--- trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/03/21 17:42:12	378
+++ trunk/OOPSE/libmdtools/DumpWriter.cpp	2003/03/26 22:24:49	415
@@ -11,10 +11,8 @@
 #include "ReadWrite.hpp"
 #include "simError.h"
 
+#define GAME_OVER -1
 
-
-
-
 DumpWriter::DumpWriter( SimInfo* the_entry_plug ){
 
   entry_plug = the_entry_plug;
@@ -122,146 +120,98 @@ void DumpWriter::writeDump( double currentTime ){
   outFile.flush();
 
 #else // is_mpi
-
-  int masterIndex;
-  int nodeAtomsStart;
-  int nodeAtomsEnd;
-  int mpiErr;
-  int sendError;
-  int procIndex;
-    
+  
   MPI_Status istatus[MPI_STATUS_SIZE];
-
-    
+  
   // write out header and node 0's coordinates
-
+  
   if( worldRank == 0 ){
     outFile << mpiSim->getTotAtoms() << "\n";
-      
+    
     outFile << currentTime << "\t" 
 	    << entry_plug->box_x << "\t"
 	    << entry_plug->box_y << "\t"
 	    << entry_plug->box_z << "\n";
-
-    masterIndex = 0;
-    for( i=0; i<nAtoms; i++ ){
+    
+    for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) {
+      // Get the Node number which has this molecule:
       
-      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());
-      strcpy( writeLine, tempBuffer );
+      which_node = AtomToProcMap[i];     
+      
+      if (which_node == mpiPlug->myNode) {
+        
+        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());
+        strcpy( writeLine, tempBuffer );
 	
-      if( atoms[i]->isDirectional() ){
+        if( atoms[i]->isDirectional() ){
 	  
-	dAtom = (DirectionalAtom *)atoms[i];
-	dAtom->getQ( q );
+          dAtom = (DirectionalAtom *)atoms[i];
+          dAtom->getQ( q );
 	  
-	sprintf( tempBuffer,
-		 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
-		 q[0],
-		 q[1],
-		 q[2],
-		 q[3],
-		 dAtom->getJx(),
-		 dAtom->getJy(),
-		 dAtom->getJz());
-	strcat( writeLine, tempBuffer );
+          sprintf( tempBuffer,
+                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
+                   q[0],
+                   q[1],
+                   q[2],
+                   q[3],
+                   dAtom->getJx(),
+                   dAtom->getJy(),
+                   dAtom->getJz());
+          strcat( writeLine, tempBuffer );
+        }
+        else
+          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );       
+        
+      } else {
+        
+        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
+        MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
+                                TAKE_THIS_TAG, istatus);
       }
-      else
-	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
-	
+      
       outFile << writeLine;
-      masterIndex++;
     }
-    outFile.flush();
-  }
-
-  sprintf( checkPointMsg,
-	   "Sucessfully wrote node 0's dump configuration.\n");
-  MPIcheckPoint();
     
-  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
-       procIndex++){
-
-    if( worldRank == 0 ){
-      
-      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
-			TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
-      
-      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
-			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,TAKE_THIS_TAG,
-			  MPI_COMM_WORLD);
-	sprintf(painCave.errMsg,
-		"DumpWriter error: atoms start index (%d) for "
-		"node %d not equal to master index (%d)",
-		nodeAtomsStart,procIndex,masterIndex );
-	painCave.isFatal = 1;
-	simError();
-      }
-      
-      sendError = 0;
-      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
-			MPI_COMM_WORLD);
-      
-      // recieve the nodes writeLines
-      
-      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
-	
-	mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
-			  TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
-	
-	outFile << writeLine;
-	masterIndex++;
-      }
+    // kill everyone off:
+    for (j = 0; j < mpiPlug->numberProcessors; j++) {
+      MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG);
     }
 
-    else if( worldRank == procIndex ){
+  } else {
+    
+    done = 0;
+    while (!done) {
+      MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, 
+                              TAKE_THIS_TAG, istatus);
 
-      nodeAtomsStart = mpiSim->getMyAtomStart();
-      nodeAtomsEnd = mpiSim->getMyAtomEnd();
+      if (which_atom == GAME_OVER) {
+        done=1;
+        continue;
+      } else {
 
