# | 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 | + | |
22 | + | #define FF_DUFF 0 |
23 | + | #define FF_LJ 1 |
24 | + | |
25 | + | |
26 | SimSetup::SimSetup(){ | |
27 | stamps = new MakeStamps(); | |
28 | globals = new Globals(); | |
# | Line 66 | Line 77 | void SimSetup::createSim( void ){ | |
77 | ||
78 | MakeStamps *the_stamps; | |
79 | Globals* the_globals; | |
80 | < | int i, j; |
80 | > | int i, j, k, globalAtomIndex; |
81 | > | |
82 | > | int ensembleCase; |
83 | > | int ffCase; |
84 | > | |
85 | > | ensembleCase = -1; |
86 | > | ffCase = -1; |
87 | ||
88 | // get the stamps and globals; | |
89 | the_stamps = stamps; | |
# | Line 80 | Line 97 | void SimSetup::createSim( void ){ | |
97 | // get the ones we know are there, yet still may need some work. | |
98 | n_components = the_globals->getNComponents(); | |
99 | strcpy( force_field, the_globals->getForceField() ); | |
100 | + | |
101 | + | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
102 | + | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
103 | + | else{ |
104 | + | sprintf( painCave.errMsg, |
105 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
106 | + | force_field ); |
107 | + | painCave.isFatal = 1; |
108 | + | simError(); |
109 | + | } |
110 | + | |
111 | + | // get the ensemble: |
112 | strcpy( ensemble, the_globals->getEnsemble() ); | |
113 | + | |
114 | + | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
115 | + | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
116 | + | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
117 | + | ensembleCase = NPTi_ENS; |
118 | + | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
119 | + | else{ |
120 | + | sprintf( painCave.errMsg, |
121 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
122 | + | "reverting to NVE for this simulation.\n", |
123 | + | ensemble ); |
124 | + | painCave.isFatal = 0; |
125 | + | simError(); |
126 | + | strcpy( ensemble, "NVE" ); |
127 | + | ensembleCase = NVE_ENS; |
128 | + | } |
129 | strcpy( simnfo->ensemble, ensemble ); | |
130 | ||
131 | + | |
132 | + | // if( !strcasecmp( ensemble, "NPT" ) ) { |
133 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
134 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
135 | + | // if (the_globals->haveTargetPressure()) |
136 | + | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
137 | + | // else { |
138 | + | // sprintf( painCave.errMsg, |
139 | + | // "SimSetup error: If you use the constant pressure\n" |
140 | + | // " ensemble, you must set targetPressure.\n" |
141 | + | // " This was found in the BASS file.\n"); |
142 | + | // painCave.isFatal = 1; |
143 | + | // simError(); |
144 | + | // } |
145 | + | |
146 | + | // if (the_globals->haveTauThermostat()) |
147 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
148 | + | // else if (the_globals->haveQmass()) |
149 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
150 | + | // else { |
151 | + | // sprintf( painCave.errMsg, |
152 | + | // "SimSetup error: If you use one of the constant temperature\n" |
153 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
154 | + | // " Neither of these was found in the BASS file.\n"); |
155 | + | // painCave.isFatal = 1; |
156 | + | // simError(); |
157 | + | // } |
158 | + | |
159 | + | // if (the_globals->haveTauBarostat()) |
160 | + | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
161 | + | // else { |
162 | + | // sprintf( painCave.errMsg, |
163 | + | // "SimSetup error: If you use the constant pressure\n" |
164 | + | // " ensemble, you must set tauBarostat.\n" |
165 | + | // " This was found in the BASS file.\n"); |
166 | + | // painCave.isFatal = 1; |
167 | + | // simError(); |
168 | + | // } |
169 | + | |
170 | + | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
171 | + | // the_extendedsystem = new ExtendedSystem( simnfo ); |
172 | + | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
173 | + | |
174 | + | // if (the_globals->haveTauThermostat()) |
175 | + | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
176 | + | // else if (the_globals->haveQmass()) |
177 | + | // the_extendedsystem->setQmass(the_globals->getQmass()); |
