--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/07/09 22:14:06	586
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/10/28 16:03:37	829
@@ -1,4 +1,6 @@
-#include <cstring>
+#define _FILE_OFFSET_BITS 64
+
+#include <string.h>
 #include <iostream>
 #include <fstream>
 
@@ -70,42 +72,54 @@ void DumpWriter::writeDump( double currentTime ){
   char tempBuffer[BUFFERSIZE];
   char writeLine[BUFFERSIZE];
 
-  int i, j, which_node, done, which_atom, local_index;
+  int i;
+#ifdef IS_MPI
+  int j, which_node, done, which_atom, local_index;
+#else //is_mpi
+  int nAtoms = entry_plug->n_atoms;
+#endif //is_mpi
+
   double q[4];
   DirectionalAtom* dAtom;
-  int nAtoms = entry_plug->n_atoms;
   Atom** atoms = entry_plug->atoms;
+  double pos[3], vel[3];
     
+  
+  // write current frame to the eor file
 
+  this->writeFinal( currentTime );
+
 #ifndef IS_MPI
     
   outFile << nAtoms << "\n";
     
   outFile << currentTime << ";\t" 
-	  << entry_plug->Hmat[0] << "\t"
-	  << entry_plug->Hmat[1] << "\t"
-	  << entry_plug->Hmat[2] << ";\t"
+	  << entry_plug->Hmat[0][0] << "\t"
+	  << entry_plug->Hmat[1][0] << "\t"
+	  << entry_plug->Hmat[2][0] << ";\t"
 
-	  << entry_plug->Hmat[3] << "\t"
-	  << entry_plug->Hmat[4] << "\t"
-	  << entry_plug->Hmat[5] << ";\t"
+	  << entry_plug->Hmat[0][1] << "\t"
+	  << entry_plug->Hmat[1][1] << "\t"
+	  << entry_plug->Hmat[2][1] << ";\t"
 
-	  << entry_plug->Hmat[6] << "\t"
-	  << entry_plug->Hmat[7] << "\t"
-	  << entry_plug->Hmat[8] << ";\n";
+	  << 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() ){
@@ -147,19 +161,19 @@ void DumpWriter::writeDump( double currentTime ){
   if( worldRank == 0 ){
     outFile << mpiSim->getTotAtoms() << "\n";
   
-    outFile << currentTime << "\t" 
-	    << entry_plug->Hmat[0] << "\t"
-	    << entry_plug->Hmat[1] << "\t"
-	    << entry_plug->Hmat[2] << "\t"
+    outFile << currentTime << ";\t" 
+	    << entry_plug->Hmat[0][0] << "\t"
+	    << entry_plug->Hmat[1][0] << "\t"
+	    << entry_plug->Hmat[2][0] << ";\t"
       
-	    << entry_plug->Hmat[3] << "\t"
-	    << entry_plug->Hmat[4] << "\t"
-	    << entry_plug->Hmat[5] << "\t"
+	    << entry_plug->Hmat[0][1] << "\t"
+	    << entry_plug->Hmat[1][1] << "\t"
+	    << entry_plug->Hmat[2][1] << ";\t"
       
-	    << entry_plug->Hmat[6] << "\t"
-	    << entry_plug->Hmat[7] << "\t"
-	    << entry_plug->Hmat[8] << "\n";
-    ;
+	    << entry_plug->Hmat[0][2] << "\t"
+	    << entry_plug->Hmat[1][2] << "\t"
+	    << entry_plug->Hmat[2][2] << ";\n";
+    
     outFile.flush();
     for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this atom;
@@ -176,15 +190,19 @@ 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() ){
@@ -266,15 +284,19 @@ 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() ){
@@ -335,10 +357,15 @@ void DumpWriter::writeFinal(double finalTime){
 
   double q[4];
   DirectionalAtom* dAtom;
-  int nAtoms = entry_plug->n_atoms;
   Atom** atoms = entry_plug->atoms;
-  int i, j, which_node, done, game_over, which_atom, local_index;
+  int i;
+#ifdef IS_MPI
+  int j, which_node, done, which_atom, local_index;
+#else //is_mpi
+  int nAtoms = entry_plug->n_atoms;
+#endif //is_mpi
   
+  double pos[3], vel[3];
   
 #ifdef IS_MPI
   if(worldRank == 0 ){
@@ -370,30 +397,33 @@ void DumpWriter::writeFinal(double finalTime){
     
   finalOut << nAtoms << "\n";
     
-  finalOut << finalTime << "\t"
-	   << entry_plug->Hmat[0] << "\t"
-	   << entry_plug->Hmat[1] << "\t"
-	   << entry_plug->Hmat[2] << "\t"
+  finalOut << finalTime << ";\t"
+	   << entry_plug->Hmat[0][0] << "\t"
+	   << entry_plug->Hmat[1][0] << "\t"
+	   << entry_plug->Hmat[2][0] << ";\t"
     
-	   << entry_plug->Hmat[3] << "\t"
-	   << entry_plug->Hmat[4] << "\t"
-	   << entry_plug->Hmat[5] << "\t"
+	   << entry_plug->Hmat[0][1] << "\t"
+	   << entry_plug->Hmat[1][1] << "\t"
+	   << entry_plug->Hmat[2][1] << ";\t"
     
-	   << entry_plug->Hmat[6] << "\t"
-	   << entry_plug->Hmat[7] << "\t"
-	   << entry_plug->Hmat[8] << "\n";
+	   << 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() ){
@@ -437,18 +467,18 @@ void DumpWriter::writeFinal(double finalTime){
   if( worldRank == 0 ){
     finalOut << mpiSim->getTotAtoms() << "\n";
     
-    finalOut << finalTime << "\t"
-	     << entry_plug->Hmat[0] << "\t"
-	     << entry_plug->Hmat[1] << "\t"
-	     << entry_plug->Hmat[2] << "\t"
+    finalOut << finalTime << ";\t"
+	     << entry_plug->Hmat[0][0] << "\t"
+	     << entry_plug->Hmat[1][0] << "\t"
+	     << entry_plug->Hmat[2][0] << ";\t"
       
-	     << entry_plug->Hmat[3] << "\t"
-	     << entry_plug->Hmat[4] << "\t"
-	     << entry_plug->Hmat[5] << "\t"
+	     << entry_plug->Hmat[0][1] << "\t"
+	     << entry_plug->Hmat[1][1] << "\t"
+	     << entry_plug->Hmat[2][1] << ";\t"
       
-	     << entry_plug->Hmat[6] << "\t"
-	     << entry_plug->Hmat[7] << "\t"
-	     << entry_plug->Hmat[8] << "\n";
+	     << 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:
@@ -462,16 +492,20 @@ void DumpWriter::writeFinal(double finalTime){
         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() ){
@@ -551,16 +585,19 @@ void DumpWriter::writeFinal(double finalTime){
       }
       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() ){