--- trunk/mdtools/md_code/InitializeFromFile.cpp	2003/01/27 21:28:19	249
+++ trunk/mdtools/md_code/InitializeFromFile.cpp	2003/01/30 20:03:37	254
@@ -71,8 +71,8 @@ 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;
 
 
@@ -207,9 +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) {
 
@@ -233,7 +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){
 	  
@@ -252,7 +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++;
       }
@@ -260,21 +260,21 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
 
 
     else if(worldRank == procIndex){
-      nodeAtomStart = mpiSim->getMyAtomStart();
-      nodeAtomEnd = 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 ){
@@ -291,7 +291,7 @@ void InitializeFromFile :: read_xyz( SimInfo* the_entr
       }
     }
     sprintf(checkPointMsg,"Node %d received initial configuration.",procIndex);
-    mpiCheckPoint();
+    MPIcheckPoint();
   }
 
 #endif