-      mpiErr = MPI_Send(&nodeAtomsStart,1,MPI_INT,0,TAKE_THIS_TAG,
-			MPI_COMM_WORLD);
-      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,TAKE_THIS_TAG,
-			MPI_COMM_WORLD);
-	
-      sendError = -1;
-      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,
-			MPI_COMM_WORLD, istatus);
-
-      if (sendError) MPIcheckPoint();
-
-      // send current node's configuration line by line.
-
-      for( i=0; i<nAtoms; i++ ){
-
+        //format the line
 	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()); // check here.
+		 atoms[which_atom]->getType(),
+		 atoms[which_atom]->getX(),
+		 atoms[which_atom]->getY(),
+		 atoms[which_atom]->getZ(),
+		 atoms[which_atom]->get_vx(),
+		 atoms[which_atom]->get_vy(),
+		 atoms[which_atom]->get_vz()); // check here.
 	strcpy( writeLine, tempBuffer );
 	  
-	if( atoms[i]->isDirectional() ){
+	if( atoms[which_atom]->isDirectional() ){
 	    
-	  dAtom = (DirectionalAtom *)atoms[i];
+	  dAtom = (DirectionalAtom *)atoms[which_atom];
 	  dAtom->getQ( q );
 	    
 	  sprintf( tempBuffer,
@@ -277,37 +227,22 @@ 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,TAKE_THIS_TAG,
-			  MPI_COMM_WORLD);
+        
+        MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
+                             TAKE_THIS_TAG);
       }
     }
-      
-    sprintf(checkPointMsg,"Node %d sent dump configuration.",
-	    procIndex);
-    MPIcheckPoint();
-  }
-    
+  }  
+  outFile.flush();
+  sprintf( checkPointMsg,
+	   "Sucessfully took a dump.\n");
+  MPIcheckPoint();
 #endif // is_mpi
 }
 
-
-
 void DumpWriter::writeFinal(){
-
-
-  const int BUFFERSIZE = 2000;
-  char tempBuffer[500];
-  char writeLine[BUFFERSIZE];
   
   char finalName[500];
-
-  int i;
-  double q[4];
-  DirectionalAtom* dAtom;
-  int nAtoms = entry_plug->n_atoms;
-  Atom** atoms = entry_plug->atoms;
-  
   ofstream finalOut;
   
 #ifdef IS_MPI
@@ -335,8 +270,7 @@ void DumpWriter::writeFinal(){
   
 #endif //is_mpi
 
-    
-
+  
 #ifndef IS_MPI
     
   finalOut << nAtoms << "\n";
@@ -380,144 +314,100 @@ void DumpWriter::writeFinal(){
     finalOut << writeLine;
   }
   finalOut.flush();
+  finalOut.close();
 
 #else // is_mpi
-
-  int masterIndex;
-  int nodeAtomsStart;
-  int nodeAtomsEnd;
-  int mpiErr;
-  int sendError;
-  int procIndex;
-    
+  
   MPI_Status istatus[MPI_STATUS_SIZE];
-
-    
+  
   // write out header and node 0's coordinates
-
+  
   if( worldRank == 0 ){
     finalOut << mpiSim->getTotAtoms() << "\n";
-      
+    
     finalOut << entry_plug->box_x << "\t"
-	     << entry_plug->box_y << "\t"
-	     << entry_plug->box_z << "\n";
+	    << entry_plug->box_y << "\t"
+	    << entry_plug->box_z << "\n";
     
-    masterIndex = 0;
-    
-    for( i=0; i<nAtoms; i++ ){
+    for (i = 0 ; i < mpiPlug->nAtomsGlobal; i++ ) {
+      // Get the Node number which has this molecule:
       
-      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());
-      strcpy( writeLine, tempBuffer );
+      which_node = AtomToProcMap[i];     
+      
+      if (which_node == mpiPlug->myNode) {
+        
+        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());
+        strcpy( writeLine, tempBuffer );
 	
-      if( atoms[i]->isDirectional() ){
+        if( atoms[i]->isDirectional() ){
 	  
-	dAtom = (DirectionalAtom *)atoms[i];
-	dAtom->getQ( q );
+          dAtom = (DirectionalAtom *)atoms[i];
+          dAtom->getQ( q );
 	  
