| /** @defgroup APOLparm APOLparm class | |
| * @brief Parameter structure for APOL-specific variables from input files | |
| */ | |
| /** | |
| * @file femparm.h | |
| * @ingroup APOLparm | |
| * @brief Contains declarations for class APOLparm | |
| * @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 */ | |
| /** | |
| * @ingroup APOLparm | |
| * @brief Define energy calculation enumeration | |
| */ | |
| enum eAPOLparm_calcEnergy { | |
| ACE_NO=0, /**< Do not perform energy calculation */ | |
| ACE_TOTAL=1, /**< Calculate total energy only */ | |
| ACE_COMPS=2 /**< Calculate per-atom energy components */ | |
| }; | |
| /** | |
| * @ingroup APOLparm | |
| * @brief Define eAPOLparm_calcEnergy enumeration as APOLparm_calcEnergy | |
| */ | |
| typedef enum eAPOLparm_calcEnergy APOLparm_calcEnergy; | |
| /** | |
| * @ingroup APOLparm | |
| * @brief Define force calculation enumeration | |
| */ | |
| enum eAPOLparm_calcForce { | |
| ACF_NO=0, /**< Do not perform force calculation */ | |
| ACF_TOTAL=1, /**< Calculate total force only */ | |
| ACF_COMPS=2 /**< Calculate per-atom force components */ | |
| }; | |
| /** | |
| * @ingroup APOLparm | |
| * @brief Define eAPOLparm_calcForce enumeration as APOLparm_calcForce | |
| */ | |
| typedef enum eAPOLparm_calcForce APOLparm_calcForce; | |
| /** | |
| * @ingroup APOLparm | |
| * @brief Define force calculation enumeration | |
| */ | |
| enum eAPOLparm_doCalc { | |
| ACD_NO=0, /**< Do not perform calculation */ | |
| ACD_YES=1, /**< Perform calculations */ | |
| ACD_ERROR=2 /**< Error setting up calculation */ | |
| }; | |
| /** | |
| * @ingroup APOLparm | |
| * @brief Define eAPOLparm_calcForce enumeration as APOLparm_calcForce | |
| */ | |
| typedef enum eAPOLparm_doCalc APOLparm_doCalc; | |
| /** | |
| * @ingroup APOLparm | |
| * @author David Gohara | |
| * @brief Parameter structure for APOL-specific variables from input files | |
| */ | |
| struct sAPOLparm { | |
| int parsed; /**< Flag: Has this structure been filled with anything other than the default values? (0 = no, 1 = yes) */ | |
| double grid[3]; /**< Grid spacing */ | |
| int setgrid; /**< Flag, @see grid */ | |
| int molid; /**< Molecule ID to perform calculation on */ | |
| int setmolid; /**< Flag, @see molid */ | |
| double bconc; /**< Vacc sphere density */ | |
| int setbconc; /**< Flag, @see bconc */ | |
| double sdens; /**< Vacc sphere density */ | |
| int setsdens; /**< Flag, @see sdens */ | |
| double dpos; /**< Atom position offset */ | |
| int setdpos; /**< Flag, @see dpos */ | |
| double press; /**< Solvent pressure */ | |
| int setpress; /**< Flag, @see press */ | |
| Vsurf_Meth srfm; /**< Surface calculation method */ | |
| int setsrfm; /**< Flag, @see srfm */ | |
| double srad; /**< Solvent radius */ | |
| int setsrad; /**< Flag, @see srad */ | |
| double swin; /**< Cubic spline window */ | |
| int setswin; /**< Flag, @see swin */ | |
| double temp; /**< Temperature (in K) */ | |
| int settemp; /**< Flag, @see temp */ | |
| double gamma; /**< Surface tension for apolar energies/forces | |
| * (in kJ/mol/A^2) */ | |
| int setgamma; /**< Flag, @see gamma */ | |
| APOLparm_calcEnergy calcenergy; /**< Energy calculation flag */ | |
| int setcalcenergy; /**< Flag, @see calcenergy */ | |
| APOLparm_calcForce calcforce; /**< Atomic forces calculation */ | |
| int setcalcforce; /**< Flag, @see calcforce */ | |
| double watsigma; /**< Water oxygen Lennard-Jones radius (A) */ | |
| double watepsilon; /**< Water oxygen Lennard-Jones well depth (kJ/mol) */ | |
| double sasa; /**< Solvent accessible surface area for this calculation */ | |
| double sav; /**< Solvent accessible volume for this calculation */ | |
| double wcaEnergy; /**< wcaEnergy */ | |
| double totForce[3]; /**< Total forces on x, y, z */ | |
| int setwat; /**< Boolean for determining if a water parameter | |
| * is supplied. Yes = 1, No = 0 */ | |
| }; | |
| /** @typedef APOLparm | |
| * @ingroup APOLparm | |
| * @brief Declaration of the APOLparm class as the APOLparm structure | |
| */ | |
| typedef struct sAPOLparm APOLparm; | |
| /* /////////////////////////////////////////////////////////////////////////// | |
| // Class NOsh: Non-inlineable methods (nosh.c) | |
| /////////////////////////////////////////////////////////////////////////// */ | |
| /** @brief Construct APOLparm | |
| * @ingroup APOLparm | |
| * @author David Gohara | |
| * @returns Newly allocated and initialized Vpmgp object | |
| */ | |
| VEXTERNC APOLparm* APOLparm_ctor(); | |
| /** @brief FORTRAN stub to construct APOLparm | |
| * @ingroup APOLparm | |
| * @author David Gohara, Yong Huang | |
| * @param thee Pointer to allocated APOLparm object | |
| * @returns Success enumeration | |
| */ | |
| VEXTERNC Vrc_Codes APOLparm_ctor2(APOLparm *thee); | |
| /** @brief Object destructor | |
| * @ingroup APOLparm | |
| * @author David Gohara | |
| * @param thee Pointer to memory location of APOLparm object | |
| */ | |
| VEXTERNC void APOLparm_dtor(APOLparm **thee); | |
| /** @brief FORTRAN stub for object destructor | |
| * @ingroup APOLparm | |
| * @author David Gohara | |
| * @param thee Pointer to APOLparm object | |
| */ | |
| VEXTERNC void APOLparm_dtor2(APOLparm *thee); | |
| /** | |
| * @brief Consistency check for parameter values stored in object | |
| * @ingroup APOLparm | |
| * @author David Gohara, Yong Huang | |
| * @param thee APOLparm object | |
| * @returns Success enumeration | |
| */ | |
| VEXTERNC Vrc_Codes APOLparm_check(APOLparm *thee); | |
| /** @brief Copy target object into thee | |
| @ingroup APOLparm | |
| @author Nathan Baker | |
| @param thee Destination object | |
| @param source Source object | |
| */ | |
| VEXTERNC void APOLparm_copy(APOLparm *thee, APOLparm *source); | |
| /** | |
| * @brief Parse an MG keyword from an input file | |
| * @ingroup MGparm | |
| * @author David Gohara | |
| * @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 APOLparm_parseToken(APOLparm *thee, char tok[VMAX_BUFSIZE], | |
| Vio *sock); | |