--- trunk/mdtools/md_code/DumpWriter.cpp	2002/12/16 21:42:14	214
+++ trunk/mdtools/md_code/DumpWriter.cpp	2003/02/03 21:15:59	261
@@ -1,24 +1,32 @@
 #include <cstring>
 #include <iostream>
 #include <fstream>
+
+#ifdef IS_MPI
 #include <mpi.h>
+#include "mpiSimulation.hpp"
+#define TAKE_THIS_TAG 0
+#endif //is_mpi
 
 #include "ReadWrite.hpp"
 #include "simError.h"
 
 
+
+
+
 DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
 
+  entry_plug = the_entry_plug;
+
 #ifdef IS_MPI
   if(worldRank == 0 ){
 #endif // is_mpi
     
-    entry_plug = the_entry_plug;
+ 
     
     strcpy( outName, entry_plug->sampleName );
     
-    std::cerr << "Opening " << outName << " for dumping.\n";
-
     outFile.open(outName, ios::out | ios::trunc );
     
     if( !outFile ){
@@ -34,6 +42,10 @@ DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
 
 #ifdef IS_MPI
   }
+
+  sprintf( checkPointMsg,
+	   "Sucessfully opened output file for dumping.\n");
+  MPIcheckPoint();
 #endif // is_mpi
 }
 
@@ -53,7 +65,7 @@ void DumpWriter::writeDump( double currentTime ){
 void DumpWriter::writeDump( double currentTime ){
   
   const int BUFFERSIZE = 2000;
-  char tempBuffer[500];
+  char tempBuffer[BUFFERSIZE];
   char writeLine[BUFFERSIZE];
 
   int i;
@@ -74,6 +86,7 @@ void DumpWriter::writeDump( double currentTime ){
     
   for( i=0; i<nAtoms; i++ ){
       
+
     sprintf( tempBuffer,
 	     "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 	     atoms[i]->getType(),
@@ -123,7 +136,7 @@ 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"
@@ -163,29 +176,33 @@ 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();
   }
+
+  sprintf( checkPointMsg,
+	   "Sucessfully wrote node 0's dump configuration.\n");
+  MPIcheckPoint();
     
-  for (procIndex = 1; procIndex < entry_plug->mpiSim->getNumberProcessors();
+  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
        procIndex++){
 
     if( worldRank == 0 ){
-	
+      
       mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
-			MPI_ANY_TAG,MPI_COMM_WORLD,istatus);
-
+			TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
+      
       mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
-			MPI_ANY_TAG,MPI_COMM_WORLD, istatus);
-	
+			TAKE_THIS_TAG,MPI_COMM_WORLD, istatus);
+      
       // Make sure where node 0 is writing to, matches where the
       // receiving node expects it to be.
-	
+      
       if (masterIndex != nodeAtomsStart){
 	sendError = 1;
-	mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,
+	mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
 			  MPI_COMM_WORLD);
 	sprintf(painCave.errMsg,
 		"DumpWriter error: atoms start index (%d) for "
@@ -194,18 +211,18 @@ void DumpWriter::writeDump( double currentTime ){
 	painCave.isFatal = 1;
 	simError();
       }
-	
+      
       sendError = 0;
-      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,
+      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
 			MPI_COMM_WORLD);
-
+      
       // recieve the nodes writeLines
-
-      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
-	  
-	mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,
-			  MPI_ANY_TAG,MPI_COMM_WORLD,istatus );
-
+      
+      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
+	
+	mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
+			  TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
+	
 	outFile << writeLine;
 	masterIndex++;
       }
@@ -213,22 +230,24 @@ void DumpWriter::writeDump( double currentTime ){
 
     else if( worldRank == procIndex ){
 
-      nodeAtomStart = entry_plug->mpiSim->getMyAtomStart();
-      nodeAtomEnd = entry_plug->mpiSim->getMyAtomEnd();
-	
-      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,MPI_ANY_TAG,
+      nodeAtomsStart = mpiSim->getMyAtomStart();
+      nodeAtomsEnd = mpiSim->getMyAtomEnd();
+
+      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,
 			MPI_COMM_WORLD);
-      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,
+      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,
 			MPI_COMM_WORLD);
 	
