--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/07/11 01:15:28	591
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/09/25 19:27:15	787
@@ -1,3 +1,5 @@
+#define _FILE_OFFSET_BITS 64
+
 #include <cstring>
 #include <iostream>
 #include <fstream>
@@ -70,11 +72,17 @@ 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];
     
 
 #ifndef IS_MPI
@@ -96,16 +104,18 @@ void DumpWriter::writeDump( double currentTime ){
     
   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() ){
@@ -176,15 +186,19 @@ 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 +280,19 @@ 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 +353,15 @@ 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 ){
@@ -385,15 +408,18 @@ void DumpWriter::writeFinal(double finalTime){
   
   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() ){
@@ -462,16 +488,20 @@ 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 +581,19 @@ 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() ){