--- trunk/src/primitives/Inversion.cpp	2008/07/14 12:35:58	1277
+++ branches/development/src/primitives/Inversion.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/Inversion.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, 
 		       Atom *atom4, InversionType *it) :
@@ -50,7 +50,7 @@ namespace oopse {
   
   void Inversion::calcForce(RealType& angle) {
     
-    // In OOPSE's version of an inversion, the central atom
+    // In OpenMD's version of an inversion, the central atom
     // comes first.  However, to get the planarity in a typical cosine
     // version of this potential (i.e. Amber-style), the central atom
     // is treated as atom *3* in a standard torsion form:
@@ -60,55 +60,60 @@ namespace oopse {
     Vector3d pos3 = atom1_->getPos();
     Vector3d pos4 = atom4_->getPos();
 
-    Vector3d r21 = pos1 - pos2;
-    Vector3d r32 = pos2 - pos3;
+    Vector3d r31 = pos1 - pos3;
+    Vector3d r23 = pos3 - pos2;
     Vector3d r43 = pos3 - pos4;
 
     //  Calculate the cross products and distances
-    Vector3d A = cross(r21, r32);
+    Vector3d A = cross(r31, r43);
     RealType rA = A.length();
-    Vector3d B = cross(r32, r43);
+    Vector3d B = cross(r43, r23);
     RealType rB = B.length();
-    Vector3d C = cross(r32, A);
-    RealType rC = C.length();
+    //Vector3d C = cross(r23, A);
+    //RealType rC = C.length();
 
     A.normalize();
     B.normalize();
-    C.normalize();
+    //C.normalize();
     
     //  Calculate the sin and cos
     RealType cos_phi = dot(A, B) ;
     if (cos_phi > 1.0) cos_phi = 1.0;
-    if (cos_phi < -1.0) cos_phi = -1.0; 
+    if (cos_phi < -1.0) cos_phi = -1.0;
 
-
     RealType dVdcosPhi;
     inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
-    Vector3d f1;
-    Vector3d f2;
-    Vector3d f3;
+    Vector3d f1 ;
+    Vector3d f2 ;
+    Vector3d f3 ;
 
     Vector3d dcosdA = (cos_phi * A - B) /rA;
     Vector3d dcosdB = (cos_phi * B - A) /rB;
 
-    f1 = dVdcosPhi * cross(r32, dcosdA);
-    f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA));
-    f3 = dVdcosPhi * cross(dcosdB, r32);
+    f1 = dVdcosPhi * cross(r43, dcosdA);
+    f2 = dVdcosPhi * ( cross(r23, dcosdB) - cross(r31, dcosdA));
+    f3 = dVdcosPhi * cross(dcosdB, r43);
 
-    // In OOPSE's version of an improper torsion, the central atom
+    // In OpenMD's version of an improper torsion, the central atom
     // comes first.  However, to get the planarity in a typical cosine
     // version of this potential (i.e. Amber-style), the central atom
     // is treated as atom *3* in a standard torsion form:
 
     //  AMBER:   I - J - K - L   (e.g. K is sp2 hybridized carbon)
-    //  OOPSE:   I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
+    //  OpenMD:  I - (J - K - L)  (e.g. I is sp2 hybridized carbon)
 
     // Confusing enough?  Good.
 
-    atom3_->addFrc(f1);
-    atom1_->addFrc(f2 - f1);
-    atom2_->addFrc(f3 - f2);
-    atom4_->addFrc(-f3);
+    atom2_->addFrc(f1);
+    atom1_->addFrc(f2 - f1 + f3);
+    atom4_->addFrc(-f2);
+    atom3_->addFrc(-f3);
+
+    atom1_->addParticlePot(potential_);
+    atom2_->addParticlePot(potential_);
+    atom3_->addParticlePot(potential_);
+    atom4_->addParticlePot(potential_);
+
     angle = acos(cos_phi) /M_PI * 180.0;
   }