--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/04/03 20:21:54	447
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/07/02 21:26:55	572
@@ -27,8 +27,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
   if(worldRank == 0 ){
 #endif // is_mpi
     
- 
-    
     strcpy( outName, entry_plug->sampleName );
     
     outFile.open(outName, ios::out | ios::trunc );
@@ -41,7 +39,7 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
       painCave.isFatal = 1;
       simError();
     }
-  
+
     //outFile.setf( ios::scientific );
 
 #ifdef IS_MPI
@@ -72,7 +70,7 @@ void DumpWriter::writeDump( double currentTime ){
   char tempBuffer[BUFFERSIZE];
   char writeLine[BUFFERSIZE];
 
-  int i, j, which_node, done, game_over, which_atom, local_index;
+  int i, j, which_node, done, which_atom, local_index;
   double q[4];
   DirectionalAtom* dAtom;
   int nAtoms = entry_plug->n_atoms;
@@ -84,9 +82,17 @@ void DumpWriter::writeDump( double currentTime ){
   outFile << nAtoms << "\n";
     
   outFile << currentTime << "\t" 
-	  << entry_plug->box_x << "\t"
-	  << entry_plug->box_y << "\t"
-	  << entry_plug->box_z << "\n";
+	  << entry_plug->Hmat[0] << "\t"
+	  << entry_plug->Hmat[1] << "\t"
+	  << entry_plug->Hmat[2] << "\t"
+
+	  << entry_plug->Hmat[3] << "\t"
+	  << entry_plug->Hmat[4] << "\t"
+	  << entry_plug->Hmat[5] << "\t"
+
+	  << entry_plug->Hmat[6] << "\t"
+	  << entry_plug->Hmat[7] << "\t"
+	  << entry_plug->Hmat[8] << "\n";
     
   for( i=0; i<nAtoms; i++ ){
       
@@ -140,11 +146,20 @@ void DumpWriter::writeDump( double currentTime ){
   
   if( worldRank == 0 ){
     outFile << mpiSim->getTotAtoms() << "\n";
-    
+  
     outFile << currentTime << "\t" 
-	    << entry_plug->box_x << "\t"
-	    << entry_plug->box_y << "\t"
-	    << entry_plug->box_z << "\n";
+	    << entry_plug->Hmat[0] << "\t"
+	    << entry_plug->Hmat[1] << "\t"
+	    << entry_plug->Hmat[2] << "\t"
+      
+	    << entry_plug->Hmat[3] << "\t"
+	    << entry_plug->Hmat[4] << "\t"
+	    << entry_plug->Hmat[5] << "\t"
+      
+	    << entry_plug->Hmat[6] << "\t"
+	    << entry_plug->Hmat[7] << "\t"
+	    << entry_plug->Hmat[8] << "\n";
+    ;
     outFile.flush();
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this atom;
@@ -309,7 +324,7 @@ void DumpWriter::writeDump( double currentTime ){
 #endif // is_mpi
 }
 
-void DumpWriter::writeFinal(){
+void DumpWriter::writeFinal(double finalTime){
 
   char finalName[500];
   ofstream finalOut;
@@ -355,9 +370,18 @@ void DumpWriter::writeFinal(){
     
   finalOut << nAtoms << "\n";
     
-  finalOut << entry_plug->box_x << "\t"
-	   << entry_plug->box_y << "\t"
-	   << entry_plug->box_z << "\n";
+  finalOut << finalTime << "\t"
+	   << entry_plug->Hmat[0] << "\t"
+	   << entry_plug->Hmat[1] << "\t"
+	   << entry_plug->Hmat[2] << "\t"
+    
+	   << entry_plug->Hmat[3] << "\t"
+	   << entry_plug->Hmat[4] << "\t"
+	   << entry_plug->Hmat[5] << "\t"
+    
+	   << entry_plug->Hmat[6] << "\t"
+	   << entry_plug->Hmat[7] << "\t"
+	   << entry_plug->Hmat[8] << "\n";
   
   for( i=0; i<nAtoms; i++ ){
       
@@ -413,9 +437,18 @@ void DumpWriter::writeFinal(){
   if( worldRank == 0 ){
     finalOut << mpiSim->getTotAtoms() << "\n";
     
-    finalOut << entry_plug->box_x << "\t"
-	    << entry_plug->box_y << "\t"
-	    << entry_plug->box_z << "\n";
+    finalOut << finalTime << "\t"
+	     << entry_plug->Hmat[0] << "\t"
+	     << entry_plug->Hmat[1] << "\t"
+	     << entry_plug->Hmat[2] << "\t"
+      
+	     << entry_plug->Hmat[3] << "\t"
+	     << entry_plug->Hmat[4] << "\t"
+	     << entry_plug->Hmat[5] << "\t"
+      
+	     << entry_plug->Hmat[6] << "\t"
+	     << entry_plug->Hmat[7] << "\t"
+	     << entry_plug->Hmat[8] << "\n";
     
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this molecule: