# | 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 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(); | |
# | Line 66 | Line 76 | void SimSetup::createSim( void ){ | |
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; | |
# | Line 80 | Line 96 | void SimSetup::createSim( void ){ | |
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_Ex" ) ) the_ff = new TraPPE_ExFF(); |
196 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
197 | < | 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", |
96 | < | force_field ); |
201 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
202 | painCave.isFatal = 1; | |
203 | simError(); | |
204 | } | |
# | Line 103 | Line 208 | void SimSetup::createSim( void ){ | |
208 | MPIcheckPoint(); | |
209 | #endif // is_mpi | |
210 | ||
106 | – | |
107 | – | |
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]; | |
# | Line 228 | Line 331 | void SimSetup::createSim( void ){ | |
331 | simnfo->n_torsions = tot_torsions; | |
332 | simnfo->n_SRI = tot_SRI; | |
333 | simnfo->n_mol = tot_nmol; | |
231 | – | |
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 | ||
239 | – | |
240 | – | |
343 | globalIndex = mpiSim->divideLabor(); | |
344 | ||
243 | – | |
244 | – | |
345 | // set up the local variables | |
346 | ||
347 | int localMol, allMol; | |
# | Line 256 | Line 356 | void SimSetup::createSim( void ){ | |
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( mol2proc[j] == worldRank ){ |
366 | > | if( mol2proc[allMol] == worldRank ){ |
367 | ||
368 | local_atoms += comp_stamps[i]->getNAtoms(); | |
369 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 268 | Line 371 | void SimSetup::createSim( void ){ | |
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 ){ | |
# | Line 316 | Line 423 | void SimSetup::createSim( void ){ | |
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 | } | |
# | Line 323 | Line 432 | void SimSetup::createSim( void ){ | |
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 | } | |
# | Line 335 | Line 451 | void SimSetup::createSim( void ){ | |
451 | ||
452 | ||
453 | if( 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 | ||
# | Line 361 | Line 479 | void SimSetup::createSim( void ){ | |
479 | ||
480 | // get some of the tricky things that may still be in the globals | |
481 | ||
482 | < | |
482 | > | double boxVector[3]; |
483 | if( the_globals->haveBox() ){ | |
484 | < | simnfo->box_x = the_globals->getBox(); |
485 | < | simnfo->box_y = the_globals->getBox(); |
486 | < | simnfo->box_z = the_globals->getBox(); |
484 | > | boxVector[0] = the_globals->getBox(); |
485 | > | boxVector[1] = the_globals->getBox(); |
486 | > | boxVector[2] = the_globals->getBox(); |
487 | > | |
488 | > | simnfo->setBox( boxVector ); |
489 | } | |
490 | else if( the_globals->haveDensity() ){ | |
491 | ||
492 | double vol; | |
493 | vol = (double)tot_nmol / the_globals->getDensity(); | |
494 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
495 | < | simnfo->box_y = simnfo->box_x; |
496 | < | simnfo->box_z = simnfo->box_x; |
494 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
495 | > | boxVector[1] = boxVector[0]; |
496 | > | boxVector[2] = boxVector[0]; |
497 | > | |
498 | > | simnfo->setBox( boxVector ); |
499 | } | |
500 | else{ | |
501 | if( !the_globals->haveBoxX() ){ | |
# | Line 382 | Line 504 | void SimSetup::createSim( void ){ | |
504 | painCave.isFatal = 1; | |
505 | simError(); | |
506 | } | |
507 | < | simnfo->box_x = the_globals->getBoxX(); |
507 | > | boxVector[0] = the_globals->getBoxX(); |
508 | ||
509 | if( !the_globals->haveBoxY() ){ | |
510 | sprintf( painCave.errMsg, | |
