routines.h File Reference
Header file for front end auxiliary routines. More...
#include "apbs/apbs.h"#include "apbs/nosh.h"#include "apbs/mgparm.h"#include "apbs/pbeparm.h"#include "apbs/femparm.h"#include "apbs/vparam.h"#include "apbs/vfetk.h"
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Data Structures | |
| struct | AtomForce |
| Structure to hold atomic forces. More... | |
Defines | |
| #define | APBSRC 13 |
| Return code for APBS during failure. | |
Typedefs | |
| typedef struct AtomForce | AtomForce |
| Define AtomForce type. | |
Functions | |
| Vparam * | loadParameter (NOsh *nosh) |
| Loads and returns parameter object. | |
| int | loadMolecules (NOsh *nosh, Vparam *param, Valist *alist[NOSH_MAXMOL]) |
| Load the molecules given in NOsh into atom lists. | |
| void | killMolecules (NOsh *nosh, Valist *alist[NOSH_MAXMOL]) |
| Destroy the loaded molecules. | |
| int | loadDielMaps (NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL]) |
| Load the dielectric maps given in NOsh into grid objects. | |
| void | killDielMaps (NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL]) |
| Destroy the loaded dielectric. | |
| int | loadKappaMaps (NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL]) |
| Load the kappa maps given in NOsh into grid objects. | |
| void | killKappaMaps (NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL]) |
| Destroy the loaded kappa maps. | |
| int | loadChargeMaps (NOsh *nosh, Vgrid *charge[NOSH_MAXMOL]) |
| Load the charge maps given in NOsh into grid objects. | |
| void | killChargeMaps (NOsh *nosh, Vgrid *charge[NOSH_MAXMOL]) |
| Destroy the loaded charge maps. | |
| void | printPBEPARM (PBEparm *pbeparm) |
| Print out generic PBE params loaded from input. | |
| void | printMGPARM (MGparm *mgparm, double realCenter[3]) |
| Print out MG-specific params loaded from input. | |
| int | initMG (int icalc, NOsh *nosh, MGparm *mgparm, PBEparm *pbeparm, double realCenter[3], Vpbe *pbe[NOSH_MAXCALC], Valist *alist[NOSH_MAXMOL], Vgrid *dielXMap[NOSH_MAXMOL], Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL], Vgrid *kappaMap[NOSH_MAXMOL], Vgrid *chargeMap[NOSH_MAXMOL], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) |
| Initialize an MG calculation. | |
| void | killMG (NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vpmgp *pmgp[NOSH_MAXCALC], Vpmg *pmg[NOSH_MAXCALC]) |
| Kill structures initialized during an MG calculation. | |
| int | solveMG (NOsh *nosh, Vpmg *pmg, MGparm_CalcType type) |
| Solve the PBE with MG. | |
| int | setPartMG (NOsh *nosh, MGparm *mgparm, Vpmg *pmg) |
| Set MG partitions for calculating observables and performing I/O. | |
| int | energyMG (NOsh *nosh, int icalc, Vpmg *pmg, int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy) |
| Calculate electrostatic energies from MG solution. | |
| void | killEnergy () |
| Kill arrays allocated for energies. | |
| int | forceMG (Vmem *mem, NOsh *nosh, PBEparm *pbeparm, MGparm *mgparm, Vpmg *pmg, int *nforce, AtomForce **atomForce, Valist *alist[NOSH_MAXMOL]) |
| Calculate forces from MG solution. | |
| void | killForce (Vmem *mem, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]) |
| Free memory from MG force calculation. | |
| void | storeAtomEnergy (Vpmg *pmg, int icalc, double **atomEnergy, int *nenergy) |
| Store energy in arrays for future use. | |
| int | writedataFlat (NOsh *nosh, Vcom *com, const char *fname, double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC], double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC], int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC], int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]) |
| Write out information to a flat file. | |
| int | writedataXML (NOsh *nosh, Vcom *com, const char *fname, double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC], double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC], int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC], int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]) |
