C translation of Holst group PMG code. More...

Macros
#define	HARMO2(a, b)
	Multigrid subroutines.

#define	MAXIONS 50
	Specifies the PDE definition for PMG to solve.

Functions
VPUBLIC void	VbuildA (int nx, int ny, int nz, int ipkey, int mgdisc, int numdia, int ipc, double rpc, double ac, double cc, double fc, double xf, double yf, double zf, double gxcf, double gycf, double gzcf, double a1cf, double a2cf, double a3cf, double ccf, double fcf)
	Build the Laplacian.

VPUBLIC void	Vbuildband (int key, int nx, int ny, int nz, int ipc, double rpc, double ac, int ipcB, double rpcB, double acB)
	Banded matrix builder.

VEXTERNC void	Vbuildband1_7 (int nx, int ny, int nz, int ipc, double rpc, double oC, double oE, double oN, double uC, int ipcB, double rpcB, double acB, int n, int m, int *lda)
	Build the operator in banded form given the 7-diagonal form.

VEXTERNC void	Vbuildband1_27 (int nx, int ny, int nz, int ipc, double rpc, double oC, double oE, double oN, double uC, double oNE, double oNW, double uE, double uW, double uN, double uS, double uNE, double uNW, double uSE, double uSW, int ipcB, double rpcB, double acB, int n, int m, int *lda)
	Build the operator in banded form given the 27-diagonal form.

VPUBLIC void	VbuildG (int nxf, int nyf, int nzf, int nxc, int nyc, int nzc, int numdia, double pcFF, double acFF, double ac)
	Build Galerkin matrix structures.

VEXTERNC void	VbuildG_1 (int nxf, int nyf, int nzf, int nx, int ny, int nz, double oPC, double oPN, double oPS, double oPE, double oPW, double oPNE, double oPNW, double oPSE, double oPSW, double uPC, double uPN, double uPS, double uPE, double uPW, double uPNE, double uPNW, double uPSE, double uPSW, double dPC, double dPN, double dPS, double dPE, double dPW, double dPNE, double dPNW, double dPSE, double dPSW, double oC, double XoC, double XoE, double XoN, double XuC, double XoNE, double XoNW, double XuE, double XuW, double XuN, double XuS, double XuNE, double XuNW, double XuSE, double XuSW)
	Computes a 27-point galerkin coarse grid matrix from a 1-point (i.e., diagonal) fine grid matrix.

VEXTERNC void	VbuildG_7 (int nxf, int nyf, int nzf, int nx, int ny, int nz, double oPC, double oPN, double oPS, double oPE, double oPW, double oPNE, double oPNW, double oPSE, double oPSW, double uPC, double uPN, double uPS, double uPE, double uPW, double uPNE, double uPNW, double uPSE, double uPSW, double dPC, double dPN, double dPS, double dPE, double dPW, double dPNE, double dPNW, double dPSE, double dPSW, double oC, double oE, double oN, double uC, double XoC, double XoE, double XoN, double XuC, double XoNE, double XoNW, double XuE, double XuW, double XuN, double XuS, double XuNE, double XuNW, double XuSE, double *XuSW)
	Computes a 27-point galerkin coarse grid matrix from a 7-point fine grid matrix.

VEXTERNC void	VbuildG_27 (int nxf, int nyf, int nzf, int nx, int ny, int nz, double oPC, double oPN, double oPS, double oPE, double oPW, double oPNE, double oPNW, double oPSE, double oPSW, double uPC, double uPN, double uPS, double uPE, double uPW, double uPNE, double uPNW, double uPSE, double uPSW, double dPC, double dPN, double dPS, double dPE, double dPW, double dPNE, double dPNW, double dPSE, double dPSW, double oC, double oE, double oN, double uC, double oNE, double oNW, double uE, double uW, double uN, double uS, double uNE, double uNW, double uSE, double uSW, double XoC, double XoE, double XoN, double XuC, double XoNE, double XoNW, double XuE, double XuW, double XuN, double XuS, double XuNE, double XuNW, double XuSE, double *XuSW)
	Compute a 27-point galerkin coarse grid matrix from a 27-point fine grid matrix.

VPUBLIC void	VbuildP (int nxf, int nyf, int nzf, int nxc, int nyc, int nzc, int mgprol, int ipc, double rpc, double pc, double ac, double xf, double yf, double zf)
	Builds prolongation matrix.

VPUBLIC void	Vcghs (int nx, int ny, int nz, int ipc, double rpc, double ac, double cc, double fc, double x, double p, double ap, double r, int itmax, int iters, double errtol, double omega, int iresid, int iadjoint)
	A collection of useful low-level routines (timing, etc).

VPUBLIC void	Vgsrb (int nx, int ny, int nz, int ipc, double rpc, double ac, double cc, double fc, double x, double w1, double w2, double r, int itmax, int iters, double errtol, double omega, int iresid, int iadjoint)
	Guass-Seidel solver.

VPUBLIC void	Vmatvec (int nx, int ny, int nz, int ipc, double rpc, double ac, double cc, double x, double *y)
	Matrix-vector multiplication routines.

VEXTERNC void	Vnmatvec (int nx, int ny, int nz, int ipc, double rpc, double ac, double cc, double x, double y, double w1)
	Break the matrix data-structure into diagonals and then call the matrix-vector routine.

VEXTERNC void	Vmresid (int nx, int ny, int nz, int ipc, double rpc, double ac, double cc, double fc, double x, double r)
	Break the matrix data-structure into diagonals and then call the residual routine.

VEXTERNC void	Vnmresid (int nx, int ny, int nz, int ipc, double rpc, double ac, double cc, double fc, double x, double r, double *w1)
	Break the matrix data-structure into diagonals and then call the residual routine.

VEXTERNC void	Vrestrc (int nxf, int nyf, int nzf, int nxc, int nyc, int nzc, double xin, double xout, double *pc)
	Apply the restriction operator.

VEXTERNC void	VinterpPMG (int nxc, int nyc, int nzc, int nxf, int nyf, int nzf, double xin, double xout, double *pc)
	Apply the prolongation operator.

VEXTERNC void	Vextrac (int nxf, int nyf, int nzf, int nxc, int ny, int nzc, double xin, double xout)
	Simple injection of a fine grid function into coarse grid.

VEXTERNC void	Vmvcs (int nx, int ny, int nz, double x, int iz, double w0, double w1, double w2, double w3, int istop, int itmax, int iters, int ierror, int nlev, int ilev, int nlev_real, int mgsolv, int iok, int iinfo, double epsiln, double errtol, double omega, int nu1, int nu2, int mgsmoo, int ipc, double rpc, double pc, double ac, double cc, double fc, double tru)
	MG helper functions.

VPUBLIC void	Vmgdriv (int iparm, double rparm, int iwork, double rwork, double u, double xf, double yf, double zf, double gxcf, double gycf, double gzcf, double a1cf, double a2cf, double a3cf, double ccf, double fcf, double *tcf)
	Multilevel solver driver.

VEXTERNC void	Vmgdriv2 (int iparm, double rparm, int nx, int ny, int nz, double u, int iz, int ipc, double rpc, double pc, double ac, double cc, double fc, double xf, double yf, double zf, double gxcf, double gycf, double gzcf, double a1cf, double a2cf, double a3cf, double ccf, double fcf, double *tcf)
	Solves the pde using the multi-grid method.

VEXTERNC void	Vmgsz (int mgcoar, int mgdisc, int mgsolv, int nx, int ny, int nz, int nlev, int nxc, int nyc, int nzc, int nf, int nc, int narr, int narrc, int n_rpc, int n_iz, int n_ipc, int iretot, int *iintot)
	This routine computes the required sizes of the real and integer work arrays for the multigrid code. these two sizes are a (complicated) function of input parameters.

VPUBLIC void	Vfmvfas (int nx, int ny, int nz, double x, int iz, double w0, double w1, double w2, double w3, double w4, int istop, int itmax, int iters, int ierror, int nlev, int ilev, int nlev_real, int mgsolv, int iok, int iinfo, double epsiln, double errtol, double omega, int nu1, int nu2, int mgsmoo, int ipc, double rpc, double pc, double ac, double cc, double fc, double *tru)
	Multigrid nonlinear solve iteration routine.

VEXTERNC void	Vmvfas (int nx, int ny, int nz, double x, int iz, double w0, double w1, double w2, double w3, double w4, int istop, int itmax, int iters, int ierror, int nlev, int ilev, int nlev_real, int mgsolv, int iok, int iinfo, double epsiln, double errtol, double omega, int nu1, int nu2, int mgsmoo, int ipc, double rpc, double pc, double ac, double cc, double fc, double *tru)
	Nonlinear multilevel method.

VPUBLIC void	Vbuildops (int nx, int ny, int nz, int nlev, int ipkey, int iinfo, int ido, int iz, int mgprol, int mgcoar, int mgsolv, int mgdisc, int ipc, double rpc, double pc, double ac, double cc, double fc, double xf, double yf, double zf, double gxcf, double gycf, double gzcf, double a1cf, double a2cf, double a3cf, double ccf, double fcf, double tcf)
	Build operators, boundary arrays, modify affine vectors ido==0: do only fine level ido==1: do only coarse levels (including second op at coarsest) ido==2: do all levels ido==3: rebuild the second operator at the coarsest level.

