--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/15 16:18:26	1113
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/05/11 16:00:22	1154
@@ -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);
@@ -538,13 +538,13 @@ void SimSetup::makeMolecules(void){
 
   // clean up the forcefield
 
-  if (!globals->haveLJrcut()){
+  if (!globals->haveRcut()){
 
     the_ff->calcRcut();
 
   } else {
     
-    the_ff->setRcut( globals->getLJrcut() );
+    the_ff->setRcut( globals->getRcut() );
   }
 
   the_ff->cleanMe();
@@ -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;
@@ -987,39 +987,38 @@ void SimSetup::finalInfoCheck(void){
     MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
 #endif //is_mpi
 
-    double theEcr, theEst;
+    double theRcut, theRsw;
 
     if (globals->getUseRF()){
       info[i].useReactionField = 1;
 
-      if (!globals->haveECR()){
+      if (!globals->haveRcut()){
         sprintf(painCave.errMsg,
-                "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
+                "SimSetup Warning: No value was set for the cutoffRadius.\n"
                 "\tOOPSE will use a default value of 15.0 angstroms"
-                "\tfor the electrostaticCutoffRadius.\n");
+                "\tfor the cutoffRadius.\n");
         painCave.isFatal = 0;
         simError();
-        theEcr = 15.0;
+        theRcut = 15.0;
       }
       else{
-        theEcr = globals->getECR();
+        theRcut = globals->getRcut();
       }
 
-      if (!globals->haveEST()){
+      if (!globals->haveRsw()){
         sprintf(painCave.errMsg,
-                "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
+                "SimSetup Warning: No value was set for switchingRadius.\n"
                 "\tOOPSE will use a default value of\n"
-                "\t0.05 * electrostaticCutoffRadius\n"
-                "\tfor the electrostaticSkinThickness\n");
+                "\t0.95 * cutoffRadius for the switchingRadius\n");
         painCave.isFatal = 0;
         simError();
-        theEst = 0.05 * theEcr;
+        theRsw = 0.95 * theRcut;
       }
       else{
-        theEst = globals->getEST();
+        theRsw = globals->getRsw();
       }
 
-      info[i].setDefaultEcr(theEcr, theEst);
+      info[i].setDefaultRcut(theRcut, theRsw);
 
       if (!globals->haveDielectric()){
         sprintf(painCave.errMsg,
@@ -1033,34 +1032,35 @@ void SimSetup::finalInfoCheck(void){
     }
     else{
       if (usesDipoles || usesCharges){
-        if (!globals->haveECR()){
+
+        if (!globals->haveRcut()){
           sprintf(painCave.errMsg,
-                  "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
+                  "SimSetup Warning: No value was set for the cutoffRadius.\n"
                   "\tOOPSE will use a default value of 15.0 angstroms"
-                  "\tfor the electrostaticCutoffRadius.\n");
-	  painCave.isFatal = 0;
-	  simError();
-	  theEcr = 15.0;
-        }
+                  "\tfor the cutoffRadius.\n");
+          painCave.isFatal = 0;
+          simError();
+          theRcut = 15.0;
+      }
         else{
-          theEcr = globals->getECR();
+          theRcut = globals->getRcut();
         }
-	
-        if (!globals->haveEST()){
+        
+        if (!globals->haveRsw()){
           sprintf(painCave.errMsg,
-                  "SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
+                  "SimSetup Warning: No value was set for switchingRadius.\n"
                   "\tOOPSE will use a default value of\n"
-                  "\t0.05 * electrostaticCutoffRadius\n"
-                  "\tfor the electrostaticSkinThickness\n");
+                  "\t0.95 * cutoffRadius for the switchingRadius\n");
           painCave.isFatal = 0;
           simError();
-          theEst = 0.05 * theEcr;
+          theRsw = 0.95 * theRcut;
         }
         else{
-          theEst = globals->getEST();
+          theRsw = globals->getRsw();
         }
+        
+        info[i].setDefaultRcut(theRcut, theRsw);
 	
-        info[i].setDefaultEcr(theEcr, theEst);
       }
     }
   }
@@ -1365,14 +1365,13 @@ 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