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#include "SRI.hpp" |
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#include "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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|
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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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|
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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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|
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r_cr1_r_cr2 = r_cr1.length * r_cr2.length; |
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|
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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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|
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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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|
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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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|
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cos_phi = cr1_dot_cr2 / r_cr1_r_cr2; |
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|
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/* adjust for the granularity of the numbers for angles near 0 or pi */ |
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|
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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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|
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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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|
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|
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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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|
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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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|
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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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|
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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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|
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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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|
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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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} |
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#include "primitives/Torsion.hpp" |
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|
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namespace oopse { |
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|
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Torsion::Torsion(Atom* atom1, Atom* atom2, Atom* atom3, Atom* atom4, TorsionType* tt) |
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: atom1_(atom1), atom2_(atom2), atom3_(atom3), atom4_(atom4) { |
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|
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} |
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|
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void Torsion::calcForce() { |
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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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Vector3d pos4 = atom4_->getPos(); |
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|
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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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|
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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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// Calculate the sin and cos |
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double cos_phi = (A*B)/(rA*rB); |
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double sin_phi = (C*B)/(rC*rB); |
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|
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double phi= -atan2(sin_phi,cos_phi); |
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|
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double firstDerivative; |
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torsionType_->calcForce(phi, firstDerivative, potential_); |
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|
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|
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Vector3d f1,f2,f3; |
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|
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// Normalize B |
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rB = 1.0/rB; |
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B *= rB; |
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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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rA = 1.0/rA; |
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A *= rA; |
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Vector3d dcosdA = rA*(cos_phi*A-B); |
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Vector3d dcosdB = rB*(cos_phi*B-A); |
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|
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K1 = K1/sin_phi; |
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|
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//simple form |
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//f1 = K1 * cross(r23, dcosdA); |
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//f3 = K1 * cross(r23, dcosdB); |
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//f2 = K1 * ( cross(r34, dcosdB) - cross(r12, dcosdA)); |
63 |
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|
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f1.x = K1*(r23.y*dcosdA.z - r23.z*dcosdA.y); |
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f1.y = K1*(r23.z*dcosdA.x - r23.x*dcosdA.z); |
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f1.z = K1*(r23.x*dcosdA.y - r23.y*dcosdA.x); |
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|
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f3.x = K1*(r23.z*dcosdB.y - r23.y*dcosdB.z); |
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f3.y = K1*(r23.x*dcosdB.z - r23.z*dcosdB.x); |
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f3.z = K1*(r23.y*dcosdB.x - r23.x*dcosdB.y); |
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|
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f2.x = K1*(r12.z*dcosdA.y - r12.y*dcosdA.z + r34.y*dcosdB.z - r34.z*dcosdB.y); |
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f2.y = K1*(r12.x*dcosdA.z - r12.z*dcosdA.x + r34.z*dcosdB.x - r34.x*dcosdB.z); |
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f2.z = K1*(r12.y*dcosdA.x - r12.x*dcosdA.y + r34.x*dcosdB.y - r34.y*dcosdB.x); |
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} else { |
76 |
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// This angle is closer to 0 or 180 than it is to |
77 |
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// 90, so use the cos version to avoid 1/sin terms |
78 |
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|
79 |
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// Normalize C |