VEXTERNC void	Vbuildstr (int nx, int ny, int nz, int nlev, int *iz)
	Build the nexted operator framework in the array iz.

VEXTERNC void	Vbuildgaler0 (int nxf, int nyf, int nzf, int nxc, int nyc, int nzc, int ipkey, int numdia, double pcFF, int ipcFF, double rpcFF, double acFF, double ccFF, double fcFF, int ipc, double rpc, double ac, double cc, double *fc)
	Form the Galerkin coarse grid system.

VPUBLIC void	Vxcopy (int nx, int ny, int nz, double x, double *y)
	A collection of useful low-level routines (timing, etc).

VEXTERNC void	Vxcopy_small (int nx, int ny, int nz, double x, double *y)
	Copy operation for a grid function with boundary values. Quite simply copies one 3d matrix to another.

VEXTERNC void	Vxcopy_large (int nx, int ny, int nz, double x, double *y)
	Copy operation for a grid function with boundary values. Quite simply copies one 3d matrix to another.

VEXTERNC void	Vxaxpy (int nx, int ny, int nz, double alpha, double x, double y)
	saxpy operation for a grid function with boundary values.

VEXTERNC double	Vxnrm1 (int nx, int ny, int nz, double x)
	Norm operation for a grid function with boundary values.

VEXTERNC double	Vxnrm2 (int nx, int ny, int nz, double x)
	Norm operation for a grid function with boundary values.

VEXTERNC double	Vxdot (int nx, int ny, int nz, double x, double *y)
	Inner product operation for a grid function with boundary values.

VEXTERNC void	Vazeros (int nx, int ny, int nz, double x)
	Zero out operation for a grid function, including boundary values.

VEXTERNC void	VfboundPMG (int ibound, int nx, int ny, int nz, double x, double gxc, double gyc, double gzc)
	Initialize a grid function to have a certain boundary value,.

VEXTERNC void	VfboundPMG00 (int nx, int ny, int nz, double x)
	Initialize a grid function to have a zero boundary value.

VEXTERNC void	Vaxrand (int nx, int ny, int nz, double x)
	Fill grid function with random values, including boundary values.

VEXTERNC void	Vxscal (int nx, int ny, int nz, double fac, double *x)
	Scale operation for a grid function with boundary values.

VEXTERNC void	Vprtmatd (int nx, int ny, int nz, int ipc, double rpc, double ac)

VPUBLIC void	Vdpbsl (double abd, int lda, int n, int m, double *b)
	LINPACK interface.

VPUBLIC void	Vmypdefinitlpbe (int tnion, double tcharge, double *tsconc)
	Set up the ionic species to be used in later calculations. This must be called before any other of the routines in this file.

VEXTERNC void	Vmypdefinitnpbe (int tnion, double tcharge, double *tsconc)
	Set up the ionic species to be used in later calculations. This must be called before any other of the routines in this file.

VEXTERNC void	Vmypdefinitsmpbe (int tnion, double tcharge, double tsconc, double smvolume, double *smsize)
	Set up the ionic species to be used in later calculations. This must be called before any other of the routines in this file.

VEXTERNC void	Vc_vec (double coef, double uin, double uout, int nx, int ny, int nz, int *ipkey)
	Define the nonlinearity (vector version)

VEXTERNC void	Vdc_vec (double coef, double uin, double uout, int nx, int ny, int nz, int *ipkey)
	Define the derivative of the nonlinearity (vector version)

VEXTERNC void	Vc_vecpmg (double coef, double uin, double uout, int nx, int ny, int nz, int *ipkey)
	Define the nonlinearity (vector version)

VEXTERNC void	Vc_vecsmpbe (double coef, double uin, double uout, int nx, int ny, int nz, int *ipkey)
	Define the nonlinearity (vector version)

VEXTERNC void	Vnewdriv (int iparm, double rparm, int iwork, double rwork, double u, double xf, double yf, double zf, double gxcf, double gycf, double gzcf, double a1cf, double a2cf, double a3cf, double ccf, double fcf, double *tcf)
	Driver for the Newton Solver.

VEXTERNC void	Vnewdriv2 (int iparm, double rparm, int nx, int ny, int nz, double u, int iz, double w1, double w2, int ipc, double rpc, double pc, double ac, double cc, double fc, double xf, double yf, double zf, double gxcf, double gycf, double gzcf, double a1cf, double a2cf, double a3cf, double ccf, double fcf, double *tcf)
	Solves using Newton's Method.

VPUBLIC void	Vfnewton (int nx, int ny, int nz, double x, int iz, double w0, double w1, double w2, double w3, int istop, int itmax, int iters, int ierror, int nlev, int ilev, int nlev_real, int mgsolv, int iok, int iinfo, double epsiln, double errtol, double omega, int nu1, int nu2, int mgsmoo, double cprime, double rhs, double xtmp, int ipc, double rpc, double pc, double ac, double cc, double fc, double *tru)
	Driver routines for the Newton method.

VEXTERNC void	Vnewton (int nx, int ny, int nz, double x, int iz, double w0, double w1, double w2, double w3, int istop, int itmax, int iters, int ierror, int nlev, int ilev, int nlev_real, int mgsolv, int iok, int iinfo, double epsiln, double errtol, double omega, int nu1, int nu2, int mgsmoo, double cprime, double rhs, double xtmp, int ipc, double rpc, double pc, double ac, double cc, double fc, double *tru)
	Inexact-newton-multilevel method.

VEXTERNC void	Vgetjac (int nx, int ny, int nz, int nlev_real, int iz, int lev, int ipkey, double x, double r, double cprime, double rhs, double cc, double *pc)
	Form the jacobian system.

VPUBLIC void	Vpower (int nx, int ny, int nz, int iz, int ilev, int ipc, double rpc, double ac, double cc, double w1, double w2, double w3, double w4, double eigmax, double eigmax_model, double tol, int itmax, int iters, int *iinfo)
	Power methods for eigenvalue estimation.

VEXTERNC void	Vipower (int nx, int ny, int nz, double u, int iz, double w0, double w1, double w2, double w3, double w4, double eigmin, double eigmin_model, double tol, int itmax, int iters, int nlev, int ilev, int nlev_real, int mgsolv, int iok, int iinfo, double epsiln, double errtol, double omega, int nu1, int nu2, int mgsmoo, int ipc, double rpc, double pc, double ac, double cc, double *tru)
	Standard inverse power method for minimum eigenvalue estimation.

VEXTERNC void	Vsmooth (int nx, int ny, int nz, int ipc, double rpc, double ac, double cc, double fc, double x, double w1, double w2, double r, int itmax, int iters, double errtol, double omega, int iresid, int iadjoint, int *meth)
	Multigrid smoothing functions.

VEXTERNC void	Vnsmooth (int nx, int ny, int nz, int ipc, double rpc, double ac, double cc, double fc, double x, double w1, double w2, double r, int itmax, int iters, double errtol, double omega, int iresid, int iadjoint, int *meth)
	call the appropriate non-linear smoothing routine.

Detailed Description

C translation of Holst group PMG code.

Macro Definition Documentation

◆ HARMO2

#define HARMO2	(		a,
			b )

Value:

(2.0 * (a) * (b) / ((a) + (b)))

Multigrid subroutines.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Definition at line 65 of file mgsubd.h.

◆ MAXIONS

#define MAXIONS 50

Specifies the PDE definition for PMG to solve.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Definition at line 62 of file mypdec.h.

Function Documentation

◆ Vaxrand()

VEXTERNC void Vaxrand	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x )

Fill grid function with random values, including boundary values.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces axrand from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
x	The 3d matrix to fill

Definition at line 291 of file mikpckd.c.

◆ Vazeros()

VEXTERNC void Vazeros	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x )

Zero out operation for a grid function, including boundary values.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces azeros from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the x dimension of the 3d matrix
nz	The size of the x dimension of the 3d matrix
x	The matrix to zero out

Definition at line 195 of file mikpckd.c.

◆ VbuildA()

VEXTERNC void VbuildA	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipkey,
		int *	mgdisc,
		int *	numdia,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	xf,
		double *	yf,
		double *	zf,
		double *	gxcf,
		double *	gycf,
		double *	gzcf,
		double *	a1cf,
		double *	a2cf,
		double *	a3cf,
		double *	ccf,
		double *	fcf )

Build the Laplacian.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Mike Holst [original], Tucker Beck [translation]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Break the matrix data-structure into diagonals and then call the matrix build routine

Author: Tucker Beck [C Translation], Michael Holst [Original]

Parameters

nx
ny
nz
ipkey
mgdisc
numdia
ipc
rpc
ac
cc
fc
xf
yf
zf
gxcf
gycf
gzcf
a1cf
a2cf
a3cf
ccf
fcf

Definition at line 57 of file buildAd.c.

◆ Vbuildband()

VEXTERNC void Vbuildband	(	int *	key,
		int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		int *	ipcB,
		double *	rpcB,
		double *	acB )

Banded matrix builder.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.gov)
* Pacific Northwest National Laboratory
*
* Additional contributing authors listed in the code documentation.
*
* Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy.
* Copyright (c) 2010-2020 Battelle Memorial Institute.
* 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 Washington University in St. Louis 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.
*
*

Author: Mike Holst and Steve Bond [original], Tucker Beck [translation]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Build and factor a banded matrix given a matrix in diagonal form.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces buildband from buildBd.f

Parameters

key
nx
ny
nz
ipc
rpc
ac
ipcB
rpcB
acB

Definition at line 57 of file buildBd.c.

