--- trunk/src/brains/SimCreator.cpp	2012/09/10 18:38:44	1796
+++ trunk/src/brains/SimCreator.cpp	2012/11/08 14:23:43	1810
@@ -255,11 +255,28 @@ namespace OpenMD {
     std::string mdRawData;
     int metaDataBlockStart = -1;
     int metaDataBlockEnd = -1;
-    int i;
+    int i, j;
     streamoff mdOffset(0);
     int mdFileVersion;
 
+    // Create a string for embedding the version information in the MetaData
+    std::string version;
+    version.assign("## Last run using OpenMD Version: ");
+    version.append(OPENMD_VERSION_MAJOR);
+    version.append(".");
+    version.append(OPENMD_VERSION_MINOR);
 
+    std::string svnrev;
+    //convert a macro from compiler to a string in c++
+    STR_DEFINE(svnrev, SVN_REV );
+    version.append(" Revision: ");
+    // If there's no SVN revision, just call this the RELEASE revision.
+    if (!svnrev.empty()) {
+      version.append(svnrev);
+    } else {
+      version.append("RELEASE");
+    }
+   
 #ifdef IS_MPI            
     const int masterNode = 0;
     if (worldRank == masterNode) {
@@ -354,12 +371,23 @@ namespace OpenMD {
 
       mdRawData.clear();
 
+      bool foundVersion = false;
+
       for (int i = 0; i < metaDataBlockEnd - metaDataBlockStart - 1; ++i) {
         mdFile_.getline(buffer, bufferSize);
-        mdRawData += buffer;
+        std::string line = trimLeftCopy(buffer);
+        j = CaseInsensitiveFind(line, "## Last run using OpenMD Version");
+        if (static_cast<size_t>(j) != string::npos) {
+          foundVersion = true;
+          mdRawData += version;
+        } else {
+          mdRawData += buffer;
+        }
         mdRawData += "\n";
       }
-
+      
+      if (!foundVersion) mdRawData += version + "\n";
+      
       mdFile_.close();
 
 #ifdef IS_MPI
@@ -544,6 +572,7 @@ namespace OpenMD {
       nTarget = (int)(precast + 0.5);
       
       for(i = 0; i < nGlobalMols; i++) {
+
         done = 0;
         loops = 0;
         
@@ -568,13 +597,15 @@ 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",
+
+            sprintf(painCave.errMsg,
+                    "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;
@@ -619,13 +650,14 @@ namespace OpenMD {
       }
       
       delete myRandom;
-      
+
       // Spray out this nonsense to all other processors:
       MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
     } else {
       
       // Listen to your marching orders from processor 0:
       MPI::COMM_WORLD.Bcast(&molToProcMap[0], nGlobalMols, MPI::INT, 0);
+
     }
     
     info->setMolToProcMap(molToProcMap);
@@ -783,6 +815,7 @@ namespace OpenMD {
     int beginRigidBodyIndex;
     int beginCutoffGroupIndex;
     int nGlobalAtoms = info->getNGlobalAtoms();
+    int nGlobalRigidBodies = info->getNGlobalRigidBodies();
     
     beginAtomIndex = 0;
     //rigidbody's index begins right after atom's
@@ -858,18 +891,25 @@ namespace OpenMD {
 #endif
     
     //fill molMembership
-    std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
+    std::vector<int> globalMolMembership(info->getNGlobalAtoms() + 
+                                         info->getNGlobalRigidBodies(), 0);
     
-    for(mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
+    for(mol = info->beginMolecule(mi); mol != NULL; 
+        mol = info->nextMolecule(mi)) {
       for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
         globalMolMembership[atom->getGlobalIndex()] = mol->getGlobalIndex();
       }
+      for (rb = mol->beginRigidBody(ri); rb != NULL; 
+           rb = mol->nextRigidBody(ri)) {
+        globalMolMembership[rb->getGlobalIndex()] = mol->getGlobalIndex();
+      }
     }
     
 #ifdef IS_MPI
-    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
+    std::vector<int> tmpMolMembership(info->getNGlobalAtoms() + 
+                                      info->getNGlobalRigidBodies(), 0);
     MPI::COMM_WORLD.Allreduce(&globalMolMembership[0], &tmpMolMembership[0], 
-                              nGlobalAtoms,
+                              nGlobalAtoms + nGlobalRigidBodies,
                               MPI::INT, MPI::SUM);
     
     info->setGlobalMolMembership(tmpMolMembership);
@@ -881,7 +921,8 @@ namespace OpenMD {
     // here the molecules are listed by their global indices.
 
     std::vector<int> nIOPerMol(info->getNGlobalMolecules(), 0);
-    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
+    for (mol = info->beginMolecule(mi); mol != NULL;
+         mol = info->nextMolecule(mi)) {
       nIOPerMol[mol->getGlobalIndex()] = mol->getNIntegrableObjects();       
     }
     
@@ -902,7 +943,8 @@ namespace OpenMD {
     }
     
     std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
-    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
+    for (mol = info->beginMolecule(mi); mol != NULL; 
+         mol = info->nextMolecule(mi)) {
       int myGlobalIndex = mol->getGlobalIndex();
       int globalIO = startingIOIndexForMol[myGlobalIndex];
       for (StuntDouble* sd = mol->beginIntegrableObject(ioi); sd != NULL;