--- branches/development/src/io/DumpWriter.cpp	2012/05/19 13:30:21	1712
+++ branches/development/src/io/DumpWriter.cpp	2012/06/10 14:05:02	1752
@@ -59,10 +59,18 @@ namespace OpenMD {
     : info_(info), filename_(info->getDumpFileName()), eorFilename_(info->getFinalConfigFileName()){
 
     Globals* simParams = info->getSimParams();
-    needCompression_ = simParams->getCompressDumpFile();
-    needForceVector_ = simParams->getOutputForceVector();
-    needParticlePot_ = simParams->getOutputParticlePotential();
-    cerr << "DW npp = " << needParticlePot_ << "\n";
+    needCompression_   = simParams->getCompressDumpFile();
+    needForceVector_   = simParams->getOutputForceVector();
+    needParticlePot_   = simParams->getOutputParticlePotential();
+    needFlucQ_         = simParams->getOutputFluctuatingCharges();
+    needElectricField_ = simParams->getOutputElectricField();
+
+    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
+      doSiteData_ = true;
+    } else {
+      doSiteData_ = false;
+    }
+
     createDumpFile_ = true;
 #ifdef HAVE_LIBZ
     if (needCompression_) {
@@ -100,9 +108,18 @@ namespace OpenMD {
     Globals* simParams = info->getSimParams();
     eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
 
-    needCompression_ = simParams->getCompressDumpFile();
-    needForceVector_ = simParams->getOutputForceVector();
-    needParticlePot_ = simParams->getOutputParticlePotential();
+    needCompression_   = simParams->getCompressDumpFile();
+    needForceVector_   = simParams->getOutputForceVector();
+    needParticlePot_   = simParams->getOutputParticlePotential();
+    needFlucQ_         = simParams->getOutputFluctuatingCharges();
+    needElectricField_ = simParams->getOutputElectricField();
+
+    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
+      doSiteData_ = true;
+    } else {
+      doSiteData_ = false;
+    }
+
     createDumpFile_ = true;
 #ifdef HAVE_LIBZ
     if (needCompression_) {
@@ -140,10 +157,18 @@ namespace OpenMD {
     Globals* simParams = info->getSimParams();
     eorFilename_ = filename_.substr(0, filename_.rfind(".")) + ".eor";    
     
-    needCompression_ = simParams->getCompressDumpFile();
-    needForceVector_ = simParams->getOutputForceVector();
-    needParticlePot_ = simParams->getOutputParticlePotential();
-    
+    needCompression_   = simParams->getCompressDumpFile();
+    needForceVector_   = simParams->getOutputForceVector();
+    needParticlePot_   = simParams->getOutputParticlePotential();
+    needFlucQ_         = simParams->getOutputFluctuatingCharges();
+    needElectricField_ = simParams->getOutputElectricField();
+
+    if (needParticlePot_ || needFlucQ_ || needElectricField_) {
+      doSiteData_ = true;
+    } else {
+      doSiteData_ = false;
+    }
+
 #ifdef HAVE_LIBZ
     if (needCompression_) {
       filename_ += ".gz";
@@ -277,6 +302,8 @@ namespace OpenMD {
     StuntDouble* integrableObject;
     SimInfo::MoleculeIterator mi;
     Molecule::IntegrableObjectIterator ii;
+    RigidBody::AtomIterator ai;
+    Atom* atom;
 
