev[3], nlev; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:127:9: warning: unused variable 'i' [-Wunused-variable] int i, tdime[3], ti, tnlev[3], nlev; ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c: In function 'BEMparm_copy': /builddir/build/BUILD/apbs-3.0.0/src/generic/bemparm.c:176:9: warning: unused variable 'i' [-Wunused-variable] int i; ^ [ 16%] Building C object src/generic/CMakeFiles/apbs_generic.dir/geoflowparm.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c: In function 'GEOFLOWparm_ctor2': /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.c:79:9: warning: unused variable 'i' [-Wunused-variable] int i; ^ [ 17%] Building C object src/generic/CMakeFiles/apbs_generic.dir/apolparm.c.o [ 18%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vacc.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'VaccSurf_dtor': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:841:11: warning: variable 'mem' set but not used [-Wunused-but-set-variable] Vmem *mem; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_splineAccGradAtomNorm3': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1104:27: warning: variable 'e5' set but not used [-Wunused-but-set-variable] double e, e2, e3, e4, e5; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_atomdSASA': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1338:12: warning: variable 'ts' set but not used [-Wunused-but-set-variable] time_t ts; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1335:15: warning: variable 'ref' set but not used [-Wunused-but-set-variable] VaccSurf *ref; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_totalAtomdSASA': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1395:15: warning: variable 'ref' set but not used [-Wunused-but-set-variable] VaccSurf *ref; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1392:23: warning: variable 'tRad' set but not used [-Wunused-but-set-variable] double *temp_Pos, tRad; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1391:9: warning: variable 'iatom' set but not used [-Wunused-but-set-variable] int iatom; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_totalAtomdSAV': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1454:15: warning: variable 'ref' set but not used [-Wunused-but-set-variable] VaccSurf *ref; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1451:23: warning: variable 'tRad' set but not used [-Wunused-but-set-variable] double *temp_Pos, tRad; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1450:9: warning: variable 'iatom' set but not used [-Wunused-but-set-variable] int iatom; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_wcaEnergyAtom': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1584:9: warning: variable 'npts' set but not used [-Wunused-but-set-variable] int npts[3]; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c: In function 'Vacc_wcaForceAtom': /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1807:12: warning: variable 'ts' set but not used [-Wunused-but-set-variable] time_t ts; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vacc.c:1764:9: warning: variable 'npts' set but not used [-Wunused-but-set-variable] npts[3], ^~~~ [ 20%] Building C object src/generic/CMakeFiles/apbs_generic.dir/valist.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c: In function 'Valist_readPQR': /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:618:10: warning: unused variable 'chs' [-Wunused-variable] char chs[VMAX_BUFSIZE]; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c: In function 'Valist_readXML': /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:834:17: warning: 'radius' may be used uninitialized in this function [-Wmaybe-uninitialized] Vatom_setRadius(nextAtom, radius); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:833:17: warning: 'charge' may be used uninitialized in this function [-Wmaybe-uninitialized] Vatom_setCharge(nextAtom, charge); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:831:48: warning: 'z' may be used uninitialized in this function [-Wmaybe-uninitialized] pos[0] = x; pos[1] = y; pos[2] = z; ~~~~~~~^~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:736:15: warning: 'y' may be used uninitialized in this function [-Wmaybe-uninitialized] double x, y, z, charge, radius, dtmp; ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/valist.c:736:12: warning: 'x' may be used uninitialized in this function [-Wmaybe-uninitialized] double x, y, z, charge, radius, dtmp; ^ [ 21%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vatom.c.o [ 22%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vpbe.c.o [ 23%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vcap.c.o [ 24%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vclist.c.o [ 25%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vstring.c.o [ 27%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vparam.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c: In function 'Vparam_readXMLFile': /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:389:69: warning: 'nalloc' may be used uninitialized in this function [-Wmaybe-uninitialized] tatoms = (Vparam_AtomData*)Vmem_malloc(thee->vmem, 2*nalloc, sizeof(Vparam_AtomData)); ~^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vparam.c:309:18: warning: 'natoms' may be used uninitialized in this function [-Wmaybe-uninitialized] int i, ires, natoms, nalloc, ralloc; ^~~~~~ [ 28%] Building C object src/generic/CMakeFiles/apbs_generic.dir/vgreen.c.o /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function 'Vgreen_coulomb_direct': /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:31: warning: unused variable 'fz' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:27: warning: unused variable 'fy' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:23: warning: unused variable 'fx' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:16: warning: unused variable 'qtemp' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:229:13: warning: unused variable 'q' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function 'Vgreen_coulomb': /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:264:9: warning: unused variable 'iatom' [-Wunused-variable] int iatom, ipos; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:31: warning: unused variable 'fz' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:27: warning: unused variable 'fy' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:23: warning: unused variable 'fx' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:16: warning: unused variable 'qtemp' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:263:13: warning: unused variable 'q' [-Wunused-variable] double *q, qtemp, fx, fy, fz; ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:45: warning: unused variable 'scale' [-Wunused-variable] double *apos, charge, dist, dx, dy, dz, scale; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:41: warning: unused variable 'dz' [-Wunused-variable] double *apos, charge, dist, dx, dy, dz, scale; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:37: warning: unused variable 'dy' [-Wunused-variable] double *apos, charge, dist, dx, dy, dz, scale; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:33: warning: unused variable 'dx' [-Wunused-variable] double *apos, charge, dist, dx, dy, dz, scale; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:27: warning: unused variable 'dist' [-Wunused-variable] double *apos, charge, dist, dx, dy, dz, scale; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:19: warning: unused variable 'charge' [-Wunused-variable] double *apos, charge, dist, dx, dy, dz, scale; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:262:13: warning: unused variable 'apos' [-Wunused-variable] double *apos, charge, dist, dx, dy, dz, scale; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:261:12: warning: unused variable 'atom' [-Wunused-variable] Vatom *atom; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function 'Vgreen_coulombD_direct': /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:316:16: warning: unused variable 'qtemp' [-Wunused-variable] double *q, qtemp; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:316:13: warning: unused variable 'q' [-Wunused-variable] double *q, qtemp; ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c: In function 'Vgreen_coulombD': /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:368:9: warning: unused variable 'iatom' [-Wunused-variable] int iatom, ipos; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:367:16: warning: unused variable 'qtemp' [-Wunused-variable] double *q, qtemp; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:367:13: warning: unused variable 'q' [-Wunused-variable] double *q, qtemp; ^ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:60: warning: unused variable 'scale' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:56: warning: unused variable 'dx' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:52: warning: unused variable 'dz' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:48: warning: unused variable 'dy' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:40: warning: unused variable 'idist3' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:33: warning: unused variable 'dist2' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:27: warning: unused variable 'dist' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:19: warning: unused variable 'charge' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:366:13: warning: unused variable 'apos' [-Wunused-variable] double *apos, charge, dist, dist2, idist3, dy, dz, dx, scale; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:365:12: warning: unused variable 'atom' [-Wunused-variable] Vatom *atom; ^~~~ At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:525:14: warning: 'treecalc' defined but not used [-Wunused-function] VPRIVATE int treecalc(Vgreen *thee, double *xtar, double *ytar, double *ztar, ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:505:14: warning: 'treecleanup' defined but not used [-Wunused-function] VPRIVATE int treecleanup(Vgreen *thee) { ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vgreen.c:425:14: warning: 'treesetup' defined but not used [-Wunused-function] VPRIVATE int treesetup(Vgreen *thee) { ^~~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 28%] Built target apbs_generic make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 29%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildAd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c: In function 'VbuildA': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:66:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 14); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c: In function 'VbuildA_fv': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gzcf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:167:5: note: in expansion of macro 'MAT3' MAT3(gzcf, *nx, *ny, 2); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gycf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:166:5: note: in expansion of macro 'MAT3' MAT3(gycf, *nx, *nz, 2); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gxcf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:165:5: note: in expansion of macro 'MAT3' MAT3(gxcf, *ny, *nz, 2); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:164:5: note: in expansion of macro 'MAT3' MAT3( oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:163:5: note: in expansion of macro 'MAT3' MAT3( oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:162:5: note: in expansion of macro 'MAT3' MAT3( uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a3cf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:161:5: note: in expansion of macro 'MAT3' MAT3(a3cf, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a2cf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:160:5: note: in expansion of macro 'MAT3' MAT3(a2cf, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a1cf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:159:5: note: in expansion of macro 'MAT3' MAT3(a1cf, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:158:5: note: in expansion of macro 'MAT3' MAT3( oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_ccf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:157:5: note: in expansion of macro 'MAT3' MAT3( ccf, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:156:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fcf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:155:5: note: in expansion of macro 'MAT3' MAT3( fcf, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildAd.c:154:5: note: in expansion of macro 'MAT3' MAT3( fc, *nx, *ny, *nz); ^~~~ [ 30%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildBd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function 'Vbuildband': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:65:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function 'Vbuildband1_7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:133:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:132:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:131:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:130:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_acB' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:128:5: note: in expansion of macro 'MAT2' MAT2(acB, *lda, *ny-1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c: In function 'Vbuildband1_27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:213:5: note: in expansion of macro 'MAT3' MAT3(uSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:212:5: note: in expansion of macro 'MAT3' MAT3(uSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:211:5: note: in expansion of macro 'MAT3' MAT3(uNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:210:5: note: in expansion of macro 'MAT3' MAT3(uNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:208:5: note: in expansion of macro 'MAT3' MAT3( uS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:207:5: note: in expansion of macro 'MAT3' MAT3( uN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:206:5: note: in expansion of macro 'MAT3' MAT3( uW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:205:5: note: in expansion of macro 'MAT3' MAT3( uE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:203:5: note: in expansion of macro 'MAT3' MAT3(oNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:202:5: note: in expansion of macro 'MAT3' MAT3(oNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:200:5: note: in expansion of macro 'MAT3' MAT3( uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:199:5: note: in expansion of macro 'MAT3' MAT3( oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:198:5: note: in expansion of macro 'MAT3' MAT3( oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:197:5: note: in expansion of macro 'MAT3' MAT3( oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_acB' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildBd.c:195:5: note: in expansion of macro 'MAT2' MAT2(acB, *lda, *ny-1); ^~~~ [ 31%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildGd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function 'VbuildG': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:64:5: note: in expansion of macro 'MAT2' MAT2( ac, *nxc * *nyc * *nzc, 27); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_acFF' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:63:5: note: in expansion of macro 'MAT2' MAT2(acFF, *nxf * *nyf * *nzf, 27); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pcFF' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:62:5: note: in expansion of macro 'MAT2' MAT2(pcFF, *nxc * *nyc * *nzc, 27); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function 'VbuildG_1': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:216:5: note: in expansion of macro 'MAT3' MAT3(dPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:215:5: note: in expansion of macro 'MAT3' MAT3(dPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:214:5: note: in expansion of macro 'MAT3' MAT3(dPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:213:5: note: in expansion of macro 'MAT3' MAT3(dPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:212:5: note: in expansion of macro 'MAT3' MAT3( dPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:211:5: note: in expansion of macro 'MAT3' MAT3( dPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:210:5: note: in expansion of macro 'MAT3' MAT3( dPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:209:5: note: in expansion of macro 'MAT3' MAT3( dPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:208:5: note: in expansion of macro 'MAT3' MAT3( dPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:206:5: note: in expansion of macro 'MAT3' MAT3(uPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:205:5: note: in expansion of macro 'MAT3' MAT3(uPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:204:5: note: in expansion of macro 'MAT3' MAT3(uPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:203:5: note: in expansion of macro 'MAT3' MAT3(uPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:202:5: note: in expansion of macro 'MAT3' MAT3( uPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:201:5: note: in expansion of macro 'MAT3' MAT3( uPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:200:5: note: in expansion of macro 'MAT3' MAT3( uPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:199:5: note: in expansion of macro 'MAT3' MAT3( uPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:198:5: note: in expansion of macro 'MAT3' MAT3( uPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:196:5: note: in expansion of macro 'MAT3' MAT3(oPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:195:5: note: in expansion of macro 'MAT3' MAT3(oPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:194:5: note: in expansion of macro 'MAT3' MAT3(oPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:193:5: note: in expansion of macro 'MAT3' MAT3(oPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:192:5: note: in expansion of macro 'MAT3' MAT3( oPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:191:5: note: in expansion of macro 'MAT3' MAT3( oPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:190:5: note: in expansion of macro 'MAT3' MAT3( oPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:189:5: note: in expansion of macro 'MAT3' MAT3( oPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:188:5: note: in expansion of macro 'MAT3' MAT3( oPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:186:5: note: in expansion of macro 'MAT3' MAT3(XuSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:185:5: note: in expansion of macro 'MAT3' MAT3(XuSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:184:5: note: in expansion of macro 'MAT3' MAT3(XuNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:183:5: note: in expansion of macro 'MAT3' MAT3(XuNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:182:5: note: in expansion of macro 'MAT3' MAT3( XuS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:181:5: note: in expansion of macro 'MAT3' MAT3( XuN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:180:5: note: in expansion of macro 'MAT3' MAT3( XuW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:179:5: note: in expansion of macro 'MAT3' MAT3( XuE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:177:5: note: in expansion of macro 'MAT3' MAT3(XoNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:176:5: note: in expansion of macro 'MAT3' MAT3(XoNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:174:5: note: in expansion of macro 'MAT3' MAT3( XuC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:172:5: note: in expansion of macro 'MAT3' MAT3( XoN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:171:5: note: in expansion of macro 'MAT3' MAT3( XoE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:170:5: note: in expansion of macro 'MAT3' MAT3( XoC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:168:5: note: in expansion of macro 'MAT3' MAT3( oC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:21: warning: variable 'nzm1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:15: warning: variable 'nym1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:164:9: warning: variable 'nxm1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:163:33: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] int iim1, iip1, jjm1, jjp1, kkm1, kkp1; ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function 'VbuildG_7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:532:5: note: in expansion of macro 'MAT3' MAT3(dPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:531:5: note: in expansion of macro 'MAT3' MAT3(dPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:530:5: note: in expansion of macro 'MAT3' MAT3(dPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:529:5: note: in expansion of macro 'MAT3' MAT3(dPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:528:5: note: in expansion of macro 'MAT3' MAT3( dPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:527:5: note: in expansion of macro 'MAT3' MAT3( dPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:526:5: note: in expansion of macro 'MAT3' MAT3( dPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:525:5: note: in expansion of macro 'MAT3' MAT3( dPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:524:5: note: in expansion of macro 'MAT3' MAT3( dPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:522:5: note: in expansion of macro 'MAT3' MAT3(uPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:521:5: note: in expansion of macro 'MAT3' MAT3(uPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:520:5: note: in expansion of macro 'MAT3' MAT3(uPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:519:5: note: in expansion of macro 'MAT3' MAT3(uPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:518:5: note: in expansion of macro 'MAT3' MAT3( uPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:517:5: note: in expansion of macro 'MAT3' MAT3( uPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:516:5: note: in expansion of macro 'MAT3' MAT3( uPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:515:5: note: in expansion of macro 'MAT3' MAT3( uPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:514:5: note: in expansion of macro 'MAT3' MAT3( uPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:512:5: note: in expansion of macro 'MAT3' MAT3(oPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:511:5: note: in expansion of macro 'MAT3' MAT3(oPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:510:5: note: in expansion of macro 'MAT3' MAT3(oPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:509:5: note: in expansion of macro 'MAT3' MAT3(oPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:508:5: note: in expansion of macro 'MAT3' MAT3( oPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:507:5: note: in expansion of macro 'MAT3' MAT3( oPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:506:5: note: in expansion of macro 'MAT3' MAT3( oPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:505:5: note: in expansion of macro 'MAT3' MAT3( oPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:504:5: note: in expansion of macro 'MAT3' MAT3( oPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:502:5: note: in expansion of macro 'MAT3' MAT3(XuSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:501:5: note: in expansion of macro 'MAT3' MAT3(XuSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:500:5: note: in expansion of macro 'MAT3' MAT3(XuNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:499:5: note: in expansion of macro 'MAT3' MAT3(XuNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:498:5: note: in expansion of macro 'MAT3' MAT3( XuS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:497:5: note: in expansion of macro 'MAT3' MAT3( XuN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:496:5: note: in expansion of macro 'MAT3' MAT3( XuW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:495:5: note: in expansion of macro 'MAT3' MAT3( XuE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:494:5: note: in expansion of macro 'MAT3' MAT3( XuC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:492:5: note: in expansion of macro 'MAT3' MAT3(XoNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:491:5: note: in expansion of macro 