--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/07/22 16:41:08	644
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/10/28 16:03:37	829
@@ -1,5 +1,5 @@
 #include <iostream>
-#include <cmath>
+#include <math.h>
 
 #include <stdio.h>
 #include <stdlib.h>
@@ -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.
     
@@ -323,8 +319,8 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 
   char *foo; // the pointer to the current string token 
   
-  double rx, ry, rz; // position place holders
-  double vx, vy, vz; // velocity placeholders
+  double pos[3]; // position place holders
+  double vel[3]; // velocity placeholders
   double q[4]; // the quaternions
   double jx, jy, jz; // angular velocity placeholders;
   double qSqr, qLength; // needed to normalize the quaternion vector.
@@ -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++) {
@@ -377,7 +375,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  rx = atof( foo );
+  pos[0] = atof( foo );
    
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -387,7 +385,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  ry = atof( foo );
+  pos[1] = atof( foo );
      
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -397,7 +395,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  rz = atof( foo );    
+  pos[2] = atof( foo );    
 
 
   // get the velocities
@@ -410,7 +408,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vx = atof( foo );
+  vel[0] = atof( foo );
     
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -420,7 +418,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vy = atof( foo );
+  vel[1] = atof( foo );
     
   foo = strtok(NULL, " ,;\t");
   if(foo == NULL){
@@ -430,7 +428,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	     c_in_name, n_atoms, atomIndex );
     return strdup( painCave.errMsg );
   }
-  vz = atof( foo );
+  vel[2] = atof( foo );
     
     
   // get the quaternions
@@ -531,14 +529,9 @@ char* InitializeFromFile::parseDumpLine(char* readLine
   }
     
   // add the positions and velocities to the atom
-    
-  atoms[atomIndex]->setX( rx );
-  atoms[atomIndex]->setY( ry );
-  atoms[atomIndex]->setZ( rz );
     
-  atoms[atomIndex]->set_vx( vx );
-  atoms[atomIndex]->set_vy( vy );
-  atoms[atomIndex]->set_vz( vz );
+  atoms[atomIndex]->setPos( pos );
+  atoms[atomIndex]->setVel( vel );
 
   return NULL;
 }
@@ -548,7 +541,6 @@ char* InitializeFromFile::parseBoxLine(char* readLine,
 				       double &time ){
 
   char *foo; // the pointer to the current string token 
-  int j;
 
   // set the string tokenizer