# | Line 12 | Line 12 | |
---|---|---|
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 NPTi_ENS 2 |
20 | + | #define NPTf_ENS 3 |
21 | + | #define NPTim_ENS 4 |
22 | + | #define NPTfm_ENS 5 |
23 | + | |
24 | + | |
25 | + | #define FF_DUFF 0 |
26 | + | #define FF_LJ 1 |
27 | + | |
28 | + | |
29 | SimSetup::SimSetup(){ | |
30 | stamps = new MakeStamps(); | |
31 | globals = new Globals(); | |
# | Line 66 | Line 80 | void SimSetup::createSim( void ){ | |
80 | ||
81 | MakeStamps *the_stamps; | |
82 | Globals* the_globals; | |
83 | < | int i, j; |
83 | > | int i, j, k, globalAtomIndex; |
84 | > | |
85 | > | int ensembleCase; |
86 | > | int ffCase; |
87 | > | |
88 | > | ensembleCase = -1; |
89 | > | ffCase = -1; |
90 | ||
91 | // get the stamps and globals; | |
92 | the_stamps = stamps; | |
# | Line 80 | Line 100 | void SimSetup::createSim( void ){ | |
100 | // get the ones we know are there, yet still may need some work. | |
101 | n_components = the_globals->getNComponents(); | |
102 | strcpy( force_field, the_globals->getForceField() ); | |
103 | + | |
104 | + | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
105 | + | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
106 | + | else{ |
107 | + | sprintf( painCave.errMsg, |
108 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
109 | + | force_field ); |
110 | + | painCave.isFatal = 1; |
111 | + | simError(); |
112 | + | } |
113 | + | |
114 | + | // get the ensemble: |
115 | strcpy( ensemble, the_globals->getEnsemble() ); | |
116 | + | |
117 | + | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
118 | + | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
119 | + | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
120 | + | ensembleCase = NPTi_ENS; |
121 | + | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
122 | + | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
123 | + | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
124 | + | else{ |
125 | + | sprintf( painCave.errMsg, |
126 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
127 | + | "reverting to NVE for this simulation.\n", |
128 | + | ensemble ); |
129 | + | painCave.isFatal = 0; |
130 | + | simError(); |
131 | + | strcpy( ensemble, "NVE" ); |
132 | + | ensembleCase = NVE_ENS; |
133 | + | } |
134 | strcpy( simnfo->ensemble, ensemble ); | |
135 | ||
136 | + | |
137 | + | // if( !strcasecmp( ensemble, "NPT" ) ) { |
138 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
139 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
140 | + | // if (the_globals->haveTargetPressure()) |
141 | + | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
142 | + | // else { |
143 | + | // sprintf( painCave.errMsg, |
144 | + | // "SimSetup error: If you use the constant pressure\n" |
145 | + | // " ensemble, you must set targetPressure.\n" |
146 | + | // " This was found in the BASS file.\n"); |
147 | + | // painCave.isFatal = 1; |
148 | + | // simError(); |
149 | + | // } |
150 | + | |
151 | + | // if (the_globals->haveTauThermostat()) |
152 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
153 | + | // else if (the_globals->haveQmass()) |
154 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
155 | + | // else { |
156 | + | // sprintf( painCave.errMsg, |
157 | + | // "SimSetup error: If you use one of the constant temperature\n" |
158 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
159 | + | // " Neither of these was found in the BASS file.\n"); |
160 | + | // painCave.isFatal = 1; |
161 | + | // simError(); |
162 | + | // } |
163 | + | |
164 | + | // if (the_globals->haveTauBarostat()) |
165 | + | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
166 | + | // else { |
167 | + | // sprintf( painCave.errMsg, |
168 | + | // "SimSetup error: If you use the constant pressure\n" |
169 | + | // " ensemble, you must set tauBarostat.\n" |
170 | + | // " This was found in the BASS file.\n"); |
171 | + | // painCave.isFatal = 1; |
172 | + | // simError(); |
173 | + | // } |
174 | + | |
175 | + | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
176 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
177 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
178 | + | |
179 | + | // if (the_globals->haveTauThermostat()) |
180 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
181 | + | // else if (the_globals->haveQmass()) |
182 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
183 | + | // else { |
184 | + | // sprintf( painCave.errMsg, |
185 | + | // "SimSetup error: If you use one of the constant temperature\n" |
186 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
187 | + | // " Neither of these was found in the BASS file.\n"); |
188 | + | // painCave.isFatal = 1; |
189 | + | // simError(); |
190 | + | // } |
191 | + | |
192 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
193 | simnfo->usePBC = the_globals->getPBC(); | |
