| 35 |
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* |
| 36 |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
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* [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 |
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*/ |
| 42 |
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|
| 43 |
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#include "restraints/MolecularRestraint.hpp" |
| 49 |
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namespace OpenMD { |
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+ |
|
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void MolecularRestraint::calcForce(std::vector<Vector3d> struc, |
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Vector3d molCom){ |
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| 71 |
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pot_ += p; |
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|
| 74 |
< |
restInfo_[rtDisplacement] = std::make_pair(r, p); |
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> |
if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r, p); |
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|
| 76 |
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for(it = forces_.begin(); it != forces_.end(); ++it) |
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(*it) = -kDisp_ * del * scaleFactor_; |
| 86 |
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Mat3x3d R(0.0); |
| 88 |
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|
| 89 |
< |
for (int n = 0; n < struc.size(); n++){ |
| 89 |
> |
for (unsigned int n = 0; n < struc.size(); n++){ |
| 90 |
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| 91 |
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/* |
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* correlation matrix R: |
| 138 |
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Vector3d eularAngles = A.toEulerAngles(); |
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| 140 |
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| 141 |
< |
RealType twistAngle, swingAngle; |
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> |
RealType twistAngle; |
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Vector3d swingAxis; |
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Quat4d quat = A.toQuaternion(); |
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< |
quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis); |
| 146 |
> |
RealType swingX, swingY; |
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> |
quat.toSwingTwist(swingX, swingY, twistAngle); |
| 148 |
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|
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< |
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; |
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< |
RealType dTwist, dSwing, dSwingX, dSwingY; |
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> |
RealType dVdtwist, dVdswingX, dVdswingY; |
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> |
RealType dTwist, dSwingX, dSwingY; |
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RealType p; |
| 152 |
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if (restType_ & rtTwist){ |
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p = kTwist_ * (1.0 - cos(dTwist) ) ; |
| 157 |
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pot_ += p; |
| 158 |
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tBody -= dVdtwist * V3Z; |
| 159 |
< |
restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 159 |
> |
if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 160 |
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} |
| 161 |
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|
| 162 |
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// if (restType_ & rtSwing){ |
| 174 |
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p = kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 175 |
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pot_ += p; |
| 176 |
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tBody -= dVdswingX * V3X; |
| 177 |
< |
restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 177 |
> |
if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 178 |
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} |
| 179 |
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if (restType_ & rtSwingY){ |
| 180 |
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dSwingY = swingY - swingY0_; |
| 182 |
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p = kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 183 |
|
pot_ += p; |
| 184 |
|
tBody -= dVdswingY * V3Y; |
| 185 |
< |
restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 185 |
> |
if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 186 |
|
} |
| 187 |
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| 188 |
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| 190 |
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| 191 |
|
Vector3d rLab, rBody, txr, fBody, fLab; |
| 192 |
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|
| 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; |
