--- trunk/src/io/DumpReader.cpp	2012/08/22 02:28:28	1782
+++ trunk/src/io/DumpReader.cpp	2015/03/05 16:30:23	2069
@@ -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).
  */
@@ -43,6 +43,10 @@
 #define _LARGEFILE_SOURCE64 
 #define _FILE_OFFSET_BITS 64 
  
+#ifdef IS_MPI 
+#include <mpi.h> 
+#endif
+ 
 #include <sys/types.h> 
 #include <sys/stat.h> 
  
@@ -60,11 +64,7 @@
 #include "utils/StringTokenizer.hpp" 
 #include "brains/Thermo.hpp"
  
-#ifdef IS_MPI 
-#include <mpi.h> 
-#endif
  
- 
 namespace OpenMD { 
    
   DumpReader::DumpReader(SimInfo* info, const std::string& filename) 
@@ -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, 
@@ -102,8 +103,8 @@ namespace OpenMD { 
 #ifdef IS_MPI 
     
     if (worldRank == 0) { 
-#endif 
-      
+#endif
+
       delete inFile_; 
       
 #ifdef IS_MPI 
@@ -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;
         
@@ -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; 
@@ -241,7 +245,6 @@ namespace OpenMD { 
     readSet(whichFrame); 
 
     if (needCOMprops_) {
-      Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
       Thermo thermo(info_);
       Vector3d com;
 
@@ -286,16 +289,17 @@ 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_Bcast((void *)sendBuffer.c_str(), sendBufferSize, 
+                MPI_CHAR, masterNode, MPI_COMM_WORLD);     
       
       sstream.str(sendBuffer);
     } else {
       int sendBufferSize;
-      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);     
+      MPI_Bcast(&sendBufferSize, 1, MPI_INT, masterNode, MPI_COMM_WORLD);
       char * recvBuffer = new char[sendBufferSize+1];
       assert(recvBuffer);
       recvBuffer[sendBufferSize] = '\0';
-      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);     
+      MPI_Bcast(recvBuffer, sendBufferSize, MPI_CHAR, masterNode, MPI_COMM_WORLD);
       sstream.str(recvBuffer);
       delete [] recvBuffer;
     }      
@@ -503,6 +507,13 @@ namespace OpenMD { 
            eField[1] = tokenizer.nextTokenAsDouble(); 
            eField[2] = tokenizer.nextTokenAsDouble();           
            sd->setElectricField(eField);          
+           break;
+        }
+        case 's' : {
+
+           RealType sPot;
+           sPot = tokenizer.nextTokenAsDouble(); 
+           sd->setSitePotential(sPot);          
            break;
         }
         default: {
@@ -515,7 +526,6 @@ namespace OpenMD { 
 
       }
     }
-     
   } 
    
 
@@ -523,7 +533,7 @@ namespace OpenMD { 
 
     StringTokenizer tokenizer(line); 
     int nTokens; 
-     
+         
     nTokens = tokenizer.countTokens(); 
      
     if (nTokens < 2) {  
@@ -555,8 +565,11 @@ 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];
+      }
     }
 
     /**
@@ -605,6 +618,13 @@ namespace OpenMD { 
         sd->setElectricField(eField);          
         break;
       }
+      case 's' : {
+        
+        RealType sPot;
+        sPot = tokenizer.nextTokenAsDouble(); 
+        sd->setSitePotential(sPot);          
+        break;
+      }
       default: {
         sprintf(painCave.errMsg, 
                 "DumpReader Error: %s is an unrecognized type\n", type.c_str()); 
@@ -617,7 +637,7 @@ namespace OpenMD { 
   } 
   
   
-  void  DumpReader::readStuntDoubles(std::istream& inputStream) {
+    void  DumpReader::readStuntDoubles(std::istream& inputStream) {
     
     inputStream.getline(buffer, bufferSize);
     std::string line(buffer);
@@ -643,14 +663,12 @@ 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;