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root/group/trunk/OOPSE/libmdtools/DirectionalAtom.cpp
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Comparing trunk/OOPSE/libmdtools/DirectionalAtom.cpp (file contents):
Revision 599 by mmeineke, Mon Jul 14 21:48:43 2003 UTC vs.
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

# Line 1 | Line 1
1 < #include <cmath>
1 > #include <math.h>
2  
3   #include "Atom.hpp"
4 + #include "DirectionalAtom.hpp"
5 + #include "simError.h"
6 + #include "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] ){
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];
53  
54 <  this->updateU();  
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] ){
71 > void DirectionalAtom::setI( double the_I[3][3] ){  
72    
73    Ixx = the_I[0][0]; Ixy = the_I[0][1]; Ixz = the_I[0][2];
74    Iyx = the_I[1][0]; Iyy = the_I[1][1]; Iyz = the_I[1][2];
# Line 24 | Line 79 | void DirectionalAtom::setQ( double the_q[4] ){
79  
80    double q0Sqr, q1Sqr, q2Sqr, q3Sqr;
81  
82 <  q0Sqr = the_q[0] * the_q[0];
83 <  q1Sqr = the_q[1] * the_q[1];
84 <  q2Sqr = the_q[2] * the_q[2];
85 <  q3Sqr = the_q[3] * the_q[3];
86 <  
82 >  if( hasCoords ){
83 >    q0Sqr = the_q[0] * the_q[0];
84 >    q1Sqr = the_q[1] * the_q[1];
85 >    q2Sqr = the_q[2] * the_q[2];
86 >    q3Sqr = the_q[3] * the_q[3];
87 >    
88 >    
89 >    Amat[Axx] = q0Sqr + q1Sqr - q2Sqr - q3Sqr;
90 >    Amat[Axy] = 2.0 * ( the_q[1] * the_q[2] + the_q[0] * the_q[3] );
91 >    Amat[Axz] = 2.0 * ( the_q[1] * the_q[3] - the_q[0] * the_q[2] );
92 >    
93 >    Amat[Ayx] = 2.0 * ( the_q[1] * the_q[2] - the_q[0] * the_q[3] );
94 >    Amat[Ayy] = q0Sqr - q1Sqr + q2Sqr - q3Sqr;
95 >    Amat[Ayz] = 2.0 * ( the_q[2] * the_q[3] + the_q[0] * the_q[1] );
96 >    
97 >    Amat[Azx] = 2.0 * ( the_q[1] * the_q[3] + the_q[0] * the_q[2] );
98 >    Amat[Azy] = 2.0 * ( the_q[2] * the_q[3] - the_q[0] * the_q[1] );
99 >    Amat[Azz] = q0Sqr - q1Sqr -q2Sqr +q3Sqr;
100 >    
101 >    this->updateU();
102 >  }
103 >  else{
104 >    
105 >    sprintf( painCave.errMsg,
106 >             "Attempt to set Q for atom %d before coords set.\n",
107 >             index );
108 >    painCave.isFatal = 1;
109 >    simError();
110 >  }
111  
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();
112   }
113  
114   void DirectionalAtom::getA( double the_A[3][3] ){
115    
116 <  the_A[0][0] = Amat[Axx];
117 <  the_A[0][1] = Amat[Axy];
118 <  the_A[0][2] = Amat[Axz];
116 >  if( hasCoords ){
117 >    the_A[0][0] = Amat[Axx];
118 >    the_A[0][1] = Amat[Axy];
119 >    the_A[0][2] = Amat[Axz];
120 >    
121 >    the_A[1][0] = Amat[Ayx];
122 >    the_A[1][1] = Amat[Ayy];
123 >    the_A[1][2] = Amat[Ayz];
124 >    
125 >    the_A[2][0] = Amat[Azx];
126 >    the_A[2][1] = Amat[Azy];
127 >    the_A[2][2] = Amat[Azz];
128 >  }
129 >  else{
130 >    
131 >    sprintf( painCave.errMsg,
132 >             "Attempt to get Amat for atom %d before coords set.\n",
133 >             index );
134 >    painCave.isFatal = 1;
135 >    simError();
136 >  }
137  
54 –  the_A[1][0] = Amat[Ayx];
55 –  the_A[1][1] = Amat[Ayy];
56 –  the_A[1][2] = Amat[Ayz];
57 –
58 –  the_A[2][0] = Amat[Azx];
59 –  the_A[2][1] = Amat[Azy];
60 –  the_A[2][2] = Amat[Azz];
138   }
139  
140   void DirectionalAtom::printAmatIndex( void ){
141  
142 <  std::cerr << "Atom[" << index << "] index =>\n"
143 <            << "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n"
144 <            << "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n"
145 <            << "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n";
142 >  if( hasCoords ){
143 >    std::cerr << "Atom[" << index << "] index =>\n"
144 >              << "[ " << Axx << ", " << Axy << ", " << Axz << " ]\n"
145 >              << "[ " << Ayx << ", " << Ayy << ", " << Ayz << " ]\n"
146 >              << "[ " << Azx << ", " << Azy << ", " << Azz << " ]\n";
147 >  }
148 >  else{
149 >    
150 >    sprintf( painCave.errMsg,
151 >             "Attempt to print Amat indices for atom %d before coords set.\n",
152 >             index );
153 >    painCave.isFatal = 1;
154 >    simError();
155 >  }
156   }
157  
158  
159   void DirectionalAtom::getU( double the_u[3] ){
160    
161 <  the_u[0] = sux;
162 <  the_u[1] = suy;
163 <  the_u[2] = suz;
164 <
161 >  the_u[0] = sU[2][0];
162 >  the_u[1] = sU[2][1];
163 >  the_u[2] = sU[2][2];
164 >  
165    this->body2Lab( the_u );
166   }
167  
# Line 83 | Line 170 | void DirectionalAtom::getQ( double q[4] ){
170    double t, s;
171    double ad1, ad2, ad3;
172  
173 <  t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0;
87 <  if( t > 0.0 ){
173 >  if( hasCoords ){
174      
175 <    s = 0.5 / sqrt( t );
176 <    q[0] = 0.25 / s;
91 <    q[1] = (Amat[Ayz] - Amat[Azy]) * s;
92 <    q[2] = (Amat[Azx] - Amat[Axz]) * s;
93 <    q[3] = (Amat[Axy] - Amat[Ayx]) * s;
94 <  }
95 <  else{
96 <    
97 <    ad1 = fabs( Amat[Axx] );
98 <    ad2 = fabs( Amat[Ayy] );
99 <    ad3 = fabs( Amat[Azz] );
100 <
101 <    if( ad1 >= ad2 && ad1 >= ad3 ){
175 >    t = Amat[Axx] + Amat[Ayy] + Amat[Azz] + 1.0;
176 >    if( t > 0.0 ){
177        
178 <      s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] );
179 <      q[0] = (Amat[Ayz] + Amat[Azy]) / s;
180 <      q[1] = 0.5 / s;
181 <      q[2] = (Amat[Axy] + Amat[Ayx]) / s;
182 <      q[3] = (Amat[Axz] + Amat[Azx]) / s;
178 >      s = 0.5 / sqrt( t );
179 >      q[0] = 0.25 / s;
180 >      q[1] = (Amat[Ayz] - Amat[Azy]) * s;
181 >      q[2] = (Amat[Azx] - Amat[Axz]) * s;
182 >      q[3] = (Amat[Axy] - Amat[Ayx]) * s;
183      }
109 –    else if( ad2 >= ad1 && ad2 >= ad3 ){
110 –
111 –      s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0;
112 –      q[0] = (Amat[Axz] + Amat[Azx]) / s;
113 –      q[1] = (Amat[Axy] + Amat[Ayx]) / s;
114 –      q[2] = 0.5 / s;
115 –      q[3] = (Amat[Ayz] + Amat[Azy]) / s;
116 –    }
184      else{
185        
186 <      s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0;
187 <      q[0] = (Amat[Axy] + Amat[Ayx]) / s;
188 <      q[1] = (Amat[Axz] + Amat[Azx]) / s;
189 <      q[2] = (Amat[Ayz] + Amat[Azy]) / s;
190 <      q[3] = 0.5 / s;
186 >      ad1 = fabs( Amat[Axx] );
187 >      ad2 = fabs( Amat[Ayy] );
188 >      ad3 = fabs( Amat[Azz] );
189 >      
190 >      if( ad1 >= ad2 && ad1 >= ad3 ){
191 >        
192 >        s = 2.0 * sqrt( 1.0 + Amat[Axx] - Amat[Ayy] - Amat[Azz] );
193 >        q[0] = (Amat[Ayz] + Amat[Azy]) / s;
194 >        q[1] = 0.5 / s;
195 >        q[2] = (Amat[Axy] + Amat[Ayx]) / s;
