# | Line 22 | Line 22 | |
---|---|---|
22 | #define NVT_ENS 1 | |
23 | #define NPTi_ENS 2 | |
24 | #define NPTf_ENS 3 | |
25 | + | #define NPTxyz_ENS 4 |
26 | ||
27 | + | |
28 | #define FF_DUFF 0 | |
29 | #define FF_LJ 1 | |
30 | #define FF_EAM 2 | |
# | Line 90 | Line 92 | void SimSetup::createSim(void){ | |
92 | #endif // is_mpi | |
93 | ||
94 | void SimSetup::createSim(void){ | |
93 | – | int i, j, k, globalAtomIndex; |
95 | ||
96 | // gather all of the information from the Bass file | |
97 | ||
# | Line 108 | Line 109 | void SimSetup::createSim(void){ | |
109 | ||
110 | if (!isInfoArray){ | |
111 | initSystemCoords(); | |
112 | + | |
113 | + | if( !(globals->getUseInitTime()) ) |
114 | + | info[0].currentTime = 0.0; |
115 | } | |
116 | ||
117 | // make the output filenames | |
# | Line 129 | Line 133 | void SimSetup::makeMolecules(void){ | |
133 | ||
134 | ||
135 | void SimSetup::makeMolecules(void){ | |
136 | < | int k, l; |
136 | > | int k; |
137 | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; | |
138 | molInit molInfo; | |
139 | DirectionalAtom* dAtom; | |
# | Line 551 | Line 555 | void SimSetup::gatherInfo(void){ | |
555 | ||
556 | ||
557 | void SimSetup::gatherInfo(void){ | |
558 | < | int i, j, k; |
558 | > | int i; |
559 | ||
560 | ensembleCase = -1; | |
561 | ffCase = -1; | |
# | Line 601 | Line 605 | void SimSetup::gatherInfo(void){ | |
605 | } | |
606 | else if (!strcasecmp(ensemble, "NPTf")){ | |
607 | ensembleCase = NPTf_ENS; | |
608 | + | } |
609 | + | else if (!strcasecmp(ensemble, "NPTxyz")){ |
610 | + | ensembleCase = NPTxyz_ENS; |
611 | } | |
612 | else{ | |
613 | sprintf(painCave.errMsg, | |
# | Line 914 | Line 921 | void SimSetup::initSystemCoords(void){ | |
921 | if (worldRank == 0){ | |
922 | #endif //is_mpi | |
923 | inName = globals->getInitialConfig(); | |
917 | – | double* tempDouble = new double[1000000]; |
924 | fileInit = new InitializeFromFile(inName); | |
925 | #ifdef IS_MPI | |
926 | } | |
# | Line 932 | Line 938 | void SimSetup::initSystemCoords(void){ | |
938 | ||
939 | sprintf(painCave.errMsg, | |
940 | "Cannot intialize a parallel simulation without an initial configuration file.\n"); | |
941 | < | painCave.isFatal; |
941 | > | painCave.isFatal = 1;; |
942 | simError(); | |
943 | ||
944 | #else | |
# | Line 1158 | Line 1164 | void SimSetup::calcSysValues(void){ | |
1164 | } | |
1165 | ||
1166 | void SimSetup::calcSysValues(void){ | |
1167 | < | int i, j, k; |
1167 | > | int i; |
1168 | ||
1169 | int* molMembershipArray; | |
1170 | ||
# | Line 1257 | Line 1263 | void SimSetup::makeSysArrays(void){ | |
1263 | ||
1264 | ||
1265 | void SimSetup::makeSysArrays(void){ | |
1266 | < | int i, j, k, l; |
1266 | > | |
1267 | > | #ifndef IS_MPI |
1268 | > | int k, j; |
1269 | > | #endif // is_mpi |
1270 | > | int i, l; |
1271 | ||
1272 | Atom** the_atoms; | |
1273 | Molecule* the_molecules; | |
# | Line 1344 | Line 1354 | void SimSetup::makeIntegrator(void){ | |
1354 | NVT<RealIntegrator>* myNVT = NULL; | |
1355 | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; | |
1356 | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; | |
1357 | + | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1358 | ||
1359 | for (k = 0; k < nInfo; k++){ | |
1360 | switch (ensembleCase){ | |
# | Line 1466 | Line 1477 | void SimSetup::makeIntegrator(void){ | |
1477 | } | |
1478 | ||
1479 | info->the_integrator = myNPTf; | |
1480 | + | break; |
1481 | + | |
1482 | + | case NPTxyz_ENS: |
1483 | + | if (globals->haveZconstraints()){ |
1484 | + | setupZConstraint(info[k]); |
1485 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1486 | + | } |
1487 | + | else |
1488 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1489 | + | |
1490 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1491 | + | |
1492 | + | if (globals->haveTargetPressure()) |
1493 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1494 | + | else{ |
1495 | + | sprintf(painCave.errMsg, |
1496 | + | "SimSetup error: If you use a constant pressure\n" |
1497 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1498 | + | painCave.isFatal = 1; |
1499 | + | simError(); |
1500 | + | } |
1501 | + | |
1502 | + | if (globals->haveTauThermostat()) |
1503 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1504 | + | else{ |
1505 | + | sprintf(painCave.errMsg, |
1506 | + | "SimSetup error: If you use an NPT\n" |
1507 | + | " ensemble, you must set tauThermostat.\n"); |
1508 | + | painCave.isFatal = 1; |
1509 | + | simError(); |
1510 | + | } |
1511 | + | |
1512 | + | if (globals->haveTauBarostat()) |
1513 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1514 | + | else{ |
1515 | + | sprintf(painCave.errMsg, |
1516 | + | "SimSetup error: If you use an NPT\n" |
1517 | + | " ensemble, you must set tauBarostat.\n"); |
1518 | + | painCave.isFatal = 1; |
1519 | + | simError(); |
1520 | + | } |
1521 | + | |
1522 | + | info->the_integrator = myNPTxyz; |
1523 | break; | |
1524 | ||
1525 | default: |
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