◆ Vbuildband1_27()

VEXTERNC void Vbuildband1_27	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	oC,
		double *	oE,
		double *	oN,
		double *	uC,
		double *	oNE,
		double *	oNW,
		double *	uE,
		double *	uW,
		double *	uN,
		double *	uS,
		double *	uNE,
		double *	uNW,
		double *	uSE,
		double *	uSW,
		int *	ipcB,
		double *	rpcB,
		double *	acB,
		int *	n,
		int *	m,
		int *	lda )

Build the operator in banded form given the 27-diagonal form.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces buildband1_7 from buildBd.f

Parameters

nx
ny
nz
ipc
rpc
oC
oE
oN
uC
oNE
oNW
uE
uW
uN
uS
uNE
uNW
uSE
uSW
ipcB
rpcB
acB
n
m
lda

Definition at line 183 of file buildBd.c.

◆ Vbuildband1_7()

VEXTERNC void Vbuildband1_7	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	oC,
		double *	oE,
		double *	oN,
		double *	uC,
		int *	ipcB,
		double *	rpcB,
		double *	acB,
		int *	n,
		int *	m,
		int *	lda )

Build the operator in banded form given the 7-diagonal form.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces buildband1_7 from buildBd.f

Parameters

nx
ny
nz
ipc
rpc
oC
oE
oN
uC
ipcB
rpcB
acB
n
m
lda

Definition at line 119 of file buildBd.c.

◆ VbuildG()

VEXTERNC void VbuildG	(	int *	nxf,
		int *	nyf,
		int *	nzf,
		int *	nxc,
		int *	nyc,
		int *	nzc,
		int *	numdia,
		double *	pcFF,
		double *	acFF,
		double *	ac )

Build Galerkin matrix structures.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Parameters

nxf
nyf
nzf
nxc
nyc
nzc
numdia
pcFF
acFF
ac

Definition at line 57 of file buildGd.c.

◆ VbuildG_1()

VEXTERNC void VbuildG_1	(	int *	nxf,
		int *	nyf,
		int *	nzf,
		int *	nx,
		int *	ny,
		int *	nz,
		double *	oPC,
		double *	oPN,
		double *	oPS,
		double *	oPE,
		double *	oPW,
		double *	oPNE,
		double *	oPNW,
		double *	oPSE,
		double *	oPSW,
		double *	uPC,
		double *	uPN,
		double *	uPS,
		double *	uPE,
		double *	uPW,
		double *	uPNE,
		double *	uPNW,
		double *	uPSE,
		double *	uPSW,
		double *	dPC,
		double *	dPN,
		double *	dPS,
		double *	dPE,
		double *	dPW,
		double *	dPNE,
		double *	dPNW,
		double *	dPSE,
		double *	dPSW,
		double *	oC,
		double *	XoC,
		double *	XoE,
		double *	XoN,
		double *	XuC,
		double *	XoNE,
		double *	XoNW,
		double *	XuE,
		double *	XuW,
		double *	XuN,
		double *	XuS,
		double *	XuNE,
		double *	XuNW,
		double *	XuSE,
		double *	XuSW )

Computes a 27-point galerkin coarse grid matrix from a 1-point (i.e., diagonal) fine grid matrix.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces buildG_1 from buildGd.f

Expressions for the galerkin coarse grid stencil XA in terms of the fine grid matrix stencil A and the interpolation operator stencil P. these stencils have the form:

XA := array([

matrix([ [ -XdNW(i,j,k), -XdN(i,j,k), -XdNE(i,j,k) ], [ -XdW(i,j,k), -XdC(i,j,k), -XdE(i,j,k) ], [ -XdSW(i,j,k), -XdS(i,j,k), -XdSE(i,j,k) ] ]),

matrix([ [ -XoNW(i,j,k), -XoN(i,j,k), -XoNE(i,j,k) ], [ -XoW(i,j,k), XoC(i,j,k), -XoE(i,j,k) ], [ -XoSW(i,j,k), -XoS(i,j,k), -XoSE(i,j,k) ] ]),

matrix([ [ -XuNW(i,j,k), -XuN(i,j,k), -XuNE(i,j,k) ], [ -XuW(i,j,k), -XuC(i,j,k), -XuE(i,j,k) ], [ -XuSW(i,j,k), -XuS(i,j,k), -XuSE(i,j,k) ] ]) ]):

A := array([

matrix([ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ]),

matrix([ [ 0, 0, 0 ], [ 0, oC(i,j,k), 0 ], [ 0, 0, 0 ] ]),

matrix([ [ 0, 0, 0 ], [ 0, 0, 0 ], [ 0, 0, 0 ] ])

P := array([

matrix([ [ dPNW(i,j,k), dPN(i,j,k), dPNE(i,j,k) ], [ dPW(i,j,k), dPC(i,j,k), dPE(i,j,k) ], [ dPSW(i,j,k), dPS(i,j,k), dPSE(i,j,k) ] ]),

matrix([ [ oPNW(i,j,k), oPN(i,j,k), oPNE(i,j,k) ], [ oPW(i,j,k), oPC(i,j,k), oPE(i,j,k) ], [ oPSW(i,j,k), oPS(i,j,k), oPSE(i,j,k) ] ]),

matrix([ [ uPNW(i,j,k), uPN(i,j,k), uPNE(i,j,k) ], [ uPW(i,j,k), uPC(i,j,k), uPE(i,j,k) ], [ uPSW(i,j,k), uPS(i,j,k), uPSE(i,j,k) ] ]) ]):

Parameters

nxf
nyf
nzf
nx
ny
nz
oPC
oPN
oPS
oPE
oPW
oPNE
oPNW
oPSE
oPSW
uPC
uPN
uPS
uPE
uPW
uPNE
uPNW
uPSE
uPSW
dPC
dPN
dPS
dPE
dPW
dPNE
dPNW
dPSE
dPSW
oC
XoC
XoE
XoN
XuC
XoNE
XoNW
XuE
XuW
XuN
XuS
XuNE
XuNW
XuSE
XuSW

Definition at line 145 of file buildGd.c.

◆ VbuildG_27()

VEXTERNC void VbuildG_27	(	int *	nxf,
		int *	nyf,
		int *	nzf,
		int *	nx,
		int *	ny,
		int *	nz,
		double *	oPC,
		double *	oPN,
		double *	oPS,
		double *	oPE,
		double *	oPW,
		double *	oPNE,
		double *	oPNW,
		double *	oPSE,
		double *	oPSW,
		double *	uPC,
		double *	uPN,
		double *	uPS,
		double *	uPE,
		double *	uPW,
		double *	uPNE,
		double *	uPNW,
		double *	uPSE,
		double *	uPSW,
		double *	dPC,
		double *	dPN,
		double *	dPS,
		double *	dPE,
		double *	dPW,
		double *	dPNE,
		double *	dPNW,
		double *	dPSE,
		double *	dPSW,
		double *	oC,
		double *	oE,
		double *	oN,
		double *	uC,
		double *	oNE,
		double *	oNW,
		double *	uE,
		double *	uW,
		double *	uN,
		double *	uS,
		double *	uNE,
		double *	uNW,
		double *	uSE,
		double *	uSW,
		double *	XoC,
		double *	XoE,
		double *	XoN,
		double *	XuC,
		double *	XoNE,
		double *	XoNW,
		double *	XuE,
		double *	XuW,
		double *	XuN,
		double *	XuS,
		double *	XuNE,
		double *	XuNW,
		double *	XuSE,
		double *	XuSW )

Compute a 27-point galerkin coarse grid matrix from a 27-point fine grid matrix.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces buildG_27 from buildGd.f

Expressions for the galerkin coarse grid stencil XA in terms of the fine grid matrix stencil A and the interpolation operator stencil P. these stencils have the form:

XA := array([

matrix([ [ -XdNW(i,j,k), -XdN(i,j,k), -XdNE(i,j,k) ], [ -XdW(i,j,k), -XdC(i,j,k), -XdE(i,j,k) ], [ -XdSW(i,j,k), -XdS(i,j,k), -XdSE(i,j,k) ] ]),

matrix([ [ -XoNW(i,j,k), -XoN(i,j,k), -XoNE(i,j,k) ], [ -XoW(i,j,k), XoC(i,j,k), -XoE(i,j,k) ], [ -XoSW(i,j,k), -XoS(i,j,k), -XoSE(i,j,k) ] ]),

matrix([ [ -XuNW(i,j,k), -XuN(i,j,k), -XuNE(i,j,k) ], [ -XuW(i,j,k), -XuC(i,j,k), -XuE(i,j,k) ], [ -XuSW(i,j,k), -XuS(i,j,k), -XuSE(i,j,k) ] ]) ]):

A := array([

matrix([ [ -dNW(i,j,k), -dN(i,j,k), -dNE(i,j,k) ], [ -dW(i,j,k), -dC(i,j,k), -dE(i,j,k) ], [ -dSW(i,j,k), -dS(i,j,k), -dSE(i,j,k) ] ]),

matrix([ [ -oNW(i,j,k), -oN(i,j,k), -oNE(i,j,k) ], [ -oW(i,j,k), oC(i,j,k), -oE(i,j,k) ], [ -oSW(i,j,k), -oS(i,j,k), -oSE(i,j,k) ] ]),

matrix([ [ -uNW(i,j,k), -uN(i,j,k), -uNE(i,j,k) ], [ -uW(i,j,k), -uC(i,j,k), -uE(i,j,k) ], [ -uSW(i,j,k), -uS(i,j,k), -uSE(i,j,k) ] ]) ]):

