vhal.h File Reference

Contains generic macro definitions for APBS. More...

This graph shows which files directly or indirectly include this file:

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	SINH_MIN -85.0
	Used to set the min/max values acceptable for sinh chopping.
#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_FAILURE = 0, VRC_SUCCESS = 1 }
	Return code enumerations. More...
enum	eVsol_Meth
	Solution Method 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 file format. More...
enum	eVbcfl { BCFL_ZERO = 0, BCFL_SDH = 1, BCFL_MDH = 2, BCFL_UNUSED = 3, BCFL_FOCUS = 4, BCFL_MEM = 5 }
	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, VDF_MCSF = 3 }
	Format of data for APBS I/O. More...

Detailed Description

Contains generic macro definitions for APBS.

Version:

Id: vhal.h 1522 2009-12-03 19:32:11Z yhuang01

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) 2002-2009, Washington University in St. Louis.
 * Portions Copyright (c) 2002-2009.  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.
 *
 *

vhal.h File Reference

Defines

Typedefs

Enumerations

Detailed Description