--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/08/07 21:47:18	670
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/09/25 19:27:15	787
@@ -26,7 +26,8 @@ using namespace initFile;
 
 #endif // is_mpi
 
-InitializeFromFile :: InitializeFromFile( char *in_name ){
+InitializeFromFile::InitializeFromFile( char *in_name ){
+
 #ifdef IS_MPI
   if (worldRank == 0) {
 #endif
@@ -48,7 +49,7 @@ InitializeFromFile :: InitializeFromFile( char *in_nam
   return;  
 }
 
-InitializeFromFile :: ~InitializeFromFile( ){
+InitializeFromFile::~InitializeFromFile( ){
 #ifdef IS_MPI
   if (worldRank == 0) {
 #endif
@@ -71,18 +72,19 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
 
 void InitializeFromFile :: readInit( SimInfo* the_simnfo ){
 
-  int i, j, done, which_node, which_atom; // loop counter
+  int i, j;
+  
+#ifdef IS_MPI
+  int done, which_node, which_atom; // loop counter
+#endif //is_mpi
 
   const int BUFFERSIZE = 2000; // size of the read buffer
   int n_atoms; // the number of atoms
   char read_buffer[BUFFERSIZE]; //the line buffer for reading 
-#ifdef IS_MPI
-  char send_buffer[BUFFERSIZE];
-#endif
 
   char *eof_test; // ptr to see when we reach the end of the file 
   char *parseErr;
-  int procIndex;
+
   double currTime;
   double boxMat[9];
   double theBoxMat3[3][3];
@@ -102,9 +104,6 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
 
   n_atoms = atoi( read_buffer );
 
-  Atom **atoms = simnfo->atoms;
-  DirectionalAtom* dAtom;
-
   if( n_atoms != simnfo->n_atoms ){
     sprintf( painCave.errMsg,
 	     "Initialize from File error. %s n_atoms, %d, "
@@ -180,16 +179,13 @@ void InitializeFromFile :: readInit( SimInfo* the_simn
     eof_test = fgets(read_buffer, sizeof(read_buffer), c_in_file);
     if( eof_test == NULL ){
       sprintf( painCave.errMsg,
-	       "Error reading 1st line of %d \n ",c_in_name);
+	       "Error reading 1st line of %s \n ",c_in_name);
       haveError = 1;
       simError();
     }
     
     n_atoms = atoi( read_buffer );
     
-    Atom **atoms = simnfo->atoms;
-    DirectionalAtom* dAtom;
- 
     // Check to see that the number of atoms in the intial configuration file is the
     // same as declared in simBass.
     
@@ -332,9 +328,11 @@ char* InitializeFromFile::parseDumpLine(char* readLine
   Atom **atoms = simnfo->atoms;
   DirectionalAtom* dAtom;
   
-  int j, n_atoms, atomIndex;
+  int n_atoms, atomIndex;
 
 #ifdef IS_MPI
+  int j;
+
   n_atoms = mpiSim->getTotAtoms();
   atomIndex=-1;        
   for (j=0; j < mpiSim->getMyNlocal(); j++) {
@@ -543,7 +541,6 @@ char* InitializeFromFile::parseBoxLine(char* readLine,
 				       double &time ){
 
   char *foo; // the pointer to the current string token 
-  int j;
 
   // set the string tokenizer