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#include <cmath> |
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#include <math.h> |
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#include "Atom.hpp" |
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#include "simError.h" |
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void DirectionalAtom::zeroForces() { |
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if( hasCoords ){ |
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frc[offsetX] = 0.0; |
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else{ |
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sprintf( painCave.errMsg, |
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"Attempted to set Atom %d coordinates with an unallocated " |
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"SimState object.\n" ); |
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"SimState object.\n", index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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hasCoords = true; |
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mu[index] = myMu; |
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*mu = myMu; |
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} |
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double DirectionalAtom::getMu( void ) { |
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if( hasCoords ){ |
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return mu[index]; |
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return *mu; |
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} |
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else{ |
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return myMu; |
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} |
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return 0; |
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} |
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void DirectionalAtom::setMu( double the_mu ) { |
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if( hasCoords ){ |
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mu[index] = the_mu; |
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*mu = the_mu; |
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myMu = the_mu; |
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} |
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else{ |
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the_I[2][0] = Izx; |
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the_I[2][1] = Izy; |
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the_I[2][2] = Izz; |
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} |
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void DirectionalAtom::getGrad( double grad[6] ) { |
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double myEuler[3]; |
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double phi, theta, psi; |
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double cphi, sphi, ctheta, stheta; |
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double ephi[3]; |
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double etheta[3]; |
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double epsi[3]; |
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this->getEulerAngles(myEuler); |
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phi = myEuler[0]; |
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theta = myEuler[1]; |
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psi = myEuler[2]; |
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cphi = cos(phi); |
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sphi = sin(phi); |
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ctheta = cos(theta); |
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stheta = sin(theta); |
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// get unit vectors along the phi, theta and psi rotation axes |
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ephi[0] = 0.0; |
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ephi[1] = 0.0; |
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ephi[2] = 1.0; |
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etheta[0] = cphi; |
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etheta[1] = sphi; |
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etheta[2] = 0.0; |
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epsi[0] = stheta * cphi; |
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epsi[1] = stheta * sphi; |
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epsi[2] = ctheta; |
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for (int j = 0 ; j<3; j++) |
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grad[j] = frc[j]; |
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grad[3] = 0; |
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grad[4] = 0; |
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grad[5] = 0; |
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for (int j = 0; j < 3; j++ ) { |
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grad[3] += trq[j]*ephi[j]; |
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grad[4] += trq[j]*etheta[j]; |
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grad[5] += trq[j]*epsi[j]; |
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} |
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} |
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/** |
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* getEulerAngles computes a set of Euler angle values consistent |
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* with an input rotation matrix. They are returned in the following |
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* order: |
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* myEuler[0] = phi; |
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* myEuler[1] = theta; |
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* myEuler[2] = psi; |
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*/ |
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void DirectionalAtom::getEulerAngles(double myEuler[3]) { |
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// We use so-called "x-convention", which is the most common definition. |
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// In this convention, the rotation given by Euler angles (phi, theta, psi), where the first |
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// rotation is by an angle phi about the z-axis, the second is by an angle |
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// theta (0 <= theta <= 180)about the x-axis, and thethird is by an angle psi about the |
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//z-axis (again). |
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double phi,theta,psi,eps; |
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double pi; |
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double cphi,ctheta,cpsi; |
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double sphi,stheta,spsi; |
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double b[3]; |
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int flip[3]; |
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// set the tolerance for Euler angles and rotation elements |
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eps = 1.0e-8; |
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theta = acos(min(1.0,max(-1.0,Amat[Azz]))); |
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ctheta = Amat[Azz]; |
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stheta = sqrt(1.0 - ctheta * ctheta); |
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// when sin(theta) is close to 0, we need to consider singularity |
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// In this case, we can assign an arbitary value to phi (or psi), and then determine |
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// the psi (or phi) or vice-versa. We'll assume that phi always gets the rotation, and psi is 0 |
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// in cases of singularity. |
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// we use atan2 instead of atan, since atan2 will give us -Pi to Pi. |
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// Since 0 <= theta <= 180, sin(theta) will be always non-negative. Therefore, it never |
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// change the sign of both of the parameters passed to atan2. |
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if (fabs(stheta) <= eps){ |
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psi = 0.0; |
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phi = atan2(-Amat[Ayx], Amat[Axx]); |
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} |
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// we only have one unique solution |
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else{ |
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phi = atan2(Amat[Azx], -Amat[Azy]); |
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psi = atan2(Amat[Axz], Amat[Ayz]); |
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} |
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//wrap phi and psi, make sure they are in the range from 0 to 2*Pi |
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//if (phi < 0) |
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// phi += M_PI; |
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//if (psi < 0) |
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// psi += M_PI; |
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myEuler[0] = phi; |
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myEuler[1] = theta; |
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myEuler[2] = psi; |
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return; |
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} |
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double DirectionalAtom::max(double x, double y) { |
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return (x > y) ? x : y; |
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} |
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double DirectionalAtom::min(double x, double y) { |
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return (x > y) ? y : x; |
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} |