194 | ||
195 | + | int usesDipoles = 0; |
196 | + | switch( ffCase ){ |
197 | ||
198 | + | case FF_DUFF: |
199 | + | the_ff = new DUFF(); |
200 | + | usesDipoles = 1; |
201 | + | break; |
202 | ||
203 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
204 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
205 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
206 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
207 | < | else{ |
203 | > | case FF_LJ: |
204 | > | the_ff = new LJFF(); |
205 | > | break; |
206 | > | |
207 | > | default: |
208 | sprintf( painCave.errMsg, | |
209 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
98 | < | force_field ); |
209 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
210 | painCave.isFatal = 1; | |
211 | simError(); | |
212 | } | |
# | Line 105 | Line 216 | void SimSetup::createSim( void ){ | |
216 | MPIcheckPoint(); | |
217 | #endif // is_mpi | |
218 | ||
108 | – | |
109 | – | |
219 | // get the components and calculate the tot_nMol and indvidual n_mol | |
220 | the_components = the_globals->getComponents(); | |
221 | components_nmol = new int[n_components]; | |
# | Line 230 | Line 339 | void SimSetup::createSim( void ){ | |
339 | simnfo->n_torsions = tot_torsions; | |
340 | simnfo->n_SRI = tot_SRI; | |
341 | simnfo->n_mol = tot_nmol; | |
233 | – | |
342 | ||
343 | + | simnfo->molMembershipArray = new int[tot_atoms]; |
344 | + | |
345 | #ifdef IS_MPI | |
346 | ||
347 | // divide the molecules among processors here. | |
348 | ||
349 | mpiSim = new mpiSimulation( simnfo ); | |
350 | ||
241 | – | |
242 | – | |
351 | globalIndex = mpiSim->divideLabor(); | |
352 | ||
245 | – | |
246 | – | |
353 | // set up the local variables | |
354 | ||
355 | int localMol, allMol; | |
356 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
357 | + | |
358 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
359 | + | int* molCompType = mpiSim->getMolComponentType(); |
360 | ||
361 | allMol = 0; | |
362 | localMol = 0; | |
# | Line 255 | Line 364 | void SimSetup::createSim( void ){ | |
364 | local_bonds = 0; | |
365 | local_bends = 0; | |
366 | local_torsions = 0; | |
367 | + | globalAtomIndex = 0; |
368 | + | |
369 | + | |
370 | for( i=0; i<n_components; i++ ){ | |
371 | ||
372 | for( j=0; j<components_nmol[i]; j++ ){ | |
373 | ||
374 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
374 | > | if( mol2proc[allMol] == worldRank ){ |
375 | ||
376 | local_atoms += comp_stamps[i]->getNAtoms(); | |
377 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 268 | Line 379 | void SimSetup::createSim( void ){ | |
379 | local_torsions += comp_stamps[i]->getNTorsions(); | |
380 | localMol++; | |
381 | } | |
382 | < | allMol++; |
382 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
383 | > | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
384 | > | globalAtomIndex++; |
385 | > | } |
386 | > | |
387 | > | allMol++; |
388 | } | |
389 | } | |
390 | local_SRI = local_bonds + local_bends + local_torsions; | |
391 | ||
276 | – | |
392 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
393 | ||
394 | if( local_atoms != simnfo->n_atoms ){ | |
395 | sprintf( painCave.errMsg, | |
396 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
397 | < | " localAtom (%d) are note equal.\n", |
397 | > | " localAtom (%d) are not equal.\n", |
398 | simnfo->n_atoms, | |
399 | local_atoms ); | |
400 | painCave.isFatal = 1; | |
# | Line 304 | Line 419 | void SimSetup::createSim( void ){ | |
419 | Atom::createArrays(simnfo->n_atoms); | |
420 | the_atoms = new Atom*[simnfo->n_atoms]; | |
421 | the_molecules = new Molecule[simnfo->n_mol]; | |
422 | + | int molIndex; |
423 | ||
424 | + | // initialize the molecule's stampID's |
425 | ||
426 | + | #ifdef IS_MPI |
427 | + | |
428 | + | |
429 | + | molIndex = 0; |
430 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
431 | + | |
432 | + | if(mol2proc[i] == worldRank ){ |
433 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
434 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
435 | + | the_molecules[molIndex].setGlobalIndex( i ); |
436 | + | molIndex++; |
437 | + | } |
438 | + | } |
439 | + | |
440 | + | #else // is_mpi |
441 | + | |
442 | + | molIndex = 0; |
443 | + | globalAtomIndex = 0; |
444 | + | for(i=0; i<n_components; i++){ |
445 | + | for(j=0; j<components_nmol[i]; j++ ){ |
446 | + | the_molecules[molIndex].setStampID( i ); |
447 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
448 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
449 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
450 | + | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
451 | + | globalAtomIndex++; |
452 | + | } |
453 | + | molIndex++; |
454 | + | } |
455 | + | } |
456 | + | |
457 | + | |
458 | + | #endif // is_mpi |
459 | + | |
460 | + | |
461 | if( simnfo->n_SRI ){ | |
