--- trunk/src/primitives/GhostBend.cpp	2005/01/12 22:41:40	246
+++ trunk/src/primitives/GhostBend.cpp	2009/11/25 20:02:06	1390
@@ -1,4 +1,4 @@
- /*
+/*
  * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
@@ -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.
@@ -37,61 +28,74 @@
  * 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/GhostBend.hpp"
 #include "primitives/DirectionalAtom.hpp"
-namespace oopse {
+namespace OpenMD {
 
-/**@todo still a lot left to improve*/
-void GhostBend::calcForce() {
+  /**@todo still a lot left to improve*/
+  void GhostBend::calcForce(RealType& angle) {
     DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_);
     
     Vector3d pos1 = atom1_->getPos();
     Vector3d pos2 = ghostAtom->getPos();
-
+    
     Vector3d r12 = pos1 - pos2;
-    double d12 = r12.length();
-
-    double d12inv = 1.0 / d12;
-
+    RealType d12 = r12.length();
+    
+    RealType d12inv = 1.0 / d12;
+    
     Vector3d r32 = ghostAtom->getElectroFrame().getColumn(2);
-    double d32 = r32.length();
-
-    double d32inv = 1.0 / d32;
-
-    double cosTheta = dot(r12, r32) / (d12 * d32);
-
+    RealType d32 = r32.length();
+    
+    RealType d32inv = 1.0 / d32;
+    
+    RealType cosTheta = dot(r12, r32) / (d12 * d32);
+    
     //check roundoff     
     if (cosTheta > 1.0) {
-        cosTheta = 1.0;
+      cosTheta = 1.0;
     } else if (cosTheta < -1.0) {
-        cosTheta = -1.0;
+      cosTheta = -1.0;
     }
-
-    double theta = acos(cosTheta);
-
-    double firstDerivative;
-
-    bendType_->calcForce(theta, firstDerivative, potential_);
-
-    double sinTheta = sqrt(1.0 - cosTheta * cosTheta);
-
+    
+    RealType theta = acos(cosTheta);
+    
+    RealType firstDerivative;
+    
+    bendType_->calcForce(theta, potential_, firstDerivative);
+    
+    RealType sinTheta = sqrt(1.0 - cosTheta * cosTheta);
+    
     if (fabs(sinTheta) < 1.0E-12) {
-        sinTheta = 1.0E-12;
+      sinTheta = 1.0E-12;
     }
-
-    double commonFactor1 = -firstDerivative / sinTheta * d12inv;
-    double commonFactor2 = -firstDerivative / sinTheta * d32inv;
-
+    
+    RealType commonFactor1 = -firstDerivative / sinTheta * d12inv;
+    RealType commonFactor2 = -firstDerivative / sinTheta * d32inv;
+    
     Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv);
     Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv);
     atom1_->addFrc(force1);
     ghostAtom->addFrc(-force1);
     /**@todo test correctness */
-    ghostAtom->addTrq(cross(r32, force3) );
+    ghostAtom->addTrq(cross(r32, force3) );    
 
-}
+    atom1_->addParticlePot(potential_);
+    ghostAtom->addParticlePot(potential_);
 
-} //end namespace oopse
+    angle = theta /M_PI * 180.0;
+    
+  }  
+} //end namespace OpenMD