--- trunk/src/primitives/Inversion.cpp	2008/10/21 18:23:31	1309
+++ trunk/src/primitives/Inversion.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.
@@ -37,20 +28,33 @@
  * 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/Inversion.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   Inversion::Inversion(Atom *atom1, Atom *atom2, Atom *atom3, 
 		       Atom *atom4, InversionType *it) :
     atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), 
     inversionType_(it) { }
   
-  void Inversion::calcForce(RealType& angle) {
+  void Inversion::calcForce(RealType& angle, bool doParticlePot) {
     
-    // 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:
@@ -94,13 +98,13 @@ namespace oopse {
     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.
 
@@ -109,11 +113,13 @@ namespace oopse {
     atom4_->addFrc(-f2);
     atom3_->addFrc(-f3);
 
-    atom1_->addParticlePot(potential_);
-    atom2_->addParticlePot(potential_);
-    atom3_->addParticlePot(potential_);
-    atom4_->addParticlePot(potential_);
-
+    if (doParticlePot) { 
+      atom1_->addParticlePot(potential_);
+      atom2_->addParticlePot(potential_);
+      atom3_->addParticlePot(potential_);
+      atom4_->addParticlePot(potential_);
+    }
+    
     angle = acos(cos_phi) /M_PI * 180.0;
   }