178 | + | // else { |
179 | + | // sprintf( painCave.errMsg, |
180 | + | // "SimSetup error: If you use one of the constant temperature\n" |
181 | + | // " ensembles, you must set either tauThermostat or qMass.\n" |
182 | + | // " Neither of these was found in the BASS file.\n"); |
183 | + | // painCave.isFatal = 1; |
184 | + | // simError(); |
185 | + | // } |
186 | + | |
187 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
188 | simnfo->usePBC = the_globals->getPBC(); | |
189 | ||
190 | + | int usesDipoles = 0; |
191 | + | switch( ffCase ){ |
192 | ||
193 | + | case FF_DUFF: |
194 | + | the_ff = new DUFF(); |
195 | + | usesDipoles = 1; |
196 | + | break; |
197 | ||
198 | < | if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF(); |
199 | < | else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF(); |
200 | < | else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
201 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
202 | < | else{ |
198 | > | case FF_LJ: |
199 | > | the_ff = new LJFF(); |
200 | > | break; |
201 | > | |
202 | > | default: |
203 | sprintf( painCave.errMsg, | |
204 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
98 | < | force_field ); |
204 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
205 | painCave.isFatal = 1; | |
206 | simError(); | |
207 | } | |
# | Line 105 | Line 211 | void SimSetup::createSim( void ){ | |
211 | MPIcheckPoint(); | |
212 | #endif // is_mpi | |
213 | ||
108 | – | |
109 | – | |
214 | // get the components and calculate the tot_nMol and indvidual n_mol | |
215 | the_components = the_globals->getComponents(); | |
216 | components_nmol = new int[n_components]; | |
# | Line 230 | Line 334 | void SimSetup::createSim( void ){ | |
334 | simnfo->n_torsions = tot_torsions; | |
335 | simnfo->n_SRI = tot_SRI; | |
336 | simnfo->n_mol = tot_nmol; | |
233 | – | |
337 | ||
338 | + | simnfo->molMembershipArray = new int[tot_atoms]; |
339 | + | |
340 | #ifdef IS_MPI | |
341 | ||
342 | // divide the molecules among processors here. | |
343 | ||
344 | mpiSim = new mpiSimulation( simnfo ); | |
345 | ||
241 | – | |
242 | – | |
346 | globalIndex = mpiSim->divideLabor(); | |
347 | ||
245 | – | |
246 | – | |
348 | // set up the local variables | |
349 | ||
350 | int localMol, allMol; | |
351 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
352 | + | |
353 | + | int* mol2proc = mpiSim->getMolToProcMap(); |
354 | + | int* molCompType = mpiSim->getMolComponentType(); |
355 | ||
356 | allMol = 0; | |
357 | localMol = 0; | |
# | Line 255 | Line 359 | void SimSetup::createSim( void ){ | |
359 | local_bonds = 0; | |
360 | local_bends = 0; | |
361 | local_torsions = 0; | |
362 | + | globalAtomIndex = 0; |
363 | + | |
364 | + | |
365 | for( i=0; i<n_components; i++ ){ | |
366 | ||
367 | for( j=0; j<components_nmol[i]; j++ ){ | |
368 | ||
369 | < | if( mpiSim->getMyMolStart() <= allMol && |
263 | < | allMol <= mpiSim->getMyMolEnd() ){ |
369 | > | if( mol2proc[allMol] == worldRank ){ |
370 | ||
371 | local_atoms += comp_stamps[i]->getNAtoms(); | |
372 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 268 | Line 374 | void SimSetup::createSim( void ){ | |
374 | local_torsions += comp_stamps[i]->getNTorsions(); | |
375 | localMol++; | |
376 | } | |
377 | < | allMol++; |
377 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
378 | > | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
379 | > | globalAtomIndex++; |
380 | > | } |
381 | > | |
382 | > | allMol++; |
383 | } | |
384 | } | |
385 | local_SRI = local_bonds + local_bends + local_torsions; | |
386 | ||
276 | – | |
387 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
388 | ||
389 | if( local_atoms != simnfo->n_atoms ){ | |
390 | sprintf( painCave.errMsg, | |
391 | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" | |
392 | < | " localAtom (%d) are note equal.\n", |
392 | > | " localAtom (%d) are not equal.\n", |
393 | simnfo->n_atoms, | |
394 | local_atoms ); | |
395 | painCave.isFatal = 1; | |
# | Line 304 | Line 414 | void SimSetup::createSim( void ){ | |
414 | Atom::createArrays(simnfo->n_atoms); | |