462 | < | the_sris = new SRI*[simnfo->n_SRI]; |
463 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
462 | > | |
463 | > | Exclude::createArray(simnfo->n_SRI); |
464 | > | the_excludes = new Exclude*[simnfo->n_SRI]; |
465 | > | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
466 | simnfo->globalExcludes = new int; | |
467 | < | simnfo->n_exclude = tot_SRI; |
467 | > | simnfo->n_exclude = simnfo->n_SRI; |
468 | } | |
469 | else{ | |
470 | ||
471 | < | the_excludes = new int[2]; |
472 | < | the_excludes[0] = 0; |
473 | < | the_excludes[1] = 0; |
471 | > | Exclude::createArray( 1 ); |
472 | > | the_excludes = new Exclude*; |
473 | > | the_excludes[0] = new Exclude(0); |
474 | > | the_excludes[0]->setPair( 0,0 ); |
475 | simnfo->globalExcludes = new int; | |
476 | simnfo->globalExcludes[0] = 0; | |
477 | < | |
323 | < | simnfo->n_exclude = 1; |
477 | > | simnfo->n_exclude = 0; |
478 | } | |
479 | ||
480 | // set the arrays into the SimInfo object | |
481 | ||
482 | simnfo->atoms = the_atoms; | |
483 | < | simnfo->sr_interactions = the_sris; |
483 | > | simnfo->molecules = the_molecules; |
484 | simnfo->nGlobalExcludes = 0; | |
485 | simnfo->excludes = the_excludes; | |
486 | ||
487 | ||
488 | // get some of the tricky things that may still be in the globals | |
489 | ||
490 | < | 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 |
360 | < | |
490 | > | double boxVector[3]; |
491 | if( the_globals->haveBox() ){ | |
492 | < | simnfo->box_x = the_globals->getBox(); |
493 | < | simnfo->box_y = the_globals->getBox(); |
494 | < | simnfo->box_z = the_globals->getBox(); |
492 | > | boxVector[0] = the_globals->getBox(); |
493 | > | boxVector[1] = the_globals->getBox(); |
494 | > | boxVector[2] = the_globals->getBox(); |
495 | > | |
496 | > | simnfo->setBox( boxVector ); |
497 | } | |
498 | else if( the_globals->haveDensity() ){ | |
499 | ||
500 | double vol; | |
501 | vol = (double)tot_nmol / the_globals->getDensity(); | |
502 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
503 | < | simnfo->box_y = simnfo->box_x; |
504 | < | simnfo->box_z = simnfo->box_x; |
502 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
503 | > | boxVector[1] = boxVector[0]; |
504 | > | boxVector[2] = boxVector[0]; |
505 | > | |
506 | > | simnfo->setBox( boxVector ); |
507 | } | |
508 | else{ | |
509 | if( !the_globals->haveBoxX() ){ | |
# | Line 378 | Line 512 | void SimSetup::createSim( void ){ | |
512 | painCave.isFatal = 1; | |
513 | simError(); | |
514 | } | |
515 | < | simnfo->box_x = the_globals->getBoxX(); |
515 | > | boxVector[0] = the_globals->getBoxX(); |
516 | ||
517 | if( !the_globals->haveBoxY() ){ | |
518 | sprintf( painCave.errMsg, | |
# | Line 386 | Line 520 | void SimSetup::createSim( void ){ | |
520 | painCave.isFatal = 1; | |
521 | simError(); | |
522 | } | |
523 | < | simnfo->box_y = the_globals->getBoxY(); |
523 | > | boxVector[1] = the_globals->getBoxY(); |
524 | ||
525 | if( !the_globals->haveBoxZ() ){ | |
526 | sprintf( painCave.errMsg, | |
# | Line 394 | Line 528 | void SimSetup::createSim( void ){ | |
528 | painCave.isFatal = 1; | |
529 | simError(); | |
530 | } | |
531 | < | simnfo->box_z = the_globals->getBoxZ(); |
531 | > | boxVector[2] = the_globals->getBoxZ(); |
532 | > | |
533 | > | simnfo->setBox( boxVector ); |
534 | } | |
535 | ||
536 | #ifdef IS_MPI | |
# | Line 407 | Line 543 | void SimSetup::createSim( void ){ | |
543 | ||
544 | the_ff->setSimInfo( simnfo ); | |
545 | ||
546 | < | makeAtoms(); |
546 | > | makeMolecules(); |
547 | simnfo->identArray = new int[simnfo->n_atoms]; | |
548 | for(i=0; i<simnfo->n_atoms; i++){ | |
549 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
550 | } | |
551 | ||
552 | < | if( tot_bonds ){ |
553 | < | makeBonds(); |
554 | < | } |
555 | < | |
556 | < | if( tot_bends ){ |
557 | < | makeBends(); |
558 | < | } |
559 | < | |
560 | < | if( tot_torsions ){ |
561 | < | makeTorsions(); |
562 | < | } |
563 | < | |
564 | < | |
565 | < | |
552 | > | if (the_globals->getUseRF() ) { |
553 | > | simnfo->useReactionField = 1; |
554 | > | |
555 | > | if( !the_globals->haveECR() ){ |
556 | > | sprintf( painCave.errMsg, |
557 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
558 | > | "box length for the electrostaticCutoffRadius.\n" |
559 | > | "I hope you have a very fast processor!\n"); |
560 | > | painCave.isFatal = 0; |
561 | > | simError(); |
562 | > | double smallest; |
563 | > | smallest = simnfo->boxLx; |
564 | > | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
565 | > | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
566 | > | simnfo->ecr = 0.5 * smallest; |
567 | > | } else { |
568 | > | simnfo->ecr = the_globals->getECR(); |
569 | > | } |
570 | ||
571 | + | if( !the_globals->haveEST() ){ |
572 | + | sprintf( painCave.errMsg, |
573 | + | "SimSetup Warning: using default value of 0.05 * the " |
