--- branches/development/src/io/DumpWriter.cpp	2012/06/10 14:05:02	1752
+++ branches/development/src/io/DumpWriter.cpp	2012/07/09 14:15:52	1769
@@ -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 {
@@ -257,20 +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++) {
@@ -299,7 +306,7 @@ namespace OpenMD {
 #endif
 
     Molecule* mol;
-    StuntDouble* integrableObject;
+    StuntDouble* sd;
     SimInfo::MoleculeIterator mi;
     Molecule::IntegrableObjectIterator ii;
     RigidBody::AtomIterator ai;
@@ -314,9 +321,9 @@ namespace OpenMD {
     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
 
       
-      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL;  
-           integrableObject = mol->nextIntegrableObject(ii)) { 	
-          os << prepareDumpLine(integrableObject);
+      for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
+           sd = mol->nextIntegrableObject(ii)) { 	
+          os << prepareDumpLine(sd);
           
       }
     }    
@@ -326,16 +333,16 @@ namespace OpenMD {
       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)) { 	
+        for (sd = mol->beginIntegrableObject(ii); sd != NULL;  
+           sd = mol->nextIntegrableObject(ii)) { 	
 
-          int ioIndex = integrableObject->getGlobalIntegrableObjectIndex();
+          int ioIndex = sd->getGlobalIntegrableObjectIndex();
           // do one for the IO itself
-          os << prepareSiteLine(integrableObject, ioIndex, 0);
+          os << prepareSiteLine(sd, ioIndex, 0);
 
-          if (integrableObject->isRigidBody()) {
+          if (sd->isRigidBody()) {
             
-            RigidBody* rb = static_cast<RigidBody*>(integrableObject);
+            RigidBody* rb = static_cast<RigidBody*>(sd);
             int siteIndex = 0;
             for (atom = rb->beginAtom(ai); atom != NULL;  
                  atom = rb->nextAtom(ai)) { 	                                        
@@ -356,9 +363,9 @@ namespace OpenMD {
     for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
 
 
-      for (integrableObject = mol->beginIntegrableObject(ii); integrableObject != NULL; 
-           integrableObject = mol->nextIntegrableObject(ii)) { 	
-          buffer += prepareDumpLine(integrableObject);
+      for (sd = mol->beginIntegrableObject(ii); sd != NULL; 
+           sd = mol->nextIntegrableObject(ii)) { 	
+          buffer += prepareDumpLine(sd);
       }
     }
     
@@ -408,16 +415,16 @@ namespace OpenMD {
 
   }
 
-  std::string DumpWriter::prepareDumpLine(StuntDouble* integrableObject) {
+  std::string DumpWriter::prepareDumpLine(StuntDouble* sd) {
 	
-    int index = integrableObject->getGlobalIntegrableObjectIndex();
+    int index = sd->getGlobalIntegrableObjectIndex();
     std::string type("pv");
     std::string line;
     char tempBuffer[4096];
 
     Vector3d pos;
     Vector3d vel;
-    pos = integrableObject->getPos();
+    pos = sd->getPos();
 
     if (isinf(pos[0]) || isnan(pos[0]) || 
         isinf(pos[1]) || isnan(pos[1]) || 
@@ -429,7 +436,7 @@ namespace OpenMD {
       simError();
     }
 
-    vel = integrableObject->getVel();		
+    vel = sd->getVel();		
 
     if (isinf(vel[0]) || isnan(vel[0]) || 
         isinf(vel[1]) || isnan(vel[1]) || 
@@ -446,11 +453,11 @@ namespace OpenMD {
             vel[0], vel[1], vel[2]);		        
     line += tempBuffer;
 
-    if (integrableObject->isDirectional()) {
+    if (sd->isDirectional()) {
       type += "qj";
       Quat4d q;
       Vector3d ji;
-      q = integrableObject->getQ();
+      q = sd->getQ();
 
       if (isinf(q[0]) || isnan(q[0]) || 
           isinf(q[1]) || isnan(q[1]) || 
@@ -463,7 +470,7 @@ namespace OpenMD {
         simError();
       }
 