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rC = 1.0/rC; |
81 |
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C *= rC; |
82 |
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Vector3d dsindC = rC*(sin_phi*C-B); |
83 |
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Vector3d dsindB = rB*(sin_phi*B-C); |
84 |
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|
85 |
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K1 = -K1/cos_phi; |
86 |
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|
87 |
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f1.x = K1*((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 = K1*((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 = K1*((r23.x*r23.x + r23.y*r23.y)*dsindC.z - r23.z*r23.x*dsindC.x - r23.z*r23.y*dsindC.y); |
90 |
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|
91 |
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f3 = K1 *cross(dsindB,r23); |
92 |
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|
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f2.x = K1*(-(r23.y*r12.y + r23.z*r12.z)*dsindC.x + (2.0*r23.x*r12.y - r12.x*r23.y)*dsindC.y |
94 |
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+ (2.0*r23.x*r12.z - r12.x*r23.z)*dsindC.z + dsindB.z*r34.y - dsindB.y*r34.z); |
95 |
> |
f2.y = K1*(-(r23.z*r12.z + r23.x*r12.x)*dsindC.y + (2.0*r23.y*r12.z - r12.y*r23.z)*dsindC.z |
96 |
> |
+ (2.0*r23.y*r12.x - r12.y*r23.x)*dsindC.x + dsindB.x*r34.z - dsindB.z*r34.x); |
97 |
> |
f2.z = K1*(-(r23.x*r12.x + r23.y*r12.y)*dsindC.z + (2.0*r23.z*r12.x - r12.z*r23.x)*dsindC.x |
98 |
> |
+(2.0*r23.z*r12.y - r12.z*r23.y)*dsindC.y + dsindB.y*r34.x - dsindB.x*r34.y); |
99 |
> |
} |
100 |
> |
|
101 |
> |
atom1_->addFrc(f1); |
102 |
> |
atom2_->addFrc(f2 - f1); |
103 |
> |
atom3_->addFrc(f3 - f2); |
104 |
> |
atom4_->addFrc(-f3); |
105 |
> |
|
106 |
> |
} |
107 |
> |
|
108 |
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|
109 |
> |
double K=0; // energy |
110 |
> |
double K1=0; // force |
111 |
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|
112 |
> |
// get the dihedral information |
113 |
> |
int multiplicity = value->multiplicity; |
114 |
> |
|
115 |
> |
// Loop through the multiple parameter sets for this |
116 |
> |
// bond. We will only loop more than once if this |
117 |
> |
// has multiple parameter sets from Charmm22 |
118 |
> |
for (int mult_num=0; mult_num<multiplicity; mult_num++) |
119 |
> |
{ |
120 |
> |
/* get angle information */ |
121 |
> |
double k = value->values[mult_num].k * scale; |
122 |
> |
double delta = value->values[mult_num].delta; |
123 |
> |
int n = value->values[mult_num].n; |
124 |
> |
|
125 |
> |
// Calculate the energy |
126 |
> |
if (n) |
127 |
> |
{ |
128 |
> |
// Periodicity is greater than 0, so use cos form |
129 |
> |
K += k*(1+cos(n*phi + delta)); |
130 |
> |
K1 += -n*k*sin(n*phi + delta); |
131 |
> |
} |
132 |
> |
else |
133 |
> |
{ |
134 |
> |
// Periodicity is 0, so just use the harmonic form |
135 |
> |
double diff = phi-delta; |
136 |
> |
if (diff < -PI) diff += TWOPI; |
137 |
> |
else if (diff > PI) diff -= TWOPI; |
138 |
> |
|
139 |
> |
K += k*diff*diff; |
140 |
> |
K1 += 2.0*k*diff; |
141 |
> |
} |
142 |
> |
} /* for multiplicity */ |
143 |
> |
|
144 |
> |
|
145 |
> |
void Torsion::calc_forces(){ |
146 |
> |
|
147 |
> |
/********************************************************************** |
148 |
> |
* |
149 |
> |
* initialize vectors |
150 |
> |
* |
151 |
> |
***********************************************************************/ |
152 |
> |
|
153 |
> |
vect r_ab; /* the vector whose origin is a and end is b */ |
154 |
> |
vect r_cb; /* the vector whose origin is c and end is b */ |
155 |
> |
vect r_cd; /* the vector whose origin is c and end is b */ |
156 |
> |
vect r_cr1; /* the cross product of r_ab and r_cb */ |
157 |
> |
vect r_cr2; /* the cross product of r_cb and r_cd */ |
