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root/group/trunk/OOPSE/libmdtools/DirectionalAtom.cpp
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Comparing trunk/OOPSE/libmdtools/DirectionalAtom.cpp (file contents):
Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 1046 by tim, Tue Feb 10 21:33:44 2004 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2  
3   #include "Atom.hpp"
4 + #include "simError.h"
5  
6  
7  
8 + 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 +
28 + void DirectionalAtom::setCoords(void){
29 +
30 +  if( myConfig->isAllocated() ){
31 +
32 +    myConfig->getAtomPointers( index,
33 +                     &pos,
34 +                     &vel,
35 +                     &frc,
36 +                     &trq,
37 +                     &Amat,
38 +                     &mu,  
39 +                     &ul );
40 +  }
41 +  else{
42 +    sprintf( painCave.errMsg,
43 +             "Attempted to set Atom %d  coordinates with an unallocated "
44 +             "SimState object.\n", index );
45 +    painCave.isFatal = 1;
46 +    simError();
47 +  }
48 +
49 +  hasCoords = true;
50 +
51 +  *mu = myMu;
52 +
53 + }
54 +
55 + double DirectionalAtom::getMu( void ) {
56 +
57 +  if( hasCoords ){
58 +    return *mu;
59 +  }
60 +  else{
61 +    return myMu;
62 +  }
63 + }
64 +
65 + void DirectionalAtom::setMu( double the_mu ) {
66 +
67 +  if( hasCoords ){
68 +    *mu = the_mu;
69 +    myMu = the_mu;
70 +  }
71 +  else{
72 +    myMu = the_mu;
73 +  }
74 + }
75 +
76   void DirectionalAtom::setA( double the_A[3][3] ){
8 –  
9 –  Amat[Axx] = the_A[0][0]; Amat[Axy] = the_A[0][1]; Amat[Axz] = the_A[0][2];
10 –  Amat[Ayx] = the_A[1][0]; Amat[Ayy] = the_A[1][1]; Amat[Ayz] = the_A[1][2];
11 –  Amat[Azx] = the_A[2][0]; Amat[Azy] = the_A[2][1]; Amat[Azz] = the_A[2][2];
77  
78 <  this->updateU();  
78 >  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   }
94  
95   void DirectionalAtom::setI( double the_I[3][3] ){
# Line 24 | Line 103 | void DirectionalAtom::setQ( double the_q[4] ){
103  
104    double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
105  
106 <  q0Sqr = the_q[0] * the_q[0];
107 <  q1Sqr = the_q[1] * the_q[1];
108 <  q2Sqr = the_q[2] * the_q[2];
109 <  q3Sqr = the_q[3] * the_q[3];
110 <  
106 >  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  
33 –  Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr;
34 –  Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] );
35 –  Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] );
36 –  
37 –  Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] );
38 –  Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr;
39 –  Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] );
40 –
41 –  Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] );
42 –  Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] );
43 –  Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr;
44 –
45 –  this->updateU();
136   }
137  
138   void DirectionalAtom::getA( double the_A[3][3] ){
139    
140 <  the_A[0][0] = Amat[Axx];
141 <  the_A[0][1] = Amat[Axy];
142 <  the_A[0][2] = Amat[Axz];
140 >  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  
162 <  the_A[1][0] = Amat[Ayx];
55 <  the_A[1][1] = Amat[Ayy];
56 <  the_A[1][2] = Amat[Ayz];
162 > }
163  
164 <  the_A[2][0] = Amat[Azx];
165 <  the_A[2][1] = Amat[Azy];
166 <  the_A[2][2] = Amat[Azz];
164 > void DirectionalAtom::printAmatIndex( void ){
165 >
166 >  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   }
181  
182  
# Line 75 | Line 194 | void DirectionalAtom::getQ( double q[4] ){
194    double t, s;
195    double ad1, ad2, ad3;
196  
197 <  t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0;
79 <  if( t > 0.0 ){
197 >  if( hasCoords ){
198      
199 <    s = 0.5 / sqrt( t );
200 <    q[0] = 0.25 / s;
83 <    q[1] = (Amat[Ayz] - Amat[Azy]) * s;
84 <    q[2] = (Amat[Azx] - Amat[Axz]) * s;
85 <    q[3] = (Amat[Axy] - Amat[Ayx]) * s;
86 <  }
87 <  else{
88 <    
89 <    ad1 = fabs( Amat[Axx] );
90 <    ad2 = fabs( Amat[Ayy] );
91 <    ad3 = fabs( Amat[Azz] );
92 <
93 <    if( ad1 >= ad2 && ad1 >= ad3 ){
199 >    t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0;
200 >    if( t > 0.0 ){
201        
202 <      s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] );
203 <      q[0] = (Amat[Ayz] + Amat[Azy]) / s;
204 <      q[1] = 0.5 / s;
205 <      q[2] = (Amat[Axy] + Amat[Ayx]) / s;
206 <      q[3] = (Amat[Axz] + Amat[Azx]) / s;
202 >      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      }
101 –    else if( ad2 >= ad1 && ad2 >= ad3 ){
102 –
103 –      s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0;
104 –      q[0] = (Amat[Axz] + Amat[Azx]) / s;
105 –      q[1] = (Amat[Axy] + Amat[Ayx]) / s;
106 –      q[2] = 0.5 / s;
107 –      q[3] = (Amat[Ayz] + Amat[Azy]) / s;
108 –    }
208      else{
209        
210 <      s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0;
211 <      q[0] = (Amat[Axy] + Amat[Ayx]) / s;
212 <      q[1] = (Amat[Axz] + Amat[Azx]) / s;
213 <      q[2] = (Amat[Ayz] + Amat[Azy]) / s;
214 <      q[3] = 0.5 / s;
210 >      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      }
239    }
240 +  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   }
249  
250  
