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10f2621 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 | /** @defgroup PBEparm PBEparm class
* @brief Parameter structure for PBE variables independent of solver
*/
/**
* @file pbeparm.h
* @ingroup PBEparm
* @brief Contains declarations for class PBEparm
* @version $Id$
* @author Nathan A. Baker
*
* @attention
* @verbatim
*
* APBS -- Adaptive Poisson-Boltzmann Solver
*
* Nathan A. Baker (nathan.baker@pnnl.gov)
* Pacific Northwest National Laboratory
*
* Additional contributing authors listed in the code documentation.
*
* Copyright (c) 2010-2020 Battelle Memorial Institute. Developed at the
* Pacific Northwest National Laboratory, operated by Battelle Memorial
* Institute, Pacific Northwest Division for the U.S. Department of 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 the developer 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.
*
* @endverbatim
*/
#ifndef _PBEPARM_H_
#define _PBEPARM_H_
#include "apbscfg.h"
#include "maloc/maloc.h"
#include "generic/vhal.h"
#include "generic/vstring.h"
/** @brief Number of things that can be written out in a single calculation
* @ingroup PBEparm
*/
#define PBEPARM_MAXWRITE 20
/**
* @ingroup PBEparm
* @brief Define energy calculation enumeration
*/
enum ePBEparm_calcEnergy {
PCE_NO=0, /**< Do not perform energy calculation */
PCE_TOTAL=1, /**< Calculate total energy only */
PCE_COMPS=2 /**< Calculate per-atom energy components */
};
/**
* @ingroup PBEparm
* @brief Define ePBEparm_calcEnergy enumeration as PBEparm_calcEnergy
*/
typedef enum ePBEparm_calcEnergy PBEparm_calcEnergy;
/**
* @ingroup PBEparm
* @brief Define force calculation enumeration
*/
enum ePBEparm_calcForce {
PCF_NO=0, /**< Do not perform force calculation */
PCF_TOTAL=1, /**< Calculate total force only */
PCF_COMPS=2 /**< Calculate per-atom force components */
};
/**
* @ingroup PBEparm
* @brief Define ePBEparm_calcForce enumeration as PBEparm_calcForce
*/
typedef enum ePBEparm_calcForce PBEparm_calcForce;
/**
* @ingroup PBEparm
* @author Nathan Baker
* @brief Parameter structure for PBE variables from input files
* @note If you add/delete/change something in this class, the member
* functions -- especially PBEparm_copy -- must be modified
* accordingly
*/
struct sPBEparm {
int molid; /**< Molecule ID to perform calculation on */
int setmolid; /**< Flag, @see molid */
int useDielMap; /**< Indicates whether we use external
* dielectric maps (note plural) */
int dielMapID; /**< Dielectric map ID (if used) */
int useKappaMap; /**< Indicates whether we use an external
* kappa map */
int kappaMapID; /**< Kappa map ID (if used) */
int usePotMap; /**< Indicates whether we use an external
* kappa map */
int potMapID; /**< Kappa map ID (if used) */
int useChargeMap; /**< Indicates whether we use an external
* charge distribution map */
int chargeMapID; /**< Charge distribution map ID (if used) */
Vhal_PBEType pbetype; /**< Which version of the PBE are we solving? */
int setpbetype; /**< Flag, @see pbetype */
Vbcfl bcfl; /**< Boundary condition method */
int setbcfl; /**< Flag, @see bcfl */
int nion; /**< Number of counterion species */
int setnion; /**< Flag, @see nion */
double ionq[MAXION]; /**< Counterion charges (in e) */
double ionc[MAXION]; /**< Counterion concentrations (in M) */
double ionr[MAXION]; /**< Counterion radii (in A) */
int setion[MAXION]; /**< Flag, @see ionq */
double pdie; /**< Solute dielectric */
int setpdie; /**< Flag, @see pdie */
double sdens; /**< Vacc sphere density */
int setsdens; /**< Flag, @see sdens */
double sdie; /**< Solvent dielectric */
int setsdie; /**< Flag, @see sdie */
Vsurf_Meth srfm; /**< Surface calculation method */
int setsrfm; /**< Flag, @see srfm */
double srad; /**< Solvent radius */
int setsrad; /**< Flag, @see srad */
double swin; /**< Cubic spline window */
int setswin; /**< Flag, @see swin */
double temp; /**< Temperature (in K) */
int settemp; /**< Flag, @see temp */
double smsize; /**< SMPBE size */
int setsmsize; /**< Flag, @see temp */
double smvolume; /**< SMPBE size */
int setsmvolume; /**< Flag, @see temp */
PBEparm_calcEnergy calcenergy; /**< Energy calculation flag */
int setcalcenergy; /**< Flag, @see calcenergy */
PBEparm_calcForce calcforce; /**< Atomic forces calculation */
int setcalcforce; /**< Flag, @see calcforce */
/*----------------------------------------------------------------*/
/* Added by Michael Grabe */
/*----------------------------------------------------------------*/
double zmem; /**< z value of membrane bottom */
int setzmem; /**< Flag */
double Lmem; /**< membrane width */
int setLmem; /**< Flag */
double mdie; /**< membrane dielectric constant */
int setmdie; /**< Flag */
double memv; /**< Membrane potential */
int setmemv; /**< Flag */
/*----------------------------------------------------------------*/
int numwrite; /**< Number of write statements encountered */
char writestem[PBEPARM_MAXWRITE][VMAX_ARGLEN]; /**< File stem to write
* data to */
Vdata_Type writetype[PBEPARM_MAXWRITE]; /**< What data to write */
Vdata_Format writefmt[PBEPARM_MAXWRITE]; /**< File format to write data
* in */
int writemat; /**< Write out the operator matrix?
