1 |
gezelter |
829 |
#include <math.h> |
2 |
mmeineke |
377 |
|
3 |
|
|
#include "Atom.hpp" |
4 |
mmeineke |
670 |
#include "simError.h" |
5 |
mmeineke |
377 |
|
6 |
gezelter |
878 |
|
7 |
|
|
|
8 |
mmeineke |
670 |
void DirectionalAtom::zeroForces() { |
9 |
|
|
if( hasCoords ){ |
10 |
|
|
frc[offsetX] = 0.0; |
11 |
|
|
frc[offsetY] = 0.0; |
12 |
|
|
frc[offsetZ] = 0.0; |
13 |
|
|
|
14 |
|
|
trq[offsetX] = 0.0; |
15 |
|
|
trq[offsetY] = 0.0; |
16 |
|
|
trq[offsetZ] = 0.0; |
17 |
|
|
} |
18 |
|
|
else{ |
19 |
|
|
|
20 |
|
|
sprintf( painCave.errMsg, |
21 |
|
|
"Attempt to zero frc and trq for atom %d before coords set.\n", |
22 |
|
|
index ); |
23 |
|
|
painCave.isFatal = 1; |
24 |
|
|
simError(); |
25 |
|
|
} |
26 |
|
|
} |
27 |
mmeineke |
377 |
|
28 |
tim |
689 |
void DirectionalAtom::setCoords(void){ |
29 |
mmeineke |
414 |
|
30 |
tim |
689 |
if( myConfig->isAllocated() ){ |
31 |
|
|
|
32 |
|
|
myConfig->getAtomPointers( index, |
33 |
|
|
&pos, |
34 |
|
|
&vel, |
35 |
|
|
&frc, |
36 |
|
|
&trq, |
37 |
|
|
&Amat, |
38 |
|
|
&mu, |
39 |
|
|
&ul ); |
40 |
mmeineke |
670 |
} |
41 |
|
|
else{ |
42 |
|
|
sprintf( painCave.errMsg, |
43 |
tim |
689 |
"Attempted to set Atom %d coordinates with an unallocated " |
44 |
mmeineke |
787 |
"SimState object.\n", index ); |
45 |
mmeineke |
670 |
painCave.isFatal = 1; |
46 |
|
|
simError(); |
47 |
|
|
} |
48 |
tim |
689 |
|
49 |
|
|
hasCoords = true; |
50 |
|
|
|
51 |
mmeineke |
690 |
*mu = myMu; |
52 |
tim |
689 |
|
53 |
|
|
} |
54 |
|
|
|
55 |
|
|
double DirectionalAtom::getMu( void ) { |
56 |
|
|
|
57 |
|
|
if( hasCoords ){ |
58 |
mmeineke |
690 |
return *mu; |
59 |
tim |
689 |
} |
60 |
|
|
else{ |
61 |
|
|
return myMu; |
62 |
|
|
} |
63 |
mmeineke |
670 |
} |
64 |
|
|
|
65 |
|
|
void DirectionalAtom::setMu( double the_mu ) { |
66 |
|
|
|
67 |
|
|
if( hasCoords ){ |
68 |
mmeineke |
690 |
*mu = the_mu; |
69 |
tim |
689 |
myMu = the_mu; |
70 |
mmeineke |
670 |
} |
71 |
|
|
else{ |
72 |
tim |
689 |
myMu = the_mu; |
73 |
mmeineke |
670 |
} |
74 |
|
|
} |
75 |
|
|
|
76 |
mmeineke |
377 |
void DirectionalAtom::setA( double the_A[3][3] ){ |
77 |
|
|
|
78 |
mmeineke |
670 |
if( hasCoords ){ |
79 |
|
|
Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2]; |
80 |
|
|
Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2]; |
81 |
|
|
Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2]; |
82 |
|
|
|
83 |
|
|
this->updateU(); |
84 |
|
|
} |
85 |
|
|
else{ |
86 |
|
|
|
87 |
|
|
sprintf( painCave.errMsg, |
88 |
|
|
"Attempt to set Amat for atom %d before coords set.\n", |
