--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/03/26 22:24:49	415
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/03/26 23:14:02	416
@@ -4,6 +4,7 @@
 
 #ifdef IS_MPI
 #include <mpi.h>
+#include <mpi++.h>
 #include "mpiSimulation.hpp"
 #define TAKE_THIS_TAG 0
 #endif //is_mpi
@@ -11,8 +12,6 @@
 #include "ReadWrite.hpp"
 #include "simError.h"
 
-#define GAME_OVER -1
-
 DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
 
   entry_plug = the_entry_plug;
@@ -66,7 +65,7 @@ void DumpWriter::writeDump( double currentTime ){
   char tempBuffer[BUFFERSIZE];
   char writeLine[BUFFERSIZE];
 
-  int i;
+  int i, j, which_node, done, game_over, which_atom;
   double q[4];
   DirectionalAtom* dAtom;
   int nAtoms = entry_plug->n_atoms;
@@ -120,9 +119,10 @@ void DumpWriter::writeDump( double currentTime ){
   outFile.flush();
 
 #else // is_mpi
+
+  MPI::Status istatus;
+  int *AtomToProcMap = mpiSim->getAtomToProcMap();
   
-  MPI_Status istatus[MPI_STATUS_SIZE];
-  
   // write out header and node 0's coordinates
   
   if( worldRank == 0 ){
@@ -133,12 +133,12 @@ void DumpWriter::writeDump( double currentTime ){
 	    << entry_plug->box_y << "\t"
 	    << entry_plug->box_z << "\n";
     
-    for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) {
+    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this molecule:
       
       which_node = AtomToProcMap[i];     
       
-      if (which_node == mpiPlug->myNode) {
+      if (which_node == mpiSim->getMyNode()) {
         
         sprintf( tempBuffer,
                  "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
@@ -173,7 +173,7 @@ void DumpWriter::writeDump( double currentTime ){
       } else {
         
         MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
-        MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
+        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
                                 TAKE_THIS_TAG, istatus);
       }
       
@@ -181,18 +181,19 @@ void DumpWriter::writeDump( double currentTime ){
     }
     
     // kill everyone off:
-    for (j = 0; j < mpiPlug->numberProcessors; j++) {
-      MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG);
+    game_over = -1;
+    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
+      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG);
     }
 
   } else {
     
     done = 0;
     while (!done) {
-      MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, 
+      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, 
                               TAKE_THIS_TAG, istatus);
 
-      if (which_atom == GAME_OVER) {
+      if (which_atom == -1) {
         done=1;
         continue;
       } else {
@@ -241,10 +242,21 @@ void DumpWriter::writeFinal(){
 }
 
 void DumpWriter::writeFinal(){
-  
+
   char finalName[500];
   ofstream finalOut;
+
+  const int BUFFERSIZE = 2000;
+  char tempBuffer[BUFFERSIZE];
+  char writeLine[BUFFERSIZE];  
+
+  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;
   
+  
 #ifdef IS_MPI
   if(worldRank == 0 ){
 #endif // is_mpi
@@ -278,7 +290,7 @@ void DumpWriter::writeFinal(){
   finalOut << entry_plug->box_x << "\t"
 	   << entry_plug->box_y << "\t"
 	   << entry_plug->box_z << "\n";
-    
+  
   for( i=0; i<nAtoms; i++ ){
       
     sprintf( tempBuffer,
@@ -318,8 +330,9 @@ void DumpWriter::writeFinal(){
 
 #else // is_mpi
   
-  MPI_Status istatus[MPI_STATUS_SIZE];
-  
+  MPI::Status istatus;
+  int *AtomToProcMap = mpiSim->getAtomToProcMap();
+
   // write out header and node 0's coordinates
   
   if( worldRank == 0 ){
@@ -329,12 +342,12 @@ void DumpWriter::writeFinal(){
 	    << entry_plug->box_y << "\t"
 	    << entry_plug->box_z << "\n";
     
-    for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) {
+    for (i = 0 ; i < mpiSim->getTotAtoms(); i++ ) {
       // Get the Node number which has this molecule:
       
       which_node = AtomToProcMap[i];     
       
-      if (which_node == mpiPlug->myNode) {
+      if (which_node == mpiSim->getMyNode()) {
         
         sprintf( tempBuffer,
                  "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
@@ -369,7 +382,7 @@ void DumpWriter::writeFinal(){
       } else {
         
         MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
-        MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
+        MPI::COMM_WORLD.Recv(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
                                 TAKE_THIS_TAG, istatus);
       }
       
@@ -377,18 +390,19 @@ void DumpWriter::writeFinal(){
     }
     
     // kill everyone off:
-    for (j = 0; j < mpiPlug->numberProcessors; j++) {
-      MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG);
+    game_over = -1;
+    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {
+      MPI::COMM_WORLD.Send(&game_over, 1, MPI_INT, j, TAKE_THIS_TAG);
     }
 
   } else {
     
     done = 0;
     while (!done) {
-      MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, 
-                              TAKE_THIS_TAG, istatus);
+      MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, 
+                           TAKE_THIS_TAG, istatus);
 
-      if (which_atom == GAME_OVER) {
+      if (which_atom == -1) {
         done=1;
         continue;
       } else {