P := array([

matrix([ [ dPNW(i,j,k), dPN(i,j,k), dPNE(i,j,k) ], [ dPW(i,j,k), dPC(i,j,k), dPE(i,j,k) ], [ dPSW(i,j,k), dPS(i,j,k), dPSE(i,j,k) ] ]),

matrix([ [ oPNW(i,j,k), oPN(i,j,k), oPNE(i,j,k) ], [ oPW(i,j,k), oPC(i,j,k), oPE(i,j,k) ], [ oPSW(i,j,k), oPS(i,j,k), oPSE(i,j,k) ] ]),

matrix([ [ uPNW(i,j,k), uPN(i,j,k), uPNE(i,j,k) ], [ uPW(i,j,k), uPC(i,j,k), uPE(i,j,k) ], [ uPSW(i,j,k), uPS(i,j,k), uPSE(i,j,k) ] ]) ]):

in addition, A is assumed to be symmetric so that:

oS := proc(x,y,z) RETURN( oN(x,y-1,z) ): end: oW := proc(x,y,z) RETURN( oE(x-1,y,z) ): end: oSE := proc(x,y,z) RETURN( oNW(x+1,y-1,z) ): end: oSW := proc(x,y,z) RETURN( oNE(x-1,y-1,z) ): end:

dC := proc(x,y,z) RETURN( uC(x,y,z-1) ): end: dW := proc(x,y,z) RETURN( uE(x-1,y,z-1) ): end: dE := proc(x,y,z) RETURN( uW(x+1,y,z-1) ): end:

dN := proc(x,y,z) RETURN( uS(x,y+1,z-1) ): end: dNW := proc(x,y,z) RETURN( uSE(x-1,y+1,z-1) ): end: dNE := proc(x,y,z) RETURN( uSW(x+1,y+1,z-1) ): end:

dS := proc(x,y,z) RETURN( uN(x,y-1,z-1) ): end: dSW := proc(x,y,z) RETURN( uNE(x-1,y-1,z-1) ): end: dSE := proc(x,y,z) RETURN( uNW(x+1,y-1,z-1) ): end:

Parameters

nxf
nyf
nzf
nx
ny
nz
oPC
oPN
oPS
oPE
oPW
oPNE
oPNW
oPSE
oPSW
uPC
uPN
uPS
uPE
uPW
uPNE
uPNW
uPSE
uPSW
dPC
dPN
dPS
dPE
dPW
dPNE
dPNW
dPSE
dPSW
oC
oE
oN
uC
oNE
oNW
uE
uW
uN
uS
uNE
uNW
uSE
uSW
XoC
XoE
XoN
XuC
XoNE
XoNW
XuE
XuW
XuN
XuS
XuNE
XuNW
XuSE
XuSW

Definition at line 1252 of file buildGd.c.

◆ VbuildG_7()

VEXTERNC void VbuildG_7	(	int *	nxf,
		int *	nyf,
		int *	nzf,
		int *	nx,
		int *	ny,
		int *	nz,
		double *	oPC,
		double *	oPN,
		double *	oPS,
		double *	oPE,
		double *	oPW,
		double *	oPNE,
		double *	oPNW,
		double *	oPSE,
		double *	oPSW,
		double *	uPC,
		double *	uPN,
		double *	uPS,
		double *	uPE,
		double *	uPW,
		double *	uPNE,
		double *	uPNW,
		double *	uPSE,
		double *	uPSW,
		double *	dPC,
		double *	dPN,
		double *	dPS,
		double *	dPE,
		double *	dPW,
		double *	dPNE,
		double *	dPNW,
		double *	dPSE,
		double *	dPSW,
		double *	oC,
		double *	oE,
		double *	oN,
		double *	uC,
		double *	XoC,
		double *	XoE,
		double *	XoN,
		double *	XuC,
		double *	XoNE,
		double *	XoNW,
		double *	XuE,
		double *	XuW,
		double *	XuN,
		double *	XuS,
		double *	XuNE,
		double *	XuNW,
		double *	XuSE,
		double *	XuSW )

Computes a 27-point galerkin coarse grid matrix from a 7-point fine grid matrix.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces buildG_7 from buildGd.f

Expressions for the galerkin coarse grid stencil XA in terms of the fine grid matrix stencil A and the interpolation operator stencil P. these stencils have the form:

XA := array([

matrix([ [ -XdNW(i,j,k), -XdN(i,j,k), -XdNE(i,j,k) ], [ -XdW(i,j,k), -XdC(i,j,k), -XdE(i,j,k) ], [ -XdSW(i,j,k), -XdS(i,j,k), -XdSE(i,j,k) ] ]),

matrix([ [ -XoNW(i,j,k), -XoN(i,j,k), -XoNE(i,j,k) ], [ -XoW(i,j,k), XoC(i,j,k), -XoE(i,j,k) ], [ -XoSW(i,j,k), -XoS(i,j,k), -XoSE(i,j,k) ] ]),

matrix([ [ -XuNW(i,j,k), -XuN(i,j,k), -XuNE(i,j,k) ], [ -XuW(i,j,k), -XuC(i,j,k), -XuE(i,j,k) ], [ -XuSW(i,j,k), -XuS(i,j,k), -XuSE(i,j,k) ] ]) ]):

A := array([

matrix([ [ 0, 0, 0 ], [ 0, -dC(i,j,k), 0 ], [ 0, 0, 0 ] ]),

matrix([ [ 0, -oN(i,j,k), 0 ], [ -oW(i,j,k), oC(i,j,k), -oE(i,j,k) ], [ 0, -oS(i,j,k), 0 ] ]),

matrix([ [ 0, 0, 0 ], [ 0, -uC(i,j,k), 0 ], [ 0, 0, 0 ] ])

P := array([

matrix([ [ dPNW(i,j,k), dPN(i,j,k), dPNE(i,j,k) ], [ dPW(i,j,k), dPC(i,j,k), dPE(i,j,k) ], [ dPSW(i,j,k), dPS(i,j,k), dPSE(i,j,k) ] ]),

matrix([ [ oPNW(i,j,k), oPN(i,j,k), oPNE(i,j,k) ], [ oPW(i,j,k), oPC(i,j,k), oPE(i,j,k) ], [ oPSW(i,j,k), oPS(i,j,k), oPSE(i,j,k) ] ]),

matrix([ [ uPNW(i,j,k), uPN(i,j,k), uPNE(i,j,k) ], [ uPW(i,j,k), uPC(i,j,k), uPE(i,j,k) ], [ uPSW(i,j,k), uPS(i,j,k), uPSE(i,j,k) ] ]) ]):

in addition, A is assumed to be symmetric so that:

oS := proc(x,y,z) RETURN( oN(x,y-1,z) ): end: oW := proc(x,y,z) RETURN( oE(x-1,y,z) ): end: dC := proc(x,y,z) RETURN( uC(x,y,z-1) ): end:

Parameters

nxf
nyf
nzf
nx
ny
nz
oPC
oPN
oPS
oPE
oPW
oPNE
oPNW
oPSE
oPSW
uPC
uPN
uPS
uPE
uPW
uPNE
uPNW
uPSE
uPSW
dPC
dPN
dPS
dPE
dPW
dPNE
dPNW
dPSE
dPSW
oC
oE
oN
uC
XoC
XoE
XoN
XuC
XoNE
XoNW
XuE
XuW
XuN
XuS
XuNE
XuNW
XuSE
XuSW

Definition at line 450 of file buildGd.c.

◆ Vbuildgaler0()

VEXTERNC void Vbuildgaler0	(	int *	nxf,
		int *	nyf,
		int *	nzf,
		int *	nxc,
		int *	nyc,
		int *	nzc,
		int *	ipkey,
		int *	numdia,
		double *	pcFF,
		int *	ipcFF,
		double *	rpcFF,
		double *	acFF,
		double *	ccFF,
		double *	fcFF,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	fc )

Form the Galerkin coarse grid system.

Note: Although the fine grid matrix may be 7 or 27 diagonal, the coarse grid matrix is always 27 diagonal. (only 14 stored due to symmetry.)

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces buildgaler0 from mgsubd.f

Parameters

nxf
nyf
nzf
nxc
nyc
nzc
ipkey
numdia
pcFF
ipcFF
rpcFF
acFF
ccFF
fcFF
ipc
rpc
ac
cc
fc

Definition at line 341 of file mgsubd.c.

