--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/15 16:18:26	1113
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/28 22:06:29	1139
@@ -464,11 +464,11 @@ void SimSetup::makeMolecules(void){
             // used for the exclude list:
             
 #ifdef IS_MPI
-            exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
-            exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
+            exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
+            exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
 #else
-            exI = tempI + 1;
-            exJ = tempJ + 1;
+            exI = molInfo.myAtoms[tempI]->getIndex() + 1;
+            exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
 #endif
             
             info[k].excludes->addPair(exI, exJ);
@@ -834,7 +834,7 @@ void SimSetup::gatherInfo(void){
   }
 
   //check whether sample time, status time, thermal time and reset time are divisble by dt
-  if (!isDivisible(globals->getSampleTime(), globals->getDt())){
+  if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
     sprintf(painCave.errMsg,
             "Sample time is not divisible by dt.\n"
             "\tThis will result in samples that are not uniformly\n"
@@ -844,7 +844,7 @@ void SimSetup::gatherInfo(void){
     simError();    
   }
 
-  if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
+  if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
     sprintf(painCave.errMsg,
             "Status time is not divisible by dt.\n"
             "\tThis will result in status reports that are not uniformly\n"
@@ -880,12 +880,10 @@ void SimSetup::gatherInfo(void){
     if (globals->haveSampleTime()){
       info[i].sampleTime = globals->getSampleTime();
       info[i].statusTime = info[i].sampleTime;
-      info[i].thermalTime = info[i].sampleTime;
     }
     else{
       info[i].sampleTime = globals->getRunTime();
       info[i].statusTime = info[i].sampleTime;
-      info[i].thermalTime = info[i].sampleTime;
     }
 
     if (globals->haveStatusTime()){
@@ -894,6 +892,8 @@ void SimSetup::gatherInfo(void){
 
     if (globals->haveThermalTime()){
       info[i].thermalTime = globals->getThermalTime();
+    } else {
+      info[i].thermalTime = globals->getRunTime();
     }
 
     info[i].resetIntegrator = 0;
@@ -911,6 +911,8 @@ void SimSetup::gatherInfo(void){
 
     info[i].useInitXSstate = globals->getUseInitXSstate();
     info[i].orthoTolerance = globals->getOrthoBoxTolerance();
+    info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
+
     
   }
   
@@ -1365,14 +1367,13 @@ void SimSetup::mpiMolDivide(void){
   int localMol, allMol;
   int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
   int local_rigid;
-  vector<int> globalAtomIndex;
   vector<int> globalMolIndex;
 
   mpiSim = new mpiSimulation(info);
 
   mpiSim->divideLabor();
   globalAtomIndex = mpiSim->getGlobalAtomIndex();
-  globalMolIndex = mpiSim->getGlobalMolIndex();
+  //globalMolIndex = mpiSim->getGlobalMolIndex();
 
   // set up the local variables