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root/OpenMD/trunk/src/restraints/ObjectRestraint.cpp
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Comparing trunk/src/restraints/ObjectRestraint.cpp (file contents):
Revision 1442 by gezelter, Mon May 10 17:28:26 2010 UTC vs.
Revision 1973 by gezelter, Thu Mar 6 19:34:22 2014 UTC

# Line 35 | Line 35
35   *                                                                      
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).                        
38 > * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
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/ObjectRestraint.hpp"
# Line 51 | Line 52 | namespace OpenMD {
52        RealType r = del.length();
53        Vector3d frc = -kDisp_ * del;
54        RealType p = 0.5 * kDisp_ * del.lengthSquare();
55 +
56        pot_ = p;
57        force_ = frc * scaleFactor_;
58        restInfo_[rtDisplacement] = std::make_pair(r,p);
# Line 70 | Line 72 | namespace OpenMD {
72  
73        Quat4d quat = temp.toQuaternion();
74  
75 <      RealType twistAngle, swingAngle;
75 >      RealType twistAngle;
76        Vector3d swingAxis;
77        RealType swingX, swingY;
78        
79        quat.toSwingTwist(swingX, swingY, twistAngle);
80  
79 –
80 –      RealType dVdtwist, dVdswingX, dVdswingY;
81 –      RealType dTwist, dSwingX, dSwingY;
81        RealType p;
82        Vector3d tTwist, tSwing;
83  
84        if (restType_ & rtTwist){
85 <        dTwist = twistAngle - twist0_;
86 <        dVdtwist = kTwist_ * sin(dTwist);
85 >        RealType dTwist = twistAngle - twist0_;
86 >        RealType dVdtwist = kTwist_ * sin(dTwist);
87          p = kTwist_ * (1.0 - cos(dTwist) );
88          pot_ += p;
89          tBody -= dVdtwist * V3Z;
# Line 92 | Line 91 | namespace OpenMD {
91        }
92  
93        if (restType_ & rtSwingX){
94 <        dSwingX = swingX - swingX0_;
95 <        dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
94 >        RealType dSwingX = swingX - swingX0_;
95 >        RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
96          p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
97          pot_ += p;
98          tBody -= dVdswingX * V3X;
# Line 101 | Line 100 | namespace OpenMD {
100        }
101  
102        if (restType_ & rtSwingY){
103 <        dSwingY = swingY - swingY0_;
104 <        dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
103 >        RealType dSwingY = swingY - swingY0_;
104 >        RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
105          p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
106          pot_ += p;
107          tBody -= dVdswingY * V3Y;

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