--- trunk/src/primitives/GhostTorsion.cpp	2005/04/15 22:04:00	507
+++ trunk/src/primitives/GhostTorsion.cpp	2010/06/17 14:48:02	1446
@@ -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.
@@ -37,62 +28,79 @@
  * 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) {}
-
-  void GhostTorsion::calcForce() {
+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);
-
+    Vector3d r43 = ghostAtom->getA().getColumn(2);
+    
     //  Calculate the cross products and distances
     Vector3d A = cross(r21, r32);
-    double rA = A.length();
+    RealType rA = A.length();
     Vector3d B = cross(r32, r43);
-    double rB = B.length();
-    Vector3d C = cross(r32, A);
-    double rC = C.length();
+    RealType rB = B.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
-    double cos_phi = dot(A, B) ;
-    double sin_phi = dot(C, B);
-
-    double dVdPhi;
-    torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi);
-
+    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;
-
-    double dVdcosPhi = -dVdPhi / sin_phi;
-
+    
     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;
+  }
 }