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#include "primitives/Torsion.hpp" |
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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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atom1_(atom1), |
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atom2_(atom2), |
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atom3_(atom3), |
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atom4_(atom4) { } |
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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 pos4 = atom4_->getPos(); |
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Vector3d r12 = pos1 - pos2; |
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Vector3d r23 = pos2 - pos3; |
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Vector3d r34 = pos3 - pos4; |
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// Calculate the cross products and distances |
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Vector3d A = cross(r12, r23); |
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double rA = A.length(); |
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Vector3d B = cross(r23, r34); |
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double rB = B.length(); |
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Vector3d C = cross(r23, A); |
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double rC = C.length(); |
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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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Vector3d f1; |
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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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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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f1 = dVdcosPhi * cross(r23, dcosdA); |
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f2 = dVdcosPhi * ( cross(r34, dcosdB) - cross(r12, dcosdA)); |
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f3 = dVdcosPhi * cross(r23, dcosdB); |
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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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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*((r23.y()*r23.y() + r23.z()*r23.z())*dsindC.x() - r23.x()*r23.y()*dsindC.y() - r23.x()*r23.z()*dsindC.z()); |
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f1.y() = dVdsinPhi*((r23.z()*r23.z() + r23.x()*r23.x())*dsindC.y() - r23.y()*r23.z()*dsindC.z() - r23.y()*r23.x()*dsindC.x()); |
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f1.z() = dVdsinPhi*((r23.x()*r23.x() + r23.y()*r23.y())*dsindC.z() - r23.z()*r23.x()*dsindC.x() - r23.z()*r23.y()*dsindC.y()); |
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f2.x() = dVdsinPhi*(-(r23.y()*r12.y() + r23.z()*r12.z())*dsindC.x() + (2.0*r23.x()*r12.y() - r12.x()*r23.y())*dsindC.y() |
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+ (2.0*r23.x()*r12.z() - r12.x()*r23.z())*dsindC.z() + dsindB.z()*r34.y() - dsindB.y()*r34.z()); |
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f2.y() = dVdsinPhi*(-(r23.z()*r12.z() + r23.x()*r12.x())*dsindC.y() + (2.0*r23.y()*r12.z() - r12.y()*r23.z())*dsindC.z() |
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+ (2.0*r23.y()*r12.x() - r12.y()*r23.x())*dsindC.x() + dsindB.x()*r34.z() - dsindB.z()*r34.x()); |
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f2.z() = dVdsinPhi*(-(r23.x()*r12.x() + r23.y()*r12.y())*dsindC.z() + (2.0*r23.z()*r12.x() - r12.z()*r23.x())*dsindC.x() |
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+(2.0*r23.z()*r12.y() - r12.z()*r23.y())*dsindC.y() + dsindB.y()*r34.x() - dsindB.x()*r34.y()); |
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f3 = dVdsinPhi * cross(dsindB, r23); |
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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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} |
