--- branches/development/src/io/DumpReader.cpp	2012/06/10 14:05:02	1752
+++ branches/development/src/io/DumpReader.cpp	2012/09/06 19:44:06	1794
@@ -58,16 +58,13 @@
 #include "utils/simError.h" 
 #include "utils/MemoryUtils.hpp" 
 #include "utils/StringTokenizer.hpp" 
+#include "brains/Thermo.hpp"
  
 #ifdef IS_MPI 
- 
 #include <mpi.h> 
-#define TAKE_THIS_TAG_CHAR 0 
-#define TAKE_THIS_TAG_INT 1 
+#endif
  
-#endif // is_mpi 
  
- 
 namespace OpenMD { 
    
   DumpReader::DumpReader(SimInfo* info, const std::string& filename) 
@@ -78,7 +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, 
@@ -229,7 +227,9 @@ 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; 
@@ -245,20 +245,18 @@ namespace OpenMD { 
 
     if (needCOMprops_) {
       Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot();
+      Thermo thermo(info_);
       Vector3d com;
-      Vector3d comvel;
-      Vector3d comw;
-      if (needPos_ && needVel_){
-	info_->getComAll(com, comvel);
-	comw = info_->getAngularMomentum();
-      }else{
-	com = info_->getCom();
-	comvel = 0.0;
-	comw   = 0.0;
-      }
-      s->setCOMprops(com, comvel, comw);      
+
+      if (needPos_ && needVel_) {
+        Vector3d comvel;
+        Vector3d comw;
+        thermo.getComAll(com, comvel);
+        comw = thermo.getAngularMomentum();
+      } else {
+        com = thermo.getCom();
+      }                    
     }
-
   } 
    
   void DumpReader::readSet(int whichFrame) {     
@@ -357,9 +355,9 @@ namespace OpenMD { 
 
     int index = tokenizer.nextTokenAsInt();
  
-    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
+    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
 
-    if (integrableObject == NULL) {
+    if (sd == NULL) {
       return;
     }
     std::string type = tokenizer.nextToken(); 
@@ -379,7 +377,7 @@ namespace OpenMD { 
       }
     }
     
-    if (integrableObject->isDirectional()) {
+    if (sd->isDirectional()) {
       if (needQuaternion_) {
         found = type.find("q");      
         if (found == std::string::npos) {
@@ -402,7 +400,7 @@ namespace OpenMD { 
             pos[1] = tokenizer.nextTokenAsDouble(); 
             pos[2] = tokenizer.nextTokenAsDouble(); 
             if (needPos_) { 
-              integrableObject->setPos(pos); 
+              sd->setPos(pos); 
             }             
             break;
         }
@@ -412,14 +410,14 @@ namespace OpenMD { 
             vel[1] = tokenizer.nextTokenAsDouble(); 
             vel[2] = tokenizer.nextTokenAsDouble(); 
             if (needVel_) { 
-              integrableObject->setVel(vel); 
+              sd->setVel(vel); 
             } 
             break;
         }
 
         case 'q' : {
            Quat4d q;
-           if (integrableObject->isDirectional()) { 
+           if (sd->isDirectional()) { 
               
              q[0] = tokenizer.nextTokenAsDouble(); 
              q[1] = tokenizer.nextTokenAsDouble(); 
@@ -438,19 +436,19 @@ namespace OpenMD { 
               
              q.normalize(); 
              if (needQuaternion_) {            
-               integrableObject->setQ(q); 
+               sd->setQ(q); 
              }               
            }            
            break;
         }  
         case 'j' : {
           Vector3d ji;
-          if (integrableObject->isDirectional()) {
+          if (sd->isDirectional()) {
              ji[0] = tokenizer.nextTokenAsDouble(); 
              ji[1] = tokenizer.nextTokenAsDouble(); 
              ji[2] = tokenizer.nextTokenAsDouble(); 
              if (needAngMom_) { 
-               integrableObject->setJ(ji); 
+               sd->setJ(ji); 
              } 
           }
           break;
@@ -461,7 +459,7 @@ namespace OpenMD { 
           force[0] = tokenizer.nextTokenAsDouble(); 
           force[1] = tokenizer.nextTokenAsDouble(); 
           force[2] = tokenizer.nextTokenAsDouble();           
-          integrableObject->setFrc(force); 
+          sd->setFrc(force); 
           break;
         }
         case 't' : {
@@ -470,35 +468,35 @@ namespace OpenMD { 
            torque[0] = tokenizer.nextTokenAsDouble(); 
            torque[1] = tokenizer.nextTokenAsDouble(); 
            torque[2] = tokenizer.nextTokenAsDouble();           
-           integrableObject->setTrq(torque);          
+           sd->setTrq(torque);          
            break;
         }
         case 'u' : {
 
