--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/13 16:26:03	1104
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/28 22:06:29	1139
@@ -147,13 +147,6 @@ void SimSetup::createSim(void){
   // make the output filenames
 
   makeOutNames();
-
-  if (globals->haveMinimizer())
-    // make minimizer
-    makeMinimizer();
-  else
-    // make the integrator
-    makeIntegrator();
   
 #ifdef IS_MPI
   mpiSim->mpiRefresh();
@@ -162,6 +155,14 @@ void SimSetup::createSim(void){
   // initialize the Fortran
 
   initFortran();
+
+  if (globals->haveMinimizer())
+    // make minimizer
+    makeMinimizer();
+  else
+    // make the integrator
+    makeIntegrator();
+
 }
 
 
@@ -190,6 +191,8 @@ void SimSetup::makeMolecules(void){
   set<int> skipList;
 
   double phi, theta, psi;
+  char* molName;
+  char rbName[100];
 
   //init the forceField paramters
 
@@ -206,6 +209,7 @@ void SimSetup::makeMolecules(void){
 
     for (i = 0; i < info[k].n_mol; i++){
       stampID = info[k].molecules[i].getStampID();
+      molName = comp_stamps[stampID]->getID();
 
       molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
       molInfo.nBonds = comp_stamps[stampID]->getNBonds();
@@ -259,13 +263,13 @@ void SimSetup::makeMolecules(void){
         else{
 
           molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
+
         }
 
         molInfo.myAtoms[j]->setType(currentAtom->getType());
-
 #ifdef IS_MPI
 
-        molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
+        molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
 
 #endif // is_mpi
       } 
@@ -406,6 +410,9 @@ void SimSetup::makeMolecules(void){
         info[k].excludes->addPair(exK, exL);
       }
 
+      
+      molInfo.myRigidBodies.clear();
+      
       for (j = 0; j < molInfo.nRigidBodies; j++){
 
         currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
@@ -414,6 +421,9 @@ void SimSetup::makeMolecules(void){
         // Create the Rigid Body:
 
         myRB = new RigidBody();
+
+        sprintf(rbName,"%s_RB_%d", molName, j);
+        myRB->setType(rbName);
         
         for (rb1 = 0; rb1 < nMembers; rb1++) {
 
@@ -454,11 +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);
@@ -473,6 +483,9 @@ void SimSetup::makeMolecules(void){
 
       // After this is all set up, scan through the atoms to 
       // see if they can be added to the integrableObjects:
+
+      molInfo.myIntegrableObjects.clear();
+      
 
       for (j = 0; j < molInfo.nAtoms; j++){
 
@@ -821,7 +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"
@@ -831,7 +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"
@@ -867,12 +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()){
@@ -881,6 +892,8 @@ void SimSetup::gatherInfo(void){
 
     if (globals->haveThermalTime()){
       info[i].thermalTime = globals->getThermalTime();
+    } else {
+      info[i].thermalTime = globals->getRunTime();
     }
 
     info[i].resetIntegrator = 0;
@@ -898,6 +911,8 @@ void SimSetup::gatherInfo(void){
 
     info[i].useInitXSstate = globals->getUseInitXSstate();
     info[i].orthoTolerance = globals->getOrthoBoxTolerance();
+    info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
+
     
   }
   
@@ -951,6 +966,7 @@ void SimSetup::finalInfoCheck(void){
 void SimSetup::finalInfoCheck(void){
   int index;
   int usesDipoles;
+  int usesCharges;
   int i;
 
   for (i = 0; i < nInfo; i++){
@@ -962,7 +978,12 @@ void SimSetup::finalInfoCheck(void){
       usesDipoles = (info[i].atoms[index])->hasDipole();
       index++;
     }
-
+    index = 0;
+    usesCharges = 0;
+    while ((index < info[i].n_atoms) && !usesCharges){
+      usesCharges= (info[i].atoms[index])->hasCharge();
+      index++;
+    }
 #ifdef IS_MPI
     int myUse = usesDipoles;
     MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
@@ -1013,7 +1034,7 @@ void SimSetup::finalInfoCheck(void){
       info[i].dielectric = globals->getDielectric();
     }
     else{
-      if (usesDipoles){
+      if (usesDipoles || usesCharges){
         if (!globals->haveECR()){
           sprintf(painCave.errMsg,
                   "SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
@@ -1346,10 +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> globalMolIndex;
 
   mpiSim = new mpiSimulation(info);
 
-  globalIndex = mpiSim->divideLabor();
+  mpiSim->divideLabor();
+  globalAtomIndex = mpiSim->getGlobalAtomIndex();
+  //globalMolIndex = mpiSim->getGlobalMolIndex();
 
   // set up the local variables 
 
@@ -1363,7 +1387,7 @@ void SimSetup::mpiMolDivide(void){
   local_bends = 0;
   local_torsions = 0;
   local_rigid = 0;
-  globalAtomIndex = 0;
+  globalAtomCounter = 0;
 
   for (i = 0; i < n_components; i++){
     for (j = 0; j < components_nmol[i]; j++){
@@ -1376,8 +1400,8 @@ void SimSetup::mpiMolDivide(void){
         localMol++;
       }      
       for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
-        info[0].molMembershipArray[globalAtomIndex] = allMol;
-        globalAtomIndex++;
+        info[0].molMembershipArray[globalAtomCounter] = allMol;
+        globalAtomCounter++;
       }
 
       allMol++;
@@ -1445,15 +1469,15 @@ void SimSetup::makeSysArrays(void){
 #else // is_mpi
 
     molIndex = 0;
-    globalAtomIndex = 0;
+    globalAtomCounter = 0;
     for (i = 0; i < n_components; i++){
       for (j = 0; j < components_nmol[i]; j++){
         the_molecules[molIndex].setStampID(i);
         the_molecules[molIndex].setMyIndex(molIndex);
         the_molecules[molIndex].setGlobalIndex(molIndex);
         for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
-          info[l].molMembershipArray[globalAtomIndex] = molIndex;
-          globalAtomIndex++;
+          info[l].molMembershipArray[globalAtomCounter] = molIndex;
+          globalAtomCounter++;
         }
         molIndex++;
       }