| 1 |
gezelter |
829 |
#include <math.h> |
| 2 |
mmeineke |
377 |
|
| 3 |
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#include "Atom.hpp" |
| 4 |
gezelter |
1097 |
#include "DirectionalAtom.hpp" |
| 5 |
mmeineke |
670 |
#include "simError.h" |
| 6 |
gezelter |
1097 |
#include "MatVec3.h" |
| 7 |
mmeineke |
377 |
|
| 8 |
mmeineke |
670 |
void DirectionalAtom::zeroForces() { |
| 9 |
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if( hasCoords ){ |
| 10 |
gezelter |
1097 |
|
| 11 |
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Atom::zeroForces(); |
| 12 |
mmeineke |
670 |
|
| 13 |
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trq[offsetX] = 0.0; |
| 14 |
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trq[offsetY] = 0.0; |
| 15 |
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trq[offsetZ] = 0.0; |
| 16 |
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} |
| 17 |
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else{ |
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| 19 |
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sprintf( painCave.errMsg, |
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"Attempt to zero frc and trq for atom %d before coords set.\n", |
| 21 |
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index ); |
| 22 |
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painCave.isFatal = 1; |
| 23 |
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simError(); |
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} |
| 25 |
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} |
| 26 |
mmeineke |
377 |
|
| 27 |
tim |
689 |
void DirectionalAtom::setCoords(void){ |
| 28 |
mmeineke |
414 |
|
| 29 |
tim |
689 |
if( myConfig->isAllocated() ){ |
| 30 |
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| 31 |
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myConfig->getAtomPointers( index, |
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&pos, |
| 33 |
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&vel, |
| 34 |
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&frc, |
| 35 |
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&trq, |
| 36 |
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&Amat, |
| 37 |
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&mu, |
| 38 |
tim |
1136 |
&ul, |
| 39 |
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&rc, |
| 40 |
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&massRatio); |
| 41 |
mmeineke |
670 |
} |
| 42 |
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else{ |
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sprintf( painCave.errMsg, |
| 44 |
tim |
689 |
"Attempted to set Atom %d coordinates with an unallocated " |
| 45 |
mmeineke |
787 |
"SimState object.\n", index ); |
| 46 |
mmeineke |
670 |
painCave.isFatal = 1; |
| 47 |
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simError(); |
| 48 |
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} |
| 49 |
tim |
689 |
|
| 50 |
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hasCoords = true; |
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| 52 |
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} |
| 53 |
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| 54 |
mmeineke |
377 |
void DirectionalAtom::setA( double the_A[3][3] ){ |
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mmeineke |
670 |
if( hasCoords ){ |
| 57 |
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Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
| 58 |
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Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
| 59 |
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Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
| 60 |
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| 61 |
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this->updateU(); |
| 62 |
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} |
| 63 |
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else{ |
| 64 |
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| 65 |
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sprintf( painCave.errMsg, |
| 66 |
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"Attempt to set Amat for atom %d before coords set.\n", |
| 67 |
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index ); |