-      ji = integrableObject->getJ();
+      ji = sd->getJ();
 
       if (isinf(ji[0]) || isnan(ji[0]) || 
           isinf(ji[1]) || isnan(ji[1]) || 
@@ -483,7 +490,7 @@ namespace OpenMD {
 
     if (needForceVector_) {
       type += "f";
-      Vector3d frc = integrableObject->getFrc();
+      Vector3d frc = sd->getFrc();
       if (isinf(frc[0]) || isnan(frc[0]) || 
           isinf(frc[1]) || isnan(frc[1]) || 
           isinf(frc[2]) || isnan(frc[2]) ) {      
@@ -497,9 +504,9 @@ namespace OpenMD {
               frc[0], frc[1], frc[2]);
       line += tempBuffer;
       
-      if (integrableObject->isDirectional()) {
+      if (sd->isDirectional()) {
         type += "t";
-        Vector3d trq = integrableObject->getTrq();        
+        Vector3d trq = sd->getTrq();        
         if (isinf(trq[0]) || isnan(trq[0]) || 
             isinf(trq[1]) || isnan(trq[1]) || 
             isinf(trq[2]) || isnan(trq[2]) ) {      
@@ -519,7 +526,7 @@ namespace OpenMD {
     return std::string(tempBuffer);
   }
 
-  std::string DumpWriter::prepareSiteLine(StuntDouble* integrableObject, int ioIndex, int siteIndex) {
+  std::string DumpWriter::prepareSiteLine(StuntDouble* sd, int ioIndex, int siteIndex) {
 	
 
     std::string id;
@@ -527,7 +534,7 @@ namespace OpenMD {
     std::string line;
     char tempBuffer[4096];
 
-    if (integrableObject->isRigidBody()) {
+    if (sd->isRigidBody()) {
       sprintf(tempBuffer, "%10d           ", ioIndex);
       id = std::string(tempBuffer);
     } else {
@@ -537,7 +544,7 @@ namespace OpenMD {
               
     if (needFlucQ_) {
       type += "cw";
-      RealType fqPos = integrableObject->getFlucQPos();
+      RealType fqPos = sd->getFlucQPos();
       if (isinf(fqPos) || isnan(fqPos) ) {      
         sprintf( painCave.errMsg,
                  "DumpWriter detected a numerical error writing the"
@@ -548,7 +555,7 @@ namespace OpenMD {
       sprintf(tempBuffer, " %13e ", fqPos);
       line += tempBuffer;
     
-      RealType fqVel = integrableObject->getFlucQVel();
+      RealType fqVel = sd->getFlucQVel();
       if (isinf(fqVel) || isnan(fqVel) ) {      
         sprintf( painCave.errMsg,
                  "DumpWriter detected a numerical error writing the"
@@ -561,7 +568,7 @@ namespace OpenMD {
 
       if (needForceVector_) {
         type += "g";
-        RealType fqFrc = integrableObject->getFlucQFrc();        
+        RealType fqFrc = sd->getFlucQFrc();        
         if (isinf(fqFrc) || isnan(fqFrc) ) {      
           sprintf( painCave.errMsg,
                    "DumpWriter detected a numerical error writing the"
@@ -576,7 +583,7 @@ namespace OpenMD {
 
     if (needElectricField_) {
       type += "e";
-      Vector3d eField= integrableObject->getElectricField();
+      Vector3d eField= sd->getElectricField();
       if (isinf(eField[0]) || isnan(eField[0]) || 
           isinf(eField[1]) || isnan(eField[1]) || 
           isinf(eField[2]) || isnan(eField[2]) ) {      
@@ -594,7 +601,7 @@ namespace OpenMD {
 
     if (needParticlePot_) {
       type += "u";
-      RealType particlePot = integrableObject->getParticlePot();
+      RealType particlePot = sd->getParticlePot();
       if (isinf(particlePot) || isnan(particlePot)) {      
         sprintf( painCave.errMsg,
                  "DumpWriter detected a numerical error writing the particle "
@@ -678,7 +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 {