89 |
|
|
index ); |
90 |
|
|
painCave.isFatal = 1; |
91 |
|
|
simError(); |
92 |
|
|
} |
93 |
mmeineke |
377 |
} |
94 |
|
|
|
95 |
|
|
void DirectionalAtom::setI( double the_I[3][3] ){ |
96 |
|
|
|
97 |
|
|
Ixx = the_I[0][0]; Ixy = the_I[0][1]; Ixz = the_I[0][2]; |
98 |
|
|
Iyx = the_I[1][0]; Iyy = the_I[1][1]; Iyz = the_I[1][2]; |
99 |
|
|
Izx = the_I[2][0]; Izy = the_I[2][1]; Izz = the_I[2][2]; |
100 |
|
|
} |
101 |
|
|
|
102 |
|
|
void DirectionalAtom::setQ( double the_q[4] ){ |
103 |
|
|
|
104 |
|
|
double q0Sqr, q1Sqr, q2Sqr, q3Sqr; |
105 |
|
|
|
106 |
mmeineke |
670 |
if( hasCoords ){ |
107 |
|
|
q0Sqr = the_q[0] * the_q[0]; |
108 |
|
|
q1Sqr = the_q[1] * the_q[1]; |
109 |
|
|
q2Sqr = the_q[2] * the_q[2]; |
110 |
|
|
q3Sqr = the_q[3] * the_q[3]; |
111 |
|
|
|
112 |
|
|
|
113 |
|
|
Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr; |
114 |
|
|
Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] ); |
115 |
|
|
Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] ); |
116 |
|
|
|
117 |
|
|
Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] ); |
118 |
|
|
Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr; |
119 |
|
|
Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] ); |
120 |
|
|
|
121 |
|
|
Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] ); |
122 |
|
|
Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] ); |
123 |
|
|
Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr; |
124 |
|
|
|
125 |
|
|
this->updateU(); |
126 |
|
|
} |
127 |
|
|
else{ |
128 |
|
|
|
129 |
|
|
sprintf( painCave.errMsg, |
130 |
|
|
"Attempt to set Q for atom %d before coords set.\n", |
131 |
|
|
index ); |
132 |
|
|
painCave.isFatal = 1; |
133 |
|
|
simError(); |
134 |
|
|
} |
135 |
mmeineke |
377 |
|
136 |
|
|
} |
137 |
|
|
|
138 |
|
|
void DirectionalAtom::getA( double the_A[3][3] ){ |
139 |
|
|
|
140 |
mmeineke |
670 |
if( hasCoords ){ |
141 |
|
|
the_A[0][0] = Amat[Axx]; |
142 |
|
|
the_A[0][1] = Amat[Axy]; |
143 |
|
|
the_A[0][2] = Amat[Axz]; |
144 |
|
|
|
145 |
|
|
the_A[1][0] = Amat[Ayx]; |
146 |
|
|
the_A[1][1] = Amat[Ayy]; |
147 |
|
|
the_A[1][2] = Amat[Ayz]; |
148 |
|
|
|
149 |
|
|
the_A[2][0] = Amat[Azx]; |
150 |
|
|
the_A[2][1] = Amat[Azy]; |
151 |
|
|
the_A[2][2] = Amat[Azz]; |
152 |
|
|
} |
153 |
|
|
else{ |
154 |
|
|
|
155 |
|
|
sprintf( painCave.errMsg, |
156 |
|
|
"Attempt to get Amat for atom %d before coords set.\n", |
157 |
|
|
index ); |
158 |
|
|
painCave.isFatal = 1; |
159 |
|
|
simError(); |
160 |
|
|
} |
161 |
mmeineke |
377 |
|
162 |
|
|
} |
163 |
|