'MAT3' MAT3(XoNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:490:5: note: in expansion of macro 'MAT3' MAT3( XoN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:489:5: note: in expansion of macro 'MAT3' MAT3( XoE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:488:5: note: in expansion of macro 'MAT3' MAT3( XoC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:486:5: note: in expansion of macro 'MAT3' MAT3( uC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:484:5: note: in expansion of macro 'MAT3' MAT3( oN, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:483:5: note: in expansion of macro 'MAT3' MAT3( oE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:482:5: note: in expansion of macro 'MAT3' MAT3( oC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:21: warning: variable 'nzm1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:15: warning: variable 'nym1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:473:9: warning: variable 'nxm1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:472:9: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] int kkm1, kkp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:469:28: warning: variable 'kp2' set but not used [-Wunused-but-set-variable] int km1, kp1, km2, kp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:469:22: warning: variable 'km2' set but not used [-Wunused-but-set-variable] int km1, kp1, km2, kp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:468:28: warning: variable 'jp2' set but not used [-Wunused-but-set-variable] int jm1, jp1, jm2, jp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:467:28: warning: variable 'ip2' set but not used [-Wunused-but-set-variable] int im1, ip1, im2, ip2; ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c: In function 'VbuildG_27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1380:5: note: in expansion of macro 'MAT3' MAT3(dPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1379:5: note: in expansion of macro 'MAT3' MAT3(dPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1378:5: note: in expansion of macro 'MAT3' MAT3(dPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1377:5: note: in expansion of macro 'MAT3' MAT3(dPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1376:5: note: in expansion of macro 'MAT3' MAT3( dPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1375:5: note: in expansion of macro 'MAT3' MAT3( dPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1374:5: note: in expansion of macro 'MAT3' MAT3( dPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1373:5: note: in expansion of macro 'MAT3' MAT3( dPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1372:5: note: in expansion of macro 'MAT3' MAT3( dPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1370:5: note: in expansion of macro 'MAT3' MAT3(uPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1369:5: note: in expansion of macro 'MAT3' MAT3(uPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1368:5: note: in expansion of macro 'MAT3' MAT3(uPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1367:5: note: in expansion of macro 'MAT3' MAT3(uPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1366:5: note: in expansion of macro 'MAT3' MAT3( uPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1365:5: note: in expansion of macro 'MAT3' MAT3( uPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1364:5: note: in expansion of macro 'MAT3' MAT3( uPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1363:5: note: in expansion of macro 'MAT3' MAT3( uPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1362:5: note: in expansion of macro 'MAT3' MAT3( uPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1360:5: note: in expansion of macro 'MAT3' MAT3(oPSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1359:5: note: in expansion of macro 'MAT3' MAT3(oPSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1358:5: note: in expansion of macro 'MAT3' MAT3(oPNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1357:5: note: in expansion of macro 'MAT3' MAT3(oPNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1356:5: note: in expansion of macro 'MAT3' MAT3( oPW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1355:5: note: in expansion of macro 'MAT3' MAT3( oPE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1354:5: note: in expansion of macro 'MAT3' MAT3( oPS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1353:5: note: in expansion of macro 'MAT3' MAT3( oPN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1352:5: note: in expansion of macro 'MAT3' MAT3( oPC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1350:5: note: in expansion of macro 'MAT3' MAT3(XuSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1349:5: note: in expansion of macro 'MAT3' MAT3(XuSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1348:5: note: in expansion of macro 'MAT3' MAT3(XuNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1347:5: note: in expansion of macro 'MAT3' MAT3(XuNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1346:5: note: in expansion of macro 'MAT3' MAT3( XuS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1345:5: note: in expansion of macro 'MAT3' MAT3( XuN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1344:5: note: in expansion of macro 'MAT3' MAT3( XuW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1343:5: note: in expansion of macro 'MAT3' MAT3( XuE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XuC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1342:5: note: in expansion of macro 'MAT3' MAT3( XuC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1340:5: note: in expansion of macro 'MAT3' MAT3(XoNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1339:5: note: in expansion of macro 'MAT3' MAT3(XoNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1338:5: note: in expansion of macro 'MAT3' MAT3( XoN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1337:5: note: in expansion of macro 'MAT3' MAT3( XoE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_XoC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1336:5: note: in expansion of macro 'MAT3' MAT3( XoC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1334:5: note: in expansion of macro 'MAT3' MAT3( uSW, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1333:5: note: in expansion of macro 'MAT3' MAT3( uSE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1332:5: note: in expansion of macro 'MAT3' MAT3( uNW, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1331:5: note: in expansion of macro 'MAT3' MAT3( uNE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1330:5: note: in expansion of macro 'MAT3' MAT3( uS, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1329:5: note: in expansion of macro 'MAT3' MAT3( uN, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1328:5: note: in expansion of macro 'MAT3' MAT3( uW, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1327:5: note: in expansion of macro 'MAT3' MAT3( uE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1326:5: note: in expansion of macro 'MAT3' MAT3( uC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1324:5: note: in expansion of macro 'MAT3' MAT3( oNW, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1323:5: note: in expansion of macro 'MAT3' MAT3( oNE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1322:5: note: in expansion of macro 'MAT3' MAT3( oN, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1321:5: note: in expansion of macro 'MAT3' MAT3( oE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1320:5: note: in expansion of macro 'MAT3' MAT3( oC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:21: warning: variable 'nzm1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:15: warning: variable 'nym1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1277:9: warning: variable 'nxm1' set but not used [-Wunused-but-set-variable] int nxm1, nym1, nzm1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1276:9: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] int kkm1, kkp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1273:28: warning: variable 'kp2' set but not used [-Wunused-but-set-variable] int km1, kp1, km2, kp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildGd.c:1273:22: warning: variable 'km2' set but not used [-Wunused-but-set-variable] int km1, kp1, km2, kp2; ^~~ [ 32%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/buildPd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildP': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:67:5: note: in expansion of macro 'MAT2' MAT2(ac, *nxf * *nyf * *nzf, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:66:5: note: in expansion of macro 'MAT2' MAT2(pc, *nxc * *nyc * *nzc, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildP_trilin': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:101:5: note: in expansion of macro 'MAT2' MAT2(pc, *nxc * *nyc * *nzc, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildPb_trilin': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:163:5: note: in expansion of macro 'MAT3' MAT3(dPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:162:5: note: in expansion of macro 'MAT3' MAT3(dPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:161:5: note: in expansion of macro 'MAT3' MAT3(dPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:160:5: note: in expansion of macro 'MAT3' MAT3(dPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:158:5: note: in expansion of macro 'MAT3' MAT3( dPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:157:5: note: in expansion of macro 'MAT3' MAT3( dPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:156:5: note: in expansion of macro 'MAT3' MAT3( dPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:155:5: note: in expansion of macro 'MAT3' MAT3( dPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:154:5: note: in expansion of macro 'MAT3' MAT3( dPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:152:5: note: in expansion of macro 'MAT3' MAT3(uPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:151:5: note: in expansion of macro 'MAT3' MAT3(uPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:150:5: note: in expansion of macro 'MAT3' MAT3(uPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:149:5: note: in expansion of macro 'MAT3' MAT3(uPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:147:5: note: in expansion of macro 'MAT3' MAT3( uPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:146:5: note: in expansion of macro 'MAT3' MAT3( uPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:145:5: note: in expansion of macro 'MAT3' MAT3( uPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:144:5: note: in expansion of macro 'MAT3' MAT3( uPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:143:5: note: in expansion of macro 'MAT3' MAT3( uPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:141:5: note: in expansion of macro 'MAT3' MAT3(oPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:140:5: note: in expansion of macro 'MAT3' MAT3(oPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:139:5: note: in expansion of macro 'MAT3' MAT3(oPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:138:5: note: in expansion of macro 'MAT3' MAT3(oPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:136:5: note: in expansion of macro 'MAT3' MAT3( oPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:135:5: note: in expansion of macro 'MAT3' MAT3( oPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:134:5: note: in expansion of macro 'MAT3' MAT3( oPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:133:5: note: in expansion of macro 'MAT3' MAT3( oPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:132:5: note: in expansion of macro 'MAT3' MAT3( oPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildP_op7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:212:5: note: in expansion of macro 'MAT2' MAT2(pc, *nxc * *nyc * *nzc, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:211:5: note: in expansion of macro 'MAT2' MAT2(ac, *nxf * *nyf * *nzf, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildPb_op7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:287:5: note: in expansion of macro 'MAT3' MAT3(dPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:286:5: note: in expansion of macro 'MAT3' MAT3(dPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:285:5: note: in expansion of macro 'MAT3' MAT3(dPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:284:5: note: in expansion of macro 'MAT3' MAT3(dPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:283:5: note: in expansion of macro 'MAT3' MAT3( dPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:282:5: note: in expansion of macro 'MAT3' MAT3( dPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:281:5: note: in expansion of macro 'MAT3' MAT3( dPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:280:5: note: in expansion of macro 'MAT3' MAT3( dPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:279:5: note: in expansion of macro 'MAT3' MAT3( dPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:278:5: note: in expansion of macro 'MAT3' MAT3(uPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:277:5: note: in expansion of macro 'MAT3' MAT3(uPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:276:5: note: in expansion of macro 'MAT3' MAT3(uPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:275:5: note: in expansion of macro 'MAT3' MAT3(uPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:274:5: note: in expansion of macro 'MAT3' MAT3( uPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:273:5: note: in expansion of macro 'MAT3' MAT3( uPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:272:5: note: in expansion of macro 'MAT3' MAT3( uPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:271:5: note: in expansion of macro 'MAT3' MAT3( uPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:270:5: note: in expansion of macro 'MAT3' MAT3( uPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:269:5: note: in expansion of macro 'MAT3' MAT3(oPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:268:5: note: in expansion of macro 'MAT3' MAT3(oPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:267:5: note: in expansion of macro 'MAT3' MAT3(oPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:266:5: note: in expansion of macro 'MAT3' MAT3(oPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:265:5: note: in expansion of macro 'MAT3' MAT3( oPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:264:5: note: in expansion of macro 'MAT3' MAT3( oPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:263:5: note: in expansion of macro 'MAT3' MAT3( oPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:262:5: note: in expansion of macro 'MAT3' MAT3( oPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:261:5: note: in expansion of macro 'MAT3' MAT3( oPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:260:5: note: in expansion of macro 'MAT3' MAT3( uC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:259:5: note: in expansion of macro 'MAT3' MAT3( oN, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:258:5: note: in expansion of macro 'MAT3' MAT3( oE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:257:5: note: in expansion of macro 'MAT3' MAT3( oC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:32: warning: variable 'eighth' set but not used [-Wunused-but-set-variable] double won, half, quarter, eighth; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:23: warning: variable 'quarter' set but not used [-Wunused-but-set-variable] double won, half, quarter, eighth; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:255:17: warning: variable 'half' set but not used [-Wunused-but-set-variable] double won, half, quarter, eighth; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:253:15: warning: variable 'kkp1' set but not used [-Wunused-but-set-variable] int kkm1, kkp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:253:9: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] int kkm1, kkp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:252:15: warning: variable 'jjp1' set but not used [-Wunused-but-set-variable] int jjm1, jjp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:252:9: warning: variable 'jjm1' set but not used [-Wunused-but-set-variable] int jjm1, jjp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:251:15: warning: variable 'iip1' set but not used [-Wunused-but-set-variable] int iim1, iip1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:251:9: warning: variable 'iim1' set but not used [-Wunused-but-set-variable] int iim1, iip1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:250:16: warning: variable 'kp2' set but not used [-Wunused-but-set-variable] int km2, kp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:250:10: warning: variable 'km2' set but not used [-Wunused-but-set-variable] int km2, kp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:248:16: warning: variable 'jp2' set but not used [-Wunused-but-set-variable] int jm2, jp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:248:10: warning: variable 'jm2' set but not used [-Wunused-but-set-variable] int jm2, jp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:246:16: warning: variable 'ip2' set but not used [-Wunused-but-set-variable] int im2, ip2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:246:10: warning: variable 'im2' set but not used [-Wunused-but-set-variable] int im2, ip2; ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildP_op27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:728:5: note: in expansion of macro 'MAT2' MAT2(pc, *nxc * *nyc * *nzc, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:727:5: note: in expansion of macro 'MAT2' MAT2(ac, *nxf * *nyf * *nzf, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c: In function 'VbuildPb_op27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:818:7: note: in expansion of macro 'MAT3' MAT3(dPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:817:7: note: in expansion of macro 'MAT3' MAT3(dPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:816:7: note: in expansion of macro 'MAT3' MAT3(dPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:815:7: note: in expansion of macro 'MAT3' MAT3(dPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:814:7: note: in expansion of macro 'MAT3' MAT3( dPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:813:7: note: in expansion of macro 'MAT3' MAT3( dPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:812:7: note: in expansion of macro 'MAT3' MAT3( dPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:811:7: note: in expansion of macro 'MAT3' MAT3( dPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:810:7: note: in expansion of macro 'MAT3' MAT3( dPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:809:7: note: in expansion of macro 'MAT3' MAT3(uPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:808:7: note: in expansion of macro 'MAT3' MAT3(uPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:807:7: note: in expansion of macro 'MAT3' MAT3(uPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:806:7: note: in expansion of macro 'MAT3' MAT3(uPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:805:7: note: in expansion of macro 'MAT3' MAT3( uPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:804:7: note: in expansion of macro 'MAT3' MAT3( uPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:803:7: note: in expansion of macro 'MAT3' MAT3( uPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:802:7: note: in expansion of macro 'MAT3' MAT3( uPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:801:7: note: in expansion of macro 'MAT3' MAT3( uPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:800:7: note: in expansion of macro 'MAT3' MAT3(oPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:799:7: note: in expansion of macro 'MAT3' MAT3(oPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:798:7: note: in expansion of macro 'MAT3' MAT3(oPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:797:7: note: in expansion of macro 'MAT3' MAT3(oPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:796:7: note: in expansion of macro 'MAT3' MAT3( oPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:795:7: note: in expansion of macro 'MAT3' MAT3( oPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:794:7: note: in expansion of macro 'MAT3' MAT3( oPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:793:7: note: in expansion of macro 'MAT3' MAT3( oPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:792:7: note: in expansion of macro 'MAT3' MAT3( oPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:791:7: note: in expansion of macro 'MAT3' MAT3( uSW, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:790:7: note: in expansion of macro 'MAT3' MAT3( uSE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:789:7: note: in expansion of macro 'MAT3' MAT3( uNW, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:788:7: note: in expansion of macro 'MAT3' MAT3( uNE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:787:7: note: in expansion of macro 'MAT3' MAT3( uS, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:786:7: note: in expansion of macro 'MAT3' MAT3( uN, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:785:7: note: in expansion of macro 'MAT3' MAT3( uW, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:784:7: note: in expansion of macro 'MAT3' MAT3( uE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:783:7: note: in expansion of macro 'MAT3' MAT3( oNW, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:782:7: note: in expansion of macro 'MAT3' MAT3( oNE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:781:7: note: in expansion of macro 'MAT3' MAT3( uC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:780:7: note: in expansion of macro 'MAT3' MAT3( oN, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:779:7: note: in expansion of macro 'MAT3' MAT3( oE, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:778:7: note: in expansion of macro 'MAT3' MAT3( oC, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:34: warning: variable 'eighth' set but not used [-Wunused-but-set-variable] double won, half, quarter, eighth; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:25: warning: variable 'quarter' set but not used [-Wunused-but-set-variable] double won, half, quarter, eighth; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:776:19: warning: variable 'half' set but not used [-Wunused-but-set-variable] double won, half, quarter, eighth; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:774:17: warning: variable 'kkp1' set but not used [-Wunused-but-set-variable] int kkm1, kkp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:774:11: warning: variable 'kkm1' set but not used [-Wunused-but-set-variable] int kkm1, kkp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:773:17: warning: variable 'jjp1' set but not used [-Wunused-but-set-variable] int jjm1, jjp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:773:11: warning: variable 'jjm1' set but not used [-Wunused-but-set-variable] int jjm1, jjp1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:772:17: warning: variable 'iip1' set but not used [-Wunused-but-set-variable] int iim1, iip1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:772:11: warning: variable 'iim1' set but not used [-Wunused-but-set-variable] int iim1, iip1; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:771:18: warning: variable 'kp2' set but not used [-Wunused-but-set-variable] int km2, kp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:771:12: warning: variable 'km2' set but not used [-Wunused-but-set-variable] int km2, kp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:769:18: warning: variable 'jp2' set but not used [-Wunused-but-set-variable] int jm2, jp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:769:12: warning: variable 'jm2' set but not used [-Wunused-but-set-variable] int jm2, jp2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:767:18: warning: variable 'ip2' set but not used [-Wunused-but-set-variable] int im2, ip2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/buildPd.c:767:12: warning: variable 'im2' set but not used [-Wunused-but-set-variable] int im2, ip2; ^~~ [ 34%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/cgd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c: In function 