APBS
1.4.1
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Contains generic macro definitions for APBS. More...
#include "stdio.h"
Go to the source code of this file.
Macros | |
#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. More... | |
#define | MAX_SPHERE_PTS 50000 |
Maximum number of points on a sphere. More... | |
#define | VAPBS_FRONT 1 |
Face definition for a volume. More... | |
#define | VAPBS_UP 2 |
Face definition for a volume. More... | |
#define | VAPBS_LEFT 3 |
Face definition for a volume. More... | |
#define | VAPBS_BACK 4 |
Face definition for a volume. More... | |
#define | VAPBS_DOWN 5 |
Face definition for a volume. More... | |
#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 | MAX_HASH_DIM 75 |
#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. More... | |
#define | VEMBED(rctag) |
Allows embedding of RCS ID tags in object files. More... | |
#define | PRINT_FUNC __PRETTY_FUNCTION__ |
#define | OS_SEP_STR "/" |
#define | OS_SEP_CHAR '/' |
#define | ANNOUNCE_FUNCTION |
#define | WARN_UNTESTED |
#define | WARN_PARTTESTED |
#define | VCHANNELEDMESSAGE0(channel, msg) |
#define | VCHANNELEDMESSAGE1(channel, msg, arg0) |
#define | VCHANNELEDMESSAGE2(channel, msg, arg0, arg1) |
#define | VCHANNELEDMESSAGE3(channel, msg, arg0, arg1, arg2) |
#define | VMESSAGE0(msg) VCHANNELEDMESSAGE0(0, msg) |
#define | VMESSAGE1(msg, arg0) VCHANNELEDMESSAGE1(0, msg, arg0) |
#define | VMESSAGE2(msg, arg0, arg1) VCHANNELEDMESSAGE2(0, msg, arg0, arg1) |
#define | VMESSAGE3(msg, arg0, arg1, arg2) VCHANNELEDMESSAGE3(0, msg, arg0, arg1, arg2) |
#define | VERRMSG0(msg) VCHANNELEDMESSAGE0(2, msg) |
#define | VERRMSG1(msg, arg0) VCHANNELEDMESSAGE1(2, msg, arg0) |
#define | VERRMSG2(msg, arg0, arg1) VCHANNELEDMESSAGE2(2, msg, arg0, arg1) |
#define | VERRMSG3(msg, arg0, arg1, arg2) VCHANNELEDMESSAGE3(2, msg, arg0, arg1, arg2) |
#define | VASSERT_MSG0(cnd, msg) |
#define | VASSERT_MSG1(cnd, msg, arg) |
#define | VASSERT_MSG2(cnd, msg, arg0, arg1) |
#define | VWARN_MSG0(cnd, msg) |
#define | VWARN_MSG1(cnd, msg, arg0) |
#define | VWARN_MSG2(cnd, msg, arg0, arg1) |
#define | VABORT_MSG0(msg) |
#define | VABORT_MSG1(msg, arg) |
#define | VABORT_MSG2(msg, arg0, arg1) |
#define | PRINT_INT(expr) |
#define | PRINT_DBL(expr) |
#define | VMALLOC(vmem, n, type) ((type*)Vmem_malloc(vmem, n, sizeof(type))) |
#define | VFREE(vmem, n, type, ptr) (Vmem_free(vmem, n, sizeof(type), (void **)&(ptr))) |
#define | VFILL(vec, n, val) |
#define | VCOPY(srcvec, dstvec, i, n) |
#define | VAT(array, i) ((array)[(i) - 1]) |
#define | RAT(array, i) ((array) + i - 1) |
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. More... | |
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. 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_NRPBE, 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 { 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. More... | |
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. 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_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. More... | |
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. More... | |
Functions | |
char * | wrap_text (char *str, int right_margin, int left_padding) |
Variables | |
FILE * | data |
Contains generic macro definitions for APBS.
* * 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) 2010-2012 Battelle Memorial Institute. Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific Northwest Division for the U.S. Department Energy. 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 * 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. * *
Definition in file vhal.h.
#define PRINT_FUNC __PRETTY_FUNCTION__ |
#define VABORT_MSG0 | ( | msg | ) |
#define VABORT_MSG1 | ( | msg, | |
arg | |||
) |
#define VABORT_MSG2 | ( | msg, | |
arg0, | |||
arg1 | |||
) |
#define VASSERT_MSG0 | ( | cnd, | |
msg | |||
) |
#define VASSERT_MSG1 | ( | cnd, | |
msg, | |||
arg | |||
) |
#define VASSERT_MSG2 | ( | cnd, | |
msg, | |||
arg0, | |||
arg1 | |||
) |
#define VCHANNELEDMESSAGE0 | ( | channel, | |
msg | |||
) |
#define VCHANNELEDMESSAGE1 | ( | channel, | |
msg, | |||
arg0 | |||
) |
#define VCHANNELEDMESSAGE2 | ( | channel, | |
msg, | |||
arg0, | |||
arg1 | |||
) |
#define VCHANNELEDMESSAGE3 | ( | channel, | |
msg, | |||
arg0, | |||
arg1, | |||
arg2 | |||
) |
#define VCOPY | ( | srcvec, | |
dstvec, | |||
i, | |||
n | |||
) |
#define VFILL | ( | vec, | |
n, | |||
val | |||
) |
#define VWARN_MSG0 | ( | cnd, | |
msg | |||
) |
#define VWARN_MSG1 | ( | cnd, | |
msg, | |||
arg0 | |||
) |