196 >        q[3] = (Amat[Axz] + Amat[Azx]) / s;
197 >      }
198 >      else if( ad2 >= ad1 && ad2 >= ad3 ){
199 >        
200 >        s = sqrt( 1.0 + Amat[Ayy] - Amat[Axx] - Amat[Azz] ) * 2.0;
201 >        q[0] = (Amat[Axz] + Amat[Azx]) / s;
202 >        q[1] = (Amat[Axy] + Amat[Ayx]) / s;
203 >        q[2] = 0.5 / s;
204 >        q[3] = (Amat[Ayz] + Amat[Azy]) / s;
205 >      }
206 >      else{
207 >        
208 >        s = sqrt( 1.0 + Amat[Azz] - Amat[Axx] - Amat[Ayy] ) * 2.0;
209 >        q[0] = (Amat[Axy] + Amat[Ayx]) / s;
210 >        q[1] = (Amat[Axz] + Amat[Azx]) / s;
211 >        q[2] = (Amat[Ayz] + Amat[Azy]) / s;
212 >        q[3] = 0.5 / s;
213 >      }
214      }
215    }
216 +  else{
217 +    
218 +    sprintf( painCave.errMsg,
219 +             "Attempt to get Q for atom %d before coords set.\n",
220 +             index );
221 +    painCave.isFatal = 1;
222 +    simError();
223 +  }
224   }
225  
226 + void DirectionalAtom::setUnitFrameFromEuler(double phi,
227 +                                            double theta,
228 +                                            double psi) {
229  
230 < void DirectionalAtom::setEuler( double phi, double theta, double psi ){
230 >  double myA[3][3];
231 >  double uFrame[3][3];
232 >  double len;
233 >  int i, j;
234    
235 <  Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
236 <  Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
237 <  Amat[Axz] = sin(theta) * sin(psi);
235 >  myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
236 >  myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
237 >  myA[0][2] = sin(theta) * sin(psi);
238    
239 <  Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
240 <  Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
241 <  Amat[Ayz] = sin(theta) * cos(psi);
239 >  myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
240 >  myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
241 >  myA[1][2] = sin(theta) * cos(psi);
242 >  
243 >  myA[2][0] = sin(phi) * sin(theta);
244 >  myA[2][1] = -cos(phi) * sin(theta);
245 >  myA[2][2] = cos(theta);
246 >  
247 >  // Make the unit Frame:
248  
249 <  Amat[Azx] = sin(phi) * sin(theta);
250 <  Amat[Azy] = -cos(phi) * sin(theta);
251 <  Amat[Azz] = cos(theta);
249 >  for (i=0; i < 3; i++)
250 >    for (j=0; j < 3; j++)
251 >      uFrame[i][j] = 0.0;
252  
253 <  this->updateU();
253 >  for (i=0; i < 3; i++)
254 >    uFrame[i][i] = 1.0;
255 >
256 >  // rotate by the given rotation matrix:
257 >
258 >  matMul3(myA, uFrame, sU);
259 >
260 >  // renormalize column vectors:
261 >
262 >  for (i=0; i < 3; i++) {
263 >    len = 0.0;
264 >    for (j = 0; j < 3; j++) {
265 >      len += sU[i][j]*sU[i][j];
266 >    }
267 >    len = sqrt(len);
268 >    for (j = 0; j < 3; j++) {
269 >      sU[i][j] /= len;    
270 >    }
271 >  }
272 >  
273 >  // sU now contains the coordinates of the 'special' frame;
274 >    
275   }
276  
277 + void DirectionalAtom::setEuler( double phi, double theta, double psi ){
278 +  
279 +  if( hasCoords ){
280 +    Amat[Axx] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
281 +    Amat[Axy] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
282 +    Amat[Axz] = sin(theta) * sin(psi);
283 +    
