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* redistribute this software in source and binary code form, provided |
| 7 |
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* that the following conditions are met: |
| 8 |
|
* |
| 9 |
< |
* 1. Acknowledgement of the program authors must be made in any |
| 10 |
< |
* publication of scientific results based in part on use of the |
| 11 |
< |
* program. An acceptable form of acknowledgement is citation of |
| 12 |
< |
* the article in which the program was described (Matthew |
| 13 |
< |
* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
| 14 |
< |
* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
| 15 |
< |
* Parallel Simulation Engine for Molecular Dynamics," |
| 16 |
< |
* J. Comput. Chem. 26, pp. 252-271 (2005)) |
| 17 |
< |
* |
| 18 |
< |
* 2. Redistributions of source code must retain the above copyright |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
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* distribution. |
| 28 |
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* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
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* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 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, 234107 (2008). |
| 39 |
+ |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
+ |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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|
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#include "restraints/MolecularRestraint.hpp" |
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|
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//using namespace JAMA; |
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|
|
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< |
namespace oopse { |
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> |
namespace OpenMD { |
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|
|
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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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|
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|
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pot_ += p; |
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|
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< |
restInfo_[rtDisplacement] = std::make_pair(r, p); |
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> |
if (printRest_) restInfo_[rtDisplacement] = std::make_pair(r, p); |
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|
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for(it = forces_.begin(); it != forces_.end(); ++it) |
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(*it) = -kDisp_ * del * scaleFactor_; |
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|
|
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Mat3x3d R(0.0); |
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|
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< |
for (int n = 0; n < struc.size(); n++){ |
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> |
for (unsigned int n = 0; n < struc.size(); n++){ |
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|
|
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/* |
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* correlation matrix R: |
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|
Vector3d eularAngles = A.toEulerAngles(); |
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|
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|
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< |
RealType twistAngle, swingAngle; |
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> |
RealType twistAngle; |
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Vector3d swingAxis; |
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|
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Quat4d quat = A.toQuaternion(); |
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|
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< |
quat.getTwistSwingAxisAngle(twistAngle, swingAngle, swingAxis); |
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> |
RealType swingX, swingY; |
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> |
quat.toSwingTwist(swingX, swingY, twistAngle); |
| 148 |
|
|
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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; |
| 155 |
< |
RealType dTwist, dSwing, dSwingX, dSwingY; |
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> |
RealType dVdtwist, dVdswingX, dVdswingY; |
| 150 |
> |
RealType dTwist, dSwingX, dSwingY; |
| 151 |
|
RealType p; |
| 152 |
|
|
| 153 |
|
if (restType_ & rtTwist){ |
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|
dTwist = twistAngle - twist0_; |
| 155 |
< |
dVdtwist = kTwist_ * sin(dTwist) ; |
| 156 |
< |
p = kTwist_ * (1.0 - cos(dTwist) ) ; |
| 155 |
> |
/// dVdtwist = kTwist_ * sin(dTwist) ; |
| 156 |
> |
/// p = kTwist_ * (1.0 - cos(dTwist) ) ; |
| 157 |
> |
dVdtwist = kTwist_ * dTwist; |
| 158 |
> |
p = 0.5 * kTwist_ * dTwist * dTwist; |
| 159 |
|
pot_ += p; |
| 160 |
|
tBody -= dVdtwist * V3Z; |
| 161 |
< |
restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 161 |
> |
if (printRest_) restInfo_[rtTwist] = std::make_pair(twistAngle, p); |
| 162 |
|
} |
| 163 |
|
|
| 167 |
– |
// if (restType_ & rtSwing){ |
| 168 |
– |
// dSwing = swingAngle - swing0_; |
| 169 |
– |
// dVdswing = kSwing_ * 2.0 * sin(2.0 * dSwing); |
| 170 |
– |
// p = kSwing_ * (1.0 - cos(2.0 * dSwing)); |
| 171 |
– |
// pot_ += p; |
| 172 |
– |
// tBody -= dVdswing * swingAxis; |
| 173 |
– |
// restInfo_[rtSwing] = std::make_pair(swingAngle, p); |
| 174 |
– |
// } |
| 175 |
– |
|
| 164 |
|
if (restType_ & rtSwingX){ |
| 165 |
|
dSwingX = swingX - swingX0_; |
| 166 |
< |
dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX); |
| 167 |
< |
p = kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 166 |
> |
/// dVdswingX = kSwingX_ * 2.0 * sin(2.0 * dSwingX); |
| 167 |
> |
/// p = kSwingX_ * (1.0 - cos(2.0 * dSwingX)); |
| 168 |
> |
dVdswingX = kSwingX_ * dSwingX; |
| 169 |
> |
p = 0.5 * kSwingX_ * dSwingX * dSwingX; |
| 170 |
|
pot_ += p; |
| 171 |
|
tBody -= dVdswingX * V3X; |
| 172 |
< |
restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 172 |
> |
if (printRest_) restInfo_[rtSwingX] = std::make_pair(swingX, p); |
| 173 |
|
} |
| 174 |
|
if (restType_ & rtSwingY){ |
| 175 |
|
dSwingY = swingY - swingY0_; |
| 176 |
< |
dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY); |
| 177 |
< |
p = kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 176 |
> |
/// dVdswingY = kSwingY_ * 2.0 * sin(2.0 * dSwingY); |
| 177 |
> |
/// p = kSwingY_ * (1.0 - cos(2.0 * dSwingY)); |
| 178 |
> |
dVdswingY = kSwingY_ * dSwingY; |
| 179 |
> |
p = 0.5 * kSwingX_ * dSwingY * dSwingY; |
| 180 |
|
pot_ += p; |
| 181 |
|
tBody -= dVdswingY * V3Y; |
| 182 |
< |
restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 182 |
> |
if (printRest_) restInfo_[rtSwingY] = std::make_pair(swingY, p); |
| 183 |
|
} |
| 184 |
|
|
| 185 |
|
|
| 187 |
|
|
| 188 |
|
Vector3d rLab, rBody, txr, fBody, fLab; |
| 189 |
|
|
| 190 |
< |
for (int i = 0; i < struc.size(); i++) { |
| 190 |
> |
for (unsigned int i = 0; i < struc.size(); i++) { |
| 191 |
|
|
| 192 |
|
rLab = struc[i]; |
| 193 |
|
rBody = A * rLab; |