'Vcghs': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/cgd.c:99:24: warning: 'rhok1' may be used uninitialized in this function [-Wmaybe-uninitialized] beta = rhok2 / rhok1; ~~~~~~^~~~~~~ [ 35%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/gsd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function 'Vgsrb': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:67:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function 'Vgsrb7x': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:116:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:115:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:114:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:113:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro 'MAT3' MAT3( r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_r' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro 'MAT3' MAT3( r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_r' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:111:5: note: in expansion of macro 'MAT3' MAT3( r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w2' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro 'MAT3' MAT3(w2, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_w2' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro 'MAT3' MAT3(w2, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_w2' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:110:5: note: in expansion of macro 'MAT3' MAT3(w2, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro 'MAT3' MAT3(w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_w1' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro 'MAT3' MAT3(w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_w1' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:109:5: note: in expansion of macro 'MAT3' MAT3(w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:108:5: note: in expansion of macro 'MAT3' MAT3( x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:107:5: note: in expansion of macro 'MAT3' MAT3(fc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:106:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c: In function 'Vgsrb27x': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:208:5: note: in expansion of macro 'MAT3' MAT3(uSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:207:5: note: in expansion of macro 'MAT3' MAT3(uSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:206:5: note: in expansion of macro 'MAT3' MAT3(uNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:205:5: note: in expansion of macro 'MAT3' MAT3(uNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:204:5: note: in expansion of macro 'MAT3' MAT3( uS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:203:5: note: in expansion of macro 'MAT3' MAT3( uN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:202:5: note: in expansion of macro 'MAT3' MAT3( uW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:201:5: note: in expansion of macro 'MAT3' MAT3( uE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:199:5: note: in expansion of macro 'MAT3' MAT3(oNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:198:5: note: in expansion of macro 'MAT3' MAT3(oNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:196:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:195:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:194:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:193:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro 'MAT3' MAT3( r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_r' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro 'MAT3' MAT3( r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_r' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:191:5: note: in expansion of macro 'MAT3' MAT3( r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w2' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro 'MAT3' MAT3(w2, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_w2' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro 'MAT3' MAT3(w2, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_w2' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:190:5: note: in expansion of macro 'MAT3' MAT3(w2, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro 'MAT3' MAT3(w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_w1' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro 'MAT3' MAT3(w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_w1' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:189:5: note: in expansion of macro 'MAT3' MAT3(w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:188:5: note: in expansion of macro 'MAT3' MAT3( x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:187:5: note: in expansion of macro 'MAT3' MAT3(fc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:186:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:182:9: warning: variable 'istep' set but not used [-Wunused-but-set-variable] int istep; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:17: warning: variable 'k2' set but not used [-Wunused-but-set-variable] int i2, j2, k2; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:13: warning: variable 'j2' set but not used [-Wunused-but-set-variable] int i2, j2, k2; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:180:9: warning: variable 'i2' set but not used [-Wunused-but-set-variable] int i2, j2, k2; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:17: warning: variable 'k1' set but not used [-Wunused-but-set-variable] int i1, j1, k1; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:13: warning: variable 'j1' set but not used [-Wunused-but-set-variable] int i1, j1, k1; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/gsd.c:179:9: warning: variable 'i1' set but not used [-Wunused-but-set-variable] int i1, j1, k1; ^~ [ 36%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/matvecd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.h:55, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmatvec7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:87:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmatvec7_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:112:5: note: in expansion of macro 'MAT3' MAT3(y, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:111:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:110:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:109:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:108:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:107:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:106:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmatvec27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:139:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmatvec27_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:184:5: note: in expansion of macro 'MAT3' MAT3(uSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:183:5: note: in expansion of macro 'MAT3' MAT3(uSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:182:5: note: in expansion of macro 'MAT3' MAT3(uNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:181:5: note: in expansion of macro 'MAT3' MAT3(uNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:180:5: note: in expansion of macro 'MAT3' MAT3(uS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:179:5: note: in expansion of macro 'MAT3' MAT3(uN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:178:5: note: in expansion of macro 'MAT3' MAT3(uW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:177:5: note: in expansion of macro 'MAT3' MAT3(uE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:176:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:174:5: note: in expansion of macro 'MAT3' MAT3(oNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:173:5: note: in expansion of macro 'MAT3' MAT3(oNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:172:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:171:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:170:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:168:5: note: in expansion of macro 'MAT3' MAT3(y, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:167:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:166:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmatvec7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:263:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmatvecd7_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:292:5: note: in expansion of macro 'MAT3' MAT3(w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:291:5: note: in expansion of macro 'MAT3' MAT3( y, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:290:5: note: in expansion of macro 'MAT3' MAT3( x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:289:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_cc' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_cc' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:288:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:287:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:286:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:285:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmatvec27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:322:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmatvecd27_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:370:5: note: in expansion of macro 'MAT3' MAT3( w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:369:5: note: in expansion of macro 'MAT3' MAT3( y, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:368:5: note: in expansion of macro 'MAT3' MAT3( x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:367:5: note: in expansion of macro 'MAT3' MAT3( oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_cc' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_cc' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:366:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:365:5: note: in expansion of macro 'MAT3' MAT3(uSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:364:5: note: in expansion of macro 'MAT3' MAT3(uSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:363:5: note: in expansion of macro 'MAT3' MAT3(uNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:362:5: note: in expansion of macro 'MAT3' MAT3(uNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:361:5: note: in expansion of macro 'MAT3' MAT3( uS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:360:5: note: in expansion of macro 'MAT3' MAT3( uN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:359:5: note: in expansion of macro 'MAT3' MAT3( uW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:358:5: note: in expansion of macro 'MAT3' MAT3( uE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:357:5: note: in expansion of macro 'MAT3' MAT3(oNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:356:5: note: in expansion of macro 'MAT3' MAT3(oNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:355:5: note: in expansion of macro 'MAT3' MAT3( uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:354:5: note: in expansion of macro 'MAT3' MAT3( oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:353:5: note: in expansion of macro 'MAT3' MAT3( oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmresid7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:451:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmresid7_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:476:5: note: in expansion of macro 'MAT3' MAT3(r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:475:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:474:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:473:5: note: in expansion of macro 'MAT3' MAT3(fc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:472:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:471:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:470:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:469:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmresid27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:503:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vmresid27_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:550:5: note: in expansion of macro 'MAT3' MAT3(uSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:549:5: note: in expansion of macro 'MAT3' MAT3(uSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:548:5: note: in expansion of macro 'MAT3' MAT3(uNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:547:5: note: in expansion of macro 'MAT3' MAT3(uNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:546:5: note: in expansion of macro 'MAT3' MAT3(uS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:545:5: note: in expansion of macro 'MAT3' MAT3(uN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:544:5: note: in expansion of macro 'MAT3' MAT3(uW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:543:5: note: in expansion of macro 'MAT3' MAT3(uE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:542:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:540:5: note: in expansion of macro 'MAT3' MAT3(oNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:539:5: note: in expansion of macro 'MAT3' MAT3(oNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:538:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:537:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:536:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:534:5: note: in expansion of macro 'MAT3' MAT3(r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:533:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:532:5: note: in expansion of macro 'MAT3' MAT3(fc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:531:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmresid7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:623:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmresid7_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:650:5: note: in expansion of macro 'MAT3' MAT3(w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:649:5: note: in expansion of macro 'MAT3' MAT3( r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:648:5: note: in expansion of macro 'MAT3' MAT3( x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:647:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:646:5: note: in expansion of macro 'MAT3' MAT3(fc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_cc' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_cc' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:645:5: note: in expansion of macro 'MAT3' MAT3(cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:644:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:643:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:642:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmresid27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:681:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vnmresid27_1s': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_w1' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:727:5: note: in expansion of macro 'MAT3' MAT3( w1, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_r' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:726:5: note: in expansion of macro 'MAT3' MAT3( r, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:725:5: note: in expansion of macro 'MAT3' MAT3( x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:724:5: note: in expansion of macro 'MAT3' MAT3(uSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:723:5: note: in expansion of macro 'MAT3' MAT3(uSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:722:5: note: in expansion of macro 'MAT3' MAT3(uNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:721:5: note: in expansion of macro 'MAT3' MAT3(uNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:720:5: note: in expansion of macro 'MAT3' MAT3( uS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:719:5: note: in expansion of macro 'MAT3' MAT3( uN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:718:5: note: in expansion of macro 'MAT3' MAT3( uW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:717:5: note: in expansion of macro 'MAT3' MAT3( uE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:716:5: note: in expansion of macro 'MAT3' MAT3(oNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:715:5: note: in expansion of macro 'MAT3' MAT3(oNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:714:5: note: in expansion of macro 'MAT3' MAT3( uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:713:5: note: in expansion of macro 'MAT3' MAT3( oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:712:5: note: in expansion of macro 'MAT3' MAT3( oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:711:5: note: in expansion of macro 'MAT3' MAT3( fc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_cc' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_cc' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:710:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:709:5: note: in expansion of macro 'MAT3' MAT3( oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vrestrc': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:786:5: note: in expansion of macro 'MAT2' MAT2(pc, *nxc * *nyc * *nzc, 1 ); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vrestrc2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:852:5: note: in expansion of macro 'MAT3' MAT3(dPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:851:5: note: in expansion of macro 'MAT3' MAT3(dPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:850:5: note: in expansion of macro 'MAT3' MAT3(dPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:849:5: note: in expansion of macro 'MAT3' MAT3(dPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:847:5: note: in expansion of macro 'MAT3' MAT3(dPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:846:5: note: in expansion of macro 'MAT3' MAT3(dPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:845:5: note: in expansion of macro 'MAT3' MAT3(dPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:844:5: note: in expansion of macro 'MAT3' MAT3(dPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:843:5: note: in expansion of macro 'MAT3' MAT3(dPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:841:5: note: in expansion of macro 'MAT3' MAT3(uPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:840:5: note: in expansion of macro 'MAT3' MAT3(uPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:839:5: note: in expansion of macro 'MAT3' MAT3(uPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:838:5: note: in expansion of macro 'MAT3' MAT3(uPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:836:5: note: in expansion of macro 'MAT3' MAT3(uPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:835:5: note: in expansion of macro 'MAT3' MAT3(uPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:834:5: note: in expansion of macro 'MAT3' MAT3(uPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:833:5: note: in expansion of macro 'MAT3' MAT3(uPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:832:5: note: in expansion of macro 'MAT3' MAT3(uPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:830:5: note: in expansion of macro 'MAT3' MAT3(oPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:829:5: note: in expansion of macro 'MAT3' MAT3(oPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:828:5: note: in expansion of macro 'MAT3' MAT3(oPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:827:5: note: in expansion of macro 'MAT3' MAT3(oPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:825:5: note: in expansion of macro 'MAT3' MAT3(oPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:824:5: note: in expansion of macro 'MAT3' MAT3(oPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:823:5: note: in expansion of macro 'MAT3' MAT3(oPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:822:5: note: in expansion of macro 'MAT3' MAT3(oPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:821:5: note: in expansion of macro 'MAT3' MAT3(oPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xout' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:819:5: note: in expansion of macro 'MAT3' MAT3(xout, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xin' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:818:5: note: in expansion of macro 'MAT3' MAT3(xin, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:816:12: warning: variable 'dimfac' set but not used [-Wunused-but-set-variable] double dimfac; ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.h:55, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'VinterpPMG': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_pc' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:920:5: note: in expansion of macro 'MAT2' MAT2(pc, *nxc * *nyc * *nzc, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'VinterpPMG2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:982:5: note: in expansion of macro 'MAT3' MAT3(dPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:981:5: note: in expansion of macro 'MAT3' MAT3(dPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:980:5: note: in expansion of macro 'MAT3' MAT3(dPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:979:5: note: in expansion of macro 'MAT3' MAT3(dPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:977:5: note: in expansion of macro 'MAT3' MAT3( dPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:976:5: note: in expansion of macro 'MAT3' MAT3( dPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:975:5: note: in expansion of macro 'MAT3' MAT3( dPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:974:5: note: in expansion of macro 'MAT3' MAT3( dPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_dPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:973:5: note: in expansion of macro 'MAT3' MAT3( dPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:971:5: note: in expansion of macro 'MAT3' MAT3(uPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:970:5: note: in expansion of macro 'MAT3' MAT3(uPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:969:5: note: in expansion of macro 'MAT3' MAT3(uPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:968:5: note: in expansion of macro 'MAT3' MAT3(uPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:966:5: note: in expansion of macro 'MAT3' MAT3( uPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:965:5: note: in expansion of macro 'MAT3' MAT3( uPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:964:5: note: in expansion of macro 'MAT3' MAT3( uPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:963:5: note: in expansion of macro 'MAT3' MAT3( uPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:962:5: note: in expansion of macro 'MAT3' MAT3( uPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:960:5: note: in expansion of macro 'MAT3' MAT3(oPSW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:959:5: note: in expansion of macro 'MAT3' MAT3(oPSE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:958:5: note: in expansion of macro 'MAT3' MAT3(oPNW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:957:5: note: in expansion of macro 'MAT3' MAT3(oPNE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:955:5: note: in expansion of macro 'MAT3' MAT3( oPW, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:954:5: note: in expansion of macro 'MAT3' MAT3( oPE, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:953:5: note: in expansion of macro 'MAT3' MAT3( oPS, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:952:5: note: in expansion of macro 'MAT3' MAT3( oPN, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oPC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro 'MAT3' MAT3( oPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:78:9: warning: unused variable 'dy_oPC' [-Wunused-variable] int dy_##mat = dy; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro 'MAT3' MAT3( oPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:77:9: warning: unused variable 'dx_oPC' [-Wunused-variable] int dx_##mat = dx; \ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:951:5: note: in expansion of macro 'MAT3' MAT3( oPC, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xout' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:949:5: note: in expansion of macro 'MAT3' MAT3(xout, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xin' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:948:5: note: in expansion of macro 'MAT3' MAT3( xin, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c: In function 'Vextrac': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xout' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:1086:5: note: in expansion of macro 'MAT3' MAT3(xout, *nxc, *nyc, *nzc); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_xin' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/matvecd.c:1085:5: note: in expansion of macro 'MAT3' MAT3( xin, *nxf, *nyf, *nzf); ^~~~ [ 37%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgcsd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c: In function 'Vmvcs': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:99:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:303:13: warning: 'rsnrm' may be used uninitialized in this function [-Wmaybe-uninitialized] Vprtstp(*iok, *iters, rsnrm, rsden, orsnrm); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgcsd.c:562:37: warning: 'rsden' may be used uninitialized in this function [-Wmaybe-uninitialized] } while (*iters<*itmax && (rsnrm/rsden) > *errtol); ~~~~~~^~~~~~~ [ 38%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgdrvd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function 'Vmgdriv': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:85:9: warning: unused variable 'ierror' [-Wunused-variable] int ierror = 0; ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.h:62, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function 'Vmgdriv2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:267:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, nlev); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:234:12: warning: unused variable 'tsolve' [-Wunused-variable] double tsolve = 0.0; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:233:12: warning: unused variable 'tsetupc' [-Wunused-variable] double tsetupc = 0.0; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:232:12: warning: unused variable 'tsetupf' [-Wunused-variable] double tsetupf = 0.0; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:231:12: warning: unused variable 'oh' [-Wunused-variable] double oh = 0.0; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:230:12: warning: unused variable 'bf' [-Wunused-variable] double bf = 0.0; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:226:12: warning: unused variable 'epsmac' [-Wunused-variable] double epsmac = 0.0; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c: In function 'Vmgsz': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:580:22: warning: 'num_narrc_oper' may be used uninitialized in this function [-Wmaybe-uninitialized] int num_nf_oper, num_narrc_oper; ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:656:13: warning: 'n_band' may be used uninitialized in this function [-Wmaybe-uninitialized] *iretot = num_narr * *narr ~~~~~~~~~~~~~~~~ + (num_nf + num_nf_oper) * *nf ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + (num_narrc + num_narrc_oper) * *narrc ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + n_band ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgdrvd.c:654:41: warning: 'num_nf_oper' may be used uninitialized in this function [-Wmaybe-uninitialized] + (num_nf + num_nf_oper) * *nf ~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ [ 40%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgsubd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function 'Vbuildops': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:83:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, *nlev); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function 'Vbuildstr': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:266:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, *nlev); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function 'Vbuildcopy0': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fcf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:628:5: note: in expansion of macro 'MAT3' MAT3( fcf, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_ccf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:627:5: note: in expansion of macro 'MAT3' MAT3( ccf, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_tcf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:626:5: note: in expansion of macro 'MAT3' MAT3( tcf, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a3cf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:625:5: note: in expansion of macro 'MAT3' MAT3(a3cf, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a2cf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:624:5: note: in expansion of macro 'MAT3' MAT3(a2cf, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a1cf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:623:5: note: in expansion of macro 'MAT3' MAT3(a1cf, *nxf, *nyf, *nzf); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gzcf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:622:5: note: in expansion of macro 'MAT3' MAT3(gzcf, *nxf, *nyf, 4); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gycf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:621:5: note: in expansion of macro 'MAT3' MAT3(gycf, *nxf, *nzf, 4); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gxcf' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:620:5: note: in expansion of macro 'MAT3' MAT3(gxcf, *nyf, *nzf, 4); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_tc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:619:5: note: in expansion of macro 'MAT3' MAT3( tc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_fc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:618:5: note: in expansion of macro 'MAT3' MAT3( fc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_cc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:617:5: note: in expansion of macro 'MAT3' MAT3( cc, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a3c' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:616:5: note: in expansion of macro 'MAT3' MAT3( a3c, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a2c' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:615:5: note: in expansion of macro 'MAT3' MAT3( a2c, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_a1c' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:614:5: note: in expansion of macro 'MAT3' MAT3( a1c, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gzc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:613:5: note: in expansion of macro 'MAT3' MAT3( gzc, *nx, *ny, 4); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gyc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:612:5: note: in expansion of macro 'MAT3' MAT3( gyc, *nx, *nz, 4); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gxc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:611:5: note: in expansion of macro 'MAT3' MAT3( gxc, *ny, *nz, 4); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c: In function 'Vbuildalg': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgsubd.c:914:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, *nlev); ^~~~ [ 41%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mikpckd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxcopy': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:60:5: note: in expansion of macro 'MAT3' MAT3(y, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:59:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxcopy_small': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:78:5: note: in expansion of macro 'MAT3' MAT3(y, *nx - 2, *ny - 2, *nz - 2); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:77:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxcopy_large': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:99:5: note: in expansion of macro 'MAT3' MAT3(y, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:98:5: note: in expansion of macro 'MAT3' MAT3(x, *nx - 2, *ny - 2, *nz - 2); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxaxpy': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:117:5: note: in expansion of macro 'MAT3' MAT3(y, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:116:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxnrm1': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:136:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxnrm2': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:157:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxdot': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_y' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:182:5: note: in expansion of macro 'MAT3' MAT3(y, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:181:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vazeros': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:198:9: warning: unused variable 'nproc' [-Wunused-variable] int nproc = 1; ^~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'VfboundPMG': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gzc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:218:5: note: in expansion of macro 'MAT3' MAT3(gzc, *nx, *ny, 2); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gyc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:217:5: note: in expansion of macro 'MAT3' MAT3(gyc, *nx, *nz, 2); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_gxc' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:216:5: note: in expansion of macro 'MAT3' MAT3(gxc, *ny, *nz, 2); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:215:5: note: in expansion of macro 'MAT3' MAT3( x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'VfboundPMG00': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:262:5: note: in expansion of macro 'MAT3' MAT3( x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vaxrand': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:295:12: warning: variable 'xdum' set but not used [-Wunused-but-set-variable] double xdum; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:293:33: warning: variable 'iflag' set but not used [-Wunused-but-set-variable] int n, i, ii, ipara, ivect, iflag; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:293:26: warning: variable 'ivect' set but not used [-Wunused-but-set-variable] int n, i, ii, ipara, ivect, iflag; ^~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.h:58, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vxscal': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_x' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:322:5: note: in expansion of macro 'MAT3' MAT3(x, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vprtmatd': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_ac' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:337:5: note: in expansion of macro 'MAT2' MAT2(ac, *nx * *ny * *nz, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vprtmatd7': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:370:5: note: in expansion of macro 'MAT3' MAT3(uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:369:5: note: in expansion of macro 'MAT3' MAT3(oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:368:5: note: in expansion of macro 'MAT3' MAT3(oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:367:5: note: in expansion of macro 'MAT3' MAT3(oC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c: In function 'Vprtmatd27': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:415:5: note: in expansion of macro 'MAT3' MAT3(uSW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uSE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:414:5: note: in expansion of macro 'MAT3' MAT3(uSE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:413:5: note: in expansion of macro 'MAT3' MAT3(uNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:412:5: note: in expansion of macro 'MAT3' MAT3(uNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uS' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:411:5: note: in expansion of macro 'MAT3' MAT3( uS, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:410:5: note: in expansion of macro 'MAT3' MAT3( uN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:409:5: note: in expansion of macro 'MAT3' MAT3( uW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:408:5: note: in expansion of macro 'MAT3' MAT3( uE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNW' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:407:5: note: in expansion of macro 'MAT3' MAT3(oNW, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oNE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:406:5: note: in expansion of macro 'MAT3' MAT3(oNE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_uC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:405:5: note: in expansion of macro 'MAT3' MAT3( uC, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oN' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:404:5: note: in expansion of macro 'MAT3' MAT3( oN, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oE' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:403:5: note: in expansion of macro 'MAT3' MAT3( oE, *nx, *ny, *nz); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_oC' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mikpckd.c:402:5: note: in expansion of macro 'MAT3' MAT3( oC, *nx, *ny, *nz); ^~~~ [ 42%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mlinpckd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c: In function 'Vdpbsl': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_abd' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:62:5: note: in expansion of macro 'MAT2' MAT2(abd, *lda, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c: In function 'Vdpbfa': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_abd' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mlinpckd.c:199:5: note: in expansion of macro 'MAT2' MAT2(abd, *lda, 1); ^~~~ [ 43%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mypdec.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vmypdefinitsmpbe': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:96:9: warning: unused variable 'i' [-Wunused-variable] int i; ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vc_vecsmpbe': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:26: warning: variable 'ivect' set but not used [-Wunused-but-set-variable] int n, i, ii, ipara, ivect; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:19: warning: variable 'ipara' set but not used [-Wunused-but-set-variable] int n, i, ii, ipara, ivect; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:223:15: warning: unused variable 'ii' [-Wunused-variable] int n, i, ii, ipara, ivect; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:222:9: warning: unused variable 'iion' [-Wunused-variable] int iion; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:28: warning: unused variable 'fact' [-Wunused-variable] double argument, poly, fact; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:22: warning: unused variable 'poly' [-Wunused-variable] double argument, poly, fact; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:219:12: warning: unused variable 'argument' [-Wunused-variable] double argument, poly, fact; ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:218:29: warning: unused variable 'am_pos' [-Wunused-variable] double am_zero, am_neg, am_pos; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:218:21: warning: unused variable 'am_neg' [-Wunused-variable] double am_zero, am_neg, am_pos; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:217:18: warning: unused variable 'zu2' [-Wunused-variable] double zcf2, zu2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:217:12: warning: unused variable 'zcf2' [-Wunused-variable] double zcf2, zu2; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:216:9: warning: unused variable 'ideg' [-Wunused-variable] int ideg; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vdc_vec': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:345:9: warning: unused variable 'n' [-Wunused-variable] int n = *nx * *ny * *nz; ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:344:9: warning: unused variable 'i' [-Wunused-variable] int i; ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vdc_vecpmg': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:360:28: warning: unused variable 'fact' [-Wunused-variable] double argument, poly, fact; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:360:22: warning: unused variable 'poly' [-Wunused-variable] double argument, poly, fact; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:357:9: warning: unused variable 'ideg' [-Wunused-variable] int ideg, iion; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c: In function 'Vdc_vecsmpbe': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:433:16: warning: variable 'ivect' set but not used [-Wunused-but-set-variable] int ipara, ivect; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:433:9: warning: variable 'ipara' set but not used [-Wunused-but-set-variable] int ipara, ivect; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:432:15: warning: unused variable 'ii' [-Wunused-variable] int n, i, ii; ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:28: warning: unused variable 'fact' [-Wunused-variable] double argument, poly, fact; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:22: warning: unused variable 'poly' [-Wunused-variable] double argument, poly, fact; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:429:12: warning: unused variable 'argument' [-Wunused-variable] double argument, poly, fact; ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:428:29: warning: unused variable 'am_pos' [-Wunused-variable] double am_zero, am_neg, am_pos; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:428:21: warning: unused variable 'am_neg' [-Wunused-variable] double am_zero, am_neg, am_pos; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:427:18: warning: unused variable 'zu2' [-Wunused-variable] double zcf2, zu2; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:427:12: warning: unused variable 'zcf2' [-Wunused-variable] double zcf2, zu2; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:426:15: warning: unused variable 'iion' [-Wunused-variable] int ideg, iion; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mypdec.c:426:9: warning: unused variable 'ideg' [-Wunused-variable] int ideg, iion; ^~~~ [ 44%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newtond.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:56: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function 'Vfnewton': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:77:5: note: in expansion of macro 'MAT2' MAT2( iz, 50, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function 'Vnewton': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:187:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c: In function 'Vgetjac': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newtond.c:560:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, 1); ^~~~ [ 45%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/newdrvd.c.o /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c: In function 'Vnewdriv': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:86:9: warning: unused variable 'maxlev' [-Wunused-variable] int maxlev; /// @todo: Doc ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:85:9: warning: unused variable 'ierror' [-Wunused-variable] int ierror; /// @todo: Doc ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c: In function 'Vnewdriv2': /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:223:9: warning: unused variable 'i' [-Wunused-variable] int i; ^ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:221:12: warning: unused variable 'orsnrm_t' [-Wunused-variable] double orsnrm_t; ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:220:12: warning: unused variable 'rsden_t' [-Wunused-variable] double rsden_t; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:219:12: warning: unused variable 'rsnrm_t' [-Wunused-variable] double rsnrm_t; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:218:9: warning: unused variable 'iters_t' [-Wunused-variable] int iters_t; ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:217:9: warning: unused variable 'iok_t' [-Wunused-variable] int iok_t; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:215:9: warning: unused variable 'numlev' [-Wunused-variable] int numlev; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:210:12: warning: unused variable 'tsolve' [-Wunused-variable] double tsolve; /// @todo: Doc ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:209:12: warning: unused variable 'tsetupc' [-Wunused-variable] double tsetupc; /// @todo: Doc ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:208:12: warning: unused variable 'tsetupf' [-Wunused-variable] double tsetupf; /// @todo: Doc ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:207:12: warning: unused variable 'oh' [-Wunused-variable] double oh; /// @todo: Doc ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:206:12: warning: unused variable 'bf' [-Wunused-variable] double bf; /// @todo: Doc ^~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:204:12: warning: variable 'omegal' set but not used [-Wunused-but-set-variable] double omegal; /// @todo: Doc ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/newdrvd.c:202:12: warning: unused variable 'epsmac' [-Wunused-variable] double epsmac; /// @todo: Doc ^~~~~~ [ 47%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/powerd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function 'Vpower': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:74:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:71:9: warning: unused variable 'skipIters' [-Wunused-variable] int skipIters = 0; ^~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function 'Vipower': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:188:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, 1); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c: In function 'Vmpower': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/powerd.c:311:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, 1); ^~~~ [ 48%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/smoothd.c.o [ 49%] Building C object src/pmgc/CMakeFiles/apbs_pmgc.dir/mgfasd.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c: In function 'Vfmvfas': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:79:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, *nlev); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:74:12: warning: variable 'errd' set but not used [-Wunused-but-set-variable] double errd; ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/smoothd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.h:57, from /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:55: /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c: In function 'Vmvfas': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:66:9: warning: unused variable 'dy_iz' [-Wunused-variable] int dy_##mat = dy ^~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:182:5: note: in expansion of macro 'MAT2' MAT2(iz, 50, *nlev); ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:171:33: warning: unused variable 'ivariv' [-Wunused-variable] int itmax_s, iters_s, nuuu, ivariv, mgsmoo_s, iresid; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:359:13: warning: 'rsnrm' may be used uninitialized in this function [-Wmaybe-uninitialized] Vprtstp(*iok, *iters, rsnrm, rsden, orsnrm); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/pmgc/mgfasd.c:597:24: warning: 'rsden' may be used uninitialized in this function [-Wmaybe-uninitialized] if ((rsnrm / rsden) <= *errtol) ~~~~~~~^~~~~~~~ make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 49%] Built target apbs_pmgc make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 50%] Linking C shared library ../lib/libapbs.so make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 50%] Built target apbs make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 51%] Building C object src/CMakeFiles/apbs-bin.dir/main.c.o /builddir/build/BUILD/apbs-3.0.0/src/main.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/src/main.c:117:11: warning: unused variable 'gm' [-Wunused-variable] void *gm[NOSH_MAXMOL]; ^~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:116:11: warning: variable 'fetk' set but not used [-Wunused-but-set-variable] void *fetk[NOSH_MAXCALC]; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:96:18: warning: unused variable 'geoflowparm' [-Wunused-variable] GEOFLOWparm *geoflowparm = VNULL; ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:92:14: warning: unused variable 'feparm' [-Wunused-variable] FEMparm *feparm = VNULL; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/main.c:86:17: warning: unused variable 'te' [-Wunused-variable] clock_t ts, te; ^~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/main.c:70: /builddir/build/BUILD/apbs-3.0.0/src/main.