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Defines | |
#define | APBS_TIMER_WALL_CLOCK 26 |
APBS total execution timer ID. | |
#define | APBS_TIMER_SETUP 27 |
APBS setup timer ID. | |
#define | APBS_TIMER_SOLVER 28 |
APBS solver timer ID. | |
#define | APBS_TIMER_ENERGY 29 |
APBS energy timer ID. | |
#define | APBS_TIMER_FORCE 30 |
APBS force timer ID. | |
#define | APBS_TIMER_TEMP1 31 |
APBS temp timer #1 ID. | |
#define | APBS_TIMER_TEMP2 32 |
APBS temp timer #2 ID. | |
#define | MAXMOL 5 |
The maximum number of molecules that can be involved in a single PBE calculation. | |
#define | MAXION 10 |
The maximum number of ion species that can be involved in a single PBE calculation. | |
#define | MAXFOCUS 5 |
The maximum number of times an MG calculation can be focused. | |
#define | VMGNLEV 4 |
Minimum number of levels in a multigrid calculations. | |
#define | VREDFRAC 0.25 |
Maximum reduction of grid spacing during a focusing calculation. | |
#define | VAPBS_NVS 4 |
Number of vertices per simplex (hard-coded to 3D). | |
#define | VAPBS_DIM 3 |
Our dimension. | |
#define | VAPBS_RIGHT 0 |
Face definition for a volume. | |
#define | VAPBS_FRONT 1 |
Face definition for a volume. | |
#define | VAPBS_UP 2 |
Face definition for a volume. | |
#define | VAPBS_LEFT 3 |
Face definition for a volume. | |
#define | VAPBS_BACK 4 |
Face definition for a volume. | |
#define | VAPBS_DOWN 5 |
Face definition for a volume. | |
#define | VPMGSMALL 1e-12 |
A small number used in Vpmg to decide if points are on/off grid-lines or non-zer0 (etc.). | |
#define | VF77_MANGLE(name, NAME) name |
Name-mangling macro for using FORTRAN functions in C code. | |
#define | VFLOOR(value) floor(value) |
Wrapped floor to fix floating point issues in the Intel compiler. | |
#define | VEMBED(rctag) |
Allows embedding of RCS ID tags in object files. | |
Typedefs | |
typedef enum eVsurf_Meth | Vsurf_Meth |
Declaration of the Vsurf_Meth type as the Vsurf_Meth enum. | |
typedef enum eVhal_PBEType | Vhal_PBEType |
Declaration of the Vhal_PBEType type as the Vhal_PBEType enum. | |
typedef enum eVhal_IPKEYType | Vhal_IPKEYType |
Declaration of the Vhal_IPKEYType type as the Vhal_IPKEYType enum. | |
typedef enum eVhal_NONLINType | Vhal_NONLINType |
Declaration of the Vhal_NONLINType type as the Vhal_NONLINType enum. | |
typedef enum eVoutput_Format | Voutput_Format |
Declaration of the Voutput_Format type as the VOutput_Format enum. | |
typedef enum eVbcfl | Vbcfl |
Declare Vbcfl type. | |
typedef enum eVchrg_Meth | Vchrg_Meth |
Declaration of the Vchrg_Meth type as the Vchrg_Meth enum. | |
typedef enum eVchrg_Src | Vchrg_Src |
Declaration of the Vchrg_Src type as the Vchrg_Meth enum. | |
typedef enum eVdata_Type | Vdata_Type |
Declaration of the Vdata_Type type as the Vdata_Type enum. | |
typedef enum eVdata_Format | Vdata_Format |
Declaration of the Vdata_Format type as the Vdata_Format enum. | |
Enumerations | |
enum | eVrc_Codes { VRC_WARNING = -1 } |
Return code enumerations. More... | |
enum | eVsurf_Meth { VSM_MOL = 0, VSM_MOLSMOOTH = 1, VSM_SPLINE = 2, VSM_SPLINE3 = 3, VSM_SPLINE4 = 4 } |
Types of molecular surface definitions. More... | |
enum | eVhal_PBEType { PBE_LPBE, PBE_NPBE, PBE_LRPBE , PBE_SMPBE } |
Version of PBE to solve. More... | |
enum | eVhal_IPKEYType { IPKEY_SMPBE = -2, IPKEY_LPBE, IPKEY_NPBE } |
Type of ipkey to use for MG methods. More... | |
enum | eVhal_NONLINType |
Type of nonlinear to use for MG methods. | |
enum | eVoutput_Format { OUTPUT_NULL, OUTPUT_FLAT, OUTPUT_XML } |
Output file format. More... | |
enum | eVbcfl { BCFL_ZERO = 0, BCFL_SDH = 1, BCFL_MDH = 2, BCFL_UNUSED = 3, BCFL_FOCUS = 4 } |
Types of boundary conditions. More... | |
enum | eVchrg_Meth { VCM_TRIL = 0, VCM_BSPL2 = 1, VCM_BSPL4 = 2 } |
Types of charge discretization methods. More... | |
enum | eVchrg_Src { VCM_CHARGE = 0, VCM_PERMANENT = 1, VCM_INDUCED = 2, VCM_NLINDUCED = 3 } |
Charge source. More... | |
enum | eVdata_Type { VDT_CHARGE, VDT_POT, VDT_SMOL, VDT_SSPL, VDT_VDW, VDT_IVDW, VDT_LAP, VDT_EDENS, VDT_NDENS, VDT_QDENS, VDT_DIELX, VDT_DIELY, VDT_DIELZ, VDT_KAPPA } |
Types of (scalar) data that can be written out of APBS. More... | |
enum | eVdata_Format { VDF_DX = 0, VDF_UHBD = 1, VDF_AVS = 2 } |
Format of data that can be written out of APBS. More... |
* * 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) 2002-2007. 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 * * Linking APBS statically or dynamically with other modules is making a * combined work based on APBS. Thus, the terms and conditions of the GNU * General Public License cover the whole combination. * * SPECIAL GPL EXCEPTION * In addition, as a special exception, the copyright holders of APBS * give you permission to combine the APBS program with free software * programs and libraries that are released under the GNU LGPL or with * code included in releases of ISIM, Ion Simulator Interface, PMV, PyMOL * SMOL, VMD, and Vision. Such combined software may be linked with APBS and * redistributed together in original or modified form as mere aggregation * without requirement that the entire work be under the scope of the GNU * General Public License. This special exception permission is also extended * to any software listed in the SPECIAL GPL EXCEPTION clauses by the PMG, * FEtk, MC, or MALOC libraries. * * Note that people who make modified versions of APBS are not obligated * to grant this special exception for their modified versions; it is * their choice whether to do so. The GNU General Public License gives * permission to release a modified version without this exception; this * exception also makes it possible to release a modified version which * carries forward this exception. * *