# | Line 390 | Line 512 | void SimSetup::createSim( void ){ | |
512 | painCave.isFatal = 1; | |
513 | simError(); | |
514 | } | |
515 | < | simnfo->box_y = the_globals->getBoxY(); |
515 | > | boxVector[1] = the_globals->getBoxY(); |
516 | ||
517 | if( !the_globals->haveBoxZ() ){ | |
518 | sprintf( painCave.errMsg, | |
# | Line 398 | Line 520 | void SimSetup::createSim( void ){ | |
520 | painCave.isFatal = 1; | |
521 | simError(); | |
522 | } | |
523 | < | simnfo->box_z = the_globals->getBoxZ(); |
523 | > | boxVector[2] = the_globals->getBoxZ(); |
524 | > | |
525 | > | simnfo->setBox( boxVector ); |
526 | } | |
527 | ||
528 | #ifdef IS_MPI | |
# | Line 428 | Line 552 | void SimSetup::createSim( void ){ | |
552 | painCave.isFatal = 0; | |
553 | simError(); | |
554 | double smallest; | |
555 | < | smallest = simnfo->box_x; |
556 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
557 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
555 | > | smallest = simnfo->boxLx; |
556 | > | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
557 | > | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
558 | simnfo->ecr = 0.5 * smallest; | |
559 | } else { | |
560 | simnfo->ecr = the_globals->getECR(); | |
# | Line 458 | Line 582 | void SimSetup::createSim( void ){ | |
582 | } | |
583 | simnfo->dielectric = the_globals->getDielectric(); | |
584 | } else { | |
585 | < | if (simnfo->n_dipoles) { |
585 | > | if (usesDipoles) { |
586 | ||
587 | if( !the_globals->haveECR() ){ | |
588 | sprintf( painCave.errMsg, | |
589 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
589 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
590 | "box length for the electrostaticCutoffRadius.\n" | |
591 | "I hope you have a very fast processor!\n"); | |
592 | painCave.isFatal = 0; | |
593 | simError(); | |
594 | double smallest; | |
595 | < | smallest = simnfo->box_x; |
596 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
597 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
595 | > | smallest = simnfo->boxLx; |
596 | > | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
597 | > | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
598 | simnfo->ecr = 0.5 * smallest; | |
599 | } else { | |
600 | simnfo->ecr = the_globals->getECR(); | |
# | Line 478 | Line 602 | void SimSetup::createSim( void ){ | |
602 | ||
603 | if( !the_globals->haveEST() ){ | |
604 | sprintf( painCave.errMsg, | |
605 | < | "SimSetup Warning: using default value of 5% of the" |
605 | > | "SimSetup Warning: using default value of 5%% of the " |
606 | "electrostaticCutoffRadius for the " | |
607 | "electrostaticSkinThickness\n" | |
608 | ); | |
# | Line 649 | Line 773 | void SimSetup::createSim( void ){ | |
773 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
774 | ||
775 | ||
776 | < | // // make the longe range forces and the integrator |
777 | < | |
778 | < | // new AllLong( simnfo ); |
779 | < | |
780 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
657 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
776 | > | // make the integrator |
777 | > | |
778 | > | |
779 | > | NVT* myNVT = NULL; |
780 | > | switch( ensembleCase ){ |
781 | ||
782 | + | case NVE_ENS: |
783 | + | new NVE( simnfo, the_ff ); |
784 | + | break; |
785 | ||
786 | + | case NVT_ENS: |
787 | + | myNVT = new NVT( simnfo, the_ff ); |
788 | + | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
789 | ||
790 | + | if (the_globals->haveTauThermostat()) |
791 | + | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
792 | + | // else if (the_globals->haveQmass()) |
793 | + | // myNVT->setQmass(the_globals->getQmass()); |