415 | the_atoms = new Atom*[simnfo->n_atoms]; | |
416 | the_molecules = new Molecule[simnfo->n_mol]; | |
417 | + | int molIndex; |
418 | + | |
419 | + | // initialize the molecule's stampID's |
420 | + | |
421 | + | #ifdef IS_MPI |
422 | + | |
423 | + | |
424 | + | molIndex = 0; |
425 | + | for(i=0; i<mpiSim->getTotNmol(); i++){ |
426 | + | |
427 | + | if(mol2proc[i] == worldRank ){ |
428 | + | the_molecules[molIndex].setStampID( molCompType[i] ); |
429 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
430 | + | the_molecules[molIndex].setGlobalIndex( i ); |
431 | + | molIndex++; |
432 | + | } |
433 | + | } |
434 | + | |
435 | + | #else // is_mpi |
436 | + | |
437 | + | molIndex = 0; |
438 | + | globalAtomIndex = 0; |
439 | + | for(i=0; i<n_components; i++){ |
440 | + | for(j=0; j<components_nmol[i]; j++ ){ |
441 | + | the_molecules[molIndex].setStampID( i ); |
442 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
443 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
444 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
445 | + | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
446 | + | globalAtomIndex++; |
447 | + | } |
448 | + | molIndex++; |
449 | + | } |
450 | + | } |
451 | + | |
452 | ||
453 | + | #endif // is_mpi |
454 | ||
455 | + | |
456 | if( simnfo->n_SRI ){ | |
457 | + | |
458 | Exclude::createArray(simnfo->n_SRI); | |
459 | the_excludes = new Exclude*[simnfo->n_SRI]; | |
460 | + | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
461 | simnfo->globalExcludes = new int; | |
462 | < | simnfo->n_exclude = tot_SRI; |
462 | > | simnfo->n_exclude = simnfo->n_SRI; |
463 | } | |
464 | else{ | |
465 | ||
# | Line 326 | Line 475 | void SimSetup::createSim( void ){ | |
475 | // set the arrays into the SimInfo object | |
476 | ||
477 | simnfo->atoms = the_atoms; | |
478 | < | simnfo->sr_interactions = the_sris; |
478 | > | simnfo->molecules = the_molecules; |
479 | simnfo->nGlobalExcludes = 0; | |
480 | simnfo->excludes = the_excludes; | |
481 | ||
482 | ||
483 | // get some of the tricky things that may still be in the globals | |
484 | ||
485 | < | |
485 | > | double boxVector[3]; |
486 | if( the_globals->haveBox() ){ | |
487 | < | simnfo->box_x = the_globals->getBox(); |
488 | < | simnfo->box_y = the_globals->getBox(); |
489 | < | simnfo->box_z = the_globals->getBox(); |
487 | > | boxVector[0] = the_globals->getBox(); |
488 | > | boxVector[1] = the_globals->getBox(); |
489 | > | boxVector[2] = the_globals->getBox(); |
490 | > | |
491 | > | simnfo->setBox( boxVector ); |
492 | } | |
493 | else if( the_globals->haveDensity() ){ | |
494 | ||
495 | double vol; | |
496 | vol = (double)tot_nmol / the_globals->getDensity(); | |
497 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
498 | < | simnfo->box_y = simnfo->box_x; |
499 | < | simnfo->box_z = simnfo->box_x; |
497 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
498 | > | boxVector[1] = boxVector[0]; |
499 | > | boxVector[2] = boxVector[0]; |
500 | > | |
501 | > | simnfo->setBox( boxVector ); |
502 | } | |
503 | else{ | |
504 | if( !the_globals->haveBoxX() ){ | |
# | Line 354 | Line 507 | void SimSetup::createSim( void ){ | |
507 | painCave.isFatal = 1; | |
508 | simError(); | |
509 | } | |
510 | < | simnfo->box_x = the_globals->getBoxX(); |
510 | > | boxVector[0] = the_globals->getBoxX(); |
511 | ||
512 | if( !the_globals->haveBoxY() ){ | |
513 | sprintf( painCave.errMsg, | |
# | Line 362 | Line 515 | void SimSetup::createSim( void ){ | |
515 | painCave.isFatal = 1; | |
516 | simError(); | |
517 | } | |
518 | < | simnfo->box_y = the_globals->getBoxY(); |
518 | > | boxVector[1] = the_globals->getBoxY(); |
519 | ||
520 | if( !the_globals->haveBoxZ() ){ | |
521 | sprintf( painCave.errMsg, | |
# | Line 370 | Line 523 | void SimSetup::createSim( void ){ | |
523 | painCave.isFatal = 1; | |
524 | simError(); | |
525 | } | |
526 | < | simnfo->box_z = the_globals->getBoxZ(); |
526 | > | boxVector[2] = the_globals->getBoxZ(); |
527 | > | |
528 | > | simnfo->setBox( boxVector ); |
529 | } | |
530 | ||
531 | #ifdef IS_MPI | |
# | Line 383 | Line 538 | void SimSetup::createSim( void ){ | |
538 | ||
