File size: 12,789 Bytes
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 | /** @defgroup Vgreen Vgreen class
* @brief Provides capabilities for pointwise evaluation of free space
* Green's function for point charges in a uniform dielectric.
* @note Right now, these are very slow methods without any fast multipole
* acceleration.
*
* @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
*/
/**
* @file vgreen.h
* @ingroup Vgreen
* @brief Contains declarations for class Vgreen
* @version $Id$
* @author Nathan A. Baker
*/
#ifndef _VGREEN_H_
#define _VGREEN_H_
#include "apbscfg.h"
#include "maloc/maloc.h"
#include "generic/vhal.h"
#include "generic/vunit.h"
#include "generic/vatom.h"
#include "generic/valist.h"
/**
* @ingroup Vgreen
* @author Nathan Baker
* @brief Contains public data members for Vgreen class/module
*/
struct sVgreen {
Valist *alist; /**< Atom (charge) list for Green's function */
Vmem *vmem; /**< Memory management object */
double *xp; /**< Array of particle x-coordinates for use with
* treecode routines */
double *yp; /**< Array of particle y-coordinates for use with
* treecode routines */
double *zp; /**< Array of particle z-coordinates for use with
* treecode routines */
double *qp; /**< Array of particle charges for use with
* treecode routines */
int np; /**< Set to size of above arrays */
};
/**
* @ingroup Vgreen
* @brief Declaration of the Vgreen class as the Vgreen structure
*/
typedef struct sVgreen Vgreen;
/* ///////////////////////////////////////////////////////////////////////////
// Class Vgreen: Inlineable methods (vgreen.c)
/////////////////////////////////////////////////////////////////////////// */
#if !defined(VINLINE_VGREEN)
/** @brief Get the atom list associated with this Green's function object
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Vgreen object
* @return Pointer to Valist object associated with this Green's function
* object
*/
VEXTERNC Valist* Vgreen_getValist(Vgreen *thee);
/** @brief Return the memory used by this structure (and its contents)
* in bytes
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Vgreen object
* @return The memory used by this structure and its contents in bytes
*/
VEXTERNC unsigned long int Vgreen_memChk(Vgreen *thee);
#else /* if defined(VINLINE_VGREEN) */
# define Vgreen_getValist(thee) ((thee)->alist)
# define Vgreen_memChk(thee) (Vmem_bytes((thee)->vmem))
#endif /* if !defined(VINLINE_VGREEN) */
/* ///////////////////////////////////////////////////////////////////////////
// Class Vgreen: Non-Inlineable methods (vgreen.c)
/////////////////////////////////////////////////////////////////////////// */
/** @brief Construct the Green's function oracle
* @ingroup Vgreen
* @author Nathan Baker
* @param alist Atom (charge) list associated with object
* @return Pointer to newly allocated Green's function oracle
*/
VEXTERNC Vgreen* Vgreen_ctor(Valist *alist);
/** @brief FORTRAN stub to construct the Green's function oracle
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Pointer to memory allocated for object
* @param alist Atom (charge) list associated with object
* @return 1 if successful, 0 otherwise
*/
VEXTERNC int Vgreen_ctor2(Vgreen *thee, Valist *alist);
/** @brief Destruct the Green's function oracle
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Pointer to memory location for object
*/
VEXTERNC void Vgreen_dtor(Vgreen **thee);
/** @brief FORTRAN stub to destruct the Green's function oracle
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Pointer to object
*/
VEXTERNC void Vgreen_dtor2(Vgreen *thee);
/** @brief Get the Green's function for Helmholtz's equation integrated over
* the atomic point charges
*
* Returns the potential \f$\phi\f$ defined by
* \f[ \phi(r) = \sum_i \frac{q_i e^{-\kappa r_i}}{r_i} \f]
*
* where \f$\kappa\f$ is the inverse screening length (in Å)
* \f$q_i\f$ is the atomic charge (in e), and \f$r_i\f$ r_i is the
* distance from atom \f$i\f$ to the observation point \f$r\f$. The
* potential is scaled to units of V.
*
* @ingroup Vgreen
* @author Nathan Baker
* @bug Not implemented yet
* @note Not implemented yet
* @param thee Vgreen object
* @param npos Number of positions to evaluate
* @param x The npos x-coordinates
* @param y The npos y-coordinates
* @param z The npos z-coordinates
* @param val The npos values
* @param kappa The value of \f$\kappa\f$ (see above)
* @return 1 if successful, 0 otherwise
*/
VEXTERNC int Vgreen_helmholtz(Vgreen *thee, int npos, double *x, double *y,
double *z, double *val, double kappa);
/** @brief Get the gradient of Green's function for Helmholtz's equation
* integrated over the atomic point charges
*
* Returns the field \f$\nabla \phi\f$ defined by
* \f[ \nabla \phi(r) = \nabla \sum_i \frac{q_i e^{-\kappa r_i}}{r_i}
* \f]
*
* where \f$\kappa\f$ is the inverse screening length (in Å).