| 68 |
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painCave.isFatal = 1; |
| 69 |
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simError(); |
| 70 |
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} |
| 71 |
mmeineke |
377 |
} |
| 72 |
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| 73 |
gezelter |
1097 |
void DirectionalAtom::setI( double the_I[3][3] ){ |
| 74 |
mmeineke |
377 |
|
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Ixx = the_I[0][0]; Ixy = the_I[0][1]; Ixz = the_I[0][2]; |
| 76 |
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Iyx = the_I[1][0]; Iyy = the_I[1][1]; Iyz = the_I[1][2]; |
| 77 |
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Izx = the_I[2][0]; Izy = the_I[2][1]; Izz = the_I[2][2]; |
| 78 |
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} |
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| 80 |
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void DirectionalAtom::setQ( double the_q[4] ){ |
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double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
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| 84 |
mmeineke |
670 |
if( hasCoords ){ |
| 85 |
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q0Sqr = the_q[0] * the_q[0]; |
| 86 |
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q1Sqr = the_q[1] * the_q[1]; |
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q2Sqr = the_q[2] * the_q[2]; |
| 88 |
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q3Sqr = the_q[3] * the_q[3]; |
| 89 |
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| 90 |
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Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
| 92 |
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Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
| 93 |
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Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
| 94 |
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| 95 |
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Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
| 96 |
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Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
| 97 |
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Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
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| 99 |
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Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
| 100 |
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Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
| 101 |
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Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
| 102 |
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| 103 |
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this->updateU(); |
| 104 |
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} |
| 105 |
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else{ |
| 106 |
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| 107 |
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sprintf( painCave.errMsg, |
| 108 |
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"Attempt to set Q for atom %d before coords set.\n", |
| 109 |
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index ); |
| 110 |
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painCave.isFatal = 1; |
| 111 |
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simError(); |
| 112 |
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} |
| 113 |
mmeineke |
377 |
|
| 114 |
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} |
| 115 |
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| 116 |
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void DirectionalAtom::getA( double the_A[3][3] ){ |
| 117 |
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| 118 |
mmeineke |
670 |
if( hasCoords ){ |
| 119 |
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the_A[0][0] = Amat[Axx]; |
| 120 |
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the_A[0][1] = Amat[Axy]; |
| 121 |
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the_A[0][2] = Amat[Axz]; |
| 122 |
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| 123 |
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the_A[1][0] = Amat[Ayx]; |