539 | the_ff->setSimInfo( simnfo ); | |
540 | ||
541 | < | makeAtoms(); |
541 | > | makeMolecules(); |
542 | simnfo->identArray = new int[simnfo->n_atoms]; | |
543 | for(i=0; i<simnfo->n_atoms; i++){ | |
544 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
545 | } | |
546 | ||
392 | – | if( tot_bonds ){ |
393 | – | makeBonds(); |
394 | – | } |
395 | – | |
396 | – | if( tot_bends ){ |
397 | – | makeBends(); |
398 | – | } |
399 | – | |
400 | – | if( tot_torsions ){ |
401 | – | makeTorsions(); |
402 | – | } |
403 | – | |
404 | – | |
547 | if (the_globals->getUseRF() ) { | |
548 | simnfo->useReactionField = 1; | |
549 | ||
# | Line 413 | Line 555 | void SimSetup::createSim( void ){ | |
555 | painCave.isFatal = 0; | |
556 | simError(); | |
557 | double smallest; | |
558 | < | smallest = simnfo->box_x; |
559 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
560 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
558 | > | smallest = simnfo->boxLx; |
559 | > | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
560 | > | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
561 | simnfo->ecr = 0.5 * smallest; | |
562 | } else { | |
563 | simnfo->ecr = the_globals->getECR(); | |
# | Line 443 | Line 585 | void SimSetup::createSim( void ){ | |
585 | } | |
586 | simnfo->dielectric = the_globals->getDielectric(); | |
587 | } else { | |
588 | < | if (simnfo->n_dipoles) { |
588 | > | if (usesDipoles) { |
589 | ||
590 | if( !the_globals->haveECR() ){ | |
591 | sprintf( painCave.errMsg, | |
592 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
592 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
593 | "box length for the electrostaticCutoffRadius.\n" | |
594 | "I hope you have a very fast processor!\n"); | |
595 | painCave.isFatal = 0; | |
596 | simError(); | |
597 | double smallest; | |
598 | < | smallest = simnfo->box_x; |
599 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
600 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
598 | > | smallest = simnfo->boxLx; |
599 | > | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
600 | > | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
601 | simnfo->ecr = 0.5 * smallest; | |
602 | } else { | |
603 | simnfo->ecr = the_globals->getECR(); | |
# | Line 463 | Line 605 | void SimSetup::createSim( void ){ | |
605 | ||
606 | if( !the_globals->haveEST() ){ | |
607 | sprintf( painCave.errMsg, | |
608 | < | "SimSetup Warning: using default value of 5% of the" |
608 | > | "SimSetup Warning: using default value of 5%% of the " |
609 | "electrostaticCutoffRadius for the " | |
610 | "electrostaticSkinThickness\n" | |
611 | ); | |
# | Line 634 | Line 776 | void SimSetup::createSim( void ){ | |
776 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
777 | ||
778 | ||
779 | < | // // make the longe range forces and the integrator |
779 | > | // make the integrator |
780 | > | |
781 | > | |
782 | > | NVT* myNVT = NULL; |
783 | > | switch( ensembleCase ){ |
784 | ||
785 | < | // new AllLong( simnfo ); |
786 | < | |
787 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 | < | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
643 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
644 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
785 | > | case NVE_ENS: |
786 | > | new NVE( simnfo, the_ff ); |
787 | > | break; |
788 | ||
789 | + | case NVT_ENS: |
790 | + | myNVT = new NVT( simnfo, the_ff ); |
791 | + | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
792 | ||
793 | + | if (the_globals->haveTauThermostat()) |
794 | + | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
795 | + | // else if (the_globals->haveQmass()) |
796 | + | // myNVT->setQmass(the_globals->getQmass()); |
797 | + | else { |
798 | + | sprintf( painCave.errMsg, |
799 | + | "SimSetup error: If you use the NVT\n" |
800 | + | " ensemble, you must set either tauThermostat or qMass.\n" |
801 | + | " Neither of these was found in the BASS file.\n"); |
802 | + | painCave.isFatal = 1; |
803 | + | simError(); |
804 | + | } |
805 | + | break; |
806 | ||
807 | + | default: |
808 | + | sprintf( painCave.errMsg, |
