--- trunk/mdtools/md_code/InitializeFromFile.cpp	2002/12/13 21:17:00	212
+++ trunk/mdtools/md_code/InitializeFromFile.cpp	2003/01/31 21:04:27	260
@@ -11,7 +11,12 @@
 #include "ReadWrite.hpp"
 #include "simError.h"
 
+#ifdef IS_MPI
+#include "mpiSimulation.hpp"
 
+#define TAKE_THIS_TAG 0
+#endif // is_mpi
+
 InitializeFromFile :: InitializeFromFile( char *in_name ){
 #ifdef IS_MPI
   if (worldRank == 0) {
@@ -68,11 +73,11 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 
   char *eof_test; // ptr to see when we reach the end of the file 
   char *parseErr;
+  int procIndex;
 
+  entry_plug = the_entry_plug;
 
-  entry_plug = the_entry_plug
 
-
 #ifndef IS_MPI
   eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
   if( eof_test == NULL ){
@@ -158,7 +163,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
     // Check to see that the number of atoms in the intial configuration file is the
     // same as declared in simBass.
     
-    if( n_atoms != entry_plug->mpiSim->getTotAtoms() ){
+    if( n_atoms != mpiSim->getTotAtoms() ){
       sprintf( painCave.errMsg,
 	       "Initialize from File error. %s n_atoms, %d, "
 	       "does not match the BASS file's n_atoms, %d.\n",
@@ -179,7 +184,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
   
     // Read Proc 0 share of the xyz file...
     masterIndex = 0;
-    for( i=0; i <= entry_plug->mpiSim->getMyAtomEnd(); i++){
+    for( i=0; i <= mpiSim->getMyAtomEnd(); i++){
     
       eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
       if(eof_test == NULL){
@@ -204,23 +209,23 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 
   sprintf(checkPointMsg,
 	  "Node 0 has successfully read positions from input file.");
-  mpiCheckPoint();
+  MPIcheckPoint();
 
-  for (procIndex = 1; procIndex < entryPlug->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,
+      mpiErr = MPI_Recv(&nodeAtomsStart,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD,
 	       istatus);
 
-      mpiErr = MPI_Recv(&nodeAtomsEnd,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
+      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,MPI_ANY_TAG,MPI_COMM_WORLD);
+	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 );
@@ -228,14 +233,14 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 	simError();
       }
       sendError = 0;
-      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
+      mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
       
-      for ( i = nodeAtomStart; i <= nodeAtomEnd, i++){
+      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,MPI_ANY_TAG,MPI_COMM_WORLD);
+	  mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,TAKE_THIS_TAG,MPI_COMM_WORLD);
 	  
 	  sprintf(painCave.errMsg,
 		  "error in reading file %s\n"
@@ -246,10 +251,10 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 	  simError();
 	}
 	
-	mpiErr = MPI_Send(read_buffer,BUFFERSIZE,MPI_CHAR,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD);
-	mpiErr = MPI_Recv(&sendError,1,MPI_INT,procIndex,MPI_ANY_TAG,MPI_COMM_WORLD,
+	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();
+	if (sendError) MPIcheckPoint();
 
 	masterIndex++;
       }
@@ -257,26 +262,26 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 
 
     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,MPI_COMM_WORLD);
-      mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
+      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,MPI_ANY_TAG,MPI_COMM_WORLD,
+      mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
 	       istatus);
-      if (sendError) mpiCheckpoint();
+      if (sendError) MPIcheckPoint();
 
-      for ( i = 0; i < entry_plug->n_atoms, i++){
+      for ( i = 0; i < entry_plug->n_atoms; i++){
 
-	mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,MPI_ANY_TAG,MPI_COMM_WORLD,
+	mpiErr = MPI_Recv(&read_buffer,BUFFERSIZE,MPI_CHAR,0,TAKE_THIS_TAG,MPI_COMM_WORLD,
 			  istatus);
 	
-	if(!strcmp(read_buffer, "ERROR")) mpiCheckPoint();
+	if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
 	
 	parseErr = parseDumpLine( read_buffer, i );
 	if( parseErr != NULL ){
 	  sendError = 1;
-	  mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
+	  mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
 
 
 	  strcpy( painCave.errMsg, parseErr );
@@ -284,18 +289,18 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 	  simError();
 	}
 	sendError = 0;
-	mpiErr = MPI_Send(&sendError,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
+	mpiErr = MPI_Send(&sendError,1,MPI_INT,0,TAKE_THIS_TAG,MPI_COMM_WORLD);
       }
     }
     sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
-    mpiCheckPoint();
+    MPIcheckPoint();
   }
 
 #endif
 }
 
 
-char* IntitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
+char* InitializeFromFile::parseDumpLine(char* readLine, int atomIndex){
 
   char *foo; // the pointer to the current string token 
   
@@ -311,10 +316,10 @@ char* IntitializeFromFile::parseDumpLine(char* readLin
   int n_atoms;
 
 #ifdef IS_MPI
-  n_atoms = entry_plug->mpiSim->getTotAtoms();
+  n_atoms = mpiSim->getTotAtoms();
 #else
   n_atoms = entry_plug->n_atoms;
-#endi // is_mpi
+#endif // is_mpi
 
 
   // set the string tokenizer