| 124 |
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the_A[1][1] = Amat[Ayy]; |
| 125 |
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the_A[1][2] = Amat[Ayz]; |
| 126 |
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| 127 |
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the_A[2][0] = Amat[Azx]; |
| 128 |
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the_A[2][1] = Amat[Azy]; |
| 129 |
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the_A[2][2] = Amat[Azz]; |
| 130 |
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} |
| 131 |
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else{ |
| 132 |
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| 133 |
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sprintf( painCave.errMsg, |
| 134 |
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"Attempt to get Amat for atom %d before coords set.\n", |
| 135 |
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index ); |
| 136 |
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painCave.isFatal = 1; |
| 137 |
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simError(); |
| 138 |
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} |
| 139 |
mmeineke |
377 |
|
| 140 |
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} |
| 141 |
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| 142 |
mmeineke |
597 |
void DirectionalAtom::printAmatIndex( void ){ |
| 143 |
mmeineke |
377 |
|
| 144 |
mmeineke |
670 |
if( hasCoords ){ |
| 145 |
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std::cerr << "Atom[" << index << "] index =>\n" |
| 146 |
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<< "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n" |
| 147 |
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<< "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n" |
| 148 |
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<< "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n"; |
| 149 |
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} |
| 150 |
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else{ |
| 151 |
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| 152 |
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sprintf( painCave.errMsg, |
| 153 |
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"Attempt to print Amat indices for atom %d before coords set.\n", |
| 154 |
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index ); |
| 155 |
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painCave.isFatal = 1; |
| 156 |
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simError(); |
| 157 |
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} |
| 158 |
mmeineke |
597 |
} |
| 159 |
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| 160 |
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| 161 |
mmeineke |
377 |
void DirectionalAtom::getU( double the_u[3] ){ |
| 162 |
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gezelter |
1097 |
the_u[0] = sU[2][0]; |
| 164 |
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the_u[1] = sU[2][1]; |
| 165 |
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the_u[2] = sU[2][2]; |
| 166 |
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mmeineke |
377 |
this->body2Lab( the_u ); |
| 168 |
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} |
| 169 |
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| 170 |
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void DirectionalAtom::getQ( double q[4] ){ |
| 171 |
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| 172 |
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double t, s; |
| 173 |
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double ad1, ad2, ad3; |
| 174 |
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| 175 |
mmeineke |
670 |
if( hasCoords ){ |
| 176 |
mmeineke |
377 |
|
| 177 |
mmeineke |
670 |
t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0; |
| 178 |
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if( t > 0.0 ){ |
| 179 |
mmeineke |
377 |
|
| 180 |
mmeineke |
670 |
s = 0.5 / sqrt( t ); |
| 181 |
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q[0] = 0.25 / s; |
| 182 |
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q[1] = (Amat[Ayz] - Amat[Azy]) * s; |
| 183 |
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q[2] = (Amat[Azx] - Amat[Axz]) * s; |