* \li 0 => no
* \li 1 => yes */
int setwritemat; /**< Flag, @see writemat */
char writematstem[VMAX_ARGLEN]; /**< File stem to write mat */
int writematflag; /**< What matrix should we write:
* \li 0 => Poisson (differential operator)
* \li 1 => Poisson-Boltzmann operator linearized around
* solution (if applicable) */
/*Added for issue 482*/
char pbam_3dmapstem[VMAX_ARGLEN];
int pbam_3dmapflag;
int parsed; /**< Has this been filled with anything other
* than the default values? */
};
/**
* @ingroup PBEparm
* @brief Declaration of the PBEparm class as the PBEparm structure
*/
typedef struct sPBEparm PBEparm;
/* ///////////////////////////////////////////////////////////////////////////
// Class NOsh: Non-inlineable methods (mcsh.c)
/////////////////////////////////////////////////////////////////////////// */
/** @brief Get charge (e) of specified ion species
* @ingroup PBEparm
* @author Nathan Baker
* @returns Charge of ion species (e)
*/
VEXTERNC double PBEparm_getIonCharge(
PBEparm *thee, /**< PBEparm object */
int iion /**< Ion species ID/index */
);
/** @brief Get concentration (M) of specified ion species
* @ingroup PBEparm
* @author Nathan Baker
* @returns Concentration of ion species (M)
*/
VEXTERNC double PBEparm_getIonConc(
PBEparm *thee, /**< PBEparm object */
int iion /**< Ion species ID/index */
);
/** @brief Get radius (A) of specified ion species
* @ingroup PBEparm
* @author Nathan Baker
* @returns Radius of ion species (A)
*/
VEXTERNC double PBEparm_getIonRadius(
PBEparm *thee, /**< PBEparm object */
int iion /**< Ion species ID/index */
);
/** @brief Construct PBEparm object
* @ingroup PBEparm
* @author Nathan Baker
* @returns Newly allocated and initialized PBEparm object
*/
VEXTERNC PBEparm* PBEparm_ctor();
/** @brief FORTRAN stub to construct PBEparm object
* @ingroup PBEparm
* @author Nathan Baker
* @returns 1 if succesful, 0 otherwise
*/
VEXTERNC int PBEparm_ctor2(
PBEparm *thee /**< Memory location for object */
);
/** @brief Object destructor
* @ingroup PBEparm
* @author Nathan Baker
*/
VEXTERNC void PBEparm_dtor(
PBEparm **thee /**< Pointer to memory location of object */
);
/** @brief FORTRAN stub for object destructor
* @ingroup PBEparm
* @author Nathan Baker
*/
VEXTERNC void PBEparm_dtor2(
PBEparm *thee /**< Pointer to object to be destroyed */
);
/** @brief Consistency check for parameter values stored in object
* @ingroup PBEparm
* @author Nathan Baker
* @returns 1 if OK, 0 otherwise
*/
VEXTERNC int PBEparm_check(
PBEparm *thee /**< Object to be checked */
);
/** @brief Copy PBEparm object into thee
* @ingroup PBEparm
* @author Nathan Baker
*/
VEXTERNC void PBEparm_copy(
PBEparm *thee, /**< Target for copy */
PBEparm *parm /**< Source for copy */
);
/** @brief Parse a keyword from an input file
* @ingroup PBEparm
* @author Nathan Baker
* @return 1 if matched and assigned; -1 if matched, but there's some sort
* of error (i.e., too few args); 0 if not matched
*/
VEXTERNC int PBEparm_parseToken(
PBEparm *thee, /**< Parsing object */
char tok[VMAX_BUFSIZE], /**< Token to parse */
Vio *sock /**< Socket for additional tokens */
);
#endif
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