--- trunk/mdtools/md_code/DumpWriter.cpp	2002/12/16 21:42:14	214
+++ trunk/mdtools/md_code/DumpWriter.cpp	2003/01/30 20:03:37	254
@@ -1,12 +1,19 @@
 #include <cstring>
 #include <iostream>
 #include <fstream>
+
+#ifdef IS_MPI
 #include <mpi.h>
+#include "mpiSimulation.hpp"
+#endif //is_mpi
 
 #include "ReadWrite.hpp"
 #include "simError.h"
 
 
+
+
+
 DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
 
 #ifdef IS_MPI
@@ -123,7 +130,7 @@ void DumpWriter::writeDump( double currentTime ){
   // write out header and node 0's coordinates
 
   if( worldRank == 0 ){
-    outFile << entry_plug->mpiSim->getTotAtoms() << "\n";
+    outFile << mpiSim->getTotAtoms() << "\n";
       
     outFile << currentTime << "\t" 
 	    << entry_plug->box_x << "\t"
@@ -163,13 +170,13 @@ void DumpWriter::writeDump( double currentTime ){
       else
 	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
 	
-      outfile << writeLine;
+      outFile << writeLine;
       masterIndex++;
     }
     outFile.flush();
   }
     
-  for (procIndex = 1; procIndex < entry_plug->mpiSim->getNumberProcessors();
+  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
        procIndex++){
 
     if( worldRank == 0 ){
@@ -201,9 +208,9 @@ void DumpWriter::writeDump( double currentTime ){
 
       // recieve the nodes writeLines
 
-      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
+      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
 	  
-	mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,
+	mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
 			  MPI_ANY_TAG,MPI_COMM_WORLD,istatus );
 
 	outFile << writeLine;
@@ -213,8 +220,8 @@ void DumpWriter::writeDump( double currentTime ){
 
     else if( worldRank == procIndex ){
 
-      nodeAtomStart = entry_plug->mpiSim->getMyAtomStart();
-      nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd();
+      nodeAtomsStart = mpiSim->getMyAtomStart();
+      nodeAtomsEnd = mpiSim->getMyAtomEnd();
 	
       mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,
 			MPI_COMM_WORLD);
@@ -223,7 +230,7 @@ void DumpWriter::writeDump( double currentTime ){
 	
       mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,
 			MPI_COMM_WORLD, istatus);
-      if (sendError) mpiCheckpoint();
+      if (sendError) MPIcheckPoint();
 
       // send current node's configuration line by line.
 
@@ -266,7 +273,7 @@ void DumpWriter::writeDump( double currentTime ){
       
     sprintf(checkPointMsg,"Node %d sent dump configuration.",
 	    procIndex);
-    mpiCheckPoint();
+    MPIcheckPoint();
   }
     
 #endif // is_mpi
@@ -311,8 +318,8 @@ void DumpWriter::writeFinal(){
 #ifdef IS_MPI
   }
   
-  sprintf(checkPointMsg,"Opened file for final configuration\n",procIndex);
-  mpiCheckPoint();  
+  sprintf(checkPointMsg,"Opened file for final configuration\n");
+  MPIcheckPoint();  
   
 #endif //is_mpi
 
@@ -322,10 +329,9 @@ void DumpWriter::writeFinal(){
     
   finalOut << nAtoms << "\n";
     
-  finalOut << currentTime << "\t" 
-	  << entry_plug->box_x << "\t"
-	  << entry_plug->box_y << "\t"
-	  << entry_plug->box_z << "\n";
+  finalOut << entry_plug->box_x << "\t"
+	   << entry_plug->box_y << "\t"
+	   << entry_plug->box_z << "\n";
     
   for( i=0; i<nAtoms; i++ ){
       
@@ -378,13 +384,12 @@ void DumpWriter::writeFinal(){
   // write out header and node 0's coordinates
 
   if( worldRank == 0 ){
-    finalOut << entry_plug->mpiSim->getTotAtoms() << "\n";
+    finalOut << mpiSim->getTotAtoms() << "\n";
       
-    finalOut << currentTime << "\t" 
-	    << entry_plug->box_x << "\t"
-	    << entry_plug->box_y << "\t"
-	    << entry_plug->box_z << "\n";
-
+    finalOut << entry_plug->box_x << "\t"
+	     << entry_plug->box_y << "\t"
+	     << entry_plug->box_z << "\n";
+    
     masterIndex = 0;
     for( i=0; i<nAtoms; i++ ){
       
@@ -418,13 +423,13 @@ void DumpWriter::writeFinal(){
       else
 	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
 	
-      outfile << writeLine;
+      outFile << writeLine;
       masterIndex++;
     }
     finalOut.flush();
   }
     
-  for (procIndex = 1; procIndex < entry_plug->mpiSim->getNumberProcessors();
+  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
        procIndex++){
 
     if( worldRank == 0 ){
@@ -456,9 +461,9 @@ void DumpWriter::writeFinal(){
 
       // recieve the nodes writeLines
 
-      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
+      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
 	  
-	mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,
+	mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
 			  MPI_ANY_TAG,MPI_COMM_WORLD,istatus );
 
 	finalOut << writeLine;
@@ -470,8 +475,8 @@ void DumpWriter::writeFinal(){
 
     else if( worldRank == procIndex ){
 
-      nodeAtomStart = entry_plug->mpiSim->getMyAtomStart();
-      nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd();
+      nodeAtomsStart = mpiSim->getMyAtomStart();
+      nodeAtomsEnd = mpiSim->getMyAtomEnd();
 	
       mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,
 			MPI_COMM_WORLD);
@@ -480,7 +485,7 @@ void DumpWriter::writeFinal(){
 	
       mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,
 			MPI_COMM_WORLD, istatus);
-      if (sendError) mpiCheckpoint();
+      if (sendError) MPIcheckPoint();
 
       // send current node's configuration line by line.
 
@@ -523,7 +528,7 @@ void DumpWriter::writeFinal(){
       
     sprintf(checkPointMsg,"Node %d sent dump configuration.",
 	    procIndex);
-    mpiCheckPoint();
+    MPIcheckPoint();
   }
 
   if( worldRank == 0 ) finalOut.close();