--- trunk/src/restraints/MolecularRestraint.cpp	2010/05/10 17:28:26	1442
+++ trunk/src/restraints/MolecularRestraint.cpp	2014/10/16 19:13:51	2024
@@ -35,8 +35,9 @@
  *                                                                      
  * [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).                        
+ * [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/MolecularRestraint.hpp"
@@ -70,7 +71,7 @@ namespace OpenMD {
 
       pot_ += p;
 
-      restInfo_[rtDisplacement] = std::make_pair(r, p);
+      if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r, p);
 
       for(it = forces_.begin(); it != forces_.end(); ++it)
         (*it) = -kDisp_ * del * scaleFactor_;
@@ -85,7 +86,7 @@ namespace OpenMD {
       
       Mat3x3d R(0.0);
       
-      for (int n = 0; n < struc.size(); n++){
+      for (unsigned int n = 0; n < struc.size(); n++){
 
         /*
          * correlation matrix R:   
@@ -137,51 +138,48 @@ namespace OpenMD {
       Vector3d eularAngles = A.toEulerAngles();
 
 
-      RealType twistAngle, swingAngle;
+      RealType twistAngle;
       Vector3d swingAxis;
 
       Quat4d quat = A.toQuaternion();  
 
-      RealType tw, sx, sy, ttw, swingX, swingY;
+      RealType swingX, swingY;
       quat.toSwingTwist(swingX, swingY, twistAngle);
 
-      RealType dVdtwist, dVdswing, dVdswingX, dVdswingY;
-      RealType dTwist, dSwing, dSwingX, dSwingY;
+      RealType dVdtwist, dVdswingX, dVdswingY;
+      RealType dTwist, dSwingX, dSwingY;
       RealType p;
 
       if (restType_ & rtTwist){
         dTwist = twistAngle - twist0_;
-        dVdtwist = kTwist_ * sin(dTwist) ;
-        p = kTwist_ * (1.0 - cos(dTwist) ) ;
+        /// dVdtwist = kTwist_ * sin(dTwist) ;
+        /// p = kTwist_ * (1.0 - cos(dTwist) ) ;
+        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_ & rtSwing){
-//         dSwing = swingAngle - swing0_;
-//         dVdswing = kSwing_ * 2.0 * sin(2.0 * dSwing);
-//         p = kSwing_ * (1.0 - cos(2.0 * dSwing));
-//         pot_ += p;
-//         tBody -= dVdswing * swingAxis;
-//         restInfo_[rtSwing] = std::make_pair(swingAngle, p);
-//       }
-
       if (restType_ & rtSwingX){
         dSwingX = swingX - swingX0_;
-        dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX);
-        p = kSwingX_ * (1.0 - cos(2.0 * dSwingX));
+        /// dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX);
+        /// p = kSwingX_ * (1.0 - cos(2.0 * dSwingX));
+        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_ * 2.0 * sin(2.0 * dSwingY);
-        p = kSwingY_ * (1.0 - cos(2.0 * dSwingY));
+        /// dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY);
+        /// p = kSwingY_ * (1.0 - cos(2.0 * dSwingY));
+        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);
       }
 
             
@@ -189,7 +187,7 @@ namespace OpenMD {
       
       Vector3d rLab, rBody, txr, fBody, fLab;
 
-      for (int i = 0; i < struc.size(); i++) {
+      for (unsigned int i = 0; i < struc.size(); i++) {
                    
         rLab = struc[i];        
         rBody = A * rLab;