| 12 |
|
#include "mpiSimulation.hpp" |
| 13 |
|
#endif |
| 14 |
|
|
| 15 |
+ |
// some defines for ensemble and Forcefield cases |
| 16 |
+ |
|
| 17 |
+ |
#define NVE_ENS 0 |
| 18 |
+ |
#define NVT_ENS 1 |
| 19 |
+ |
#define NPT_ENS 2 |
| 20 |
+ |
|
| 21 |
+ |
#define FF_DUFF 0 |
| 22 |
+ |
#define FF_LJ 1 |
| 23 |
+ |
|
| 24 |
+ |
|
| 25 |
|
SimSetup::SimSetup(){ |
| 26 |
|
stamps = new MakeStamps(); |
| 27 |
|
globals = new Globals(); |
| 76 |
|
|
| 77 |
|
MakeStamps *the_stamps; |
| 78 |
|
Globals* the_globals; |
| 79 |
< |
int i, j; |
| 79 |
> |
int i, j, k, globalAtomIndex; |
| 80 |
> |
|
| 81 |
> |
int ensembleCase; |
| 82 |
> |
int ffCase; |
| 83 |
> |
|
| 84 |
> |
ensembleCase = -1; |
| 85 |
> |
ffCase = -1; |
| 86 |
|
|
| 87 |
|
// get the stamps and globals; |
| 88 |
|
the_stamps = stamps; |
| 96 |
|
// get the ones we know are there, yet still may need some work. |
| 97 |
|
n_components = the_globals->getNComponents(); |
| 98 |
|
strcpy( force_field, the_globals->getForceField() ); |
| 99 |
+ |
|
| 100 |
+ |
if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
| 101 |
+ |
else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
| 102 |
+ |
else{ |
| 103 |
+ |
sprintf( painCave.errMsg, |
| 104 |
+ |
"SimSetup Error. Unrecognized force field -> %s\n", |
| 105 |
+ |
force_field ); |
| 106 |
+ |
painCave.isFatal = 1; |
| 107 |
+ |
simError(); |
| 108 |
+ |
} |
| 109 |
+ |
|
| 110 |
+ |
// get the ensemble: |
| 111 |
|
strcpy( ensemble, the_globals->getEnsemble() ); |
| 112 |
+ |
|
| 113 |
+ |
if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
| 114 |
+ |
else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
| 115 |
+ |
else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS; |
| 116 |
+ |
else{ |
| 117 |
+ |
sprintf( painCave.errMsg, |
| 118 |
+ |
"SimSetup Warning. Unrecognized Ensemble -> %s, " |
| 119 |
+ |
"reverting to NVE for this simulation.\n", |
| 120 |
+ |
ensemble ); |
| 121 |
+ |
painCave.isFatal = 0; |
| 122 |
+ |
simError(); |
| 123 |
+ |
strcpy( ensemble, "NVE" ); |
| 124 |
+ |
ensembleCase = NVE_ENS; |
| 125 |
+ |
} |
| 126 |
|
strcpy( simnfo->ensemble, ensemble ); |
| 127 |
+ |
|
| 128 |
+ |
|
| 129 |
+ |
// if( !strcasecmp( ensemble, "NPT" ) ) { |
| 130 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
| 131 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
| 132 |
+ |
// if (the_globals->haveTargetPressure()) |
| 133 |
+ |
// the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
| 134 |
+ |
// else { |
| 135 |
+ |
// sprintf( painCave.errMsg, |
| 136 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
| 137 |
+ |
// " ensemble, you must set targetPressure.\n" |
| 138 |
+ |
// " This was found in the BASS file.\n"); |
| 139 |
+ |
// painCave.isFatal = 1; |
| 140 |
+ |
// simError(); |
| 141 |
+ |
// } |
| 142 |
+ |
|
| 143 |
+ |
// if (the_globals->haveTauThermostat()) |
| 144 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
| 145 |
+ |
// else if (the_globals->haveQmass()) |
| 146 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
| 147 |
+ |
// else { |
| 148 |
+ |
// sprintf( painCave.errMsg, |
| 149 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
| 150 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
| 151 |
+ |
// " Neither of these was found in the BASS file.\n"); |
| 152 |
+ |
// painCave.isFatal = 1; |
| 153 |
+ |
// simError(); |
| 154 |
+ |
// } |
| 155 |
|
|
| 156 |
+ |
// if (the_globals->haveTauBarostat()) |
| 157 |
+ |
// the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
| 158 |
+ |
// else { |
| 159 |
+ |
// sprintf( painCave.errMsg, |
| 160 |
+ |
// "SimSetup error: If you use the constant pressure\n" |
| 161 |
+ |
// " ensemble, you must set tauBarostat.\n" |
| 162 |
+ |
// " This was found in the BASS file.\n"); |
| 163 |
+ |
// painCave.isFatal = 1; |
| 164 |
+ |
// simError(); |
| 165 |
+ |
// } |
| 166 |
+ |
|
| 167 |
+ |
// } else if ( !strcasecmp( ensemble, "NVT") ) { |
| 168 |
+ |
// the_extendedsystem = new ExtendedSystem( simnfo ); |
| 169 |
+ |
// the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
| 170 |
+ |
|
| 171 |
+ |
// if (the_globals->haveTauThermostat()) |
| 172 |
+ |
// the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
| 173 |
+ |
// else if (the_globals->haveQmass()) |
| 174 |
+ |
// the_extendedsystem->setQmass(the_globals->getQmass()); |
| 175 |
+ |
// else { |
| 176 |
+ |
// sprintf( painCave.errMsg, |
| 177 |
+ |
// "SimSetup error: If you use one of the constant temperature\n" |
| 178 |
+ |
// " ensembles, you must set either tauThermostat or qMass.\n" |
| 179 |
+ |
// " Neither of these was found in the BASS file.\n"); |
| 180 |
+ |
// painCave.isFatal = 1; |
| 181 |
+ |
// simError(); |
| 182 |
+ |
// } |
| 183 |
+ |
|
| 184 |
|
strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
| 185 |
|
simnfo->usePBC = the_globals->getPBC(); |
| 186 |
|
|
| 187 |
+ |
int usesDipoles = 0; |
| 188 |
+ |
switch( ffCase ){ |
| 189 |
|
|
| 190 |
+ |
case FF_DUFF: |
| 191 |
+ |
the_ff = new DUFF(); |
| 192 |
+ |
usesDipoles = 1; |
| 193 |
+ |
break; |
| 194 |
|
|
| 195 |
< |
if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
| 196 |
< |
else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
| 197 |
< |
else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
| 198 |
< |
else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
| 199 |
< |
else{ |
| 195 |
> |
case FF_LJ: |
| 196 |
> |
the_ff = new LJFF(); |
| 197 |
> |
break; |
| 198 |
> |
|
| 199 |
> |
default: |
| 200 |
|
sprintf( painCave.errMsg, |
| 201 |
< |
"SimSetup Error. Unrecognized force field -> %s\n", |
| 98 |
< |
force_field ); |
| 201 |
> |
"SimSetup Error. Unrecognized force field in case statement.\n"); |
| 202 |
|
painCave.isFatal = 1; |
| 203 |
|
simError(); |
| 204 |
|
} |
| 208 |
|
MPIcheckPoint(); |
| 209 |
|
#endif // is_mpi |
| 210 |
|
|
| 108 |
– |
|
| 109 |
– |
|
| 211 |
|
// get the components and calculate the tot_nMol and indvidual n_mol |
| 212 |
|
the_components = the_globals->getComponents(); |
| 213 |
|
components_nmol = new int[n_components]; |
| 331 |
|
simnfo->n_torsions = tot_torsions; |
| 332 |
|
simnfo->n_SRI = tot_SRI; |
| 333 |
|
simnfo->n_mol = tot_nmol; |
| 233 |
– |
|
| 334 |
|
|
| 335 |
+ |
simnfo->molMembershipArray = new int[tot_atoms]; |
| 336 |
+ |
|
| 337 |
|
#ifdef IS_MPI |
| 338 |
|
|
| 339 |
|
// divide the molecules among processors here. |
| 340 |
|
|
| 341 |
|
mpiSim = new mpiSimulation( simnfo ); |
| 342 |
|
|
| 241 |
– |
|
| 242 |
– |
|
| 343 |
|
globalIndex = mpiSim->divideLabor(); |
| 344 |
|
|
| 245 |
– |
|
| 246 |
– |
|
| 345 |
|
// set up the local variables |
| 346 |
|
|
| 347 |
|
int localMol, allMol; |
| 348 |
|
int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
| 349 |
+ |
|
| 350 |
+ |
int* mol2proc = mpiSim->getMolToProcMap(); |
| 351 |
+ |
int* molCompType = mpiSim->getMolComponentType(); |
| 352 |
|
|
| 353 |
|
allMol = 0; |
| 354 |
|
localMol = 0; |
| 356 |
|
local_bonds = 0; |
| 357 |
|
local_bends = 0; |
| 358 |
|
local_torsions = 0; |
| 359 |
+ |
globalAtomIndex = 0; |
| 360 |
+ |
|
| 361 |
+ |
|
| 362 |
|
for( i=0; i<n_components; i++ ){ |
| 363 |
|
|
| 364 |
|
for( j=0; j<components_nmol[i]; j++ ){ |
| 365 |
|
|
| 366 |
< |
if( mpiSim->getMyMolStart() <= allMol && |
| 263 |
< |
allMol <= mpiSim->getMyMolEnd() ){ |
| 366 |
> |
if( mol2proc[allMol] == worldRank ){ |
| 367 |
|
|
| 368 |
|
local_atoms += comp_stamps[i]->getNAtoms(); |
| 369 |
|
local_bonds += comp_stamps[i]->getNBonds(); |
| 371 |
|
local_torsions += comp_stamps[i]->getNTorsions(); |
| 372 |
|
localMol++; |
| 373 |
|
} |
| 374 |
< |
allMol++; |
| 374 |
> |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 375 |
> |
simnfo->molMembershipArray[globalAtomIndex] = allMol; |
| 376 |
> |
globalAtomIndex++; |
| 377 |
> |
} |
| 378 |
> |
|
| 379 |
> |
allMol++; |
| 380 |
|
} |
| 381 |
|
} |
| 382 |
|
local_SRI = local_bonds + local_bends + local_torsions; |
| 383 |
|
|
| 276 |
– |
|
| 384 |
|
simnfo->n_atoms = mpiSim->getMyNlocal(); |
| 385 |
|
|
| 386 |
|
if( local_atoms != simnfo->n_atoms ){ |
| 387 |
|
sprintf( painCave.errMsg, |
| 388 |
|
"SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
| 389 |
< |
" localAtom (%d) are note equal.\n", |
| 389 |
> |
" localAtom (%d) are not equal.\n", |
| 390 |
|
simnfo->n_atoms, |
| 391 |
|
local_atoms ); |
| 392 |
|
painCave.isFatal = 1; |
| 411 |
|
Atom::createArrays(simnfo->n_atoms); |
| 412 |
|
the_atoms = new Atom*[simnfo->n_atoms]; |
| 413 |
|
the_molecules = new Molecule[simnfo->n_mol]; |
| 414 |
+ |
int molIndex; |
| 415 |
|
|
| 416 |
+ |
// initialize the molecule's stampID's |
| 417 |
|
|
| 418 |
+ |
#ifdef IS_MPI |
| 419 |
+ |
|
| 420 |
+ |
|
| 421 |
+ |
molIndex = 0; |
| 422 |
+ |
for(i=0; i<mpiSim->getTotNmol(); i++){ |
| 423 |
+ |
|
| 424 |
+ |
if(mol2proc[i] == worldRank ){ |
| 425 |
+ |
the_molecules[molIndex].setStampID( molCompType[i] ); |
| 426 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 427 |
+ |
the_molecules[molIndex].setGlobalIndex( i ); |
| 428 |
+ |
molIndex++; |
| 429 |
+ |
} |
| 430 |
+ |
} |
| 431 |
+ |
|
| 432 |
+ |
#else // is_mpi |
| 433 |
+ |
|
| 434 |
+ |
molIndex = 0; |
| 435 |
+ |
globalAtomIndex = 0; |
| 436 |
+ |
for(i=0; i<n_components; i++){ |
| 437 |
+ |
for(j=0; j<components_nmol[i]; j++ ){ |
| 438 |
+ |
the_molecules[molIndex].setStampID( i ); |
| 439 |
+ |
the_molecules[molIndex].setMyIndex( molIndex ); |
| 440 |
+ |
the_molecules[molIndex].setGlobalIndex( molIndex ); |
| 441 |
+ |
for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
| 442 |
+ |
simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
| 443 |
+ |
globalAtomIndex++; |
| 444 |
+ |
} |
| 445 |
+ |
molIndex++; |
| 446 |
+ |
} |
| 447 |
+ |
} |
| 448 |
+ |
|
| 449 |
+ |
|
| 450 |
+ |
#endif // is_mpi |
| 451 |
+ |
|
| 452 |
+ |
|
| 453 |
|
if( simnfo->n_SRI ){ |
| 454 |
< |
the_sris = new SRI*[simnfo->n_SRI]; |
| 455 |
< |
the_excludes = new int[2 * simnfo->n_SRI]; |
| 454 |
> |
|
| 455 |
> |
Exclude::createArray(simnfo->n_SRI); |
| 456 |
> |
the_excludes = new Exclude*[simnfo->n_SRI]; |
| 457 |
> |
for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
| 458 |
|
simnfo->globalExcludes = new int; |
| 459 |
< |
simnfo->n_exclude = tot_SRI; |
| 459 |
> |
simnfo->n_exclude = simnfo->n_SRI; |
| 460 |
|
} |
| 461 |
|
else{ |
| 462 |
|
|
| 463 |
< |
the_excludes = new int[2]; |
| 464 |
< |
the_excludes[0] = 0; |
| 465 |
< |
the_excludes[1] = 0; |
| 463 |
> |
Exclude::createArray( 1 ); |
| 464 |
> |
the_excludes = new Exclude*; |
| 465 |
> |
the_excludes[0] = new Exclude(0); |
| 466 |
> |
the_excludes[0]->setPair( 0,0 ); |
| 467 |
|
simnfo->globalExcludes = new int; |
| 468 |
|
simnfo->globalExcludes[0] = 0; |
| 469 |
< |
|
| 323 |
< |
simnfo->n_exclude = 1; |
| 469 |
> |
simnfo->n_exclude = 0; |
| 470 |
|
} |
| 471 |
|
|
| 472 |
|
// set the arrays into the SimInfo object |
| 473 |
|
|
| 474 |
|
simnfo->atoms = the_atoms; |
| 475 |
< |
simnfo->sr_interactions = the_sris; |
| 475 |
> |
simnfo->molecules = the_molecules; |
| 476 |
|
simnfo->nGlobalExcludes = 0; |
| 477 |
|
simnfo->excludes = the_excludes; |
| 478 |
|
|
| 479 |
|
|
| 480 |
|
// get some of the tricky things that may still be in the globals |
| 481 |
|
|
| 336 |
– |
if( simnfo->n_dipoles ){ |
| 337 |
– |
|
| 338 |
– |
if( !the_globals->haveRRF() ){ |
| 339 |
– |
sprintf( painCave.errMsg, |
| 340 |
– |
"SimSetup Error, system has dipoles, but no rRF was set.\n"); |
| 341 |
– |
painCave.isFatal = 1; |
| 342 |
– |
simError(); |
| 343 |
– |
} |
| 344 |
– |
if( !the_globals->haveDielectric() ){ |
| 345 |
– |
sprintf( painCave.errMsg, |
| 346 |
– |
"SimSetup Error, system has dipoles, but no" |
| 347 |
– |
" dielectric was set.\n" ); |
| 348 |
– |
painCave.isFatal = 1; |
| 349 |
– |
simError(); |
| 350 |
– |
} |
| 351 |
– |
|
| 352 |
– |
simnfo->rRF = the_globals->getRRF(); |
| 353 |
– |
simnfo->dielectric = the_globals->getDielectric(); |
| 354 |
– |
} |
| 355 |
– |
|
| 356 |
– |
#ifdef IS_MPI |
| 357 |
– |
strcpy( checkPointMsg, "rRf and dielectric check out" ); |
| 358 |
– |
MPIcheckPoint(); |
| 359 |
– |
#endif // is_mpi |
| 482 |
|
|
| 483 |
|
if( the_globals->haveBox() ){ |
| 484 |
|
simnfo->box_x = the_globals->getBox(); |
| 529 |
|
|
| 530 |
|
the_ff->setSimInfo( simnfo ); |
| 531 |
|
|
| 532 |
< |
makeAtoms(); |
| 532 |
> |
makeMolecules(); |
| 533 |
|
simnfo->identArray = new int[simnfo->n_atoms]; |
| 534 |
|
for(i=0; i<simnfo->n_atoms; i++){ |
| 535 |
|
simnfo->identArray[i] = the_atoms[i]->getIdent(); |
| 536 |
|
} |
| 537 |
|
|
| 538 |
< |
if( tot_bonds ){ |
| 539 |
< |
makeBonds(); |
| 540 |
< |
} |
| 541 |
< |
|
| 542 |
< |
if( tot_bends ){ |
| 543 |
< |
makeBends(); |
| 544 |
< |
} |
| 545 |
< |
|
| 546 |
< |
if( tot_torsions ){ |
| 547 |
< |
makeTorsions(); |
| 548 |
< |
} |
| 549 |
< |
|
| 550 |
< |
|
| 551 |
< |
|
| 538 |
> |
if (the_globals->getUseRF() ) { |
| 539 |
> |
simnfo->useReactionField = 1; |
| 540 |
> |
|
| 541 |
> |
if( !the_globals->haveECR() ){ |
| 542 |
> |
sprintf( painCave.errMsg, |
| 543 |
> |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 544 |
> |
"box length for the electrostaticCutoffRadius.\n" |
| 545 |
> |
"I hope you have a very fast processor!\n"); |
| 546 |
> |
painCave.isFatal = 0; |
| 547 |
> |
simError(); |
| 548 |
> |
double smallest; |
| 549 |
> |
smallest = simnfo->box_x; |
| 550 |
> |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
| 551 |
> |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
| 552 |
> |
simnfo->ecr = 0.5 * smallest; |
| 553 |
> |
} else { |
| 554 |
> |
simnfo->ecr = the_globals->getECR(); |
| 555 |
> |
} |
| 556 |
|
|
| 557 |
+ |
if( !the_globals->haveEST() ){ |
| 558 |
+ |
sprintf( painCave.errMsg, |
| 559 |
+ |
"SimSetup Warning: using default value of 0.05 * the " |
| 560 |
+ |
"electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
| 561 |
+ |
); |
| 562 |
+ |
painCave.isFatal = 0; |
| 563 |
+ |
simError(); |
| 564 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
| 565 |
+ |
} else { |
| 566 |
+ |
simnfo->est = the_globals->getEST(); |
| 567 |
+ |
} |
| 568 |
+ |
|
| 569 |
+ |
if(!the_globals->haveDielectric() ){ |
| 570 |
+ |
sprintf( painCave.errMsg, |
| 571 |
+ |
"SimSetup Error: You are trying to use Reaction Field without" |
| 572 |
+ |
"setting a dielectric constant!\n" |
| 573 |
+ |
); |
| 574 |
+ |
painCave.isFatal = 1; |
