--- trunk/src/primitives/GhostTorsion.cpp	2008/01/23 16:38:22	1211
+++ trunk/src/primitives/GhostTorsion.cpp	2013/06/16 15:15:42	1879
@@ -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.
@@ -37,17 +28,30 @@
  * 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, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
+#include "config.h"
+#include <cmath>
+
 #include "primitives/GhostTorsion.hpp"
 
-namespace oopse {
+namespace OpenMD {
   
   GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2,  
                              DirectionalAtom* ghostAtom, TorsionType *tt) 
     : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {}
   
-  void GhostTorsion::calcForce(RealType& angle) {
+  void GhostTorsion::calcForce(RealType& angle, bool doParticlePot) {
     DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom3_);    
     
     Vector3d pos1 = atom1_->getPos();
@@ -56,19 +60,24 @@ namespace oopse {
     
     Vector3d r21 = pos1 - pos2;
     Vector3d r32 = pos2 - pos3;
-    Vector3d r43 = ghostAtom->getElectroFrame().getColumn(2);
+    Vector3d r43 = ghostAtom->getA().transpose().getColumn(2);
     
     //  Calculate the cross products and distances
     Vector3d A = cross(r21, r32);
     RealType rA = A.length();
     Vector3d B = cross(r32, r43);
     RealType rB = B.length();
-    Vector3d C = cross(r32, A);
-    RealType rC = C.length();
+
+    /* 
+       If either of the two cross product vectors is tiny, that means
+       the three atoms involved are colinear, and the torsion angle is
+       going to be undefined.  The easiest check for this problem is
+       to use the product of the two lengths.
+    */
+    if (rA * rB < OpenMD::epsilon) return;
     
     A.normalize();
     B.normalize();
-    C.normalize();
     
     //  Calculate the sin and cos
     RealType cos_phi = dot(A, B) ;
@@ -91,6 +100,12 @@ namespace oopse {
     f3.negate();
     ghostAtom->addTrq(cross(r43, f3));    
     
+    if (doParticlePot) {
+      atom1_->addParticlePot(potential_);
+      atom2_->addParticlePot(potential_);
+      ghostAtom->addParticlePot(potential_);
+    }
+
     angle = acos(cos_phi) /M_PI * 180.0;
   }
 }