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#include <cmath> |
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#include "Atom.hpp" |
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double* Atom::pos; // the position array |
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double* Atom::vel; // the velocity array |
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double* Atom::frc; // the forc array |
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double* Atom::trq; // the torque vector ( space fixed ) |
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double* Atom::Amat; // the rotation matrix |
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double* Atom::mu; // the array of dipole moments |
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double* Atom::ul; // the lab frame unit directional vector |
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void DirectionalAtom::setA( double the_A[3][3] ){ |
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Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
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Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
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Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
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this->updateU(); |
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} |
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void DirectionalAtom::setI( double the_I[3][3] ){ |
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Ixx = the_I[0][0]; Ixy = the_I[0][1]; Ixz = the_I[0][2]; |
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Iyx = the_I[1][0]; Iyy = the_I[1][1]; Iyz = the_I[1][2]; |
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Izx = the_I[2][0]; Izy = the_I[2][1]; Izz = the_I[2][2]; |
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} |
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void DirectionalAtom::setQ( double the_q[4] ){ |
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double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
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q0Sqr = the_q[0] * the_q[0]; |
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q1Sqr = the_q[1] * the_q[1]; |
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q2Sqr = the_q[2] * the_q[2]; |
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q3Sqr = the_q[3] * the_q[3]; |
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Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
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Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
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Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
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Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
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Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
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Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
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Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
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Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
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Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
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this->updateU(); |
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} |
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void DirectionalAtom::getA( double the_A[3][3] ){ |
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the_A[0][0] = Amat[Axx]; |
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the_A[0][1] = Amat[Axy]; |
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the_A[0][2] = Amat[Axz]; |
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the_A[1][0] = Amat[Ayx]; |
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the_A[1][1] = Amat[Ayy]; |
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the_A[1][2] = Amat[Ayz]; |
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the_A[2][0] = Amat[Azx]; |
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the_A[2][1] = Amat[Azy]; |
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the_A[2][2] = Amat[Azz]; |
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} |
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void DirectionalAtom::getU( double the_u[3] ){ |
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the_u[0] = sux; |
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the_u[1] = suy; |
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the_u[2] = suz; |
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this->body2Lab( the_u ); |
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} |
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void DirectionalAtom::getQ( double q[4] ){ |
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double t, s; |
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double ad1, ad2, ad3; |
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t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0; |
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if( t > 0.0 ){ |
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s = 0.5 / sqrt( t ); |
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q[0] = 0.25 / s; |
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q[1] = (Amat[Ayz] - Amat[Azy]) * s; |
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q[2] = (Amat[Azx] - Amat[Axz]) * s; |
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q[3] = (Amat[Axy] - Amat[Ayx]) * s; |
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} |
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else{ |
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ad1 = fabs( Amat[Axx] ); |
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ad2 = fabs( Amat[Ayy] ); |
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ad3 = fabs( Amat[Azz] ); |
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if( ad1 >= ad2 && ad1 >= ad3 ){ |
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s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] ); |
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q[0] = (Amat[Ayz] + Amat[Azy]) / s; |
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q[1] = 0.5 / s; |
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q[2] = (Amat[Axy] + Amat[Ayx]) / s; |
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q[3] = (Amat[Axz] + Amat[Azx]) / s; |
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} |
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else if( ad2 >= ad1 && ad2 >= ad3 ){ |
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s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0; |
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q[0] = (Amat[Axz] + Amat[Azx]) / s; |
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q[1] = (Amat[Axy] + Amat[Ayx]) / s; |
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q[2] = 0.5 / s; |
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q[3] = (Amat[Ayz] + Amat[Azy]) / s; |
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} |
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else{ |
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s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
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q[0] = (Amat[Axy] + Amat[Ayx]) / s; |
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q[1] = (Amat[Axz] + Amat[Azx]) / s; |
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q[2] = (Amat[Ayz] + Amat[Azy]) / s; |
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q[3] = 0.5 / s; |
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} |
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} |
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} |
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void DirectionalAtom::setEuler( double phi, double theta, double psi ){ |
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Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
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Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
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Amat[Axz] = sin(theta) * sin(psi); |
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Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
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Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
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Amat[Ayz] = sin(theta) * cos(psi); |
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Amat[Azx] = sin(phi) * sin(theta); |
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Amat[Azy] = -cos(phi) * sin(theta); |
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Amat[Azz] = cos(theta); |
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this->updateU(); |
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} |
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void DirectionalAtom::lab2Body( double r[3] ){ |
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double rl[3]; // the lab frame vector |
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rl[0] = r[0]; |
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rl[1] = r[1]; |
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rl[2] = r[2]; |
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r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
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r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
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r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
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} |
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void DirectionalAtom::body2Lab( double r[3] ){ |
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double rb[3]; // the body frame vector |
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rb[0] = r[0]; |
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rb[1] = r[1]; |
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rb[2] = r[2]; |
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r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
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r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
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r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
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} |
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void DirectionalAtom::updateU( void ){ |
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ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz); |
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ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz); |
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ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz); |
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} |
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