# | Line 66 | Line 66 | void SimSetup::createSim( void ){ | |
---|---|---|
66 | ||
67 | MakeStamps *the_stamps; | |
68 | Globals* the_globals; | |
69 | + | ExtendedSystem* the_extendedsystem; |
70 | int i, j; | |
71 | ||
72 | // get the stamps and globals; | |
# | Line 80 | Line 81 | void SimSetup::createSim( void ){ | |
81 | // get the ones we know are there, yet still may need some work. | |
82 | n_components = the_globals->getNComponents(); | |
83 | strcpy( force_field, the_globals->getForceField() ); | |
84 | + | |
85 | + | // get the ensemble and set up an extended system if we need it: |
86 | 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 | + | } |
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, |
145 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 | + | "reverting to NVE for this simulation.\n", |
147 | + | ensemble ); |
148 | + | painCave.isFatal = 0; |
149 | + | simError(); |
150 | + | strcpy( ensemble, "NVE" ); |
151 | + | } |
152 | strcpy( simnfo->ensemble, ensemble ); | |
153 | ||
154 | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); | |
155 | simnfo->usePBC = the_globals->getPBC(); | |
156 | ||
157 | < | |
158 | < | |
159 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF(); |
160 | < | else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
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, | |
165 | "SimSetup Error. Unrecognized force field -> %s\n", | |
# | Line 240 | Line 310 | void SimSetup::createSim( void ){ | |
310 | ||
311 | globalIndex = mpiSim->divideLabor(); | |
312 | ||
243 | – | |
244 | – | |
313 | // set up the local variables | |
314 | ||
315 | int localMol, allMol; | |
# | Line 316 | Line 384 | void SimSetup::createSim( void ){ | |
384 | ||
385 | if(mol2proc[i] == worldRank ){ | |
386 | the_molecules[molIndex].setStampID( molCompType[i] ); | |
387 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
388 | molIndex++; | |
389 | } | |
390 | } | |
# | Line 326 | Line 395 | void SimSetup::createSim( void ){ | |
395 | for(i=0; i<n_components; i++){ | |
396 | for(j=0; j<components_nmol[i]; j++ ){ | |
397 | the_molecules[molIndex].setStampID( i ); | |
398 | + | the_molecules[molIndex].setMyIndex( molIndex ); |
399 | molIndex++; | |
400 | } | |
401 | } | |
# | Line 336 | Line 406 | void SimSetup::createSim( void ){ | |
406 | ||
407 | if( simnfo->n_SRI ){ | |
408 | ||
339 | – | std::cerr << "n_SRI = " << simnfo->n_SRI << "\n"; |
340 | – | |
409 | Exclude::createArray(simnfo->n_SRI); | |
410 | the_excludes = new Exclude*[simnfo->n_SRI]; | |
411 | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); | |
412 | simnfo->globalExcludes = new int; | |
413 | < | simnfo->n_exclude = tot_SRI; |
413 | > | simnfo->n_exclude = simnfo->n_SRI; |
414 | } | |
415 | else{ | |
416 | ||
# | Line 462 | Line 530 | void SimSetup::createSim( void ){ | |
530 | } | |
531 | simnfo->dielectric = the_globals->getDielectric(); | |
532 | } else { | |
533 | < | if (simnfo->n_dipoles) { |
533 | > | if (usesDipoles) { |
534 | ||
535 | if( !the_globals->haveECR() ){ | |
536 | sprintf( painCave.errMsg, | |
537 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
537 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
538 | "box length for the electrostaticCutoffRadius.\n" | |
539 | "I hope you have a very fast processor!\n"); | |
540 | painCave.isFatal = 0; | |
# | Line 482 | Line 550 | void SimSetup::createSim( void ){ | |
550 | ||
551 | if( !the_globals->haveEST() ){ | |
552 | sprintf( painCave.errMsg, | |
553 | < | "SimSetup Warning: using default value of 5% of the" |
553 | > | "SimSetup Warning: using default value of 5%% of the " |
554 | "electrostaticCutoffRadius for the " | |
555 | "electrostaticSkinThickness\n" | |
556 | ); | |
# | Line 657 | Line 725 | void SimSetup::createSim( void ){ | |
725 | ||
726 | // new AllLong( simnfo ); | |
727 | ||
660 | – | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
661 | – | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
728 | ||
729 | < | |
729 | > | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
730 | > | new Symplectic(simnfo, the_ff, the_extendedsystem); |
731 | > | std::cerr << "called new Symplecic\n"; |
732 | > | fprintf( stderr, "called new Symplectic. stderr\n" ); |
733 | > | } |
734 | > | else if( !strcmp( force_field, "LJ" ) ){ |
735 | > | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
736 | > | std::cerr << "called new Verlet\n"; |
737 | > | fprintf( stderr, "called new Verlet. stderr\n" ); |
738 | > | } |
739 | > | else { |
740 | > | std::cerr << "I'm a bug.\n"; |
741 | > | fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
742 | > | } |
743 | > | #ifdef IS_MPI |
744 | > | mpiSim->mpiRefresh(); |
745 | > | #endif |
746 | ||
747 | // initialize the Fortran | |
748 | < | |
748 | > | |
749 | > | |
750 | simnfo->refreshSim(); | |
751 | ||
752 | if( !strcmp( simnfo->mixingRule, "standard") ){ | |
# | Line 782 | Line 865 | void SimSetup::makeMolecules( void ){ | |
865 | theBonds[j].a = currentBond->getA() + atomOffset; | |
866 | theBonds[j].b = currentBond->getB() + atomOffset; | |
867 | ||
868 | < | exI = theBonds[i].a; |
869 | < | exJ = theBonds[i].b; |
868 | > | exI = theBonds[j].a; |
869 | > | exJ = theBonds[j].b; |
870 | ||
871 | // exclude_I must always be the smaller of the pair | |
872 | if( exI > exJ ){ | |
# | Line 799 | Line 882 | void SimSetup::makeMolecules( void ){ | |
882 | ||
883 | the_excludes[j+excludeOffset]->setPair( exI, exJ ); | |
884 | #else // isn't MPI | |
885 | + | |
886 | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); | |
887 | #endif //is_mpi | |
888 | } | |
# | Line 836 | Line 920 | void SimSetup::makeMolecules( void ){ | |
920 | ||
921 | default: | |
922 | sprintf( painCave.errMsg, | |
923 | < | "SimSetup Error: ghostVectorSource was neiter a " |
923 | > | "SimSetup Error: ghostVectorSource was neither a " |
924 | "double nor an int.\n" | |
925 | "-->Bend[%d] in %s\n", | |
926 | j, comp_stamps[stampID]->getID() ); | |
# | Line 930 | Line 1014 | void SimSetup::makeMolecules( void ){ | |
1014 | ||
1015 | ||
1016 | the_molecules[i].initialize( info ); | |
1017 | + | |
1018 | + | |
1019 | atomOffset += info.nAtoms; | |
1020 | delete[] theBonds; | |
1021 | delete[] theBends; | |
1022 | delete[] theTorsions; | |
1023 | } | |
1024 | ||
1025 | + | #ifdef IS_MPI |
1026 | + | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1027 | + | MPIcheckPoint(); |
1028 | + | #endif // is_mpi |
1029 | + | |
1030 | // clean up the forcefield | |
1031 | the_ff->calcRcut(); | |
1032 | the_ff->cleanMe(); | |
1033 | + | |
1034 | } | |
1035 | ||
1036 | void SimSetup::initFromBass( void ){ |
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