◆ Vbuildops()

VEXTERNC void Vbuildops	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	nlev,
		int *	ipkey,
		int *	iinfo,
		int *	ido,
		int *	iz,
		int *	mgprol,
		int *	mgcoar,
		int *	mgsolv,
		int *	mgdisc,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	xf,
		double *	yf,
		double *	zf,
		double *	gxcf,
		double *	gycf,
		double *	gzcf,
		double *	a1cf,
		double *	a2cf,
		double *	a3cf,
		double *	ccf,
		double *	fcf,
		double *	tcf )

Build operators, boundary arrays, modify affine vectors ido==0: do only fine level ido==1: do only coarse levels (including second op at coarsest) ido==2: do all levels ido==3: rebuild the second operator at the coarsest level.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Note: The fine level must be build before any coarse levels.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Replaces buildops from mgsubd.f

Parameters

nx
ny
nz
nlev
ipkey
iinfo
ido
iz
mgprol
mgcoar
mgsolv
mgdisc
ipc
rpc
pc
ac
cc
fc
xf
yf
zf
gxcf
gycf
gzcf
a1cf
a2cf
a3cf
ccf
fcf
tcf

Definition at line 57 of file mgsubd.c.

◆ VbuildP()

VEXTERNC void VbuildP	(	int *	nxf,
		int *	nyf,
		int *	nzf,
		int *	nxc,
		int *	nyc,
		int *	nzc,
		int *	mgprol,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	xf,
		double *	yf,
		double *	zf )

Builds prolongation matrix.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Parameters

nxf
nyf
nzf
nxc
nyc
nzc
mgprol
ipc
rpc
pc
ac
xf
yf
zf

Definition at line 57 of file buildPd.c.

◆ Vbuildstr()

VEXTERNC void Vbuildstr	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	nlev,
		int *	iz )

Build the nexted operator framework in the array iz.

Note: iz(50,i) indexes into the gridfcn arrays for each level i=(1,...,nlev+1) as follows:

fun(i) = fun (iz(1,i)) bndx(i) = bndx(iz(2,i)) bndy(i) = bndy(iz(3,i)) bndz(i) = bndz(iz(4,i)) ipc(i) = ipc(iz(5,i)) rpc(i) = rpc(iz(6,i)) oper(i) = oper(iz(7,i)) grdx(i) = brdx(iz(8,i)) grdy(i) = brdy(iz(9,i)) grdz(i) = brdz(iz(10,i))

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces buildstr from mgsubd.f

Parameters

nx
ny
nz
nlev
iz

Definition at line 257 of file mgsubd.c.

◆ Vc_vec()

VEXTERNC void Vc_vec	(	double *	coef,
		double *	uin,
		double *	uout,
		int *	nx,
		int *	ny,
		int *	nz,
		int *	ipkey )

Define the nonlinearity (vector version)

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces c_vec from mypde.f

Parameters

coef
uin
uout
nx
ny
nz
ipkey

Definition at line 121 of file mypdec.c.

◆ Vc_vecpmg()

VEXTERNC void Vc_vecpmg	(	double *	coef,
		double *	uin,
		double *	uout,
		int *	nx,
		int *	ny,
		int *	nz,
		int *	ipkey )

Define the nonlinearity (vector version)

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces c_vecpmg from mypde.f

Parameters

coef
uin
uout
nx
ny
nz
ipkey

Definition at line 133 of file mypdec.c.

◆ Vc_vecsmpbe()

VEXTERNC void Vc_vecsmpbe	(	double *	coef,
		double *	uin,
		double *	uout,
		int *	nx,
		int *	ny,
		int *	nz,
		int *	ipkey )

Define the nonlinearity (vector version)

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces c_vecpmg from mypde.f

Parameters

coef
uin
uout
nx
ny
nz
ipkey

Definition at line 213 of file mypdec.c.

◆ Vcghs()

VEXTERNC void Vcghs	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	x,
		double *	p,
		double *	ap,
		double *	r,
		int *	itmax,
		int *	iters,
		double *	errtol,
		double *	omega,
		int *	iresid,
		int *	iadjoint )

A collection of useful low-level routines (timing, etc).

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Parameters

nx
ny
nz
ipc
rpc
ac
cc
fc
x
p
ap
r
itmax
iters
errtol
omega
iresid
iadjoint

Definition at line 57 of file cgd.c.

◆ Vdc_vec()

VEXTERNC void Vdc_vec	(	double *	coef,
		double *	uin,
		double *	uout,
		int *	nx,
		int *	ny,
		int *	nz,
		int *	ipkey )

Define the derivative of the nonlinearity (vector version)

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces dc_vec from mypde.f

Parameters

coef
uin
uout
nx
ny
nz
ipkey

Definition at line 341 of file mypdec.c.

◆ Vdpbsl()

VEXTERNC void Vdpbsl	(	double *	abd,
		int *	lda,
		int *	n,
		int *	m,
		double *	b )

LINPACK interface.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Solves the double precision symmetric positive definite band system A*X = B using the factors computed by dpbco or dpbfa

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: A division by zero will occur if the input factor contains a zero on the diagonal. Technically this indicates singularity, but it is usually caused by imporper subroutine arugments. It will not occur if the subroutines are called correctly and info == 0; Replaces dpbsl from mgsubd.f

Parameters

abd	The output from dpbco or dpbfa
lda	The leading dimension of the array abd
n	The order of the matrix a
m	The number of diagonals above the main diagonal
b	The right hand side vector

Definition at line 57 of file mlinpckd.c.

◆ Vextrac()

VEXTERNC void Vextrac	(	int *	nxf,
		int *	nyf,
		int *	nzf,
		int *	nxc,
		int *	ny,
		int *	nzc,
		double *	xin,
		double *	xout )

Simple injection of a fine grid function into coarse grid.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces extrac from matvecd.f

Parameters

nxf
nyf
nzf
nxc
ny
nzc
xin
xout

Definition at line 1078 of file matvecd.c.

◆ VfboundPMG()

VEXTERNC void VfboundPMG	(	int *	ibound,
		int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		double *	gxc,
		double *	gyc,
		double *	gzc )

Initialize a grid function to have a certain boundary value,.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces fboundPMG from mikpckd.f

Parameters

ibound
nx
ny
nz
x
gxc
gyc
gzc

Definition at line 209 of file mikpckd.c.

◆ VfboundPMG00()

VEXTERNC void VfboundPMG00	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x )

Initialize a grid function to have a zero boundary value.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces fboundPMG00 from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
x	The 3d matrix to initialize

Definition at line 258 of file mikpckd.c.

◆ Vfmvfas()

VEXTERNC void Vfmvfas	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		int *	iz,
		double *	w0,
		double *	w1,
		double *	w2,
		double *	w3,
		double *	w4,
		int *	istop,
		int *	itmax,
		int *	iters,
		int *	ierror,
		int *	nlev,
		int *	ilev,
		int *	nlev_real,
		int *	mgsolv,
		int *	iok,
		int *	iinfo,
		double *	epsiln,
		double *	errtol,
		double *	omega,
		int *	nu1,
		int *	nu2,
		int *	mgsmoo,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	tru )

Multigrid nonlinear solve iteration routine.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Nested iteration for a nonlinear multilevel method. Algorithm: nonlinear multigrid iteration (fas)

this routine is the full multigrid front-end for a multigrid v-cycle solver. in other words, at repeatedly calls the v-cycle multigrid solver on successively finer and finer grids.

Note

Author: Tucker Beck [C Translation], Michael Holst [Original]

Replaces fmvfas from mgfasd.f

Parameters

nx
ny
nz
x
iz
w0
w1
w2
w3
w4
istop
itmax
iters
ierror
nlev
ilev
nlev_real
mgsolv
iok
iinfo
epsiln
errtol
omega
nu1
nu2
mgsmoo
ipc
rpc
pc
ac
cc
fc
tru

Definition at line 57 of file mgfasd.c.

◆ Vfnewton()

VPUBLIC void Vfnewton	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		int *	iz,
		double *	w0,
		double *	w1,
		double *	w2,
		double *	w3,
		int *	istop,
		int *	itmax,
		int *	iters,
		int *	ierror,
		int *	nlev,
		int *	ilev,
		int *	nlev_real,
		int *	mgsolv,
		int *	iok,
		int *	iinfo,
		double *	epsiln,
		double *	errtol,
		double *	omega,
		int *	nu1,
		int *	nu2,
		int *	mgsmoo,
		double *	cprime,
		double *	rhs,
		double *	xtmp,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	tru )

Driver routines for the Newton method.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Nested iteration for an inexact-newton-multilevel method.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces fnewton from newtond.f

Parameters

nx
ny
nz
x
iz
w0
w1
w2
w3
istop
itmax
iters
ierror
nlev
ilev
nlev_real
mgsolv
iok
iinfo
epsiln
errtol
omega
nu1
nu2
mgsmoo
cprime
rhs
xtmp
ipc
rpc
pc
ac
cc
fc
tru

Definition at line 58 of file newtond.c.

◆ Vgetjac()

VEXTERNC void Vgetjac	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	nlev_real,
		int *	iz,
		int *	lev,
		int *	ipkey,
		double *	x,
		double *	r,
		double *	cprime,
		double *	rhs,
		double *	cc,
		double *	pc )

Form the jacobian system.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces getjac from newtond.f

Parameters

nx
ny
nz
nlev_real
iz
lev
ipkey
x
r
cprime
rhs
cc
pc

Definition at line 550 of file newtond.c.

◆ Vgsrb()

VEXTERNC void Vgsrb	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	x,
		double *	w1,
		double *	w2,
		double *	r,
		int *	itmax,
		int *	iters,
		double *	errtol,
		double *	omega,
		int *	iresid,
		int *	iadjoint )

Guass-Seidel solver.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Call the fast diagonal iterative method.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces gsrb from gsd.f

Parameters

nx
ny
nz
ipc
rpc
ac
cc
fc
x
w1
w2
r
itmax
iters
errtol
omega
iresid
iadjoint

Definition at line 57 of file gsd.c.

