--- branches/development/src/io/DumpWriter.cpp	2012/06/06 02:18:54	1746
+++ branches/development/src/io/DumpWriter.cpp	2012/07/06 22:01:58	1767
@@ -44,13 +44,19 @@
 #include "primitives/Molecule.hpp"
 #include "utils/simError.h"
 #include "io/basic_teebuf.hpp"
+#ifdef HAVE_ZLIB
 #include "io/gzstream.hpp"
+#endif
 #include "io/Globals.hpp"
 
+#ifdef _MSC_VER
+#define isnan(x) _isnan((x))
+#define isinf(x) (!_finite(x) && !_isnan(x))
+#endif
 
 #ifdef IS_MPI
 #include <mpi.h>
-#endif //is_mpi
+#endif
 
 using namespace std;
 namespace OpenMD {
@@ -65,6 +71,12 @@ namespace OpenMD {
     needFlucQ_         = simParams->getOutputFluctuatingCharges();
     needElectricField_ = simParams->getOutputElectricField();
 
+    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
+      doSiteData_ = true;
+    } else {
+      doSiteData_ = false;
+    }
+
     createDumpFile_ = true;
 #ifdef HAVE_LIBZ
     if (needCompression_) {
@@ -107,6 +119,12 @@ namespace OpenMD {
     needParticlePot_   = simParams->getOutputParticlePotential();
     needFlucQ_         = simParams->getOutputFluctuatingCharges();
     needElectricField_ = simParams->getOutputElectricField();
+
+    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
+      doSiteData_ = true;
+    } else {
+      doSiteData_ = false;
+    }
 
     createDumpFile_ = true;
 #ifdef HAVE_LIBZ
@@ -151,6 +169,12 @@ namespace OpenMD {
     needFlucQ_         = simParams->getOutputFluctuatingCharges();
     needElectricField_ = simParams->getOutputElectricField();
 
+    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
+      doSiteData_ = true;
+    } else {
+      doSiteData_ = false;
+    }
+
 #ifdef HAVE_LIBZ
     if (needCompression_) {
       filename_ += ".gz";
@@ -239,20 +263,21 @@ namespace OpenMD {
             hmat(0, 2), hmat(1, 2), hmat(2, 2));
     os << buffer;
 
-    RealType chi = s->getChi();
-    RealType integralOfChiDt = s->getIntegralOfChiDt();
-    if (isinf(chi) || isnan(chi) || 
-        isinf(integralOfChiDt) || isnan(integralOfChiDt)) {      
+    pair<RealType, RealType> thermostat = s->getThermostat();
+
+    if (isinf(thermostat.first)  || isnan(thermostat.first) || 
+        isinf(thermostat.second) || isnan(thermostat.second)) {      
       sprintf( painCave.errMsg,
                "DumpWriter detected a numerical error writing the thermostat");
       painCave.isFatal = 1;
       simError();
     }
-    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", chi, integralOfChiDt);
+    sprintf(buffer, "  Thermostat: %.10g , %.10g\n", thermostat.first, 
+            thermostat.second);
     os << buffer;
 
     Mat3x3d eta;
-    eta = s->getEta();
+    eta = s->getBarostat();
 
     for (unsigned int i = 0; i < 3; i++) {
       for (unsigned int j = 0; j < 3; j++) {
@@ -284,6 +309,8 @@ namespace OpenMD {
     StuntDouble* integrableObject;
     SimInfo::MoleculeIterator mi;
     Molecule::IntegrableObjectIterator ii;
+    RigidBody::AtomIterator ai;
+    Atom* atom;
 
 #ifndef IS_MPI
     os << "  <Snapshot>\n";
@@ -301,7 +328,32 @@ namespace OpenMD {
       }
     }    
     os << "    </StuntDoubles>\n";
-    
+
+    if (doSiteData_) {
+      os << "    <SiteData>\n";
+      for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
+               
+        for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
+           integrableObject = mol->nextIntegrableObject(ii)) { 	
+
+          int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
+          // do one for the IO itself
+          os << prepareSiteLine(integrableObject, ioIndex, 0);
+
+          if (integrableObject->isRigidBody()) {
+            
+            RigidBody* rb = static_cast<RigidBody*>(integrableObject);
+            int siteIndex = 0;
+            for (atom = rb->beginAtom(ai); atom != NULL;  
+                 atom = rb->nextAtom(ai)) { 	                                        
+              os << prepareSiteLine(atom, ioIndex, siteIndex);
+              siteIndex++;
+            }
+          }
+        }
+      }    
+      os << "    </SiteData>\n";
+    }
     os << "  </Snapshot>\n";
 