| 575 |
+ |
simError(); |
| 576 |
+ |
} |
| 577 |
+ |
simnfo->dielectric = the_globals->getDielectric(); |
| 578 |
+ |
} else { |
| 579 |
+ |
if (usesDipoles) { |
| 580 |
+ |
|
| 581 |
+ |
if( !the_globals->haveECR() ){ |
| 582 |
+ |
sprintf( painCave.errMsg, |
| 583 |
+ |
"SimSetup Warning: using default value of 1/2 the smallest " |
| 584 |
+ |
"box length for the electrostaticCutoffRadius.\n" |
| 585 |
+ |
"I hope you have a very fast processor!\n"); |
| 586 |
+ |
painCave.isFatal = 0; |
| 587 |
+ |
simError(); |
| 588 |
+ |
double smallest; |
| 589 |
+ |
smallest = simnfo->box_x; |
| 590 |
+ |
if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
| 591 |
+ |
if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
| 592 |
+ |
simnfo->ecr = 0.5 * smallest; |
| 593 |
+ |
} else { |
| 594 |
+ |
simnfo->ecr = the_globals->getECR(); |
| 595 |
+ |
} |
| 596 |
+ |
|
| 597 |
+ |
if( !the_globals->haveEST() ){ |
| 598 |
+ |
sprintf( painCave.errMsg, |
| 599 |
+ |
"SimSetup Warning: using default value of 5%% of the " |
| 600 |
+ |
"electrostaticCutoffRadius for the " |
| 601 |
+ |
"electrostaticSkinThickness\n" |
| 602 |
+ |
); |
| 603 |
+ |
painCave.isFatal = 0; |
| 604 |
+ |
simError(); |
| 605 |
+ |
simnfo->est = 0.05 * simnfo->ecr; |
| 606 |
+ |
} else { |
| 607 |
+ |
simnfo->est = the_globals->getEST(); |
| 608 |
+ |
} |
| 609 |
+ |
} |
| 610 |
+ |
} |
| 611 |
|
|
| 612 |
+ |
#ifdef IS_MPI |
| 613 |
+ |
strcpy( checkPointMsg, "electrostatic parameters check out" ); |
| 614 |
+ |
MPIcheckPoint(); |
| 615 |
+ |
#endif // is_mpi |
| 616 |
|
|
| 617 |
|
if( the_globals->haveInitialConfig() ){ |
| 618 |
|
|
| 767 |
|
if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
| 768 |
|
|
| 769 |
|
|
| 770 |
< |
// // make the longe range forces and the integrator |
| 770 |
> |
// make the integrator |
| 771 |
> |
|
| 772 |
> |
|
| 773 |
> |
NVT* myNVT = NULL; |
| 774 |
> |
switch( ensembleCase ){ |
| 775 |
|
|
| 776 |
< |
// new AllLong( simnfo ); |
| 776 |
> |
case NVE_ENS: |
| 777 |
> |
new NVE( simnfo, the_ff ); |
| 778 |
> |
break; |
| 779 |
|
|
| 780 |
< |
if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
| 781 |
< |
if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
| 782 |
< |
if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
| 593 |
< |
if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
| 780 |
> |
case NVT_ENS: |
| 781 |
> |
myNVT = new NVT( simnfo, the_ff ); |
| 782 |
> |
myNVT->setTargetTemp(the_globals->getTargetTemp()); |
| 783 |
|
|
| 784 |
+ |
if (the_globals->haveTauThermostat()) |
| 785 |
+ |
myNVT->setTauThermostat(the_globals->getTauThermostat()); |
| 786 |
+ |
else if (the_globals->haveQmass()) |
| 787 |
+ |
myNVT->setQmass(the_globals->getQmass()); |
| 788 |
+ |
else { |
| 789 |
+ |
sprintf( painCave.errMsg, |
| 790 |
+ |
"SimSetup error: If you use the NVT\n" |
| 791 |
+ |
" ensemble, you must set either tauThermostat or qMass.\n" |
| 792 |
+ |
" Neither of these was found in the BASS file.\n"); |
| 793 |
+ |
painCave.isFatal = 1; |
| 794 |
+ |
simError(); |
| 795 |
+ |
} |
| 796 |
+ |
break; |
| 797 |
|
|
| 798 |
+ |
default: |
| 799 |
+ |
sprintf( painCave.errMsg, |
| 800 |
+ |
"SimSetup Error. Unrecognized ensemble in case statement.\n"); |
| 801 |
+ |
painCave.isFatal = 1; |
| 802 |
+ |
simError(); |
| 803 |
+ |
} |
| 804 |
|
|
| 805 |
+ |
|
| 806 |
+ |
#ifdef IS_MPI |
| 807 |
+ |
mpiSim->mpiRefresh(); |
| 808 |
+ |
#endif |
| 809 |
+ |
|
| 810 |
|
// initialize the Fortran |
| 811 |
< |
|
| 811 |
> |
|
| 812 |
> |
|
| 813 |
|
simnfo->refreshSim(); |
| 814 |
|
|
| 815 |
|
if( !strcmp( simnfo->mixingRule, "standard") ){ |
| 834 |
|
#endif // is_mpi |
| 835 |
|
} |
| 836 |
|
|
| 623 |
– |
void SimSetup::makeAtoms( void ){ |
| 837 |
|
|
| 838 |
< |
int i, j, k, index; |
| 626 |
< |
double ux, uy, uz, uSqr, u; |
| 627 |
< |
AtomStamp* current_atom; |
| 838 |
> |
void SimSetup::makeMolecules( void ){ |
| 839 |
|
|
| 840 |
+ |
int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
| 841 |
+ |
molInit info; |
| 842 |
|
DirectionalAtom* dAtom; |
| 843 |
< |
int molIndex, molStart, molEnd, nMemb, lMolIndex; |
| 843 |
> |
LinkedAssign* extras; |
| 844 |
> |
LinkedAssign* current_extra; |
| 845 |
> |
AtomStamp* currentAtom; |
| 846 |
> |
BondStamp* currentBond; |
| 847 |
> |
BendStamp* currentBend; |
| 848 |
> |
TorsionStamp* currentTorsion; |
| 849 |
|
|
| 850 |
< |
lMolIndex = 0; |
| 851 |
< |
molIndex = 0; |
| 852 |
< |
index = 0; |
| 635 |
< |
for( i=0; i<n_components; i++ ){ |
| 850 |
> |
bond_pair* theBonds; |
| 851 |
> |
bend_set* theBends; |
| 852 |
> |
torsion_set* theTorsions; |
| 853 |
|
|
| 854 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 854 |
> |
|
| 855 |
> |
//init the forceField paramters |
| 856 |
|
|
| 857 |
< |
#ifdef IS_MPI |