794 | + | else { |
795 | + | sprintf( painCave.errMsg, |
796 | + | "SimSetup error: If you use the NVT\n" |
797 | + | " ensemble, you must set either tauThermostat or qMass.\n" |
798 | + | " Neither of these was found in the BASS file.\n"); |
799 | + | painCave.isFatal = 1; |
800 | + | simError(); |
801 | + | } |
802 | + | break; |
803 | + | |
804 | + | default: |
805 | + | sprintf( painCave.errMsg, |
806 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
807 | + | painCave.isFatal = 1; |
808 | + | simError(); |
809 | + | } |
810 | + | |
811 | + | |
812 | + | #ifdef IS_MPI |
813 | + | mpiSim->mpiRefresh(); |
814 | + | #endif |
815 | + | |
816 | // initialize the Fortran | |
817 | < | |
817 | > | |
818 | > | |
819 | simnfo->refreshSim(); | |
820 | ||
821 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 778 | Line 934 | void SimSetup::makeMolecules( void ){ | |
934 | theBonds[j].a = currentBond->getA() + atomOffset; | |
935 | theBonds[j].b = currentBond->getB() + atomOffset; | |
936 | ||
937 | < | exI = theBonds[i].a; |
938 | < | exJ = theBonds[i].b; |
937 | > | exI = theBonds[j].a; |
938 | > | exJ = theBonds[j].b; |
939 | ||
940 | // exclude_I must always be the smaller of the pair | |
941 | if( exI > exJ ){ | |
# | Line 795 | Line 951 | void SimSetup::makeMolecules( void ){ | |
951 | ||
952 | the_excludes[j+excludeOffset]->setPair( exI, exJ ); | |
953 | #else // isn't MPI | |
954 | + | |
955 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
956 | #endif //is_mpi | |
957 | } | |
# | Line 832 | Line 989 | void SimSetup::makeMolecules( void ){ | |
989 | ||
990 | default: | |
991 | sprintf( painCave.errMsg, | |
992 | < | "SimSetup Error: ghostVectorSource was neiter a " |
992 | > | "SimSetup Error: ghostVectorSource was neither a " |
993 | "double nor an int.\n" | |
994 | "-->Bend[%d] in %s\n", | |
995 | j, comp_stamps[stampID]->getID() ); | |
# | Line 926 | Line 1083 | void SimSetup::makeMolecules( void ){ | |
1083 | ||
1084 | ||
1085 | the_molecules[i].initialize( info ); | |
1086 | + | |
1087 | + | |
1088 | atomOffset += info.nAtoms; | |
1089 | delete[] theBonds; | |
1090 | delete[] theBends; | |
1091 | delete[] theTorsions; | |
1092 | } | |
1093 | + | |
1094 | + | #ifdef IS_MPI |
1095 | + | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1096 | + | MPIcheckPoint(); |
1097 | + | #endif // is_mpi |
1098 | ||
1099 | // clean up the forcefield | |
1100 | the_ff->calcRcut(); | |
1101 | the_ff->cleanMe(); | |
1102 | + | |
1103 | } | |
1104 | ||
1105 | void SimSetup::initFromBass( void ){ | |
# | Line 956 | Line 1121 | void SimSetup::initFromBass( void ){ | |
1121 | have_extra =1; | |
1122 | ||
1123 | n_cells = (int)temp3 - 1; | |
1124 | < | cellx = simnfo->box_x / temp3; |
1125 | < | celly = simnfo->box_y / temp3; |
1126 | < | cellz = simnfo->box_z / temp3; |
1124 | > | cellx = simnfo->boxLx / temp3; |
1125 | > | celly = simnfo->boxLy / temp3; |
1126 | > | cellz = simnfo->boxLz / temp3; |
1127 | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); | |
1128 | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); | |
1129 | n_per_extra = (int)ceil( temp1 ); | |
# | Line 973 | Line 1138 | void SimSetup::initFromBass( void ){ | |
1138 | } | |
1139 | else{ | |
1140 | n_cells = (int)temp3; | |
1141 | < | cellx = simnfo->box_x / temp3; |
1142 | < | celly = simnfo->box_y / temp3; |
1143 | < | cellz = simnfo->box_z / temp3; |
1141 | > | cellx = simnfo->boxLx / temp3; |
1142 | > | celly = simnfo->boxLy / temp3; |
1143 | > | cellz = simnfo->boxLz / temp3; |
1144 | } | |
1145 | ||
1146 | current_mol = 0; |
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