--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/03/21 17:42:12	378
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/03/27 01:49:45	417
@@ -12,8 +12,9 @@
 #include "simError.h"
 
 #ifdef IS_MPI
+#include <mpi.h>
+#include <mpi++.h>
 #include "mpiSimulation.hpp"
-
 #define TAKE_THIS_TAG 0
 #endif // is_mpi
 
@@ -62,7 +63,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 
 void InitializeFromFile :: read_xyz( SimInfo* the_entry_plug ){
 
-  int i; // loop counter
+  int i, j, done, which_node, which_atom; // loop counter
 
   const int BUFFERSIZE = 2000; // size of the read buffer
   int n_atoms; // the number of atoms
@@ -138,14 +139,9 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
   // MPI Section of code..........
 #else //IS_MPI
 
-  int masterIndex;
-  int nodeAtomsStart;
-  int nodeAtomsEnd;
-  int mpiErr;
-  int sendError;
+  MPI::Status istatus;
+  int *AtomToProcMap = mpiSim->getAtomToProcMap();
 
-  MPI_Status istatus[MPI_STATUS_SIZE];
-
   if (worldRank == 0) {
     eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
     if( eof_test == NULL ){
@@ -182,10 +178,9 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
       simError();
     }
   
-    // Read Proc 0 share of the xyz file...
-    masterIndex = 0;
-    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
-    
+
+    for (i=0 ; i < mpiSim->getTotAtoms(); i++) {
+      
       eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
       if(eof_test == NULL){
 	sprintf(painCave.errMsg,
@@ -197,109 +192,52 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 	simError();
       }
     
-      parseErr = parseDumpLine( read_buffer, i );
-      if( parseErr != NULL ){
-	strcpy( painCave.errMsg, parseErr );
-	painCave.isFatal = 1;
-	simError();
-      }    
-      masterIndex++;
-    }
-  }
-
-  sprintf(checkPointMsg,
-	  "Node 0 has successfully read positions from input file.");
-  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 reading from, 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,
-		"Initialize from file error: atoms start index (%d) for "
-		"node %d not equal to master index (%d)",nodeAtomsStart,procIndex,masterIndex );
-	painCave.isFatal = 1;
-	simError();
+      // Get the Node number which wants this atom:
+      which_node = AtomToProcMap[i];     
+      if (which_node == mpiSim->getMyNode()) {
+        parseErr = parseDumpLine( read_buffer, i );
+        if( parseErr != NULL ){
+          strcpy( painCave.errMsg, parseErr );
+          painCave.isFatal = 1;
+          simError();
+        }    
+      } else {
+        MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, which_node, 
+                             TAKE_THIS_TAG);
+        MPI::COMM_WORLD.Send(&i, 1, MPI_INT, which_node, TAKE_THIS_TAG);
       }
-      sendError = 0;
-      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
-      
-      for ( i = nodeAtomsStart; i <= nodeAtomsEnd; i++){
-	eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
-	if(eof_test == NULL){
-	  
-	  sprintf(read_buffer,"ERROR");
-	  mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
-	  
-	  sprintf(painCave.errMsg,
-		  "error in reading file %s\n"
-		  "natoms  = %d; index = %d\n"
-		  "error reading the line from the file.\n",
-		  c_in_name, n_atoms, i );
-	  painCave.isFatal = 1;
-	  simError();
-	}
-	
-	mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
-	mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
-			  istatus);
-	if (sendError) MPIcheckPoint();
-
-	masterIndex++;
-      }
+    }
+    sprintf(read_buffer, "GAMEOVER");
+    for (j = 0; j < mpiSim->getNumberProcessors(); j++) {      
+      MPI::COMM_WORLD.Send(read_buffer, BUFFERSIZE, MPI_CHAR, j, 
+                           TAKE_THIS_TAG);
     }
 
+  } else {
 
-    else if(worldRank == procIndex){
-      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();
-
-      for ( i = 0; i < entry_plug->n_atoms; i++){
-
-	mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
-			  istatus);
-	
-	if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
-	
-	parseErr = parseDumpLine( read_buffer, i );
-	if( parseErr != NULL ){
-	  sendError = 1;
-	  mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
-
-
-	  strcpy( painCave.errMsg, parseErr );
-	  painCave.isFatal = 1;
-	  simError();
-	}
-	sendError = 0;
-	mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
+    done = 0;
+    while (!done) {
+      MPI::COMM_WORLD.Recv(read_buffer, BUFFERSIZE, MPI_CHAR, 0, 
+                           TAKE_THIS_TAG, istatus);
+      if (strcmp(read_buffer, "GAMEOVER")) {
+        done = 1;
+        continue;
+      } else {
+        MPI::COMM_WORLD.Recv(&which_atom, 1, MPI_INT, 0, 
+                             TAKE_THIS_TAG, istatus);
+        parseErr = parseDumpLine( read_buffer, which_atom );
+        if( parseErr != NULL ){
+          strcpy( painCave.errMsg, parseErr );
+          painCave.isFatal = 1;
+          simError();
+        } 
       }
     }
-    sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
-    MPIcheckPoint();
   }
-
+        
 #endif
 }
 
-
 char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
 
   char *foo; // the pointer to the current string token