--- trunk/src/restraints/MolecularRestraint.cpp	2009/09/07 16:31:51	1360
+++ trunk/src/restraints/MolecularRestraint.cpp	2013/06/16 15:15:42	1879
@@ -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.
@@ -37,6 +28,16 @@
  * 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/MolecularRestraint.hpp"
@@ -46,8 +47,9 @@
 
 //using namespace JAMA;
 
-namespace oopse {
+namespace OpenMD {
 
+
   void MolecularRestraint::calcForce(std::vector<Vector3d> struc, 
                                      Vector3d molCom){
 
@@ -84,7 +86,7 @@ namespace oopse {
       
       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 oopse {
       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){
@@ -195,7 +190,7 @@ namespace oopse {
       
       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;