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namespace oopse { |
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< |
void DLM::doRotate(StuntDouble* sd, Vector3d& ji, double dt) { |
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< |
double dt2 = 0.5 * dt; |
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< |
double angle; |
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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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RealType angle; |
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RotMat3x3d A = sd->getA(); |
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Mat3x3d I = sd->getI(); |
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} |
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< |
void DLM::rotateStep(int axes1, int axes2, double angle, Vector3d& ji, RotMat3x3d& A) { |
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> |
void DLM::rotateStep(int axes1, int axes2, RealType angle, Vector3d& ji, RotMat3x3d& A) { |
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< |
double sinAngle; |
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double cosAngle; |
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double angleSqr; |
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< |
double angleSqrOver4; |
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double top, bottom; |
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> |
RealType sinAngle; |
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RealType cosAngle; |
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RealType angleSqr; |
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RealType angleSqrOver4; |
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RealType top, bottom; |
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RotMat3x3d tempA(A); // initialize the tempA |
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Vector3d tempJ(0.0); |
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// use a small angle aproximation for sin and cosine |
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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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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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< |
//cosAngle = top / bottom; |
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//sinAngle = angle / bottom; |
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cosAngle = cos(angle); |
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sinAngle = sin(angle); |
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cosAngle = top / bottom; |
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sinAngle = angle / bottom; |
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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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rot(axes1, axes1) = cosAngle; |
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rot(axes2, axes2) = cosAngle; |
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// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
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ji = rot * ji; |
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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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< |
A = rot * A; //? A = A* rot.transpose(); |
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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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A = rot * A; |
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} |
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