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#include "primitives/SRI.hpp" |
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#include "primitives/Atom.hpp" |
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#include <math.h> |
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#include <iostream> |
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#include <stdlib.h> |
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#include "primitives/Torsion.hpp" |
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void Torsion::set_atoms( Atom &a, Atom &b, Atom &c, Atom &d){ |
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c_p_a = &a; |
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c_p_b = &b; |
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c_p_c = &c; |
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c_p_d = &d; |
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} |
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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::calc_forces(){ |
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|
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/********************************************************************** |
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* |
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* initialize vectors |
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* |
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***********************************************************************/ |
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|
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vect r_ab; /* the vector whose origin is a and end is b */ |
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vect r_cb; /* the vector whose origin is c and end is b */ |
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vect r_cd; /* the vector whose origin is c and end is b */ |
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vect r_cr1; /* the cross product of r_ab and r_cb */ |
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vect r_cr2; /* the cross product of r_cb and r_cd */ |
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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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double r_cr1_x2; /* the components of r_cr1 squared */ |
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double r_cr1_y2; |
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double r_cr1_z2; |
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|
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double r_cr2_x2; /* the components of r_cr2 squared */ |
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double r_cr2_y2; |
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double r_cr2_z2; |
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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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double r_cr1_sqr; /* the length of r_cr1 squared */ |
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double r_cr2_sqr; /* the length of r_cr2 squared */ |
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|
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double r_cr1_r_cr2; /* the length of r_cr1 * length of r_cr2 */ |
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|
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double aR[3], bR[3], cR[3], dR[3]; |
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double aF[3], bF[3], cF[3], dF[3]; |
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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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c_p_a->getPos( aR ); |
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c_p_b->getPos( bR ); |
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c_p_c->getPos( cR ); |
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c_p_d->getPos( dR ); |
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A.normalize(); |
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B.normalize(); |
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C.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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r_ab.x = bR[0] - aR[0]; |
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r_ab.y = bR[1] - aR[1]; |
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r_ab.z = bR[2] - aR[2]; |
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r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z)); |
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double dVdPhi; |
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torsionType_->calcForce(cos_phi, sin_phi, potential_, dVdPhi); |
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r_cb.x = bR[0] - cR[0]; |
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r_cb.y = bR[1] - cR[1]; |
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r_cb.z = bR[2] - cR[2]; |
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r_cb.length = sqrt((r_cb.x * r_cb.x + r_cb.y * r_cb.y + r_cb.z * r_cb.z)); |
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Vector3d f1; |
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Vector3d f2; |
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Vector3d f3; |
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r_cd.x = dR[0] - cR[0]; |
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r_cd.y = dR[1] - cR[1]; |
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r_cd.z = dR[2] - cR[2]; |
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r_cd.length = sqrt((r_cd.x * r_cd.x + r_cd.y * r_cd.y + r_cd.z * r_cd.z)); |
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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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r_cr1.x = r_ab.y * r_cb.z - r_cb.y * r_ab.z; |
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r_cr1.y = r_ab.z * r_cb.x - r_cb.z * r_ab.x; |
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r_cr1.z = r_ab.x * r_cb.y - r_cb.x * r_ab.y; |
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r_cr1_x2 = r_cr1.x * r_cr1.x; |
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r_cr1_y2 = r_cr1.y * r_cr1.y; |
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r_cr1_z2 = r_cr1.z * r_cr1.z; |
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r_cr1_sqr = r_cr1_x2 + r_cr1_y2 + r_cr1_z2; |
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r_cr1.length = sqrt(r_cr1_sqr); |
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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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r_cr2.x = r_cb.y * r_cd.z - r_cd.y * r_cb.z; |
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r_cr2.y = r_cb.z * r_cd.x - r_cd.z * r_cb.x; |
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r_cr2.z = r_cb.x * r_cd.y - r_cd.x * r_cb.y; |
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r_cr2_x2 = r_cr2.x * r_cr2.x; |
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r_cr2_y2 = r_cr2.y * r_cr2.y; |
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r_cr2_z2 = r_cr2.z * r_cr2.z; |
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r_cr2_sqr = r_cr2_x2 + r_cr2_y2 + r_cr2_z2; |
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r_cr2.length = sqrt(r_cr2_sqr); |
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double dVdcosPhi = dVdPhi / sin_phi; |
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r_cr1_r_cr2 = r_cr1.length * r_cr2.length; |
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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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/********************************************************************** |
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* |
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* dot product and angle calculations |