◆ VinterpPMG()

VEXTERNC void VinterpPMG	(	int *	nxc,
		int *	nyc,
		int *	nzc,
		int *	nxf,
		int *	nyf,
		int *	nzf,
		double *	xin,
		double *	xout,
		double *	pc )

Apply the prolongation operator.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces interpPMG from matvecd.f

Parameters

nxc
nyc
nzc
nxf
nyf
nzf
xin
xout
pc

Definition at line 915 of file matvecd.c.

◆ Vipower()

VEXTERNC void Vipower	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	u,
		int *	iz,
		double *	w0,
		double *	w1,
		double *	w2,
		double *	w3,
		double *	w4,
		double *	eigmin,
		double *	eigmin_model,
		double *	tol,
		int *	itmax,
		int *	iters,
		int *	nlev,
		int *	ilev,
		int *	nlev_real,
		int *	mgsolv,
		int *	iok,
		int *	iinfo,
		double *	epsiln,
		double *	errtol,
		double *	omega,
		int *	nu1,
		int *	nu2,
		int *	mgsmoo,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	tru )

Standard inverse power method for minimum eigenvalue estimation.

Note

To test, note that the 3d laplacean has min/max eigenvalues:

 lambda_min = 6 - 2*dcos(pi/(nx-1))
                - 2*dcos(pi/(ny-1))
                - 2*dcos(pi/(nz-1))

 lambda_max = 6 - 2*dcos((nx-2)*pi/(nx-1))
                - 2*dcos((ny-2)*pi/(ny-1))
                - 2*dcos((nz-2)*pi/(nz-1))

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces ipower from powerd.f

Parameters

nx
ny
nz
u
iz
w0
w1
w2
w3
w4
eigmin
eigmin_model
tol
itmax
iters
nlev
ilev
nlev_real
mgsolv
iok
iinfo
epsiln
errtol
omega
nu1
nu2
mgsmoo
ipc
rpc
pc
ac
cc
tru

Definition at line 165 of file powerd.c.

◆ Vmatvec()

VEXTERNC void Vmatvec	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	x,
		double *	y )

Matrix-vector multiplication routines.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Break the matrix data-structure into diagonals and then call the matrix-vector routine.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces matvec from matvecd.f

Parameters

nx
ny
nz
ipc
rpc
ac
cc
x
y

Definition at line 57 of file matvecd.c.

◆ Vmgdriv()

VEXTERNC void Vmgdriv	(	int *	iparm,
		double *	rparm,
		int *	iwork,
		double *	rwork,
		double *	u,
		double *	xf,
		double *	yf,
		double *	zf,
		double *	gxcf,
		double *	gycf,
		double *	gzcf,
		double *	a1cf,
		double *	a2cf,
		double *	a3cf,
		double *	ccf,
		double *	fcf,
		double *	tcf )

Multilevel solver driver.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy.
* Portions Copyright (c) 2002-2012, 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [C Translation], Michael Holst [Original]

Replaces mgdriv from mgdrvd.f

Parameters

iparm
rparm
iwork
rwork
u
xf
yf
zf
gxcf
gycf
gzcf
a1cf
a2cf
a3cf
ccf
fcf
tcf

Definition at line 57 of file mgdrvd.c.

◆ Vmgdriv2()

VEXTERNC void Vmgdriv2	(	int *	iparm,
		double *	rparm,
		int *	nx,
		int *	ny,
		int *	nz,
		double *	u,
		int *	iz,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	xf,
		double *	yf,
		double *	zf,
		double *	gxcf,
		double *	gycf,
		double *	gzcf,
		double *	a1cf,
		double *	a2cf,
		double *	a3cf,
		double *	ccf,
		double *	fcf,
		double *	tcf )

Solves the pde using the multi-grid method.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Replaces mgdriv2 from mgdrvd.f

This routine uses a multigrid method to solve the following three-dimensional, 2nd order elliptic partial differential equation:

 lu = f, u in omega
  u = g, u on boundary of omega

where

 omega = [xmin,xmax]x[ymin,ymax]x[zmin,zmax]

the multigrid code requires the operator in the form:

 - \nabla \cdot (a \nabla u) + c(u) = f

with

a(x,y,z),f(x,y,z), scalar functions (possibly discontinuous)
on omega.  (discontinuities must be along fine grid lines).
boundary function g(x,y,z) is smooth on boundary of omega.

the function c(u) is a possibly nonlinear function of the
unknown u, and varies (possibly discontinuously) with the
spatial position also.

user inputs:

the user must provide the coefficients of the differential
operator, some initial parameter settings in an integer and a
real parameter array, and various work arrays.

Parameters

iparm
rparm
nx
ny
nz
u
iz
ipc
rpc
pc
ac
cc
fc
xf
yf
zf
gxcf
gycf
gzcf
a1cf
a2cf
a3cf
ccf
fcf
tcf

Definition at line 190 of file mgdrvd.c.

◆ Vmgsz()

VEXTERNC void Vmgsz	(	int *	mgcoar,
		int *	mgdisc,
		int *	mgsolv,
		int *	nx,
		int *	ny,
		int *	nz,
		int *	nlev,
		int *	nxc,
		int *	nyc,
		int *	nzc,
		int *	nf,
		int *	nc,
		int *	narr,
		int *	narrc,
		int *	n_rpc,
		int *	n_iz,
		int *	n_ipc,
		int *	iretot,
		int *	iintot )

This routine computes the required sizes of the real and integer work arrays for the multigrid code. these two sizes are a (complicated) function of input parameters.

The work arrays must have been declared in the calling program as:

double precision rwork(iretot)
integer          iwork(iintot)

where:

iretot   = function_of(mgcoar,mgdisc,mgsolv,nx,ny,nz,nlev)
iintot   = function_of(mgcoar,mgdisc,mgsolv,nx,ny,nz,nlev)

mgcoar   = coarsening technique:
           0=standard discretization
           1=averaged coefficient + standard discretization
           2=algebraic galerkin coarsening

mgdisc   = discretization technique:
           0=box method
           1=fem method

mgsolv   = coarse grid solver:
           0=conjugate gradients
           1=symmetric banded linpack solver

nx,ny,nz = grid dimensions in each direction,
           including boundary points

nlev     = the number of multigrid levels desired for the
           method.

other parameters:

nf       = number of unknowns on the finest mesh
         = nx * ny * nz

nc       = number of unknowns on the coarsest mesh

narr     = storage for one vector on all the meshes

narrc    = storage for one vector on all the meshes but the finest

the work arrays rwork and iwork will be chopped into smaller pieces according to:

double precision ac(STORE)         (system operators on all levels)
double precision pc(27*narrc)      (prol. opers for coarse levels)
double precision cc(narr),fc(narr) (helmholtz term, rhs -- all levels)
double precision rpc(100*(nlev+1)) (real info for all levels)
integer          ipc(100*(nlev+1)) (integer info for all levels)
integer          iz(50,nlev+1),    (pointers into ac,pc,cc,fc,etc.)

where STORE depends on the discretization, coarsening, and coarse grid solver:

STORE =  4*nf +  4*narrc + NBAND*nc (mgdisc=box, mgcoar=stan/harm)
   or =  4*nf + 14*narrc + NBAND*nc (mgdisc=box, mgcoar=gal)
   or = 14*nf + 14*narrc + NBAND*nc (mgdisc=fem, mgcoar=stan/harm/gal)

NBAND = 0                           (mgsolv=iterative)
   or = 1+(nxc-2)*(nyc-2)           (mgsolv=7-pt banded linpack)
   or = 1+(nxc-2)*(nyc-2)+(nxc-2)+1 (mgsolv=27-pt banded linpack)

Author: Tucker Beck [C Translation], Michael Holst [Original]

Replaces mgsz from mgdrvd.f

Parameters

mgcoar
mgdisc
mgsolv
nx
ny
nz
nlev
nxc
nyc
nzc
nf
nc
narr
narrc
n_rpc
n_iz
n_ipc
iretot
iintot

Definition at line 562 of file mgdrvd.c.

◆ Vmresid()

VEXTERNC void Vmresid	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	x,
		double *	r )

Break the matrix data-structure into diagonals and then call the residual routine.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces mresid from matvecd.f

Parameters

nx
ny
nz
ipc
rpc
ac
cc
fc
x
r

Definition at line 426 of file matvecd.c.