| 640 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 641 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 642 |
< |
#endif // is_mpi |
| 857 |
> |
the_ff->readParams(); |
| 858 |
|
|
| 859 |
< |
molStart = index; |
| 860 |
< |
nMemb = comp_stamps[i]->getNAtoms(); |
| 646 |
< |
for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
| 647 |
< |
|
| 648 |
< |
current_atom = comp_stamps[i]->getAtom( k ); |
| 649 |
< |
if( current_atom->haveOrientation() ){ |
| 650 |
< |
|
| 651 |
< |
dAtom = new DirectionalAtom(index); |
| 652 |
< |
simnfo->n_oriented++; |
| 653 |
< |
the_atoms[index] = dAtom; |
| 654 |
< |
|
| 655 |
< |
ux = current_atom->getOrntX(); |
| 656 |
< |
uy = current_atom->getOrntY(); |
| 657 |
< |
uz = current_atom->getOrntZ(); |
| 658 |
< |
|
| 659 |
< |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 660 |
< |
|
| 661 |
< |
u = sqrt( uSqr ); |
| 662 |
< |
ux = ux / u; |
| 663 |
< |
uy = uy / u; |
| 664 |
< |
uz = uz / u; |
| 665 |
< |
|
| 666 |
< |
dAtom->setSUx( ux ); |
| 667 |
< |
dAtom->setSUy( uy ); |
| 668 |
< |
dAtom->setSUz( uz ); |
| 669 |
< |
} |
| 670 |
< |
else{ |
| 671 |
< |
the_atoms[index] = new GeneralAtom(index); |
| 672 |
< |
} |
| 673 |
< |
the_atoms[index]->setType( current_atom->getType() ); |
| 674 |
< |
the_atoms[index]->setIndex( index ); |
| 675 |
< |
|
| 676 |
< |
// increment the index and repeat; |
| 677 |
< |
index++; |
| 678 |
< |
} |
| 679 |
< |
|
| 680 |
< |
molEnd = index -1; |
| 681 |
< |
the_molecules[lMolIndex].setNMembers( nMemb ); |
| 682 |
< |
the_molecules[lMolIndex].setStartAtom( molStart ); |
| 683 |
< |
the_molecules[lMolIndex].setEndAtom( molEnd ); |
| 684 |
< |
the_molecules[lMolIndex].setStampID( i ); |
| 685 |
< |
lMolIndex++; |
| 859 |
> |
|
| 860 |
> |
// init the atoms |
| 861 |
|
|
| 862 |
< |
#ifdef IS_MPI |
| 863 |
< |
} |
| 864 |
< |
#endif //is_mpi |
| 865 |
< |
|
| 866 |
< |
molIndex++; |
| 692 |
< |
} |
| 693 |
< |
} |
| 694 |
< |
|
| 695 |
< |
#ifdef IS_MPI |
| 696 |
< |
for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
| 862 |
> |
double ux, uy, uz, u, uSqr; |
| 863 |
> |
|
| 864 |
> |
atomOffset = 0; |
| 865 |
> |
excludeOffset = 0; |
| 866 |
> |
for(i=0; i<simnfo->n_mol; i++){ |
| 867 |
|
|
| 868 |
< |
delete[] globalIndex; |
| 868 |
> |
stampID = the_molecules[i].getStampID(); |
| 869 |
|
|
| 870 |
< |
mpiSim->mpiRefresh(); |
| 871 |
< |
#endif //IS_MPI |
| 872 |
< |
|
| 873 |
< |
the_ff->initializeAtoms(); |
| 874 |
< |
} |
| 705 |
< |
|
| 706 |
< |
void SimSetup::makeBonds( void ){ |
| 870 |
> |
info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
| 871 |
> |
info.nBonds = comp_stamps[stampID]->getNBonds(); |
| 872 |
> |
info.nBends = comp_stamps[stampID]->getNBends(); |
| 873 |
> |
info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
| 874 |
> |
info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
| 875 |
|
|
| 876 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 877 |
< |
bond_pair* the_bonds; |
| 878 |
< |
BondStamp* current_bond; |
| 876 |
> |
info.myAtoms = &the_atoms[atomOffset]; |
| 877 |
> |
info.myExcludes = &the_excludes[excludeOffset]; |
| 878 |
> |
info.myBonds = new Bond*[info.nBonds]; |
| 879 |
> |
info.myBends = new Bend*[info.nBends]; |
| 880 |
> |
info.myTorsions = new Torsion*[info.nTorsions]; |
| 881 |
|
|
| 882 |
< |
the_bonds = new bond_pair[tot_bonds]; |
| 883 |
< |
index = 0; |
| 884 |
< |
offset = 0; |
| 885 |
< |
molIndex = 0; |
| 886 |
< |
|
| 887 |
< |
for( i=0; i<n_components; i++ ){ |
| 888 |
< |
|
| 889 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 890 |
< |
|
| 891 |
< |
#ifdef IS_MPI |
| 722 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 723 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 724 |
< |
#endif // is_mpi |
| 882 |
> |
theBonds = new bond_pair[info.nBonds]; |
| 883 |
> |
theBends = new bend_set[info.nBends]; |
| 884 |
> |
theTorsions = new torsion_set[info.nTorsions]; |
| 885 |
> |
|
| 886 |
> |
// make the Atoms |
| 887 |
> |
|
| 888 |
> |
for(j=0; j<info.nAtoms; j++){ |
| 889 |
> |
|
| 890 |
> |
currentAtom = comp_stamps[stampID]->getAtom( j ); |
| 891 |
> |
if( currentAtom->haveOrientation() ){ |
| 892 |
|
|
| 893 |
< |
for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
| 894 |
< |
|
| 895 |
< |
current_bond = comp_stamps[i]->getBond( k ); |
| 729 |
< |
the_bonds[index].a = current_bond->getA() + offset; |
| 730 |
< |
the_bonds[index].b = current_bond->getB() + offset; |
| 731 |
< |
|
| 732 |
< |
exI = the_bonds[index].a; |
| 733 |
< |
exJ = the_bonds[index].b; |
| 734 |
< |
|
| 735 |
< |
// exclude_I must always be the smaller of the pair |
| 736 |
< |
if( exI > exJ ){ |
| 737 |
< |
tempEx = exI; |
| 738 |
< |
exI = exJ; |
| 739 |
< |
exJ = tempEx; |
| 740 |
< |
} |
| 741 |
< |
|
| 742 |
< |
|
| 743 |