     os.flush();
@@ -470,27 +522,33 @@ namespace OpenMD {
       }      
     }
 
-    if (needParticlePot_) {
-      type += "u";
-      RealType particlePot = integrableObject->getParticlePot();
-      if (isinf(particlePot) || isnan(particlePot)) {      
-        sprintf( painCave.errMsg,
-                 "DumpWriter detected a numerical error writing the particle "
-                 " potential for object %d", index);      
-        painCave.isFatal = 1;
-        simError();
-      }
-      sprintf(tempBuffer, " %13e", particlePot);
-      line += tempBuffer;
+    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
+    return std::string(tempBuffer);
+  }
+
+  std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
+	
+
+    std::string id;
+    std::string type;
+    std::string line;
+    char tempBuffer[4096];
+
+    if (integrableObject->isRigidBody()) {
+      sprintf(tempBuffer, "%10d           ", ioIndex);
+      id = std::string(tempBuffer);
+    } else {
+      sprintf(tempBuffer, "%10d %10d", ioIndex, siteIndex);
+      id = std::string(tempBuffer);
     }
-    
+              
     if (needFlucQ_) {
       type += "cw";
       RealType fqPos = integrableObject->getFlucQPos();
       if (isinf(fqPos) || isnan(fqPos) ) {      
         sprintf( painCave.errMsg,
                  "DumpWriter detected a numerical error writing the"
-                 " fluctuating charge for object %d", index);      
+                 " fluctuating charge for object %s", id.c_str());      
         painCave.isFatal = 1;
         simError();
       }
@@ -501,7 +559,7 @@ namespace OpenMD {
       if (isinf(fqVel) || isnan(fqVel) ) {      
         sprintf( painCave.errMsg,
                  "DumpWriter detected a numerical error writing the"
-                 " fluctuating charge velocity for object %d", index);      
+                 " fluctuating charge velocity for object %s", id.c_str());      
         painCave.isFatal = 1;
         simError();
       }
@@ -514,7 +572,7 @@ namespace OpenMD {
         if (isinf(fqFrc) || isnan(fqFrc) ) {      
           sprintf( painCave.errMsg,
                    "DumpWriter detected a numerical error writing the"
-                   " fluctuating charge force for object %d", index);      
+                   " fluctuating charge force for object %s", id.c_str());      
           painCave.isFatal = 1;
           simError();
         }
@@ -531,7 +589,7 @@ namespace OpenMD {
           isinf(eField[2]) || isnan(eField[2]) ) {      
         sprintf( painCave.errMsg,
                  "DumpWriter detected a numerical error writing the electric"
-                 " field for object %d", index);      
+                 " field for object %s", id.c_str());      
         painCave.isFatal = 1;
         simError();
       }
@@ -540,7 +598,23 @@ namespace OpenMD {
       line += tempBuffer;
     }
 
-    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
+
+    if (needParticlePot_) {
+      type += "u";
+      RealType particlePot = integrableObject->getParticlePot();
+      if (isinf(particlePot) || isnan(particlePot)) {      
+        sprintf( painCave.errMsg,
+                 "DumpWriter detected a numerical error writing the particle "
+                 " potential for object %s", id.c_str());      
+        painCave.isFatal = 1;
+        simError();
+      }
+      sprintf(tempBuffer, " %13e", particlePot);
+      line += tempBuffer;
+    }
+    
+
+    sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
     return std::string(tempBuffer);
   }
 
@@ -611,7 +685,7 @@ namespace OpenMD {
   std::ostream* DumpWriter::createOStream(const std::string& filename) {
 
     std::ostream* newOStream;
-#ifdef HAVE_LIBZ 
+#ifdef HAVE_ZLIB
     if (needCompression_) {
       newOStream = new ogzstream(filename.c_str());
     } else {