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mmeineke |
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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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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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dx = c_p_a->getX() - c_p_b->getX(); |
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dy = c_p_a->getY() - c_p_b->getY(); |
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dz = c_p_a->getZ() - c_p_b->getZ(); |
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gx = c_p_c->getX() - c_p_b->getX(); |
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gy = c_p_c->getY() - c_p_b->getY(); |
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gz = c_p_c->getZ() - c_p_b->getZ(); |
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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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c_p_a->addFx(daxi); |
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c_p_a->addFy(dayi); |
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c_p_a->addFz(dazi); |
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c_p_b->addFx(daxj); |
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c_p_b->addFy(dayj); |
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c_p_b->addFz(dazj); |
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c_p_c->addFx(daxk); |
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c_p_c->addFy(dayk); |
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c_p_c->addFz(dazk); |
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return; |
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} |
