| 1 |
#include <math.h> |
| 2 |
|
| 3 |
#include "primitives/Atom.hpp" |
| 4 |
#include "primitives/DirectionalAtom.hpp" |
| 5 |
#include "utils/simError.h" |
| 6 |
#include "math/MatVec3.h" |
| 7 |
|
| 8 |
void DirectionalAtom::zeroForces() { |
| 9 |
if( hasCoords ){ |
| 10 |
|
| 11 |
Atom::zeroForces(); |
| 12 |
|
| 13 |
trq[offsetX] = 0.0; |
| 14 |
trq[offsetY] = 0.0; |
| 15 |
trq[offsetZ] = 0.0; |
| 16 |
} |
| 17 |
else{ |
| 18 |
|
| 19 |
sprintf( painCave.errMsg, |
| 20 |
"Attempt to zero frc and trq for atom %d before coords set.\n", |
| 21 |
index ); |
| 22 |
painCave.isFatal = 1; |
| 23 |
simError(); |
| 24 |
} |
| 25 |
} |
| 26 |
|
| 27 |
void DirectionalAtom::setCoords(void){ |
| 28 |
|
| 29 |
if( myConfig->isAllocated() ){ |
| 30 |
|
| 31 |
myConfig->getAtomPointers( index, |
| 32 |
&pos, |
| 33 |
&vel, |
| 34 |
&frc, |
| 35 |
&trq, |
| 36 |
&Amat, |
| 37 |
&mu, |
| 38 |
&ul); |
| 39 |
} |
| 40 |
else{ |
| 41 |
sprintf( painCave.errMsg, |
| 42 |
"Attempted to set Atom %d coordinates with an unallocated " |
| 43 |
"SimState object.\n", index ); |
| 44 |
painCave.isFatal = 1; |
| 45 |
simError(); |
| 46 |
} |
| 47 |
|
| 48 |
hasCoords = true; |
| 49 |
|
| 50 |
} |
| 51 |
|
| 52 |
void DirectionalAtom::setA( double the_A[3][3] ){ |
| 53 |
|
| 54 |
if( hasCoords ){ |
| 55 |
Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
| 56 |
Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
| 57 |
Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
| 58 |
|
| 59 |
this->updateU(); |
| 60 |
} |
| 61 |
else{ |
| 62 |
|
| 63 |
sprintf( painCave.errMsg, |
| 64 |
"Attempt to set Amat for atom %d before coords set.\n", |
| 65 |
index ); |
| 66 |
painCave.isFatal = 1; |
| 67 |
simError(); |
| 68 |
} |
| 69 |
} |
| 70 |
|
| 71 |
void DirectionalAtom::setI( double the_I[3][3] ){ |
| 72 |
|
| 73 |
int n_linear_coords, i, j; |
| 74 |
|
| 75 |
Ixx = the_I[0][0]; Ixy = the_I[0][1]; Ixz = the_I[0][2]; |
| 76 |
Iyx = the_I[1][0]; Iyy = the_I[1][1]; Iyz = the_I[1][2]; |
| 77 |
Izx = the_I[2][0]; Izy = the_I[2][1]; Izz = the_I[2][2]; |
| 78 |
|
| 79 |
n_linear_coords = 0; |
| 80 |
|
| 81 |
for (i = 0; i<3; i++) { |
| 82 |
if (fabs(the_I[i][i]) < momIntTol) { |
| 83 |
is_linear = true; |
| 84 |
n_linear_coords++; |
| 85 |
linear_axis = i; |
| 86 |
} |
| 87 |
} |
| 88 |
|
| 89 |
if (n_linear_coords > 1) { |
| 90 |
sprintf( painCave.errMsg, |
| 91 |
"DirectionalAtom error.\n" |
| 92 |
"\tOOPSE was told to set more than one axis in this\n" |
| 93 |
"\tDirectionalAtom to a vanishing moment of inertia.\n" |
| 94 |
"\tThis should not be a DirectionalAtom. Use an Atom.\n" |
| 95 |
); |
| 96 |
painCave.isFatal = 1; |
| 97 |
simError(); |
| 98 |
} |
| 99 |
|
| 100 |
|
| 101 |
} |
| 102 |
|
| 103 |
void DirectionalAtom::setQ( double the_q[4] ){ |
| 104 |
|
| 105 |