809 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
810 | + | painCave.isFatal = 1; |
811 | + | simError(); |
812 | + | } |
813 | + | |
814 | + | |
815 | + | #ifdef IS_MPI |
816 | + | mpiSim->mpiRefresh(); |
817 | + | #endif |
818 | + | |
819 | // initialize the Fortran | |
820 | < | |
820 | > | |
821 | > | |
822 | simnfo->refreshSim(); | |
823 | ||
824 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 683 | Line 855 | void SimSetup::makeMolecules( void ){ | |
855 | BondStamp* currentBond; | |
856 | BendStamp* currentBend; | |
857 | TorsionStamp* currentTorsion; | |
858 | + | |
859 | + | bond_pair* theBonds; |
860 | + | bend_set* theBends; |
861 | + | torsion_set* theTorsions; |
862 | + | |
863 | ||
864 | //init the forceField paramters | |
865 | ||
866 | the_ff->readParams(); | |
867 | ||
868 | ||
869 | < | // init the molecules |
869 | > | // init the atoms |
870 | ||
871 | + | double ux, uy, uz, u, uSqr; |
872 | + | |
873 | atomOffset = 0; | |
874 | excludeOffset = 0; | |
875 | for(i=0; i<simnfo->n_mol; i++){ | |
# | Line 707 | Line 886 | void SimSetup::makeMolecules( void ){ | |
886 | info.myExcludes = &the_excludes[excludeOffset]; | |
887 | info.myBonds = new Bond*[info.nBonds]; | |
888 | info.myBends = new Bend*[info.nBends]; | |
889 | < | info.myTorsions = new Torsions*[info.nTorsions]; |
889 | > | info.myTorsions = new Torsion*[info.nTorsions]; |
890 | ||
891 | theBonds = new bond_pair[info.nBonds]; | |
892 | theBends = new bend_set[info.nBends]; | |
# | Line 717 | Line 896 | void SimSetup::makeMolecules( void ){ | |
896 | ||
897 | for(j=0; j<info.nAtoms; j++){ | |
898 | ||
899 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
899 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
900 | if( currentAtom->haveOrientation() ){ | |
901 | ||
902 | dAtom = new DirectionalAtom(j + atomOffset); | |
# | Line 758 | Line 937 | void SimSetup::makeMolecules( void ){ | |
937 | theBonds[j].a = currentBond->getA() + atomOffset; | |
938 | theBonds[j].b = currentBond->getB() + atomOffset; | |
939 | ||
940 | < | exI = theBonds[i].a; |
941 | < | exJ = theBonds[i].b; |
940 | > | exI = theBonds[j].a; |
941 | > | exJ = theBonds[j].b; |
942 | ||
943 | // exclude_I must always be the smaller of the pair | |
944 | if( exI > exJ ){ | |
# | Line 775 | Line 954 | void SimSetup::makeMolecules( void ){ | |
954 | ||
955 | the_excludes[j+excludeOffset]->setPair( exI, exJ ); | |
956 | #else // isn't MPI | |
957 | + | |
958 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
959 | #endif //is_mpi | |
960 | } | |
# | Line 790 | Line 970 | void SimSetup::makeMolecules( void ){ | |
970 | ||
971 | if( currentBend->haveExtras() ){ | |
972 | ||
973 | < | extras = current_bend->getExtras(); |
973 | > | extras = currentBend->getExtras(); |
974 | current_extra = extras; | |
975 | ||
976 | while( current_extra != NULL ){ | |
# | Line 812 | Line 992 | void SimSetup::makeMolecules( void ){ | |
992 | ||
993 | default: | |
994 | sprintf( painCave.errMsg, | |
995 | < | "SimSetup Error: ghostVectorSource was neiter a " |
995 | > | "SimSetup Error: ghostVectorSource was neither a " |
996 | "double nor an int.\n" | |
997 | "-->Bend[%d] in %s\n", | |
998 | j, comp_stamps[stampID]->getID() ); | |
# | Line 897 | Line 1077 | void SimSetup::makeMolecules( void ){ | |
1077 | excludeOffset += info.nTorsions; | |
1078 | ||
1079 | ||
1080 | + | // send the arrays off to the forceField for init. |
1081 | ||
1082 | + | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1083 | + | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1084 | + | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1085 | + | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1086 | ||
1087 | ||
1088 | < | |
904 | < | |
905 | < | |
906 | < | void SimSetup::makeAtoms( void ){ |
907 | < | |
908 | < | int i, j, k, index; |
909 | < | double ux, uy, uz, uSqr, u; |
910 | < | AtomStamp* current_atom; |
911 | < | |
912 | < | DirectionalAtom* dAtom; |
913 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
914 | < | |
915 | < | lMolIndex = 0; |
916 | < | molIndex = 0; |
917 | < | index = 0; |
