| 1 |
#include <cmath> |
| 2 |
|
| 3 |
#include "Atom.hpp" |
| 4 |
#include "simError.h" |
| 5 |
|
| 6 |
void DirectionalAtom::zeroForces() { |
| 7 |
if( hasCoords ){ |
| 8 |
frc[offsetX] = 0.0; |
| 9 |
frc[offsetY] = 0.0; |
| 10 |
frc[offsetZ] = 0.0; |
| 11 |
|
| 12 |
trq[offsetX] = 0.0; |
| 13 |
trq[offsetY] = 0.0; |
| 14 |
trq[offsetZ] = 0.0; |
| 15 |
} |
| 16 |
else{ |
| 17 |
|
| 18 |
sprintf( painCave.errMsg, |
| 19 |
"Attempt to zero frc and trq for atom %d before coords set.\n", |
| 20 |
index ); |
| 21 |
painCave.isFatal = 1; |
| 22 |
simError(); |
| 23 |
} |
| 24 |
} |
| 25 |
|
| 26 |
double DirectionalAtom::getMu( void ) { |
| 27 |
|
| 28 |
if( hasCoords ){ |
| 29 |
return mu[index]; |
| 30 |
} |
| 31 |
else{ |
| 32 |
|
| 33 |
sprintf( painCave.errMsg, |
| 34 |
"Attempt to get Mu for atom %d before coords set.\n", |
| 35 |
index ); |
| 36 |
painCave.isFatal = 1; |
| 37 |
simError(); |
| 38 |
} |
| 39 |
return 0; |
| 40 |
} |
| 41 |
|
| 42 |
void DirectionalAtom::setMu( double the_mu ) { |
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|
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if( hasCoords ){ |
| 45 |
mu[index] = the_mu; |
| 46 |
} |
| 47 |
else{ |
| 48 |
|
| 49 |
sprintf( painCave.errMsg, |
| 50 |
"Attempt to set Mu for atom %d before coords set.\n", |
| 51 |
index ); |
| 52 |
painCave.isFatal = 1; |
| 53 |
simError(); |
| 54 |
} |
| 55 |
} |
| 56 |
|
| 57 |
void DirectionalAtom::setA( double the_A[3][3] ){ |
| 58 |
|
| 59 |
if( hasCoords ){ |
| 60 |
Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
| 61 |
Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
| 62 |
Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
| 63 |
|
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this->updateU(); |
| 65 |
} |
| 66 |
else{ |
| 67 |
|
| 68 |
sprintf( painCave.errMsg, |
| 69 |
"Attempt to set Amat for atom %d before coords set.\n", |
| 70 |
index ); |
| 71 |
painCave.isFatal = 1; |
| 72 |
simError(); |
| 73 |
} |
| 74 |
} |
| 75 |
|
| 76 |
void DirectionalAtom::setI( double the_I[3][3] ){ |
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|
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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]; |
| 81 |
} |
| 82 |
|
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void DirectionalAtom::setQ( double the_q[4] ){ |
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|
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double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
| 86 |
|
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if( hasCoords ){ |
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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]; |
| 91 |
q3Sqr = the_q[3] * the_q[3]; |
| 92 |
|
| 93 |
|
| 94 |
Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
| 95 |
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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|
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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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|
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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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|
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this->updateU(); |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
| 111 |
"Attempt to set Q for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
| 114 |
simError(); |
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} |
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|
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} |
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|
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void DirectionalAtom::getA( double the_A[3][3] ){ |
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|
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if( hasCoords ){ |
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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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|
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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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|
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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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else{ |
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|
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sprintf( painCave.errMsg, |
| 137 |
"Attempt to get Amat for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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} |
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|
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void DirectionalAtom::printAmatIndex( void ){ |
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|
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if( hasCoords ){ |
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std::cerr << "Atom[" << index << "] index =>\n" |
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<< "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n" |
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<< "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n" |
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<< "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n"; |
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} |
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else{ |
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|
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sprintf( painCave.errMsg, |
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"Attempt to print Amat indices for atom %d before coords set.\n", |
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index ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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|
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void DirectionalAtom::getU( double the_u[3] ){ |
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|
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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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|
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this->body2Lab( the_u ); |
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} |
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|
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void DirectionalAtom::getQ( double q[4] ){ |
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|
