Defines | Typedefs | Enumerations

src/generic/apbs/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 MAX_SPHERE_PTS   50000
 Maximum number of points on a sphere.
#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 values acceptable for sinh chopping.
#define SINH_MAX   85.0
 Used to set the 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 eVrc_Codes Vrc_Codes
typedef enum eVsol_Meth Vsol_Meth
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, VRC_FAILURE = 0, VRC_SUCCESS = 1 }
 

Return code enumerations.

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enum  eVsol_Meth {
  VSOL_CGMG, VSOL_Newton, VSOL_MG, VSOL_CG,
  VSOL_SOR, VSOL_RBGS, VSOL_WJ, VSOL_Richardson,
  VSOL_CGMGAqua, VSOL_NewtonAqua
}
 

Solution Method enumerations.

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enum  eVsurf_Meth {
  VSM_MOL = 0, VSM_MOLSMOOTH = 1, VSM_SPLINE = 2, VSM_SPLINE3 = 3,
  VSM_SPLINE4 = 4
}
 

Types of molecular surface definitions.

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enum  eVhal_PBEType {
  PBE_LPBE, PBE_NPBE, PBE_LRPBE, PBE_NRPBE,
  PBE_SMPBE
}
 

Version of PBE to solve.

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enum  eVhal_IPKEYType { IPKEY_SMPBE = -2, IPKEY_LPBE, IPKEY_NPBE }
 

Type of ipkey to use for MG methods.

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enum  eVhal_NONLINType {
  NONLIN_LPBE = 0, NONLIN_NPBE, NONLIN_SMPBE, NONLIN_LPBEAQUA,
  NONLIN_NPBEAQUA
}
 

Type of nonlinear to use for MG methods.


enum  eVoutput_Format { OUTPUT_NULL, OUTPUT_FLAT }
 

Output file format.

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enum  eVbcfl {
  BCFL_ZERO = 0, BCFL_SDH = 1, BCFL_MDH = 2, BCFL_UNUSED = 3,
  BCFL_FOCUS = 4, BCFL_MEM = 5, BCFL_MAP = 6
}
 

Types of boundary conditions.

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enum  eVchrg_Meth { VCM_TRIL = 0, VCM_BSPL2 = 1, VCM_BSPL4 = 2 }
 

Types of charge discretization methods.

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enum  eVchrg_Src { VCM_CHARGE = 0, VCM_PERMANENT = 1, VCM_INDUCED = 2, VCM_NLINDUCED = 3 }
 

Charge source.

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enum  eVdata_Type {
  VDT_CHARGE, VDT_POT, VDT_ATOMPOT, 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.

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enum  eVdata_Format {
  VDF_DX = 0, VDF_UHBD = 1, VDF_AVS = 2, VDF_MCSF = 3,
  VDF_GZ = 4, VDF_FLAT = 5
}
 

Format of data for APBS I/O.

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Detailed Description

Contains generic macro definitions for APBS.

Version:
Id:
vhal.h 1605 2010-09-13 15:12:09Z yhuang01
Author:
Nathan A. Baker
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, Pacific Northwest National Laboratory.  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
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 * 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
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Definition in file vhal.h.