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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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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, 234107 (2008). |
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* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
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* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
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*/ |
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#include "config.h" |
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#include <cmath> |
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|
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#include "primitives/GhostTorsion.hpp" |
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namespace oopse { |
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GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2, DirectionalAtom* ghostAtom, |
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TorsionType *tt) : Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {} |
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|
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void GhostTorsion::calcForce() { |
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DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atom2_); |
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|
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = atom2_->getPos(); |
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namespace OpenMD { |
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|
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GhostTorsion::GhostTorsion(Atom *atom1, Atom *atom2, |
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DirectionalAtom* ghostAtom, TorsionType *tt) |
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: Torsion(atom1, atom2, ghostAtom, ghostAtom, tt) {} |
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|
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void GhostTorsion::calcForce(RealType& angle, bool doParticlePot) { |
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DirectionalAtom* ghostAtom = static_cast<DirectionalAtom*>(atoms_[2]); |
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|
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Vector3d pos1 = atoms_[0]->getPos(); |
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Vector3d pos2 = atoms_[1]->getPos(); |
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Vector3d pos3 = ghostAtom->getPos(); |
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Vector3d r21 = pos1 - pos2; |
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Vector3d r32 = pos2 - pos3; |
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Vector3d r43 = ghostAtom->getElectroFrame().getColumn(2); |
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Vector3d r43 = ghostAtom->getA().transpose().getColumn(2); |
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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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// 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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double dVdPhi; |
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torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi); |
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RealType cos_phi = dot(A, B) ; |
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RealType dVdcosPhi; |
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torsionType_->calcForce(cos_phi, potential_, dVdcosPhi); |
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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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double dVdcosPhi = -dVdPhi / sin_phi; |
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Vector3d f1 = dVdcosPhi * cross(r32, dcosdA); |
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Vector3d f2 = dVdcosPhi * ( cross(r43, dcosdB) - cross(r21, dcosdA)); |
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Vector3d f3 = dVdcosPhi * cross(dcosdB, r32); |
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atom1_->addFrc(f1); |
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atom2_->addFrc(f2 - f1); |
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atoms_[0]->addFrc(f1); |
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atoms_[1]->addFrc(f2 - f1); |
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ghostAtom->addFrc(-f2); |
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f3.negate(); |
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ghostAtom->addTrq(cross(r43, f3)); |
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} |
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if (doParticlePot) { |
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atoms_[0]->addParticlePot(potential_); |
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atoms_[1]->addParticlePot(potential_); |
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ghostAtom->addParticlePot(potential_); |
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} |
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angle = acos(cos_phi) /M_PI * 180.0; |
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} |
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} |
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