--- trunk/OOPSE/libmdtools/SimSetup.cpp	2003/09/22 21:23:25	780
+++ trunk/OOPSE/libmdtools/SimSetup.cpp	2003/09/25 19:27:15	787
@@ -90,7 +90,6 @@ void SimSetup::createSim(void){
 #endif // is_mpi
 
 void SimSetup::createSim(void){
-  int i, j, k, globalAtomIndex;
 
   // gather all of the information from the Bass file
 
@@ -129,7 +128,7 @@ void SimSetup::makeMolecules(void){
 
 
 void SimSetup::makeMolecules(void){
-  int k, l;
+  int k;
   int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
   molInit molInfo;
   DirectionalAtom* dAtom;
@@ -551,7 +550,7 @@ void SimSetup::gatherInfo(void){
 
 
 void SimSetup::gatherInfo(void){
-  int i, j, k;
+  int i;
 
   ensembleCase = -1;
   ffCase = -1;
@@ -914,7 +913,6 @@ void SimSetup::initSystemCoords(void){
     if (worldRank == 0){
 #endif //is_mpi
       inName = globals->getInitialConfig();
-      double* tempDouble = new double[1000000];
       fileInit = new InitializeFromFile(inName);
 #ifdef IS_MPI
     }
@@ -932,7 +930,7 @@ void SimSetup::initSystemCoords(void){
 
     sprintf(painCave.errMsg,
             "Cannot intialize a parallel simulation without an initial configuration file.\n");
-    painCave.isFatal;
+    painCave.isFatal = 1;;
     simError();
 
 #else
@@ -1158,7 +1156,7 @@ void SimSetup::calcSysValues(void){
 }
 
 void SimSetup::calcSysValues(void){
-  int i, j, k;
+  int i;
 
   int* molMembershipArray;
 
@@ -1257,7 +1255,11 @@ void SimSetup::makeSysArrays(void){
 
 
 void SimSetup::makeSysArrays(void){
-  int i, j, k, l;
+ 
+#ifndef IS_MPI
+  int k, j;
+#endif // is_mpi
+  int i, l;
 
   Atom** the_atoms;
   Molecule* the_molecules;
@@ -1340,6 +1342,7 @@ void SimSetup::makeIntegrator(void){
 void SimSetup::makeIntegrator(void){
   int k;
 
+  NVE<RealIntegrator>* myNVE = NULL;
   NVT<RealIntegrator>* myNVT = NULL;
   NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
   NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
@@ -1349,10 +1352,13 @@ void SimSetup::makeIntegrator(void){
       case NVE_ENS:
         if (globals->haveZconstraints()){
           setupZConstraint(info[k]);
-          new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
+          myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
         }
-        else
-          new NVE<RealIntegrator>(&(info[k]), the_ff);
+        else{
+          myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
+	}
+	
+	info->the_integrator = myNVE;
         break;
 
       case NVT_ENS:
@@ -1374,6 +1380,8 @@ void SimSetup::makeIntegrator(void){
           painCave.isFatal = 1;
           simError();
         }
+
+	info->the_integrator = myNVT;
         break;
 
       case NPTi_ENS:
@@ -1415,6 +1423,8 @@ void SimSetup::makeIntegrator(void){
           painCave.isFatal = 1;
           simError();
         }
+
+	info->the_integrator = myNPTi;
         break;
 
       case NPTf_ENS:
@@ -1456,6 +1466,8 @@ void SimSetup::makeIntegrator(void){
           painCave.isFatal = 1;
           simError();
         }
+
+	info->the_integrator = myNPTf;
         break;
 
       default: