| 1 |
< |
#include "primitives/SRI.hpp" |
| 2 |
< |
#include "primitives/Atom.hpp" |
| 3 |
< |
#include <math.h> |
| 4 |
< |
#include <iostream> |
| 5 |
< |
#include <stdlib.h> |
| 6 |
< |
|
| 7 |
< |
|
| 8 |
< |
|
| 9 |
< |
Bond::Bond(){ |
| 10 |
< |
|
| 11 |
< |
c_constraint = NULL; |
| 12 |
< |
c_is_constrained = 0; |
| 13 |
< |
} |
| 14 |
< |
|
| 15 |
< |
void Bond::set_atoms( Atom &a, Atom &b ){ |
| 16 |
< |
|
| 17 |
< |
c_p_a = &a; |
| 18 |
< |
c_p_b = &b; |
| 19 |
< |
} |
| 20 |
< |
|
| 21 |
< |
void Bond::constrain(double bond_distance){ |
| 22 |
< |
|
| 23 |
< |
double dsqr = bond_distance * bond_distance; |
| 24 |
< |
|
| 25 |
< |
c_is_constrained = 1; |
| 26 |
< |
|
| 27 |
< |
c_constraint = new Constraint(); |
| 28 |
< |
c_constraint->set_a( c_p_a->getIndex() ); |
| 29 |
< |
c_constraint->set_b( c_p_b->getIndex() ); |
| 30 |
< |
c_constraint->set_dsqr( dsqr ); |
| 31 |
< |
} |
| 32 |
< |
|
| 33 |
< |
Bond::~Bond(){ |
| 34 |
< |
delete c_constraint; |
| 35 |
< |
c_constraint = 0; |
| 36 |
< |
} |
| 37 |
< |
|
| 38 |
< |
void Bond::calc_forces(){ |
| 39 |
< |
|
| 40 |
< |
/* return 0 if the bond is constrained and stop wasting cpu */ |
| 41 |
< |
|
| 42 |
< |
if(c_is_constrained){ |
| 43 |
< |
|
| 44 |
< |
c_potential_E = 0.0; |
| 45 |
< |
return; |
| 46 |
< |
} |
| 47 |
< |
|
| 48 |
< |
vect r_ab; /*the vector whose origin is a and end is b */ |
| 49 |
< |
double force; /* the force scaling factor. */ |
| 50 |
< |
double Fab_x; /*the x,y, and z components of the force */ |
| 51 |
< |
double Fab_y; |
| 52 |
< |
double Fab_z; |
| 53 |
< |
|
| 54 |
< |
double aR[3], bR[3]; |
| 55 |
< |
double aF[3], bF[3]; |
| 56 |
< |
|
| 57 |
< |
/* initialize the vector */ |
| 58 |
< |
|
| 59 |
< |
c_p_a->getPos(aR); |
| 60 |
< |
c_p_b->getPos(bR); |
| 61 |
< |
|
| 62 |
< |
r_ab.x = bR[0] - aR[0]; |
| 63 |
< |
r_ab.y = bR[1] - aR[1]; |
| 64 |
< |
r_ab.z = bR[2] - aR[2]; |
| 65 |
< |
|
| 66 |
< |
r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z)); |
| 67 |
< |
|
| 68 |
< |
/* calculate the force here */ |
| 69 |
< |
|
| 70 |
< |
force = bond_force(r_ab.length); |
| 71 |
< |
|
| 72 |
< |
Fab_x = -force * r_ab.x / r_ab.length; |
| 73 |
< |
Fab_y = -force * r_ab.y / r_ab.length; |
| 74 |
< |
Fab_z = -force * r_ab.z / r_ab.length; |
| 75 |
< |
|
| 76 |
< |
aF[0] = Fab_x; |
| 77 |
< |
aF[1] = Fab_y; |
| 78 |
< |
aF[2] = Fab_z; |
| 79 |
< |
|
| 80 |
< |
bF[0] = -Fab_x; |
| 81 |
< |
bF[1] = -Fab_y; |
| 82 |
< |
bF[2] = -Fab_z; |
| 83 |
< |
|
| 84 |
< |
c_p_a->addFrc(aF); |
| 85 |
< |
c_p_b->addFrc(bF); |
| 86 |
< |
|
| 87 |
< |
return; |
| 88 |
< |
} |
| 1 |
> |
