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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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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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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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force = torsion_force(cos_phi); |
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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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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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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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} |
