/** @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 */ #ifndef _MGPARM_H_ #define _MGPARM_H_ /* Generic header files */ #include "maloc/maloc.h" #include "generic/vhal.h" #include "generic/vstring.h" /** * @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); #endif