--- trunk/src/primitives/GhostTorsion.cpp	2006/05/17 21:51:42	963
+++ trunk/src/primitives/GhostTorsion.cpp	2009/11/25 20:02:06	1390
@@ -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.
@@ -37,26 +28,36 @@
  * 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/GhostTorsion.hpp"
 
-namespace oopse {
-
-  GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2,  DirectionalAtom* ghostAtom,
-			     TorsionType *tt) : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {}
-
+namespace OpenMD {
+  
+  GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2,  
+                             DirectionalAtom* ghostAtom, TorsionType *tt) 
+    : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {}
+  
   void GhostTorsion::calcForce(RealType& angle) {
     DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_);    
-
+    
     Vector3d pos1 = atom1_->getPos();
     Vector3d pos2 = atom2_->getPos();
     Vector3d pos3 = ghostAtom->getPos();
-
+    
     Vector3d r21 = pos1 - pos2;
     Vector3d r32 = pos2 - pos3;
     Vector3d r43 = ghostAtom->getElectroFrame().getColumn(2);
-
+    
     //  Calculate the cross products and distances
     Vector3d A = cross(r21, r32);
     RealType rA = A.length();
@@ -64,34 +65,37 @@ namespace oopse {
     RealType rB = B.length();
     Vector3d C = cross(r32, A);
     RealType rC = C.length();
-
+    
     A.normalize();
     B.normalize();
     C.normalize();
     
     //  Calculate the sin and cos
     RealType cos_phi = dot(A, B) ;
-
+    
     RealType dVdcosPhi;
     torsionType_->calcForce(cos_phi, potential_, dVdcosPhi);
-
+    
     Vector3d dcosdA = (cos_phi * A - B) /rA;
     Vector3d dcosdB = (cos_phi * B - A) /rB;
-
+    
     Vector3d f1 = dVdcosPhi * cross(r32, dcosdA);
     Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
     Vector3d f3 = dVdcosPhi * cross(dcosdB, r32);
-
+    
     atom1_->addFrc(f1);
     atom2_->addFrc(f2 - f1);
-
+    
     ghostAtom->addFrc(-f2);
-
+    
     f3.negate();
     ghostAtom->addTrq(cross(r43, f3));    
+    
+    atom1_->addParticlePot(potential_);
+    atom2_->addParticlePot(potential_);
+    ghostAtom->addParticlePot(potential_);
 
     angle = acos(cos_phi) /M_PI * 180.0;
   }
-
 }