--- trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/12 20:32:20	1097
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2004/04/15 16:18:26	1113
@@ -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();
@@ -162,12 +155,20 @@ void SimSetup::createSim(void){
   // initialize the Fortran
 
   initFortran();
+
+  if (globals->haveMinimizer())
+    // make minimizer
+    makeMinimizer();
+  else
+    // make the integrator
+    makeIntegrator();
+
 }
 
 
 void SimSetup::makeMolecules(void){
   int i, j, k;
-  int exI, exJ, exK, exL, slI;
+  int exI, exJ, exK, exL, slI, slJ;
   int tempI, tempJ, tempK, tempL;
   int molI;
   int stampID, atomOffset, rbOffset;
@@ -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++) {
 
@@ -465,8 +475,44 @@ void SimSetup::makeMolecules(void){
             
           }
         }
+
+        molInfo.myRigidBodies.push_back(myRB);
+        info[k].rigidBodies.push_back(myRB);
       }
       
+
+      // 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++){
+
+#ifdef IS_MPI
+        slJ = molInfo.myAtoms[j]->getGlobalIndex();
+#else
+        slJ = j+atomOffset;
+#endif
+
+        // if they aren't on the skip list, then they can be integrated
+
+        if (skipList.find(slJ) == skipList.end()) {
+          mySD = (StuntDouble *) molInfo.myAtoms[j];
+          info[k].integrableObjects.push_back(mySD);
+          molInfo.myIntegrableObjects.push_back(mySD);
+        }
+      }
+
+      // all rigid bodies are integrated:
+
+      for (j = 0; j < molInfo.nRigidBodies; j++) {
+        mySD = (StuntDouble *) molInfo.myRigidBodies[j];
+        info[k].integrableObjects.push_back(mySD);      
+        molInfo.myIntegrableObjects.push_back(mySD);
+      }
+    
+      
       // send the arrays off to the forceField for init.
       
       the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
@@ -482,28 +528,7 @@ void SimSetup::makeMolecules(void){
       delete[] theBonds;
       delete[] theBends;
       delete[] theTorsions;
-    }
-
-    // build up the integrableObjects vector:
-
-    for (i = 0; i < info[k].n_atoms; i++) {
-      
-#ifdef IS_MPI
-      slI = info[k].atoms[i]->getGlobalIndex();
-#else
-      slI = i;
-#endif
-
-      if (skipList.find(slI) == skipList.end()) {
-        mySD = (StuntDouble *) info[k].atoms[i];
-        info[k].integrableObjects.push_back(mySD);
-      }
-    }
-    for (i = 0; i < info[k].rigidBodies.size(); i++) {
-      mySD = (StuntDouble *) info[k].rigidBodies[i];
-      info[k].integrableObjects.push_back(mySD);      
-    }
-    
+    }    
   }
 
 #ifdef IS_MPI
@@ -939,6 +964,7 @@ void SimSetup::finalInfoCheck(void){
 void SimSetup::finalInfoCheck(void){
   int index;
   int usesDipoles;
+  int usesCharges;
   int i;
 
   for (i = 0; i < nInfo; i++){
@@ -950,7 +976,12 @@ 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);
@@ -1001,7 +1032,7 @@ 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"
@@ -1334,10 +1365,14 @@ 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);
 
-  globalIndex = mpiSim->divideLabor();
+  mpiSim->divideLabor();
+  globalAtomIndex = mpiSim->getGlobalAtomIndex();
+  globalMolIndex = mpiSim->getGlobalMolIndex();
 
   // set up the local variables 
 
@@ -1351,7 +1386,7 @@ 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++){
@@ -1364,8 +1399,8 @@ 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++;
@@ -1433,15 +1468,15 @@ 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++;
       }