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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* 1. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* 2. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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* |
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* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
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* research, please cite the appropriate papers when you publish your |
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* work. Good starting points are: |
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* |
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* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
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* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
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+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
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* [4] Vardeman & Gezelter, in progress (2009). |
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*/ |
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|
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#include "DLM.hpp" |
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|
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namespace oopse { |
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namespace OpenMD { |
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|
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void DLM::doRotate(StuntDouble* sd, Vector3d& ji, RealType dt) { |
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RealType dt2 = 0.5 * dt; |
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RotMat3x3d rot = RotMat3x3d::identity(); // initalize rot as a unit matrix |
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|
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// use a small angle aproximation for sin and cosine |
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/* |
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angleSqr = angle * angle; |
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angleSqrOver4 = angleSqr / 4.0; |
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top = 1.0 - angleSqrOver4; |
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bottom = 1.0 + angleSqrOver4; |
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|
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//angleSqr = angle * angle; |
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//angleSqrOver4 = angleSqr / 4.0; |
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//top = 1.0 - angleSqrOver4; |
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//bottom = 1.0 + angleSqrOver4; |
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|
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//cosAngle = top / bottom; |
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//sinAngle = angle / bottom; |
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cosAngle = top / bottom; |
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sinAngle = angle / bottom; |
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*/ |
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// or don't use the small angle approximation: |
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cosAngle = cos(angle); |
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sinAngle = sin(angle); |
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+ |
|
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rot(axes1, axes1) = cosAngle; |
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rot(axes2, axes2) = cosAngle; |
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|
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// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
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ji = rot * ji; |
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|
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// rotate the Rotation matrix acording to: |
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// A[][] = A[][] * transpose(rot[][]) |
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// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
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// This code comes from converting an algorithm detailed in |
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// J. Chem. Phys. 107 (15), pp. 5840-5851 by Dullweber, |
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// Leimkuhler and McLachlan (DLM) for use in our code. |
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> |
// In Appendix A, the DLM paper has the change to the rotation |
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// matrix as: Q = Q * rot.transpose(), but our rotation matrix |
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> |
// A is actually equivalent to Q.transpose(). This fact can be |
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> |
// seen on page 5849 of the DLM paper where a lab frame |
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> |
// dipole \mu_i(t) is expressed in terms of a body-fixed |
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// reference orientation, \bar{\mu_i} and the rotation matrix, Q: |
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// \mu_i(t) = Q * \bar{\mu_i} |
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// Our code computes lab frame vectors from body-fixed reference |
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// vectors using: |
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// v_{lab} = A.transpose() * v_{body} |
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// (See StuntDouble.hpp for confirmation of this fact). |
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// |
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// So, using the identity: |
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// (A * B).transpose() = B.transpose() * A.transpose(), we |
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// get the equivalent of Q = Q * rot.transpose() for our code to be: |
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|
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< |
A = rot * A; //? A = A* rot.transpose(); |
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A = rot * A; |
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|
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} |
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|