| Write out information to an XML file. | |
| int | writedataMG (int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg) |
| Write out observables from MG calculation to file. | |
| int | writematMG (int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg) |
| Write out operator matrix from MG calculation to file. | |
| double | returnEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
| Access net local energy. | |
| int | printEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
| Combine and pretty-print energy data (deprecated...see printElecEnergy). | |
| int | printElecEnergy (Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint) |
| Combine and pretty-print energy data. | |
| int | printApolEnergy (NOsh *nosh, int iprint) |
| Combine and pretty-print energy data. | |
| int | printForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) |
| Combine and pretty-print force data (deprecated...see printElecForce). | |
| int | printElecForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) |
| Combine and pretty-print force data. | |
| int | printApolForce (Vcom *com, NOsh *nosh, int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC], int i) |
| Combine and pretty-print force data. | |
| void | startVio () |
| Wrapper to start MALOC Vio layer. | |
| void | printFEPARM (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Print out FE-specific params loaded from input. | |
| int | energyFE (NOsh *nosh, int icalc, Vfetk *fetk[NOSH_MAXCALC], int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy, double *dielEnergy) |
| Calculate electrostatic energies from FE solution. | |
| Vrc_Codes | initFE (int icalc, NOsh *nosh, FEMparm *feparm, PBEparm *pbeparm, Vpbe *pbe[NOSH_MAXCALC], Valist *alist[NOSH_MAXMOL], Vfetk *fetk[NOSH_MAXCALC], Gem *gm[NOSH_MAXCALC]) |
| Initialize FE solver objects. | |
| void | killFE (NOsh *nosh, Vpbe *pbe[NOSH_MAXCALC], Vfetk *fetk[NOSH_MAXCALC], Gem *gem[NOSH_MAXMOL]) |
| Kill structures initialized during an FE calculation. | |
| int | preRefineFE (int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Pre-refine mesh before solve. | |
| int | partFE (int i, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Partition mesh (if applicable). | |
| int | solveFE (int i, NOsh *nosh, PBEparm *pbeparm, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Solve-estimate-refine. | |
| int | postRefineFE (int icalc, NOsh *nosh, FEMparm *feparm, Vfetk *fetk[NOSH_MAXCALC]) |
| Estimate error, mark mesh, and refine mesh after solve. | |
| int | writedataFE (int rank, NOsh *nosh, PBEparm *pbeparm, Vfetk *fetk) |
| Write FEM data to files. | |
| int | energyAPOL (APOLparm *apolparm, double sasa, double sav, double atomsasa[], double atomwcaEnergy[], int numatoms) |
| Calculate non-polar energies. | |
| int | forceAPOL (Vacc *acc, Vmem *mem, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist, Vclist *clist) |
| Calculate non-polar forces. | |
| int | initAPOL (NOsh *nosh, Vmem *mem, Vparam *param, APOLparm *apolparm, int *nforce, AtomForce **atomForce, Valist *alist) |
| Upperlevel routine to the non-polar energy and force routines. | |
| Vrc_Codes | loadMeshes (NOsh *nosh, Gem *gm[NOSH_MAXMOL]) |
| Load the meshes given in NOsh into geometry objects. | |
| void | killMeshes (NOsh *nosh, Gem *alist[NOSH_MAXMOL]) |
| Destroy the loaded meshes. | |
Detailed Description
Header file for front end auxiliary routines.
- Version:
- Id
- routines.h 1368 2009-05-02 00:32:09Z yhuang01
- Attention:
* * APBS -- Adaptive Poisson-Boltzmann Solver * * Nathan A. Baker (baker@biochem.wustl.edu) * Dept. of Biochemistry and Molecular Biophysics * Center for Computational Biology * Washington University in St. Louis * * Additional contributing authors listed in the code documentation. * * Copyright (c) 2002-2009, Washington University in St. Louis. * Portions Copyright (c) 2002-2009. 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 Washington University in St. Louis 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. * *
