# | Line 12 | Line 12 | |
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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 | < | ExtendedSystem* the_extendedsystem; |
80 | < | 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 82 | Line 97 | void SimSetup::createSim( void ){ | |
97 | n_components = the_globals->getNComponents(); | |
98 | strcpy( force_field, the_globals->getForceField() ); | |
99 | ||
100 | < | // get the ensemble and set up an extended system if we need it: |
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() ); | |
87 | – | if( !strcasecmp( ensemble, "NPT" ) ) { |
88 | – | the_extendedsystem = new ExtendedSystem( simnfo ); |
89 | – | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
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 | – | } |
112 | ||
113 | < | if (the_globals->haveTauThermostat()) |
114 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
115 | < | else if (the_globals->haveQmass()) |
116 | < | 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 { |
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", | |
# | Line 148 | Line 121 | void SimSetup::createSim( void ){ | |
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 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
189 | < | the_ff = new TraPPE_ExFF(); |
188 | > | switch( ffCase ){ |
189 | > | |
190 | > | case FF_DUFF: |
191 | > | the_ff = new DUFF(); |
192 | usesDipoles = 1; | |
193 | < | } |
194 | < | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
195 | < | else{ |
193 | > | break; |
194 | > | |
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", |
166 | < | force_field ); |
201 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
202 | painCave.isFatal = 1; | |
203 | simError(); | |
204 | } | |
# | Line 173 | Line 208 | void SimSetup::createSim( void ){ | |
208 | MPIcheckPoint(); | |
209 | #endif // is_mpi | |
210 | ||
176 | – | |
177 | – | |
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 298 | Line 331 | void SimSetup::createSim( void ){ | |
331 | simnfo->n_torsions = tot_torsions; | |
332 | simnfo->n_SRI = tot_SRI; | |
333 | simnfo->n_mol = tot_nmol; | |
301 | – | |
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 | ||
309 | – | |
310 | – | |
343 | globalIndex = mpiSim->divideLabor(); | |
344 | ||
345 | // set up the local variables | |
# | Line 324 | 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++ ){ | |
# | Line 336 | 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 | ||
344 | – | |
384 | simnfo->n_atoms = mpiSim->getMyNlocal(); | |
385 | ||
386 | if( local_atoms != simnfo->n_atoms ){ | |
# | Line 393 | 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 487 | Line 531 | void SimSetup::createSim( void ){ | |
531 | ||
532 | makeMolecules(); | |
533 | simnfo->identArray = new int[simnfo->n_atoms]; | |
490 | – | simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
534 | for(i=0; i<simnfo->n_atoms; i++){ | |
535 | simnfo->identArray[i] = the_atoms[i]->getIdent(); | |
493 | – | } |
494 | – | for(i=0; i< simnfo->n_mol; i++) { |
495 | – | the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
536 | } | |
537 | ||
538 | if (the_globals->getUseRF() ) { | |
# | Line 727 | 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 | ||
772 | < | // new AllLong( simnfo ); |
772 | > | switch( ensembleCase ){ |
773 | ||
774 | + | case NVE_ENS: |
775 | + | new NVE( simnfo, the_ff ); |
776 | + | break; |
777 | ||
778 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
779 | < | new Symplectic(simnfo, the_ff, the_extendedsystem); |
780 | < | } |
781 | < | else if( !strcmp( force_field, "LJ" ) ){ |
782 | < | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
740 | < | } |
741 | < | else { |
742 | < | std::cerr << "I'm a bug.\n"; |
743 | < | fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
778 | > | default: |
779 | > | sprintf( painCave.errMsg, |
780 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
781 | > | painCave.isFatal = 1; |
782 | > | simError(); |
783 | } | |
784 | + | |
785 | + | |
786 | #ifdef IS_MPI | |
787 | mpiSim->mpiRefresh(); | |
788 | #endif |
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