918 | < | for( i=0; i<n_components; i++ ){ |
919 | < | |
920 | < | for( j=0; j<components_nmol[i]; j++ ){ |
921 | < | |
922 | < | #ifdef IS_MPI |
923 | < | if( mpiSim->getMyMolStart() <= molIndex && |
924 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
925 | < | #endif // is_mpi |
1088 | > | the_molecules[i].initialize( info ); |
1089 | ||
927 | – | molStart = index; |
928 | – | nMemb = comp_stamps[i]->getNAtoms(); |
929 | – | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
930 | – | |
931 | – | current_atom = comp_stamps[i]->getAtom( k ); |
932 | – | if( current_atom->haveOrientation() ){ |
933 | – | |
934 | – | dAtom = new DirectionalAtom(index); |
935 | – | simnfo->n_oriented++; |
936 | – | the_atoms[index] = dAtom; |
937 | – | |
938 | – | ux = current_atom->getOrntX(); |
939 | – | uy = current_atom->getOrntY(); |
940 | – | uz = current_atom->getOrntZ(); |
941 | – | |
942 | – | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
943 | – | |
944 | – | u = sqrt( uSqr ); |
945 | – | ux = ux / u; |
946 | – | uy = uy / u; |
947 | – | uz = uz / u; |
948 | – | |
949 | – | dAtom->setSUx( ux ); |
950 | – | dAtom->setSUy( uy ); |
951 | – | dAtom->setSUz( uz ); |
952 | – | } |
953 | – | else{ |
954 | – | the_atoms[index] = new GeneralAtom(index); |
955 | – | } |
956 | – | the_atoms[index]->setType( current_atom->getType() ); |
957 | – | the_atoms[index]->setIndex( index ); |
958 | – | |
959 | – | // increment the index and repeat; |
960 | – | index++; |
961 | – | } |
962 | – | |
963 | – | molEnd = index -1; |
964 | – | the_molecules[lMolIndex].setNMembers( nMemb ); |
965 | – | the_molecules[lMolIndex].setStartAtom( molStart ); |
966 | – | the_molecules[lMolIndex].setEndAtom( molEnd ); |
967 | – | the_molecules[lMolIndex].setStampID( i ); |
968 | – | lMolIndex++; |
1090 | ||
1091 | < | #ifdef IS_MPI |
1092 | < | } |
1093 | < | #endif //is_mpi |
1094 | < | |
974 | < | molIndex++; |
975 | < | } |
976 | < | } |
977 | < | |
978 | < | #ifdef IS_MPI |
979 | < | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
980 | < | |
981 | < | delete[] globalIndex; |
982 | < | |
983 | < | mpiSim->mpiRefresh(); |
984 | < | #endif //IS_MPI |
985 | < | |
986 | < | the_ff->initializeAtoms(); |
987 | < | } |
988 | < | |
989 | < | void SimSetup::makeBonds( void ){ |
990 | < | |
991 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
992 | < | bond_pair* the_bonds; |
993 | < | BondStamp* current_bond; |
994 | < | |
995 | < | the_bonds = new bond_pair[tot_bonds]; |
996 | < | index = 0; |
997 | < | offset = 0; |
998 | < | molIndex = 0; |
999 | < | |
1000 | < | for( i=0; i<n_components; i++ ){ |
1001 | < | |
1002 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1003 | < | |
1004 | < | #ifdef IS_MPI |
1005 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1006 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1007 | < | #endif // is_mpi |
1008 | < | |
1009 | < | for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){ |
1010 | < | |
1011 | < | current_bond = comp_stamps[i]->getBond( k ); |
1012 | < | the_bonds[index].a = current_bond->getA() + offset; |
1013 | < | the_bonds[index].b = current_bond->getB() + offset; |
1014 | < | |
1015 | < | exI = the_bonds[index].a; |
1016 | < | exJ = the_bonds[index].b; |
1017 | < | |
1018 | < | // exclude_I must always be the smaller of the pair |
1019 | < | if( exI > exJ ){ |
1020 | < | tempEx = exI; |
1021 | < | exI = exJ; |
1022 | < | exJ = tempEx; |
1023 | < | } |
1024 | < | |
1025 | < | |
1026 | < | #ifdef IS_MPI |
1027 | < | |
1028 | < | the_excludes[index*2] = |
1029 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1030 | < | the_excludes[index*2 + 1] = |
1031 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1032 | < | |
1033 | < | #else // isn't MPI |
1034 | < | |
1035 | < | the_excludes[index*2] = exI + 1; |
1036 | < | the_excludes[index*2 + 1] = exJ + 1; |
1037 | < | // fortran index from 1 (hence the +1 in the indexing) |
1038 | < | #endif //is_mpi |
1039 | < | |
1040 | < | // increment the index and repeat; |
1041 | < | index++; |
1042 | < | } |
1043 | < | offset += comp_stamps[i]->getNAtoms(); |
1044 | < | |
