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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. |
| 11 |
|
* |
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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 |
| 14 |
|
* 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 "primitives/Torsion.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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Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4, |
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TorsionType *tt) : |
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atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4), torsionType_(tt) { } |
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|
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void Torsion::calcForce() { |
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> |
void Torsion::calcForce(RealType& angle) { |
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|
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = atom2_->getPos(); |
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Vector3d pos3 = atom3_->getPos(); |
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|
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// Calculate the cross products and distances |
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Vector3d A = cross(r21, r32); |
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double rA = A.length(); |
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> |
RealType rA = A.length(); |
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Vector3d B = cross(r32, r43); |
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double rB = B.length(); |
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Vector3d C = cross(r32, A); |
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double rC = C.length(); |
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> |
RealType rB = B.length(); |
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|
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/* |
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If either of the two cross product vectors is tiny, that means |
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the three atoms involved are colinear, and the torsion angle is |
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going to be undefined. The easiest check for this problem is |
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to use the product of the two lengths. |
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*/ |
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if (rA * rB < OpenMD::epsilon) return; |
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|
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A.normalize(); |
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B.normalize(); |
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C.normalize(); |
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B.normalize(); |
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|
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// Calculate the sin and cos |
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double cos_phi = dot(A, B) ; |
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double sin_phi = dot(C, B); |
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|
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double dVdPhi; |
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torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi); |
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|
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Vector3d f1; |
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Vector3d f2; |
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Vector3d f3; |
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|
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// Next, we want to calculate the forces. In order |
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// to do that, we first need to figure out whether the |
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// sin or cos form will be more stable. For this, |
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// just look at the value of phi |
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//if (fabs(sin_phi) > 0.1) { |
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// use the sin version to avoid 1/cos terms |
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|
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> |
RealType cos_phi = dot(A, B) ; |
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if (cos_phi > 1.0) cos_phi = 1.0; |
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if (cos_phi < -1.0) cos_phi = -1.0; |
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|
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RealType dVdcosPhi; |
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torsionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
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Vector3d f1 ; |
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> |
Vector3d f2 ; |
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> |
Vector3d f3 ; |
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> |
|
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Vector3d dcosdA = (cos_phi * A - B) /rA; |
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Vector3d dcosdB = (cos_phi * B - A) /rB; |
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|
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double dVdcosPhi = -dVdPhi / sin_phi; |
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< |
|
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> |
|
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f1 = dVdcosPhi * cross(r32, dcosdA); |
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f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
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f3 = dVdcosPhi * cross(dcosdB, r32); |
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< |
|
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/** @todo fix below block, must be something wrong with the sign somewhere */ |
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//} else { |
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// This angle is closer to 0 or 180 than it is to |
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// 90, so use the cos version to avoid 1/sin terms |
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|
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//double dVdsinPhi = dVdPhi /cos_phi; |
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//Vector3d dsindB = (sin_phi * B - C) /rB; |
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//Vector3d dsindC = (sin_phi * C - B) /rC; |
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|
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< |
//f1.x() = dVdsinPhi*((r32.y()*r32.y() + r32.z()*r32.z())*dsindC.x() - r32.x()*r32.y()*dsindC.y() - r32.x()*r32.z()*dsindC.z()); |
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|
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//f1.y() = dVdsinPhi*((r32.z()*r32.z() + r32.x()*r32.x())*dsindC.y() - r32.y()*r32.z()*dsindC.z() - r32.y()*r32.x()*dsindC.x()); |
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|
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< |
//f1.z() = dVdsinPhi*((r32.x()*r32.x() + r32.y()*r32.y())*dsindC.z() - r32.z()*r32.x()*dsindC.x() - r32.z()*r32.y()*dsindC.y()); |
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|
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< |
//f2.x() = dVdsinPhi*(-(r32.y()*r21.y() + r32.z()*r21.z())*dsindC.x() + (2.0*r32.x()*r21.y() - r21.x()*r32.y())*dsindC.y() |
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//+ (2.0*r32.x()*r21.z() - r21.x()*r32.z())*dsindC.z() + dsindB.z()*r43.y() - dsindB.y()*r43.z()); |
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|
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< |
//f2.y() = dVdsinPhi*(-(r32.z()*r21.z() + r32.x()*r21.x())*dsindC.y() + (2.0*r32.y()*r21.z() - r21.y()*r32.z())*dsindC.z() |
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//+ (2.0*r32.y()*r21.x() - r21.y()*r32.x())*dsindC.x() + dsindB.x()*r43.z() - dsindB.z()*r43.x()); |
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|
| 120 |
< |
//f2.z() = dVdsinPhi*(-(r32.x()*r21.x() + r32.y()*r21.y())*dsindC.z() + (2.0*r32.z()*r21.x() - r21.z()*r32.x())*dsindC.x() |
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//+(2.0*r32.z()*r21.y() - r21.z()*r32.y())*dsindC.y() + dsindB.y()*r43.x() - dsindB.x()*r43.y()); |
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< |
|
| 123 |
< |
//f3 = dVdsinPhi * cross(r32, dsindB); |
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< |
|
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< |
//} |
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< |
|
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> |
|
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atom1_->addFrc(f1); |
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atom2_->addFrc(f2 - f1); |
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atom3_->addFrc(f3 - f2); |
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atom4_->addFrc(-f3); |
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< |
} |
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< |
|
| 100 |
> |
|
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> |
atom1_->addParticlePot(potential_); |
| 102 |
> |
atom2_->addParticlePot(potential_); |
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> |
atom3_->addParticlePot(potential_); |
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> |
atom4_->addParticlePot(potential_); |
| 105 |
> |
|
| 106 |
> |
angle = acos(cos_phi) /M_PI * 180.0; |
| 107 |
> |
} |
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|
} |