double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
| 106 |
|
| 107 |
if( hasCoords ){ |
| 108 |
q0Sqr = the_q[0] * the_q[0]; |
| 109 |
q1Sqr = the_q[1] * the_q[1]; |
| 110 |
q2Sqr = the_q[2] * the_q[2]; |
| 111 |
q3Sqr = the_q[3] * the_q[3]; |
| 112 |
|
| 113 |
|
| 114 |
Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
| 115 |
Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
| 116 |
Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
| 117 |
|
| 118 |
Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
| 119 |
Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
| 120 |
Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
| 121 |
|
| 122 |
Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
| 123 |
Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
| 124 |
Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
| 125 |
|
| 126 |
this->updateU(); |
| 127 |
} |
| 128 |
else{ |
| 129 |
|
| 130 |
sprintf( painCave.errMsg, |
| 131 |
"Attempt to set Q for atom %d before coords set.\n", |
| 132 |
index ); |
| 133 |
painCave.isFatal = 1; |
| 134 |
simError(); |
| 135 |
} |
| 136 |
|
| 137 |
} |
| 138 |
|
| 139 |
void DirectionalAtom::getA( double the_A[3][3] ){ |
| 140 |
|
| 141 |
if( hasCoords ){ |
| 142 |
the_A[0][0] = Amat[Axx]; |
| 143 |
the_A[0][1] = Amat[Axy]; |
| 144 |
the_A[0][2] = Amat[Axz]; |
| 145 |
|
| 146 |
the_A[1][0] = Amat[Ayx]; |
| 147 |
the_A[1][1] = Amat[Ayy]; |
| 148 |
the_A[1][2] = Amat[Ayz]; |
| 149 |
|
| 150 |
the_A[2][0] = Amat[Azx]; |
| 151 |
the_A[2][1] = Amat[Azy]; |
| 152 |
the_A[2][2] = Amat[Azz]; |
| 153 |
} |
| 154 |
else{ |
| 155 |
|
| 156 |
sprintf( painCave.errMsg, |
| 157 |
"Attempt to get Amat for atom %d before coords set.\n", |
| 158 |
index ); |
| 159 |
painCave.isFatal = 1; |
| 160 |
simError(); |
| 161 |
} |
| 162 |
|
| 163 |
} |
| 164 |
|
| 165 |
void DirectionalAtom::printAmatIndex( void ){ |
| 166 |
|
| 167 |
if( hasCoords ){ |
| 168 |
std::cerr << "Atom[" << index << "] index =>\n" |
| 169 |
<< "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n" |
| 170 |
<< "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n" |
| 171 |
<< "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n"; |
| 172 |
} |
| 173 |
else{ |
| 174 |
|
| 175 |
sprintf( painCave.errMsg, |
| 176 |
"Attempt to print Amat indices for atom %d before coords set.\n", |
| 177 |
index ); |
| 178 |
painCave.isFatal = 1; |
| 179 |
simError(); |
| 180 |
} |
| 181 |
} |
| 182 |
|
| 183 |
|
| 184 |
void DirectionalAtom::getU( double the_u[3] ){ |
| 185 |
|
| 186 |
the_u[0] = sU[2][0]; |
| 187 |
the_u[1] = sU[2][1]; |
| 188 |
the_u[2] = sU[2][2]; |
| 189 |
|
| 190 |
this->body2Lab( the_u ); |
| 191 |
} |
| 192 |
|
| 193 |
void DirectionalAtom::getQ( double q[4] ){ |
| 194 |
|
| 195 |
double t, s; |
| 196 |
double ad1, ad2, ad3; |
| 197 |