574 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
575 | + | ); |
576 | + | painCave.isFatal = 0; |
577 | + | simError(); |
578 | + | simnfo->est = 0.05 * simnfo->ecr; |
579 | + | } else { |
580 | + | simnfo->est = the_globals->getEST(); |
581 | + | } |
582 | + | |
583 | + | if(!the_globals->haveDielectric() ){ |
584 | + | sprintf( painCave.errMsg, |
585 | + | "SimSetup Error: You are trying to use Reaction Field without" |
586 | + | "setting a dielectric constant!\n" |
587 | + | ); |
588 | + | painCave.isFatal = 1; |
589 | + | simError(); |
590 | + | } |
591 | + | simnfo->dielectric = the_globals->getDielectric(); |
592 | + | } else { |
593 | + | if (usesDipoles) { |
594 | + | |
595 | + | if( !the_globals->haveECR() ){ |
596 | + | sprintf( painCave.errMsg, |
597 | + | "SimSetup Warning: using default value of 1/2 the smallest " |
598 | + | "box length for the electrostaticCutoffRadius.\n" |
599 | + | "I hope you have a very fast processor!\n"); |
600 | + | painCave.isFatal = 0; |
601 | + | simError(); |
602 | + | double smallest; |
603 | + | smallest = simnfo->boxLx; |
604 | + | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
605 | + | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
606 | + | simnfo->ecr = 0.5 * smallest; |
607 | + | } else { |
608 | + | simnfo->ecr = the_globals->getECR(); |
609 | + | } |
610 | + | |
611 | + | if( !the_globals->haveEST() ){ |
612 | + | sprintf( painCave.errMsg, |
613 | + | "SimSetup Warning: using default value of 5%% of the " |
614 | + | "electrostaticCutoffRadius for the " |
615 | + | "electrostaticSkinThickness\n" |
616 | + | ); |
617 | + | painCave.isFatal = 0; |
618 | + | simError(); |
619 | + | simnfo->est = 0.05 * simnfo->ecr; |
620 | + | } else { |
621 | + | simnfo->est = the_globals->getEST(); |
622 | + | } |
623 | + | } |
624 | + | } |
625 | ||
626 | + | #ifdef IS_MPI |
627 | + | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
628 | + | MPIcheckPoint(); |
629 | + | #endif // is_mpi |
630 | ||
631 | if( the_globals->haveInitialConfig() ){ | |
632 | ||
# | Line 583 | Line 781 | void SimSetup::createSim( void ){ | |
781 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
782 | ||
783 | ||
784 | < | // // make the longe range forces and the integrator |
784 | > | // make the integrator |
785 | > | |
786 | > | |
787 | > | NVT* myNVT = NULL; |
788 | > | NPTi* myNPTi = NULL; |
789 | > | NPTf* myNPTf = NULL; |
790 | > | NPTim* myNPTim = NULL; |
791 | > | NPTfm* myNPTfm = NULL; |
792 | ||
793 | < | // new AllLong( simnfo ); |
793 | > | switch( ensembleCase ){ |
794 | ||
795 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
796 | < | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
797 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
798 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
795 | > | case NVE_ENS: |
796 | > | new NVE( simnfo, the_ff ); |
797 | > | break; |
798 | > | |
799 | > | case NVT_ENS: |
800 | > | myNVT = new NVT( simnfo, the_ff ); |
801 | > | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
802 | > | |
803 | > | if (the_globals->haveTauThermostat()) |
804 | > | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
805 | > | |
806 | > | else { |
807 | > | sprintf( painCave.errMsg, |
808 | > | "SimSetup error: If you use the NVT\n" |
809 | > | " ensemble, you must set tauThermostat.\n"); |
810 | > | painCave.isFatal = 1; |
811 | > | simError(); |
812 | > | } |
813 | > | break; |
814 | > | |
815 | > | case NPTi_ENS: |
816 | > | myNPTi = new NPTi( simnfo, the_ff ); |
817 | > | myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
818 | > | |
819 | > | if (the_globals->haveTargetPressure()) |
820 | > | myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
821 | > | else { |
822 | > | sprintf( painCave.errMsg, |
823 | > | "SimSetup error: If you use a constant pressure\n" |
824 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
825 | > | painCave.isFatal = 1; |
826 | > | simError(); |
827 | > | } |
828 | > | |
829 | > | if( the_globals->haveTauThermostat() ) |
830 | > | myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
831 | > | else{ |
832 | > | sprintf( painCave.errMsg, |
833 | > | "SimSetup error: If you use an NPT\n" |
834 | > | " ensemble, you must set tauThermostat.\n"); |
835 | > | painCave.isFatal = 1; |
836 | > | simError(); |
837 | > | } |
838 | > | |
839 | > | if( the_globals->haveTauBarostat() ) |
840 | > | myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
841 | > | else{ |
842 | > | sprintf( painCave.errMsg, |
843 | > | "SimSetup error: If you use an NPT\n" |
844 | > | " ensemble, you must set tauBarostat.\n"); |
845 | > | painCave.isFatal = 1; |
846 | > | simError(); |
847 | > | } |
848 | > | break; |
849 | > | |
850 | > | case NPTf_ENS: |
851 | > | myNPTf = new NPTf( simnfo, the_ff ); |
852 | > | myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
853 | ||
