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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: |
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* |
| 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 |
|
* 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, 24107 (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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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); |
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|
|
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< |
RealType tw, sx, sy, ttw, swingX, swingY; |
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quat.toTwistSwing(tw, sx, sy); |
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quat.toSwingTwist(swingX, swingY, ttw); |
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< |
|
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< |
// std::cerr << eularAngles << "\t[" << twistAngle << "," << swingAngle << |
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// "]\t[" << tw << "," << sx << "," << sy << "]\t[" << ttw << |
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// "," << 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; |
| 150 |
> |
RealType dTwist, dSwingX, dSwingY; |
| 151 |
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RealType p; |
| 152 |
|
|
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|
if (restType_ & rtTwist){ |
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|
| 191 |
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Vector3d rLab, rBody, txr, fBody, fLab; |
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|
|
| 193 |
< |
for (int i = 0; i < struc.size(); i++) { |
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> |
for (unsigned int i = 0; i < struc.size(); i++) { |
| 194 |
|
|
| 195 |
|
rLab = struc[i]; |
| 196 |
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rBody = A * rLab; |