< |
#ifdef IS_MPI |
| 744 |
< |
|
| 745 |
< |
the_excludes[index*2] = |
| 746 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 747 |
< |
the_excludes[index*2 + 1] = |
| 748 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 749 |
< |
|
| 750 |
< |
#else // isn't MPI |
| 751 |
< |
|
| 752 |
< |
the_excludes[index*2] = exI + 1; |
| 753 |
< |
the_excludes[index*2 + 1] = exJ + 1; |
| 754 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
| 755 |
< |
#endif //is_mpi |
| 756 |
< |
|
| 757 |
< |
// increment the index and repeat; |
| 758 |
< |
index++; |
| 759 |
< |
} |
| 760 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 893 |
> |
dAtom = new DirectionalAtom(j + atomOffset); |
| 894 |
> |
simnfo->n_oriented++; |
| 895 |
> |
info.myAtoms[j] = dAtom; |
| 896 |
|
|
| 897 |
< |
#ifdef IS_MPI |
| 897 |
> |
ux = currentAtom->getOrntX(); |
| 898 |
> |
uy = currentAtom->getOrntY(); |
| 899 |
> |
uz = currentAtom->getOrntZ(); |
| 900 |
> |
|
| 901 |
> |
uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
| 902 |
> |
|
| 903 |
> |
u = sqrt( uSqr ); |
| 904 |
> |
ux = ux / u; |
| 905 |
> |
uy = uy / u; |
| 906 |
> |
uz = uz / u; |
| 907 |
> |
|
| 908 |
> |
dAtom->setSUx( ux ); |
| 909 |
> |
dAtom->setSUy( uy ); |
| 910 |
> |
dAtom->setSUz( uz ); |
| 911 |
|
} |
| 912 |
< |
#endif //is_mpi |
| 912 |
> |
else{ |
| 913 |
> |
info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
| 914 |
> |
} |
| 915 |
> |
info.myAtoms[j]->setType( currentAtom->getType() ); |
| 916 |
> |
|
| 917 |
> |
#ifdef IS_MPI |
| 918 |
|
|
| 919 |
< |
molIndex++; |
| 920 |
< |
} |
| 921 |
< |
} |
| 919 |
> |
info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
| 920 |
> |
|
| 921 |
> |
#endif // is_mpi |
| 922 |
> |
} |
| 923 |
> |
|
| 924 |
> |
// make the bonds |
| 925 |
> |
for(j=0; j<info.nBonds; j++){ |
| 926 |
> |
|
| 927 |
> |
currentBond = comp_stamps[stampID]->getBond( j ); |
| 928 |
> |
theBonds[j].a = currentBond->getA() + atomOffset; |
| 929 |
> |
theBonds[j].b = currentBond->getB() + atomOffset; |
| 930 |
|
|
| 931 |
< |
the_ff->initializeBonds( the_bonds ); |
| 932 |
< |
} |
| 931 |
> |
exI = theBonds[j].a; |
| 932 |
> |
exJ = theBonds[j].b; |
| 933 |
|
|
| 934 |
< |
void SimSetup::makeBends( void ){ |
| 935 |
< |
|
| 936 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 937 |
< |
bend_set* the_bends; |
| 938 |
< |
BendStamp* current_bend; |
| 939 |
< |
LinkedAssign* extras; |
| 779 |
< |
LinkedAssign* current_extra; |
| 780 |
< |
|
| 781 |
< |
|
| 782 |
< |
the_bends = new bend_set[tot_bends]; |
| 783 |
< |
index = 0; |
| 784 |
< |
offset = 0; |
| 785 |
< |
molIndex = 0; |
| 786 |
< |
for( i=0; i<n_components; i++ ){ |
| 787 |
< |
|
| 788 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 789 |
< |
|
| 934 |
> |
// exclude_I must always be the smaller of the pair |
| 935 |
> |
if( exI > exJ ){ |
| 936 |
> |
tempEx = exI; |
| 937 |
> |
exI = exJ; |
| 938 |
> |
exJ = tempEx; |
| 939 |
> |
} |
| 940 |
|
#ifdef IS_MPI |
| 941 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 942 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 943 |
< |
#endif // is_mpi |
| 941 |
> |
tempEx = exI; |
| 942 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 943 |
> |
tempEx = exJ; |
| 944 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 945 |
> |
|
| 946 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 947 |
> |
#else // isn't MPI |
| 948 |
|
|
| 949 |
< |
for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
| 949 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 950 |
> |
#endif //is_mpi |
| 951 |
> |
} |
| 952 |
> |
excludeOffset += info.nBonds; |
| 953 |
> |
|
| 954 |
> |
//make the bends |
| 955 |
> |
for(j=0; j<info.nBends; j++){ |
| 956 |
> |
|
| 957 |
> |
currentBend = comp_stamps[stampID]->getBend( j ); |
| 958 |
> |
theBends[j].a = currentBend->getA() + atomOffset; |
| 959 |
> |
theBends[j].b = currentBend->getB() + atomOffset; |
| 960 |
> |
theBends[j].c = currentBend->getC() + atomOffset; |
| 961 |
|
|
| 962 |
< |
current_bend = comp_stamps[i]->getBend( k ); |
| 798 |
< |
the_bends[index].a = current_bend->getA() + offset; |
| 799 |
< |
the_bends[index].b = current_bend->getB() + offset; |
| 800 |
< |
the_bends[index].c = current_bend->getC() + offset; |
| 801 |
< |
|
| 802 |
< |
if( current_bend->haveExtras() ){ |
| 962 |
> |
if( currentBend->haveExtras() ){ |
| 963 |
|
|
| 964 |
< |
extras = current_bend->getExtras(); |
| 965 |
< |
current_extra = extras; |
| 964 |
> |
extras = currentBend->getExtras(); |
| 965 |
> |
current_extra = extras; |
| 966 |
|
|
| 967 |
< |
while( current_extra != NULL ){ |
| 968 |
< |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 967 |
> |
while( current_extra != NULL ){ |
| 968 |
> |
if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
