--- trunk/src/io/DumpReader.cpp	2012/08/22 02:28:28	1782
+++ trunk/src/io/DumpReader.cpp	2013/07/03 20:21:00	1897
@@ -35,7 +35,7 @@
  *                                                                      
  * [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).          
+ * [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).
  */
@@ -75,7 +75,8 @@ namespace OpenMD { 
     if (worldRank == 0) { 
 #endif 
       
-      inFile_ = new std::ifstream(filename_.c_str()); 
+      inFile_ = new std::ifstream(filename_.c_str(),   
+                                  ifstream::in | ifstream::binary); 
       
       if (inFile_->fail()) { 
 	sprintf(painCave.errMsg, 
@@ -127,7 +128,7 @@ namespace OpenMD { 
   } 
    
   void DumpReader::scanFile(void) { 
-    int lineNo = 0; 
+
     std::streampos prevPos;
     std::streampos  currPos; 
     
@@ -140,7 +141,8 @@ namespace OpenMD { 
       prevPos = currPos;
       bool foundOpenSnapshotTag = false;
       bool foundClosedSnapshotTag = false;
-      bool foundOpenSiteDataTag = false;
+
+      int lineNo = 0; 
       while(inFile_->getline(buffer, bufferSize)) {
         ++lineNo;
         
@@ -201,7 +203,7 @@ namespace OpenMD { 
 #ifdef IS_MPI 
     } 
      
-    MPI_Bcast(&nframes_, 1, MPI_INT, 0, MPI_COMM_WORLD); 
+    MPI::COMM_WORLD.Bcast(&nframes_, 1, MPI::INT, 0); 
     
 #endif // is_mpi 
     
@@ -226,7 +228,9 @@ namespace OpenMD { 
       needVel_ = false; 
     } 
      
-    if (storageLayout & DataStorage::dslAmat || storageLayout & DataStorage::dslElectroFrame) { 
+    if (storageLayout & DataStorage::dslAmat || 
+        storageLayout & DataStorage::dslDipole || 
+        storageLayout & DataStorage::dslQuadrupole) { 
       needQuaternion_ = true; 
     } else { 
       needQuaternion_ = false; 
@@ -285,17 +289,18 @@ 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;
     }      
@@ -523,7 +528,7 @@ namespace OpenMD { 
 
     StringTokenizer tokenizer(line); 
     int nTokens; 
-     
+         
     nTokens = tokenizer.countTokens(); 
      
     if (nTokens < 2) {  
@@ -555,8 +560,11 @@ namespace OpenMD { 
     if (i >> siteIndex) {
       // chew up this token and parse as an int:
       siteIndex = tokenizer.nextTokenAsInt();
-      RigidBody* rb = static_cast<RigidBody*>(sd);
-      sd = rb->getAtoms()[siteIndex];
+
+      if (sd->isRigidBody()) {
+        RigidBody* rb = static_cast<RigidBody*>(sd);
+        sd = rb->getAtoms()[siteIndex];
+      }
     }
 
     /**
@@ -643,14 +651,12 @@ namespace OpenMD { 
 
   void  DumpReader::readSiteData(std::istream& inputStream) {
 
-    inputStream.getline(buffer, bufferSize);
     std::string line(buffer);
-    
-    if (line.find("<SiteData>") == std::string::npos) {
-      // site data isn't required for a simulation, so skip
-      return;
-    }
 
+    // We already found the starting <SiteData> tag or we wouldn't be
+    // here, so just start parsing until we get to the ending
+    // </SiteData> tag:
+    
     while(inputStream.getline(buffer, bufferSize)) {
       line = buffer;