| 184 |
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q[3] = (Amat[Axy] - Amat[Ayx]) * s; |
| 185 |
mmeineke |
377 |
} |
| 186 |
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else{ |
| 187 |
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| 188 |
mmeineke |
670 |
ad1 = fabs( Amat[Axx] ); |
| 189 |
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ad2 = fabs( Amat[Ayy] ); |
| 190 |
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ad3 = fabs( Amat[Azz] ); |
| 191 |
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| 192 |
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if( ad1 >= ad2 && ad1 >= ad3 ){ |
| 193 |
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| 194 |
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s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] ); |
| 195 |
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q[0] = (Amat[Ayz] + Amat[Azy]) / s; |
| 196 |
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q[1] = 0.5 / s; |
| 197 |
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q[2] = (Amat[Axy] + Amat[Ayx]) / s; |
| 198 |
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q[3] = (Amat[Axz] + Amat[Azx]) / s; |
| 199 |
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} |
| 200 |
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else if( ad2 >= ad1 && ad2 >= ad3 ){ |
| 201 |
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| 202 |
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s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0; |
| 203 |
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q[0] = (Amat[Axz] + Amat[Azx]) / s; |
| 204 |
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q[1] = (Amat[Axy] + Amat[Ayx]) / s; |
| 205 |
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q[2] = 0.5 / s; |
| 206 |
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q[3] = (Amat[Ayz] + Amat[Azy]) / s; |
| 207 |
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} |
| 208 |
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else{ |
| 209 |
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| 210 |
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s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
| 211 |
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q[0] = (Amat[Axy] + Amat[Ayx]) / s; |
| 212 |
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q[1] = (Amat[Axz] + Amat[Azx]) / s; |
| 213 |
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q[2] = (Amat[Ayz] + Amat[Azy]) / s; |
| 214 |
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q[3] = 0.5 / s; |
| 215 |
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} |
| 216 |
mmeineke |
377 |
} |
| 217 |
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} |
| 218 |
mmeineke |
670 |
else{ |
| 219 |
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| 220 |
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sprintf( painCave.errMsg, |
| 221 |
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"Attempt to get Q for atom %d before coords set.\n", |
| 222 |
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index ); |
| 223 |
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painCave.isFatal = 1; |
| 224 |
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simError(); |
| 225 |
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} |
| 226 |
mmeineke |
377 |
} |
| 227 |
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| 228 |
gezelter |
1097 |
void DirectionalAtom::setUnitFrameFromEuler(double phi, |
| 229 |
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double theta, |
| 230 |
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double psi) { |
| 231 |
mmeineke |
377 |
|
| 232 |
gezelter |
1097 |
double myA[3][3]; |
| 233 |
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double uFrame[3][3]; |
| 234 |
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double len; |
| 235 |
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int i, j; |
| 236 |
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| 237 |
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myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 238 |
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myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 239 |
