# | Line 90 | Line 90 | void SimSetup::createSim(void){ | |
---|---|---|
90 | #endif // is_mpi | |
91 | ||
92 | void SimSetup::createSim(void){ | |
93 | – | int i, j, k, globalAtomIndex; |
93 | ||
94 | // gather all of the information from the Bass file | |
95 | ||
# | Line 108 | Line 107 | void SimSetup::createSim(void){ | |
107 | ||
108 | if (!isInfoArray){ | |
109 | initSystemCoords(); | |
110 | + | |
111 | + | if( !(globals->getUseInitTime()) ) |
112 | + | info[0].currentTime = 0.0; |
113 | } | |
114 | ||
115 | // make the output filenames | |
# | Line 129 | Line 131 | void SimSetup::makeMolecules(void){ | |
131 | ||
132 | ||
133 | void SimSetup::makeMolecules(void){ | |
134 | < | int k, l; |
134 | > | int k; |
135 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
136 | molInit molInfo; | |
137 | DirectionalAtom* dAtom; | |
# | Line 551 | Line 553 | void SimSetup::gatherInfo(void){ | |
553 | ||
554 | ||
555 | void SimSetup::gatherInfo(void){ | |
556 | < | int i, j, k; |
556 | > | int i; |
557 | ||
558 | ensembleCase = -1; | |
559 | ffCase = -1; | |
# | Line 914 | Line 916 | void SimSetup::initSystemCoords(void){ | |
916 | if (worldRank == 0){ | |
917 | #endif //is_mpi | |
918 | inName = globals->getInitialConfig(); | |
917 | – | double* tempDouble = new double[1000000]; |
919 | fileInit = new InitializeFromFile(inName); | |
920 | #ifdef IS_MPI | |
921 | } | |
# | Line 932 | Line 933 | void SimSetup::initSystemCoords(void){ | |
933 | ||
934 | sprintf(painCave.errMsg, | |
935 | "Cannot intialize a parallel simulation without an initial configuration file.\n"); | |
936 | < | painCave.isFatal; |
936 | > | painCave.isFatal = 1;; |
937 | simError(); | |
938 | ||
939 | #else | |
# | Line 1158 | Line 1159 | void SimSetup::calcSysValues(void){ | |
1159 | } | |
1160 | ||
1161 | void SimSetup::calcSysValues(void){ | |
1162 | < | int i, j, k; |
1162 | > | int i; |
1163 | ||
1164 | int* molMembershipArray; | |
1165 | ||
# | Line 1257 | Line 1258 | void SimSetup::makeSysArrays(void){ | |
1258 | ||
1259 | ||
1260 | void SimSetup::makeSysArrays(void){ | |
1261 | < | int i, j, k, l; |
1261 | > | |
1262 | > | #ifndef IS_MPI |
1263 | > | int k, j; |
1264 | > | #endif // is_mpi |
1265 | > | int i, l; |
1266 | ||
1267 | Atom** the_atoms; | |
1268 | Molecule* the_molecules; | |
# | Line 1340 | Line 1345 | void SimSetup::makeIntegrator(void){ | |
1345 | void SimSetup::makeIntegrator(void){ | |
1346 | int k; | |
1347 | ||
1348 | + | NVE<RealIntegrator>* myNVE = NULL; |
1349 | NVT<RealIntegrator>* myNVT = NULL; | |
1350 | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; | |
1351 | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; | |
# | Line 1349 | Line 1355 | void SimSetup::makeIntegrator(void){ | |
1355 | case NVE_ENS: | |
1356 | if (globals->haveZconstraints()){ | |
1357 | setupZConstraint(info[k]); | |
1358 | < | new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1358 | > | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1359 | } | |
1360 | < | else |
1361 | < | new NVE<RealIntegrator>(&(info[k]), the_ff); |
1360 | > | else{ |
1361 | > | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1362 | > | } |
1363 | > | |
1364 | > | info->the_integrator = myNVE; |
1365 | break; | |
1366 | ||
1367 | case NVT_ENS: | |
# | Line 1374 | Line 1383 | void SimSetup::makeIntegrator(void){ | |
1383 | painCave.isFatal = 1; | |
1384 | simError(); | |
1385 | } | |
1386 | + | |
1387 | + | info->the_integrator = myNVT; |
1388 | break; | |
1389 | ||
1390 | case NPTi_ENS: | |
# | Line 1415 | Line 1426 | void SimSetup::makeIntegrator(void){ | |
1426 | painCave.isFatal = 1; | |
1427 | simError(); | |
1428 | } | |
1429 | + | |
1430 | + | info->the_integrator = myNPTi; |
1431 | break; | |
1432 | ||
1433 | case NPTf_ENS: | |
# | Line 1456 | Line 1469 | void SimSetup::makeIntegrator(void){ | |
1469 | painCave.isFatal = 1; | |
1470 | simError(); | |
1471 | } | |
1472 | + | |
1473 | + | info->the_integrator = myNPTf; |
1474 | break; | |
1475 | ||
1476 | default: |
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+ | Added lines |
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> | Changed lines |