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/main.c:70: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/main.c:70: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/main.c:70: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 52%] Building C object src/CMakeFiles/apbs-bin.dir/routines.c.o /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'loadDielMaps': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:296:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (ii=0; ii<(nx*ny*nz); ii++) ^~~ /builddir/build/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' sum = sum*hx*hy*hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:331:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (ii=0; ii<(nx*ny*nz); ii++) ^~~ /builddir/build/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' sum = sum*hx*hy*hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:420:17: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (ii=0; ii<(nx*ny*nz); ii++) ^~~ /builddir/build/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' sum = sum*hx*hy*hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:454:9: warning: this 'for' clause does not guard... [-Wmisleading-indentation] for (ii=0; ii<(nx*ny*nz); ii++) ^~~ /builddir/build/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' sum = sum*hx*hy*hzed; ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1234:12: warning: variable 'iparm' set but not used [-Wunused-but-set-variable] iparm, ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'energyMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1584:13: warning: variable 'mgparm' set but not used [-Wunused-but-set-variable] MGparm *mgparm; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1803:10: warning: variable 'mxtype' set but not used [-Wunused-but-set-variable] char mxtype[3]; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printApolForce': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3485:12: warning: variable 'scalar' set but not used [-Wunused-but-set-variable] scalar, ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:3484:12: warning: variable 'temp' set but not used [-Wunused-but-set-variable] double temp, ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'initAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4496:12: warning: variable 'sav' set but not used [-Wunused-but-set-variable] sav, /**< @todo document */ ^~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4495:12: warning: variable 'sasa' set but not used [-Wunused-but-set-variable] double sasa, /**< @todo document */ ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4489:12: warning: unused variable 'ts' [-Wunused-variable] time_t ts; /**< Temporary timing variable for debugging (PCE) */ ^~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'forceAPOL': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4753:13: warning: unused variable 'apos' [-Wunused-variable] *apos; ^~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c:4737:46: warning: unused variable 'ts_sub' [-Wunused-variable] time_t ts, ts_main, ts_sub; ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/routines.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writematMG': /builddir/build/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=] sprintf(writematstem, "%s-PE%d", pbeparm->writematstem,nosh->proc_rank); ^~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1038 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writematstem, "mat"); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataFlat': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:1906:44: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] double conversion, ltenergy, gtenergy, scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataXML': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2140:44: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] double conversion, ltenergy, gtenergy, scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'writedataMG': /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "dxbin"); ^~ ~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "txt"); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "dx.gz"); ^~ ~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 7 and 1030 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "mcsf"); ^~ ~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 6 and 1029 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "ucd"); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "grd"); ^~ ~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 5 and 1028 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/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=] sprintf(outpath, "%s.%s", writestem, "dx"); ^~ ~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/src/routines.c:54: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 4 and 1027 bytes into a destination of size 1024 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'returnEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2762:12: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2795:12: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printElecEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2863:12: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/routines.c: In function 'printApolEnergy': /builddir/build/BUILD/apbs-3.0.0/src/routines.c:2970:29: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] gtenergy += (scalar * ((apolparm->gamma*apolparm->sasa) + ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (apolparm->press*apolparm->sav) + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ (apolparm->wcaEnergy))); ~~~~~~~~~~~~~~~~~~~~~~~ [ 54%] Linking C executable ../bin/apbs make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 54%] Built target apbs-bin make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 55%] Building C object tools/mesh/CMakeFiles/value.dir/value.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:37:9: warning: unused variable 'inorm' [-Wunused-variable] int inorm; ^~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:8: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/value.c:8: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 56%] Linking C executable ../bin/value make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 56%] Built target value make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 57%] Building C object tools/mesh/CMakeFiles/mgmesh.dir/mgmesh.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mgmesh.c:10: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mgmesh.c:10: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mgmesh.c:10: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mgmesh.c:10: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 58%] Linking C executable ../bin/mgmesh make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 58%] Built target mgmesh make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 60%] Building C object tools/mesh/CMakeFiles/dxmath.dir/dxmath.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:41:10: warning: unused variable 'format' [-Wunused-variable] char format[VMAX_BUFSIZE]; ^~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:13: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dxmath.c:13: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 61%] Linking C executable ../bin/dxmath make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 61%] Built target dxmath make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 62%] Building C object tools/mesh/CMakeFiles/mergedx.dir/mergedx.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:8: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: 'nz' may be used uninitialized in this function [-Wmaybe-uninitialized] 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/tools/mesh/mergedx.c:81:13: warning: 'ny' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx.c:81:13: warning: 'nx' may be used uninitialized in this function [-Wmaybe-uninitialized] [ 63%] Linking C executable ../bin/mergedx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 63%] Built target mergedx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 64%] Building C object tools/mesh/CMakeFiles/smooth.dir/smooth.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:13: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/smooth.c:163:8: warning: 'format' may be used uninitialized in this function [-Wmaybe-uninitialized] if (format == VDF_DX) { ^ [ 65%] Linking C executable ../bin/smooth make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 65%] Built target smooth make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 67%] Building C object tools/mesh/CMakeFiles/similarity.dir/similarity.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:13: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:13: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/similarity.c:422:10: warning: 'format' may be used uninitialized in this function [-Wmaybe-uninitialized] if (!readGrid(&scalar1, scalar1Path, format)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 68%] Linking C executable ../bin/similarity make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 68%] Built target similarity make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 69%] Building C object tools/mesh/CMakeFiles/multivalue.dir/multivalue.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/multivalue.c:46: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/multivalue.c:46: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/multivalue.c:46: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/multivalue.c:46: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 70%] Linking C executable ../bin/multivalue make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 70%] Built target multivalue make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 71%] Building C object tools/mesh/CMakeFiles/benchmark.dir/benchmark.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:28:12: warning: unused variable 'grid' [-Wunused-variable] Vgrid *grid; ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:58: warning: unused variable 'sum' [-Wunused-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:51: warning: unused variable 'value' [-Wunused-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:44: warning: unused variable 'pt' [-Wunused-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:38: warning: variable 'zmin' set but not used [-Wunused-but-set-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:32: warning: variable 'ymin' set but not used [-Wunused-but-set-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:26: warning: variable 'xmin' set but not used [-Wunused-but-set-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:20: warning: variable 'hzed' set but not used [-Wunused-but-set-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:16: warning: variable 'hx' set but not used [-Wunused-but-set-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:18:12: warning: variable 'hy' set but not used [-Wunused-but-set-variable] double hy, hx, hzed, xmin, ymin, zmin, pt[3], value, sum, dtmp; ^~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:27: warning: unused variable 'k' [-Wunused-variable] int nx, ny, nz, i, j, k, itmp; ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:24: warning: unused variable 'j' [-Wunused-variable] int nx, ny, nz, i, j, k, itmp; ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:17:21: warning: unused variable 'i' [-Wunused-variable] int nx, ny, nz, i, j, k, itmp; ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:8: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/benchmark.c:8: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 72%] Linking C executable ../bin/benchmark make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 72%] Built target benchmark make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 74%] Building C object tools/mesh/CMakeFiles/uhbd_asc2bin.dir/uhbd_asc2bin.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:3: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/src/generic/vmatrix.h:79:9: warning: unused variable 'dz_grid' [-Wunused-variable] int dz_##mat = dz ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:24:5: note: in expansion of macro 'MAT3' MAT3(grid, MXGRD, MXGRD, MXGRD); ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:3: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:3: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:3: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c:3: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/uhbd_asc2bin.c: In function 'main': /builddir/build/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] scanf("%s", flnm); ^~~~~~~~~~~~~~~~~ /builddir/build/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] scanf("%s", newfile); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%s", title); ^~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &scale); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &dum2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &grdflg); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &idum2); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &km); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &one); ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &km); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &im); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &jm); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &km); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &h); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &ox); ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &oy); ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &oz); ^~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &dum3); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &dum4); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &dum5); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &dum6); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &dum7); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", &dum8); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &idum3); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &idum4); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &kk); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &im); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%d", &jm); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/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] fscanf(inFile, "%lf", RAT3(grid, i, j, k)); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Linking C executable ../bin/uhbd_asc2bin make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 75%] Built target uhbd_asc2bin make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 76%] Building C object tools/mesh/CMakeFiles/analysis.dir/analysis.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:14: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: 'minG2pt[2]' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Min gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ minG2pt[0], minG2pt[1], minG2pt[2]); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: 'minG2pt[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:292:5: warning: 'minG2pt[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: 'minSpt[2]' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ minSpt[0], minSpt[1], minSpt[2]); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: 'maxG2pt[2]' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Max gradient-squared value location = (%4.3f, %4.3f, %4.3f)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ maxG2pt[0], maxG2pt[1], maxG2pt[2]); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: 'maxG2pt[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:288:5: warning: 'maxG2pt[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: 'maxSpt[2]' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ maxSpt[0], maxSpt[1], maxSpt[2]); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: 'maxSpt[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: 'minSpt[1]' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Min scalar value location = (%4.3f, %4.3f, %4.3f)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ minSpt[0], minSpt[1], minSpt[2]); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:284:5: warning: 'minSpt[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:290:5: warning: 'minG2' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Min gradient-squared value = %1.12E\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ minG2); ~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:286:5: warning: 'maxG2' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Max gradient-squared value = %1.12E\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ maxG2); ~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:278:5: warning: 'maxS' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Max scalar value = %1.12E\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ maxS); ~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:280:5: warning: 'maxSpt[0]' may be used uninitialized in this function [-Wmaybe-uninitialized] Vnm_print(1, "Max scalar value location = (%4.3f, %4.3f, %4.3f)\n", ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ maxSpt[0], maxSpt[1], maxSpt[2]); ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/analysis.c:182:14: warning: 'format' may be used uninitialized in this function [-Wmaybe-uninitialized] if (!readGrid(&mask, maskPath, format)) { ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 77%] Linking C executable ../bin/analysis make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 77%] Built target analysis make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 78%] Building C object tools/mesh/CMakeFiles/dx2mol.dir/dx2mol.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:28:12: warning: unused variable 'avg' [-Wunused-variable] double avg; ^~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:19: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:19: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:19: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2mol.c:19: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 80%] Linking C executable ../bin/dx2mol make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 80%] Built target dx2mol make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 81%] Building C object tools/mesh/CMakeFiles/mergedx2.dir/mergedx2.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx2.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx2.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx2.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/mergedx2.c:8: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 82%] Linking C executable ../bin/mergedx2 make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 82%] Built target mergedx2 make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 83%] Building C object tools/mesh/CMakeFiles/dx2uhbd.dir/dx2uhbd.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:25:10: warning: unused variable 'avg' [-Wunused-variable] double avg; ^~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:19: warning: unused variable 'k' [-Wunused-variable] size_t u, i, j, k, nx, ny, nz; ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:16: warning: unused variable 'j' [-Wunused-variable] size_t u, i, j, k, nx, ny, nz; ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:13: warning: unused variable 'i' [-Wunused-variable] size_t u, i, j, k, nx, ny, nz; ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:24:10: warning: unused variable 'u' [-Wunused-variable] size_t u, i, j, k, nx, ny, nz; ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:17: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:17: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:17: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/dx2uhbd.c:17: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 84%] Linking C executable ../bin/dx2uhbd make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 84%] Built target dx2uhbd make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 85%] Building C object tools/mesh/CMakeFiles/del2dx.dir/del2dx.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:57: warning: variable 'extent' set but not used [-Wunused-but-set-variable] float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:43: warning: unused variable 'xdata' [-Wunused-variable] float val, xmax, scale, oldmid[3], temp, xdata, range, extent, origin[3], delta[3]; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:45:8: warning: unused variable 'val' [-Wunused-variable] 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/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:16: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:16: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:16: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:16: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:76:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&igrid, 1, sizeof(int), pfile); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:89:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(buffer, 1, sizeof(char) * 10, pfile); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:97:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(data, tot_grid, sizeof(float), pfile); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:103:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(&scale, 1, sizeof(float), pfile); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/del2dx.c:106:2: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result] fread(oldmid, 3, sizeof(float), pfile); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Linking C executable ../bin/del2dx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 87%] Built target del2dx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 88%] Building C object tools/mesh/CMakeFiles/tensor2dx.dir/tensor2dx.c.o /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:12: warning: unused variable 'index' [-Wunused-variable] int i,j,k,index,icol; ^~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:10: warning: unused variable 'k' [-Wunused-variable] int i,j,k,index,icol; ^ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:42:8: warning: unused variable 'j' [-Wunused-variable] int i,j,k,index,icol; ^ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:14: /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:14: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:14: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:97:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile1,"%lf %lf %lf",&origin_xyz[0],&origin_xyz[1],&origin_xyz[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:98:2: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile1,"%lf %lf %lf",&gspace[0],&gspace[1],&gspace[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:137:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:138:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:139:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:140:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:155:7: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile2,"%i %i %i",&itmp[0],&itmp[1],&itmp[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:156:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile2,"%lf %lf %lf",&datapt[0],&tmp[1],&tmp[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:157:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile2,"%lf %lf %lf",&tmp[0],&datapt[1],&tmp[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/tools/mesh/tensor2dx.c:158:3: warning: ignoring return value of 'fscanf', declared with attribute warn_unused_result [-Wunused-result] fscanf(pfile2,"%lf %lf %lf",&tmp[0],&tmp[1],&datapt[2]); ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 89%] Linking C executable ../bin/tensor2dx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 89%] Built target tensor2dx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 90%] Building C object tools/manip/CMakeFiles/born.dir/born.c.o In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/born.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/born.