251   void DirectionalAtom::setEuler( double phi, double theta, double psi ){
252    
253 <  Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
254 <  Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
255 <  Amat[Axz] = sin(theta) * sin(psi);
256 <  
257 <  Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
258 <  Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
259 <  Amat[Ayz] = sin(theta) * cos(psi);
260 <
261 <  Amat[Azx] = sin(phi) * sin(theta);
262 <  Amat[Azy] = -cos(phi) * sin(theta);
263 <  Amat[Azz] = cos(theta);
264 <
265 <  this->updateU();
253 >  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   }
277  
278  
# Line 140 | Line 280 | void DirectionalAtom::lab2Body( double r[3] ){
280  
281    double rl[3]; // the lab frame vector
282    
283 <  rl[0] = r[0];
284 <  rl[1] = r[1];
285 <  rl[2] = r[2];
283 >  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  
147 –  r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]);
148 –  r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]);
149 –  r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]);
301   }
302  
303   void DirectionalAtom::body2Lab( double r[3] ){
304  
305    double rb[3]; // the body frame vector
306    
307 <  rb[0] = r[0];
308 <  rb[1] = r[1];
309 <  rb[2] = r[2];
310 <
311 <  r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]);
312 <  r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]);
313 <  r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]);
307 >  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   }
325  
326   void DirectionalAtom::updateU( void ){
327  
328 <  ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz);
329 <  ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz);
330 <  ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz);
328 >  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   }
342  
343 + 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 +  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 + }
373 +
374 + void DirectionalAtom::addTrq( double theT[3] ){
375 +  
376 +  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 + }
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 +
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 +
433 +  etheta[0] = cphi;
434 +  etheta[1] = sphi;
435 +  etheta[2] = 0.0;
436 +  
437 +  epsi[0] = stheta * cphi;
438 +  epsi[1] = stheta * sphi;
439 +  epsi[2] = ctheta;
440 +  
441 +  for (int j = 0 ; j<3; j++)
442 +    grad[j] = frc[j];
443 +
444 +  grad[3] = 0;
445 +  grad[4] = 0;
446 +  grad[5] = 0;
447 +
448 +  for (int j = 0; j < 3; j++ ) {
449 +    
450 +    grad[3] += trq[j]*ephi[j];
451 +    grad[4] += trq[j]*etheta[j];
452 +    grad[5] += trq[j]*epsi[j];
453 +    
454 +  }
455 +
456 + }
457 +
458 + /**
459 +  * getEulerAngles computes a set of Euler angle values consistent
460 +  *  with an input rotation matrix.  They are returned in the following
461 +  * order:
462 +  *  myEuler[0] = phi;
463 +  *  myEuler[1] = theta;
464 +  *  myEuler[2] = psi;
465 + */
466 + void DirectionalAtom::getEulerAngles(double myEuler[3]) {
467 +
468 +  // We use so-called "x-convention", which is the most common definition.
469 +  // In this convention, the rotation given by Euler angles (phi, theta, psi), where the first
470 +  // rotation is by an angle phi about the z-axis, the second is by an angle  
471 +  // theta (0 <= theta <= 180)about the x-axis, and thethird is by an angle psi about the
472 +  //z-axis (again).
473 +  
474 +  
475 +  double phi,theta,psi,eps;
476 +  double pi;
477 +  double cphi,ctheta,cpsi;
478 +  double sphi,stheta,spsi;
479 +  double b[3];
480 +  int flip[3];
481 +
482 +  // set the tolerance for Euler angles and rotation elements
483 +  
484 +  eps = 1.0e-8;
485 +
486 +  theta = acos(min(1.0,max(-1.0,Amat[Azz])));
487 +  ctheta = Amat[Azz];
488 +  stheta = sqrt(1.0 - ctheta * ctheta);
489 +
490 +  // when sin(theta) is close to 0, we need to consider singularity
491 +  // In this case, we can assign an arbitary value to phi (or psi), and then determine
492 +  // the psi (or phi) or vice-versa. We'll assume that phi always gets the rotation, and psi is 0
493 +  // in cases of singularity.  
494 +  // we use atan2 instead of atan, since atan2 will give us -Pi to Pi.
495 +  // Since 0 <= theta <= 180, sin(theta) will be always non-negative. Therefore, it never
496 +  // change the sign of both of the parameters passed to atan2.
497 +  
498 +  if (fabs(stheta) <= eps){
499 +    psi = 0.0;
500 +    phi = atan2(-Amat[Ayx], Amat[Axx]);  
501 +  }
502 +  // we only have one unique solution
503 +  else{    
504 +      phi = atan2(Amat[Azx], -Amat[Azy]);
505 +      psi = atan2(Amat[Axz], Amat[Ayz]);
506 +  }
507 +
508 +  //wrap phi and psi, make sure they are in the range from 0 to 2*Pi
509 +  //if (phi < 0)
510 +  //  phi += M_PI;
511 +
512 +  //if (psi < 0)
513 +  //  psi += M_PI;
514 +
515 +  myEuler[0] = phi;
516 +  myEuler[1] = theta;
517 +  myEuler[2] = psi;
518 +  
519 +  return;
520 + }
521 +
522 + double DirectionalAtom::max(double x, double  y) {  
523 +  return (x > y) ? x : y;
524 + }
525 +
526 + double DirectionalAtom::min(double x, double  y) {  
527 +  return (x > y) ? y : x;
528 + }

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