* \f$q_i\f$ is the atomic charge (in e), and \f$r_i\f$ r_i is the
* distance from atom \f$i\f$ to the observation point \f$r\f$. The
* potential is scaled to units of V/Å.
*
* @ingroup Vgreen
* @author Nathan Baker
* @bug Not implemented yet
* @note Not implemented yet
* @param thee Vgreen object
* @param npos The number of positions to evaluate
* @param x The npos x-coordinates
* @param y The npos y-coordinates
* @param z The npos z-coordinates
* @param gradx The npos gradient x-components
* @param grady The npos gradient y-components
* @param gradz The npos gradient z-components
* @param kappa The value of \f$\kappa\f$ (see above)
* @return int 1 if sucessful, 0 otherwise
*/
VEXTERNC int Vgreen_helmholtzD(Vgreen *thee, int npos, double *x, double *y,
double *z, double *gradx, double *grady, double *gradz, double kappa);
/** @brief Get the Coulomb's Law Green's function (solution to Laplace's
* equation) integrated over the atomic point charges using direct
* summation
*
* Returns the potential \f$\phi\f$ defined by
* \f[ \phi(r) = \sum_i \frac{q_i}{r_i} \f]
* where \f$q_i\f$ is the atomic charge (in e) and \f$r_i\f$ is the
* distance to the observation point \f$r\f$. The potential is
* scaled to units of V.
*
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Vgreen object
* @param npos The number of positions to evaluate
* @param x The npos x-coordinates
* @param y The npos y-coordinates
* @param z The npos z-coordinates
* @param val The npos values
* @return 1 if successful, 0 otherwise
*/
VEXTERNC int Vgreen_coulomb_direct(Vgreen *thee, int npos, double *x,
double *y, double *z, double *val);
/** @brief Get the Coulomb's Law Green's function (solution to Laplace's
* equation) integrated over the atomic point charges using direct
* summation or H. E. Johnston, R. Krasny FMM library (if available)
*
* Returns the potential \f$\phi\f$ defined by
* \f[ \phi(r) = \sum_i \frac{q_i}{r_i} \f]
* where \f$q_i\f$ is the atomic charge (in e) and \f$r_i\f$ is the
* distance to the observation point \f$r\f$. The potential is
* scaled to units of V.
*
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Vgreen object
* @param npos The number of positions to evaluate
* @param x The npos x-coordinates
* @param y The npos y-coordinates
* @param z The npos z-coordinates
* @param val The npos values
* @return 1 if successful, 0 otherwise
*/
VEXTERNC int Vgreen_coulomb(Vgreen *thee, int npos, double *x, double *y,
double *z, double *val);
/** @brief Get gradient of the Coulomb's Law Green's function (solution to
* Laplace's equation) integrated over the atomic point charges using
* direct summation
*
* Returns the field \f$\nabla \phi\f$ defined by
* \f[ \nabla \phi(r) = \sum_i \frac{q_i}{r_i} \f]
* where \f$q_i\f$ is the atomic charge (in e) and \f$r_i\f$ is the
* distance to the observation point \f$r\f$. The field is
* scaled to units of V/Å.
*
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Vgreen object
* @param npos The number of positions to evaluate
* @param x The npos x-coordinates
* @param y The npos y-coordinates
* @param z The npos z-coordinates
* @param pot The npos potential values
* @param gradx The npos gradient x-components
* @param grady The npos gradient y-components
* @param gradz The npos gradient z-components
* @return 1 if successful, 0 otherwise
*/
VEXTERNC int Vgreen_coulombD_direct(Vgreen *thee, int npos, double *x,
double *y, double *z, double *pot, double *gradx, double *grady, double
*gradz);
/** @brief Get gradient of the Coulomb's Law Green's function (solution to
* Laplace's equation) integrated over the atomic point charges using
* either direct summation or H. E. Johnston/R. Krasny FMM library
* (if available)
*
* Returns the field \f$\nabla \phi\f$ defined by
* \f[ \nabla \phi(r) = \sum_i \frac{q_i}{r_i} \f]
* where \f$q_i\f$ is the atomic charge (in e) and \f$r_i\f$ is the
* distance to the observation point \f$r\f$. The field is
* scaled to units of V/Å.
*
* @ingroup Vgreen
* @author Nathan Baker
* @param thee Vgreen object
* @param npos The number of positions to evaluate
* @param x The npos x-coordinates
* @param y The npos y-coordinates
* @param z The npos z-coordinates
* @param pot The npos potential values
* @param gradx The npos gradient x-components
* @param grady The npos gradient y-components
* @param gradz The npos gradient z-components
* @return 1 if successful, 0 otherwise
*/
VEXTERNC int Vgreen_coulombD(Vgreen *thee, int npos, double *x, double *y,
double *z, double *pot, double *gradx, double *grady, double *gradz);
#endif /* ifndef _VGREEN_H_ */
|