|
| 198 |
if( hasCoords ){ |
| 199 |
|
| 200 |
t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0; |
| 201 |
if( t > 0.0 ){ |
| 202 |
|
| 203 |
s = 0.5 / sqrt( t ); |
| 204 |
q[0] = 0.25 / s; |
| 205 |
q[1] = (Amat[Ayz] - Amat[Azy]) * s; |
| 206 |
q[2] = (Amat[Azx] - Amat[Axz]) * s; |
| 207 |
q[3] = (Amat[Axy] - Amat[Ayx]) * s; |
| 208 |
} |
| 209 |
else{ |
| 210 |
|
| 211 |
ad1 = fabs( Amat[Axx] ); |
| 212 |
ad2 = fabs( Amat[Ayy] ); |
| 213 |
ad3 = fabs( Amat[Azz] ); |
| 214 |
|
| 215 |
if( ad1 >= ad2 && ad1 >= ad3 ){ |
| 216 |
|
| 217 |
s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] ); |
| 218 |
q[0] = (Amat[Ayz] + Amat[Azy]) / s; |
| 219 |
q[1] = 0.5 / s; |
| 220 |
q[2] = (Amat[Axy] + Amat[Ayx]) / s; |
| 221 |
q[3] = (Amat[Axz] + Amat[Azx]) / s; |
| 222 |
} |
| 223 |
else if( ad2 >= ad1 && ad2 >= ad3 ){ |
| 224 |
|
| 225 |
s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0; |
| 226 |
q[0] = (Amat[Axz] + Amat[Azx]) / s; |
| 227 |
q[1] = (Amat[Axy] + Amat[Ayx]) / s; |
| 228 |
q[2] = 0.5 / s; |
| 229 |
q[3] = (Amat[Ayz] + Amat[Azy]) / s; |
| 230 |
} |
| 231 |
else{ |
| 232 |
|
| 233 |
s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
| 234 |
q[0] = (Amat[Axy] + Amat[Ayx]) / s; |
| 235 |
q[1] = (Amat[Axz] + Amat[Azx]) / s; |
| 236 |
q[2] = (Amat[Ayz] + Amat[Azy]) / s; |
| 237 |
q[3] = 0.5 / s; |
| 238 |
} |
| 239 |
} |
| 240 |
} |
| 241 |
else{ |
| 242 |
|
| 243 |
sprintf( painCave.errMsg, |
| 244 |
"Attempt to get Q for atom %d before coords set.\n", |
| 245 |
index ); |
| 246 |
painCave.isFatal = 1; |
| 247 |
simError(); |
| 248 |
} |
| 249 |
} |
| 250 |
|
| 251 |
void DirectionalAtom::setUnitFrameFromEuler(double phi, |
| 252 |
double theta, |
| 253 |
double psi) { |
| 254 |
|
| 255 |
double myA[3][3]; |
| 256 |
double uFrame[3][3]; |
| 257 |
double len; |
| 258 |
int i, j; |
| 259 |
|
| 260 |
myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 261 |
myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 262 |
myA[0][2] = sin(theta) * sin(psi); |
| 263 |
|
| 264 |
myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 265 |
myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 266 |
myA[1][2] = sin(theta) * cos(psi); |
| 267 |
|
| 268 |
myA[2][0] = sin(phi) * sin(theta); |
| 269 |
myA[2][1] = -cos(phi) * sin(theta); |
| 270 |
myA[2][2] = cos(theta); |
| 271 |
|
| 272 |
// Make the unit Frame: |
| 273 |
|
| 274 |
for (i=0; i < 3; i++) |
| 275 |
for (j=0; j < 3; j++) |
| 276 |
uFrame[i][j] = 0.0; |
| 277 |
|
| 278 |
for (i=0; i < 3; i++) |
| 279 |
uFrame[i][i] = 1.0; |
| 280 |
|
| 281 |
// rotate by the given rotation matrix: |
| 282 |
|
| 283 |
matMul3(myA, uFrame, sU); |
| 284 |
|
| 285 |
// renormalize column vectors: |
| 286 |
|
| 287 |
for (i=0; i < 3; i++) { |
| 288 |
len = 0.0; |
| 289 |
for (j = 0; j < 3; j++) { |
| 290 |
len += sU[i][j]*sU[i][j]; |
| 291 |
} |
| 292 |
len = sqrt(len); |
| 293 |
for (j = 0; j < 3; j++) { |
| 294 |
sU[i][j] /= len; |
| 295 |
} |
| 296 |
} |
| 297 |
|
| 298 |
// sU now contains the coordinates of the 'special' frame; |
| 299 |
|
| 300 |
} |
| 301 |
|
| 302 |
void DirectionalAtom::setEuler( double phi, double theta, double psi ){ |
| 303 |
|
| 304 |
if( hasCoords ){ |
| 305 |
Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
| 306 |
Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
| 307 |
Amat[Axz] = sin(theta) * sin(psi); |
| 308 |
|
| 309 |
Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
| 310 |
Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
| 311 |
Amat[Ayz] = sin(theta) * cos(psi); |
| 312 |
|
| 313 |
Amat[Azx] = sin(phi) * sin(theta); |
| 314 |
Amat[Azy] = -cos(phi) * sin(theta); |
| 315 |
Amat[Azz] = cos(theta); |
| 316 |
|
| 317 |
this->updateU(); |
| 318 |
} |
| 319 |
else{ |
| 320 |
|
| 321 |
sprintf( painCave.errMsg, |
| 322 |
"Attempt to set Euler angles for atom %d before coords set.\n", |
| 323 |
index ); |
| 324 |
painCave.isFatal = 1; |
| 325 |
simError(); |
| 326 |
} |
| 327 |
} |
| 328 |
|
| 329 |
|
| 330 |
void DirectionalAtom::lab2Body( double r[3] ){ |
| 331 |
|
| 332 |
double rl[3]; // the lab frame vector |
| 333 |
|
| 334 |
if( hasCoords ){ |
| 335 |
rl[0] = r[0]; |
| 336 |
rl[1] = r[1]; |
| 337 |
rl[2] = r[2]; |
| 338 |
|
| 339 |
r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
| 340 |
r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
| 341 |
r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
| 342 |
} |
| 343 |
else{ |
| 344 |
|
| 345 |
sprintf( painCave.errMsg, |
| 346 |
"Attempt to convert lab2body for atom %d before coords set.\n", |
| 347 |
index ); |
| 348 |
painCave.isFatal = 1; |
| 349 |
simError(); |
| 350 |
} |
| 351 |
|
| 352 |
} |
| 353 |
|
| 354 |
void DirectionalAtom::rotateBy( double by_A[3][3]) { |
| 355 |
|
| 356 |
// Check this |
| 357 |
|
| 358 |
double r00, r01, r02, r10, r11, r12, r20, r21, r22; |
| 359 |
|
| 360 |
if( hasCoords ){ |
| 361 |
|
| 362 |
r00 = by_A[0][0]*Amat[Axx] + by_A[0][1]*Amat[Ayx] + by_A[0][2]*Amat[Azx]; |
| 363 |
r01 = by_A[0][0]*Amat[Axy] + by_A[0][1]*Amat[Ayy] + by_A[0][2]*Amat[Azy]; |
| 364 |
r02 = by_A[0][0]*Amat[Axz] + by_A[0][1]*Amat[Ayz] + by_A[0][2]*Amat[Azz]; |
| 365 |
|
| 366 |
r10 = by_A[1][0]*Amat[Axx] + by_A[1][1]*Amat[Ayx] + by_A[1][2]*Amat[Azx]; |
| 367 |
r11 = by_A[1][0]*Amat[Axy] + by_A[1][1]*Amat[Ayy] + by_A[1][2]*Amat[Azy]; |
| 368 |
r12 = by_A[1][0]*Amat[Axz] + by_A[1][1]*Amat[Ayz] + by_A[1][2]*Amat[Azz]; |
| 369 |
|
| 370 |
r20 = by_A[2][0]*Amat[Axx] + by_A[2][1]*Amat[Ayx] + by_A[2][2]*Amat[Azx]; |
| 371 |
r21 = by_A[2][0]*Amat[Axy] + by_A[2][1]*Amat[Ayy] + by_A[2][2]*Amat[Azy]; |
| 372 |
