--- trunk/src/restraints/ObjectRestraint.cpp	2009/09/07 16:31:51	1360
+++ trunk/src/restraints/ObjectRestraint.cpp	2015/03/05 16:30:23	2069
@@ -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 +28,34 @@
  * 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 "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_;
+      if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r,p);
     }
   }
     
@@ -65,50 +69,51 @@ namespace oopse {
       Vector3d tBody(0.0);
       
       RotMat3x3d temp = A * refA_.transpose();
-
       Quat4d quat = temp.toQuaternion();
 
-      RealType twistAngle, swingAngle;
+      RealType twistAngle;
       Vector3d swingAxis;
-      RealType tw, swingX, swingY;
+      RealType swingX, swingY;
       
-      quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
-      quat.toSwingTwist(tw, swingX, swingY);
-      
-      RealType dVdtwist, dVdswingX, dVdswingY;
-      RealType dTwist, dSwingX, dSwingY;
+      quat.toSwingTwist(swingX, swingY, twistAngle);
+
+
       RealType p;
       Vector3d tTwist, tSwing;
 
       if (restType_ & rtTwist){
-        dTwist = twistAngle - twist0_;
-        dVdtwist = kTwist_ * sin(dTwist);
-        p = kTwist_ * (1.0 - cos(dTwist) );
+        RealType dTwist = twistAngle - twist0_;      
+        /// RealType dVdtwist = kTwist_ * sin(dTwist);
+        /// p = kTwist_ * (1.0 - cos(dTwist) );
+        RealType dVdtwist = kTwist_ * dTwist;
+        p = 0.5 * kTwist_ * dTwist * dTwist;
         pot_ += p;
         tBody -= dVdtwist * V3Z;
-        restInfo_[rtTwist] = std::make_pair(twistAngle, p);
+        if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p);
       }
 
       if (restType_ & rtSwingX){
-        dSwingX = swingX - swingX0_;
-        dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
-        p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
+        RealType dSwingX = swingX - swingX0_;
+        /// RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
+        /// p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
+        RealType dVdswingX = kSwingX_ * dSwingX;        
+        p = 0.5 * kSwingX_ * dSwingX * dSwingX;
         pot_ += p;
         tBody -= dVdswingX * V3X;
-        restInfo_[rtSwingX] = std::make_pair(swingX, p);
+        if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p);
       }
 
       if (restType_ & rtSwingY){
-        dSwingY = swingY - swingY0_;
-        dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
-        p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
+        RealType dSwingY = swingY - swingY0_;
+        /// RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
+        /// p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
+        RealType dVdswingY = kSwingY_ * dSwingY;        
+        p = 0.5 * kSwingX_ * dSwingY * dSwingY;
         pot_ += p;
         tBody -= dVdswingY * V3Y;
-        restInfo_[rtSwingY] = std::make_pair(swingY, p);
+        if (printRest_) 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_;      
     }