854 | + | if (the_globals->haveTargetPressure()) |
855 | + | myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
856 | + | else { |
857 | + | sprintf( painCave.errMsg, |
858 | + | "SimSetup error: If you use a constant pressure\n" |
859 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
860 | + | painCave.isFatal = 1; |
861 | + | simError(); |
862 | + | } |
863 | ||
864 | + | if( the_globals->haveTauThermostat() ) |
865 | + | myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
866 | + | else{ |
867 | + | sprintf( painCave.errMsg, |
868 | + | "SimSetup error: If you use an NPT\n" |
869 | + | " ensemble, you must set tauThermostat.\n"); |
870 | + | painCave.isFatal = 1; |
871 | + | simError(); |
872 | + | } |
873 | ||
874 | + | if( the_globals->haveTauBarostat() ) |
875 | + | myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
876 | + | else{ |
877 | + | sprintf( painCave.errMsg, |
878 | + | "SimSetup error: If you use an NPT\n" |
879 | + | " ensemble, you must set tauBarostat.\n"); |
880 | + | painCave.isFatal = 1; |
881 | + | simError(); |
882 | + | } |
883 | + | break; |
884 | + | |
885 | + | case NPTim_ENS: |
886 | + | myNPTim = new NPTim( simnfo, the_ff ); |
887 | + | myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
888 | + | |
889 | + | if (the_globals->haveTargetPressure()) |
890 | + | myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
891 | + | else { |
892 | + | sprintf( painCave.errMsg, |
893 | + | "SimSetup error: If you use a constant pressure\n" |
894 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
895 | + | painCave.isFatal = 1; |
896 | + | simError(); |
897 | + | } |
898 | + | |
899 | + | if( the_globals->haveTauThermostat() ) |
900 | + | myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
901 | + | else{ |
902 | + | sprintf( painCave.errMsg, |
903 | + | "SimSetup error: If you use an NPT\n" |
904 | + | " ensemble, you must set tauThermostat.\n"); |
905 | + | painCave.isFatal = 1; |
906 | + | simError(); |
907 | + | } |
908 | + | |
909 | + | if( the_globals->haveTauBarostat() ) |
910 | + | myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
911 | + | else{ |
912 | + | sprintf( painCave.errMsg, |
913 | + | "SimSetup error: If you use an NPT\n" |
914 | + | " ensemble, you must set tauBarostat.\n"); |
915 | + | painCave.isFatal = 1; |
916 | + | simError(); |
917 | + | } |
918 | + | break; |
919 | + | |
920 | + | case NPTfm_ENS: |
921 | + | myNPTfm = new NPTfm( simnfo, the_ff ); |
922 | + | myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
923 | + | |
924 | + | if (the_globals->haveTargetPressure()) |
925 | + | myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
926 | + | else { |
927 | + | sprintf( painCave.errMsg, |
928 | + | "SimSetup error: If you use a constant pressure\n" |
929 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
930 | + | painCave.isFatal = 1; |
931 | + | simError(); |
932 | + | } |
933 | + | |
934 | + | if( the_globals->haveTauThermostat() ) |
935 | + | myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
936 | + | else{ |
937 | + | sprintf( painCave.errMsg, |
938 | + | "SimSetup error: If you use an NPT\n" |
939 | + | " ensemble, you must set tauThermostat.\n"); |
940 | + | painCave.isFatal = 1; |
941 | + | simError(); |
942 | + | } |
943 | + | |
944 | + | if( the_globals->haveTauBarostat() ) |
945 | + | myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
946 | + | else{ |
947 | + | sprintf( painCave.errMsg, |
948 | + | "SimSetup error: If you use an NPT\n" |
949 | + | " ensemble, you must set tauBarostat.\n"); |
950 | + | painCave.isFatal = 1; |
951 | + | simError(); |
952 | + | } |
953 | + | break; |
954 | + | |
955 | + | default: |
956 | + | sprintf( painCave.errMsg, |
957 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
958 | + | painCave.isFatal = 1; |
959 | + | simError(); |
960 | + | } |
961 | + | |
962 | + | |
963 | + | #ifdef IS_MPI |
964 | + | mpiSim->mpiRefresh(); |
965 | + | #endif |
966 | + | |
967 | // initialize the Fortran | |
968 | < | |
968 | > | |
969 | > | |
970 | simnfo->refreshSim(); | |
971 | ||
972 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 620 | Line 991 | void SimSetup::createSim( void ){ | |
991 | #endif // is_mpi | |
992 | } | |
993 | ||
623 | – | void SimSetup::makeAtoms( void ){ |
994 | ||
995 | < | int i, j, k, index; |
626 | < | double ux, uy, uz, uSqr, u; |
627 | < | AtomStamp* current_atom; |
995 | > | void SimSetup::makeMolecules( void ){ |
996 | ||
997 | + | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
998 | + | molInit info; |
999 | DirectionalAtom* dAtom; | |
1000 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
1000 | > | LinkedAssign* extras; |
1001 | > | LinkedAssign* current_extra; |
1002 | > | AtomStamp* currentAtom; |
1003 | > | BondStamp* currentBond; |
1004 | > | BendStamp* currentBend; |