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/born.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/born.c:8: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 91%] Linking C executable ../bin/born make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 91%] Built target born make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 92%] Building C object tools/manip/CMakeFiles/coulomb.dir/coulomb.c.o /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c: In function 'main': /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:20:12: warning: unused variable 'j' [-Wunused-variable] int i, j; ^ /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:18:34: warning: unused variable 'disp' [-Wunused-variable] double *pos, energy, zmagic, disp[3], force[3]; ^~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:8: /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:8: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/tools/manip/coulomb.c:8: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 94%] Linking C executable ../bin/coulomb make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 94%] Built target coulomb make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Scanning dependencies of target apbslib_swig_compilation make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 95%] Swig compile apbslib.i for python make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 95%] Built target apbslib_swig_compilation make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 96%] Building C object tools/python/CMakeFiles/_apbslib.dir/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c.o /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: In function 'getPotentials': /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3601:12: warning: unused variable 'rc' [-Wunused-variable] int i, rc, nx, ny, nz; ^~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: In function 'getForces': /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3655:31: warning: unused variable 'npholder' [-Wunused-variable] PyObject *npvalues, *np, *npholder; ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3655:26: warning: unused variable 'np' [-Wunused-variable] PyObject *npvalues, *np, *npholder; ^~ /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3655:15: warning: unused variable 'npvalues' [-Wunused-variable] PyObject *npvalues, *np, *npholder; ^~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3048: /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3048: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3048: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/src/routines.h:64, from /builddir/build/BUILD/apbs-3.0.0/build/tools/python/CMakeFiles/_apbslib.dir/apbslibPYTHON_wrap.c:3048: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ [ 97%] Linking C shared library ../../lib/_apbslib.so make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 97%] Built target _apbslib make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 98%] Building C object contrib/iapbs/src/CMakeFiles/iapbs.dir/apbs_driver.c.o /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'apbsdrv_': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:278:5: warning: multi-line comment [-Wcomment] // Vnm_print(1,"\nError you must provide a parameter file if you\n" \ ^ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:110:21: warning: unused variable 'isolve' [-Wunused-variable] int rank, size, isolve, debug, natom; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:98:11: warning: unused variable 'gm' [-Wunused-variable] void *gm[NOSH_MAXMOL]; ^~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:97:11: warning: variable 'fetk' set but not used [-Wunused-but-set-variable] void *fetk[NOSH_MAXCALC]; ^~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:85:14: warning: unused variable 'feparm' [-Wunused-variable] FEMparm *feparm = VNULL; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'setupString': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:938:64: warning: implicit declaration of function 'getpid'; did you mean 'getenv'? [-Wimplicit-function-declaration] sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); ^~~~~~ getenv /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:938:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict] sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); ^~~~~~ ~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:77, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:11: /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: At top level: /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:169:20: warning: 'GEOFLOWparm_parseVDW' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseVDW(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/geoflowparm.h:171:20: warning: 'GEOFLOWparm_parseETOL' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes GEOFLOWparm_parseETOL(GEOFLOWparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:78, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:11: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:251:20: warning: 'PBAMparm_parseSalt' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:260:20: warning: 'PBAMparm_parseRunType' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:269:20: warning: 'PBAMparm_parseRunName' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:278:20: warning: 'PBAMparm_parseRandorient' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:287:20: warning: 'PBAMparm_parsePBCS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:296:20: warning: 'PBAMparm_parseUnits' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:305:20: warning: 'PBAMparm_parse3Dmap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:314:20: warning: 'PBAMparm_parseGrid2D' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:323:20: warning: 'PBAMparm_parseDX' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:332:20: warning: 'PBAMparm_parseGridPts' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:341:20: warning: 'PBAMparm_parseTermcombine' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:350:20: warning: 'PBAMparm_parseDiff' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbamparm.h:359:20: warning: 'PBAMparm_parseXYZ' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/generic/nosh.h:79, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:70, from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:11: /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:199:20: warning: 'PBSAMparm_parseTolsp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseTolsp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:208:20: warning: 'PBSAMparm_parseSurf' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseSurf(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:217:20: warning: 'PBSAMparm_parseImat' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseImat(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:226:20: warning: 'PBSAMparm_parseExp' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseExp(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/generic/pbsamparm.h:235:20: warning: 'PBSAMparm_parseMSMS' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes PBSAMparm_parseMSMS(PBSAMparm *thee, Vio *sock); ^~~~~~~~~~~~~~~~~~~ In file included from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:93, from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:11: /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:811:15: warning: 'bcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:834:15: warning: 'bcolcomp2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:863:15: warning: 'bcolcomp3' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp3( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:885:15: warning: 'bcolcomp4' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcolcomp4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:910:15: warning: 'pcolcomp' declared 'static' but never defined [-Wunused-function] VPRIVATE void pcolcomp( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:933:17: warning: 'bspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline2( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:942:17: warning: 'dbspline2' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline2( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:951:17: warning: 'VFCHI4' declared 'static' but never defined [-Wunused-function] VPRIVATE double VFCHI4( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:961:17: warning: 'bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double bspline4( ^~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:970:17: warning: 'dbspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double dbspline4( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:979:17: warning: 'd2bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d2bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:988:17: warning: 'd3bspline4' declared 'static' but never defined [-Wunused-function] VPRIVATE double d3bspline4( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:998:17: warning: 'Vpmg_polarizEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_polarizEnergy( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1009:17: warning: 'Vpmg_qfEnergyPoint' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyPoint( ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1020:17: warning: 'Vpmg_qfEnergyVolume' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qfEnergyVolume( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1031:15: warning: 'Vpmg_splineSelect' declared 'static' but never defined [-Wunused-function] VPRIVATE void Vpmg_splineSelect( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1047:15: warning: 'focusFillBound' declared 'static' but never defined [-Wunused-function] VPRIVATE void focusFillBound( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1058:15: warning: 'bcfl1' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl1( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1080:15: warning: 'bcfl2' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcfl2( ^~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1109:15: warning: 'multipolebc' declared 'static' but never defined [-Wunused-function] VPRIVATE void multipolebc( ^~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1126:17: warning: 'bcfl1sp' declared 'static' but never defined [-Wunused-function] VPRIVATE double bcfl1sp( ^~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1139:15: warning: 'bcCalc' declared 'static' but never defined [-Wunused-function] VPRIVATE void bcCalc( ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1147:15: warning: 'fillcoCoef' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoef( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1155:15: warning: 'fillcoCoefMap' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMap( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1164:15: warning: 'fillcoCoefMol' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMol( ^~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1173:15: warning: 'fillcoCoefMolIon' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolIon( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1182:15: warning: 'fillcoCoefMolDiel' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDiel( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1191:15: warning: 'fillcoCoefMolDielNoSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielNoSmooth( ^~~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1208:15: warning: 'fillcoCoefMolDielSmooth' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefMolDielSmooth( ^~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1217:15: warning: 'fillcoCoefSpline' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline( ^~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1226:15: warning: 'fillcoCoefSpline3' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline3( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1235:15: warning: 'fillcoCoefSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoCoefSpline4( ^~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1244:20: warning: 'fillcoCharge' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoCharge( ^~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1253:20: warning: 'fillcoChargeMap' declared 'static' but never defined [-Wunused-function] VPRIVATE Vrc_Codes fillcoChargeMap( ^~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1261:15: warning: 'fillcoChargeSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline1( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1269:15: warning: 'fillcoChargeSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoChargeSpline2( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1277:15: warning: 'fillcoPermanentMultipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoPermanentMultipole( ^~~~~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1285:15: warning: 'fillcoInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoInducedDipole( ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1294:15: warning: 'fillcoNLInducedDipole' declared 'static' but never defined [-Wunused-function] VPRIVATE void fillcoNLInducedDipole( ^~~~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1304:15: warning: 'extEnergy' declared 'static' but never defined [-Wunused-function] VPRIVATE void extEnergy( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1317:15: warning: 'qfForceSpline1' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline1( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1327:15: warning: 'qfForceSpline2' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline2( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1337:15: warning: 'qfForceSpline4' declared 'static' but never defined [-Wunused-function] VPRIVATE void qfForceSpline4( ^~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1351:15: warning: 'zlapSolve' declared 'static' but never defined [-Wunused-function] VPRIVATE void zlapSolve( ^~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1364:15: warning: 'markSphere' declared 'static' but never defined [-Wunused-function] VPRIVATE void markSphere( ^~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1384:17: warning: 'Vpmg_qmEnergySMPBE' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergySMPBE(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/src/mg/vpmg.h:1385:17: warning: 'Vpmg_qmEnergyNONLIN' declared 'static' but never defined [-Wunused-function] VPRIVATE double Vpmg_qmEnergyNONLIN(Vpmg *thee, int extFlag); ^~~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'setupString': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:938:26: warning: 'write pot dx iapbs-pot-' directive writing 23 bytes into a region of size between 1 and 4096 [-Wformat-overflow=] sprintf(string, "%swrite pot dx iapbs-pot-%d\n", string, getpid()); ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:873, from /usr/include/maloc/maloc_base.h:80, from /usr/include/maloc/maloc.h:38, from /builddir/build/BUILD/apbs-3.0.0/src/apbs.h:67, from /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:11: /usr/include/bits/stdio2.h:36:10: note: '__builtin___sprintf_chk' output between 26 and 4131 bytes into a destination of size 4096 return __builtin___sprintf_chk (__s, __USE_FORTIFY_LEVEL - 1, ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __glibc_objsize (__s), __fmt, ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ __va_arg_pack ()); ~~~~~~~~~~~~~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'getElecEnergy': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:1038:32: warning: 'scalar' may be used uninitialized in this function [-Wmaybe-uninitialized] double ltenergy, gtenergy, scalar; ^~~~~~ /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c: In function 'apbsdrv_': /builddir/build/BUILD/apbs-3.0.0/contrib/iapbs/src/apbs_driver.c:549:42: warning: 'outputformat' may be used uninitialized in this function [-Wmaybe-uninitialized] if ((pbeparm->calcenergy == PCE_COMPS) && (outputformat != OUTPUT_NULL)){ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [100%] Linking C static library ../../../lib/libiapbs.a make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [100%] Built target iapbs make[1]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' make: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' + exit 0 Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.DzKBLJ + umask 022 + cd /builddir/build/BUILD + '[' /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 '!=' / ']' + rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 ++ dirname /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 + mkdir -p /builddir/build/BUILDROOT + mkdir /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 + cd apbs-3.0.0 + /usr/bin/make install DESTDIR=/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 'INSTALL=/usr/bin/install -p' -C build make: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[1]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs_routines make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 1%] Built target apbs_routines make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs_mg make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 7%] Built target apbs_mg make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs_generic make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 28%] Built target apbs_generic make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs_pmgc make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 49%] Built target apbs_pmgc make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 50%] Built target apbs make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target apbs-bin make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 54%] Built target apbs-bin make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target value make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 56%] Built target value make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target mgmesh make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 58%] Built target mgmesh make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target dxmath make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 61%] Built target dxmath make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target mergedx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 63%] Built target mergedx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target smooth make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 65%] Built target smooth make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target similarity make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 68%] Built target similarity make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target multivalue make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 70%] Built target multivalue make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target benchmark make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 72%] Built target benchmark make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target uhbd_asc2bin make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 75%] Built target uhbd_asc2bin make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target analysis make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 77%] Built target analysis make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target dx2mol make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 80%] Built target dx2mol make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target mergedx2 make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 82%] Built target mergedx2 make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target dx2uhbd make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 84%] Built target dx2uhbd make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target del2dx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 87%] Built target del2dx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target tensor2dx make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 89%] Built target tensor2dx make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target born make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 91%] Built target born make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target coulomb make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 94%] Built target coulomb make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 95%] Built target apbslib_swig_compilation make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target _apbslib make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [ 97%] Built target _apbslib make[2]: Entering directory '/builddir/build/BUILD/apbs-3.0.0/build' Consolidate compiler generated dependencies of target iapbs make[2]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' [100%] Built target iapbs make[1]: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' Install the project... -- Install configuration: "Release" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/coulomb -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/born -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/tensor2dx -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/del2dx -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/dx2uhbd -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/mergedx2 -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/dx2mol -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/analysis -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/uhbd_asc2bin -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/benchmark -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/multivalue -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/similarity -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/smooth -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/mergedx -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/dxmath -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/mgmesh -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs/tools/bin/value -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/libapbs.so.1 -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/libapbs.so.1" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/libapbs.so -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/apbscfg.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/apbs.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/routines.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/nosh.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/mgparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/femparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/pbamparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/pbsamparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/pbeparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/bemparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/geoflowparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/apolparm.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vacc.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/valist.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vatom.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vpbe.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vcap.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vclist.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vstring.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vparam.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vgreen.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vmatrix.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vhal.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/generic/vunit.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/buildAd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/buildBd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/buildGd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/buildPd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/cgd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/gsd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/matvecd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/mgcsd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/mgdrvd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/mgsubd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/mikpckd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/mlinpckd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/mypdec.