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Comparing:
trunk/src/restraints/MolecularRestraint.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/restraints/MolecularRestraint.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

# Line 36 | Line 36
36   * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).            
37   * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
38   * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
39 < * [4]  Vardeman & Gezelter, in progress (2009).                        
39 > * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40 > * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41   */
42  
43   #include "restraints/MolecularRestraint.hpp"
# Line 48 | Line 49 | namespace OpenMD {
49  
50   namespace OpenMD {
51  
52 +
53    void MolecularRestraint::calcForce(std::vector<Vector3d> struc,
54                                       Vector3d molCom){
55  
# Line 84 | Line 86 | namespace OpenMD {
86        
87        Mat3x3d R(0.0);
88        
89 <      for (int n = 0; n < struc.size(); n++){
89 >      for (unsigned int n = 0; n < struc.size(); n++){
90  
91          /*
92           * correlation matrix R:  
# Line 136 | Line 138 | namespace OpenMD {
138        Vector3d eularAngles = A.toEulerAngles();
139  
140  
141 <      RealType twistAngle, swingAngle;
141 >      RealType twistAngle;
142        Vector3d swingAxis;
143  
144        Quat4d quat = A.toQuaternion();  
145  
146 <      quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis);
146 >      RealType swingX, swingY;
147 >      quat.toSwingTwist(swingX, swingY, twistAngle);
148  
149 <      RealType tw, sx, sy, ttw, swingX, swingY;
150 <      quat.toTwistSwing(tw, sx, sy);
148 <      quat.toSwingTwist(swingX, swingY, ttw);
149 <
150 <      // std::cerr << eularAngles << "\t[" << twistAngle << "," << swingAngle <<
151 <      // "]\t[" << tw << "," << sx << "," << sy << "]\t[" << ttw <<
152 <      // "," << ssx << "," << ssy << "]" << std::endl;
153 <
154 <      RealType dVdtwist, dVdswing, dVdswingX, dVdswingY;
155 <      RealType dTwist, dSwing, dSwingX, dSwingY;
149 >      RealType dVdtwist, dVdswingX, dVdswingY;
150 >      RealType dTwist, dSwingX, dSwingY;
151        RealType p;
152  
153        if (restType_ & rtTwist){
# Line 195 | Line 190 | namespace OpenMD {
190        
191        Vector3d rLab, rBody, txr, fBody, fLab;
192  
193 <      for (int i = 0; i < struc.size(); i++) {
193 >      for (unsigned int i = 0; i < struc.size(); i++) {
194                    
195          rLab = struc[i];        
196          rBody = A * rLab;

Comparing:
trunk/src/restraints/MolecularRestraint.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/restraints/MolecularRestraint.cpp (property svn:keywords), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

# Line 0 | Line 1
1 + Author Id Revision Date

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