1005 | > | TorsionStamp* currentTorsion; |
1006 | ||
1007 | < | lMolIndex = 0; |
1008 | < | molIndex = 0; |
1009 | < | index = 0; |
635 | < | for( i=0; i<n_components; i++ ){ |
636 | < | |
637 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1007 | > | bond_pair* theBonds; |
1008 | > | bend_set* theBends; |
1009 | > | torsion_set* theTorsions; |
1010 | ||
1011 | < | #ifdef IS_MPI |
1012 | < | if( mpiSim->getMyMolStart() <= molIndex && |
641 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
642 | < | #endif // is_mpi |
1011 | > | |
1012 | > | //init the forceField paramters |
1013 | ||
1014 | < | molStart = index; |
645 | < | 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++; |
1014 | > | the_ff->readParams(); |
1015 | ||
1016 | < | #ifdef IS_MPI |
1017 | < | } |
689 | < | #endif //is_mpi |
690 | < | |
691 | < | molIndex++; |
692 | < | } |
693 | < | } |
1016 | > | |
1017 | > | // init the atoms |
1018 | ||
1019 | < | #ifdef IS_MPI |
1020 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
1019 | > | double ux, uy, uz, u, uSqr; |
1020 | > | |
1021 | > | atomOffset = 0; |
1022 | > | excludeOffset = 0; |
1023 | > | for(i=0; i<simnfo->n_mol; i++){ |
1024 | ||
1025 | < | delete[] globalIndex; |
1025 | > | stampID = the_molecules[i].getStampID(); |
1026 | ||
1027 | < | mpiSim->mpiRefresh(); |
1028 | < | #endif //IS_MPI |
1029 | < | |
1030 | < | the_ff->initializeAtoms(); |
1031 | < | } |
1027 | > | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
1028 | > | info.nBonds = comp_stamps[stampID]->getNBonds(); |
1029 | > | info.nBends = comp_stamps[stampID]->getNBends(); |
1030 | > | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
1031 | > | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
1032 | ||
1033 | < | void SimSetup::makeBonds( void ){ |
1033 | > | info.myAtoms = &the_atoms[atomOffset]; |
1034 | > | info.myExcludes = &the_excludes[excludeOffset]; |
1035 | > | info.myBonds = new Bond*[info.nBonds]; |
1036 | > | info.myBends = new Bend*[info.nBends]; |
1037 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
1038 | ||
1039 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1040 | < | bond_pair* the_bonds; |
1041 | < | BondStamp* current_bond; |
1042 | < | |
1043 | < | the_bonds = new bond_pair[tot_bonds]; |
1044 | < | index = 0; |
1045 | < | offset = 0; |
1046 | < | molIndex = 0; |
1047 | < | |
1048 | < | for( i=0; i<n_components; i++ ){ |
718 | < | |
719 | < | for( j=0; j<components_nmol[i]; j++ ){ |
720 | < | |
721 | < | #ifdef IS_MPI |
722 | < | if( mpiSim->getMyMolStart() <= molIndex && |
723 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
724 | < | #endif // is_mpi |
1039 | > | theBonds = new bond_pair[info.nBonds]; |
1040 | > | theBends = new bend_set[info.nBends]; |
1041 | > | theTorsions = new torsion_set[info.nTorsions]; |
1042 | > | |
1043 | > | // make the Atoms |
1044 | > | |
1045 | > | for(j=0; j<info.nAtoms; j++){ |
1046 | > | |
1047 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
1048 | > | if( currentAtom->haveOrientation() ){ |
1049 | ||
1050 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
1051 | < | |
1052 | < | 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(); |
1050 | > | dAtom = new DirectionalAtom(j + atomOffset); |
1051 | > | simnfo->n_oriented++; |
1052 | > | info.myAtoms[j] = dAtom; |
1053 | ||
1054 | < | #ifdef IS_MPI |
1054 | > | ux = currentAtom->getOrntX(); |
1055 | > | uy = currentAtom->getOrntY(); |
1056 | > | uz = currentAtom->getOrntZ(); |
1057 | > | |
1058 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
1059 | > | |
1060 | > | u = sqrt( uSqr ); |
1061 | > | ux = ux / u; |
1062 | > | uy = uy / u; |
1063 | > | uz = uz / u; |
1064 | > | |
1065 | > | dAtom->setSUx( ux ); |
1066 | > | dAtom->setSUy( uy ); |
1067 | > | dAtom->setSUz( uz ); |
1068 | } | |
1069 | < | #endif //is_mpi |
1069 | > | else{ |
1070 | > | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
1071 | > | } |
1072 | > | info.myAtoms[j]->setType( currentAtom->getType() ); |
1073 | > | |
1074 | > | #ifdef IS_MPI |
1075 | ||
1076 | < | molIndex++; |
1077 | < | } |
1078 | < | } |
1076 | > | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1077 | > | |
1078 | > | #endif // is_mpi |
1079 | > | } |
1080 | > | |
1081 | > | // make the bonds |
1082 | > | for(j=0; j<info.nBonds; j++){ |
1083 | > | |
1084 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
1085 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
1086 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
1087 | ||
1088 | < | the_ff->initializeBonds( the_bonds ); |
1089 | < | } |
1088 | > | exI = theBonds[j].a; |
1089 | > | exJ = theBonds[j].b; |
1090 | ||
1091 | < | void SimSetup::makeBends( void ){ |
1092 | < | |
1093 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1094 | < | bend_set* the_bends; |
1095 | < | BendStamp* current_bend; |
