| /** @defgroup PBEparm PBEparm class | |
| * @brief Parameter structure for PBE variables independent of solver | |
| */ | |
| /** | |
| * @file pbeparm.h | |
| * @ingroup PBEparm | |
| * @brief Contains declarations for class PBEparm | |
| * @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 | |
| */ | |
| /** @brief Number of things that can be written out in a single calculation | |
| * @ingroup PBEparm | |
| */ | |
| /** | |
| * @ingroup PBEparm | |
| * @brief Define energy calculation enumeration | |
| */ | |
| enum ePBEparm_calcEnergy { | |
| PCE_NO=0, /**< Do not perform energy calculation */ | |
| PCE_TOTAL=1, /**< Calculate total energy only */ | |
| PCE_COMPS=2 /**< Calculate per-atom energy components */ | |
| }; | |
| /** | |
| * @ingroup PBEparm | |
| * @brief Define ePBEparm_calcEnergy enumeration as PBEparm_calcEnergy | |
| */ | |
| typedef enum ePBEparm_calcEnergy PBEparm_calcEnergy; | |
| /** | |
| * @ingroup PBEparm | |
| * @brief Define force calculation enumeration | |
| */ | |
| enum ePBEparm_calcForce { | |
| PCF_NO=0, /**< Do not perform force calculation */ | |
| PCF_TOTAL=1, /**< Calculate total force only */ | |
| PCF_COMPS=2 /**< Calculate per-atom force components */ | |
| }; | |
| /** | |
| * @ingroup PBEparm | |
| * @brief Define ePBEparm_calcForce enumeration as PBEparm_calcForce | |
| */ | |
| typedef enum ePBEparm_calcForce PBEparm_calcForce; | |
| /** | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| * @brief Parameter structure for PBE variables from input files | |
| * @note If you add/delete/change something in this class, the member | |
| * functions -- especially PBEparm_copy -- must be modified | |
| * accordingly | |
| */ | |
| struct sPBEparm { | |
| int molid; /**< Molecule ID to perform calculation on */ | |
| int setmolid; /**< Flag, @see molid */ | |
| int useDielMap; /**< Indicates whether we use external | |
| * dielectric maps (note plural) */ | |
| int dielMapID; /**< Dielectric map ID (if used) */ | |
| int useKappaMap; /**< Indicates whether we use an external | |
| * kappa map */ | |
| int kappaMapID; /**< Kappa map ID (if used) */ | |
| int usePotMap; /**< Indicates whether we use an external | |
| * kappa map */ | |
| int potMapID; /**< Kappa map ID (if used) */ | |
| int useChargeMap; /**< Indicates whether we use an external | |
| * charge distribution map */ | |
| int chargeMapID; /**< Charge distribution map ID (if used) */ | |
| Vhal_PBEType pbetype; /**< Which version of the PBE are we solving? */ | |
| int setpbetype; /**< Flag, @see pbetype */ | |
| Vbcfl bcfl; /**< Boundary condition method */ | |
| int setbcfl; /**< Flag, @see bcfl */ | |
| int nion; /**< Number of counterion species */ | |
| int setnion; /**< Flag, @see nion */ | |
| double ionq[MAXION]; /**< Counterion charges (in e) */ | |
| double ionc[MAXION]; /**< Counterion concentrations (in M) */ | |
| double ionr[MAXION]; /**< Counterion radii (in A) */ | |
| int setion[MAXION]; /**< Flag, @see ionq */ | |
| double pdie; /**< Solute dielectric */ | |
| int setpdie; /**< Flag, @see pdie */ | |
| double sdens; /**< Vacc sphere density */ | |
| int setsdens; /**< Flag, @see sdens */ | |
| double sdie; /**< Solvent dielectric */ | |
| int setsdie; /**< Flag, @see sdie */ | |
| 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 smsize; /**< SMPBE size */ | |
| int setsmsize; /**< Flag, @see temp */ | |
| double smvolume; /**< SMPBE size */ | |
| int setsmvolume; /**< Flag, @see temp */ | |
| PBEparm_calcEnergy calcenergy; /**< Energy calculation flag */ | |
| int setcalcenergy; /**< Flag, @see calcenergy */ | |
| PBEparm_calcForce calcforce; /**< Atomic forces calculation */ | |
| int setcalcforce; /**< Flag, @see calcforce */ | |
| /*----------------------------------------------------------------*/ | |
| /* Added by Michael Grabe */ | |
| /*----------------------------------------------------------------*/ | |
| double zmem; /**< z value of membrane bottom */ | |
| int setzmem; /**< Flag */ | |
| double Lmem; /**< membrane width */ | |
| int setLmem; /**< Flag */ | |
| double mdie; /**< membrane dielectric constant */ | |
