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* @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
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