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myA[0][2] = sin(theta) * sin(psi); |
| 240 |
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| 241 |
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myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 242 |
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myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 243 |
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myA[1][2] = sin(theta) * cos(psi); |
| 244 |
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| 245 |
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myA[2][0] = sin(phi) * sin(theta); |
| 246 |
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myA[2][1] = -cos(phi) * sin(theta); |
| 247 |
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myA[2][2] = cos(theta); |
| 248 |
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| 249 |
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// Make the unit Frame: |
| 250 |
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| 251 |
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for (i=0; i < 3; i++) |
| 252 |
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for (j=0; j < 3; j++) |
| 253 |
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uFrame[i][j] = 0.0; |
| 254 |
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| 255 |
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for (i=0; i < 3; i++) |
| 256 |
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uFrame[i][i] = 1.0; |
| 257 |
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| 258 |
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// rotate by the given rotation matrix: |
| 259 |
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| 260 |
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matMul3(myA, uFrame, sU); |
| 261 |
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| 262 |
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// renormalize column vectors: |
| 263 |
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| 264 |
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for (i=0; i < 3; i++) { |
| 265 |
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len = 0.0; |
| 266 |
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for (j = 0; j < 3; j++) { |
| 267 |
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len += sU[i][j]*sU[i][j]; |
| 268 |
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} |
| 269 |
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len = sqrt(len); |
| 270 |
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for (j = 0; j < 3; j++) { |
| 271 |
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sU[i][j] /= len; |
| 272 |
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} |
| 273 |
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} |
| 274 |
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| 275 |
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// sU now contains the coordinates of the 'special' frame; |
| 276 |
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| 277 |
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} |
| 278 |
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| 279 |
mmeineke |
377 |
void DirectionalAtom::setEuler( double phi, double theta, double psi ){ |
| 280 |
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| 281 |
mmeineke |
670 |
if( hasCoords ){ |
| 282 |
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Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 283 |
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Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 284 |
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Amat[Axz] = sin(theta) * sin(psi); |
| 285 |
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| 286 |
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Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 287 |
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Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 288 |
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Amat[Ayz] = sin(theta) * cos(psi); |
| 289 |
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| 290 |
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Amat[Azx] = sin(phi) * sin(theta); |
| 291 |
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Amat[Azy] = -cos(phi) * sin(theta); |
| 292 |