            RealType particlePot;
            particlePot = tokenizer.nextTokenAsDouble(); 
-           integrableObject->setParticlePot(particlePot);          
+           sd->setParticlePot(particlePot);          
            break;
         }
         case 'c' : {
 
            RealType flucQPos;
            flucQPos = tokenizer.nextTokenAsDouble(); 
-           integrableObject->setFlucQPos(flucQPos);          
+           sd->setFlucQPos(flucQPos);          
            break;
         }
         case 'w' : {
 
            RealType flucQVel;
            flucQVel = tokenizer.nextTokenAsDouble(); 
-           integrableObject->setFlucQVel(flucQVel);          
+           sd->setFlucQVel(flucQVel);          
            break;
         }
         case 'g' : {
 
            RealType flucQFrc;
            flucQFrc = tokenizer.nextTokenAsDouble(); 
-           integrableObject->setFlucQFrc(flucQFrc);          
+           sd->setFlucQFrc(flucQFrc);          
            break;
         }
         case 'e' : {
@@ -507,7 +505,7 @@ namespace OpenMD { 
            eField[0] = tokenizer.nextTokenAsDouble(); 
            eField[1] = tokenizer.nextTokenAsDouble(); 
            eField[2] = tokenizer.nextTokenAsDouble();           
-           integrableObject->setElectricField(eField);          
+           sd->setElectricField(eField);          
            break;
         }
         default: {
@@ -543,11 +541,10 @@ namespace OpenMD { 
      */
 
     int index = tokenizer.nextTokenAsInt();
-    StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index);
-    if (integrableObject == NULL) {
+    StuntDouble* sd = info_->getIOIndexToIntegrableObject(index);
+    if (sd == NULL) {
       return;
     }
-    StuntDouble* sd = integrableObject;
 
     /**
      * Test to see if the next token is an integer or not.  If not,
@@ -561,7 +558,7 @@ namespace OpenMD { 
     if (i >> siteIndex) {
       // chew up this token and parse as an int:
       siteIndex = tokenizer.nextTokenAsInt();
-      RigidBody* rb = static_cast<RigidBody*>(integrableObject);
+      RigidBody* rb = static_cast<RigidBody*>(sd);
       sd = rb->getAtoms()[siteIndex];
     }
 
@@ -714,10 +711,10 @@ namespace OpenMD { 
         hmat(2, 2) = tokenizer.nextTokenAsDouble(); 
         s->setHmat(hmat);      
       } else if (propertyName == "Thermostat") {
-        RealType chi = tokenizer.nextTokenAsDouble();
-        RealType integralOfChiDt = tokenizer.nextTokenAsDouble();
-        s->setChi(chi); 
-        s->setIntegralOfChiDt(integralOfChiDt);        
+        pair<RealType, RealType> thermostat;
+        thermostat.first = tokenizer.nextTokenAsDouble();
+        thermostat.second = tokenizer.nextTokenAsDouble();
+        s->setThermostat(thermostat); 
      } else if (propertyName == "Barostat") {
         Mat3x3d eta;
         eta(0, 0) = tokenizer.nextTokenAsDouble(); 
@@ -729,7 +726,7 @@ namespace OpenMD { 
         eta(2, 0) = tokenizer.nextTokenAsDouble(); 
         eta(2, 1) = tokenizer.nextTokenAsDouble(); 
         eta(2, 2) = tokenizer.nextTokenAsDouble(); 
-        s->setEta(eta); 
+        s->setBarostat(eta); 
       } else {
         sprintf(painCave.errMsg, 
                 "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str());