 #ifndef IS_MPI
     os << "  <Snapshot>\n";
@@ -294,7 +321,32 @@ 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();
@@ -431,10 +483,7 @@ namespace OpenMD {
 
     if (needForceVector_) {
       type += "f";
-      Vector3d frc;
-
-      frc = integrableObject->getFrc();
-
+      Vector3d frc = integrableObject->getFrc();
       if (isinf(frc[0]) || isnan(frc[0]) || 
           isinf(frc[1]) || isnan(frc[1]) || 
           isinf(frc[2]) || isnan(frc[2]) ) {      
@@ -450,10 +499,7 @@ namespace OpenMD {
       
       if (integrableObject->isDirectional()) {
         type += "t";
-        Vector3d trq;
-        
-        trq = integrableObject->getTrq();
-        
+        Vector3d trq = integrableObject->getTrq();        
         if (isinf(trq[0]) || isnan(trq[0]) || 
             isinf(trq[1]) || isnan(trq[1]) || 
             isinf(trq[2]) || isnan(trq[2]) ) {      
@@ -462,23 +508,97 @@ namespace OpenMD {
                    " for object %d", index);      
           painCave.isFatal = 1;
           simError();
-        }
-        
+        }        
         sprintf(tempBuffer, " %13e %13e %13e",
                 trq[0], trq[1], trq[2]);
         line += tempBuffer;
       }      
     }
-    if (needParticlePot_) {
-      type += "u";
-      RealType particlePot;
+
+    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
+    return std::string(tempBuffer);
+  }
 
-      particlePot = integrableObject->getParticlePot();
+  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 %s", id.c_str());      
+        painCave.isFatal = 1;
+        simError();
+      }
+      sprintf(tempBuffer, " %13e ", fqPos);
+      line += tempBuffer;
+    
+      RealType fqVel = integrableObject->getFlucQVel();
+      if (isinf(fqVel) || isnan(fqVel) ) {      
+        sprintf( painCave.errMsg,
+                 "DumpWriter detected a numerical error writing the"
+                 " fluctuating charge velocity for object %s", id.c_str());      
+        painCave.isFatal = 1;
+        simError();
+      }
+      sprintf(tempBuffer, " %13e ", fqVel);
+      line += tempBuffer;
+
+      if (needForceVector_) {
+        type += "g";
+        RealType fqFrc = integrableObject->getFlucQFrc();        
+        if (isinf(fqFrc) || isnan(fqFrc) ) {      
+          sprintf( painCave.errMsg,
+                   "DumpWriter detected a numerical error writing the"
+                   " fluctuating charge force for object %s", id.c_str());      
+          painCave.isFatal = 1;
+          simError();
+        }
+        sprintf(tempBuffer, " %13e ", fqFrc);        
+        line += tempBuffer;
+      }
+    }
+
+    if (needElectricField_) {
+      type += "e";
+      Vector3d eField= integrableObject->getElectricField();
+      if (isinf(eField[0]) || isnan(eField[0]) || 
+          isinf(eField[1]) || isnan(eField[1]) || 
+          isinf(eField[2]) || isnan(eField[2]) ) {      
+        sprintf( painCave.errMsg,
+                 "DumpWriter detected a numerical error writing the electric"
+                 " field for object %s", id.c_str());      
+        painCave.isFatal = 1;
+        simError();
+      }
+      sprintf(tempBuffer, " %13e %13e %13e",
+              eField[0], eField[1], eField[2]);
+      line += tempBuffer;
+    }
+
+
+    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);      
+                 " potential for object %s", id.c_str());      
         painCave.isFatal = 1;
         simError();
       }
@@ -486,7 +606,8 @@ namespace OpenMD {
       line += tempBuffer;
     }
     
-    sprintf(tempBuffer, "%10d %7s %s\n", index, type.c_str(), line.c_str());
+
+    sprintf(tempBuffer, "%s %7s %s\n", id.c_str(), type.c_str(), line.c_str());
     return std::string(tempBuffer);
   }
 
@@ -567,7 +688,7 @@ namespace OpenMD {
     newOStream = new std::ofstream(filename.c_str());
 #endif
     //write out MetaData first
-    (*newOStream) << "<OpenMD version=1>" << std::endl;
+    (*newOStream) << "<OpenMD version=2>" << std::endl;
     (*newOStream) << "  <MetaData>" << std::endl;
     (*newOStream) << info_->getRawMetaData();
     (*newOStream) << "  </MetaData>" << std::endl;