--- trunk/src/restraints/MolecularRestraint.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/restraints/MolecularRestraint.cpp	2014/09/22 19:18:35	2020
@@ -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"
@@ -48,6 +49,7 @@ namespace OpenMD {
 
 namespace OpenMD {
 
+
   void MolecularRestraint::calcForce(std::vector<Vector3d> struc, 
                                      Vector3d molCom){
 
@@ -69,7 +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_;
@@ -84,7 +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:   
@@ -136,23 +138,16 @@ namespace OpenMD {
       Vector3d eularAngles = A.toEulerAngles();
 
 
-      RealType twistAngle, swingAngle;
+      RealType twistAngle;
       Vector3d swingAxis;
 
       Quat4d quat = A.toQuaternion();  
 
-      quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
+      RealType swingX, swingY;
+      quat.toSwingTwist(swingX, swingY, twistAngle);
 
-      RealType tw, sx, sy, ttw, swingX, swingY;
-      quat.toTwistSwing(tw, sx, sy);
-      quat.toSwingTwist(swingX, swingY, ttw);
-
-      // std::cerr << eularAngles << "\t[" << twistAngle << "," << swingAngle << 
-      // "]\t[" << tw << "," << sx << "," << sy << "]\t[" << ttw <<
-      // "," << ssx << "," << ssy << "]" << std::endl;
-
-      RealType dVdtwist, dVdswing, dVdswingX, dVdswingY;
-      RealType dTwist, dSwing, dSwingX, dSwingY;
+      RealType dVdtwist, dVdswingX, dVdswingY;
+      RealType dTwist, dSwingX, dSwingY;
       RealType p;
 
       if (restType_ & rtTwist){
@@ -161,7 +156,7 @@ namespace OpenMD {
         p = kTwist_ * (1.0 - cos(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){
@@ -179,7 +174,7 @@ namespace OpenMD {
         p = kSwingX_ * (1.0 - cos(2.0 * 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_;
@@ -187,7 +182,7 @@ namespace OpenMD {
         p = kSwingY_ * (1.0 - cos(2.0 * dSwingY));
         pot_ += p;
         tBody -= dVdswingY * V3Y;
-        restInfo_[rtSwingY] = std::make_pair(swingY, p);
+        if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p);
       }
 
             
@@ -195,7 +190,7 @@ 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;