#include "primitives/SRI.hpp" |
| 2 |
> |
#include "primitives/Atom.hpp" |
| 3 |
> |
#include <math.h> |
| 4 |
> |
#include <iostream> |
| 5 |
> |
#include <stdlib.h> |
| 6 |
> |
|
| 7 |
> |
|
| 8 |
> |
|
| 9 |
> |
Bond::Bond(){ |
| 10 |
> |
|
| 11 |
> |
c_constraint = NULL; |
| 12 |
> |
c_is_constrained = 0; |
| 13 |
> |
} |
| 14 |
> |
|
| 15 |
> |
void Bond::set_atoms( Atom &a, Atom &b ){ |
| 16 |
> |
|
| 17 |
> |
c_p_a = &a; |
| 18 |
> |
c_p_b = &b; |
| 19 |
> |
} |
| 20 |
> |
|
| 21 |
> |
void Bond::constrain(double bond_distance){ |
| 22 |
> |
|
| 23 |
> |
double dsqr = bond_distance * bond_distance; |
| 24 |
> |
|
| 25 |
> |
c_is_constrained = 1; |
| 26 |
> |
|
| 27 |
> |
c_constraint = new Constraint(); |
| 28 |
> |
c_constraint->set_a( c_p_a->getIndex() ); |
| 29 |
> |
c_constraint->set_b( c_p_b->getIndex() ); |
| 30 |
> |
c_constraint->set_dsqr( dsqr ); |
| 31 |
> |
} |
| 32 |
> |
|
| 33 |
> |
Bond::~Bond(){ |
| 34 |
> |
delete c_constraint; |
| 35 |
> |
c_constraint = 0; |
| 36 |
> |
} |
| 37 |
> |
|
| 38 |
> |
void Bond::calc_forces(){ |
| 39 |
> |
|
| 40 |
> |
/* return 0 if the bond is constrained and stop wasting cpu */ |
| 41 |
> |
|
| 42 |
> |
if(c_is_constrained){ |
| 43 |
> |
|
| 44 |
> |
c_potential_E = 0.0; |
| 45 |
> |
return; |
| 46 |
> |
} |
| 47 |
> |
|
| 48 |
> |
vect r_ab; /*the vector whose origin is a and end is b */ |
| 49 |
> |
double force; /* the force scaling factor. */ |
| 50 |
> |
double Fab_x; /*the x,y, and z components of the force */ |
| 51 |
> |
double Fab_y; |
| 52 |
> |
double Fab_z; |
| 53 |
> |
|
| 54 |
> |
double aR[3], bR[3]; |
| 55 |
> |
double aF[3], bF[3]; |
| 56 |
> |
|
| 57 |
> |
/* initialize the vector */ |
| 58 |
> |
|
| 59 |
> |
aR = c_p_a->getPos(); |
| 60 |
> |
bR = c_p_b->getPos(); |
| 61 |
> |
|
| 62 |
> |
r_ab.x = bR[0] - aR[0]; |
| 63 |
> |
r_ab.y = bR[1] - aR[1]; |
| 64 |
> |
r_ab.z = bR[2] - aR[2]; |
| 65 |
> |
|
| 66 |
> |
r_ab.length = sqrt((r_ab.x * r_ab.x + r_ab.y * r_ab.y + r_ab.z * r_ab.z)); |
| 67 |
> |
|
| 68 |
> |
/* calculate the force here */ |
| 69 |
> |
|
| 70 |
> |
force = bond_force(r_ab.length); |
| 71 |
> |
|
| 72 |
> |
Fab_x = -force * r_ab.x / r_ab.length; |
| 73 |
> |
Fab_y = -force * r_ab.y / r_ab.length; |
| 74 |
> |
Fab_z = -force * r_ab.z / r_ab.length; |
| 75 |
> |
|
| 76 |
> |
aF[0] = Fab_x; |
| 77 |
> |
aF[1] = Fab_y; |
| 78 |
> |
aF[2] = Fab_z; |
| 79 |
> |
|
| 80 |
> |
bF[0] = -Fab_x; |
| 81 |
> |
bF[1] = -Fab_y; |
| 82 |
> |
bF[2] = -Fab_z; |
| 83 |
> |
|
| 84 |
> |
c_p_a->addFrc(aF); |
| 85 |
> |
c_p_b->addFrc(bF); |
| 86 |
> |
|
| 87 |
> |
return; |
| 88 |
> |
} |
