--- trunk/src/primitives/Inversion.cpp	2008/09/10 19:51:45	1290
+++ 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.
@@ -37,12 +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"
-#include "fstream"
 
-namespace oopse {
+namespace OpenMD {
 
   Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, 
 		       Atom *atom4, InversionType *it) :
@@ -51,32 +50,24 @@ 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:
 
     Vector3d pos1 = atom2_->getPos();
-    Vector3d pos2 = atom1_->getPos();
-    Vector3d pos3 = atom4_->getPos();
-    Vector3d pos4 = atom3_->getPos();
+    Vector3d pos2 = atom3_->getPos();
+    Vector3d pos3 = atom1_->getPos();
+    Vector3d pos4 = atom4_->getPos();
 
-   /*std::ofstream myfile;
-   myfile.open("Inversion", std::ios::app);       
-   myfile << atom1_->getType() << " - atom1; "
-              << atom2_->getType() << " - atom2; "
-              << atom3_->getType() << " - atom3; "
-              << atom4_->getType() << " - atom4; "
-              << std::endl;
-*/
-    Vector3d r21 = pos1 - pos2;
-    Vector3d r32 = pos2 - pos3;
-    Vector3d r42 = pos2 - pos4;
+    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, r42);
+    Vector3d B = cross(r43, r23);
     RealType rB = B.length();
     //Vector3d C = cross(r23, A);
     //RealType rC = C.length();
@@ -87,14 +78,10 @@ namespace oopse {
     
     //  Calculate the sin and cos
     RealType cos_phi = dot(A, B) ;
-    if (cos_phi > 1.0) {cos_phi = 1.0; std::cout << "!!!! cos_phi is bigger than 1.0" 
-                                                 << std::endl;}
-    if (cos_phi < -1.0) {cos_phi = -1.0; std::cout << "!!!! cos_phi is less than -1.0" 
-                                                   << std::endl;}
-    //std::cout << "We actually use this inversion!!!!" << std::endl;
+    if (cos_phi > 1.0) cos_phi = 1.0;
+    if (cos_phi < -1.0) cos_phi = -1.0;
 
     RealType dVdcosPhi;
-    //cos_phi = 2.0*cos_phi*cos_phi - 1.0;
     inversionType_->calcForce(cos_phi, potential_, dVdcosPhi);
     Vector3d f1 ;
     Vector3d f2 ;
@@ -103,17 +90,17 @@ namespace oopse {
     Vector3d dcosdA = (cos_phi * A - B) /rA;
     Vector3d dcosdB = (cos_phi * B - A) /rB;
 
-    f1 = dVdcosPhi * cross(r32, dcosdA);
-    f2 = dVdcosPhi * ( cross(r42, 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.
 
@@ -122,6 +109,11 @@ namespace oopse {
     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;
   }