# | Line 67 | Line 67 | void SimSetup::createSim( void ){ | |
---|---|---|
67 | MakeStamps *the_stamps; | |
68 | Globals* the_globals; | |
69 | ExtendedSystem* the_extendedsystem; | |
70 | < | int i, j; |
70 | > | int i, j, k, globalAtomIndex; |
71 | ||
72 | // get the stamps and globals; | |
73 | the_stamps = stamps; | |
# | Line 87 | Line 87 | void SimSetup::createSim( void ){ | |
87 | if( !strcasecmp( ensemble, "NPT" ) ) { | |
88 | the_extendedsystem = new ExtendedSystem( simnfo ); | |
89 | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); | |
90 | < | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
90 | > | if (the_globals->haveTargetPressure()) |
91 | > | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 | > | else { |
93 | > | sprintf( painCave.errMsg, |
94 | > | "SimSetup error: If you use the constant pressure\n" |
95 | > | " ensemble, you must set targetPressure.\n" |
96 | > | " This was found in the BASS file.\n"); |
97 | > | painCave.isFatal = 1; |
98 | > | simError(); |
99 | > | } |
100 | > | |
101 | > | if (the_globals->haveTauThermostat()) |
102 | > | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 | > | else if (the_globals->haveQmass()) |
104 | > | the_extendedsystem->setQmass(the_globals->getQmass()); |
105 | > | else { |
106 | > | sprintf( painCave.errMsg, |
107 | > | "SimSetup error: If you use one of the constant temperature\n" |
108 | > | " ensembles, you must set either tauThermostat or qMass.\n" |
109 | > | " Neither of these was found in the BASS file.\n"); |
110 | > | painCave.isFatal = 1; |
111 | > | simError(); |
112 | > | } |
113 | > | |
114 | > | if (the_globals->haveTauBarostat()) |
115 | > | the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 | > | else { |
117 | > | sprintf( painCave.errMsg, |
118 | > | "SimSetup error: If you use the constant pressure\n" |
119 | > | " ensemble, you must set tauBarostat.\n" |
120 | > | " This was found in the BASS file.\n"); |
121 | > | painCave.isFatal = 1; |
122 | > | simError(); |
123 | > | } |
124 | > | |
125 | } else if ( !strcasecmp( ensemble, "NVT") ) { | |
126 | the_extendedsystem = new ExtendedSystem( simnfo ); | |
127 | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); | |
128 | + | |
129 | + | if (the_globals->haveTauThermostat()) |
130 | + | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 | + | else if (the_globals->haveQmass()) |
132 | + | the_extendedsystem->setQmass(the_globals->getQmass()); |
133 | + | else { |
134 | + | sprintf( painCave.errMsg, |
135 | + | "SimSetup error: If you use one of the constant temperature\n" |
136 | + | " ensembles, you must set either tauThermostat or qMass.\n" |
137 | + | " Neither of these was found in the BASS file.\n"); |
138 | + | painCave.isFatal = 1; |
139 | + | simError(); |
140 | + | } |
141 | + | |
142 | } else if ( !strcasecmp( ensemble, "NVE") ) { | |
143 | } else { | |
144 | sprintf( painCave.errMsg, | |
# | Line 106 | Line 154 | void SimSetup::createSim( void ){ | |
154 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
155 | simnfo->usePBC = the_globals->getPBC(); | |
156 | ||
157 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
157 | > | int usesDipoles = 0; |
158 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
159 | > | the_ff = new TraPPE_ExFF(); |
160 | > | usesDipoles = 1; |
161 | > | } |
162 | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); | |
163 | else{ | |
164 | sprintf( painCave.errMsg, | |
# | Line 246 | Line 298 | void SimSetup::createSim( void ){ | |
298 | simnfo->n_torsions = tot_torsions; | |
299 | simnfo->n_SRI = tot_SRI; | |
300 | simnfo->n_mol = tot_nmol; | |
249 | – | |
301 | ||
302 | + | simnfo->molMembershipArray = new int[tot_atoms]; |
303 | + | |
304 | #ifdef IS_MPI | |
305 | ||
306 | // divide the molecules among processors here. | |
307 | ||
308 | mpiSim = new mpiSimulation( simnfo ); | |
309 | ||
257 | – | |
258 | – | |