r22 = by_A[2][0]*Amat[Axz] + by_A[2][1]*Amat[Ayz] + by_A[2][2]*Amat[Azz]; |
| 373 |
|
| 374 |
Amat[Axx] = r00; Amat[Axy] = r01; Amat[Axz] = r02; |
| 375 |
Amat[Ayx] = r10; Amat[Ayy] = r11; Amat[Ayz] = r12; |
| 376 |
Amat[Azx] = r20; Amat[Azy] = r21; Amat[Azz] = r22; |
| 377 |
|
| 378 |
} |
| 379 |
else{ |
| 380 |
|
| 381 |
sprintf( painCave.errMsg, |
| 382 |
"Attempt to rotate frame for atom %d before coords set.\n", |
| 383 |
index ); |
| 384 |
painCave.isFatal = 1; |
| 385 |
simError(); |
| 386 |
} |
| 387 |
|
| 388 |
} |
| 389 |
|
| 390 |
|
| 391 |
void DirectionalAtom::body2Lab( double r[3] ){ |
| 392 |
|
| 393 |
double rb[3]; // the body frame vector |
| 394 |
|
| 395 |
if( hasCoords ){ |
| 396 |
rb[0] = r[0]; |
| 397 |
rb[1] = r[1]; |
| 398 |
rb[2] = r[2]; |
| 399 |
|
| 400 |
r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
| 401 |
r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
| 402 |
r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
| 403 |
} |
| 404 |
else{ |
| 405 |
|
| 406 |
sprintf( painCave.errMsg, |
| 407 |
"Attempt to convert body2lab for atom %d before coords set.\n", |
| 408 |
index ); |
| 409 |
painCave.isFatal = 1; |
| 410 |
simError(); |
| 411 |
} |
| 412 |
} |
| 413 |
|
| 414 |
void DirectionalAtom::updateU( void ){ |
| 415 |
|
| 416 |
if( hasCoords ){ |
| 417 |
ul[offsetX] = (Amat[Axx] * sU[2][0]) + |
| 418 |
(Amat[Ayx] * sU[2][1]) + (Amat[Azx] * sU[2][2]); |
| 419 |
ul[offsetY] = (Amat[Axy] * sU[2][0]) + |
| 420 |
(Amat[Ayy] * sU[2][1]) + (Amat[Azy] * sU[2][2]); |
| 421 |
ul[offsetZ] = (Amat[Axz] * sU[2][0]) + |
| 422 |
(Amat[Ayz] * sU[2][1]) + (Amat[Azz] * sU[2][2]); |
| 423 |
} |
| 424 |
else{ |
| 425 |
|
| 426 |
sprintf( painCave.errMsg, |
| 427 |
"Attempt to updateU for atom %d before coords set.\n", |
| 428 |
index ); |
| 429 |
painCave.isFatal = 1; |
| 430 |
simError(); |
| 431 |
} |
| 432 |
} |
| 433 |
|
| 434 |
void DirectionalAtom::getJ( double theJ[3] ){ |
| 435 |
|
| 436 |
theJ[0] = jx; |
| 437 |
theJ[1] = jy; |
| 438 |
theJ[2] = jz; |
| 439 |
} |
| 440 |
|
| 441 |
void DirectionalAtom::setJ( double theJ[3] ){ |
| 442 |
|
| 443 |
jx = theJ[0]; |
| 444 |
jy = theJ[1]; |
| 445 |
jz = theJ[2]; |
| 446 |
} |
| 447 |
|
| 448 |
void DirectionalAtom::getTrq( double theT[3] ){ |
| 449 |
|
| 450 |
if( hasCoords ){ |
| 451 |
theT[0] = trq[offsetX]; |
| 452 |
theT[1] = trq[offsetY]; |
| 453 |
theT[2] = trq[offsetZ]; |
| 454 |
} |
| 455 |
else{ |
| 456 |
|
| 457 |
sprintf( painCave.errMsg, |
| 458 |
"Attempt to get Trq for atom %d before coords set.\n", |
| 459 |
index ); |
| 460 |
painCave.isFatal = 1; |
| 461 |
simError(); |
| 462 |
} |
| 463 |
} |
| 464 |
|
| 465 |
void DirectionalAtom::addTrq( double theT[3] ){ |
| 466 |
|
| 467 |
if( hasCoords ){ |
| 468 |
trq[offsetX] += theT[0]; |
| 469 |
trq[offsetY] += theT[1]; |
