--- trunk/src/primitives/Bend.cpp	2006/05/17 21:51:42	963
+++ branches/development/src/primitives/Bend.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.
@@ -37,66 +28,77 @@
  * 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/Bend.hpp"
 
-namespace oopse {
-
+namespace OpenMD {
+  
   /**@todo still a lot left to improve*/
   void Bend::calcForce(RealType& angle) {
     Vector3d pos1 = atom1_->getPos();
     Vector3d pos2 = atom2_->getPos();
     Vector3d pos3 = atom3_->getPos();
-
+    
     Vector3d r21 = pos1 - pos2;
     RealType d21 = r21.length();
-
+    
     RealType d21inv = 1.0 / d21;
-
+    
     Vector3d r23 = pos3 - pos2;
     RealType d23 = r23.length();
-
+    
     RealType d23inv = 1.0 / d23;
-
+    
     RealType cosTheta = dot(r21, r23) / (d21 * d23);
-
+    
     //check roundoff     
     if (cosTheta > 1.0) {
       cosTheta = 1.0;
     } else if (cosTheta < -1.0) {
       cosTheta = -1.0;
     }
-
+    
     RealType theta = acos(cosTheta);
-
+    
     RealType dVdTheta;
 
     bendType_->calcForce(theta, potential_, dVdTheta);
-    //std::cout << atom1_->getType() << "\t" << atom2_->getType() << "\t" << atom3_->getType() << "\t";
-    //std::cout << "theta = " << theta/M_PI * 180.0 <<", potential = " << potential_ << std::endl;
-
+    
     RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta);
-
+    
     if (fabs(sinTheta) < 1.0E-6) {
       sinTheta = 1.0E-6;
     }
-
+    
     RealType commonFactor1 = dVdTheta / sinTheta * d21inv;
     RealType commonFactor2 = dVdTheta / sinTheta * d23inv;
-
+    
     Vector3d force1 = commonFactor1 * (r23 * d23inv - r21*d21inv*cosTheta);
     Vector3d force3 = commonFactor2 * (r21 * d21inv - r23*d23inv*cosTheta);
 
-    //total force in current bend is zero
+    // Total force in current bend is zero
     Vector3d force2 = force1 + force3;
     force2 *= -1.0;
-
+    
     atom1_->addFrc(force1);
     atom2_->addFrc(force2);
     atom3_->addFrc(force3);
 
+    atom1_->addParticlePot(potential_);
+    atom2_->addParticlePot(potential_);
+    atom3_->addParticlePot(potential_);
+   
     angle = theta /M_PI * 180.0;
   }
 
-} //end namespace oopse
+} //end namespace OpenMD