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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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namespace oopse { |
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Torsion::Torsion(Atom *atom1, Atom *atom2, Atom *atom3, Atom *atom4, |
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TorsionType *tt) : |
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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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void Torsion::calcForce() { |
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void Torsion::calcForce() { |
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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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Vector3d f2; |
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Vector3d f3; |
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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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if (fabs(sin_phi) > 0.5) { |
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//use the sin version to prevent potential singularities |
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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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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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double dVdcosPhi = -dVdPhi / sin_phi; |
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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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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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/** @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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} else { |
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//use the cos version to prevent potential singularities |
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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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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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//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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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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//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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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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//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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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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//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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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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//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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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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//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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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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//f3 = dVdsinPhi * cross(r32, dsindB); |
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f3 = dVdsinPhi * cross(dsindB, r32); |
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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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} |
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} |
