# | Line 22 | Line 22 | |
---|---|---|
22 | #define NVT_ENS 1 | |
23 | #define NPTi_ENS 2 | |
24 | #define NPTf_ENS 3 | |
25 | – | #define NPTim_ENS 4 |
26 | – | #define NPTfm_ENS 5 |
25 | ||
26 | #define FF_DUFF 0 | |
27 | #define FF_LJ 1 | |
# | Line 92 | Line 90 | void SimSetup::createSim(void){ | |
90 | #endif // is_mpi | |
91 | ||
92 | void SimSetup::createSim(void){ | |
95 | – | int i, j, k, globalAtomIndex; |
93 | ||
94 | // gather all of the information from the Bass file | |
95 | ||
# | Line 110 | 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 131 | 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 553 | 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 604 | Line 604 | void SimSetup::gatherInfo(void){ | |
604 | else if (!strcasecmp(ensemble, "NPTf")){ | |
605 | ensembleCase = NPTf_ENS; | |
606 | } | |
607 | – | else if (!strcasecmp(ensemble, "NPTim")){ |
608 | – | ensembleCase = NPTim_ENS; |
609 | – | } |
610 | – | else if (!strcasecmp(ensemble, "NPTfm")){ |
611 | – | ensembleCase = NPTfm_ENS; |
612 | – | } |
607 | else{ | |
608 | sprintf(painCave.errMsg, | |
609 | "SimSetup Warning. Unrecognized Ensemble -> %s, " | |
# | Line 686 | Line 680 | void SimSetup::gatherInfo(void){ | |
680 | ||
681 | if (globals->haveThermalTime()){ | |
682 | info[i].thermalTime = globals->getThermalTime(); | |
683 | + | } |
684 | + | |
685 | + | info[i].resetIntegrator = 0; |
686 | + | if( globals->haveResetTime() ){ |
687 | + | info[i].resetTime = globals->getResetTime(); |
688 | + | info[i].resetIntegrator = 1; |
689 | } | |
690 | ||
691 | // check for the temperature set flag | |
# | Line 916 | Line 916 | void SimSetup::initSystemCoords(void){ | |
916 | if (worldRank == 0){ | |
917 | #endif //is_mpi | |
918 | inName = globals->getInitialConfig(); | |
919 | – | double* tempDouble = new double[1000000]; |
919 | fileInit = new InitializeFromFile(inName); | |
920 | #ifdef IS_MPI | |
921 | } | |
# | Line 934 | 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 1160 | 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 1259 | 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 1342 | 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<RealIntegrator>* myNPTi = NULL; |
1351 | < | NPTf<RealIntegrator>* myNPTf = NULL; |
1348 | < | NPTim<RealIntegrator>* myNPTim = NULL; |
1349 | < | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1350 | > | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1351 | > | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1352 | ||
1353 | for (k = 0; k < nInfo; k++){ | |
1354 | switch (ensembleCase){ | |
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 1378 | 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: | |
1391 | if (globals->haveZconstraints()){ | |
1392 | setupZConstraint(info[k]); | |
1393 | < | myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff); |
1393 | > | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1394 | } | |
1395 | else | |
1396 | < | myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff); |
1396 | > | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1397 | ||
1398 | myNPTi->setTargetTemp(globals->getTargetTemp()); | |
1399 | ||
# | Line 1419 | 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: | |
1434 | if (globals->haveZconstraints()){ | |
1435 | setupZConstraint(info[k]); | |
1436 | < | myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff); |
1436 | > | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1437 | } | |
1438 | else | |
1439 | < | myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff); |
1439 | > | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1440 | ||
1441 | myNPTf->setTargetTemp(globals->getTargetTemp()); | |
1442 | ||
# | Line 1460 | Line 1469 | void SimSetup::makeIntegrator(void){ | |
1469 | painCave.isFatal = 1; | |
1470 | simError(); | |
1471 | } | |
1463 | – | break; |
1472 | ||
1473 | < | case NPTim_ENS: |
1466 | < | if (globals->haveZconstraints()){ |
1467 | < | setupZConstraint(info[k]); |
1468 | < | myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff); |
1469 | < | } |
1470 | < | else |
1471 | < | myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff); |
1472 | < | |
1473 | < | myNPTim->setTargetTemp(globals->getTargetTemp()); |
1474 | < | |
1475 | < | if (globals->haveTargetPressure()) |
1476 | < | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1477 | < | else{ |
1478 | < | sprintf(painCave.errMsg, |
1479 | < | "SimSetup error: If you use a constant pressure\n" |
1480 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
1481 | < | painCave.isFatal = 1; |
1482 | < | simError(); |
1483 | < | } |
1484 | < | |
1485 | < | if (globals->haveTauThermostat()) |
1486 | < | myNPTim->setTauThermostat(globals->getTauThermostat()); |
1487 | < | else{ |
1488 | < | sprintf(painCave.errMsg, |
1489 | < | "SimSetup error: If you use an NPT\n" |
1490 | < | " ensemble, you must set tauThermostat.\n"); |
1491 | < | painCave.isFatal = 1; |
1492 | < | simError(); |
1493 | < | } |
1494 | < | |
1495 | < | if (globals->haveTauBarostat()) |
1496 | < | myNPTim->setTauBarostat(globals->getTauBarostat()); |
1497 | < | else{ |
1498 | < | sprintf(painCave.errMsg, |
1499 | < | "SimSetup error: If you use an NPT\n" |
1500 | < | " ensemble, you must set tauBarostat.\n"); |
1501 | < | painCave.isFatal = 1; |
1502 | < | simError(); |
1503 | < | } |
1473 | > | info->the_integrator = myNPTf; |
1474 | break; | |
1475 | ||
1506 | – | case NPTfm_ENS: |
1507 | – | if (globals->haveZconstraints()){ |
1508 | – | setupZConstraint(info[k]); |
1509 | – | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff); |
1510 | – | } |
1511 | – | else |
1512 | – | myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff); |
1513 | – | |
1514 | – | myNPTfm->setTargetTemp(globals->getTargetTemp()); |
1515 | – | |
1516 | – | if (globals->haveTargetPressure()) |
1517 | – | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1518 | – | else{ |
1519 | – | sprintf(painCave.errMsg, |
1520 | – | "SimSetup error: If you use a constant pressure\n" |
1521 | – | " ensemble, you must set targetPressure in the BASS file.\n"); |
1522 | – | painCave.isFatal = 1; |
1523 | – | simError(); |
1524 | – | } |
1525 | – | |
1526 | – | if (globals->haveTauThermostat()) |
1527 | – | myNPTfm->setTauThermostat(globals->getTauThermostat()); |
1528 | – | else{ |
1529 | – | sprintf(painCave.errMsg, |
1530 | – | "SimSetup error: If you use an NPT\n" |
1531 | – | " ensemble, you must set tauThermostat.\n"); |
1532 | – | painCave.isFatal = 1; |
1533 | – | simError(); |
1534 | – | } |
1535 | – | |
1536 | – | if (globals->haveTauBarostat()) |
1537 | – | myNPTfm->setTauBarostat(globals->getTauBarostat()); |
1538 | – | else{ |
1539 | – | sprintf(painCave.errMsg, |
1540 | – | "SimSetup error: If you use an NPT\n" |
1541 | – | " ensemble, you must set tauBarostat.\n"); |
1542 | – | painCave.isFatal = 1; |
1543 | – | simError(); |
1544 | – | } |
1545 | – | break; |
1546 | – | |
1476 | default: | |
1477 | sprintf(painCave.errMsg, | |
1478 | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |