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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp
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Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 1113 by tim, Thu Apr 15 16:18:26 2004 UTC vs.
Revision 1139 by gezelter, Wed Apr 28 22:06:29 2004 UTC

# 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 911 | Line 911 | void SimSetup::gatherInfo(void){
911  
912      info[i].useInitXSstate = globals->getUseInitXSstate();
913      info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914 +    info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
915 +
916      
917    }
918    
# Line 1365 | Line 1367 | void SimSetup::mpiMolDivide(void){
1367    int localMol, allMol;
1368    int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1369    int local_rigid;
1368 –  vector<int> globalAtomIndex;
1370    vector<int> globalMolIndex;
1371  
1372    mpiSim = new mpiSimulation(info);
1373  
1374    mpiSim->divideLabor();
1375    globalAtomIndex = mpiSim->getGlobalAtomIndex();
1376 <  globalMolIndex = mpiSim->getGlobalMolIndex();
1376 >  //globalMolIndex = mpiSim->getGlobalMolIndex();
1377  
1378    // set up the local variables
1379  

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