-      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,
+      sendError = -1;
+      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,
 			MPI_COMM_WORLD, istatus);
-      if (sendError) mpiCheckpoint();
+
+      if (sendError) MPIcheckPoint();
 
       // send current node's configuration line by line.
 
       for( i=0; i<nAtoms; i++ ){
-	  
+
 	sprintf( tempBuffer,
 		 "%s\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t",
 		 atoms[i]->getType(),
@@ -237,7 +256,7 @@ void DumpWriter::writeDump( double currentTime ){
 		 atoms[i]->getZ(),
 		 atoms[i]->get_vx(),
 		 atoms[i]->get_vy(),
-		 atoms[i]->get_vz());
+		 atoms[i]->get_vz()); // check here.
 	strcpy( writeLine, tempBuffer );
 	  
 	if( atoms[i]->isDirectional() ){
@@ -259,14 +278,14 @@ void DumpWriter::writeDump( double currentTime ){
 	else
 	  strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
 	  
-	mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,
+	mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,
 			  MPI_COMM_WORLD);
       }
     }
       
     sprintf(checkPointMsg,"Node %d sent dump configuration.",
 	    procIndex);
-    mpiCheckPoint();
+    MPIcheckPoint();
   }
     
 #endif // is_mpi
@@ -311,8 +330,8 @@ 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 +341,9 @@ 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++ ){
       
@@ -378,14 +396,14 @@ 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++ ){
       
       sprintf( tempBuffer,
@@ -418,29 +436,29 @@ void DumpWriter::writeFinal(){
       else
 	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
 	
-      outfile << writeLine;
+      finalOut << writeLine;
       masterIndex++;
     }
     finalOut.flush();
   }
     
-  for (procIndex = 1; procIndex < entry_plug->mpiSim->getNumberProcessors();
+  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
        procIndex++){
 
     if( worldRank == 0 ){
 	
       mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
-			MPI_ANY_TAG,MPI_COMM_WORLD,istatus);
+			TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
 
       mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
-			MPI_ANY_TAG,MPI_COMM_WORLD, istatus);
+			TAKE_THIS_TAG,MPI_COMM_WORLD, istatus);
 	
       // Make sure where node 0 is writing to, matches where the
       // receiving node expects it to be.
 	
       if (masterIndex != nodeAtomsStart){
 	sendError = 1;
-	mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,
+	mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
 			  MPI_COMM_WORLD);
 	sprintf(painCave.errMsg,
 		"DumpWriter error: atoms start index (%d) for "
@@ -451,15 +469,15 @@ void DumpWriter::writeFinal(){
       }
 	
       sendError = 0;
-      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,
+      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
 			MPI_COMM_WORLD);
 
       // 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,
-			  MPI_ANY_TAG,MPI_COMM_WORLD,istatus );
+	mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
+			  TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
 
 	finalOut << writeLine;
 	masterIndex++;
@@ -470,17 +488,17 @@ 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,
+      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,
 			MPI_COMM_WORLD);
-      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,
+      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,
 			MPI_COMM_WORLD);
 	
-      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_TAG,
+      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,
 			MPI_COMM_WORLD, istatus);
-      if (sendError) mpiCheckpoint();
+      if (sendError) MPIcheckPoint();
 
       // send current node's configuration line by line.
 
@@ -516,14 +534,14 @@ void DumpWriter::writeFinal(){
 	else
 	  strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
 	  
-	mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,
+	mpiErr = MPI_Send(writeLine,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,
 			  MPI_COMM_WORLD);
       }
     }
       
     sprintf(checkPointMsg,"Node %d sent dump configuration.",
 	    procIndex);
-    mpiCheckPoint();
+    MPIcheckPoint();
   }
 
   if( worldRank == 0 ) finalOut.close();