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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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|
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|
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Bond::Bond(){ |
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|
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c_constraint = NULL; |
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c_is_constrained = 0; |
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} |
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|
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void Bond::set_atoms( Atom &a, Atom &b ){ |
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|
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c_p_a = &a; |
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c_p_b = &b; |
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} |
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|
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void Bond::constrain(double bond_distance){ |
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|
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double dsqr = bond_distance * bond_distance; |
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|
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c_is_constrained = 1; |
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|
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c_constraint = new Constraint(); |
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c_constraint->set_a( c_p_a->getIndex() ); |
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c_constraint->set_b( c_p_b->getIndex() ); |
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c_constraint->set_dsqr( dsqr ); |
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} |
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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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|
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void Bond::calc_forces(){ |
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|
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/* return 0 if the bond is constrained and stop wasting cpu */ |
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|
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if(c_is_constrained){ |
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|
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c_potential_E = 0.0; |
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return; |
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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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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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|
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/* initialize the vector */ |
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|
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r_ab.x = c_p_b->getX() - c_p_a->getX(); |
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r_ab.y = c_p_b->getY() - c_p_a->getY(); |
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r_ab.z = c_p_b->getZ() - c_p_a->getZ(); |
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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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/* calculate the force here */ |
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|
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force = bond_force(r_ab.length); |
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|
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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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|
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c_p_a->addFx(Fab_x); |
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c_p_a->addFy(Fab_y); |
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c_p_a->addFz(Fab_z); |
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|
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c_p_b->addFx(-Fab_x); |
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c_p_b->addFy(-Fab_y); |
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c_p_b->addFz(-Fab_z); |
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|
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return; |
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} |