| 969 |
|
|
| 970 |
< |
switch( current_extra->getType() ){ |
| 811 |
< |
|
| 812 |
< |
case 0: |
| 813 |
< |
the_bends[index].ghost = |
| 814 |
< |
current_extra->getInt() + offset; |
| 815 |
< |
the_bends[index].isGhost = 1; |
| 816 |
< |
break; |
| 817 |
< |
|
| 818 |
< |
case 1: |
| 819 |
< |
the_bends[index].ghost = |
| 820 |
< |
(int)current_extra->getDouble() + offset; |
| 821 |
< |
the_bends[index].isGhost = 1; |
| 822 |
< |
break; |
| 823 |
< |
|
| 824 |
< |
default: |
| 825 |
< |
sprintf( painCave.errMsg, |
| 826 |
< |
"SimSetup Error: ghostVectorSource was neiter a " |
| 827 |
< |
"double nor an int.\n" |
| 828 |
< |
"-->Bend[%d] in %s\n", |
| 829 |
< |
k, comp_stamps[i]->getID() ); |
| 830 |
< |
painCave.isFatal = 1; |
| 831 |
< |
simError(); |
| 832 |
< |
} |
| 833 |
< |
} |
| 970 |
> |
switch( current_extra->getType() ){ |
| 971 |
|
|
| 972 |
< |
else{ |
| 973 |
< |
|
| 974 |
< |
sprintf( painCave.errMsg, |
| 975 |
< |
"SimSetup Error: unhandled bend assignment:\n" |
| 976 |
< |
" -->%s in Bend[%d] in %s\n", |
| 977 |
< |
current_extra->getlhs(), |
| 978 |
< |
k, comp_stamps[i]->getID() ); |
| 979 |
< |
painCave.isFatal = 1; |
| 980 |
< |
simError(); |
| 981 |
< |
} |
| 972 |
> |
case 0: |
| 973 |
> |
theBends[j].ghost = |
| 974 |
> |
current_extra->getInt() + atomOffset; |
| 975 |
> |
theBends[j].isGhost = 1; |
| 976 |
> |
break; |
| 977 |
> |
|
| 978 |
> |
case 1: |
| 979 |
> |
theBends[j].ghost = |
| 980 |
> |
(int)current_extra->getDouble() + atomOffset; |
| 981 |
> |
theBends[j].isGhost = 1; |
| 982 |
> |
break; |
| 983 |
|
|
| 984 |
< |
current_extra = current_extra->getNext(); |
| 984 |
> |
default: |
| 985 |
> |
sprintf( painCave.errMsg, |
| 986 |
> |
"SimSetup Error: ghostVectorSource was neither a " |
| 987 |
> |
"double nor an int.\n" |
| 988 |
> |
"-->Bend[%d] in %s\n", |
| 989 |
> |
j, comp_stamps[stampID]->getID() ); |
| 990 |
> |
painCave.isFatal = 1; |
| 991 |
> |
simError(); |
| 992 |
|
} |
| 993 |
|
} |
| 994 |
|
|
| 850 |
– |
if( !the_bends[index].isGhost ){ |
| 851 |
– |
|
| 852 |
– |
exI = the_bends[index].a; |
| 853 |
– |
exJ = the_bends[index].c; |
| 854 |
– |
} |
| 995 |
|
else{ |
| 996 |
|
|
| 997 |
< |
exI = the_bends[index].a; |
| 998 |
< |
exJ = the_bends[index].b; |
| 997 |
> |
sprintf( painCave.errMsg, |
| 998 |
> |
"SimSetup Error: unhandled bend assignment:\n" |
| 999 |
> |
" -->%s in Bend[%d] in %s\n", |
| 1000 |
> |
current_extra->getlhs(), |
| 1001 |
> |
j, comp_stamps[stampID]->getID() ); |
| 1002 |
> |
painCave.isFatal = 1; |
| 1003 |
> |
simError(); |
| 1004 |
|
} |
| 1005 |
|
|
| 1006 |
< |
// exclude_I must always be the smaller of the pair |
| 862 |
< |
if( exI > exJ ){ |
| 863 |
< |
tempEx = exI; |
| 864 |
< |
exI = exJ; |
| 865 |
< |
exJ = tempEx; |
| 866 |
< |
} |
| 867 |
< |
|
| 868 |
< |
|
| 869 |
< |
#ifdef IS_MPI |
| 870 |
< |
|
| 871 |
< |
the_excludes[(index + tot_bonds)*2] = |
| 872 |
< |
the_atoms[exI]->getGlobalIndex() + 1; |
| 873 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = |
| 874 |
< |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 875 |
< |
|
| 876 |
< |
#else // isn't MPI |
| 877 |
< |
|
| 878 |
< |
the_excludes[(index + tot_bonds)*2] = exI + 1; |
| 879 |
< |
the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
| 880 |
< |
// fortran index from 1 (hence the +1 in the indexing) |
| 881 |
< |
#endif //is_mpi |
| 882 |
< |
|
| 883 |
< |
|
| 884 |
< |
// increment the index and repeat; |
| 885 |
< |
index++; |
| 1006 |
> |
current_extra = current_extra->getNext(); |
| 1007 |
|
} |
| 1008 |
< |
offset += comp_stamps[i]->getNAtoms(); |
| 1008 |
> |
} |
| 1009 |
> |
|
| 1010 |
> |
if( !theBends[j].isGhost ){ |
| 1011 |
> |
|
| 1012 |
> |
exI = theBends[j].a; |
| 1013 |
> |
exJ = theBends[j].c; |
| 1014 |
> |
} |
| 1015 |
> |
else{ |
| 1016 |
|
|
| 1017 |
< |
#ifdef IS_MPI |
| 1017 |
> |
exI = theBends[j].a; |
| 1018 |
> |
exJ = theBends[j].b; |
| 1019 |
|
} |
| 1020 |
< |
#endif //is_mpi |
| 1020 |
> |
|
| 1021 |
> |
// exclude_I must always be the smaller of the pair |
| 1022 |
> |
if( exI > exJ ){ |
| 1023 |
> |
tempEx = exI; |
| 1024 |
> |
exI = exJ; |
| 1025 |
> |
exJ = tempEx; |
| 1026 |
> |
} |
| 1027 |
> |
#ifdef IS_MPI |
| 1028 |
> |
tempEx = exI; |
| 1029 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1030 |
> |
tempEx = exJ; |
| 1031 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1032 |
> |
|
| 1033 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 1034 |
> |
#else // isn't MPI |
| 1035 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 1036 |
> |
#endif //is_mpi |
| 1037 |
> |
} |
| 1038 |
> |
excludeOffset += info.nBends; |
| 1039 |
|
|
| 1040 |
< |
molIndex++; |
| 1040 |
> |
for(j=0; j<info.nTorsions; j++){ |
| 1041 |
> |
|
| 1042 |
> |
currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
