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vhal.h File Reference

Contains generic macro definitions for APBS. More...

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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...


Detailed Description

Contains generic macro definitions for APBS.

Version:
Id
vhal.h 1092 2007-04-27 15:05:41Z sdg0919
Author:
Nathan A. Baker
Attention:
 *
 * 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.
 *
 * 

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