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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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Bond::Bond(){
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c_constraint = NULL;
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c_is_constrained = 0;
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}
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void Bond::set_atoms( Atom &a, Atom &b ){
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c_p_a = &a;
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c_p_b = &b;
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}
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void Bond::constrain(double bond_distance){
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double dsqr = bond_distance * bond_distance;
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c_is_constrained = 1;
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c_constraint = new Constraint();
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c_constraint->set_a( c_p_a->getLocalIndex() );
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c_constraint->set_b( c_p_b->getLocalIndex() );
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c_constraint->set_dsqr( dsqr );
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}
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Bond::~Bond(){
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delete c_constraint;
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c_constraint = 0;
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}
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void Bond::calc_forces(){
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/* return 0 if the bond is constrained and stop wasting cpu */
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if(c_is_constrained){
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c_potential_E = 0.0;
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return;
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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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double force; /* the force scaling factor. */
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double Fab_x; /*the x,y, and z components of the force */
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double Fab_y;
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double Fab_z;
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Vector3d aR, bR;
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Vector3d aF, bF;
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/* initialize the vector */
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aR = c_p_a->getPos();
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bR = c_p_b->getPos();
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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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/* calculate the force here */
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force = bond_force(r_ab.length);
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Fab_x = -force * r_ab.x / r_ab.length;
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Fab_y = -force * r_ab.y / r_ab.length;
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Fab_z = -force * r_ab.z / r_ab.length;
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aF[0] = Fab_x;
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aF[1] = Fab_y;
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aF[2] = Fab_z;
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bF[0] = -Fab_x;
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bF[1] = -Fab_y;
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bF[2] = -Fab_z;
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c_p_a->addFrc(aF);
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c_p_b->addFrc(bF);
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return;
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}
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