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/newtond.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/newdrvd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/powerd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/smoothd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/pmgc/mgfasd.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/mg/vgrid.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/mg/vmgrid.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/mg/vopot.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/mg/vpmg.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/apbs/mg/vpmgp.h -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mgmesh -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mgmesh" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/smooth -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/smooth" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dxmath -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dxmath" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx2 -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx2" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/value -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/value" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/multivalue -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/multivalue" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/benchmark -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/benchmark" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/similarity -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/similarity" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/analysis -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/analysis" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2mol -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2mol" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2uhbd -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2uhbd" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/del2dx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/del2dx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/tensor2dx -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/tensor2dx" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/uhbd_asc2bin -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/uhbd_asc2bin" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/coulomb -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/coulomb" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/born -- Set runtime path of "/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/born" to "/usr/lib" -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib/libiapbs.a -- Installing: /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/include/iapbs/apbs_driver.h make: Leaving directory '/builddir/build/BUILD/apbs-3.0.0/build' + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/coulomb + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/coulomb /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-coulomb + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/coulomb + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/born + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/born /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-born + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/born + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mgmesh + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mgmesh /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mgmesh + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mgmesh + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dxmath + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dxmath /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dxmath + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dxmath + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx2 + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx2 /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mergedx2 + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx2 + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mergedx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/mergedx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/value + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/value /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-value + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/value + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/uhbd_asc2bin + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/uhbd_asc2bin /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-uhbd_asc2bin + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/uhbd_asc2bin + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/smooth + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/smooth /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-smooth + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/smooth + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2mol + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2mol /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dx2mol + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2mol + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2uhbd + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2uhbd /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dx2uhbd + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/dx2uhbd + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/similarity + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/similarity /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-similarity + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/similarity + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/multivalue + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/multivalue /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-multivalue + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/multivalue + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/benchmark + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/benchmark /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-benchmark + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/benchmark + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/analysis + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/analysis /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-analysis + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/analysis + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/del2dx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/del2dx /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-del2dx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/del2dx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/{coulomb,born,mgmesh,dxmath,mergedx2,mergedx,value,uhbd_asc2bin,smooth,dx2mol,dx2uhbd,similarity,multivalue,benchmark,analysis,del2dx,tensor2dx} ++ basename /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/tensor2dx + cp -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/tensor2dx /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-tensor2dx + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/tensor2dx + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-coulomb + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-born + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mgmesh + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dxmath + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mergedx2 + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mergedx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-value + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-uhbd_asc2bin + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-smooth + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dx2mol + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dx2uhbd + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-similarity + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-multivalue + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-benchmark + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-analysis + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-del2dx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + for bin in /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/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/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-tensor2dx + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs + chrpath -d /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/libapbs.so.1 + mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/python3.6/site-packages/apbs + install -pm 755 tools/manip/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/python3.6/site-packages/apbs/ + pathfix.py -pn -i /usr/bin/python3.6 /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/python3.6/site-packages/apbs/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/python3.6/site-packages/apbs/psize.py: updating + ln -s /usr/lib64/python3.6/site-packages/apbs/psize.py /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-psize.py + install -pm 755 build/lib/_apbslib.so /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/python3.6/site-packages/apbs/ + rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/apbs ++ find /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 -type f '(' -name '*.a' ')' + for i in `find /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 -type f \( -name "*.a" \)` + rm -f /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib/libiapbs.a + /usr/lib/rpm/find-debuginfo.sh -j2 --strict-build-id -m -i --build-id-seed 3.0.0-17.el8 --unique-debug-suffix -3.0.0-17.el8.x86_64 --unique-debug-src-base apbs-3.0.0-17.el8.x86_64 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 110000000 -S debugsourcefiles.list /builddir/build/BUILD/apbs-3.0.0 extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-analysis extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-benchmark extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-born extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-coulomb extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-del2dx extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dx2mol extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dx2uhbd extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-dxmath extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mergedx extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mergedx2 extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-mgmesh extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-multivalue extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-similarity extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-smooth extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-tensor2dx extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-uhbd_asc2bin extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/bin/apbs-value extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/libapbs.so.1 extracting debug info from /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/python3.6/site-packages/apbs/_apbslib.so /usr/lib/rpm/sepdebugcrcfix: Updated 20 CRC32s, 0 CRC32s did match. 5169 blocks + /usr/lib/rpm/check-buildroot + /usr/lib/rpm/redhat/brp-ldconfig /sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory + /usr/lib/rpm/brp-compress + /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip + /usr/lib/rpm/brp-python-bytecompile '' 1 Bytecompiling .py files below /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib/debug/usr/lib64/python3.6 using /usr/libexec/platform-python Bytecompiling .py files below /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64/python3.6 using /usr/libexec/platform-python + /usr/lib/rpm/brp-python-hardlink + PYTHON3=/usr/bin/python3.6 + /usr/lib/rpm/redhat/brp-mangle-shebangs Executing(%check): /bin/sh -e /var/tmp/rpm-tmp.vXsQmQ + umask 022 + cd /builddir/build/BUILD ~/build/BUILD/apbs-3.0.0/tests ~/build/BUILD/apbs-3.0.0 + cd apbs-3.0.0 + pushd tests + export LD_LIBRARY_PATH=/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64 + LD_LIBRARY_PATH=/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/lib64 + /usr/bin/python3.6 ./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: 0.001028 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-auto.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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: 0.779440 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-auto.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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: 0.730351 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE0.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE1.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE2.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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 = 8.142935605696E+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 8.142935605696E+02 1.485255306569E+03 2.977178707146E+02 8.799304557596E+02 1.542873949141E+03 -5.761864257239E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE3.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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) = -5.762728344954E+01 kJ/mol Global net ELEC energy = -5.762728344954E+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 -5.762728344954E+01 RESULT 960.7073836226 RESULT 3257.1427835731997 RESULT 5941.0039478710005 RESULT 1190.8714828309999 RESULT 3519.7218230368003 RESULT 6171.495796544 RESULT -230.49184867463003 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: 3.447477 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 4 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE0.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE1.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE2.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE3.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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: 3.439330 seconds -------------------------------------------------------------------------------- Total elapsed time: 8.397626 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for actin-dimer-auto section -------------------------------------------------------------------------------- Testing input file apbs-mol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-auto.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 1.048683058623E+02 kJ/mol Global net ELEC energy = 1.048683058623E+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 104.8683058623 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 1.048683058623E+02 against expected result 1.048683E+02 *** PASSED *** Elapsed time: 46.118844 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-auto.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-auto.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 1.095841077689E+02 kJ/mol Global net ELEC energy = 1.095841077689E+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 109.5841077689 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 1.095841077689E+02 against expected result 1.095841E+02 *** PASSED *** Elapsed time: 37.314026 seconds -------------------------------------------------------------------------------- Total elapsed time: 83.432870 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: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE0.in 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 Jan 30 2023 at 11:38:48 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. 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. 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 = 1.307364282738E+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 = 2.287357981689E+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! ---------------------------------------- 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 = 3.595556713401E+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) = 8.344489735013E+00 kJ/mol Global net ELEC energy = 8.344489735013E+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 1.307364282738E+04 2.892640552270E+03 2.287357981689E+04 4.237489755360E+03 3.595556713401E+04 8.344489735013E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE1.in 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 Jan 30 2023 at 11:38:48 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. 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. 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 = 9.271349239954E+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 = -9.159185455930E-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! ---------------------------------------- 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 = 9.271249973273E+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) = -9.010749548238E-01 kJ/mol Global net ELEC energy = -9.010749548238E-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 9.271349239954E+04 1.084559511557E-01 9.159185455930E-02 1.161009682231E+04 9.271249973273E+04 -9.010749548238E-01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE2.in 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 Jan 30 2023 at 11:38:48 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. 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. 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! ---------------------------------------- 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) = 3.002011083291E+01 kJ/mol Global net ELEC energy = 3.002011083291E+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 3.002011083291E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE3.in 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 Jan 30 2023 at 11:38:48 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. 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. 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! ---------------------------------------- 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) = 8.710240552211E+00 kJ/mol Global net ELEC energy = 8.710240552211E+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 8.710240552211E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE4.in 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 Jan 30 2023 at 11:38:48 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. 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. 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 = 3.216054441666E+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 = 1.273875050379E+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! ---------------------------------------- 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 = 1.306246439444E+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) = 2.108446480094E+01 kJ/mol Global net ELEC energy = 2.108446480094E+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 3.216054441666E+03 1.620207421716E+04 1.273875050379E+05 1.666622027749E+04 1.306246439444E+05 2.108446480094E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE5.in 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 Jan 30 2023 at 11:38:48 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. 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. 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 = 1.662571883858E+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 = -4.013366922344E-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! ---------------------------------------- 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 = 1.662768924081E+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) = 2.371738924682E+00 kJ/mol Global net ELEC energy = 2.371738924682E+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 1.662571883858E+04 4.370921758038E-01 4.013366922344E-01 2.115105077953E+03 1.662768924081E+04 2.371738924682E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE6.in 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 Jan 30 2023 at 11:38:48 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. 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. 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! ---------------------------------------- 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) = -1.892943480838E+00 kJ/mol Global net ELEC energy = -1.892943480838E+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 -1.892943480838E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-parallel-PE7.in 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 Jan 30 2023 at 11:38:48 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. 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. 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! ---------------------------------------- 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) = 3.043753521009E+01 kJ/mol Global net ELEC energy = 3.043753521009E+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 3.043753521009E+01 RESULT 35927.59777074854 RESULT 287991.6813140391 RESULT 36005.78432292607 RESULT 288019.58583029587 RESULT 72040.017332199 RESULT 576102.8221066899 RESULT 98.1745616201842 Testing computed result 3.592759777075E+04 against expected result 3.592760E+04 *** PASSED *** Testing computed result 2.879916813140E+05 against expected result 2.879917E+05 *** PASSED *** Testing computed result 3.600578432293E+04 against expected result 3.600578E+04 *** PASSED *** Testing computed result 2.880195858303E+05 against expected result 2.880196E+05 *** PASSED *** Testing computed result 7.204001733220E+04 against expected result 7.204002E+04 *** PASSED *** Testing computed result 5.761028221067E+05 against expected result 5.761028E+05 *** PASSED *** Testing computed result 9.817456162018E+01 against expected result 9.817456E+01 *** PASSED *** Elapsed time: 146.722927 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-parallel.in Splitting the input file into 8 separate files using the inputgen utility BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE0.in 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 Jan 30 2023 at 11:38:48 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. 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. 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 = 1.306912276054E+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 = 2.288057348250E+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! ---------------------------------------- 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 = 3.595842845220E+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) = 8.732209150883E+00 kJ/mol Global net ELEC energy = 8.732209150883E+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 1.306912276054E+04 2.977036667733E+03 2.288057348250E+04 4.356039288708E+03 3.595842845220E+04 8.732209150883E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE1.in 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 Jan 30 2023 at 11:38:48 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. 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. 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 = 9.276168507128E+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 = -1.129046670919E-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! ---------------------------------------- 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 = 9.276041697078E+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) = -1.155195837104E+00 kJ/mol Global net ELEC energy = -1.155195837104E+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 9.276168507128E+04 1.420924995464E-01 1.129046670919E-01 1.183791435221E+04 9.276041697078E+04 -1.155195837104E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE2.in 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 Jan 30 2023 at 11:38:48 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. 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. 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! ---------------------------------------- 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) = 3.228473728525E+01 kJ/mol Global net ELEC energy = 3.228473728525E+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 3.228473728525E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE3.in 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 Jan 30 2023 at 11:38:48 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. 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. 