--- trunk/src/io/RestReader.cpp	2010/01/22 21:31:12	1409
+++ branches/development/src/io/RestReader.cpp	2013/05/17 14:41:42	1875
@@ -35,8 +35,9 @@
  *                                                                      
  * [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).                        
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */ 
 
  
@@ -67,7 +68,7 @@ namespace OpenMD { 
 namespace OpenMD { 
 
   void RestReader::scanFile(){
-    int lineNo = 0; 
+
     std::streampos prevPos;
     std::streampos  currPos;
     
@@ -81,7 +82,7 @@ namespace OpenMD { 
       prevPos = currPos;
       
       bool foundOpenSnapshotTag = false;
-      
+      int lineNo = 0;       
       while(!foundOpenSnapshotTag && inFile_->getline(buffer, bufferSize)) {
         ++lineNo;
         
@@ -96,7 +97,7 @@ namespace OpenMD { 
       
 #ifdef IS_MPI 
     }
-    MPI_Bcast(&framePos_, 1, MPI_INT, 0, MPI_COMM_WORLD); 
+    MPI::COMM_WORLD.Bcast(&framePos_, 1, MPI::INT, 0);
 #endif // is_mpi 
   } 
 
@@ -131,17 +132,18 @@ namespace OpenMD { 
       }
       
       int sendBufferSize = sendBuffer.size();
-      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
-      MPI_Bcast((void *)sendBuffer.c_str(), sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
+      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
+      MPI::COMM_WORLD.Bcast((void *)sendBuffer.c_str(), sendBufferSize, 
+                            MPI::CHAR, masterNode);
       
       sstream.str(sendBuffer);
     } else {
       int sendBufferSize;
-      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
+      MPI::COMM_WORLD.Bcast(&sendBufferSize, 1, MPI::INT, masterNode);
       char * recvBuffer = new char[sendBufferSize+1];
       assert(recvBuffer);
       recvBuffer[sendBufferSize] = '\0';
-      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
+      MPI::COMM_WORLD.Bcast(recvBuffer, sendBufferSize, MPI::CHAR, masterNode);
       sstream.str(recvBuffer);
       delete [] recvBuffer;
     }      
@@ -279,9 +281,9 @@ namespace OpenMD { 
 
     int index = tokenizer.nextTokenAsInt();
 
-    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
+    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
 
-    if (integrableObject == NULL) {
+    if (sd == NULL) {
       return;
     }
   
@@ -309,7 +311,7 @@ namespace OpenMD { 
       }
 
       case 'q' : {
-        if (integrableObject->isDirectional()) { 
+        if (sd->isDirectional()) { 
           
           q[0] = tokenizer.nextTokenAsDouble(); 
           q[1] = tokenizer.nextTokenAsDouble(); 
@@ -331,7 +333,7 @@ namespace OpenMD { 
       }  
       case 'j' : {
         Vector3d ji;
-        if (integrableObject->isDirectional()) {
+        if (sd->isDirectional()) {
           ji[0] = tokenizer.nextTokenAsDouble(); 
           ji[1] = tokenizer.nextTokenAsDouble(); 
           ji[2] = tokenizer.nextTokenAsDouble(); 
@@ -365,8 +367,7 @@ namespace OpenMD { 
       all_pos_[index] = pos;      
         
       // is this io restrained?
-      GenericData* data = integrableObject->getPropertyByName("Restraint");
-      ObjectRestraint* oRest;
+      GenericData* data = sd->getPropertyByName("Restraint");
       
       if (data != NULL) {
         // make sure we can reinterpret the generic data as restraint data:
@@ -374,9 +375,9 @@ namespace OpenMD { 
         if (restData != NULL) {
           // make sure we can reinterpet the restraint data as a pointer to
             // an ObjectRestraint:
-          oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
+          ObjectRestraint* oRest = dynamic_cast<ObjectRestraint*>(restData->getData());
           if (oRest != NULL) {          
-            if (integrableObject->isDirectional()) {
+            if (sd->isDirectional()) {
               oRest->setReferenceStructure(pos, q.toRotationMatrix3());
             } else {                           
               oRest->setReferenceStructure(pos);