| 1043 |
> |
theTorsions[j].a = currentTorsion->getA() + atomOffset; |
| 1044 |
> |
theTorsions[j].b = currentTorsion->getB() + atomOffset; |
| 1045 |
> |
theTorsions[j].c = currentTorsion->getC() + atomOffset; |
| 1046 |
> |
theTorsions[j].d = currentTorsion->getD() + atomOffset; |
| 1047 |
> |
|
| 1048 |
> |
exI = theTorsions[j].a; |
| 1049 |
> |
exJ = theTorsions[j].d; |
| 1050 |
> |
|
| 1051 |
> |
// exclude_I must always be the smaller of the pair |
| 1052 |
> |
if( exI > exJ ){ |
| 1053 |
> |
tempEx = exI; |
| 1054 |
> |
exI = exJ; |
| 1055 |
> |
exJ = tempEx; |
| 1056 |
> |
} |
| 1057 |
> |
#ifdef IS_MPI |
| 1058 |
> |
tempEx = exI; |
| 1059 |
> |
exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1060 |
> |
tempEx = exJ; |
| 1061 |
> |
exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
| 1062 |
> |
|
| 1063 |
> |
the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
| 1064 |
> |
#else // isn't MPI |
| 1065 |
> |
the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
| 1066 |
> |
#endif //is_mpi |
| 1067 |
|
} |
| 1068 |
< |
} |
| 1068 |
> |
excludeOffset += info.nTorsions; |
| 1069 |
|
|
| 1070 |
< |
#ifdef IS_MPI |
| 1071 |
< |
sprintf( checkPointMsg, |
| 899 |
< |
"Successfully created the bends list.\n" ); |
| 900 |
< |
MPIcheckPoint(); |
| 901 |
< |
#endif // is_mpi |
| 902 |
< |
|
| 1070 |
> |
|
| 1071 |
> |
// send the arrays off to the forceField for init. |
| 1072 |
|
|
| 1073 |
< |
the_ff->initializeBends( the_bends ); |
| 1074 |
< |
} |
| 1073 |
> |
the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
| 1074 |
> |
the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
| 1075 |
> |
the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
| 1076 |
> |
the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
| 1077 |
|
|
| 907 |
– |
void SimSetup::makeTorsions( void ){ |
| 1078 |
|
|
| 1079 |
< |
int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
| 910 |
< |
torsion_set* the_torsions; |
| 911 |
< |
TorsionStamp* current_torsion; |
| 1079 |
> |
the_molecules[i].initialize( info ); |
| 1080 |
|
|
| 913 |
– |
the_torsions = new torsion_set[tot_torsions]; |
| 914 |
– |
index = 0; |
| 915 |
– |
offset = 0; |
| 916 |
– |
molIndex = 0; |
| 917 |
– |
for( i=0; i<n_components; i++ ){ |
| 1081 |
|
|
| 1082 |
< |
for( j=0; j<components_nmol[i]; j++ ){ |
| 1082 |
> |
atomOffset += info.nAtoms; |
| 1083 |
> |
delete[] theBonds; |
| 1084 |
> |
delete[] theBends; |
| 1085 |
> |
delete[] theTorsions; |
| 1086 |
> |
} |
| 1087 |
|
|
| 1088 |
|
#ifdef IS_MPI |
| 1089 |
< |
if( mpiSim->getMyMolStart() <= molIndex && |
| 1090 |
< |
molIndex <= mpiSim->getMyMolEnd() ){ |
| 1091 |
< |
#endif // is_mpi |
| 1089 |
> |
sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
| 1090 |
> |
MPIcheckPoint(); |
| 1091 |
> |
#endif // is_mpi |
| 1092 |
|
|
| 1093 |
< |
for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
| 1093 |
> |
// clean up the forcefield |
| 1094 |
> |
the_ff->calcRcut(); |
| 1095 |
> |
the_ff->cleanMe(); |
| 1096 |
|
|
| 928 |
– |
current_torsion = comp_stamps[i]->getTorsion( k ); |
| 929 |
– |
the_torsions[index].a = current_torsion->getA() + offset; |
| 930 |
– |
the_torsions[index].b = current_torsion->getB() + offset; |
| 931 |
– |
the_torsions[index].c = current_torsion->getC() + offset; |
| 932 |
– |
the_torsions[index].d = current_torsion->getD() + offset; |
| 933 |
– |
|
| 934 |
– |
exI = the_torsions[index].a; |
| 935 |
– |
exJ = the_torsions[index].d; |
| 936 |
– |
|
| 937 |
– |
|
| 938 |
– |
// exclude_I must always be the smaller of the pair |
| 939 |
– |
if( exI > exJ ){ |
| 940 |
– |
tempEx = exI; |
| 941 |
– |
exI = exJ; |
| 942 |
– |
exJ = tempEx; |
| 943 |
– |
} |
| 944 |
– |
|
| 945 |
– |
|
| 946 |
– |
#ifdef IS_MPI |
| 947 |
– |
|
| 948 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = |
| 949 |
– |
the_atoms[exI]->getGlobalIndex() + 1; |
| 950 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
| 951 |
– |
the_atoms[exJ]->getGlobalIndex() + 1; |
| 952 |
– |
|
| 953 |
– |
#else // isn't MPI |
| 954 |
– |
|
| 955 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
| 956 |
– |
the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
| 957 |
– |
// fortran indexes from 1 (hence the +1 in the indexing) |
| 958 |
– |
#endif //is_mpi |
| 959 |
– |
|
| 960 |
– |
|
| 961 |
– |
// increment the index and repeat; |
| 962 |
– |
index++; |
| 963 |
– |
} |
| 964 |
– |
offset += comp_stamps[i]->getNAtoms(); |
| 965 |
– |
|
| 966 |
– |
#ifdef IS_MPI |
| 967 |
– |
} |
| 968 |
– |
#endif //is_mpi |
| 969 |
– |
|
| 970 |
– |
molIndex++; |
| 971 |
– |
} |
| 972 |
– |
} |
| 973 |
– |
|
| 974 |
– |
the_ff->initializeTorsions( the_torsions ); |
| 1097 |
|
} |
| 1098 |
|
|
| 1099 |
|
void SimSetup::initFromBass( void ){ |