|
|
164 |
mmeineke |
597 |
void DirectionalAtom::printAmatIndex( void ){ |
165 |
mmeineke |
377 |
|
166 |
mmeineke |
670 |
if( hasCoords ){ |
167 |
|
|
std::cerr << "Atom[" << index << "] index =>\n" |
168 |
|
|
<< "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n" |
169 |
|
|
<< "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n" |
170 |
|
|
<< "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n"; |
171 |
|
|
} |
172 |
|
|
else{ |
173 |
|
|
|
174 |
|
|
sprintf( painCave.errMsg, |
175 |
|
|
"Attempt to print Amat indices for atom %d before coords set.\n", |
176 |
|
|
index ); |
177 |
|
|
painCave.isFatal = 1; |
178 |
|
|
simError(); |
179 |
|
|
} |
180 |
mmeineke |
597 |
} |
181 |
|
|
|
182 |
|
|
|
183 |
mmeineke |
377 |
void DirectionalAtom::getU( double the_u[3] ){ |
184 |
|
|
|
185 |
|
|
the_u[0] = sux; |
186 |
|
|
the_u[1] = suy; |
187 |
|
|
the_u[2] = suz; |
188 |
|
|
|
189 |
|
|
this->body2Lab( the_u ); |
190 |
|
|
} |
191 |
|
|
|
192 |
|
|
void DirectionalAtom::getQ( double q[4] ){ |
193 |
|
|
|
194 |
|
|
double t, s; |
195 |
|
|
double ad1, ad2, ad3; |
196 |
|
|
|
197 |
mmeineke |
670 |
if( hasCoords ){ |
198 |
mmeineke |
377 |
|
199 |
mmeineke |
670 |
t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0; |
200 |
|
|
if( t > 0.0 ){ |
201 |
mmeineke |
377 |
|
202 |
mmeineke |
670 |
s = 0.5 / sqrt( t ); |
203 |
|
|
q[0] = 0.25 / s; |
204 |
|
|
q[1] = (Amat[Ayz] - Amat[Azy]) * s; |
205 |
|
|
q[2] = (Amat[Azx] - Amat[Axz]) * s; |
206 |
|
|
q[3] = (Amat[Axy] - Amat[Ayx]) * s; |
207 |
mmeineke |
377 |
} |
208 |
|
|
else{ |
209 |
|
|
|
210 |
mmeineke |
670 |
ad1 = fabs( Amat[Axx] ); |
211 |
|
|
ad2 = fabs( Amat[Ayy] ); |
212 |
|
|
ad3 = fabs( Amat[Azz] ); |
213 |
|
|
|
214 |
|
|
if( ad1 >= ad2 && ad1 >= ad3 ){ |
215 |
|
|
|
216 |
|
|
s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] ); |
217 |
|
|
q[0] = (Amat[Ayz] + Amat[Azy]) / s; |
218 |
|
|
q[1] = 0.5 / s; |
219 |
|
|
q[2] = (Amat[Axy] + Amat[Ayx]) / s; |
220 |
|
|
q[3] = (Amat[Axz] + Amat[Azx]) / s; |
221 |
|
|
} |
222 |
|
|
else if( ad2 >= ad1 && ad2 >= ad3 ){ |
223 |
|
|
|
224 |
|
|
s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0; |
225 |
|
|
q[0] = (Amat[Axz] + Amat[Azx]) / s; |
226 |
|
|
q[1] = (Amat[Axy] + Amat[Ayx]) / s; |
227 |
|
|
q[2] = 0.5 / s; |
228 |
|
|
q[3] = (Amat[Ayz] + Amat[Azy]) / s; |
229 |
|
|
} |
230 |
|
|
else{ |
231 |
|
|
|
232 |
|
|
s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0; |
233 |
|
|
q[0] = (Amat[Axy] + Amat[Ayx]) / s; |
234 |
|
|
q[1] = (Amat[Axz] + Amat[Azx]) / s; |
