--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/04/03 20:21:54	447
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/08/26 20:12:51	723
@@ -1,3 +1,5 @@
+#define _FILE_OFFSET_BITS 64
+
 #include <cstring>
 #include <iostream>
 #include <fstream>
@@ -27,8 +29,6 @@ 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 +41,7 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
       painCave.isFatal = 1;
       simError();
     }
-  
+
     //outFile.setf( ios::scientific );
 
 #ifdef IS_MPI
@@ -72,34 +72,46 @@ 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;
   Atom** atoms = entry_plug->atoms;
+
+  double pos[3], vel[3];
     
 
 #ifndef IS_MPI
     
   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++ ){
       
+    atoms[i]->getPos(pos);
+    atoms[i]->getVel(vel);
 
     sprintf( tempBuffer,
 	     "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 	     atoms[i]->getType(),
-	     atoms[i]->getX(),
-	     atoms[i]->getY(),
-	     atoms[i]->getZ(),
-	     atoms[i]->get_vx(),
-	     atoms[i]->get_vy(),
-	     atoms[i]->get_vz());
+	     pos[0],
+	     pos[1],
+	     pos[2],
+	     vel[0],
+	     vel[1],
+	     vel[2]);
     strcpy( writeLine, tempBuffer );
 
     if( atoms[i]->isDirectional() ){
@@ -140,11 +152,20 @@ 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;
@@ -161,15 +182,19 @@ void DumpWriter::writeDump( double currentTime ){
         }
         if (local_index != -1) {
           //format the line
+	  
+	  atoms[local_index]->getPos(pos);
+	  atoms[local_index]->getVel(vel);
+
           sprintf( tempBuffer,
                    "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
                    atoms[local_index]->getType(),
-                   atoms[local_index]->getX(),
-                   atoms[local_index]->getY(),
-                   atoms[local_index]->getZ(),
-                   atoms[local_index]->get_vx(),
-                   atoms[local_index]->get_vy(),
-                   atoms[local_index]->get_vz()); // check here.
+		   pos[0],
+		   pos[1],
+		   pos[2],
+		   vel[0],
+		   vel[1],
+		   vel[2]); // check here.
           strcpy( writeLine, tempBuffer );
 	  
           if( atoms[local_index]->isDirectional() ){
@@ -251,15 +276,19 @@ void DumpWriter::writeDump( double currentTime ){
       }
       if (local_index != -1) {
 	//format the line
+
+	atoms[local_index]->getPos(pos);
+	atoms[local_index]->getVel(vel);
+
 	sprintf( tempBuffer,
 		 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 		 atoms[local_index]->getType(),
-		 atoms[local_index]->getX(),
-		 atoms[local_index]->getY(),
-		 atoms[local_index]->getZ(),
-		 atoms[local_index]->get_vx(),
-		 atoms[local_index]->get_vy(),
-		 atoms[local_index]->get_vz()); // check here.
+		 pos[0],
+		 pos[1],
+		 pos[2],
+		 vel[0],
+		 vel[1],
+		 vel[2]); // check here.
 	strcpy( writeLine, tempBuffer );
 	
 	if( atoms[local_index]->isDirectional() ){
@@ -309,7 +338,7 @@ void DumpWriter::writeDump( double currentTime ){
 #endif // is_mpi
 }
 
-void DumpWriter::writeFinal(){
+void DumpWriter::writeFinal(double finalTime){
 
   char finalName[500];
   ofstream finalOut;
@@ -324,6 +353,7 @@ void DumpWriter::writeFinal(){
   Atom** atoms = entry_plug->atoms;
   int i, j, which_node, done, game_over, which_atom, local_index;
   
+  double pos[3], vel[3];
   
 #ifdef IS_MPI
   if(worldRank == 0 ){
@@ -355,21 +385,33 @@ 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++ ){
       
+    atoms[i]->getPos(pos);
+    atoms[i]->getVel(vel);
+    
     sprintf( tempBuffer,
 	     "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 	     atoms[i]->getType(),
-	     atoms[i]->getX(),
-	     atoms[i]->getY(),
-	     atoms[i]->getZ(),
-	     atoms[i]->get_vx(),
-	     atoms[i]->get_vy(),
-	     atoms[i]->get_vz());
+	     pos[0],
+	     pos[1],
+	     pos[2],
+	     vel[0],
+	     vel[1],
+	     vel[2]);
     strcpy( writeLine, tempBuffer );
 
     if( atoms[i]->isDirectional() ){
@@ -413,9 +455,18 @@ 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:
@@ -429,16 +480,20 @@ void DumpWriter::writeFinal(){
         for (j=0; (j<mpiSim->getMyNlocal()) && (local_index < 0); j++) {
           if (atoms[j]->getGlobalIndex() == which_atom) local_index = j;
         }
-        if (local_index != -1) {        
+        if (local_index != -1) {    
+
+	  atoms[local_index]->getPos(pos);
+	  atoms[local_index]->getVel(vel);
+	  
 	  sprintf( tempBuffer,
 		   "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 		   atoms[local_index]->getType(),
-		   atoms[local_index]->getX(),
-		   atoms[local_index]->getY(),
-		   atoms[local_index]->getZ(),
-		   atoms[local_index]->get_vx(),
-		   atoms[local_index]->get_vy(),
-		   atoms[local_index]->get_vz());
+		   pos[0],
+		   pos[1],
+		   pos[2],
+		   vel[0],
+		   vel[1],
+		   vel[2]);
 	  strcpy( writeLine, tempBuffer );
 	  
 	  if( atoms[local_index]->isDirectional() ){
@@ -518,16 +573,19 @@ void DumpWriter::writeFinal(){
       }
       if (local_index != -1) {
 
+	atoms[local_index]->getPos(pos);
+	atoms[local_index]->getVel(vel);
+
 	//format the line
 	sprintf( tempBuffer,
 		 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 		 atoms[local_index]->getType(),
-		 atoms[local_index]->getX(),
-		 atoms[local_index]->getY(),
-		 atoms[local_index]->getZ(),
-		 atoms[local_index]->get_vx(),
-		 atoms[local_index]->get_vy(),
-		 atoms[local_index]->get_vz()); // check here.
+		 pos[0],
+		 pos[1],
+		 pos[2],
+		 vel[0],
+		 vel[1],
+		 vel[2]); // check here.
 	strcpy( writeLine, tempBuffer );
 	
 	if( atoms[local_index]->isDirectional() ){