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Amat[Azz] = cos(theta); |
| 293 |
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| 294 |
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this->updateU(); |
| 295 |
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} |
| 296 |
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else{ |
| 297 |
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| 298 |
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sprintf( painCave.errMsg, |
| 299 |
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"Attempt to set Euler angles for atom %d before coords set.\n", |
| 300 |
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index ); |
| 301 |
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painCave.isFatal = 1; |
| 302 |
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simError(); |
| 303 |
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} |
| 304 |
mmeineke |
377 |
} |
| 305 |
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| 306 |
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| 307 |
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void DirectionalAtom::lab2Body( double r[3] ){ |
| 308 |
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| 309 |
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double rl[3]; // the lab frame vector |
| 310 |
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| 311 |
mmeineke |
670 |
if( hasCoords ){ |
| 312 |
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rl[0] = r[0]; |
| 313 |
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rl[1] = r[1]; |
| 314 |
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rl[2] = r[2]; |
| 315 |
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| 316 |
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r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
| 317 |
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r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
| 318 |
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r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
| 319 |
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} |
| 320 |
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else{ |
| 321 |
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| 322 |
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sprintf( painCave.errMsg, |
| 323 |
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"Attempt to convert lab2body for atom %d before coords set.\n", |
| 324 |
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index ); |
| 325 |
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painCave.isFatal = 1; |
| 326 |
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simError(); |
| 327 |
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} |
| 328 |
mmeineke |
377 |
|
| 329 |
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} |
| 330 |
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| 331 |
gezelter |
1097 |
void DirectionalAtom::rotateBy( double by_A[3][3]) { |
| 332 |
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| 333 |
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// Check this |
| 334 |
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| 335 |
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double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
| 336 |
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| 337 |
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if( hasCoords ){ |
| 338 |
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| 339 |
|
|
r00 = by_A[0][0]*Amat[Axx] + by_A[0][1]*Amat[Ayx] + by_A[0][2]*Amat[Azx]; |
| 340 |
|
|
r01 = by_A[0][0]*Amat[Axy] + by_A[0][1]*Amat[Ayy] + by_A[0][2]*Amat[Azy]; |
| 341 |
|
|
r02 = by_A[0][0]*Amat[Axz] + by_A[0][1]*Amat[Ayz] + by_A[0][2]*Amat[Azz]; |
| 342 |
|
|
|
| 343 |
|
|
r10 = by_A[1][0]*Amat[Axx] + by_A[1][1]*Amat[Ayx] + by_A[1][2]*Amat[Azx]; |
| 344 |
|
|
r11 = by_A[1][0]*Amat[Axy] + by_A[1][1]*Amat[Ayy] + by_A[1][2]*Amat[Azy]; |
| 345 |
|
|
r12 = by_A[1][0]*Amat[Axz] + by_A[1][1]*Amat[Ayz] + by_A[1][2]*Amat[Azz]; |
| 346 |
|
|
|
| 347 |
|
|
r20 = by_A[2][0]*Amat[Axx] + by_A[2][1]*Amat[Ayx] + by_A[2][2]*Amat[Azx]; |
| 348 |
|
|
r21 = by_A[2][0]*Amat[Axy] + by_A[2][1]*Amat[Ayy] + by_A[2][2]*Amat[Azy]; |
| 349 |
|
|
r22 = by_A[2][0]*Amat[Axz] + by_A[2][1]*Amat[Ayz] + by_A[2][2]*Amat[Azz]; |
| 350 |
|
|
|
