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 |
} |