--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/04/07 20:06:31	469
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/07/11 01:15:28	591
@@ -23,14 +23,10 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
 
   entry_plug = the_entry_plug;
 
-  std::cerr << "Look at me I'm a freebird!\n";
-
 #ifdef IS_MPI
   if(worldRank == 0 ){
 #endif // is_mpi
     
- 
-    
     strcpy( outName, entry_plug->sampleName );
     
     outFile.open(outName, ios::out | ios::trunc );
@@ -44,8 +40,6 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
       simError();
     }
 
-    std::cerr << "me TOO!\n";
-
     //outFile.setf( ios::scientific );
 
 #ifdef IS_MPI
@@ -87,10 +81,18 @@ 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";
+  outFile << currentTime << ";\t" 
+	  << entry_plug->Hmat[0][0] << "\t"
+	  << entry_plug->Hmat[1][0] << "\t"
+	  << entry_plug->Hmat[2][0] << ";\t"
+
+	  << entry_plug->Hmat[0][1] << "\t"
+	  << entry_plug->Hmat[1][1] << "\t"
+	  << entry_plug->Hmat[2][1] << ";\t"
+
+	  << entry_plug->Hmat[0][2] << "\t"
+	  << entry_plug->Hmat[1][2] << "\t"
+	  << entry_plug->Hmat[2][2] << ";\n";
     
   for( i=0; i<nAtoms; i++ ){
       
@@ -144,11 +146,20 @@ void DumpWriter::writeDump( double currentTime ){
   
   if( worldRank == 0 ){
     outFile << mpiSim->getTotAtoms() << "\n";
+  
+    outFile << currentTime << ";\t" 
+	    << entry_plug->Hmat[0][0] << "\t"
+	    << entry_plug->Hmat[1][0] << "\t"
+	    << entry_plug->Hmat[2][0] << ";\t"
+      
+	    << entry_plug->Hmat[0][1] << "\t"
+	    << entry_plug->Hmat[1][1] << "\t"
+	    << entry_plug->Hmat[2][1] << ";\t"
+      
+	    << entry_plug->Hmat[0][2] << "\t"
+	    << entry_plug->Hmat[1][2] << "\t"
+	    << entry_plug->Hmat[2][2] << ";\n";
     
-    outFile << currentTime << "\t" 
-	    << entry_plug->box_x << "\t"
-	    << entry_plug->box_y << "\t"
-	    << entry_plug->box_z << "\n";
     outFile.flush();
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this atom;
@@ -313,7 +324,7 @@ void DumpWriter::writeDump( double currentTime ){
 #endif // is_mpi
 }
 
-void DumpWriter::writeFinal(){
+void DumpWriter::writeFinal(double finalTime){
 
   char finalName[500];
   ofstream finalOut;
@@ -359,9 +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][0] << "\t"
+	   << entry_plug->Hmat[1][0] << "\t"
+	   << entry_plug->Hmat[2][0] << ";\t"
+    
+	   << entry_plug->Hmat[0][1] << "\t"
+	   << entry_plug->Hmat[1][1] << "\t"
+	   << entry_plug->Hmat[2][1] << ";\t"
+    
+	   << entry_plug->Hmat[0][2] << "\t"
+	   << entry_plug->Hmat[1][2] << "\t"
+	   << entry_plug->Hmat[2][2] << ";\n";
   
   for( i=0; i<nAtoms; i++ ){
       
@@ -417,9 +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][0] << "\t"
+	     << entry_plug->Hmat[1][0] << "\t"
+	     << entry_plug->Hmat[2][0] << ";\t"
+      
+	     << entry_plug->Hmat[0][1] << "\t"
+	     << entry_plug->Hmat[1][1] << "\t"
+	     << entry_plug->Hmat[2][1] << ";\t"
+      
+	     << entry_plug->Hmat[0][2] << "\t"
+	     << entry_plug->Hmat[1][2] << "\t"
+	     << entry_plug->Hmat[2][2] << ";\n";
     
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this molecule: