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tim |
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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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void Bend::set_atoms( Atom &a, Atom &b, Atom &c){
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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_potential_E = 0.0;
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}
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void Bend::calc_forces(){
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double dx,dy,dz,gx,gy,gz,dx2,dy2,dz2,gx2,gy2,gz2;
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double rij2, rkj2, riji2, rkji2, dot, denom, cosang, angl;
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double sina2, sinai;
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double comf2, comf3, comf4;
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double dcsidx, dcsidy, dcsidz, dcskdx, dcskdy, dcskdz;
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// double dcsjdx, dcsjdy, dcsjdz;
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double dadxi, dadyi, dadzi;
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double dadxk, dadyk, dadzk;//, dadxj, dadyj, dadzj;
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double daxi, dayi, dazi, daxk, dayk, dazk, daxj, dayj, dazj;
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double aR[3], bR[3], cR[3];
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double aF[3], bF[3], cF[3];
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aR = c_p_a->getPos();
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bR = c_p_b->getPos();
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cR = c_p_c->getPos();
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dx = aR[0] - bR[0];
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dy = aR[1] - bR[1];
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dz = aR[2] - bR[2];
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gx = cR[0] - bR[0];
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gy = cR[1] - bR[1];
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gz = cR[2] - bR[2];
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dx2 = dx * dx;
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dy2 = dy * dy;
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dz2 = dz * dz;
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gx2 = gx * gx;
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gy2 = gy * gy;
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gz2 = gz * gz;
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rij2 = dx2 + dy2 + dz2;
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rkj2 = gx2 + gy2 + gz2;
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riji2 = 1.0 / rij2;
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rkji2 = 1.0 / rkj2;
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dot = dx * gx + dy * gy + dz * gz;
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denom = sqrt((riji2 * rkji2));
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cosang = dot * denom;
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if(cosang > 1.0)cosang = 1.0;
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if(cosang < -1.0) cosang = -1.0;
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angl = acos(cosang);
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angl = angl * 180.0 / M_PI;
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sina2 = 1.0 - cosang*cosang;
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if(fabs(sina2) < 1.0E-12 ) sina2 = 1.0E-12;
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sinai = 1.0 / sqrt(sina2);
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comf2 = cosang * riji2;
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comf3 = cosang * rkji2;
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comf4 = bend_force(angl);
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dcsidx = gx*denom - comf2*dx;
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dcsidy = gy*denom - comf2*dy;
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dcsidz = gz*denom - comf2*dz;
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dcskdx = dx*denom - comf3*gx;
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dcskdy = dy*denom - comf3*gy;
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dcskdz = dz*denom - comf3*gz;
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// dcsjdx = -dcsidx - dcskdx;
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// dcsjdy = -dcsidy - dcskdy;
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// dcsjdz = -dcsidz - dcskdz;
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dadxi = -sinai*dcsidx;
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dadyi = -sinai*dcsidy;
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dadzi = -sinai*dcsidz;
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dadxk = -sinai*dcskdx;
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dadyk = -sinai*dcskdy;
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dadzk = -sinai*dcskdz;
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// dadxj = -dadxi - dadxk;
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// dadyj = -dadyi - dadyk;
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// dadzj = -dadzi - dadzk;
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daxi = comf4*dadxi;
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dayi = comf4*dadyi;
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dazi = comf4*dadzi;
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daxk = comf4*dadxk;
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dayk = comf4*dadyk;
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dazk = comf4*dadzk;
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daxj = -daxi - daxk;
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dayj = -dayi - dayk;
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dazj = -dazi - dazk;
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aF[0] = daxi;
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aF[1] = dayi;
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aF[2] = dazi;
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bF[0] = daxj;
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bF[1] = dayj;
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bF[2] = dazj;
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cF[0] = daxk;
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cF[1] = dayk;
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cF[2] = dazk;
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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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return;
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}
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