00001
00059 #ifndef _APBSROUTINES_H_
00060 #define _APBSROUTINES_H_
00061
00062 #include "apbs/apbs.h"
00063 #include "apbs/nosh.h"
00064 #include "apbs/mgparm.h"
00065 #include "apbs/pbeparm.h"
00066 #include "apbs/femparm.h"
00067 #include "apbs/vparam.h"
00068
00069
00073 #define APBSRC 13
00074
00079 struct AtomForce {
00080 double ibForce[3];
00081 double qfForce[3];
00082 double dbForce[3];
00083 double sasaForce[3];
00084 double savForce[3];
00085 double wcaForce[3];
00086 };
00087
00091 typedef struct AtomForce AtomForce;
00092
00098 Vparam* loadParameter(
00099 NOsh *nosh
00101 );
00102
00108 int loadMolecules(
00109 NOsh *nosh,
00110 Vparam *param,
00112 Valist *alist[NOSH_MAXMOL]
00114 );
00115
00122 void killMolecules(NOsh *nosh, Valist *alist[NOSH_MAXMOL]);
00123
00133 int loadDielMaps(NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL],
00134 Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL]);
00135
00144 void killDielMaps(NOsh *nosh, Vgrid *dielXMap[NOSH_MAXMOL],
00145 Vgrid *dielYMap[NOSH_MAXMOL], Vgrid *dielZMap[NOSH_MAXMOL]);
00146
00154 int loadKappaMaps(NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL]);
00155
00162 void killKappaMaps(NOsh *nosh, Vgrid *kappa[NOSH_MAXMOL]);
00163
00171 int loadChargeMaps(NOsh *nosh, Vgrid *charge[NOSH_MAXMOL]);
00172
00179 void killChargeMaps(NOsh *nosh, Vgrid *charge[NOSH_MAXMOL]);
00180
00186 void printPBEPARM(PBEparm *pbeparm);
00187
00194 void printMGPARM(MGparm *mgparm, double realCenter[3]);
00195
00201 int initMG(
00202 int icalc,
00203 NOsh *nosh,
00204 MGparm *mgparm,
00205 PBEparm *pbeparm,
00206 double realCenter[3],
00207 Vpbe *pbe[NOSH_MAXCALC],
00208 Valist *alist[NOSH_MAXMOL],
00209 Vgrid *dielXMap[NOSH_MAXMOL],
00210 Vgrid *dielYMap[NOSH_MAXMOL],
00211 Vgrid *dielZMap[NOSH_MAXMOL],
00212 Vgrid *kappaMap[NOSH_MAXMOL],
00213 Vgrid *chargeMap[NOSH_MAXMOL],
00214 Vpmgp *pmgp[NOSH_MAXCALC],
00215 Vpmg *pmg[NOSH_MAXCALC]
00216 );
00217
00223 void killMG(
00224 NOsh *nosh,
00225 Vpbe *pbe[NOSH_MAXCALC],
00226 Vpmgp *pmgp[NOSH_MAXCALC],
00227 Vpmg *pmg[NOSH_MAXCALC]
00228 );
00229
00238 int solveMG(NOsh *nosh, Vpmg *pmg, MGparm_CalcType type);
00239
00248 int setPartMG(NOsh *nosh, MGparm *mgparm, Vpmg *pmg);
00249
00263 int energyMG(NOsh* nosh, int icalc, Vpmg *pmg,
00264 int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy,
00265 double *dielEnergy);
00266
00271 void killEnergy();
00272
00286 int forceMG(Vmem *mem, NOsh *nosh, PBEparm *pbeparm, MGparm *mgparm,
00287 Vpmg *pmg, int *nforce, AtomForce **atomForce, Valist *alist[NOSH_MAXMOL]);
00288
00297 void killForce(Vmem *mem, NOsh *nosh, int nforce[NOSH_MAXCALC],
00298 AtomForce *atomForce[NOSH_MAXCALC]);
00299
00304 void storeAtomEnergy(
00305 Vpmg *pmg,
00306 int icalc,
00307 double **atomEnergy,
00308 int *nenergy
00309 );
00310
00327 int writedataFlat(NOsh *nosh, Vcom *com, const char *fname,
00328 double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC],
00329 double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC],
00330 int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC],
00331 int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]);
00332
00349 int writedataXML(NOsh *nosh, Vcom *com, const char *fname,
00350 double totEnergy[NOSH_MAXCALC], double qfEnergy[NOSH_MAXCALC],
