--- trunk/mdtools/md_code/InitializeFromFile.cpp	2002/12/13 21:17:00	212
+++ trunk/mdtools/md_code/InitializeFromFile.cpp	2003/01/30 20:03:37	254
@@ -11,6 +11,9 @@
 #include "ReadWrite.hpp"
 #include "simError.h"
 
+#ifdef IS_MPI
+#include "mpiSimulation.hpp"
+#endif // is_mpi
 
 InitializeFromFile :: InitializeFromFile( char *in_name ){
 #ifdef IS_MPI
@@ -68,11 +71,11 @@ 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 +161,7 @@ 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 +182,7 @@ 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){
@@ -204,9 +207,9 @@ 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) {
 
@@ -230,7 +233,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
       sendError = 0;
       mpiErr = MPI_Send(&sendError,1,MPI_INT,procIndex,MPI_ANY_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){
 	  
@@ -249,7 +252,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 	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,
 			  istatus);
-	if (sendError) mpiCheckpoint();
+	if (sendError) MPIcheckPoint();
 
 	masterIndex++;
       }
@@ -257,21 +260,21 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 
 
     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);
       mpiErr = MPI_Send(&nodeAtomsEnd,1,MPI_INT,0,MPI_ANY_TAG,MPI_COMM_WORLD);
       
       mpiErr = MPI_Recv(&sendError,1,MPI_INT,0,MPI_ANY_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,
 			  istatus);
 	
-	if(!strcmp(read_buffer, "ERROR")) mpiCheckPoint();
+	if(!strcmp(read_buffer, "ERROR")) MPIcheckPoint();
 	
 	parseErr = parseDumpLine( read_buffer, i );
 	if( parseErr != NULL ){
@@ -288,14 +291,14 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
       }
     }
     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 +314,10 @@ 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