◆ Vmvcs()

VEXTERNC void Vmvcs	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		int *	iz,
		double *	w0,
		double *	w1,
		double *	w2,
		double *	w3,
		int *	istop,
		int *	itmax,
		int *	iters,
		int *	ierror,
		int *	nlev,
		int *	ilev,
		int *	nlev_real,
		int *	mgsolv,
		int *	iok,
		int *	iinfo,
		double *	epsiln,
		double *	errtol,
		double *	omega,
		int *	nu1,
		int *	nu2,
		int *	mgsmoo,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	tru )

MG helper functions.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Screaming linear multilevel method.

algorithm: linear multigrid iteration (cs)

multigrid v-cycle solver.

input: (1) fine and coarse grid discrete linear operators: L_h, L_H (2) fine grid source function: f_h (3) fine grid approximate solution: u_h

output: (1) fine grid improved solution: u_h

the two-grid algorithm is: (1) pre-smooth: u1_h = smooth(L_h,f_h,u_h) (2) restrict defect: d_H = r(L_h(u1_h) - f_h) (3) solve for correction: c_H = L_H^{-1}(d_H) (4) prolongate and correct: u2_h = u1_h - p(c_H) (5) post-smooth: u_h = smooth(L_h,f_h,u2_h)

(of course, c_H is determined with another two-grid algorithm)

implementation notes: (0) "u1_h" must be kept on each level until "c_H" is computed, and then both are used to compute "u2_h". (1) "u_h" (and then "u1_h") on all levels is stored in the "x" array. (2) "d_H" is identically "f_h" for f_h on the next coarser grid. (3) "c_h" is identically "u_h" for u_h on the next coarser grid. (4) "d_H" is stored in the "r" array (must be kept for post-smooth). (5) "f_h" is stored in the "fc" array. (6) "L_h" on all levels is stored in the "ac" array. (7) signs may be reveresed; i.e., residual is used in place of the defect in places, etc.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces mvcs from mgcsd.f

New grid size

Parameters

nx
ny
nz
x
iz
w0
w1
w2
w3
istop
itmax
iters
ierror
nlev
ilev
nlev_real
mgsolv
iok
iinfo
epsiln
errtol
omega
nu1
nu2
mgsmoo
ipc
rpc
pc
ac
cc
fc
tru

Definition at line 57 of file mgcsd.c.

◆ Vmvfas()

VEXTERNC void Vmvfas	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		int *	iz,
		double *	w0,
		double *	w1,
		double *	w2,
		double *	w3,
		double *	w4,
		int *	istop,
		int *	itmax,
		int *	iters,
		int *	ierror,
		int *	nlev,
		int *	ilev,
		int *	nlev_real,
		int *	mgsolv,
		int *	iok,
		int *	iinfo,
		double *	epsiln,
		double *	errtol,
		double *	omega,
		int *	nu1,
		int *	nu2,
		int *	mgsmoo,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	tru )

Nonlinear multilevel method.

Note: Replaces mvfas from mgfasd.f

Author: Tucker Beck [C Translation], Michael Holst [Original]

Algorithm: nonlinear multigrid iteration (fas)

multigrid v-cycle solver.

input: (1) fine and coarse grid discrete nonlinear operators: L_h, L_H (2) fine grid source function: f_h (3) fine grid approximate solution: u_h

output: (1) fine grid improved solution: u_h

the two-grid algorithm is: (1) pre-smooth: u1_h = smooth(L_h,f_h,u_h) (2) restrict defect: d_H = r(L_h(u1_h) - f_h) restrict solution: u_H = r(u1_h) (3) form coarse grid rhs: f_H = L_H(u_H) - d_H solve for correction: c_H = L_H^{-1}(f_H) (4) prolongate and correct: u2_h = u1_h - p(c_H - u_H) (5) post-smooth: u_h = smooth(L_h,f_h,u2_h)

(of course, c_H is determined with another two-grid algorithm)

implementation notes: (0) "u1_h" and "u_H" must be kept on each level until "c_H" is computed, and then all three are used to compute "u2_h". (1) "u_h" (and then "u1_h") on all levels is stored in the "x" array. (2) "u_H" on all levels is stored in the "e" array. (3) "c_h" is identically "u_h" for u_h on the next coarser grid. (4) "d_H" is stored in the "r" array. (5) "f_h" and "f_H" are stored in the "fc" array. (6) "L_h" on all levels is stored in the "ac" array. (7) signs may be reveresed; i.e., residual is used in place of the defect in places, etc.

Parameters

nx
ny
nz
x
iz
w0
w1
w2
w3
w4
istop
itmax
iters
ierror
nlev
ilev
nlev_real
mgsolv
iok
iinfo
epsiln
errtol
omega
nu1
nu2
mgsmoo
ipc
rpc
pc
ac
cc
fc
tru

Definition at line 157 of file mgfasd.c.

◆ Vmypdefinitlpbe()

VEXTERNC void Vmypdefinitlpbe	(	int *	tnion,
		double *	tcharge,
		double *	tsconc )

Set up the ionic species to be used in later calculations. This must be called before any other of the routines in this file.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [C Translation], Nathan Baker [Original]

Note: Replaces mypdefinitlpbe from mypde.f

Parameters

tnion	The number if ionic species
tcharge	The charge in electrons
tsconc	Prefactor for conterion Bolzmann distribution terms. Basically a scaled concentration -(ion concentration/bulkIonicStrength)/2

Definition at line 57 of file mypdec.c.

◆ Vmypdefinitnpbe()

VEXTERNC void Vmypdefinitnpbe	(	int *	tnion,
		double *	tcharge,
		double *	tsconc )

Set up the ionic species to be used in later calculations. This must be called before any other of the routines in this file.

Author: Tucker Beck [C Translation], Nathan Baker [Original]

Note: Replaces mypdefinitnpbe from mypde.f

Parameters

tnion	The number if ionic species
tcharge	The charge in electrons
tsconc	Prefactor for conterion Bolzmann distribution terms. Basically a scaled concentration -(ion concentration/bulkIonicStrength)/2

Definition at line 75 of file mypdec.c.

◆ Vmypdefinitsmpbe()

VEXTERNC void Vmypdefinitsmpbe	(	int *	tnion,
		double *	tcharge,
		double *	tsconc,
		double *	smvolume,
		double *	smsize )

Set up the ionic species to be used in later calculations. This must be called before any other of the routines in this file.

Author: Tucker Beck [C Translation], Nathan Baker [Original]

Note: Replaces mypdefinitsmpbe from mypde.f

Parameters

tnion	The number if ionic species
tcharge	The charge in electrons
tsconc	Prefactor for conterion Bolzmann distribution terms. Basically a scaled concentration -(ion concentration/bulkIonicStrength)/2
smvolume
smsize

Definition at line 93 of file mypdec.c.

◆ Vnewdriv()

VEXTERNC void Vnewdriv	(	int *	iparm,
		double *	rparm,
		int *	iwork,
		double *	rwork,
		double *	u,
		double *	xf,
		double *	yf,
		double *	zf,
		double *	gxcf,
		double *	gycf,
		double *	gzcf,
		double *	a1cf,
		double *	a2cf,
		double *	a3cf,
		double *	ccf,
		double *	fcf,
		double *	tcf )

Driver for the Newton Solver.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Driver for a screaming inexact-newton-multilevel solver.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces newdriv from newdrvd.f

Parameters

iparm
rparm
iwork
rwork
u
xf
yf
zf
gxcf
gycf
gzcf
a1cf
a2cf
a3cf
ccf
fcf
tcf

Definition at line 57 of file newdrvd.c.

◆ Vnewdriv2()

VEXTERNC void Vnewdriv2	(	int *	iparm,
		double *	rparm,
		int *	nx,
		int *	ny,
		int *	nz,
		double *	u,
		int *	iz,
		double *	w1,
		double *	w2,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	xf,
		double *	yf,
		double *	zf,
		double *	gxcf,
		double *	gycf,
		double *	gzcf,
		double *	a1cf,
		double *	a2cf,
		double *	a3cf,
		double *	ccf,
		double *	fcf,
		double *	tcf )

Solves using Newton's Method.

Author: Tucker Beck [C Translation], Michael Holst [Original]

This routine uses a newton's method, combined with a linear multigrid iteration, to solve the following three-dimensional, 2nd order elliptic partial differential equation:

 lu = f, u in omega
  u = g, u on boundary of omega

where

 omega = [xmin,xmax]x[ymin,ymax]x[zmin,zmax]

the multigrid code requires the operator in the form:

 - \nabla \cdot (a \nabla u) + c(u) = f

with

a(x,y,z),f(x,y,z), scalar functions (possibly discontinuous)
on omega.  (discontinuities must be along fine grid lines).
boundary function g(x,y,z) is smooth on boundary of omega.

the function c(u) is a possibly nonlinear function of the
unknown u, and varies (possibly discontinuously) with the
spatial position also.

User inputs:

the user must provide the coefficients of the differential operator, some initial parameter settings in an integer and a real parameter array, and various work arrays.

Note: Replaces newdriv2 from newdrvd.f

Parameters

iparm
rparm
nx
ny
nz
u
iz
w1
w2
ipc
rpc
pc
ac
cc
fc
xf
yf
zf
gxcf
gycf
gzcf
a1cf
a2cf
a3cf
ccf
fcf
tcf

Definition at line 169 of file newdrvd.c.

◆ Vnewton()

VEXTERNC void Vnewton	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		int *	iz,
		double *	w0,
		double *	w1,
		double *	w2,
		double *	w3,
		int *	istop,
		int *	itmax,
		int *	iters,
		int *	ierror,
		int *	nlev,
		int *	ilev,
		int *	nlev_real,
		int *	mgsolv,
		int *	iok,
		int *	iinfo,
		double *	epsiln,
		double *	errtol,
		double *	omega,
		int *	nu1,
		int *	nu2,
		int *	mgsmoo,
		double *	cprime,
		double *	rhs,
		double *	xtmp,
		int *	ipc,
		double *	rpc,
		double *	pc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	tru )

Inexact-newton-multilevel method.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces newton from newtond.f

Parameters

nx
ny
nz
x
iz
w0
w1
w2
w3
istop
itmax
iters
ierror
nlev
ilev
nlev_real
mgsolv
iok
iinfo
epsiln
errtol
omega
nu1
nu2
mgsmoo
cprime
rhs
xtmp
ipc
rpc
pc
ac
cc
fc
tru

Definition at line 162 of file newtond.c.