284 +    Amat[Ayx] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
285 +    Amat[Ayy] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
286 +    Amat[Ayz] = sin(theta) * cos(psi);
287 +    
288 +    Amat[Azx] = sin(phi) * sin(theta);
289 +    Amat[Azy] = -cos(phi) * sin(theta);
290 +    Amat[Azz] = cos(theta);
291 +    
292 +    this->updateU();
293 +  }
294 +  else{
295 +    
296 +    sprintf( painCave.errMsg,
297 +             "Attempt to set Euler angles for atom %d before coords set.\n",
298 +             index );
299 +    painCave.isFatal = 1;
300 +    simError();
301 +  }
302 + }
303  
304 +
305   void DirectionalAtom::lab2Body( double r[3] ){
306  
307    double rl[3]; // the lab frame vector
308    
309 <  rl[0] = r[0];
310 <  rl[1] = r[1];
311 <  rl[2] = r[2];
309 >  if( hasCoords ){
310 >    rl[0] = r[0];
311 >    rl[1] = r[1];
312 >    rl[2] = r[2];
313 >    
314 >    r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]);
315 >    r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]);
316 >    r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]);
317 >  }
318 >  else{
319 >    
320 >    sprintf( painCave.errMsg,
321 >             "Attempt to convert lab2body for atom %d before coords set.\n",
322 >             index );
323 >    painCave.isFatal = 1;
324 >    simError();
325 >  }
326  
155 –  r[0] = (Amat[Axx] * rl[0]) + (Amat[Axy] * rl[1]) + (Amat[Axz] * rl[2]);
156 –  r[1] = (Amat[Ayx] * rl[0]) + (Amat[Ayy] * rl[1]) + (Amat[Ayz] * rl[2]);
157 –  r[2] = (Amat[Azx] * rl[0]) + (Amat[Azy] * rl[1]) + (Amat[Azz] * rl[2]);
327   }
328  
329 + void DirectionalAtom::rotateBy( double by_A[3][3]) {
330 +
331 +  // Check this
332 +  
333 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
334 +
335 +  if( hasCoords ){
336 +
337 +    r00 = by_A[0][0]*Amat[Axx] + by_A[0][1]*Amat[Ayx] + by_A[0][2]*Amat[Azx];
338 +    r01 = by_A[0][0]*Amat[Axy] + by_A[0][1]*Amat[Ayy] + by_A[0][2]*Amat[Azy];
339 +    r02 = by_A[0][0]*Amat[Axz] + by_A[0][1]*Amat[Ayz] + by_A[0][2]*Amat[Azz];
340 +    
341 +    r10 = by_A[1][0]*Amat[Axx] + by_A[1][1]*Amat[Ayx] + by_A[1][2]*Amat[Azx];
342 +    r11 = by_A[1][0]*Amat[Axy] + by_A[1][1]*Amat[Ayy] + by_A[1][2]*Amat[Azy];
343 +    r12 = by_A[1][0]*Amat[Axz] + by_A[1][1]*Amat[Ayz] + by_A[1][2]*Amat[Azz];
344 +    
345 +    r20 = by_A[2][0]*Amat[Axx] + by_A[2][1]*Amat[Ayx] + by_A[2][2]*Amat[Azx];
346 +    r21 = by_A[2][0]*Amat[Axy] + by_A[2][1]*Amat[Ayy] + by_A[2][2]*Amat[Azy];
347 +    r22 = by_A[2][0]*Amat[Axz] + by_A[2][1]*Amat[Ayz] + by_A[2][2]*Amat[Azz];
348 +    
349 +    Amat[Axx] = r00; Amat[Axy] = r01; Amat[Axz] = r02;
350 +    Amat[Ayx] = r10; Amat[Ayy] = r11; Amat[Ayz] = r12;
351 +    Amat[Azx] = r20; Amat[Azy] = r21; Amat[Azz] = r22;
352 +
353 +  }
354 +  else{
355 +    
356 +    sprintf( painCave.errMsg,
357 +             "Attempt to rotate frame for atom %d before coords set.\n",
358 +             index );
359 +    painCave.isFatal = 1;
360 +    simError();
361 +  }
362 +
363 + }
364 +
365 +
366   void DirectionalAtom::body2Lab( double r[3] ){
367  
368    double rb[3]; // the body frame vector
369    
370 <  rb[0] = r[0];
371 <  rb[1] = r[1];
372 <  rb[2] = r[2];
373 <
374 <  r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]);
