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root/OpenMD/trunk/src/restraints/ObjectRestraint.cpp
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Comparing trunk/src/restraints/ObjectRestraint.cpp (file contents):
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC vs.
Revision 2069 by gezelter, Thu Mar 5 16:30:23 2015 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).          
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   */
# Line 52 | 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);
58 >      if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r,p);
59      }
60    }
61      
# Line 68 | Line 69 | namespace OpenMD {
69        Vector3d tBody(0.0);
70        
71        RotMat3x3d temp = A * refA_.transpose();
71 –
72        Quat4d quat = temp.toQuaternion();
73  
74        RealType twistAngle;
# Line 77 | Line 77 | namespace OpenMD {
77        
78        quat.toSwingTwist(swingX, swingY, twistAngle);
79  
80 <      RealType dVdtwist, dVdswingX, dVdswingY;
81 <      RealType dTwist, dSwingX, dSwingY;
80 >
81        RealType p;
82        Vector3d tTwist, tSwing;
83  
84        if (restType_ & rtTwist){
85 <        dTwist = twistAngle - twist0_;
86 <        dVdtwist = kTwist_ * sin(dTwist);
87 <        p = kTwist_ * (1.0 - cos(dTwist) );
85 >        RealType dTwist = twistAngle - twist0_;      
86 >        /// RealType dVdtwist = kTwist_ * sin(dTwist);
87 >        /// p = kTwist_ * (1.0 - cos(dTwist) );
88 >        RealType dVdtwist = kTwist_ * dTwist;
89 >        p = 0.5 * kTwist_ * dTwist * dTwist;
90          pot_ += p;
91          tBody -= dVdtwist * V3Z;
92 <        restInfo_[rtTwist] = std::make_pair(twistAngle, p);
92 >        if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p);
93        }
94  
95        if (restType_ & rtSwingX){
96 <        dSwingX = swingX - swingX0_;
97 <        dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
98 <        p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
96 >        RealType dSwingX = swingX - swingX0_;
97 >        /// RealType dVdswingX = kSwingX_ * 0.5 * sin(2.0 * dSwingX);
98 >        /// p = 0.25 * kSwingX_ * (1.0 - cos(2.0 * dSwingX));
99 >        RealType dVdswingX = kSwingX_ * dSwingX;        
100 >        p = 0.5 * kSwingX_ * dSwingX * dSwingX;
101          pot_ += p;
102          tBody -= dVdswingX * V3X;
103 <        restInfo_[rtSwingX] = std::make_pair(swingX, p);
103 >        if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p);
104        }
105  
106        if (restType_ & rtSwingY){
107 <        dSwingY = swingY - swingY0_;
108 <        dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
109 <        p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
107 >        RealType dSwingY = swingY - swingY0_;
108 >        /// RealType dVdswingY = kSwingY_ * 0.5 * sin(2.0 * dSwingY);
109 >        /// p = 0.25 * kSwingY_ * (1.0 - cos(2.0 * dSwingY));
110 >        RealType dVdswingY = kSwingY_ * dSwingY;        
111 >        p = 0.5 * kSwingX_ * dSwingY * dSwingY;
112          pot_ += p;
113          tBody -= dVdswingY * V3Y;
114 <        restInfo_[rtSwingY] = std::make_pair(swingY, p);
114 >        if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p);
115        }
116  
117        Vector3d tLab = A.transpose() * tBody;      

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