| 351 |
|
|
Amat[Axx] = r00; Amat[Axy] = r01; Amat[Axz] = r02; |
| 352 |
|
|
Amat[Ayx] = r10; Amat[Ayy] = r11; Amat[Ayz] = r12; |
| 353 |
|
|
Amat[Azx] = r20; Amat[Azy] = r21; Amat[Azz] = r22; |
| 354 |
|
|
|
| 355 |
|
|
} |
| 356 |
|
|
else{ |
| 357 |
|
|
|
| 358 |
|
|
sprintf( painCave.errMsg, |
| 359 |
|
|
"Attempt to rotate frame for atom %d before coords set.\n", |
| 360 |
|
|
index ); |
| 361 |
|
|
painCave.isFatal = 1; |
| 362 |
|
|
simError(); |
| 363 |
|
|
} |
| 364 |
|
|
|
| 365 |
|
|
} |
| 366 |
|
|
|
| 367 |
|
|
|
| 368 |
mmeineke |
377 |
void DirectionalAtom::body2Lab( double r[3] ){ |
| 369 |
|
|
|
| 370 |
|
|
double rb[3]; // the body frame vector |
| 371 |
|
|
|
| 372 |
mmeineke |
670 |
if( hasCoords ){ |
| 373 |
|
|
rb[0] = r[0]; |
| 374 |
|
|
rb[1] = r[1]; |
| 375 |
|
|
rb[2] = r[2]; |
| 376 |
|
|
|
| 377 |
|
|
r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
| 378 |
|
|
r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
| 379 |
|
|
r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
| 380 |
|
|
} |
| 381 |
|
|
else{ |
| 382 |
|
|
|
| 383 |
|
|
sprintf( painCave.errMsg, |
| 384 |
|
|
"Attempt to convert body2lab for atom %d before coords set.\n", |
| 385 |
|
|
index ); |
| 386 |
|
|
painCave.isFatal = 1; |
| 387 |
|
|
simError(); |
| 388 |
|
|
} |
| 389 |
mmeineke |
377 |
} |
| 390 |
|
|
|
| 391 |
|
|
void DirectionalAtom::updateU( void ){ |
| 392 |
|
|
|
| 393 |
mmeineke |
670 |
if( hasCoords ){ |
| 394 |
gezelter |
1097 |
ul[offsetX] = (Amat[Axx] * sU[2][0]) + |
| 395 |
|
|
(Amat[Ayx] * sU[2][1]) + (Amat[Azx] * sU[2][2]); |
| 396 |
|
|
ul[offsetY] = (Amat[Axy] * sU[2][0]) + |
| 397 |
|
|
(Amat[Ayy] * sU[2][1]) + (Amat[Azy] * sU[2][2]); |
| 398 |
|
|
ul[offsetZ] = (Amat[Axz] * sU[2][0]) + |
| 399 |
|
|
(Amat[Ayz] * sU[2][1]) + (Amat[Azz] * sU[2][2]); |
| 400 |
mmeineke |
670 |
} |
| 401 |
|
|
else{ |
| 402 |
|
|
|
| 403 |
|
|
sprintf( painCave.errMsg, |
| 404 |
|
|
"Attempt to updateU for atom %d before coords set.\n", |
| 405 |
|
|
index ); |
| 406 |
|
|
painCave.isFatal = 1; |
| 407 |
|
|
simError(); |
| 408 |
|
|
} |
| 409 |
mmeineke |
377 |
} |
| 410 |
|
|
|
| 411 |
mmeineke |
599 |
void DirectionalAtom::getJ( double theJ[3] ){ |
| 412 |
|
|
|
| 413 |
|
|
theJ[0] = jx; |
| 414 |
|
|
theJ[1] = jy; |
| 415 |
|
|
theJ[2] = jz; |
| 416 |
|
|
} |
| 417 |
|
|
|
| 418 |
|
|
void DirectionalAtom::setJ( double theJ[3] ){ |
| 419 |
|
|
|
| 420 |
|
|
jx = theJ[0]; |
| 421 |
|
|
jy = theJ[1]; |
| 422 |
|
|
jz = theJ[2]; |
| 423 |
|
|
} |
| 424 |
|
|
|
| 425 |
|
|
void DirectionalAtom::getTrq( double theT[3] ){ |
| 426 |
|
|
|
| 427 |
mmeineke |
670 |
if( hasCoords ){ |
| 428 |
|
|
theT[0] = trq[offsetX]; |
| 429 |
|
|
theT[1] = trq[offsetY]; |
| 430 |
|
|
theT[2] = trq[offsetZ]; |
| 431 |
|
|
} |
| 432 |
|
|
else{ |
| 433 |
|
|
|
| 434 |
|
|
sprintf( painCave.errMsg, |
| 435 |
|
|
"Attempt to get Trq for atom %d before coords set.\n", |
| 436 |
|
|
index ); |
| 437 |
|
|
painCave.isFatal = 1; |
| 438 |
|
|
simError(); |
| 439 |
|
|
} |
| 440 |
mmeineke |
599 |
} |
| 441 |
|
|
|
| 442 |
|
|
void DirectionalAtom::addTrq( double theT[3] ){ |
| 443 |
|
|
|
| 444 |
mmeineke |
670 |
if( hasCoords ){ |
| 445 |
|
|
trq[offsetX] += theT[0]; |
| 446 |
|
|
trq[offsetY] += theT[1]; |
| 447 |
|
|
trq[offsetZ] += theT[2]; |
| 448 |
|
|
} |
| 449 |
|
|
else{ |
| 450 |
|
|
|
| 451 |
|
|
sprintf( painCave.errMsg, |
| 452 |
|
|
"Attempt to add Trq for atom %d before coords set.\n", |
| 453 |
|
|
index ); |
| 454 |
|
|
painCave.isFatal = 1; |
| 455 |
|
|
simError(); |
| 456 |
|
|
} |
| 457 |
mmeineke |
599 |
} |
| 458 |
|
|
|
| 459 |
|
|
|
| 460 |
|
|
void DirectionalAtom::getI( double the_I[3][3] ){ |
| 461 |
|
|
|
| 462 |
|
|
the_I[0][0] = Ixx; |
| 463 |
|
|
the_I[0][1] = Ixy; |
| 464 |
|
|
the_I[0][2] = Ixz; |
| 465 |
|
|
|
| 466 |
|
|
the_I[1][0] = Iyx; |
| 467 |
|
|
the_I[1][1] = Iyy; |
| 468 |
|
|
the_I[1][2] = Iyz; |
| 469 |
|
|
|
| 470 |
|
|
the_I[2][0] = Izx; |
| 471 |
|
|
the_I[2][1] = Izy; |
| 472 |
|
|
the_I[2][2] = Izz; |
| 473 |
|
|
} |
| 474 |
gezelter |
878 |
|
| 475 |
|
|
void DirectionalAtom::getGrad( double grad[6] ) { |
| 476 |
|
|
|
| 477 |
|
|
double myEuler[3]; |
| 478 |
|
|
double phi, theta, psi; |
| 479 |
|
|
double cphi, sphi, ctheta, stheta; |
| 480 |
|
|
double ephi[3]; |
| 481 |
|
|
double etheta[3]; |
| 482 |
|
|
double epsi[3]; |
| 483 |
|
|
|
| 484 |
