#include "maloc/maloc.h"
#include "apbs/vhal.h"
#include "apbs/vpmgp.h"
#include "apbs/vacc.h"
#include "apbs/vcap.h"
#include "apbs/vpbe.h"
#include "apbs/vgrid.h"
#include "apbs/mgparm.h"
#include "apbs/pbeparm.h"
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Data Structures | |
| struct | sVpmg |
| Contains public data members for Vpmg class/module. More... | |
Defines | |
| #define | VPMGMAXPART 2000 |
Typedefs | |
| typedef sVpmg | Vpmg |
| Declaration of the Vpmg class as the Vpmg structure. | |
Functions | |
| unsigned long int | Vpmg_memChk (Vpmg *thee) |
| Return the memory used by this structure (and its contents) in bytes. | |
| Vpmg * | Vpmg_ctor (Vpmgp *parms, Vpbe *pbe, int focusFlag, Vpmg *pmgOLD, MGparm *mgparm, PBEparm_calcEnergy energyFlag) |
| Constructor for the Vpmg class (allocates new memory). | |
| int | Vpmg_ctor2 (Vpmg *thee, Vpmgp *parms, Vpbe *pbe, int focusFlag, Vpmg *pmgOLD, MGparm *mgparm, PBEparm_calcEnergy energyFlag) |
| FORTRAN stub constructor for the Vpmg class (uses previously-allocated memory). | |
| void | Vpmg_dtor (Vpmg **thee) |
| Object destructor. | |
| void | Vpmg_dtor2 (Vpmg *thee) |
| FORTRAN stub object destructor. | |
| int | Vpmg_fillco (Vpmg *thee, Vsurf_Meth surfMeth, double splineWin, Vchrg_Meth chargeMeth, int useDielXMap, Vgrid *dielXMap, int useDielYMap, Vgrid *dielYMap, int useDielZMap, Vgrid *dielZMap, int useKappaMap, Vgrid *kappaMap, int useChargeMap, Vgrid *chargeMap) |
| Fill the coefficient arrays prior to solving the equation. | |
| int | Vpmg_solve (Vpmg *thee) |
| Solve the PBE using PMG. | |
| int | Vpmg_solveLaplace (Vpmg *thee) |
| Solve Poisson's equation with a homogeneous Laplacian operator using the solvent dielectric constant. This solution is performed by a sine wave decomposition. | |
| double | Vpmg_energy (Vpmg *thee, int extFlag) |
| Get the total electrostatic energy. | |
| double | Vpmg_qfEnergy (Vpmg *thee, int extFlag) |
| Get the "fixed charge" contribution to the electrostatic energy. | |
| double | Vpmg_qfAtomEnergy (Vpmg *thee, Vatom *atom) |
| Get the per-atom "fixed charge" contribution to the electrostatic energy. | |
| double | Vpmg_qmEnergy (Vpmg *thee, int extFlag) |
| Get the "mobile charge" contribution to the electrostatic energy. | |
| double | Vpmg_dielEnergy (Vpmg *thee, int extFlag) |
| Get the "polarization" contribution to the electrostatic energy. | |
| double | Vpmg_npEnergy (Vpmg *thee, int extFlag) |
| Get the "apolar" energy. | |
| double | Vpmg_dielGradNorm (Vpmg *thee) |
| Get the integral of the gradient of the dielectric function. | |
| int | Vpmg_force (Vpmg *thee, double *force, int atomID, Vsurf_Meth srfm, Vchrg_Meth chgm) |
| Calculate the total force on the specified atom in units of k_B T/AA. | |
| int | Vpmg_qfForce (Vpmg *thee, double *force, int atomID, Vchrg_Meth chgm) |
| Calculate the "charge-field" force on the specified atom in units of k_B T/AA. | |
| int | Vpmg_dbnpForce (Vpmg *thee, double *dbForce, double *npForce, int atomID, Vsurf_Meth srfm) |
| Calculate the dielectric boundary and apolar forces on the specified atom in units of k_B T/AA. | |
| int | Vpmg_ibForce (Vpmg *thee, double *force, int atomID, Vsurf_Meth srfm) |
| Calculate the osmotic pressure on the specified atom in units of k_B T/AA. | |
| void | Vpmg_setPart (Vpmg *thee, double lowerCorner[3], double upperCorner[3], int bflags[6]) |
| Set partition information which restricts the calculation of observables to a (rectangular) subset of the problem domain. | |
| void | Vpmg_unsetPart (Vpmg *thee) |
| Remove partition restrictions. | |
| int | Vpmg_fillArray (Vpmg *thee, double *vec, Vdata_Type type, double parm, Vhal_PBEType pbetype) |
| Fill the specified array with accessibility values. | |
| void | Vpmg_printColComp (Vpmg *thee, char path[72], char title[72], char mxtype[3], int flag) |
| Print out a column-compressed sparse matrix in Harwell-Boeing format. | |
* * APBS -- Adaptive Poisson-Boltzmann Solver * * Nathan A. Baker (baker@biochem.wustl.edu) * Dept. of Biochemistry and Molecular Biophysics * Center for Computational Biology * Washington University in St. Louis * * Additional contributing authors listed in the code documentation. * * Copyright (c) 2002-2005. Washington University in St. Louis. * All Rights Reserved. * Portions Copyright (c) 1999-2002. The Regents of the University of * California. * Portions Copyright (c) 1995. Michael Holst. * * This file is part of APBS. * * APBS is free software; you can redistribute it and/or modify * it under the terms of the GNU General Public License as published by * the Free Software Foundation; either version 2 of the License, or * (at your option) any later version. * * APBS is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU General Public License for more details. * * You should have received a copy of the GNU General Public License * along with APBS; if not, write to the Free Software * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA * *
1.3.5