# | Line 464 | Line 464 | void SimSetup::makeMolecules(void){ | |
---|---|---|
464 | // used for the exclude list: | |
465 | ||
466 | #ifdef IS_MPI | |
467 | < | exI = info[k].atoms[tempI]->getGlobalIndex() + 1; |
468 | < | exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1; |
467 | > | exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1; |
468 | > | exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1; |
469 | #else | |
470 | < | exI = tempI + 1; |
471 | < | exJ = tempJ + 1; |
470 | > | exI = molInfo.myAtoms[tempI]->getIndex() + 1; |
471 | > | exJ = molInfo.myAtoms[tempJ]->getIndex() + 1; |
472 | #endif | |
473 | ||
474 | info[k].excludes->addPair(exI, exJ); | |
# | Line 834 | Line 834 | void SimSetup::gatherInfo(void){ | |
834 | } | |
835 | ||
836 | //check whether sample time, status time, thermal time and reset time are divisble by dt | |
837 | < | if (!isDivisible(globals->getSampleTime(), globals->getDt())){ |
837 | > | if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
838 | sprintf(painCave.errMsg, | |
839 | "Sample time is not divisible by dt.\n" | |
840 | "\tThis will result in samples that are not uniformly\n" | |
# | Line 844 | Line 844 | void SimSetup::gatherInfo(void){ | |
844 | simError(); | |
845 | } | |
846 | ||
847 | < | if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){ |
847 | > | if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){ |
848 | sprintf(painCave.errMsg, | |
849 | "Status time is not divisible by dt.\n" | |
850 | "\tThis will result in status reports that are not uniformly\n" | |
# | Line 880 | Line 880 | void SimSetup::gatherInfo(void){ | |
880 | if (globals->haveSampleTime()){ | |
881 | info[i].sampleTime = globals->getSampleTime(); | |
882 | info[i].statusTime = info[i].sampleTime; | |
883 | – | info[i].thermalTime = info[i].sampleTime; |
883 | } | |
884 | else{ | |
885 | info[i].sampleTime = globals->getRunTime(); | |
886 | info[i].statusTime = info[i].sampleTime; | |
888 | – | info[i].thermalTime = info[i].sampleTime; |
887 | } | |
888 | ||
889 | if (globals->haveStatusTime()){ | |
# | Line 894 | Line 892 | void SimSetup::gatherInfo(void){ | |
892 | ||
893 | if (globals->haveThermalTime()){ | |
894 | info[i].thermalTime = globals->getThermalTime(); | |
895 | + | } else { |
896 | + | info[i].thermalTime = globals->getRunTime(); |
897 | } | |
898 | ||
899 | info[i].resetIntegrator = 0; | |
# | Line 1365 | Line 1365 | void SimSetup::mpiMolDivide(void){ | |
1365 | int localMol, allMol; | |
1366 | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; | |
1367 | int local_rigid; | |
1368 | – | vector<int> globalAtomIndex; |
1368 | vector<int> globalMolIndex; | |
1369 | ||
1370 | mpiSim = new mpiSimulation(info); | |
1371 | ||
1372 | mpiSim->divideLabor(); | |
1373 | globalAtomIndex = mpiSim->getGlobalAtomIndex(); | |
1374 | < | globalMolIndex = mpiSim->getGlobalMolIndex(); |
1374 | > | //globalMolIndex = mpiSim->getGlobalMolIndex(); |
1375 | ||
1376 | // set up the local variables | |
1377 |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |