--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/07/22 16:41:08	644
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2003/08/07 21:47:18	670
@@ -323,8 +323,8 @@ 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.
@@ -377,7 +377,7 @@ 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 +387,7 @@ 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 +397,7 @@ 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 +410,7 @@ 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 +420,7 @@ 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 +430,7 @@ 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
@@ -532,13 +532,8 @@ 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;
 }