--- trunk/src/restraints/ObjectRestraint.cpp	2009/09/07 16:31:51	1360
+++ trunk/src/restraints/ObjectRestraint.cpp	2010/01/20 16:04:40	1407
@@ -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.
@@ -37,21 +28,32 @@
  * 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 "restraints/ObjectRestraint.hpp"
 
-namespace oopse {
+namespace OpenMD {
 
   void ObjectRestraint::calcForce(Vector3d struc) {
 
     pot_ = 0.0;
-    
     if (restType_ & rtDisplacement) {
-      Vector3d del = struc - refPos_;  
+      Vector3d del = struc - refPos_;
+      RealType r = del.length();
       Vector3d frc = -kDisp_ * del;
-      pot_ += 0.5 * kDisp_ * del.lengthSquare();
+      RealType p = 0.5 * kDisp_ * del.lengthSquare();
+      pot_ = p;
       force_ = frc * scaleFactor_;
+      restInfo_[rtDisplacement] = std::make_pair(r,p);
     }
   }
     
@@ -70,11 +72,11 @@ namespace oopse {
 
       RealType twistAngle, swingAngle;
       Vector3d swingAxis;
-      RealType tw, swingX, swingY;
+      RealType swingX, swingY;
       
-      quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
-      quat.toSwingTwist(tw, swingX, swingY);
-      
+      quat.toSwingTwist(swingX, swingY, twistAngle);
+
+
       RealType dVdtwist, dVdswingX, dVdswingY;
       RealType dTwist, dSwingX, dSwingY;
       RealType p;
@@ -107,8 +109,6 @@ namespace oopse {
         restInfo_[rtSwingY] = std::make_pair(swingY, p);
       }
 
-      std::cerr << "sw = " << swingAngle << " tw = " << twistAngle << "\n";
-      std::cerr << "tbod = " << tBody << "\n";
       Vector3d tLab = A.transpose() * tBody;      
       torque_ = tLab * scaleFactor_;      
     }