| 470 |
trq[offsetZ] += theT[2]; |
| 471 |
} |
| 472 |
else{ |
| 473 |
|
| 474 |
sprintf( painCave.errMsg, |
| 475 |
"Attempt to add Trq for atom %d before coords set.\n", |
| 476 |
index ); |
| 477 |
painCave.isFatal = 1; |
| 478 |
simError(); |
| 479 |
} |
| 480 |
} |
| 481 |
|
| 482 |
|
| 483 |
void DirectionalAtom::getI( double the_I[3][3] ){ |
| 484 |
|
| 485 |
the_I[0][0] = Ixx; |
| 486 |
the_I[0][1] = Ixy; |
| 487 |
the_I[0][2] = Ixz; |
| 488 |
|
| 489 |
the_I[1][0] = Iyx; |
| 490 |
the_I[1][1] = Iyy; |
| 491 |
the_I[1][2] = Iyz; |
| 492 |
|
| 493 |
the_I[2][0] = Izx; |
| 494 |
the_I[2][1] = Izy; |
| 495 |
the_I[2][2] = Izz; |
| 496 |
} |
| 497 |
|
| 498 |
void DirectionalAtom::getGrad( double grad[6] ) { |
| 499 |
|
| 500 |
double myEuler[3]; |
| 501 |
double phi, theta, psi; |
| 502 |
double cphi, sphi, ctheta, stheta; |
| 503 |
double ephi[3]; |
| 504 |
double etheta[3]; |
| 505 |
double epsi[3]; |
| 506 |
|
| 507 |
this->getEulerAngles(myEuler); |
| 508 |
|
| 509 |
phi = myEuler[0]; |
| 510 |
theta = myEuler[1]; |
| 511 |
psi = myEuler[2]; |
| 512 |
|
| 513 |
cphi = cos(phi); |
| 514 |
sphi = sin(phi); |
| 515 |
ctheta = cos(theta); |
| 516 |
stheta = sin(theta); |
| 517 |
|
| 518 |
// get unit vectors along the phi, theta and psi rotation axes |
| 519 |
|
| 520 |
ephi[0] = 0.0; |
| 521 |
ephi[1] = 0.0; |
| 522 |
ephi[2] = 1.0; |
| 523 |
|
| 524 |
etheta[0] = cphi; |
| 525 |
etheta[1] = sphi; |
| 526 |
etheta[2] = 0.0; |
| 527 |
|
| 528 |
epsi[0] = stheta * cphi; |
| 529 |
epsi[1] = stheta * sphi; |
| 530 |
epsi[2] = ctheta; |
| 531 |
|
| 532 |
for (int j = 0 ; j<3; j++) |
| 533 |
grad[j] = frc[j]; |
| 534 |
|
| 535 |
grad[3] = 0; |
| 536 |
grad[4] = 0; |
| 537 |
grad[5] = 0; |
| 538 |
|
| 539 |
for (int j = 0; j < 3; j++ ) { |
| 540 |
|
| 541 |
grad[3] += trq[j]*ephi[j]; |
| 542 |
grad[4] += trq[j]*etheta[j]; |
| 543 |
grad[5] += trq[j]*epsi[j]; |
| 544 |
|
| 545 |
} |
| 546 |
|
| 547 |
} |
| 548 |
|
| 549 |
/** |
| 550 |
* getEulerAngles computes a set of Euler angle values consistent |
| 551 |
* with an input rotation matrix. They are returned in the following |
| 552 |
* order: |
| 553 |
* myEuler[0] = phi; |
| 554 |
* myEuler[1] = theta; |
| 555 |
* myEuler[2] = psi; |
| 556 |
*/ |
| 557 |
void DirectionalAtom::getEulerAngles(double myEuler[3]) { |
| 558 |
|
| 559 |
// We use so-called "x-convention", which is the most common definition. |
| 560 |
// In this convention, the rotation given by Euler angles (phi, theta, psi), where the first |
| 561 |
// rotation is by an angle phi about the z-axis, the second is by an angle |
| 562 |
// theta (0 <= theta <= 180)about the x-axis, and thethird is by an angle psi about the |
| 563 |
//z-axis (again). |
| 564 |
|
| 565 |
|
| 566 |
double phi,theta,psi,eps; |
| 567 |
double ctheta,stheta; |
