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#include "primitives/SRI.hpp" |
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#include "primitives/Atom.hpp" |
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#include "primitives/Bend.hpp" |
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namespace oopse { |
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#include <math.h> |
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#include <iostream> |
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#include <stdlib.h> |
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/**@todo still a lot left to improve*/ |
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void Bend::calcForce() { |
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void Bend::set_atoms( Atom &a, Atom &b, Atom &c){ |
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Vector3d pos1 = atom1_->getPos(); |
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Vector3d pos2 = atom2_->getPos(); |
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Vector3d pos3 = atom3_->getPos(); |
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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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Vector3d r12 = pos1 - pos2; |
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double d12 = r12.length(); |
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double d12inv = 1. 0 / d12; |
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Vector3d r32 = pos3 - pos2; |
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double d32 = r32.length(); |
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double d32inv = 1. 0 / d32; |
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double cosTheta = (r12*r32)/(d12*d32); |
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c_potential_E = 0.0; |
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} |
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//check roundoff |
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if (cosTheta > 1.0) { |
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cosTheta = 1.0; |
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} else if (cosTheta < -1.0) { |
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cosTheta = -1.0; |
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} |
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double theta = acos(cosTheta); |
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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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Vector3d aR, bR, cR; |
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Vector3d aF, bF, cF; |
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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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double firstDerivative; |
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bendType_->calcForce(theta, firstDerivative, potential_); |
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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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double sinTheta = sqrt(1.0 - cosTheta*cosTheta); |
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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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if(fabs(sinTheta) < 1.0E-12 ) { |
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sinTheta = 1.0E-12; |
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} |
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double commonFactor1 = - firstDerivative / sinTheta * d12inv; |
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double commonFactor2 = - firstDerivative / sinTheta * d32inv; |
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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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Vector3d force1 = commonFactor1*(r12*(d12inv*cosTheta) - r32*d32inv); |
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Vector3d force3 = commonFactor2*(r32*(d32inv*cosTheta) - r12*d12inv); |
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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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//total force in current bend is zero |
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Vector3d force2 = force1 + force3; |
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force2 *= -1.0; |
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angl = acos(cosang); |
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angl = angl * 180.0 / M_PI; |
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atom1_->addFrc( force1); |
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atom2_->addFrc(force2); |
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atom3_->addFrc(force3); |
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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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} |
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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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double k = value->k * scale; |
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double theta0 = value->theta0; |
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double diff = theta - theta0; |
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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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double energy = k *diff*diff; |
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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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double firstDerivative = 2.0 * k * diff; |
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}//end namespace oopse |
