--- trunk/src/io/DumpReader.cpp	2012/09/10 18:38:44	1796
+++ trunk/src/io/DumpReader.cpp	2014/01/16 16:00:43	1964
@@ -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> 
  
@@ -59,10 +63,6 @@
 #include "utils/MemoryUtils.hpp" 
 #include "utils/StringTokenizer.hpp" 
 #include "brains/Thermo.hpp"
- 
-#ifdef IS_MPI 
-#include <mpi.h> 
-#endif
  
  
 namespace OpenMD { 
@@ -128,7 +128,7 @@ namespace OpenMD { 
   } 
    
   void DumpReader::scanFile(void) { 
-    int lineNo = 0; 
+
     std::streampos prevPos;
     std::streampos  currPos; 
     
@@ -142,6 +142,7 @@ namespace OpenMD { 
       bool foundOpenSnapshotTag = false;
       bool foundClosedSnapshotTag = false;
 
+      int lineNo = 0; 
       while(inFile_->getline(buffer, bufferSize)) {
         ++lineNo;
         
@@ -227,7 +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; 
@@ -517,7 +520,6 @@ namespace OpenMD { 
 
       }
     }
-     
   } 
    
 
@@ -525,7 +527,7 @@ namespace OpenMD { 
 
     StringTokenizer tokenizer(line); 
     int nTokens; 
-     
+         
     nTokens = tokenizer.countTokens(); 
      
     if (nTokens < 2) {  
@@ -557,8 +559,11 @@ 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];
+      }
     }
 
     /**
@@ -645,14 +650,12 @@ 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;