| 568 |
|
| 569 |
// set the tolerance for Euler angles and rotation elements |
| 570 |
|
| 571 |
eps = 1.0e-8; |
| 572 |
|
| 573 |
theta = acos(min(1.0,max(-1.0,Amat[Azz]))); |
| 574 |
ctheta = Amat[Azz]; |
| 575 |
stheta = sqrt(1.0 - ctheta * ctheta); |
| 576 |
|
| 577 |
// when sin(theta) is close to 0, we need to consider singularity |
| 578 |
// In this case, we can assign an arbitary value to phi (or psi), and then determine |
| 579 |
// the psi (or phi) or vice-versa. We'll assume that phi always gets the rotation, and psi is 0 |
| 580 |
// in cases of singularity. |
| 581 |
// we use atan2 instead of atan, since atan2 will give us -Pi to Pi. |
| 582 |
// Since 0 <= theta <= 180, sin(theta) will be always non-negative. Therefore, it never |
| 583 |
// change the sign of both of the parameters passed to atan2. |
| 584 |
|
| 585 |
if (fabs(stheta) <= eps){ |
| 586 |
psi = 0.0; |
| 587 |
phi = atan2(-Amat[Ayx], Amat[Axx]); |
| 588 |
} |
| 589 |
// we only have one unique solution |
| 590 |
else{ |
| 591 |
phi = atan2(Amat[Azx], -Amat[Azy]); |
| 592 |
psi = atan2(Amat[Axz], Amat[Ayz]); |
| 593 |
} |
| 594 |
|
| 595 |
//wrap phi and psi, make sure they are in the range from 0 to 2*Pi |
| 596 |
//if (phi < 0) |
| 597 |
// phi += M_PI; |
| 598 |
|
| 599 |
//if (psi < 0) |
| 600 |
// psi += M_PI; |
| 601 |
|
| 602 |
myEuler[0] = phi; |
| 603 |
myEuler[1] = theta; |
| 604 |
myEuler[2] = psi; |
| 605 |
|
| 606 |
return; |
| 607 |
} |
| 608 |
|
| 609 |
double DirectionalAtom::getZangle( ){ |
| 610 |
|
| 611 |
if( hasCoords ){ |
| 612 |
return zAngle; |
| 613 |
} |
| 614 |
else{ |
| 615 |
|
| 616 |
sprintf( painCave.errMsg, |
| 617 |
"Attempt to get zAngle for atom %d before coords set.\n", |
| 618 |
index ); |
| 619 |
painCave.isFatal = 1; |
| 620 |
simError(); |
| 621 |
return 0; |
| 622 |
} |
| 623 |
} |
| 624 |
|
| 625 |
void DirectionalAtom::setZangle( double zAng ){ |
| 626 |
|
| 627 |
if( hasCoords ){ |
| 628 |
zAngle = zAng; |
| 629 |
} |
| 630 |
else{ |
| 631 |
|
| 632 |
sprintf( painCave.errMsg, |
| 633 |
"Attempt to set zAngle for atom %d before coords set.\n", |
| 634 |
index ); |
| 635 |
painCave.isFatal = 1; |
| 636 |
simError(); |
| 637 |
} |
| 638 |
} |
| 639 |
|
| 640 |
void DirectionalAtom::addZangle( double zAng ){ |
| 641 |
|
| 642 |
if( hasCoords ){ |
| 643 |
zAngle += zAng; |
| 644 |
} |
| 645 |
else{ |
| 646 |
|
| 647 |
sprintf( painCave.errMsg, |
| 648 |
"Attempt to add zAngle to atom %d before coords set.\n", |
| 649 |
index ); |
| 650 |
painCave.isFatal = 1; |
| 651 |
simError(); |
| 652 |
} |
| 653 |
} |
| 654 |
|
| 655 |
double DirectionalAtom::max(double x, double y) { |
| 656 |
return (x > y) ? x : y; |
| 657 |
} |
| 658 |
|
| 659 |
double DirectionalAtom::min(double x, double y) { |
| 660 |
return (x > y) ? y : x; |
| 661 |
} |
