| /** @defgroup MGparm MGparm class | |
| * @brief Parameter which holds useful parameters for generic multigrid | |
| * calculations | |
| */ | |
| /** | |
| * @file mgparm.h | |
| * @ingroup MGparm | |
| * @brief Contains declarations for class MGparm | |
| * @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 | |
| */ | |
| /* Generic header files */ | |
| /** | |
| * @brief Calculation type | |
| * @ingroup MGparm | |
| */ | |
| enum eMGparm_CalcType { | |
| MCT_MANUAL=0, /**< mg-manual */ | |
| MCT_AUTO=1, /**< mg-auto */ | |
| MCT_PARALLEL=2, /**< mg-para */ | |
| MCT_DUMMY=3, /**< mg-dummy */ | |
| MCT_NONE=4 /**< unspecified */ | |
| }; | |
| /** | |
| * @brief Declare MGparm_CalcType type | |
| * @ingroup MGparm | |
| */ | |
| typedef enum eMGparm_CalcType MGparm_CalcType; | |
| /** | |
| * @brief Centering method | |
| * @ingroup MGparm | |
| */ | |
| enum eMGparm_CentMeth { | |
| MCM_POINT=0, /**< Center on a point */ | |
| MCM_MOLECULE=1, /**< Center on a molecule */ | |
| MCM_FOCUS=2 /**< Determined by focusing */ | |
| }; | |
| /** | |
| * @brief Declare MGparm_CentMeth type | |
| * @ingroup MGparm | |
| */ | |
| typedef enum eMGparm_CentMeth MGparm_CentMeth; | |
| /** | |
| * @ingroup MGparm | |
| * @author Nathan Baker and Todd Dolinsky | |
| * @brief Parameter structure for MG-specific variables from input files | |
| * @note If you add/delete/change something in this class, the member | |
| * functions -- especially MGparm_copy -- must be modified | |
| * accordingly | |
| */ | |
| struct sMGparm { | |
| MGparm_CalcType type; /**< What type of MG calculation? */ | |
| int parsed; /**< Has this structure been filled? (0 = no, 1 = yes) */ | |
| /* *** GENERIC PARAMETERS *** */ | |
| int dime[3]; /**< Grid dimensions */ | |
| int setdime; /**< Flag, @see dime */ | |
| Vchrg_Meth chgm; /**< Charge discretization method */ | |
| int setchgm; /**< Flag, @see chgm */ | |
| Vchrg_Src chgs; /**< Charge source (Charge, Multipole, Induced Dipole, | |
| * NL Induced */ | |
| /* *** TYPE 0 PARAMETERS (SEQUENTIAL MANUAL) *** */ | |
| int nlev; /**< Levels in multigrid hierarchy | |
| * @deprecated Just ignored now */ | |
| int setnlev; /**< Flag, @see nlev */ | |
| double etol; /**< User-defined error tolerance */ | |
| int setetol; /**< Flag, @see etol */ | |
| double grid[3]; /**< Grid spacings */ | |
| int setgrid; /**< Flag, @see grid */ | |
| double glen[3]; /**< Grid side lengths. */ | |
| int setglen; /**< Flag, @see glen */ | |
| MGparm_CentMeth cmeth; /**< Centering method */ | |
| double center[3]; /**< Grid center. If ispart = 0, then this is | |
| * only meaningful if cmeth = 0. However, if | |
| * ispart = 1 and cmeth = MCM_PNT, then this is the | |
| * center of the non-disjoint (overlapping) | |
| * partition. If ispart = 1 and cmeth = MCM_MOL, then | |
| * this is the vector that must be added to the | |
| * center of the molecule to give the center of | |
| * the non-disjoint partition. */ | |
| int centmol; /**< Particular molecule on which we want to center the grid. | |
| This should be the appropriate index in an array of molecules, not the | |
| positive definite integer specified by the user. */ | |
| int setgcent; /**< Flag, @see cmeth */ | |
| /* ******** TYPE 1 & 2 PARAMETERS (SEQUENTIAL & PARALLEL AUTO-FOCUS) *** */ | |
| double cglen[3]; /**< Coarse grid side lengths */ | |
| int setcglen; /**< Flag, @see cglen */ | |
| double fglen[3]; /**< Fine grid side lengths */ | |
| int setfglen; /**< Flag, @see fglen */ | |
| MGparm_CentMeth ccmeth; /**< Coarse grid centering method */ | |
| double ccenter[3]; /**< Coarse grid center. */ | |
| int ccentmol; /**< Particular molecule on which we want to center the grid. | |
| This should be the appropriate index in an array of molecules, not the | |
| positive definite integer specified by the user. */ | |
| int setcgcent; /**< Flag, @see ccmeth */ | |
| MGparm_CentMeth fcmeth; /**< Fine grid centering method */ | |
| double fcenter[3]; /**< Fine grid center. */ | |
| int fcentmol; /**< Particular molecule on which we want to center the grid. | |
| This should be the appropriate index in an array of molecules, not the | |
| positive definite integer specified by the user. */ | |
| int setfgcent; /**< Flag, @see fcmeth */ | |
| /* ********* TYPE 2 PARAMETERS (PARALLEL AUTO-FOCUS) ******** */ | |
| double partDisjCenter[3]; /**< This gives the center | |
| of the disjoint partitions */ | |
| double partDisjLength[3]; /**< This gives the lengths of the disjoint | |
| * partitions */ | |
| int partDisjOwnSide[6]; /**< Tells whether the boundary points are ours | |
| * (1) or not (0) */ | |
| int pdime[3]; /**< Grid of processors to be used in calculation */ | |
| int setpdime; /**< Flag, @see pdime */ | |
| int proc_rank; /**< Rank of this processor */ | |
| int setrank; /**< Flag, @see proc_rank */ | |
| int proc_size; /**< Total number of processors */ | |
| int setsize; /**< Flag, @see proc_size */ | |
