--- trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2004/01/08 15:44:47	906
+++ trunk/OOPSE/libmdtools/InitializeFromFile.cpp	2004/04/12 20:32:20	1097
@@ -327,7 +327,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
   double pos[3]; // position place holders
   double vel[3]; // velocity placeholders
   double q[4]; // the quaternions
-  double jx, jy, jz; // angular velocity placeholders;
+  double ji[3]; // angular velocity placeholders;
   double qSqr, qLength; // needed to normalize the quaternion vector.
 
   Atom **atoms = simnfo->atoms;
@@ -490,7 +490,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	       c_in_name, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jx = atof( foo );
+    ji[0] = atof( foo );
 
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
@@ -500,7 +500,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	       c_in_name, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jy = atof(foo );
+    ji[1] = atof(foo );
 
     foo = strtok(NULL, " ,;\t");
     if(foo == NULL){
@@ -510,7 +510,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 	       c_in_name, n_atoms, atomIndex );
       return strdup( painCave.errMsg );
     }
-    jz = atof( foo );
+    ji[2] = atof( foo );
 
     dAtom = ( DirectionalAtom* )atoms[atomIndex];
 
@@ -528,9 +528,7 @@ char* InitializeFromFile::parseDumpLine(char* readLine
 
     // add the angular velocities
 
-    dAtom->setJx( jx );
-    dAtom->setJy( jy );
-    dAtom->setJz( jz );
+    dAtom->setJ( ji );
   }
 
   // add the positions and velocities to the atom
@@ -618,15 +616,22 @@ char* InitializeFromFile::parseCommentLine(char* readL
       return NULL;
     
     //get eta
-    for(int i = 0 ; i < 9; i++){
-      foo = strtok(NULL, " ,;\t");
-      if(foo == NULL){
-	sprintf( painCave.errMsg,
-		 "error in reading eta[%d] from %s\n", i, c_in_name );
-	return strdup( painCave.errMsg );
+    foo = strtok(NULL, " ,;\t\n");
+    if(foo != NULL ){
+  
+      for(int i = 0 ; i < 9; i++){
+	
+	if(foo == NULL){
+	  sprintf( painCave.errMsg,
+		   "error in reading eta[%d] from %s\n", i, c_in_name );
+	  return strdup( painCave.errMsg );
+	}
+	eta[i] = atof( foo );
+	foo = strtok(NULL, " ,;\t\n");
       }
-      eta[i] = atof( foo );
     }
+    else
+      return NULL;
     
     //push eta into SimInfo::properties which can be
     //retrieved by integrator later