--- trunk/src/brains/SimCreator.cpp	2012/08/30 17:18:22	1790
+++ trunk/src/brains/SimCreator.cpp	2012/10/01 18:21:15	1801
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ * copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
@@ -100,33 +100,33 @@ namespace OpenMD {
 #ifdef IS_MPI            
       int streamSize;
       const int masterNode = 0;
-      int commStatus;
+
       if (worldRank == masterNode) {
-        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
+        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
 #endif                 
         SimplePreprocessor preprocessor;
-        preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, ppStream);
+        preprocessor.preprocess(rawMetaDataStream, filename, startOfMetaDataBlock, 
+                                ppStream);
                 
 #ifdef IS_MPI            
         //brocasting the stream size
         streamSize = ppStream.str().size() +1;
-        commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);                   
-
-        commStatus = MPI_Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())), streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); 
-            
+        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
+        MPI::COMM_WORLD.Bcast(static_cast<void*>(const_cast<char*>(ppStream.str().c_str())),
+                              streamSize, MPI::CHAR, masterNode);
                 
       } else {
 
-        commStatus = MPI_Bcast(&mdFileVersion, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
+        MPI::COMM_WORLD.Bcast(&mdFileVersion, 1, MPI::INT, masterNode);
 
         //get stream size
-        commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);   
+        MPI::COMM_WORLD.Bcast(&streamSize, 1, MPI::LONG, masterNode);
 
         char* buf = new char[streamSize];
         assert(buf);
                 
         //receive file content
-        commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); 
+        MPI::COMM_WORLD.Bcast(buf, streamSize, MPI::CHAR, masterNode);
                 
         ppStream.str(buf);
         delete [] buf;
@@ -499,7 +499,6 @@ namespace OpenMD {
     int nTarget;
     int done;
     int i;
-    int j;
     int loops;
     int which_proc;
     int nProcessors;
@@ -507,7 +506,7 @@ namespace OpenMD {
     int nGlobalMols = info->getNGlobalMolecules();
     std::vector<int> molToProcMap(nGlobalMols, -1); // default to an error condition:
     
-    MPI_Comm_size(MPI_COMM_WORLD, &nProcessors);
+    nProcessors = MPI::COMM_WORLD.Get_size();
     
     if (nProcessors > nGlobalMols) {
       sprintf(painCave.errMsg,
@@ -545,6 +544,7 @@ namespace OpenMD {
       nTarget = (int)(precast + 0.5);
       
       for(i = 0; i < nGlobalMols; i++) {
+
         done = 0;
         loops = 0;
         
@@ -569,13 +569,15 @@ namespace OpenMD {
           // and be done with it. 
           
           if (loops > 100) {
+
             sprintf(painCave.errMsg,
-                    "I've tried 100 times to assign molecule %d to a "
-                    " processor, but can't find a good spot.\n"
-                    "I'm assigning it at random to processor %d.\n",
-                    i, which_proc);
-            
+                    "There have been 100 attempts to assign molecule %d to an\n"
+                    "\tunderworked processor, but there's no good place to\n"
+                    "\tleave it.  OpenMD is assigning it at random to processor %d.\n",
+                    i, which_proc);
+           
             painCave.isFatal = 0;
+            painCave.severity = OPENMD_INFO;
             simError();
             
             molToProcMap[i] = which_proc;
@@ -620,15 +622,14 @@ namespace OpenMD {
       }
       
       delete myRandom;
-      
+
       // Spray out this nonsense to all other processors:
-      
-      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
+      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
     } else {
       
       // Listen to your marching orders from processor 0:
-      
-      MPI_Bcast(&molToProcMap[0], nGlobalMols, MPI_INT, 0, MPI_COMM_WORLD);
+      MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
+
     }
     
     info->setMolToProcMap(molToProcMap);
@@ -852,8 +853,9 @@ namespace OpenMD {
     // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
     // docs said we could.
     std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
-    MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
-                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+    MPI::COMM_WORLD.Allreduce(&globalGroupMembership[0], 
+                              &tmpGroupMembership[0], nGlobalAtoms,
+                              MPI::INT, MPI::SUM);
     info->setGlobalGroupMembership(tmpGroupMembership);
 #else
     info->setGlobalGroupMembership(globalGroupMembership);
@@ -870,10 +872,10 @@ namespace OpenMD {
     
 #ifdef IS_MPI
     std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
+    MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], 
+                              nGlobalAtoms,
+                              MPI::INT, MPI::SUM);
     
-    MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
-                  MPI_INT, MPI_SUM, MPI_COMM_WORLD);
-    
     info->setGlobalMolMembership(tmpMolMembership);
 #else
     info->setGlobalMolMembership(globalMolMembership);
@@ -889,8 +891,8 @@ namespace OpenMD {
     
 #ifdef IS_MPI
     std::vector<int> numIntegrableObjectsPerMol(info->getNGlobalMolecules(), 0);
-    MPI_Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], 
-                  info->getNGlobalMolecules(), MPI_INT, MPI_SUM, MPI_COMM_WORLD);
+    MPI::COMM_WORLD.Allreduce(&nIOPerMol[0], &numIntegrableObjectsPerMol[0], 
+                              info->getNGlobalMolecules(), MPI::INT, MPI::SUM);
 #else
     std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
 #endif    
@@ -920,10 +922,7 @@ namespace OpenMD {
   }
   
   void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
-    Globals* simParams;
 
-    simParams = info->getSimParams();
-    
     DumpReader reader(info, mdFileName);
     int nframes = reader.getNFrames();