1096 | < | 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 | < | |
1091 | > | // exclude_I must always be the smaller of the pair |
1092 | > | if( exI > exJ ){ |
1093 | > | tempEx = exI; |
1094 | > | exI = exJ; |
1095 | > | exJ = tempEx; |
1096 | > | } |
1097 | #ifdef IS_MPI | |
1098 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1099 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1100 | < | #endif // is_mpi |
1098 | > | tempEx = exI; |
1099 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1100 | > | tempEx = exJ; |
1101 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1102 | > | |
1103 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1104 | > | #else // isn't MPI |
1105 | ||
1106 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
1106 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1107 | > | #endif //is_mpi |
1108 | > | } |
1109 | > | excludeOffset += info.nBonds; |
1110 | > | |
1111 | > | //make the bends |
1112 | > | for(j=0; j<info.nBends; j++){ |
1113 | > | |
1114 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
1115 | > | theBends[j].a = currentBend->getA() + atomOffset; |
1116 | > | theBends[j].b = currentBend->getB() + atomOffset; |
1117 | > | theBends[j].c = currentBend->getC() + atomOffset; |
1118 | ||
1119 | < | 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() ){ |
1119 | > | if( currentBend->haveExtras() ){ |
1120 | ||
1121 | < | extras = current_bend->getExtras(); |
1122 | < | current_extra = extras; |
1121 | > | extras = currentBend->getExtras(); |
1122 | > | current_extra = extras; |
1123 | ||
1124 | < | while( current_extra != NULL ){ |
1125 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1124 | > | while( current_extra != NULL ){ |
1125 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1126 | ||
1127 | < | switch( current_extra->getType() ){ |
1128 | < | |
1129 | < | case 0: |
1130 | < | the_bends[index].ghost = |
1131 | < | current_extra->getInt() + offset; |
1132 | < | the_bends[index].isGhost = 1; |
1133 | < | break; |
1127 | > | switch( current_extra->getType() ){ |
1128 | > | |
1129 | > | case 0: |
1130 | > | theBends[j].ghost = |
1131 | > | current_extra->getInt() + atomOffset; |
1132 | > | theBends[j].isGhost = 1; |
1133 | > | break; |
1134 | ||
1135 | < | case 1: |
1136 | < | the_bends[index].ghost = |
1137 | < | (int)current_extra->getDouble() + offset; |
1138 | < | the_bends[index].isGhost = 1; |
1139 | < | 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 | < | } |
1135 | > | case 1: |
1136 | > | theBends[j].ghost = |
1137 | > | (int)current_extra->getDouble() + atomOffset; |
1138 | > | theBends[j].isGhost = 1; |
1139 | > | break; |
1140 | ||
1141 | < | else{ |
1142 | < | |
1143 | < | sprintf( painCave.errMsg, |
1144 | < | "SimSetup Error: unhandled bend assignment:\n" |
1145 | < | " -->%s in Bend[%d] in %s\n", |
1146 | < | current_extra->getlhs(), |
1147 | < | k, comp_stamps[i]->getID() ); |
1148 | < | painCave.isFatal = 1; |
843 | < | simError(); |
844 | < | } |
845 | < | |
846 | < | current_extra = current_extra->getNext(); |
1141 | > | default: |
1142 | > | sprintf( painCave.errMsg, |
1143 | > | "SimSetup Error: ghostVectorSource was neither a " |
1144 | > | "double nor an int.\n" |
1145 | > | "-->Bend[%d] in %s\n", |
1146 | > | j, comp_stamps[stampID]->getID() ); |
1147 | > | painCave.isFatal = 1; |
1148 | > | simError(); |
1149 | } | |
1150 | } | |
1151 | ||
850 | – | if( !the_bends[index].isGhost ){ |
851 | – | |
852 | – | exI = the_bends[index].a; |
853 | – | exJ = the_bends[index].c; |
854 | – | } |
1152 | else{ | |
1153 | ||
1154 | < | exI = the_bends[index].a; |
1155 | < | exJ = the_bends[index].b; |
1154 | > | sprintf( painCave.errMsg, |
1155 | > | "SimSetup Error: unhandled bend assignment:\n" |
1156 | > | " -->%s in Bend[%d] in %s\n", |
1157 | > | current_extra->getlhs(), |
1158 | > | j, comp_stamps[stampID]->getID() ); |
1159 | > | painCave.isFatal = 1; |
1160 | > | simError(); |
1161 | } | |
1162 | ||
1163 | < | // 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++; |
1163 | > | current_extra = current_extra->getNext(); |
1164 | } | |
1165 | < | offset += comp_stamps[i]->getNAtoms(); |
1165 | > | } |
1166 | > | |
1167 | > | if( !theBends[j].isGhost ){ |
1168 | > | |
1169 | > | exI = theBends[j].a; |
1170 | > | exJ = theBends[j].c; |
1171 | > | } |
1172 | > | else{ |
1173 | ||
1174 | < | #ifdef IS_MPI |
1174 | > | exI = theBends[j].a; |
1175 | > | exJ = theBends[j].b; |
1176 | } | |
1177 | < | #endif //is_mpi |
1177 | > | |
1178 | > | // exclude_I must always be the smaller of the pair |
1179 | > | if( exI > exJ ){ |
1180 | > | tempEx = exI; |
1181 | > | exI = exJ; |
1182 | > | exJ = tempEx; |
1183 | > | } |
1184 | > | #ifdef IS_MPI |
1185 | > | tempEx = exI; |
1186 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1187 | > | tempEx = exJ; |
1188 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1189 | > | |
