--- trunk/src/brains/SimCreator.cpp	2008/09/10 18:11:32	1287
+++ trunk/src/brains/SimCreator.cpp	2009/11/25 20:02:06	1390
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,15 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 /**
@@ -79,7 +79,7 @@
 #include "math/ParallelRandNumGen.hpp"
 #endif
 
-namespace oopse {
+namespace OpenMD {
   
   Globals* SimCreator::parseFile(std::istream& rawMetaDataStream, const std::string& filename, int startOfMetaDataBlock ){
     Globals* simParams = NULL;
@@ -108,7 +108,7 @@ namespace oopse {
       } else {
         //get stream size
         commStatus = MPI_Bcast(&streamSize, 1, MPI_LONG, masterNode, MPI_COMM_WORLD);   
-                
+
         char* buf = new char[streamSize];
         assert(buf);
                 
@@ -116,7 +116,7 @@ namespace oopse {
         commStatus = MPI_Bcast(buf, streamSize, MPI_CHAR, masterNode, MPI_COMM_WORLD); 
                 
         ppStream.str(buf);
-        delete buf;
+        delete [] buf;
 
       }
 #endif            
@@ -214,7 +214,7 @@ namespace oopse {
       painCave.isFatal = 1;
       simError();        
     }
-    catch (OOPSEException& e) {
+    catch (OpenMDException& e) {
       sprintf(painCave.errMsg, 
               "%s\n",
               e.getMessage().c_str());
@@ -262,10 +262,16 @@ namespace oopse {
       mdFile_.getline(buffer, bufferSize);
       ++lineNo;
       std::string line = trimLeftCopy(buffer);
-      i = CaseInsensitiveFind(line, "<OOPSE");
+      i = CaseInsensitiveFind(line, "<OpenMD");
       if (static_cast<size_t>(i) == string::npos) {
+        // try the older file strings to see if that works:
+        i = CaseInsensitiveFind(line, "<OOPSE");
+      }
+      
+      if (static_cast<size_t>(i) == string::npos) {
+        // still no luck!
         sprintf(painCave.errMsg, 
-                "SimCreator: File: %s is not an OOPSE file!\n", 
+                "SimCreator: File: %s is not a valid OpenMD file!\n", 
                 mdFileName.c_str()); 
         painCave.isFatal = 1; 
         simError(); 
@@ -471,7 +477,7 @@ namespace oopse {
               "\tthe number of molecules.  This will not result in a \n"
               "\tusable division of atoms for force decomposition.\n"
               "\tEither try a smaller number of processors, or run the\n"
-              "\tsingle-processor version of OOPSE.\n", nProcessors, nGlobalMols);
+              "\tsingle-processor version of OpenMD.\n", nProcessors, nGlobalMols);
       
       painCave.isFatal = 1;
       simError();
@@ -722,7 +728,7 @@ namespace oopse {
     // to get the full globalGroupMembership array (We think).
     // This would be prettier if we could use MPI_IN_PLACE like the MPI-2
     // docs said we could.
-    std::vector<int> tmpGroupMembership(nGlobalAtoms, 0);
+    std::vector<int> tmpGroupMembership(info->getNGlobalAtoms(), 0);
     MPI_Allreduce(&globalGroupMembership[0], &tmpGroupMembership[0], nGlobalAtoms,
                   MPI_INT, MPI_SUM, MPI_COMM_WORLD);
     info->setGlobalGroupMembership(tmpGroupMembership);
@@ -734,14 +740,13 @@ namespace oopse {
     std::vector<int> globalMolMembership(info->getNGlobalAtoms(), 0);
     
     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();
       }
     }
     
 #ifdef IS_MPI
-    std::vector<int> tmpMolMembership(nGlobalAtoms, 0);
+    std::vector<int> tmpMolMembership(info->getNGlobalAtoms(), 0);
     
     MPI_Allreduce(&globalMolMembership[0], &tmpMolMembership[0], nGlobalAtoms,
                   MPI_INT, MPI_SUM, MPI_COMM_WORLD);
@@ -767,28 +772,28 @@ namespace oopse {
     std::vector<int> numIntegrableObjectsPerMol = nIOPerMol;
 #endif    
 
- std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
-
-int startingIndex = 0;
- for (int i = 0; i < info->getNGlobalMolecules(); i++) {
-  startingIOIndexForMol[i] = startingIndex;
-  startingIndex += numIntegrableObjectsPerMol[i];
- }
-
- std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
- for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
+    std::vector<int> startingIOIndexForMol(info->getNGlobalMolecules());
+    
+    int startingIndex = 0;
+    for (int i = 0; i < info->getNGlobalMolecules(); i++) {
+      startingIOIndexForMol[i] = startingIndex;
+      startingIndex += numIntegrableObjectsPerMol[i];
+    }
+    
+    std::vector<StuntDouble*> IOIndexToIntegrableObject(info->getNGlobalIntegrableObjects(), (StuntDouble*)NULL);
+    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
       int myGlobalIndex = mol->getGlobalIndex();
       int globalIO = startingIOIndexForMol[myGlobalIndex];
       for (StuntDouble* integrableObject = mol->beginIntegrableObject(ioi); integrableObject != NULL;
            integrableObject = mol->nextIntegrableObject(ioi)) {
-            integrableObject->setGlobalIntegrableObjectIndex(globalIO);
-            IOIndexToIntegrableObject[globalIO] = integrableObject;
-            globalIO++;
+        integrableObject->setGlobalIntegrableObjectIndex(globalIO);
+        IOIndexToIntegrableObject[globalIO] = integrableObject;
+        globalIO++;
       }
     }
-
-  info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
-  
+    
+    info->setIOIndexToIntegrableObject(IOIndexToIntegrableObject);
+    
   }
   
   void SimCreator::loadCoordinates(SimInfo* info, const std::string& mdFileName) {
@@ -814,6 +819,6 @@ int startingIndex = 0;
     info->getSnapshotManager()->advance();
   }
   
-} //end namespace oopse
+} //end namespace OpenMD