--- trunk/src/primitives/DirectionalAtom.cpp	2008/01/23 16:38:22	1211
+++ branches/development/src/primitives/DirectionalAtom.cpp	2010/07/09 23:08:25	1465
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,11 +28,20 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
+ * [4]  Vardeman & Gezelter, in progress (2009).                        
  */
  
 #include "primitives/DirectionalAtom.hpp"
 #include "utils/simError.h"
-namespace oopse {
+namespace OpenMD {
   
   DirectionalAtom::DirectionalAtom(DirectionalAtomType* dAtomType) 
     : Atom(dAtomType){
@@ -55,7 +55,7 @@ namespace oopse {
     int nLinearAxis = 0;
     Mat3x3d inertiaTensor = getI();
     for (int i = 0; i < 3; i++) {    
-      if (fabs(inertiaTensor(i, i)) < oopse::epsilon) {
+      if (fabs(inertiaTensor(i, i)) < OpenMD::epsilon) {
         linear_ = true;
         linearAxis_ = i;
         ++ nLinearAxis;
@@ -65,7 +65,7 @@ namespace oopse {
     if (nLinearAxis > 1) {
       sprintf( painCave.errMsg,
                "Directional Atom warning.\n"
-               "\tOOPSE found more than one axis in this directional atom with a vanishing \n"
+               "\tOpenMD found more than one axis in this directional atom with a vanishing \n"
                "\tmoment of inertia.");
       painCave.isFatal = 0;
       simError();
@@ -134,6 +134,10 @@ namespace oopse {
     ephi[1] = 0.0;
     ephi[2] = 1.0;
     
+    //etheta[0] = -sphi;
+    //etheta[1] =  cphi;
+    //etheta[2] =  0.0;
+    
     etheta[0] = cphi;
     etheta[1] = sphi;
     etheta[2] = 0.0;