375 <  r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]);
376 <  r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]);
370 >  if( hasCoords ){
371 >    rb[0] = r[0];
372 >    rb[1] = r[1];
373 >    rb[2] = r[2];
374 >    
375 >    r[0] = (Amat[Axx] * rb[0]) + (Amat[Ayx] * rb[1]) + (Amat[Azx] * rb[2]);
376 >    r[1] = (Amat[Axy] * rb[0]) + (Amat[Ayy] * rb[1]) + (Amat[Azy] * rb[2]);
377 >    r[2] = (Amat[Axz] * rb[0]) + (Amat[Ayz] * rb[1]) + (Amat[Azz] * rb[2]);
378 >  }
379 >  else{
380 >    
381 >    sprintf( painCave.errMsg,
382 >             "Attempt to convert body2lab for atom %d before coords set.\n",
383 >             index );
384 >    painCave.isFatal = 1;
385 >    simError();
386 >  }
387   }
388  
389   void DirectionalAtom::updateU( void ){
390  
391 <  ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz);
392 <  ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz);
393 <  ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz);
391 >  if( hasCoords ){
392 >    ul[offsetX] = (Amat[Axx] * sU[2][0]) +
393 >      (Amat[Ayx] * sU[2][1]) + (Amat[Azx] * sU[2][2]);
394 >    ul[offsetY] = (Amat[Axy] * sU[2][0]) +
395 >      (Amat[Ayy] * sU[2][1]) + (Amat[Azy] * sU[2][2]);
396 >    ul[offsetZ] = (Amat[Axz] * sU[2][0]) +
397 >      (Amat[Ayz] * sU[2][1]) + (Amat[Azz] * sU[2][2]);
398 >  }
399 >  else{
400 >    
401 >    sprintf( painCave.errMsg,
402 >             "Attempt to updateU for atom %d before coords set.\n",
403 >             index );
404 >    painCave.isFatal = 1;
405 >    simError();
406 >  }
407   }
408  
409   void DirectionalAtom::getJ( double theJ[3] ){
# Line 193 | Line 422 | void DirectionalAtom::getTrq( double theT[3] ){
422  
423   void DirectionalAtom::getTrq( double theT[3] ){
424    
425 <  theT[0] = trq[offsetX];
426 <  theT[1] = trq[offsetY];
427 <  theT[2] = trq[offsetZ];
425 >  if( hasCoords ){
426 >    theT[0] = trq[offsetX];
427 >    theT[1] = trq[offsetY];
428 >    theT[2] = trq[offsetZ];
429 >  }
430 >  else{
431 >    
432 >    sprintf( painCave.errMsg,
433 >             "Attempt to get Trq for atom %d before coords set.\n",
434 >             index );
435 >    painCave.isFatal = 1;
436 >    simError();
437 >  }
438   }
439  
440   void DirectionalAtom::addTrq( double theT[3] ){
441    
442 <  trq[offsetX] += theT[0];
443 <  trq[offsetY] += theT[1];
444 <  trq[offsetZ] += theT[2];
442 >  if( hasCoords ){
443 >    trq[offsetX] += theT[0];
444 >    trq[offsetY] += theT[1];
445 >    trq[offsetZ] += theT[2];
446 >  }
447 >  else{
448 >    
449 >    sprintf( painCave.errMsg,
450 >             "Attempt to add Trq for atom %d before coords set.\n",
451 >             index );
452 >    painCave.isFatal = 1;
453 >    simError();
454 >  }
455   }
456  
457  
# Line 220 | Line 469 | void DirectionalAtom::getI( double the_I[3][3] ){
469    the_I[2][1] = Izy;
470    the_I[2][2] = Izz;
471   }
472 +
473 + void DirectionalAtom::getGrad( double grad[6] ) {
474 +
475 +  double myEuler[3];
476 +  double phi, theta, psi;
477 +  double cphi, sphi, ctheta, stheta;
478 +  double ephi[3];
479 +  double etheta[3];
480 +  double epsi[3];
481 +
482 +  this->getEulerAngles(myEuler);
483 +
484 +  phi = myEuler[0];
485 +  theta = myEuler[1];
486 +  psi = myEuler[2];
487 +
488 +  cphi = cos(phi);