| double ofrac; /**< Overlap fraction between procs */ | |
| int setofrac; /**< Flag, @see ofrac */ | |
| int async; /**< Processor ID for asynchronous calculation */ | |
| int setasync; /**< Flag, @see asynch */ | |
| int nonlintype; /**< Linearity Type Method to be used */ | |
| int setnonlintype; /**< Flag, @see nonlintype */ | |
| int method; /**< Solver Method */ | |
| int setmethod; /**< Flag, @see method */ | |
| int useAqua; /**< Enable use of lpbe/aqua */ | |
| int setUseAqua; /**< Flag, @see useAqua */ | |
| }; | |
| /** @typedef MGparm | |
| * @ingroup MGparm | |
| * @brief Declaration of the MGparm class as the MGparm structure | |
| */ | |
| typedef struct sMGparm MGparm; | |
| /** @brief Get number of grid points in x direction | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns Number of grid points in the x direction | |
| */ | |
| VEXTERNC int MGparm_getNx(MGparm *thee); | |
| /** @brief Get number of grid points in y direction | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns Number of grid points in the y direction | |
| */ | |
| VEXTERNC int MGparm_getNy(MGparm *thee); | |
| /** @brief Get number of grid points in z direction | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns Number of grid points in the z direction | |
| */ | |
| VEXTERNC int MGparm_getNz(MGparm *thee); | |
| /** @brief Get grid spacing in x direction (Å) | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns Grid spacing in the x direction | |
| */ | |
| VEXTERNC double MGparm_getHx(MGparm *thee); | |
| /** @brief Get grid spacing in y direction (Å) | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns Grid spacing in the y direction | |
| */ | |
| VEXTERNC double MGparm_getHy(MGparm *thee); | |
| /** @brief Get grid spacing in z direction (Å) | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns Grid spacing in the z direction | |
| */ | |
| VEXTERNC double MGparm_getHz(MGparm *thee); | |
| /** @brief Set center x-coordinate | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @param x x-coordinate | |
| */ | |
| VEXTERNC void MGparm_setCenterX(MGparm *thee, double x); | |
| /** @brief Set center y-coordinate | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @param y y-coordinate | |
| */ | |
| VEXTERNC void MGparm_setCenterY(MGparm *thee, double y); | |
| /** @brief Set center z-coordinate | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @param z z-coordinate | |
| */ | |
| VEXTERNC void MGparm_setCenterZ(MGparm *thee, double z); | |
| /** @brief Get center x-coordinate | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns x-coordinate | |
| */ | |
| VEXTERNC double MGparm_getCenterX(MGparm *thee); | |
| /** @brief Get center y-coordinate | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns y-coordinate | |
| */ | |
| VEXTERNC double MGparm_getCenterY(MGparm *thee); | |
| /** @brief Get center z-coordinate | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns z-coordinate | |
| */ | |
| VEXTERNC double MGparm_getCenterZ(MGparm *thee); | |
| /** @brief Construct MGparm object | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param type Type of MG calculation | |
| * @returns Newly allocated and initialized MGparm object | |
| */ | |
| VEXTERNC MGparm* MGparm_ctor(MGparm_CalcType type); | |
| /** @brief FORTRAN stub to construct MGparm object | |
| * @ingroup MGparm | |
| * @author Nathan Baker and Todd Dolinsky | |
| * @param thee Space for MGparm object | |
| * @param type Type of MG calculation | |
| * @returns Success enumeration | |
| */ | |
| VEXTERNC Vrc_Codes MGparm_ctor2(MGparm *thee, MGparm_CalcType type); | |
| /** @brief Object destructor | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee Pointer to memory location of MGparm object | |
| */ | |
| VEXTERNC void MGparm_dtor(MGparm **thee); | |
| /** @brief FORTRAN stub for object destructor | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee Pointer to MGparm object | |
| */ | |
| VEXTERNC void MGparm_dtor2(MGparm *thee); | |
| /** @brief Consistency check for parameter values stored in object | |
| * @ingroup MGparm | |
| * @author Nathan Baker | |
| * @param thee MGparm object | |
| * @returns Success enumeration | |
| */ | |
| VEXTERNC Vrc_Codes MGparm_check(MGparm *thee); | |
| /** @brief Copy MGparm object into thee | |
| * @ingroup MGparm | |
| * @author Nathan Baker and Todd Dolinsky | |
| * @param thee MGparm object (target for copy) | |
| * @param parm MGparm object (source for copy) | |
| */ | |
| VEXTERNC void MGparm_copy(MGparm *thee, MGparm *parm); | |
| /** @brief Parse an MG keyword from an input file | |
| * @ingroup MGparm | |
| * @author Nathan Baker and Todd Dolinsky | |
| * @param thee MGparm object | |
| * @param tok Token to parse | |
| * @param sock Stream for more tokens | |
| * @returns Success enumeration (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 Vrc_Codes MGparm_parseToken(MGparm *thee, char tok[VMAX_BUFSIZE], | |
| Vio *sock); | |