1190 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1191 | > | #else // isn't MPI |
1192 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1193 | > | #endif //is_mpi |
1194 | > | } |
1195 | > | excludeOffset += info.nBends; |
1196 | ||
1197 | < | molIndex++; |
1198 | < | } |
1199 | < | } |
1197 | > | for(j=0; j<info.nTorsions; j++){ |
1198 | > | |
1199 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1200 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1201 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1202 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1203 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1204 | > | |
1205 | > | exI = theTorsions[j].a; |
1206 | > | exJ = theTorsions[j].d; |
1207 | ||
1208 | + | // exclude_I must always be the smaller of the pair |
1209 | + | if( exI > exJ ){ |
1210 | + | tempEx = exI; |
1211 | + | exI = exJ; |
1212 | + | exJ = tempEx; |
1213 | + | } |
1214 | #ifdef IS_MPI | |
1215 | < | sprintf( checkPointMsg, |
1216 | < | "Successfully created the bends list.\n" ); |
1217 | < | MPIcheckPoint(); |
1218 | < | #endif // is_mpi |
1219 | < | |
1215 | > | tempEx = exI; |
1216 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1217 | > | tempEx = exJ; |
1218 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1219 | > | |
1220 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1221 | > | #else // isn't MPI |
1222 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1223 | > | #endif //is_mpi |
1224 | > | } |
1225 | > | excludeOffset += info.nTorsions; |
1226 | ||
1227 | < | the_ff->initializeBends( the_bends ); |
1228 | < | } |
1227 | > | |
1228 | > | // send the arrays off to the forceField for init. |
1229 | ||
1230 | < | void SimSetup::makeTorsions( void ){ |
1230 | > | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1231 | > | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1232 | > | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1233 | > | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1234 | ||
909 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
910 | – | torsion_set* the_torsions; |
911 | – | TorsionStamp* current_torsion; |
1235 | ||
1236 | < | the_torsions = new torsion_set[tot_torsions]; |
914 | < | index = 0; |
915 | < | offset = 0; |
916 | < | molIndex = 0; |
917 | < | for( i=0; i<n_components; i++ ){ |
1236 | > | the_molecules[i].initialize( info ); |
1237 | ||
919 | – | for( j=0; j<components_nmol[i]; j++ ){ |
1238 | ||
1239 | < | #ifdef IS_MPI |
1240 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1241 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1242 | < | #endif // is_mpi |
1239 | > | atomOffset += info.nAtoms; |
1240 | > | delete[] theBonds; |
1241 | > | delete[] theBends; |
1242 | > | delete[] theTorsions; |
1243 | > | } |
1244 | ||
926 | – | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
927 | – | |
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 | – | |
1245 | #ifdef IS_MPI | |
1246 | < | |
1247 | < | the_excludes[(index + tot_bonds + tot_bends)*2] = |
1248 | < | 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 | < | |
1246 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1247 | > | MPIcheckPoint(); |
1248 | > | #endif // is_mpi |
1249 | ||
1250 | < | // increment the index and repeat; |
1251 | < | index++; |
1252 | < | } |
964 | < | offset += comp_stamps[i]->getNAtoms(); |
1250 | > | // clean up the forcefield |
1251 | > | the_ff->calcRcut(); |
1252 | > | the_ff->cleanMe(); |
1253 | ||
966 | – | #ifdef IS_MPI |
967 | – | } |
968 | – | #endif //is_mpi |
969 | – | |
970 | – | molIndex++; |
971 | – | } |
972 | – | } |
973 | – | |
974 | – | the_ff->initializeTorsions( the_torsions ); |
1254 | } | |
1255 | ||
1256 | void SimSetup::initFromBass( void ){ | |
# | Line 993 | Line 1272 | void SimSetup::initFromBass( void ){ | |
1272 | have_extra =1; | |
1273 | ||
1274 | n_cells = (int)temp3 - 1; | |
1275 | < | cellx = simnfo->box_x / temp3; |
1276 | < | celly = simnfo->box_y / temp3; |
1277 | < | cellz = simnfo->box_z / temp3; |
1275 | > | cellx = simnfo->boxLx / temp3; |
1276 | > | celly = simnfo->boxLy / temp3; |
1277 | > | cellz = simnfo->boxLz / temp3; |
1278 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
1279 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
1280 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 1010 | Line 1289 | void SimSetup::initFromBass( void ){ | |
1289 | } | |
1290 | else{ | |
1291 | n_cells = (int)temp3; | |
1292 | < | cellx = simnfo->box_x / temp3; |
1293 | < | celly = simnfo->box_y / temp3; |
1294 | < | cellz = simnfo->box_z / temp3; |
1292 | > | cellx = simnfo->boxLx / temp3; |
1293 | > | celly = simnfo->boxLy / temp3; |
1294 | > | cellz = simnfo->boxLz / temp3; |
1295 | } | |
1296 | ||
1297 | current_mol = 0; |
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