--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2004/04/14 15:37:41	1108
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2004/04/22 03:29:30	1129
@@ -92,7 +92,6 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
   char *parseErr;
 
   vector<StuntDouble*> integrableObjects;
-  vector<StuntDouble*>::iterator iter;
 
   simnfo = the_simnfo;
 
@@ -141,7 +140,7 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
 
     integrableObjects = (simnfo->molecules[i]).getIntegrableObjects();
 
-    for(iter = integrableObjects.begin(); iter!= integrableObjects.end(); iter++)
+    for(j = 0; j < integrableObjects.size(); j++){
 
       eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
       if(eof_test == NULL){
@@ -154,15 +153,15 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
         simError();
       }
       
-      parseErr = parseDumpLine( read_buffer, *iter);
+      parseErr = parseDumpLine( read_buffer, integrableObjects[j]);
       if( parseErr != NULL ){
         strcpy( painCave.errMsg, parseErr );
         painCave.isFatal = 1;
         simError();
       }
+    }
   }
 
-
   // MPI Section of code..........
 #else //IS_MPI
 
@@ -176,7 +175,9 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
   int *MolToProcMap = mpiSim->getMolToProcMap();
   int localIndex;
   int nCurObj;
+  int nItems;
 
+  nTotObjs = simnfo->getTotIntegrableObjects();
   haveError = 0;
   if (worldRank == 0) {
 
@@ -188,12 +189,12 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
       simError();
     }
 
-    nTotObjs = atoi( read_buffer );
+    nItems = atoi( read_buffer );
 
     // Check to see that the number of integrable objects  in the intial configuration file is the
     // same as declared in simBass.
 
-    if( nTotObjs != simnfo->getTotIntegrableObjects()){
+    if( nTotObjs != nItems){
       sprintf( painCave.errMsg,
 	       "Initialize from File error. %s n_atoms, %d, "
 	       "does not match the BASS file's n_atoms, %d.\n",
@@ -256,7 +257,7 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
           
           if(haveError) nodeZeroError();
 
-          parseDumpLine(read_buffer, integrableObjects[i]);
+          parseDumpLine(read_buffer, integrableObjects[j]);
            
        }
 
@@ -265,7 +266,7 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
       else{
       //molecule belongs to slave nodes
 
-        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
+        MPI_Recv(&nCurObj, 1, MPI_INT, which_node,
 	       TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
       
        for(j=0; j < integrableObjects.size(); j++){
@@ -295,6 +296,17 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
   }
   else{
   //actions taken at slave nodes
+
+    MPI_Bcast(read_buffer, BUFFERSIZE, MPI_CHAR, 0, MPI_COMM_WORLD);
+
+    parseErr = parseCommentLine( read_buffer, simnfo);
+
+    if( parseErr != NULL ){
+      strcpy( painCave.errMsg, parseErr );
+      haveError = 1;
+      simError();
+    }
+  
     for (i=0 ; i < mpiSim->getTotNmol(); i++) {
       which_node = MolToProcMap[i];
       
@@ -313,8 +325,8 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
 
         nCurObj = integrableObjects.size();
         
-        MPI_Recv(&nCurObj, 1, MPI_INT, 0,
-                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD, &istatus);
+        MPI_Send(&nCurObj, 1, MPI_INT, 0,
+                        TAKE_THIS_TAG_INT, MPI_COMM_WORLD);
 
         for(j = 0; j < integrableObjects.size(); j++){
 
@@ -618,7 +630,7 @@ char* InitializeFromFile::parseCommentLine(char* readL
     
     //push eta into SimInfo::properties which can be
     //retrieved by integrator later
-    //entry_plug->setBoxM( theBoxMat3 );
+    
     DoubleArrayData* etaValue = new DoubleArrayData();
     etaValue->setID(ETAVALUE_ID);
     etaValue->setData(eta, 9);