1045 | < | #ifdef IS_MPI |
1046 | < | } |
1047 | < | #endif //is_mpi |
1048 | < | |
1049 | < | molIndex++; |
1050 | < | } |
1051 | < | } |
1052 | < | |
1053 | < | the_ff->initializeBonds( the_bonds ); |
1054 | < | } |
1055 | < | |
1056 | < | void SimSetup::makeBends( void ){ |
1057 | < | |
1058 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1059 | < | bend_set* the_bends; |
1060 | < | BendStamp* current_bend; |
1061 | < | LinkedAssign* extras; |
1062 | < | LinkedAssign* current_extra; |
1063 | < | |
1064 | < | |
1065 | < | the_bends = new bend_set[tot_bends]; |
1066 | < | index = 0; |
1067 | < | offset = 0; |
1068 | < | molIndex = 0; |
1069 | < | for( i=0; i<n_components; i++ ){ |
1070 | < | |
1071 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1072 | < | |
1073 | < | #ifdef IS_MPI |
1074 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1075 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1076 | < | #endif // is_mpi |
1077 | < | |
1078 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
1079 | < | |
1080 | < | current_bend = comp_stamps[i]->getBend( k ); |
1081 | < | the_bends[index].a = current_bend->getA() + offset; |
1082 | < | the_bends[index].b = current_bend->getB() + offset; |
1083 | < | the_bends[index].c = current_bend->getC() + offset; |
1084 | < | |
1085 | < | if( current_bend->haveExtras() ){ |
1086 | < | |
1087 | < | extras = current_bend->getExtras(); |
1088 | < | current_extra = extras; |
1089 | < | |
1090 | < | while( current_extra != NULL ){ |
1091 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
1092 | < | |
1093 | < | switch( current_extra->getType() ){ |
1094 | < | |
1095 | < | case 0: |
1096 | < | the_bends[index].ghost = |
1097 | < | current_extra->getInt() + offset; |
1098 | < | the_bends[index].isGhost = 1; |
1099 | < | break; |
1100 | < | |
1101 | < | case 1: |
1102 | < | the_bends[index].ghost = |
1103 | < | (int)current_extra->getDouble() + offset; |
1104 | < | the_bends[index].isGhost = 1; |
1105 | < | break; |
1106 | < | |
1107 | < | default: |
1108 | < | sprintf( painCave.errMsg, |
1109 | < | "SimSetup Error: ghostVectorSource was neiter a " |
1110 | < | "double nor an int.\n" |
1111 | < | "-->Bend[%d] in %s\n", |
1112 | < | k, comp_stamps[i]->getID() ); |
1113 | < | painCave.isFatal = 1; |
1114 | < | simError(); |
1115 | < | } |
1116 | < | } |
1117 | < | |
1118 | < | else{ |
1119 | < | |
1120 | < | sprintf( painCave.errMsg, |
1121 | < | "SimSetup Error: unhandled bend assignment:\n" |
1122 | < | " -->%s in Bend[%d] in %s\n", |
1123 | < | current_extra->getlhs(), |
1124 | < | k, comp_stamps[i]->getID() ); |
1125 | < | painCave.isFatal = 1; |
1126 | < | simError(); |
1127 | < | } |
1128 | < | |
1129 | < | current_extra = current_extra->getNext(); |
1130 | < | } |
1131 | < | } |
1132 | < | |
1133 | < | if( !the_bends[index].isGhost ){ |
1134 | < | |
1135 | < | exI = the_bends[index].a; |
1136 | < | exJ = the_bends[index].c; |
1137 | < | } |
1138 | < | else{ |
1139 | < | |
1140 | < | exI = the_bends[index].a; |
1141 | < | exJ = the_bends[index].b; |
1142 | < | } |
1143 | < | |
1144 | < | // exclude_I must always be the smaller of the pair |
1145 | < | if( exI > exJ ){ |
1146 | < | tempEx = exI; |
1147 | < | exI = exJ; |
1148 | < | exJ = tempEx; |
1149 | < | } |
1150 | < | |
1151 | < | |
1152 | < | #ifdef IS_MPI |
1153 | < | |
1154 | < | the_excludes[(index + tot_bonds)*2] = |
1155 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1156 | < | the_excludes[(index + tot_bonds)*2 + 1] = |
1157 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1158 | < | |
1159 | < | #else // isn't MPI |
1160 | < | |
1161 | < | the_excludes[(index + tot_bonds)*2] = exI + 1; |
1162 | < | the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1; |
1163 | < | // fortran index from 1 (hence the +1 in the indexing) |
1164 | < | #endif //is_mpi |
1165 | < | |
1166 | < | |
1167 | < | // increment the index and repeat; |
1168 | < | index++; |
1169 | < | } |
1170 | < | offset += comp_stamps[i]->getNAtoms(); |
1171 | < | |
1172 | < | #ifdef IS_MPI |
1173 | < | } |
1174 | < | #endif //is_mpi |
1175 | < | |
1176 | < | molIndex++; |