|
|
this->getEulerAngles(myEuler); |
| 485 |
|
|
|
| 486 |
|
|
phi = myEuler[0]; |
| 487 |
|
|
theta = myEuler[1]; |
| 488 |
|
|
psi = myEuler[2]; |
| 489 |
|
|
|
| 490 |
|
|
cphi = cos(phi); |
| 491 |
|
|
sphi = sin(phi); |
| 492 |
|
|
ctheta = cos(theta); |
| 493 |
|
|
stheta = sin(theta); |
| 494 |
|
|
|
| 495 |
|
|
// get unit vectors along the phi, theta and psi rotation axes |
| 496 |
|
|
|
| 497 |
|
|
ephi[0] = 0.0; |
| 498 |
|
|
ephi[1] = 0.0; |
| 499 |
|
|
ephi[2] = 1.0; |
| 500 |
tim |
1046 |
|
| 501 |
|
|
etheta[0] = cphi; |
| 502 |
|
|
etheta[1] = sphi; |
| 503 |
gezelter |
878 |
etheta[2] = 0.0; |
| 504 |
|
|
|
| 505 |
tim |
1046 |
epsi[0] = stheta * cphi; |
| 506 |
|
|
epsi[1] = stheta * sphi; |
| 507 |
|
|
epsi[2] = ctheta; |
| 508 |
|
|
|
| 509 |
gezelter |
878 |
for (int j = 0 ; j<3; j++) |
| 510 |
|
|
grad[j] = frc[j]; |
| 511 |
|
|
|
| 512 |
tim |
1046 |
grad[3] = 0; |
| 513 |
|
|
grad[4] = 0; |
| 514 |
|
|
grad[5] = 0; |
| 515 |
|
|
|
| 516 |
gezelter |
878 |
for (int j = 0; j < 3; j++ ) { |
| 517 |
|
|
|
| 518 |
|
|
grad[3] += trq[j]*ephi[j]; |
| 519 |
|
|
grad[4] += trq[j]*etheta[j]; |
| 520 |
|
|
grad[5] += trq[j]*epsi[j]; |
| 521 |
|
|
|
| 522 |
|
|
} |
| 523 |
|
|
|
| 524 |
|
|
} |
| 525 |
|
|
|
| 526 |
tim |
1046 |
/** |
| 527 |
|
|
* getEulerAngles computes a set of Euler angle values consistent |
| 528 |
|
|
* with an input rotation matrix. They are returned in the following |
| 529 |
|
|
* order: |
| 530 |
|
|
* myEuler[0] = phi; |
| 531 |
|
|
* myEuler[1] = theta; |
| 532 |
|
|
* myEuler[2] = psi; |
| 533 |
|
|
*/ |
| 534 |
gezelter |
878 |
void DirectionalAtom::getEulerAngles(double myEuler[3]) { |
| 535 |
|
|
|
| 536 |
tim |
1046 |
// We use so-called "x-convention", which is the most common definition. |
| 537 |
|
|
// In this convention, the rotation given by Euler angles (phi, theta, psi), where the first |
| 538 |
|
|
// rotation is by an angle phi about the z-axis, the second is by an angle |
| 539 |
|
|
// theta (0 <= theta <= 180)about the x-axis, and thethird is by an angle psi about the |
| 540 |
|
|
//z-axis (again). |
| 541 |
gezelter |
878 |
|
| 542 |
tim |
1046 |
|
| 543 |
gezelter |
878 |
double phi,theta,psi,eps; |
| 544 |
|
|
double pi; |
| 545 |
|
|
double cphi,ctheta,cpsi; |
| 546 |
|
|
double sphi,stheta,spsi; |
| 547 |
|
|
double b[3]; |
| 548 |
|
|
int flip[3]; |
| 549 |
|
|
|
| 550 |
|
|
// set the tolerance for Euler angles and rotation elements |
| 551 |
|
|
|
| 552 |
|
|
eps = 1.0e-8; |
| 553 |
|
|
|
| 554 |
tim |
1046 |
theta = acos(min(1.0,max(-1.0,Amat[Azz]))); |
| 555 |
|
|
ctheta = Amat[Azz]; |
| 556 |
|
|
stheta = sqrt(1.0 - ctheta * ctheta); |
| 557 |
|
|
|
| 558 |
|
|
// when sin(theta) is close to 0, we need to consider singularity |
| 559 |
|
|
// In this case, we can assign an arbitary value to phi (or psi), and then determine |
| 560 |
|
|
// the psi (or phi) or vice-versa. We'll assume that phi always gets the rotation, and psi is 0 |
| 561 |
|
|
// in cases of singularity. |
| 562 |
|
|
// we use atan2 instead of atan, since atan2 will give us -Pi to Pi. |
| 563 |
|
|
// Since 0 <= theta <= 180, sin(theta) will be always non-negative. Therefore, it never |
| 564 |
|
|
// change the sign of both of the parameters passed to atan2. |
| 565 |
gezelter |
878 |
|
| 566 |
tim |
1046 |
if (fabs(stheta) <= eps){ |
| 567 |
|
|
psi = 0.0; |
| 568 |
|
|
phi = atan2(-Amat[Ayx], Amat[Axx]); |
| 569 |
gezelter |
878 |
} |
| 570 |
tim |
1046 |
// we only have one unique solution |
| 571 |
|
|
else{ |
| 572 |
|
|
phi = atan2(Amat[Azx], -Amat[Azy]); |
| 573 |
|
|
psi = atan2(Amat[Axz], Amat[Ayz]); |
| 574 |
|
|
} |
| 575 |
gezelter |
878 |
|
| 576 |
tim |
1046 |
//wrap phi and psi, make sure they are in the range from 0 to 2*Pi |
| 577 |
|
|
//if (phi < 0) |
| 578 |
|
|
// phi += M_PI; |
| 579 |
gezelter |
878 |
|
| 580 |
tim |
1046 |
//if (psi < 0) |
| 581 |
|
|
// psi += M_PI; |
| 582 |
gezelter |
878 |
|
| 583 |
|
|
myEuler[0] = phi; |
| 584 |
|
|
myEuler[1] = theta; |
| 585 |
|
|
myEuler[2] = psi; |
| 586 |
tim |
1046 |
|
| 587 |
gezelter |
878 |
return; |
| 588 |
|
|
} |
| 589 |
|
|
|
| 590 |
|
|
double DirectionalAtom::max(double x, double y) { |
| 591 |
|
|
return (x > y) ? x : y; |
| 592 |
|
|
} |
| 593 |
|
|
|
| 594 |
|
|
double DirectionalAtom::min(double x, double y) { |
| 595 |
|
|
return (x > y) ? y : x; |
| 596 |
|
|
} |
