# | 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" )) ffCase = NVE_ENS; |
114 | + | else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS; |
115 | + | else if( !strcasecmp( ensemble, "NPT" )) ffCase = 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 = 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 | ||
345 | // set up the local variables | |
# | Line 254 | 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 266 | 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 | ||
274 | – | |
384 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
385 | ||
386 | if( local_atoms != simnfo->n_atoms ){ | |
# | Line 314 | 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 321 | 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 334 | Line 452 | void SimSetup::createSim( void ){ | |
452 | ||
453 | if( simnfo->n_SRI ){ | |
454 | ||
337 | – | std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
338 | – | |
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 460 | Line 576 | void SimSetup::createSim( void ){ | |
576 | } | |
577 | simnfo->dielectric = the_globals->getDielectric(); | |
578 | } else { | |
579 | < | if (simnfo->n_dipoles) { |
579 | > | if (usesDipoles) { |
580 | ||
581 | if( !the_globals->haveECR() ){ | |
582 | sprintf( painCave.errMsg, | |
583 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
583 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
584 | "box length for the electrostaticCutoffRadius.\n" | |
585 | "I hope you have a very fast processor!\n"); | |
586 | painCave.isFatal = 0; | |
# | Line 480 | Line 596 | void SimSetup::createSim( void ){ | |
596 | ||
597 | if( !the_globals->haveEST() ){ | |
598 | sprintf( painCave.errMsg, | |
599 | < | "SimSetup Warning: using default value of 5% of the" |
599 | > | "SimSetup Warning: using default value of 5%% of the " |
600 | "electrostaticCutoffRadius for the " | |
601 | "electrostaticSkinThickness\n" | |
602 | ); | |
# | Line 651 | Line 767 | void SimSetup::createSim( void ){ | |
767 | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); | |
768 | ||
769 | ||
770 | < | // // make the longe range forces and the integrator |
770 | > | // make the integrator |
771 | ||
656 | – | // new AllLong( simnfo ); |
772 | ||
773 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
774 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
773 | > | if( !strcmp( ensemble, "TraPPE_Ex" ) ){ |
774 | > | new Symplectic(simnfo, the_ff, the_extendedsystem); |
775 | > | } |
776 | > | else if( !strcmp( force_field, "LJ" ) ){ |
777 | > | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
778 | > | } |
779 | ||
780 | #ifdef IS_MPI | |
781 | mpiSim->mpiRefresh(); | |
# | Line 932 | Line 1051 | void SimSetup::makeMolecules( void ){ | |
1051 | ||
1052 | ||
1053 | the_molecules[i].initialize( info ); | |
1054 | + | |
1055 | + | |
1056 | atomOffset += info.nAtoms; | |
1057 | delete[] theBonds; | |
1058 | delete[] theBends; |
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