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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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void DirectionalAtom::setA( double the_A[3][3] ){ |
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Axx = the_A[0][0]; Axy = the_A[0][1]; Axz = the_A[0][2]; |
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Ayx = the_A[1][0]; Ayy = the_A[1][1]; Ayz = the_A[1][2]; |
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Azx = the_A[2][0]; Azy = the_A[2][1]; Azz = the_A[2][2]; |
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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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Axx = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
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Axy = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
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Axz = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
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Ayx = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
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Ayy = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
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Ayz = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
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Azx = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
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Azy = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
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Azz = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
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} |
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void DirectionalAtom::getA( double the_A[3][3] ){ |
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the_A[0][0] = Axx; |
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the_A[0][1] = Axy; |
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the_A[0][2] = Axz; |
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the_A[1][0] = Ayx; |
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the_A[1][1] = Ayy; |
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the_A[1][2] = Ayz; |
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the_A[2][0] = Azx; |
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the_A[2][1] = Azy; |
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the_A[2][2] = 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 = Axx + Ayy + 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] = (Ayz - Azy) * s; |
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q[2] = (Azx - Axz) * s; |
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q[3] = (Axy - Ayx) * s; |
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} |
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else{ |
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ad1 = fabs( Axx ); |
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ad2 = fabs( Ayy ); |
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ad3 = fabs( Azz ); |
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if( ad1 >= ad2 && ad1 >= ad3 ){ |
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s = 2.0 * sqrt( 1.0 + Axx - Ayy - Azz ); |
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q[0] = (Ayz + Azy) / s; |
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q[1] = 0.5 / s; |
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q[2] = (Axy + Ayx) / s; |
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q[3] = (Axz + Azx) / s; |
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} |
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else if( ad2 >= ad1 && ad2 >= ad3 ){ |
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s = sqrt( 1.0 + Ayy - Axx - Azz ) * 2.0; |
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q[0] = (Axz + Azx) / s; |
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q[1] = (Axy + Ayx) / s; |
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q[2] = 0.5 / s; |
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q[3] = (Ayz + Azy) / s; |
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} |
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else{ |
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s = sqrt( 1.0 + Azz - Axx - Ayy ) * 2.0; |
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q[0] = (Axy + Ayx) / s; |
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q[1] = (Axz + Azx) / s; |
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q[2] = (Ayz + 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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Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
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Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
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Axz = sin(theta) * sin(psi); |
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Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
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Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
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Ayz = sin(theta) * cos(psi); |
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Azx = sin(phi) * sin(theta); |
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Azy = -cos(phi) * sin(theta); |
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Azz = cos(theta); |
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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] = (Axx * rl[0]) + (Axy * rl[1]) + (Axz * rl[2]); |
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r[1] = (Ayx * rl[0]) + (Ayy * rl[1]) + (Ayz * rl[2]); |
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r[2] = (Azx * rl[0]) + (Azy * rl[1]) + (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] = (Axx * rb[0]) + (Ayx * rb[1]) + (Azx * rb[2]); |
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r[1] = (Axy * rb[0]) + (Ayy * rb[1]) + (Azy * rb[2]); |
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r[2] = (Axz * rb[0]) + (Ayz * rb[1]) + (Azz * rb[2]); |
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} |
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