235 |
|
|
q[2] = (Amat[Ayz] + Amat[Azy]) / s; |
236 |
|
|
q[3] = 0.5 / s; |
237 |
|
|
} |
238 |
mmeineke |
377 |
} |
239 |
|
|
} |
240 |
mmeineke |
670 |
else{ |
241 |
|
|
|
242 |
|
|
sprintf( painCave.errMsg, |
243 |
|
|
"Attempt to get Q for atom %d before coords set.\n", |
244 |
|
|
index ); |
245 |
|
|
painCave.isFatal = 1; |
246 |
|
|
simError(); |
247 |
|
|
} |
248 |
mmeineke |
377 |
} |
249 |
|
|
|
250 |
|
|
|
251 |
|
|
void DirectionalAtom::setEuler( double phi, double theta, double psi ){ |
252 |
|
|
|
253 |
mmeineke |
670 |
if( hasCoords ){ |
254 |
|
|
Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi)); |
255 |
|
|
Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi)); |
256 |
|
|
Amat[Axz] = sin(theta) * sin(psi); |
257 |
|
|
|
258 |
|
|
Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi)); |
259 |
|
|
Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi)); |
260 |
|
|
Amat[Ayz] = sin(theta) * cos(psi); |
261 |
|
|
|
262 |
|
|
Amat[Azx] = sin(phi) * sin(theta); |
263 |
|
|
Amat[Azy] = -cos(phi) * sin(theta); |
264 |
|
|
Amat[Azz] = cos(theta); |
265 |
|
|
|
266 |
|
|
this->updateU(); |
267 |
|
|
} |
268 |
|
|
else{ |
269 |
|
|
|
270 |
|
|
sprintf( painCave.errMsg, |
271 |
|
|
"Attempt to set Euler angles for atom %d before coords set.\n", |
272 |
|
|
index ); |
273 |
|
|
painCave.isFatal = 1; |
274 |
|
|
simError(); |
275 |
|
|
} |
276 |
mmeineke |
377 |
} |
277 |
|
|
|
278 |
|
|
|
279 |
|
|
void DirectionalAtom::lab2Body( double r[3] ){ |
280 |
|
|
|
281 |
|
|
double rl[3]; // the lab frame vector |
282 |
|
|
|
283 |
mmeineke |
670 |
if( hasCoords ){ |
284 |
|
|
rl[0] = r[0]; |
285 |
|
|
rl[1] = r[1]; |
286 |
|
|
rl[2] = r[2]; |
287 |
|
|
|
288 |
|
|
r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]); |
289 |
|
|
r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]); |
290 |
|
|
r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]); |
291 |
|
|
} |
292 |
|
|
else{ |
293 |
|
|
|
294 |
|
|
sprintf( painCave.errMsg, |
295 |
|
|
"Attempt to convert lab2body for atom %d before coords set.\n", |
296 |
|
|
index ); |
297 |
|
|
painCave.isFatal = 1; |
298 |
|
|
simError(); |
299 |
|
|
} |
300 |
mmeineke |
377 |
|
301 |
|
|
} |
302 |
|
|
|
303 |
|
|
void DirectionalAtom::body2Lab( double r[3] ){ |
304 |
|
|
|
305 |
|
|
double rb[3]; // the body frame vector |
306 |
|
|
|
307 |
mmeineke |
670 |
if( hasCoords ){ |
308 |
|
|
rb[0] = r[0]; |
309 |
|
|
rb[1] = r[1]; |
310 |
|
|
rb[2] = r[2]; |
311 |
|
|
|
312 |
|
|
r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]); |
313 |
|
|
r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]); |
314 |
|
|
r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]); |
315 |
|
|
} |
316 |
|
|
else{ |
317 |
|
|
|
318 |
|
|
sprintf( painCave.errMsg, |
319 |
|
|
"Attempt to convert body2lab for atom %d before coords set.\n", |
320 |
|
|
index ); |
321 |
|
|
painCave.isFatal = 1; |
322 |
|
|
simError(); |
323 |
|
|
} |
324 |
mmeineke |
377 |
} |
325 |
|
|
|
326 |
|
|
void DirectionalAtom::updateU( void ){ |
327 |
|
|
|
328 |
mmeineke |
670 |
if( hasCoords ){ |
329 |
|
|
ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz); |
330 |
|
|
ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz); |
331 |
|
|
ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz); |
332 |
|
|
} |
333 |
|
|
else{ |
334 |
|
|
|
335 |
|
|
sprintf( painCave.errMsg, |
336 |
|
|
"Attempt to updateU for atom %d before coords set.\n", |
337 |
|
|
index ); |
338 |
|
|
painCave.isFatal = 1; |
339 |
|
|
simError(); |
340 |
|
|
} |
341 |
mmeineke |
377 |
} |
342 |
|
|
|
343 |
mmeineke |
599 |
void DirectionalAtom::getJ( double theJ[3] ){ |
344 |
|
|
|
345 |
|
|
theJ[0] = jx; |
346 |
|
|
theJ[1] = jy; |
347 |
|
|
theJ[2] = jz; |
348 |
|
|
} |
349 |
|
|
|
350 |
|
|
void DirectionalAtom::setJ( double theJ[3] ){ |
351 |
|
|
|
352 |
|
|
jx = theJ[0]; |
353 |
|
|
jy = theJ[1]; |
354 |
|
|
jz = theJ[2]; |
355 |
|
|
} |
356 |
|
|
|
357 |
|
|
void DirectionalAtom::getTrq( double theT[3] ){ |
358 |
|
|
|
359 |
mmeineke |
670 |
if( hasCoords ){ |
360 |
|
|
theT[0] = trq[offsetX]; |
361 |
|
|
theT[1] = trq[offsetY]; |
362 |
|
|
theT[2] = trq[offsetZ]; |
363 |
|
|
} |
364 |
|
|
else{ |
365 |
|
|
|
366 |
|
|
sprintf( painCave.errMsg, |
367 |
|
|
"Attempt to get Trq for atom %d before coords set.\n", |
368 |
|
|
index ); |
369 |
|
|
painCave.isFatal = 1; |
370 |
|
|
simError(); |
371 |
|
|
} |
372 |
mmeineke |
599 |
} |
373 |
|
|
|
374 |
|
|
void DirectionalAtom::addTrq( double theT[3] ){ |
375 |
|
|
|
376 |
mmeineke |
670 |
if( hasCoords ){ |
377 |
|
|
trq[offsetX] += theT[0]; |
378 |
|
|
trq[offsetY] += theT[1]; |
379 |
|
|
trq[offsetZ] += theT[2]; |
380 |
|
|
} |
381 |
|
|
else{ |
382 |
|
|
|
383 |
|
|
sprintf( painCave.errMsg, |
384 |
|
|
"Attempt to add Trq for atom %d before coords set.\n", |
385 |
|
|
index ); |
386 |
|
|
painCave.isFatal = 1; |
387 |
|
|
simError(); |
388 |
|
|
} |
389 |
mmeineke |
599 |
} |
390 |
|
|
|
391 |
|
|
|
392 |
|
|
void DirectionalAtom::getI( double the_I[3][3] ){ |
393 |
|
|
|
394 |
|
|
the_I[0][0] = Ixx; |
395 |
|
|
the_I[0][1] = Ixy; |