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* |
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***********************************************************************/ |
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double cr1_dot_cr2; /* the dot product of the cr1 and cr2 vectors */ |
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double cos_phi; /* the cosine of the torsion angle */ |
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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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cr1_dot_cr2 = r_cr1.x * r_cr2.x + r_cr1.y * r_cr2.y + r_cr1.z * r_cr2.z; |
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cos_phi = cr1_dot_cr2 / r_cr1_r_cr2; |
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/* adjust for the granularity of the numbers for angles near 0 or pi */ |
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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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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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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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/******************************************************************** |
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* |
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* This next section calculates derivatives needed for the force |
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* calculation |
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* |
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********************************************************************/ |
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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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/* the derivatives of cos phi with respect to the x, y, |
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and z components of vectors cr1 and cr2. */ |
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double d_cos_dx_cr1; |
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double d_cos_dy_cr1; |
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double d_cos_dz_cr1; |
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double d_cos_dx_cr2; |
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double d_cos_dy_cr2; |
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double d_cos_dz_cr2; |
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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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d_cos_dx_cr1 = r_cr2.x / r_cr1_r_cr2 - (cos_phi * r_cr1.x) / r_cr1_sqr; |
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d_cos_dy_cr1 = r_cr2.y / r_cr1_r_cr2 - (cos_phi * r_cr1.y) / r_cr1_sqr; |
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d_cos_dz_cr1 = r_cr2.z / r_cr1_r_cr2 - (cos_phi * r_cr1.z) / r_cr1_sqr; |
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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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d_cos_dx_cr2 = r_cr1.x / r_cr1_r_cr2 - (cos_phi * r_cr2.x) / r_cr2_sqr; |
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d_cos_dy_cr2 = r_cr1.y / r_cr1_r_cr2 - (cos_phi * r_cr2.y) / r_cr2_sqr; |
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d_cos_dz_cr2 = r_cr1.z / r_cr1_r_cr2 - (cos_phi * r_cr2.z) / r_cr2_sqr; |
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f3 = dVdsinPhi * cross(dsindB, r23); |
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/*********************************************************************** |
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* |
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* Calculate the actual forces and place them in the atoms. |
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* |
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***********************************************************************/ |
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} |
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double force; /*the force scaling factor */ |
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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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force = torsion_force(cos_phi); |
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|
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aF[0] = force * (d_cos_dy_cr1 * r_cb.z - d_cos_dz_cr1 * r_cb.y); |
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aF[1] = force * (d_cos_dz_cr1 * r_cb.x - d_cos_dx_cr1 * r_cb.z); |
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aF[2] = force * (d_cos_dx_cr1 * r_cb.y - d_cos_dy_cr1 * r_cb.x); |
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|
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bF[0] = force * ( d_cos_dy_cr1 * (r_ab.z - r_cb.z) |
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- d_cos_dy_cr2 * r_cd.z |
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+ d_cos_dz_cr1 * (r_cb.y - r_ab.y) |
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+ d_cos_dz_cr2 * r_cd.y); |
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bF[1] = force * ( d_cos_dx_cr1 * (r_cb.z - r_ab.z) |
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+ d_cos_dx_cr2 * r_cd.z |
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+ d_cos_dz_cr1 * (r_ab.x - r_cb.x) |
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- d_cos_dz_cr2 * r_cd.x); |
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bF[2] = force * ( d_cos_dx_cr1 * (r_ab.y - r_cb.y) |
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- d_cos_dx_cr2 * r_cd.y |
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+ d_cos_dy_cr1 * (r_cb.x - r_ab.x) |
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+ d_cos_dy_cr2 * r_cd.x); |
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|
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cF[0] = force * (- d_cos_dy_cr1 * r_ab.z |
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- d_cos_dy_cr2 * (r_cb.z - r_cd.z) |
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+ d_cos_dz_cr1 * r_ab.y |
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- d_cos_dz_cr2 * (r_cd.y - r_cb.y)); |
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cF[1] = force * ( d_cos_dx_cr1 * r_ab.z |
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- d_cos_dx_cr2 * (r_cd.z - r_cb.z) |
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- d_cos_dz_cr1 * r_ab.x |
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- d_cos_dz_cr2 * (r_cb.x - r_cd.x)); |
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cF[2] = force * (- d_cos_dx_cr1 * r_ab.y |
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- d_cos_dx_cr2 * (r_cb.y - r_cd.y) |
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+ d_cos_dy_cr1 * r_ab.x |
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- d_cos_dy_cr2 * (r_cd.x - r_cb.x)); |
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|
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dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y); |
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dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z); |
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dF[2] = force * (d_cos_dx_cr2 * r_cb.y - d_cos_dy_cr2 * r_cb.x); |
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|
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c_p_a->addFrc(aF); |
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c_p_b->addFrc(bF); |
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c_p_c->addFrc(cF); |
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c_p_d->addFrc(dF); |
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} |