158 |
> |
|
159 |
> |
double r_cr1_x2; /* the components of r_cr1 squared */ |
160 |
> |
double r_cr1_y2; |
161 |
> |
double r_cr1_z2; |
162 |
> |
|
163 |
> |
double r_cr2_x2; /* the components of r_cr2 squared */ |
164 |
> |
double r_cr2_y2; |
165 |
> |
double r_cr2_z2; |
166 |
> |
|
167 |
> |
double r_cr1_sqr; /* the length of r_cr1 squared */ |
168 |
> |
double r_cr2_sqr; /* the length of r_cr2 squared */ |
169 |
> |
|
170 |
> |
double r_cr1_r_cr2; /* the length of r_cr1 * length of r_cr2 */ |
171 |
> |
|
172 |
> |
Vector3d aR, bR, cR, dR; |
173 |
> |
Vector3d aF, bF, cF, dF; |
174 |
> |
|
175 |
> |
aR = c_p_a->getPos(); |
176 |
> |
bR = c_p_b->getPos(); |
177 |
> |
cR = c_p_c->getPos(); |
178 |
> |
dR = c_p_d->getPos(); |
179 |
> |
|
180 |
> |
r_ab.x = bR[0] - aR[0]; |
181 |
> |
r_ab.y = bR[1] - aR[1]; |
182 |
> |
r_ab.z = bR[2] - aR[2]; |
183 |
> |
r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z)); |
184 |
> |
|
185 |
> |
r_cb.x = bR[0] - cR[0]; |
186 |
> |
r_cb.y = bR[1] - cR[1]; |
187 |
> |
r_cb.z = bR[2] - cR[2]; |
188 |
> |
r_cb.length = sqrt((r_cb.x * r_cb.x + r_cb.y * r_cb.y + r_cb.z * r_cb.z)); |
189 |
> |
|
190 |
> |
r_cd.x = dR[0] - cR[0]; |
191 |
> |
r_cd.y = dR[1] - cR[1]; |
192 |
> |
r_cd.z = dR[2] - cR[2]; |
193 |
> |
r_cd.length = sqrt((r_cd.x * r_cd.x + r_cd.y * r_cd.y + r_cd.z * r_cd.z)); |
194 |
> |
|
195 |
> |
r_cr1.x = r_ab.y * r_cb.z - r_cb.y * r_ab.z; |
196 |
> |
r_cr1.y = r_ab.z * r_cb.x - r_cb.z * r_ab.x; |
197 |
> |
r_cr1.z = r_ab.x * r_cb.y - r_cb.x * r_ab.y; |
198 |
> |
r_cr1_x2 = r_cr1.x * r_cr1.x; |
199 |
> |
r_cr1_y2 = r_cr1.y * r_cr1.y; |
200 |
> |
r_cr1_z2 = r_cr1.z * r_cr1.z; |
201 |
> |
r_cr1_sqr = r_cr1_x2 + r_cr1_y2 + r_cr1_z2; |
202 |
> |
r_cr1.length = sqrt(r_cr1_sqr); |
203 |
> |
|
204 |
> |
r_cr2.x = r_cb.y * r_cd.z - r_cd.y * r_cb.z; |
205 |
> |
r_cr2.y = r_cb.z * r_cd.x - r_cd.z * r_cb.x; |
206 |
> |
r_cr2.z = r_cb.x * r_cd.y - r_cd.x * r_cb.y; |
207 |
> |
r_cr2_x2 = r_cr2.x * r_cr2.x; |
208 |
> |
r_cr2_y2 = r_cr2.y * r_cr2.y; |
209 |
> |
r_cr2_z2 = r_cr2.z * r_cr2.z; |
210 |
> |
r_cr2_sqr = r_cr2_x2 + r_cr2_y2 + r_cr2_z2; |
211 |
> |
r_cr2.length = sqrt(r_cr2_sqr); |
212 |
> |
|
213 |
> |
r_cr1_r_cr2 = r_cr1.length * r_cr2.length; |
214 |
> |
|
215 |
> |
//Vector3d pos1 = atom1_->getPos(); |
216 |
> |
//Vector3d pos2 = atom2_->getPos(); |
217 |
> |
//Vector3d pos3 = atom3_->getPos(); |
218 |
> |
//Vector3d pos4 = atom4_->getPos(); |
219 |
> |
|
220 |
> |
//Vector3d r12 = pos2 - pos1; |
221 |
> |
//Vector3d r32 = pos2 - pos3; |
222 |
> |
//Vector3d r34 = pos4 - pos3; |
223 |
> |
|
224 |
> |
//A = cross(r12, r32); |
225 |
> |
//B = cross(r32, r34); |
226 |
> |
|
227 |
> |
//rA = A.length(); |
228 |
> |
//rB = B.length(); |
229 |
> |
|
230 |
> |
/********************************************************************** |
231 |
> |
* |
232 |
> |
* dot product and angle calculations |
233 |
> |
* |
234 |
> |
***********************************************************************/ |
235 |
> |
|
236 |
> |
double cr1_dot_cr2; /* the dot product of the cr1 and cr2 vectors */ |
237 |
> |
double cos_phi; /* the cosine of the torsion angle */ |
238 |
> |
|
239 |
> |
cr1_dot_cr2 = r_cr1.x * r_cr2.x + r_cr1.y * r_cr2.y + r_cr1.z * r_cr2.z; |
240 |
> |
|
241 |
> |
cos_phi = cr1_dot_cr2 / r_cr1_r_cr2; |
242 |
> |
|
243 |
> |
/* adjust for the granularity of the numbers for angles near 0 or pi */ |
244 |
> |
|
245 |
> |
if(cos_phi > 1.0) cos_phi = 1.0; |
246 |
> |
if(cos_phi < -1.0) cos_phi = -1.0; |
247 |
> |
|
248 |
> |
//cos_phi = dot (A, B) / (rA * rB); |
249 |
> |
//if (cos_phi > 1.0) { |
250 |
> |
// cos_phi = 1.0; |
251 |
> |
//} |
252 |
> |
//if (cos_phi < -1.0) { |
253 |
> |
// cos_phi = -1.0; |
254 |
> |
//} |
255 |
> |
|
256 |
> |
|
257 |
> |
|
258 |
> |
/******************************************************************** |
259 |
> |
* |
260 |
> |
* This next section calculates derivatives needed for the force |