396 |
|
|
the_I[0][2] = Ixz; |
397 |
|
|
|
398 |
|
|
the_I[1][0] = Iyx; |
399 |
|
|
the_I[1][1] = Iyy; |
400 |
|
|
the_I[1][2] = Iyz; |
401 |
|
|
|
402 |
|
|
the_I[2][0] = Izx; |
403 |
|
|
the_I[2][1] = Izy; |
404 |
|
|
the_I[2][2] = Izz; |
405 |
|
|
} |
406 |
gezelter |
878 |
|
407 |
|
|
void DirectionalAtom::getGrad( double grad[6] ) { |
408 |
|
|
|
409 |
|
|
double myEuler[3]; |
410 |
|
|
double phi, theta, psi; |
411 |
|
|
double cphi, sphi, ctheta, stheta; |
412 |
|
|
double ephi[3]; |
413 |
|
|
double etheta[3]; |
414 |
|
|
double epsi[3]; |
415 |
|
|
|
416 |
|
|
this->getEulerAngles(myEuler); |
417 |
|
|
|
418 |
|
|
phi = myEuler[0]; |
419 |
|
|
theta = myEuler[1]; |
420 |
|
|
psi = myEuler[2]; |
421 |
|
|
|
422 |
|
|
cphi = cos(phi); |
423 |
|
|
sphi = sin(phi); |
424 |
|
|
ctheta = cos(theta); |
425 |
|
|
stheta = sin(theta); |
426 |
|
|
|
427 |
|
|
// get unit vectors along the phi, theta and psi rotation axes |
428 |
|
|
|
429 |
|
|
ephi[0] = 0.0; |
430 |
|
|
ephi[1] = 0.0; |
431 |
|
|
ephi[2] = 1.0; |
432 |
|
|
etheta[0] = -sphi; |
433 |
|
|
etheta[1] = cphi; |
434 |
|
|
etheta[2] = 0.0; |
435 |
|
|
epsi[0] = ctheta * cphi; |
436 |
|
|
epsi[1] = ctheta * sphi; |
437 |
|
|
epsi[2] = -stheta; |
438 |
|
|
|
439 |
|
|
for (int j = 0 ; j<3; j++) |
440 |
|
|
grad[j] = frc[j]; |
441 |
|
|
|
442 |
|
|
for (int j = 0; j < 3; j++ ) { |
443 |
|
|
|
444 |
|
|
grad[3] += trq[j]*ephi[j]; |
445 |
|
|
grad[4] += trq[j]*etheta[j]; |
446 |
|
|
grad[5] += trq[j]*epsi[j]; |
447 |
|
|
|
448 |
|
|
} |
449 |
|
|
|
450 |
|
|
} |
451 |
|
|
|
452 |
|
|
|
453 |
|
|
void DirectionalAtom::getEulerAngles(double myEuler[3]) { |
454 |
|
|
|
455 |
|
|
// getEulerAngles computes a set of Euler angle values consistent |
456 |
|
|
// with an input rotation matrix. They are returned in the following |
457 |
|
|
// order: |
458 |
|
|
// myEuler[0] = phi; |
459 |
|
|
// myEuler[1] = theta; |
460 |
|
|
// myEuler[2] = psi; |
461 |
|
|
|
462 |
|
|
double phi,theta,psi,eps; |
463 |
|
|
double pi; |
464 |
|
|
double cphi,ctheta,cpsi; |
465 |
|
|
double sphi,stheta,spsi; |
466 |
|
|
double b[3]; |
467 |
|
|
int flip[3]; |
468 |
|
|
|
469 |
|
|
// set the tolerance for Euler angles and rotation elements |
470 |
|
|
|
471 |
|
|
eps = 1.0e-8; |
472 |
|
|
|
473 |
|
|
// get a trial value of theta from a single rotation element |
474 |
|
|
|
475 |
|
|
theta = asin(min(1.0,max(-1.0,-Amat[Axz]))); |
476 |
|
|
ctheta = cos(theta); |
477 |
|
|
stheta = -Amat[Axz]; |
478 |
|
|
|
479 |
|
|
// set the phi/psi difference when theta is either 90 or -90 |