◆ Vnmatvec()

VEXTERNC void Vnmatvec	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	x,
		double *	y,
		double *	w1 )

Break the matrix data-structure into diagonals and then call the matrix-vector routine.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces nmatvec from matvecd.f

Parameters

nx
ny
nz
ipc
rpc
ac
cc
x
y
w1

Definition at line 232 of file matvecd.c.

◆ Vnmresid()

VEXTERNC void Vnmresid	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	x,
		double *	r,
		double *	w1 )

Break the matrix data-structure into diagonals and then call the residual routine.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces nmresid from matvecd.f

Parameters

nx
ny
nz
ipc
rpc
ac
cc
fc
x
r
w1

Definition at line 598 of file matvecd.c.

◆ Vnsmooth()

VEXTERNC void Vnsmooth	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	x,
		double *	w1,
		double *	w2,
		double *	r,
		int *	itmax,
		int *	iters,
		double *	errtol,
		double *	omega,
		int *	iresid,
		int *	iadjoint,
		int *	meth )

call the appropriate non-linear smoothing routine.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces nsmooth from nsmoothd.f

Parameters

nx
ny
nz
ipc
rpc
ac
cc
fc
x
w1
w2
r
itmax
iters
errtol
omega
iresid
iadjoint
meth

Definition at line 98 of file smoothd.c.

◆ Vpower()

VEXTERNC void Vpower	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	iz,
		int *	ilev,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	w1,
		double *	w2,
		double *	w3,
		double *	w4,
		double *	eigmax,
		double *	eigmax_model,
		double *	tol,
		int *	itmax,
		int *	iters,
		int *	iinfo )

Power methods for eigenvalue estimation.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Standard power method for maximum eigenvalue estimation of a matrix c* c*

Note: To test, note that the 3d laplacean has min/max eigenvalues: c* c* lambda_min = 6 - 2*dcos(pi/(nx-1)) c* - 2*dcos(pi/(ny-1)) c* - 2*dcos(pi/(nz-1)) c* c* lambda_max = 6 - 2*dcos((nx-2)*pi/(nx-1)) c* - 2*dcos((ny-2)*pi/(ny-1)) c* - 2*dcos((nz-2)*pi/(nz-1))

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces power from powerd.f; Vpower is yet untested as a call stack including it hasn't been found

Parameters

nx
ny
nz
iz
ilev
ipc
rpc
ac
cc
w1
w2
w3
w4
eigmax
eigmax_model
tol
itmax
iters
iinfo

Definition at line 57 of file powerd.c.

◆ Vprtmatd()

VEXTERNC void Vprtmatd	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac )

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces prtmatd from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
ipc	Integer parameters
rpc	Double parameters
ac

Definition at line 332 of file mikpckd.c.

◆ Vrestrc()

VEXTERNC void Vrestrc	(	int *	nxf,
		int *	nyf,
		int *	nzf,
		int *	nxc,
		int *	nyc,
		int *	nzc,
		double *	xin,
		double *	xout,
		double *	pc )

Apply the restriction operator.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces restrc from matvecd.f

Parameters

nxf
nyf
nzf
nxc
nyc
nzc
xin
xout
pc

Definition at line 782 of file matvecd.c.

◆ Vsmooth()

VEXTERNC void Vsmooth	(	int *	nx,
		int *	ny,
		int *	nz,
		int *	ipc,
		double *	rpc,
		double *	ac,
		double *	cc,
		double *	fc,
		double *	x,
		double *	w1,
		double *	w2,
		double *	r,
		int *	itmax,
		int *	iters,
		double *	errtol,
		double *	omega,
		int *	iresid,
		int *	iadjoint,
		int *	meth )

Multigrid smoothing functions.

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

call the appropriate linear smoothing routine.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces smooth from smoothd.f

Parameters

nx
ny
nz
ipc
rpc
ac
cc
fc
x
w1
w2
r
itmax
iters
errtol
omega
iresid
iadjoint
meth

Definition at line 58 of file smoothd.c.

◆ Vxaxpy()

VEXTERNC void Vxaxpy	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	alpha,
		double *	x,
		double *	y )

saxpy operation for a grid function with boundary values.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces xaxpy from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
alpha
x	The source matrix from which to copy data
y	The destination matrix to receive copied data

Definition at line 112 of file mikpckd.c.

◆ Vxcopy()

VEXTERNC void Vxcopy	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		double *	y )

A collection of useful low-level routines (timing, etc).

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 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 Washington University in St. Louis 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.
*
*

Author: Tucker Beck [fortran ->c translation], Michael Holst [original]

Version: $Id:

Attention

*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnl.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 Energy. Portions Copyright (c) 2002-2010, Washington University in St. Louis. Portions Copyright (c) 2002-2010, 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 Washington University in St. Louis 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.
*
*

Copy operation for a grid function with boundary values. Quite simply copies one 3d matrix to another

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces xcopy from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
x	The source matrix from which to copy data
y	The destination matrix to receive copied data

Definition at line 57 of file mikpckd.c.

◆ Vxcopy_large()

VEXTERNC void Vxcopy_large	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		double *	y )

Copy operation for a grid function with boundary values. Quite simply copies one 3d matrix to another.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces xcopy_large from mikpckd.f

Note: This function is exactly equivalent to calling xcopy_small with the matrix arguments reversed.

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
x	The source matrix from which to copy data
y	The destination matrix to receive copied data

Definition at line 91 of file mikpckd.c.

◆ Vxcopy_small()

VEXTERNC void Vxcopy_small	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		double *	y )

Copy operation for a grid function with boundary values. Quite simply copies one 3d matrix to another.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces xcopy_small from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
x	The source matrix from which to copy data
y	The destination matrix to receive copied data

Definition at line 75 of file mikpckd.c.

◆ Vxdot()

VEXTERNC double Vxdot	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x,
		double *	y )

Inner product operation for a grid function with boundary values.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces xdot from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
x	The first vector
y	The second vector

Definition at line 173 of file mikpckd.c.

◆ Vxnrm1()

VEXTERNC double Vxnrm1	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x )

Norm operation for a grid function with boundary values.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces xnrm1 from mikpckd.f

< Accumulates the calculated normal value

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
x	The matrix to normalize

Definition at line 131 of file mikpckd.c.

◆ Vxnrm2()

VEXTERNC double Vxnrm2	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	x )

Norm operation for a grid function with boundary values.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces xnrm2 from mikpckd.f

< Accumulates the calculated normal value

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
x	The matrix to normalize

Definition at line 152 of file mikpckd.c.

◆ Vxscal()

VEXTERNC void Vxscal	(	int *	nx,
		int *	ny,
		int *	nz,
		double *	fac,
		double *	x )

Scale operation for a grid function with boundary values.

Author: Tucker Beck [C Translation], Michael Holst [Original]

Note: Replaces xscal from mikpckd.f

Parameters

nx	The size of the x dimension of the 3d matrix
ny	The size of the y dimension of the 3d matrix
nz	The size of the z dimension of the 3d matrix
fac	The scaling factor
x	The 3d matrix to scale

Definition at line 318 of file mikpckd.c.

Macros

Functions

Detailed Description

Macro Definition Documentation

◆ HARMO2

◆ MAXIONS

Function Documentation

◆ Vaxrand()

◆ Vazeros()

◆ VbuildA()

◆ Vbuildband()

◆ Vbuildband1_27()

◆ Vbuildband1_7()

◆ VbuildG()

◆ VbuildG_1()

◆ VbuildG_27()

◆ VbuildG_7()

◆ Vbuildgaler0()

◆ Vbuildops()

◆ VbuildP()

◆ Vbuildstr()

◆ Vc_vec()

◆ Vc_vecpmg()

◆ Vc_vecsmpbe()

◆ Vcghs()

◆ Vdc_vec()

◆ Vdpbsl()

◆ Vextrac()

◆ VfboundPMG()

◆ VfboundPMG00()

◆ Vfmvfas()

◆ Vfnewton()

◆ Vgetjac()

◆ Vgsrb()

◆ VinterpPMG()

◆ Vipower()

◆ Vmatvec()

◆ Vmgdriv()

◆ Vmgdriv2()

◆ Vmgsz()

◆ Vmresid()

◆ Vmvcs()

◆ Vmvfas()

◆ Vmypdefinitlpbe()

◆ Vmypdefinitnpbe()

◆ Vmypdefinitsmpbe()

◆ Vnewdriv()

◆ Vnewdriv2()

◆ Vnewton()

◆ Vnmatvec()

◆ Vnmresid()

◆ Vnsmooth()

◆ Vpower()

◆ Vprtmatd()

◆ Vrestrc()

◆ Vsmooth()

◆ Vxaxpy()

◆ Vxcopy()

◆ Vxcopy_large()

◆ Vxcopy_small()

◆ Vxdot()

◆ Vxnrm1()

◆ Vxnrm2()

◆ Vxscal()