1177 | < | } |
1091 | > | atomOffset += info.nAtoms; |
1092 | > | delete[] theBonds; |
1093 | > | delete[] theBends; |
1094 | > | delete[] theTorsions; |
1095 | } | |
1096 | ||
1097 | #ifdef IS_MPI | |
1098 | < | sprintf( checkPointMsg, |
1182 | < | "Successfully created the bends list.\n" ); |
1098 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1099 | MPIcheckPoint(); | |
1100 | #endif // is_mpi | |
1185 | – | |
1101 | ||
1102 | < | the_ff->initializeBends( the_bends ); |
1103 | < | } |
1102 | > | // clean up the forcefield |
1103 | > | the_ff->calcRcut(); |
1104 | > | the_ff->cleanMe(); |
1105 | ||
1190 | – | void SimSetup::makeTorsions( void ){ |
1191 | – | |
1192 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1193 | – | torsion_set* the_torsions; |
1194 | – | TorsionStamp* current_torsion; |
1195 | – | |
1196 | – | the_torsions = new torsion_set[tot_torsions]; |
1197 | – | index = 0; |
1198 | – | offset = 0; |
1199 | – | molIndex = 0; |
1200 | – | for( i=0; i<n_components; i++ ){ |
1201 | – | |
1202 | – | for( j=0; j<components_nmol[i]; j++ ){ |
1203 | – | |
1204 | – | #ifdef IS_MPI |
1205 | – | if( mpiSim->getMyMolStart() <= molIndex && |
1206 | – | molIndex <= mpiSim->getMyMolEnd() ){ |
1207 | – | #endif // is_mpi |
1208 | – | |
1209 | – | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1210 | – | |
1211 | – | current_torsion = comp_stamps[i]->getTorsion( k ); |
1212 | – | the_torsions[index].a = current_torsion->getA() + offset; |
1213 | – | the_torsions[index].b = current_torsion->getB() + offset; |
1214 | – | the_torsions[index].c = current_torsion->getC() + offset; |
1215 | – | the_torsions[index].d = current_torsion->getD() + offset; |
1216 | – | |
1217 | – | exI = the_torsions[index].a; |
1218 | – | exJ = the_torsions[index].d; |
1219 | – | |
1220 | – | |
1221 | – | // exclude_I must always be the smaller of the pair |
1222 | – | if( exI > exJ ){ |
1223 | – | tempEx = exI; |
1224 | – | exI = exJ; |
1225 | – | exJ = tempEx; |
1226 | – | } |
1227 | – | |
1228 | – | |
1229 | – | #ifdef IS_MPI |
1230 | – | |
1231 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = |
1232 | – | the_atoms[exI]->getGlobalIndex() + 1; |
1233 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1234 | – | the_atoms[exJ]->getGlobalIndex() + 1; |
1235 | – | |
1236 | – | #else // isn't MPI |
1237 | – | |
1238 | – | the_excludes[(index + tot_bonds + tot_bends)*2] = exI + 1; |
1239 | – | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1; |
1240 | – | // fortran indexes from 1 (hence the +1 in the indexing) |
1241 | – | #endif //is_mpi |
1242 | – | |
1243 | – | |
1244 | – | // increment the index and repeat; |
1245 | – | index++; |
1246 | – | } |
1247 | – | offset += comp_stamps[i]->getNAtoms(); |
1248 | – | |
1249 | – | #ifdef IS_MPI |
1250 | – | } |
1251 | – | #endif //is_mpi |
1252 | – | |
1253 | – | molIndex++; |
1254 | – | } |
1255 | – | } |
1256 | – | |
1257 | – | the_ff->initializeTorsions( the_torsions ); |
1106 | } | |
1107 | ||
1108 | void SimSetup::initFromBass( void ){ | |
# | Line 1276 | Line 1124 | void SimSetup::initFromBass( void ){ | |
1124 | have_extra =1; | |
1125 | ||
1126 | n_cells = (int)temp3 - 1; | |
1127 | < | cellx = simnfo->box_x / temp3; |
1128 | < | celly = simnfo->box_y / temp3; |
1129 | < | cellz = simnfo->box_z / temp3; |
1127 | > | cellx = simnfo->boxLx / temp3; |
1128 | > | celly = simnfo->boxLy / temp3; |
1129 | > | cellz = simnfo->boxLz / temp3; |
1130 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
1131 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
1132 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 1293 | Line 1141 | void SimSetup::initFromBass( void ){ | |
1141 | } | |
1142 | else{ | |
1143 | n_cells = (int)temp3; | |
1144 | < | cellx = simnfo->box_x / temp3; |
1145 | < | celly = simnfo->box_y / temp3; |
1146 | < | cellz = simnfo->box_z / temp3; |
1144 | > | cellx = simnfo->boxLx / temp3; |
1145 | > | celly = simnfo->boxLy / temp3; |
1146 | > | cellz = simnfo->boxLz / temp3; |
1147 | } | |
1148 | ||
1149 | current_mol = 0; |
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