| /** @defgroup PBAMparm PBAMparm class | |
| * @brief Parameter which holds useful parameters for Poisson-boltzmann | |
| * analytical method calculations | |
| */ | |
| /** | |
| * @file pbamparm.h | |
| * @ingroup PBAMparm | |
| * @brief Contains declarations for class PBAMparm | |
| * @version $Id$ | |
| * @author Lisa Felberg | |
| * | |
| * @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 Number of things that can be written out in a single calculation | |
| * @ingroup PBAMparm | |
| */ | |
| /** | |
| * @brief Calculation type | |
| * @ingroup PBAMparm | |
| */ | |
| enum ePBAMparm_CalcType { | |
| //other methods disabled for now only auto currently implemented. | |
| //PBAMCT_MANUAL=0, /**< PBAM-manual */ | |
| PBAMCT_AUTO=1, /**< PBAM-auto */ | |
| //PBAMCT_NONE=2 /**< not defined */ | |
| }; | |
| /** | |
| * @brief Declare PBAMparm_CalcType type | |
| * @ingroup PBAMparm | |
| */ | |
| typedef enum ePBAMparm_CalcType PBAMparm_CalcType; | |
| /** | |
| * @ingroup PBAMparm | |
| * @author Andrew Stevens, Kyle Monson | |
| * @brief Parameter structure for PBAM-specific variables from input files | |
| * @note If you add/delete/change something in this class, the member | |
| * functions -- especially PBAMparm_copy -- must be modified | |
| * accordingly | |
| */ | |
| typedef struct sPBAMparm { | |
| PBAMparm_CalcType type; /**< What type of PBAM calculation? */ | |
| int parsed; /**< Has this structure been filled? (0 = no, 1 = yes) */ | |
| /* *** GENERIC PARAMETERS *** */ | |
| double salt; | |
| int setsalt; | |
| // This is the type of run you want | |
| char runtype[CHR_MAXLEN]; | |
| int setruntype; | |
| // This is the name for output files | |
| char runname[CHR_MAXLEN]; | |
| int setrunname; | |
| // For setting random orientation of molecules | |
| int setrandorient; | |
| // For periodic boundary conditions | |
| double pbcboxlen; | |
| int setpbcs; | |
| // This is units of the calculation | |
| char units[CHR_MAXLEN]; | |
| int setunits; | |
| // | |
| // ELECTROSTATICS | |
| // | |
| // For the grid, store gridpt | |
| int gridpt; | |
| int setgridpt; | |
| // For 3d map printing | |
| char map3dname[CHR_MAXLEN]; | |
| int set3dmap; | |
| // For 2D | |
| char grid2Dname[PBAMPARM_MAXWRITE][CHR_MAXLEN]; | |
| char grid2Dax[PBAMPARM_MAXWRITE][CHR_MAXLEN]; | |
| double grid2Dloc[PBAMPARM_MAXWRITE]; | |
| int grid2Dct; | |
| int setgrid2Dname; | |
| // For dx | |
| char dxname[CHR_MAXLEN]; | |
| int setdxname; | |
| // | |
| // DYNAMICS | |
| // | |
| int ntraj; | |
| int setntraj; | |
| char termcombine[CHR_MAXLEN]; | |
| int settermcombine; | |
| int diffct; | |
| char moveType[PBAMPARM_MAXMOL][CHR_MAXLEN]; | |
| double transDiff[PBAMPARM_MAXMOL]; | |
| double rotDiff[PBAMPARM_MAXMOL]; | |
| int termct; | |
| int setterm; | |
| char termnam[PBAMPARM_MAXWRITE][CHR_MAXLEN]; | |
| int termnu[PBAMPARM_MAXWRITE][1]; | |
| double termVal[PBAMPARM_MAXWRITE]; | |
| char confil[PBAMPARM_MAXWRITE][CHR_MAXLEN]; | |
| double conpad[PBAMPARM_MAXWRITE]; | |
| int confilct; | |
| int setxyz; | |
| int xyzct[PBAMPARM_MAXMOL]; | |
| char xyzfil[PBAMPARM_MAXMOL][PBAMPARM_MAXWRITE][CHR_MAXLEN]; | |
| } PBAMparm; | |
| /** @brief Construct PBAMparm object | |
| * @ingroup PBAMparm | |
| * @author Andrew Stevens, Kyle Monson | |
| * @param type Type of PBAM calculation | |
| * @returns Newly allocated and initialized PBAMparm object | |
| */ | |
| VEXTERNC PBAMparm* PBAMparm_ctor(PBAMparm_CalcType type); | |
| /** @brief FORTRAN stub to construct PBAMparm object ?????????!!!!!!! | |
| * @ingroup PBAMparm | |
| * @author Andrew Stevens, Kyle Monson | |
| * @param thee Space for PBAMparm object | |
| * @param type Type of MG calculation | |
| * @returns Success enumeration | |
| */ | |
| VEXTERNC Vrc_Codes PBAMparm_ctor2(PBAMparm *thee, PBAMparm_CalcType type); | |
| /** @brief Object destructor | |
| * @ingroup PBAMparm | |
| * @author Andrew Stevens, Kyle Monson | |
| * @param thee Pointer to memory location of PBAMparm object | |
| */ | |
| VEXTERNC void PBAMparm_dtor(PBAMparm **thee); | |
| /** @brief FORTRAN stub for object destructor ?????????!!!!!!!!!!!! | |
| * @ingroup PBAMparm | |
| * @author Andrew Stevens, Kyle Monson | |
| * @param thee Pointer to PBAMparm object | |
| */ | |
| VEXTERNC void PBAMparm_dtor2(PBAMparm *thee); | |
| /** @brief Consistency check for parameter values stored in object | |
| * @ingroup PBAMparm | |
| * @author Andrew Stevens, Kyle Monson | |
| * @param thee PBAMparm object | |
| * @returns Success enumeration | |
| */ | |
| VEXTERNC Vrc_Codes PBAMparm_check(PBAMparm *thee); | |
| /** @brief Parse an MG keyword from an input file | |
| * @ingroup PBAMparm | |
| * @author Andrew Stevens, Kyle Monson | |
| * @param thee PBAMparm 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 PBAMparm_parseToken(PBAMparm *thee, char tok[VMAX_BUFSIZE], | |
| Vio *sock); | |
| /** | |
| * @brief copy PBAMparm object int thee. | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param parm PBAMparm object. | |
| */ | |
| VEXTERNC void PBAMparm_copy(PBAMparm *thee, PBAMparm *parm); | |
| /** | |
| * @brief Find salt conc and save it as a structure variable | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param parm The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseSalt(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find runType and save it as a structure variable | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseRunType(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find runName and save it as a structure variable | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseRunName(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find randomorientation flag and save it as a boolean | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseRandorient(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find PBC flag and save the type and the boxlength | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parsePBCS(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find units flag and save units | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseUnits(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find 3D map filename and save it | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parse3Dmap(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find 2D grid filename and save it | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseGrid2D(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find DX filename and save it | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseDX(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find Grid points and save them | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseGridPts(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find Termination logic and save it | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseTermcombine(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find diffusion coeffs for each molecule and save them | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseDiff(PBAMparm *thee, Vio *sock); | |
| /** | |
| * @brief Find xyz files for each molecule for each traj and save them | |
| * @ingroup PBAMparm | |
| * @author | |
| * @param thee PBAMparm object to be copied into | |
| * @param sock The stream from which parameter is taken | |
| */ | |
| VPRIVATE Vrc_Codes PBAMparm_parseXYZ(PBAMparm *thee, Vio *sock); | |