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double t, s; |
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double ad1, ad2, ad3; |
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|
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if( hasCoords ){ |
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|
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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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|
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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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|
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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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|
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if( ad1 >= ad2 && ad1 >= ad3 ){ |
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|
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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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|
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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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|
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s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
| 214 |
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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else{ |
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|
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sprintf( painCave.errMsg, |
| 224 |
"Attempt to get Q for atom %d before coords set.\n", |
| 225 |
index ); |
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painCave.isFatal = 1; |
| 227 |
simError(); |
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} |
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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 ){ |
| 233 |
|
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if( hasCoords ){ |
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Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 236 |
Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 237 |
Amat[Axz] = sin(theta) * sin(psi); |
| 238 |
|
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Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 240 |
Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 241 |
Amat[Ayz] = sin(theta) * cos(psi); |
| 242 |
|
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Amat[Azx] = sin(phi) * sin(theta); |
| 244 |
Amat[Azy] = -cos(phi) * sin(theta); |
| 245 |
Amat[Azz] = cos(theta); |
| 246 |
|
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this->updateU(); |
| 248 |
} |
| 249 |
else{ |
| 250 |
|
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sprintf( painCave.errMsg, |
| 252 |
"Attempt to set Euler angles for atom %d before coords set.\n", |
| 253 |
index ); |
| 254 |
painCave.isFatal = 1; |
| 255 |
simError(); |
| 256 |
} |
| 257 |
} |
| 258 |
|
| 259 |
|
| 260 |
void DirectionalAtom::lab2Body( double r[3] ){ |
| 261 |
|
| 262 |
double rl[3]; // the lab frame vector |
| 263 |
|
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if( hasCoords ){ |
| 265 |
rl[0] = r[0]; |
| 266 |
rl[1] = r[1]; |
| 267 |
rl[2] = r[2]; |
| 268 |
|
| 269 |
r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
| 270 |
r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
| 271 |
r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
| 272 |
} |
| 273 |
else{ |
| 274 |
|
| 275 |
sprintf( painCave.errMsg, |
| 276 |
"Attempt to convert lab2body for atom %d before coords set.\n", |
| 277 |
index ); |
| 278 |
painCave.isFatal = 1; |
| 279 |
simError(); |
| 280 |
} |
| 281 |
|
| 282 |
} |
| 283 |
|
| 284 |
void DirectionalAtom::body2Lab( double r[3] ){ |
| 285 |
|
| 286 |
double rb[3]; // the body frame vector |
| 287 |
|
| 288 |
if( hasCoords ){ |
| 289 |
rb[0] = r[0]; |
| 290 |
rb[1] = r[1]; |
| 291 |
rb[2] = r[2]; |
| 292 |
|
| 293 |
r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
| 294 |
r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
| 295 |
r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
| 296 |
} |
| 297 |
else{ |
| 298 |
|
| 299 |
sprintf( painCave.errMsg, |
| 300 |
"Attempt to convert body2lab for atom %d before coords set.\n", |
| 301 |
index ); |
| 302 |
painCave.isFatal = 1; |
| 303 |
simError(); |
| 304 |
} |
| 305 |
} |
| 306 |
|
| 307 |
void DirectionalAtom::updateU( void ){ |
| 308 |
|
| 309 |
if( hasCoords ){ |
| 310 |
ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz); |
| 311 |
ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz); |
| 312 |
ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz); |
| 313 |
} |
| 314 |
else{ |
| 315 |
|
| 316 |
sprintf( painCave.errMsg, |
| 317 |
"Attempt to updateU for atom %d before coords set.\n", |
| 318 |
index ); |
| 319 |
painCave.isFatal = 1; |
| 320 |
simError(); |
| 321 |
} |
| 322 |
} |
| 323 |
|
| 324 |
void DirectionalAtom::getJ( double theJ[3] ){ |
| 325 |
|
| 326 |
theJ[0] = jx; |
| 327 |
theJ[1] = jy; |
| 328 |
theJ[2] = jz; |
| 329 |
} |
| 330 |
|
| 331 |
void DirectionalAtom::setJ( double theJ[3] ){ |
| 332 |
|
| 333 |
jx = theJ[0]; |
| 334 |
jy = theJ[1]; |
| 335 |
jz = theJ[2]; |
| 336 |
} |
| 337 |
|
| 338 |
void DirectionalAtom::getTrq( double theT[3] ){ |
| 339 |
|
| 340 |
if( hasCoords ){ |
| 341 |
theT[0] = trq[offsetX]; |
| 342 |
theT[1] = trq[offsetY]; |
| 343 |
theT[2] = trq[offsetZ]; |
| 344 |
} |
| 345 |
else{ |
| 346 |
|
| 347 |
sprintf( painCave.errMsg, |
| 348 |
"Attempt to get Trq for atom %d before coords set.\n", |
| 349 |
index ); |
| 350 |
painCave.isFatal = 1; |
| 351 |
simError(); |
| 352 |
} |
| 353 |
} |
| 354 |
|
| 355 |
void DirectionalAtom::addTrq( double theT[3] ){ |
| 356 |
|
| 357 |
if( hasCoords ){ |
| 358 |
trq[offsetX] += theT[0]; |
| 359 |
trq[offsetY] += theT[1]; |
| 360 |
trq[offsetZ] += theT[2]; |
| 361 |
} |
| 362 |
else{ |
| 363 |
|
| 364 |
sprintf( painCave.errMsg, |
| 365 |
"Attempt to add Trq for atom %d before coords set.\n", |
| 366 |
index ); |
| 367 |
painCave.isFatal = 1; |
| 368 |
simError(); |
| 369 |
} |
| 370 |
} |
| 371 |
|
| 372 |
|
| 373 |
void DirectionalAtom::getI( double the_I[3][3] ){ |
| 374 |
|
| 375 |
the_I[0][0] = Ixx; |
| 376 |
the_I[0][1] = Ixy; |
| 377 |
the_I[0][2] = Ixz; |
| 378 |
|
| 379 |
the_I[1][0] = Iyx; |
| 380 |
the_I[1][1] = Iyy; |
| 381 |
the_I[1][2] = Iyz; |
| 382 |
|
| 383 |
the_I[2][0] = Izx; |
| 384 |
the_I[2][1] = Izy; |
| 385 |
the_I[2][2] = Izz; |
| 386 |
} |
