| 1 |
|
| 2 |
#include <math.h>
|
| 3 |
#include <iostream>
|
| 4 |
#include <stdlib.h>
|
| 5 |
|
| 6 |
#include "utils/simError.h"
|
| 7 |
#include "primitives/SRI.hpp"
|
| 8 |
#include "primitives/Atom.hpp"
|
| 9 |
|
| 10 |
|
| 11 |
|
| 12 |
GhostBend::GhostBend( Atom &a, Atom &b ){
|
| 13 |
|
| 14 |
c_p_a = &a;
|
| 15 |
|
| 16 |
if( !b.isDirectional() ){
|
| 17 |
|
| 18 |
// if atom b is not directional, then bad things will happen
|
| 19 |
|
| 20 |
sprintf( painCave.errMsg,
|
| 21 |
" Ghost Bend error: Atom # %d of type \"%s\" is not "
|
| 22 |
"directional.\n",
|
| 23 |
b.getIndex(),
|
| 24 |
b.getType() );
|
| 25 |
painCave.isFatal = 1;
|
| 26 |
simError();
|
| 27 |
}
|
| 28 |
|
| 29 |
atomB = ( DirectionalAtom* ) &b;
|
| 30 |
|
| 31 |
c_potential_E = 0.0;
|
| 32 |
|
| 33 |
}
|
| 34 |
|
| 35 |
|
| 36 |
void GhostBend::calc_forces(){
|
| 37 |
|
| 38 |
double dx,dy,dz,gx,gy,gz,dx2,dy2,dz2,gx2,gy2,gz2;
|
| 39 |
double rij2, rkj2, riji2, rkji2, dot, denom, cosang, angl;
|
| 40 |
|
| 41 |
double sina2, sinai;
|
| 42 |
|
| 43 |
double comf2, comf3, comf4;
|
| 44 |
double dcsidx, dcsidy, dcsidz, dcskdx, dcskdy, dcskdz;
|
| 45 |
// double dcsjdx, dcsjdy, dcsjdz;
|
| 46 |
double dadxi, dadyi, dadzi;
|
| 47 |
double dadxk, dadyk, dadzk;//, dadxj, dadyj, dadzj;
|
| 48 |
double daxi, dayi, dazi, daxk, dayk, dazk, daxj, dayj, dazj;
|
| 49 |
Vector3d u;
|
| 50 |
|
| 51 |
double aR[3], bR[3];
|
| 52 |
double aF[3], bF[3], bTrq[3];
|
| 53 |
|
| 54 |
aR = c_p_a->getPos();
|
| 55 |
bR = atomB->getPos();
|
| 56 |
|
| 57 |
|
| 58 |
dx = aR[0] - bR[0];
|
| 59 |
dy = aR[1] - bR[1];
|
| 60 |
dz = aR[2] - bR[2];
|
| 61 |
|
| 62 |
u = atomB->getU();
|
| 63 |
|
| 64 |
gx = u[0];
|
| 65 |
gy = u[1];
|
| 66 |
gz = u[2];
|
| 67 |
|
| 68 |
dx2 = dx * dx;
|
| 69 |
dy2 = dy * dy;
|
| 70 |
dz2 = dz * dz;
|
| 71 |
|
| 72 |
gx2 = gx * gx;
|
| 73 |
gy2 = gy * gy;
|
| 74 |
gz2 = gz * gz;
|
| 75 |
|
| 76 |
rij2 = dx2 + dy2 + dz2;
|
| 77 |
rkj2 = gx2 + gy2 + gz2;
|
| 78 |
|
| 79 |
riji2 = 1.0 / rij2;
|
| 80 |
rkji2 = 1.0 / rkj2;
|
| 81 |
|
| 82 |
dot = dx * gx + dy * gy + dz * gz;
|
| 83 |
denom = sqrt((riji2 * rkji2));
|
| 84 |
cosang = dot * denom;
|
| 85 |
|
| 86 |
if(cosang > 1.0)cosang = 1.0;
|
| 87 |
if(cosang < -1.0) cosang = -1.0;
|
| 88 |
|
| 89 |
angl = acos(cosang);
|
| 90 |
angl = angl * 180.0 / M_PI;
|
| 91 |
|