489 +  sphi = sin(phi);
490 +  ctheta = cos(theta);
491 +  stheta = sin(theta);
492 +
493 +  // get unit vectors along the phi, theta and psi rotation axes
494 +
495 +  ephi[0] = 0.0;
496 +  ephi[1] = 0.0;
497 +  ephi[2] = 1.0;
498 +
499 +  etheta[0] = cphi;
500 +  etheta[1] = sphi;
501 +  etheta[2] = 0.0;
502 +  
503 +  epsi[0] = stheta * cphi;
504 +  epsi[1] = stheta * sphi;
505 +  epsi[2] = ctheta;
506 +  
507 +  for (int j = 0 ; j<3; j++)
508 +    grad[j] = frc[j];
509 +
510 +  grad[3] = 0;
511 +  grad[4] = 0;
512 +  grad[5] = 0;
513 +
514 +  for (int j = 0; j < 3; j++ ) {
515 +    
516 +    grad[3] += trq[j]*ephi[j];
517 +    grad[4] += trq[j]*etheta[j];
518 +    grad[5] += trq[j]*epsi[j];
519 +    
520 +  }
521 +
522 + }
523 +
524 + /**
525 +  * getEulerAngles computes a set of Euler angle values consistent
526 +  *  with an input rotation matrix.  They are returned in the following
527 +  * order:
528 +  *  myEuler[0] = phi;
529 +  *  myEuler[1] = theta;
530 +  *  myEuler[2] = psi;
531 + */
532 + void DirectionalAtom::getEulerAngles(double myEuler[3]) {
533 +
534 +  // We use so-called "x-convention", which is the most common definition.
535 +  // In this convention, the rotation given by Euler angles (phi, theta, psi), where the first
536 +  // rotation is by an angle phi about the z-axis, the second is by an angle  
537 +  // theta (0 <= theta <= 180)about the x-axis, and thethird is by an angle psi about the
538 +  //z-axis (again).
539 +  
540 +  
541 +  double phi,theta,psi,eps;
542 +  double pi;
543 +  double cphi,ctheta,cpsi;
544 +  double sphi,stheta,spsi;
545 +  double b[3];
546 +  int flip[3];
547 +
548 +  // set the tolerance for Euler angles and rotation elements
549 +  
550 +  eps = 1.0e-8;
551 +
552 +  theta = acos(min(1.0,max(-1.0,Amat[Azz])));
553 +  ctheta = Amat[Azz];
554 +  stheta = sqrt(1.0 - ctheta * ctheta);
555 +
556 +  // when sin(theta) is close to 0, we need to consider singularity
557 +  // In this case, we can assign an arbitary value to phi (or psi), and then determine
558 +  // the psi (or phi) or vice-versa. We'll assume that phi always gets the rotation, and psi is 0
559 +  // in cases of singularity.  
560 +  // we use atan2 instead of atan, since atan2 will give us -Pi to Pi.
561 +  // Since 0 <= theta <= 180, sin(theta) will be always non-negative. Therefore, it never
562 +  // change the sign of both of the parameters passed to atan2.
563 +  
564 +  if (fabs(stheta) <= eps){
565 +    psi = 0.0;
566 +    phi = atan2(-Amat[Ayx], Amat[Axx]);  
567 +  }
568 +  // we only have one unique solution
569 +  else{    
570 +      phi = atan2(Amat[Azx], -Amat[Azy]);
571 +      psi = atan2(Amat[Axz], Amat[Ayz]);
572 +  }
573 +
574 +  //wrap phi and psi, make sure they are in the range from 0 to 2*Pi
575 +  //if (phi < 0)
576 +  //  phi += M_PI;
577 +
578 +  //if (psi < 0)
579 +  //  psi += M_PI;
580 +
581 +  myEuler[0] = phi;
582 +  myEuler[1] = theta;
583 +  myEuler[2] = psi;
584 +  
585 +  return;
586 + }
587 +
588 + double DirectionalAtom::max(double x, double  y) {  
589 +  return (x > y) ? x : y;
590 + }
591 +
592 + double DirectionalAtom::min(double x, double  y) {  
593 +  return (x > y) ? y : x;
594 + }

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