480 |
|
|
|
481 |
|
|
if (fabs(ctheta) <= eps) { |
482 |
|
|
phi = 0.0; |
483 |
|
|
if (fabs(Amat[Azx]) < eps) { |
484 |
|
|
psi = asin(min(1.0,max(-1.0,-Amat[Ayx]/Amat[Axz]))); |
485 |
|
|
} else { |
486 |
|
|
if (fabs(Amat[Ayx]) < eps) { |
487 |
|
|
psi = acos(min(1.0,max(-1.0,-Amat[Azx]/Amat[Axz]))); |
488 |
|
|
} else { |
489 |
|
|
psi = atan(Amat[Ayx]/Amat[Azx]); |
490 |
|
|
} |
491 |
|
|
} |
492 |
|
|
} |
493 |
|
|
|
494 |
|
|
// set the phi and psi values for all other theta values |
495 |
|
|
|
496 |
|
|
else { |
497 |
|
|
if (fabs(Amat[Axx]) < eps) { |
498 |
|
|
phi = asin(min(1.0,max(-1.0,Amat[Axy]/ctheta))); |
499 |
|
|
} else { |
500 |
|
|
if (fabs(Amat[Axy]) < eps) { |
501 |
|
|
phi = acos(min(1.0,max(-1.0,Amat[Axx]/ctheta))); |
502 |
|
|
} else { |
503 |
|
|
phi = atan(Amat[Axy]/Amat[Axx]); |
504 |
|
|
} |
505 |
|
|
} |
506 |
|
|
if (fabs(Amat[Azz]) < eps) { |
507 |
|
|
psi = asin(min(1.0,max(-1.0,Amat[Ayz]/ctheta))); |
508 |
|
|
} else { |
509 |
|
|
if (fabs(Amat[Ayz]) < eps) { |
510 |
|
|
psi = acos(min(1.0,max(-1.0,Amat[Azz]/ctheta))); |
511 |
|
|
} |
512 |
|
|
psi = atan(Amat[Ayz]/Amat[Azz]); |
513 |
|
|
} |
514 |
|
|
} |
515 |
|
|
|
516 |
|
|
// find sine and cosine of the trial phi and psi values |
517 |
|
|
|
518 |
|
|
cphi = cos(phi); |
519 |
|
|
sphi = sin(phi); |
520 |
|
|
cpsi = cos(psi); |
521 |
|
|
spsi = sin(psi); |
522 |
|
|
|
523 |
|
|
// reconstruct the diagonal of the rotation matrix |
524 |
|
|
|
525 |
|
|
b[0] = ctheta * cphi; |
526 |
|
|
b[1] = spsi*stheta*sphi + cpsi*cphi; |
527 |
|
|
b[2] = ctheta * cpsi; |
528 |
|
|
|
529 |
|
|
// compare the correct matrix diagonal to rebuilt diagonal |
530 |
|
|
|
531 |
|
|
for (int i = 0; i < 3; i++) { |
532 |
|
|
flip[i] = 0; |
533 |
|
|
if (fabs(Amat[3*i + i] - b[i]) > eps) flip[i] = 1; |
534 |
|
|
} |
535 |
|
|
|
536 |
|
|
// alter Euler angles to get correct rotation matrix values |
537 |
|
|
|
538 |
|
|
if (flip[0] && flip[1]) phi = phi - copysign(M_PI,phi); |
539 |
|
|
if (flip[0] && flip[2]) theta = -theta + copysign(M_PI, theta); |
540 |
|
|
if (flip[1] && flip[2]) psi = psi - copysign(M_PI, psi); |
541 |
|
|
|
542 |
|
|
myEuler[0] = phi; |
543 |
|
|
myEuler[1] = theta; |
544 |
|
|
myEuler[2] = psi; |
545 |
|
|
|
546 |
|
|
return; |
547 |
|
|
} |
548 |
|
|
|
549 |
|
|
double DirectionalAtom::max(double x, double y) { |
550 |
|
|
return (x > y) ? x : y; |
551 |
|
|
} |
552 |
|
|
|
553 |
|
|
double DirectionalAtom::min(double x, double y) { |
554 |
|
|
return (x > y) ? y : x; |
555 |
|
|
} |