| int setmdie; /**< Flag */ | |
| double memv; /**< Membrane potential */ | |
| int setmemv; /**< Flag */ | |
| /*----------------------------------------------------------------*/ | |
| int numwrite; /**< Number of write statements encountered */ | |
| char writestem[PBEPARM_MAXWRITE][VMAX_ARGLEN]; /**< File stem to write | |
| * data to */ | |
| Vdata_Type writetype[PBEPARM_MAXWRITE]; /**< What data to write */ | |
| Vdata_Format writefmt[PBEPARM_MAXWRITE]; /**< File format to write data | |
| * in */ | |
| int writemat; /**< Write out the operator matrix? | |
| * \li 0 => no | |
| * \li 1 => yes */ | |
| int setwritemat; /**< Flag, @see writemat */ | |
| char writematstem[VMAX_ARGLEN]; /**< File stem to write mat */ | |
| int writematflag; /**< What matrix should we write: | |
| * \li 0 => Poisson (differential operator) | |
| * \li 1 => Poisson-Boltzmann operator linearized around | |
| * solution (if applicable) */ | |
| /*Added for issue 482*/ | |
| char pbam_3dmapstem[VMAX_ARGLEN]; | |
| int pbam_3dmapflag; | |
| int parsed; /**< Has this been filled with anything other | |
| * than the default values? */ | |
| }; | |
| /** | |
| * @ingroup PBEparm | |
| * @brief Declaration of the PBEparm class as the PBEparm structure | |
| */ | |
| typedef struct sPBEparm PBEparm; | |
| /* /////////////////////////////////////////////////////////////////////////// | |
| // Class NOsh: Non-inlineable methods (mcsh.c) | |
| /////////////////////////////////////////////////////////////////////////// */ | |
| /** @brief Get charge (e) of specified ion species | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| * @returns Charge of ion species (e) | |
| */ | |
| VEXTERNC double PBEparm_getIonCharge( | |
| PBEparm *thee, /**< PBEparm object */ | |
| int iion /**< Ion species ID/index */ | |
| ); | |
| /** @brief Get concentration (M) of specified ion species | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| * @returns Concentration of ion species (M) | |
| */ | |
| VEXTERNC double PBEparm_getIonConc( | |
| PBEparm *thee, /**< PBEparm object */ | |
| int iion /**< Ion species ID/index */ | |
| ); | |
| /** @brief Get radius (A) of specified ion species | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| * @returns Radius of ion species (A) | |
| */ | |
| VEXTERNC double PBEparm_getIonRadius( | |
| PBEparm *thee, /**< PBEparm object */ | |
| int iion /**< Ion species ID/index */ | |
| ); | |
| /** @brief Construct PBEparm object | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| * @returns Newly allocated and initialized PBEparm object | |
| */ | |
| VEXTERNC PBEparm* PBEparm_ctor(); | |
| /** @brief FORTRAN stub to construct PBEparm object | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| * @returns 1 if succesful, 0 otherwise | |
| */ | |
| VEXTERNC int PBEparm_ctor2( | |
| PBEparm *thee /**< Memory location for object */ | |
| ); | |
| /** @brief Object destructor | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void PBEparm_dtor( | |
| PBEparm **thee /**< Pointer to memory location of object */ | |
| ); | |
| /** @brief FORTRAN stub for object destructor | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void PBEparm_dtor2( | |
| PBEparm *thee /**< Pointer to object to be destroyed */ | |
| ); | |
| /** @brief Consistency check for parameter values stored in object | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| * @returns 1 if OK, 0 otherwise | |
| */ | |
| VEXTERNC int PBEparm_check( | |
| PBEparm *thee /**< Object to be checked */ | |
| ); | |
| /** @brief Copy PBEparm object into thee | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| */ | |
| VEXTERNC void PBEparm_copy( | |
| PBEparm *thee, /**< Target for copy */ | |
| PBEparm *parm /**< Source for copy */ | |
| ); | |
| /** @brief Parse a keyword from an input file | |
| * @ingroup PBEparm | |
| * @author Nathan Baker | |
| * @return 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 int PBEparm_parseToken( | |
| PBEparm *thee, /**< Parsing object */ | |
| char tok[VMAX_BUFSIZE], /**< Token to parse */ | |
| Vio *sock /**< Socket for additional tokens */ | |
| ); | |