| 92 |
sina2 = 1.0 - cosang*cosang;
|
| 93 |
if(fabs(sina2) < 1.0E-12 ) sina2 = 1.0E-12;
|
| 94 |
sinai = 1.0 / sqrt(sina2);
|
| 95 |
|
| 96 |
comf2 = cosang * riji2;
|
| 97 |
comf3 = cosang * rkji2;
|
| 98 |
comf4 = bend_force(angl);
|
| 99 |
|
| 100 |
dcsidx = gx*denom - comf2*dx;
|
| 101 |
dcsidy = gy*denom - comf2*dy;
|
| 102 |
dcsidz = gz*denom - comf2*dz;
|
| 103 |
|
| 104 |
dcskdx = dx*denom - comf3*gx;
|
| 105 |
dcskdy = dy*denom - comf3*gy;
|
| 106 |
dcskdz = dz*denom - comf3*gz;
|
| 107 |
|
| 108 |
// dcsjdx = -dcsidx - dcskdx;
|
| 109 |
// dcsjdy = -dcsidy - dcskdy;
|
| 110 |
// dcsjdz = -dcsidz - dcskdz;
|
| 111 |
|
| 112 |
dadxi = -sinai*dcsidx;
|
| 113 |
dadyi = -sinai*dcsidy;
|
| 114 |
dadzi = -sinai*dcsidz;
|
| 115 |
|
| 116 |
dadxk = -sinai*dcskdx;
|
| 117 |
dadyk = -sinai*dcskdy;
|
| 118 |
dadzk = -sinai*dcskdz;
|
| 119 |
|
| 120 |
// dadxj = -dadxi - dadxk;
|
| 121 |
// dadyj = -dadyi - dadyk;
|
| 122 |
// dadzj = -dadzi - dadzk;
|
| 123 |
|
| 124 |
daxi = comf4*dadxi;
|
| 125 |
dayi = comf4*dadyi;
|
| 126 |
dazi = comf4*dadzi;
|
| 127 |
|
| 128 |
daxk = comf4*dadxk;
|
| 129 |
dayk = comf4*dadyk;
|
| 130 |
dazk = comf4*dadzk;
|
| 131 |
|
| 132 |
daxj = -daxi - daxk;
|
| 133 |
dayj = -dayi - dayk;
|
| 134 |
dazj = -dazi - dazk;
|
| 135 |
|
| 136 |
aF[0] = daxi;
|
| 137 |
aF[1] = dayi;
|
| 138 |
aF[2] = dazi;
|
| 139 |
|
| 140 |
bF[0] = daxj + daxk;
|
| 141 |
bF[1] = dayj + dayk;
|
| 142 |
bF[2] = dazj + dazk;
|
| 143 |
|
| 144 |
bTrq[0] = gy*dazk - gz*dayk;
|
| 145 |
bTrq[1] = gz*daxk - gx*dazk;
|
| 146 |
bTrq[2] = gx*dayk - gy*daxk;
|
| 147 |
|
| 148 |
|
| 149 |
c_p_a->addFrc( aF );
|
| 150 |
atomB->addFrc( bF );
|
| 151 |
atomB->addTrq( bTrq );
|
| 152 |
|
| 153 |
return;
|
| 154 |
}
|
| 155 |
|
| 156 |
void GhostBend::setConstants( double the_c1, double the_c2, double the_c3,
|
| 157 |
double the_Th0 ){
|
| 158 |
c1 = the_c1;
|
| 159 |
c2 = the_c2;
|
| 160 |
c3 = the_c3;
|
| 161 |
theta0 = the_Th0;
|
| 162 |
}
|
| 163 |
|
| 164 |
|
| 165 |
double GhostBend::bend_force( double theta ){
|
| 166 |
|
| 167 |
double dt, dt2;
|
| 168 |
double force;
|
| 169 |
|
| 170 |
dt = ( theta - theta0 ) * M_PI / 180.0;
|
| 171 |
dt2 = dt * dt;
|
| 172 |
|
| 173 |
c_potential_E = ( c1 * dt2 ) + ( c2 * dt ) + c3;
|
| 174 |
force = -( ( 2.0 * c1 * dt ) + c2 );
|
| 175 |
return force;
|
| 176 |
}
|