310 | globalIndex = mpiSim->divideLabor(); | |
311 | ||
312 | // set up the local variables | |
# | Line 272 | Line 323 | void SimSetup::createSim( void ){ | |
323 | local_bonds = 0; | |
324 | local_bends = 0; | |
325 | local_torsions = 0; | |
326 | + | globalAtomIndex = 0; |
327 | + | |
328 | + | |
329 | for( i=0; i<n_components; i++ ){ | |
330 | ||
331 | for( j=0; j<components_nmol[i]; j++ ){ | |
332 | ||
333 | < | if( mol2proc[j] == worldRank ){ |
333 | > | if( mol2proc[allMol] == worldRank ){ |
334 | ||
335 | local_atoms += comp_stamps[i]->getNAtoms(); | |
336 | local_bonds += comp_stamps[i]->getNBonds(); | |
# | Line 284 | Line 338 | void SimSetup::createSim( void ){ | |
338 | local_torsions += comp_stamps[i]->getNTorsions(); | |
339 | localMol++; | |
340 | } | |
341 | < | allMol++; |
341 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
342 | > | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
343 | > | globalAtomIndex++; |
344 | > | } |
345 | > | |
346 | > | allMol++; |
347 | } | |
348 | } | |
349 | local_SRI = local_bonds + local_bends + local_torsions; | |
350 | ||
292 | – | |
351 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
352 | ||
353 | if( local_atoms != simnfo->n_atoms ){ | |
# | Line 333 | Line 391 | void SimSetup::createSim( void ){ | |
391 | if(mol2proc[i] == worldRank ){ | |
392 | the_molecules[molIndex].setStampID( molCompType[i] ); | |
393 | the_molecules[molIndex].setMyIndex( molIndex ); | |
394 | + | the_molecules[molIndex].setGlobalIndex( i ); |
395 | molIndex++; | |
396 | } | |
397 | } | |
# | Line 340 | Line 399 | void SimSetup::createSim( void ){ | |
399 | #else // is_mpi | |
400 | ||
401 | molIndex = 0; | |
402 | + | globalAtomIndex = 0; |
403 | for(i=0; i<n_components; i++){ | |
404 | for(j=0; j<components_nmol[i]; j++ ){ | |
405 | the_molecules[molIndex].setStampID( i ); | |
406 | the_molecules[molIndex].setMyIndex( molIndex ); | |
407 | + | the_molecules[molIndex].setGlobalIndex( molIndex ); |
408 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
409 | + | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
410 | + | globalAtomIndex++; |
411 | + | } |
412 | molIndex++; | |
413 | } | |
414 | } | |
# | Line 478 | Line 543 | void SimSetup::createSim( void ){ | |
543 | } | |
544 | simnfo->dielectric = the_globals->getDielectric(); | |
545 | } else { | |
546 | < | if (simnfo->n_dipoles) { |
546 | > | if (usesDipoles) { |
547 | ||
548 | if( !the_globals->haveECR() ){ | |
549 | sprintf( painCave.errMsg, | |
550 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
550 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
551 | "box length for the electrostaticCutoffRadius.\n" | |
552 | "I hope you have a very fast processor!\n"); | |
553 | painCave.isFatal = 0; | |
# | Line 498 | Line 563 | void SimSetup::createSim( void ){ | |
563 | ||
564 | if( !the_globals->haveEST() ){ | |
565 | sprintf( painCave.errMsg, | |
566 | < | "SimSetup Warning: using default value of 5% of the" |
566 | > | "SimSetup Warning: using default value of 5%% of the " |
567 | "electrostaticCutoffRadius for the " | |
568 | "electrostaticSkinThickness\n" | |
569 | ); | |
# | Line 673 | Line 738 | void SimSetup::createSim( void ){ | |
738 | ||
739 | // new AllLong( simnfo ); | |
740 | ||
741 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo, |
742 | < | the_ff, |
743 | < | the_extendedsystem); |
744 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, |
745 | < | the_ff, |
746 | < | the_extendedsystem ); |
741 | > | |
742 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
743 | > | new Symplectic(simnfo, the_ff, the_extendedsystem); |
744 | > | } |
745 | > | else if( !strcmp( force_field, "LJ" ) ){ |
746 | > | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
747 | > | } |
748 | ||
749 | #ifdef IS_MPI | |
750 | mpiSim->mpiRefresh(); |
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