-	sprintf( tempBuffer,
-		 "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
-		 q[0],
-		 q[1],
-		 q[2],
-		 q[3],
-		 dAtom->getJx(),
-		 dAtom->getJy(),
-		 dAtom->getJz());
-	strcat( writeLine, tempBuffer );
+          sprintf( tempBuffer,
+                   "%lf\t%lf\t%lf\t%lf\t%lf\t%lf\t%lf\n",
+                   q[0],
+                   q[1],
+                   q[2],
+                   q[3],
+                   dAtom->getJx(),
+                   dAtom->getJy(),
+                   dAtom->getJz());
+          strcat( writeLine, tempBuffer );
+        }
+        else
+          strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );       
+        
+      } else {
+        
+        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
+        MPI::COMM_WORLD.Receive(writeLine, BUFFERSIZE, MPI_CHAR, which_node,
+                                TAKE_THIS_TAG, istatus);
       }
-      else
-	strcat( writeLine, "0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\n" );
-	
+      
       finalOut << writeLine;
-      masterIndex++;
     }
-    finalOut.flush();
-  }
     
-  for (procIndex = 1; procIndex < mpiSim->getNumberProcessors();
-       procIndex++){
-
-    if( worldRank == 0 ){
-	
-      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,
-			TAKE_THIS_TAG,MPI_COMM_WORLD,istatus);
-
-      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,
-			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,TAKE_THIS_TAG,
-			  MPI_COMM_WORLD);
-	sprintf(painCave.errMsg,
-		"DumpWriter error: atoms start index (%d) for "
-		"node %d not equal to master index (%d)",
-		nodeAtomsStart,procIndex,masterIndex );
-	painCave.isFatal = 1;
-	simError();
-      }
-	
-      sendError = 0;
-      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,
-			MPI_COMM_WORLD);
-
-      // recieve the nodes writeLines
-
-      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
-	  
-	mpiErr = MPI_Recv(writeLine,BUFFERSIZE,MPI_CHAR,procIndex,
-			  TAKE_THIS_TAG,MPI_COMM_WORLD,istatus );
-
-	finalOut << writeLine;
-	masterIndex++;
-      }
-
-      finalOut.flush();
+    // kill everyone off:
+    for (j = 0; j < mpiPlug->numberProcessors; j++) {
+      MPI::COMM_WORLD.Send(GAME_OVER, 1, MPI_INT, j, TAKE_THIS_TAG);
     }
 
-    else if( worldRank == procIndex ){
+  } else {
+    
+    done = 0;
+    while (!done) {
+      MPI::COMM_WORLD.Receive(&which_atom, 1, MPI_INT, 0, 
+                              TAKE_THIS_TAG, istatus);
 
-      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,TAKE_THIS_TAG,
-			MPI_COMM_WORLD);
-	
-      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,
-			MPI_COMM_WORLD, istatus);
-      if (sendError) MPIcheckPoint();
+      if (which_atom == GAME_OVER) {
+        done=1;
+        continue;
+      } else {
 
-      // send current node's configuration line by line.
-
-      for( i=0; i<nAtoms; i++ ){
-	  
+        //format the line
 	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());
+		 atoms[which_atom]->getType(),
+		 atoms[which_atom]->getX(),
+		 atoms[which_atom]->getY(),
+		 atoms[which_atom]->getZ(),
+		 atoms[which_atom]->get_vx(),
+		 atoms[which_atom]->get_vy(),
+		 atoms[which_atom]->get_vz()); // check here.
 	strcpy( writeLine, tempBuffer );
 	  
-	if( atoms[i]->isDirectional() ){
+	if( atoms[which_atom]->isDirectional() ){
 	    
-	  dAtom = (DirectionalAtom *)atoms[i];
+	  dAtom = (DirectionalAtom *)atoms[which_atom];
 	  dAtom->getQ( q );
 	    
 	  sprintf( tempBuffer,
@@ -533,19 +423,17 @@ 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,TAKE_THIS_TAG,
-			  MPI_COMM_WORLD);
+        
+        MPI::COMM_WORLD.Send(writeLine, BUFFERSIZE, MPI_CHAR, 0, 
+                             TAKE_THIS_TAG);
       }
     }
-      
-    sprintf(checkPointMsg,"Node %d sent dump configuration.",
-	    procIndex);
-    MPIcheckPoint();
-  }
+  }  
+  finalOut.flush();
+  sprintf( checkPointMsg,
+	   "Sucessfully took a dump.\n");
+  MPIcheckPoint();
 
-  if( worldRank == 0 ) finalOut.close();
-
-    
+  if( worldRank == 0 ) finalOut.close();    
 #endif // is_mpi
 }