261 |
> |
* calculation |
262 |
> |
* |
263 |
> |
********************************************************************/ |
264 |
> |
|
265 |
> |
|
266 |
> |
/* the derivatives of cos phi with respect to the x, y, |
267 |
> |
and z components of vectors cr1 and cr2. */ |
268 |
> |
double d_cos_dx_cr1; |
269 |
> |
double d_cos_dy_cr1; |
270 |
> |
double d_cos_dz_cr1; |
271 |
> |
double d_cos_dx_cr2; |
272 |
> |
double d_cos_dy_cr2; |
273 |
> |
double d_cos_dz_cr2; |
274 |
> |
|
275 |
> |
d_cos_dx_cr1 = r_cr2.x / r_cr1_r_cr2 - (cos_phi * r_cr1.x) / r_cr1_sqr; |
276 |
> |
d_cos_dy_cr1 = r_cr2.y / r_cr1_r_cr2 - (cos_phi * r_cr1.y) / r_cr1_sqr; |
277 |
> |
d_cos_dz_cr1 = r_cr2.z / r_cr1_r_cr2 - (cos_phi * r_cr1.z) / r_cr1_sqr; |
278 |
> |
|
279 |
> |
d_cos_dx_cr2 = r_cr1.x / r_cr1_r_cr2 - (cos_phi * r_cr2.x) / r_cr2_sqr; |
280 |
> |
d_cos_dy_cr2 = r_cr1.y / r_cr1_r_cr2 - (cos_phi * r_cr2.y) / r_cr2_sqr; |
281 |
> |
d_cos_dz_cr2 = r_cr1.z / r_cr1_r_cr2 - (cos_phi * r_cr2.z) / r_cr2_sqr; |
282 |
> |
|
283 |
> |
//Vector3d dcosdA = B /(rA * rB) - cos_phi /(rA * rA) * A; |
284 |
> |
//Vector3d dcosdA = 1.0 /rA * (B.normalize() - cos_phi * A.normalize()); |
285 |
> |
//Vector3d dcosdB = 1.0 /rB * (A.normalize() - cos_phi * B.normalize()); |
286 |
> |
|
287 |
> |
/*********************************************************************** |
288 |
> |
* |
289 |
> |
* Calculate the actual forces and place them in the atoms. |
290 |
> |
* |
291 |
> |
***********************************************************************/ |
292 |
> |
|
293 |
> |
double force; /*the force scaling factor */ |
294 |
> |
|
295 |
> |
force = torsion_force(cos_phi); |
296 |
> |
|
297 |
> |
aF[0] = force * (d_cos_dy_cr1 * r_cb.z - d_cos_dz_cr1 * r_cb.y); |
298 |
> |
aF[1] = force * (d_cos_dz_cr1 * r_cb.x - d_cos_dx_cr1 * r_cb.z); |
299 |
> |
aF[2] = force * (d_cos_dx_cr1 * r_cb.y - d_cos_dy_cr1 * r_cb.x); |
300 |
> |
|
301 |
> |
bF[0] = force * ( d_cos_dy_cr1 * (r_ab.z - r_cb.z) |
302 |
> |
- d_cos_dy_cr2 * r_cd.z |
303 |
> |
+ d_cos_dz_cr1 * (r_cb.y - r_ab.y) |
304 |
> |
+ d_cos_dz_cr2 * r_cd.y); |
305 |
> |
bF[1] = force * ( d_cos_dx_cr1 * (r_cb.z - r_ab.z) |
306 |
> |
+ d_cos_dx_cr2 * r_cd.z |
307 |
> |
+ d_cos_dz_cr1 * (r_ab.x - r_cb.x) |
308 |
> |
- d_cos_dz_cr2 * r_cd.x); |
309 |
> |
bF[2] = force * ( d_cos_dx_cr1 * (r_ab.y - r_cb.y) |
310 |
> |
- d_cos_dx_cr2 * r_cd.y |
311 |
> |
+ d_cos_dy_cr1 * (r_cb.x - r_ab.x) |
312 |
> |
+ d_cos_dy_cr2 * r_cd.x); |
313 |
> |
|
314 |
> |
cF[0] = force * (- d_cos_dy_cr1 * r_ab.z |
315 |
> |
- d_cos_dy_cr2 * (r_cb.z - r_cd.z) |
316 |
> |
+ d_cos_dz_cr1 * r_ab.y |
317 |
> |
- d_cos_dz_cr2 * (r_cd.y - r_cb.y)); |
318 |
> |
cF[1] = force * ( d_cos_dx_cr1 * r_ab.z |
319 |
> |
- d_cos_dx_cr2 * (r_cd.z - r_cb.z) |
320 |
> |
- d_cos_dz_cr1 * r_ab.x |
321 |
> |
- d_cos_dz_cr2 * (r_cb.x - r_cd.x)); |
322 |
> |
cF[2] = force * (- d_cos_dx_cr1 * r_ab.y |
323 |
> |
- d_cos_dx_cr2 * (r_cb.y - r_cd.y) |
324 |
> |
+ d_cos_dy_cr1 * r_ab.x |
325 |
> |
- d_cos_dy_cr2 * (r_cd.x - r_cb.x)); |
326 |
> |
|
327 |
> |
dF[0] = force * (d_cos_dy_cr2 * r_cb.z - d_cos_dz_cr2 * r_cb.y); |
328 |
> |
dF[1] = force * (d_cos_dz_cr2 * r_cb.x - d_cos_dx_cr2 * r_cb.z); |
329 |
> |
dF[2] = force * (d_cos_dx_cr2 * r_cb.y - d_cos_dy_cr2 * r_cb.x); |
330 |
> |
|
331 |
> |
|
332 |
> |
c_p_a->addFrc(aF); |
333 |
> |
c_p_b->addFrc(bF); |
334 |
> |
c_p_c->addFrc(cF); |
335 |
> |
c_p_d->addFrc(dF); |
336 |
> |
|
337 |
> |
//double firstDerivative; |
338 |
> |
//bondType_->calcForce(cos_phi, firstDerivative, potential_); |
339 |
> |
//f1 = force * cross (dcosdA, r32); |
340 |
> |
//f2 = |
341 |
> |
//f3 = |
342 |
> |
//f4 = force * cross(dcosdB, r32); |
343 |
> |
//atom1_->addFrc(f1); |
344 |
> |
//atom2_->addFrc(f2); |
345 |
> |
//atom3_->addFrc(f3); |
346 |
> |
//atom4_->addFrc(f4); |
347 |
> |
|
348 |
> |
|
349 |
> |
} |
350 |
> |
|
351 |
> |
} |