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! ---------------------------------------- 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) = 9.405155087999E+00 kJ/mol Global net ELEC energy = 9.405155087999E+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 9.405155087999E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE4.in 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 Jan 30 2023 at 11:38:48 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. 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. 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 = 3.215581388579E+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 = 1.274227930024E+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! ---------------------------------------- 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 = 1.306747503910E+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) = 3.637600005489E+01 kJ/mol Global net ELEC energy = 3.637600005489E+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 3.215581388579E+03 1.644646339930E+04 1.274227930024E+05 1.689865332202E+04 1.306747503910E+05 3.637600005489E+01 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE5.in 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 Jan 30 2023 at 11:38:48 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. 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. 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 = 1.663590032901E+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 = -4.849499127484E-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! ---------------------------------------- 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 = 1.663641996916E+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) = 1.004590063265E+00 kJ/mol Global net ELEC energy = 1.004590063265E+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 1.663590032901E+04 4.710032885061E-01 4.849499127484E-01 2.189033693728E+03 1.663641996916E+04 1.004590063265E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE6.in 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 Jan 30 2023 at 11:38:48 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. 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. 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! ---------------------------------------- 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) = -1.699465221463E+00 kJ/mol Global net ELEC energy = -1.699465221463E+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 -1.699465221463E+00 BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-parallel-PE7.in 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 Jan 30 2023 at 11:38:48 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. 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. 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! ---------------------------------------- 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 288124.794774701 RESULT 36694.74744055409 RESULT 288128.90380424313 RESULT 73413.59604699901 RESULT 576361.14712166 RESULT 115.54206772935 Testing computed result 3.660573843587E+04 against expected result 3.660574E+04 *** PASSED *** Testing computed result 2.881247947747E+05 against expected result 2.881248E+05 *** PASSED *** Testing computed result 3.669474744055E+04 against expected result 3.669475E+04 *** PASSED *** Testing computed result 2.881289038042E+05 against expected result 2.881289E+05 *** PASSED *** Testing computed result 7.341359604700E+04 against expected result 7.341360E+04 *** PASSED *** Testing computed result 5.763611471217E+05 against expected result 5.763611E+05 *** PASSED *** Testing computed result 1.155420677293E+02 against expected result 1.155421E+02 *** PASSED *** Elapsed time: 123.540816 seconds -------------------------------------------------------------------------------- Total elapsed time: 270.263743 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for alkanes section -------------------------------------------------------------------------------- Testing input file alkanes.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: alkanes.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 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 Jan 30 2023 at 11:38:48 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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: 14.217421 seconds -------------------------------------------------------------------------------- Total elapsed time: 14.217421 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for FKBP section -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7h-dmso-mol.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 1.500810086372E+01 kJ/mol Global net ELEC energy = 1.500810086372E+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 15.00810086372 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 1.500810086372E+01 against expected result 1.500810E+01 *** PASSED *** Elapsed time: 6.617214 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7h-dmso-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7h-dmso-smol.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 1.624454192072E+01 kJ/mol Global net ELEC energy = 1.624454192072E+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 16.24454192072 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 1.624454192072E+01 against expected result 1.624454E+01 *** PASSED *** Elapsed time: 6.346477 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7i-dss-mol.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 1.442499933668E+01 kJ/mol Global net ELEC energy = 1.442499933668E+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 14.42499933668 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 1.442499933668E+01 against expected result 1.442501E+01 *** PASSED *** Elapsed time: 6.548847 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file 1d7i-dss-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: 1d7i-dss-smol.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 1.545150742844E+01 kJ/mol Global net ELEC energy = 1.545150742844E+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 15.45150742844 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 1.545150742844E+01 against expected result 1.545150E+01 *** PASSED *** Elapsed time: 6.347613 seconds -------------------------------------------------------------------------------- Total elapsed time: 25.860151 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for hca-bind section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = -5.246475812665E+01 kJ/mol Global net ELEC energy = -5.246475812665E+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 -52.46475812665 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 -5.246475812665E+01 against expected result -5.246476E+01 *** PASSED *** Elapsed time: 4.968391 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = -5.405979017066E+01 kJ/mol Global net ELEC energy = -5.405979017066E+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 -54.05979017066 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 -5.405979017066E+01 against expected result -5.405978E+01 *** PASSED *** Elapsed time: 4.648004 seconds -------------------------------------------------------------------------------- Total elapsed time: 9.616395 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ionize section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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 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 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: 1.406562 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in ---------------------------------------------------------------------- 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 Jan 30 2023 at 11:38:48 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 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 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) = -4.721246714829E+02 kJ/mol Global net ELEC energy = -4.721246714829E+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 -472.1246714829 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 -4.721246714829E+02 against expected result -4.721247E+02 *** PASSED *** Elapsed time: 1.343506 seconds -------------------------------------------------------------------------------- Total elapsed time: 2.750068 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-pmf section -------------------------------------------------------------------------------- Testing input file ion-pmf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: ion-pmf.in asc_getToken: Error occurred (bailing out). Vio_scanf: Format problem with input. 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 Jan 30 2023 at 11:38:48 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 9.130e-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 -2.767e-05 tot 1 -2.723e-02 9.133e-07 9.133e-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 -2.767e-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: -6.909718359932E+00 WCA energy for atom 1: -6.909422551724E+00 Total WCA energy: -13.8191 kJ/mol Total non-polar energy = -1.365308087297E+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 8.398642197666E+01 -1.324564548552E-05 -1.613435632529E-05 ib 0 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 0 6.148357059184E+00 -2.667517425897E-05 -5.378919678211E-05 tot 0 9.013477903584E+01 -3.992081974449E-05 -6.992355310740E-05 qf 1 -8.466423642736E+01 -1.836748045969E-05 -3.062224428458E-05 ib 1 0.000000000000E+00 0.000000000000E+00 0.000000000000E+00 db 1 2.882739230548E+00 -3.149946357588E-05 -6.291495506459E-05 tot 1 -8.178149719681E+01 -4.986694403557E-05 -9.353719934917E-05 tot all 8.353281839029E+00 -8.978776378007E-05 -1.634607524566E-04 print APOL energy 1 (asolv) end Global net APOL energy = -1.365308087297E+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 -5.826577086437E-01 -2.766670515801E-05 -2.766670515838E-05 tot 0 -1.158042745197E+01 -2.766670515801E-05 -2.766670515838E-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 5.826560767576E-01 -2.767485007141E-05 -2.767485007183E-05 tot 1 1.170128043265E+01 -2.767485007141E-05 -2.767485007183E-05 tot all 1.208529806779E-01 -5.534155522943E-05 -5.534155523021E-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 -13.65308087297 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: 7.850282 seconds -------------------------------------------------------------------------------- Total elapsed time: 7.850282 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for ion-protein section -------------------------------------------------------------------------------- Testing input file apbs-mol-pdiel2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-pdiel2.in 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 Jan 30 2023 at 11:38:48 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. 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. 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: 8.436093 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-pdiel2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-pdiel2.in 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 Jan 30 2023 at 11:38:48 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. 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. 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: 7.347708 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-pdiel12.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-pdiel12.in 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 Jan 30 2023 at 11:38:48 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. 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. 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: 6.608488 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-pdiel12.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-pdiel12.in 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 Jan 30 2023 at 11:38:48 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. 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. 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: 6.906777 seconds -------------------------------------------------------------------------------- Total elapsed time: 29.299066 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for pka-lig section -------------------------------------------------------------------------------- Testing input file apbs-mol-vdw.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-vdw.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 8.083515648730E+00 kJ/mol Global net ELEC energy = 8.083515648730E+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 8.08351564873 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 8.083515648730E+00 against expected result 8.083516E+00 *** PASSED *** Elapsed time: 6.640726 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-vdw.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-vdw.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 2.096300255723E+01 kJ/mol Global net ELEC energy = 2.096300255723E+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 20.96300255723 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 2.096300255723E+01 against expected result 2.096296E+01 *** PASSED *** Elapsed time: 5.800911 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-mol-surf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol-surf.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 1.192607686581E+02 kJ/mol Global net ELEC energy = 1.192607686581E+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 119.2607686581 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 1.192607686581E+02 against expected result 1.192608E+02 *** PASSED *** Elapsed time: 6.025723 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol-surf.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol-surf.in 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 Jan 30 2023 at 11:38:48 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. 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. 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: 5.677763 seconds -------------------------------------------------------------------------------- Total elapsed time: 24.145123 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for point-pmf section -------------------------------------------------------------------------------- Testing input file complex-0_1.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_1.in 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 Jan 30 2023 at 11:38:48 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. 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. 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: 0.296012 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_2.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_2.in 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 Jan 30 2023 at 11:38:48 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. 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. 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) = 8.906694086750E+00 kJ/mol Global net ELEC energy = 8.906694086750E+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 8.90669408675 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 8.906694086750E+00 against expected result 8.906694E+00 *** PASSED *** Elapsed time: 0.296599 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_3.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_3.in 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 Jan 30 2023 at 11:38:48 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. 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. 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: 0.296315 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file complex-0_4.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: complex-0_4.in 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 Jan 30 2023 at 11:38:48 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. 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. 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: 0.296769 seconds -------------------------------------------------------------------------------- Total elapsed time: 1.185695 seconds Test results have been logged -------------------------------------------------------------------------------- Running tests for solv section -------------------------------------------------------------------------------- Testing input file apbs-mol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-mol.in 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 Jan 30 2023 at 11:38:48 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. 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) = -3.624863488074E+01 kJ/mol Global net ELEC energy = -3.624863488074E+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 -36.24863488074 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 -3.624863488074E+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: 0.432069 seconds -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Testing input file apbs-smol.in BINARY: /builddir/build/BUILD/apbs-3.0.0/build/bin/apbs INPUT: apbs-smol.in 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 Jan 30 2023 at 11:38:48 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. 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) = -3.757593772493E+01 kJ/mol Global net ELEC energy = -3.757593772493E+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 -37.57593772493 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 -3.757593772493E+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: 0.440002 seconds -------------------------------------------------------------------------------- Total elapsed time: 0.872071 seconds Test results have been logged -------------------------------------------------------------------------------- + exit 0 Processing files: apbs-3.0.0-17.el8.x86_64 Provides: apbs = 3.0.0-17.el8 apbs(x86-64) = 3.0.0-17.el8 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_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libgomp.so.1()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmaloc.so.1()(64bit) libpthread.so.0()(64bit) libstdc++.so.6()(64bit) rtld(GNU_HASH) Processing files: apbs-tools-3.0.0-17.el8.x86_64 Provides: apbs-tools = 3.0.0-17.el8 apbs-tools(x86-64) = 3.0.0-17.el8 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_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(64bit) libgomp.so.1()(64bit) libm.so.6()(64bit) libm.so.6(GLIBC_2.2.5)(64bit) libmaloc.so.1()(64bit) libpthread.so.0()(64bit) libstdc++.so.6()(64bit) rtld(GNU_HASH) Processing files: apbs-libs-3.0.0-17.el8.x86_64 Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.U6MSh4 + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + DOCDIR=/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/doc/apbs-libs + export LC_ALL=C + LC_ALL=C + export DOCDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/doc/apbs-libs + cp -pr README.md /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/doc/apbs-libs + exit 0 Executing(%license): /bin/sh -e /var/tmp/rpm-tmp.OVxdt1 + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + LICENSEDIR=/builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/licenses/apbs-libs + export LC_ALL=C + LC_ALL=C + export LICENSEDIR + /usr/bin/mkdir -p /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/licenses/apbs-libs + cp -pr LICENSE.md /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/licenses/apbs-libs + cp -pr COPYING /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/licenses/apbs-libs + cp -pr contrib/iapbs/iapbs-COPYING /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/licenses/apbs-libs + cp -pr contrib/iapbs/iapbs-LGPLv2 /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64/usr/share/licenses/apbs-libs + exit 0 Provides: apbs-libs = 3.0.0-17.el8 apbs-libs(x86-64) = 3.0.0-17.el8 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_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(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_2.2.5)(64bit) libpthread.so.0()(64bit) rtld(GNU_HASH) Processing files: apbs-devel-3.0.0-17.el8.x86_64 Provides: apbs-devel = 3.0.0-17.el8 apbs-devel(x86-64) = 3.0.0-17.el8 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: python3-apbs-3.0.0-17.el8.x86_64 Provides: python3-apbs = 3.0.0-17.el8 python3-apbs(x86-64) = 3.0.0-17.el8 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/python3.6 libc.so.6()(64bit) libc.so.6(GLIBC_2.14)(64bit) libc.so.6(GLIBC_2.2.5)(64bit) libc.so.6(GLIBC_2.3.4)(64bit) libc.so.6(GLIBC_2.4)(64bit) libc.so.6(GLIBC_2.7)(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_2.2.5)(64bit) libmaloc.so.1()(64bit) libpthread.so.0()(64bit) libpython3.6m.so.1.0()(64bit) libstdc++.so.6()(64bit) python(abi) = 3.6 rtld(GNU_HASH) Obsoletes: apbs-libs < 0:3.0.0-11 Processing files: apbs-debugsource-3.0.0-17.el8.x86_64 Provides: apbs-debugsource = 3.0.0-17.el8 apbs-debugsource(x86-64) = 3.0.0-17.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Processing files: apbs-debuginfo-3.0.0-17.el8.x86_64 Provides: apbs-debuginfo = 3.0.0-17.el8 apbs-debuginfo(x86-64) = 3.0.0-17.el8 debuginfo(build-id) = 77a04cff154c93b130aa9c3a529700d5fbb64339 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(x86-64) = 3.0.0-17.el8 Processing files: apbs-tools-debuginfo-3.0.0-17.el8.x86_64 Provides: apbs-tools-debuginfo = 3.0.0-17.el8 apbs-tools-debuginfo(x86-64) = 3.0.0-17.el8 debuginfo(build-id) = 0cf136f18efd7df2e8739b4265e5e5ba02a445d0 debuginfo(build-id) = 3042d8b998bafe63d2ad7a5acd24ec78da1bf224 debuginfo(build-id) = 5ebe40adeb2ee2d2ee0ebe293d9103e134ac6413 debuginfo(build-id) = 7622f6940eca4d6f81d3cc09053562379f5d2033 debuginfo(build-id) = 7a0fee357674f28be73928647a4ef207a6c039b0 debuginfo(build-id) = 7d96f8757c436a1b750b0b81b0113d6bd32bca6f debuginfo(build-id) = 87bcce5ee6c432af953b0bb2dd897137904286fa debuginfo(build-id) = 87d638ae5a2ae92e4d8efbdba900ba78c209db9c debuginfo(build-id) = 99f500e4333af99603a32ff3ebbe2d46d268cd4f debuginfo(build-id) = b1b0dc8d95121a5871dd2bb56a2fdcbc031fd5be debuginfo(build-id) = b55bc20c97ec81a738ae941efc41bb46a99577f9 debuginfo(build-id) = b6fd9dc498ba61e8119cc3f1ad04fea763d717bb debuginfo(build-id) = c7422a01b9e7cf673a52f4fa1c117381daddd39e debuginfo(build-id) = d8ecc1c6e462419dd8223644219d798f3f179478 debuginfo(build-id) = e2c3cc1b3a79c61937225abe6ae0381beca15424 debuginfo(build-id) = ee9726872759449c375412b8cf6e9d3e82f3261d debuginfo(build-id) = f15d45e65e27ecf09e714287453400d8ae56635e Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(x86-64) = 3.0.0-17.el8 Processing files: apbs-libs-debuginfo-3.0.0-17.el8.x86_64 Provides: apbs-libs-debuginfo = 3.0.0-17.el8 apbs-libs-debuginfo(x86-64) = 3.0.0-17.el8 debuginfo(build-id) = 1dc19f686b580c04c467e7dd2045e594e7868a26 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(x86-64) = 3.0.0-17.el8 Processing files: python3-apbs-debuginfo-3.0.0-17.el8.x86_64 Provides: debuginfo(build-id) = c7c5d52889f23b8363f295f40b81beac5dc1317e python3-apbs-debuginfo = 3.0.0-17.el8 python3-apbs-debuginfo(x86-64) = 3.0.0-17.el8 Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1 Recommends: apbs-debugsource(x86-64) = 3.0.0-17.el8 Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 Wrote: /builddir/build/RPMS/apbs-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-tools-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-libs-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-devel-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/python3-apbs-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-debugsource-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-debuginfo-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-tools-debuginfo-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/apbs-libs-debuginfo-3.0.0-17.el8.x86_64.rpm Wrote: /builddir/build/RPMS/python3-apbs-debuginfo-3.0.0-17.el8.x86_64.rpm Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.s5g047 + umask 022 + cd /builddir/build/BUILD + cd apbs-3.0.0 + /usr/bin/rm -rf /builddir/build/BUILDROOT/apbs-3.0.0-17.el8.x86_64 + exit 0 Finish: rpmbuild apbs-3.0.0-17.el8.src.rpm Finish: build phase for apbs-3.0.0-17.el8.src.rpm INFO: chroot_scan: 3 files copied to /var/lib/copr-rpmbuild/results/chroot_scan INFO: /var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/root/var/log/dnf.rpm.log /var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/root/var/log/dnf.librepo.log /var/lib/mock/rhel+epel-8-x86_64-1675078509.656443/root/var/log/dnf.log INFO: Done(/var/lib/copr-rpmbuild/results/apbs-3.0.0-17.el8.src.rpm) Config(child) 9 minutes 5 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