00351 double qmEnergy[NOSH_MAXCALC], double dielEnergy[NOSH_MAXCALC],
00352 int nenergy[NOSH_MAXCALC], double *atomEnergy[NOSH_MAXCALC],
00353 int nforce[NOSH_MAXCALC], AtomForce *atomForce[NOSH_MAXCALC]);
00354
00364 int writedataMG(int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg);
00365
00375 int writematMG(int rank, NOsh *nosh, PBEparm *pbeparm, Vpmg *pmg);
00376
00386 double returnEnergy(Vcom *com, NOsh *nosh, double totEnergy[NOSH_MAXCALC], int iprint);
00387
00393 int printEnergy(
00394 Vcom *com,
00395 NOsh *nosh,
00396 double totEnergy[NOSH_MAXCALC],
00398 int iprint
00399 );
00400
00406 int printElecEnergy(
00407 Vcom *com,
00408 NOsh *nosh,
00409 double totEnergy[NOSH_MAXCALC],
00411 int iprint
00412 );
00413
00419 int printApolEnergy(
00420 NOsh *nosh,
00421 int iprint
00422 );
00423
00429 int printForce(
00430 Vcom *com,
00431 NOsh *nosh,
00432 int nforce[NOSH_MAXCALC],
00433 AtomForce *atomForce[NOSH_MAXCALC],
00434 int i
00435 );
00436
00442 int printElecForce(
00443 Vcom *com,
00444 NOsh *nosh,
00445 int nforce[NOSH_MAXCALC],
00446 AtomForce *atomForce[NOSH_MAXCALC],
00447 int i
00448 );
00449
00455 int printApolForce(
00456 Vcom *com,
00457 NOsh *nosh,
00458 int nforce[NOSH_MAXCALC],
00459 AtomForce *atomForce[NOSH_MAXCALC],
00460 int i
00461 );
00462
00467 void startVio();
00468
00469 #ifdef HAVE_MC_H
00470 #include "apbs/vfetk.h"
00471
00480 void printFEPARM(int icalc, NOsh *nosh, FEMparm *feparm,
00481 Vfetk *fetk[NOSH_MAXCALC]);
00482
00497 int energyFE(NOsh* nosh, int icalc, Vfetk *fetk[NOSH_MAXCALC],
00498 int *nenergy, double *totEnergy, double *qfEnergy, double *qmEnergy,
00499 double *dielEnergy);
00500
00508 Vrc_Codes initFE(
00509 int icalc,
00511 NOsh *nosh,
00512 FEMparm *feparm,
00513 PBEparm *pbeparm,
00514 Vpbe *pbe[NOSH_MAXCALC],
00515 Valist *alist[NOSH_MAXMOL],
00516 Vfetk *fetk[NOSH_MAXCALC],
00517 Gem *gm[NOSH_MAXCALC]
00518 );
00519
00525 void killFE(
00526 NOsh *nosh,
00527 Vpbe *pbe[NOSH_MAXCALC],
00528 Vfetk *fetk[NOSH_MAXCALC],
00529 Gem *gem[NOSH_MAXMOL]
00530 );
00531
00541 int preRefineFE(int i, NOsh *nosh, FEMparm *feparm,
00542 Vfetk *fetk[NOSH_MAXCALC]);
00543
00553 int partFE(int i, NOsh *nosh, FEMparm *feparm,
00554 Vfetk *fetk[NOSH_MAXCALC]);
00555
00566 int solveFE(int i, NOsh *nosh, PBEparm *pbeparm, FEMparm *feparm,
00567 Vfetk *fetk[NOSH_MAXCALC]);
00568
00581 int postRefineFE(int icalc, NOsh *nosh, FEMparm *feparm,
00582 Vfetk *fetk[NOSH_MAXCALC]);
00583
00593 int writedataFE(int rank, NOsh *nosh, PBEparm *pbeparm, Vfetk *fetk);
00594
00600 int energyAPOL(
00601 APOLparm *apolparm,
00602 double sasa,
00603 double sav,
00604 double atomsasa[],
00605 double atomwcaEnergy[],
00606 int numatoms
00607 );
00608
00614 int forceAPOL(
00615 Vacc *acc,
00616 Vmem *mem,
00617 APOLparm *apolparm,
00619 int *nforce,
00621 AtomForce **atomForce,
00623 Valist *alist,
00624 Vclist *clist
00625 );
00626
00632 int initAPOL(
00633 NOsh *nosh,
00634 Vmem *mem,
00635 Vparam *param,
00636 APOLparm *apolparm,
00637 int *nforce,
00638 AtomForce **atomForce,
00639 Valist *alist
00640 );
00641
00647 Vrc_Codes loadMeshes(
00648 NOsh *nosh,
00649 Gem *gm[NOSH_MAXMOL]
00651 );
00652
00657 void killMeshes(
00658 NOsh *nosh,
00659 Gem *alist[NOSH_MAXMOL]
00660 );
00661 #endif
00662
00663 #endif
00664
