ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/DirectionalAtom.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/DirectionalAtom.cpp (file contents):
Revision 1046 by tim, Tue Feb 10 21:33:44 2004 UTC vs.
Revision 1136 by tim, Tue Apr 27 16:26:44 2004 UTC

# Line 1 | Line 1
1   #include <math.h>
2  
3   #include "Atom.hpp"
4 + #include "DirectionalAtom.hpp"
5   #include "simError.h"
6 + #include "MatVec3.h"
7  
6 –
7 –
8   void DirectionalAtom::zeroForces() {
9    if( hasCoords ){
10 <    frc[offsetX] = 0.0;
11 <    frc[offsetY] = 0.0;
12 <    frc[offsetZ] = 0.0;
10 >
11 >    Atom::zeroForces();
12      
13      trq[offsetX] = 0.0;
14      trq[offsetY] = 0.0;
# Line 36 | Line 35 | void DirectionalAtom::setCoords(void){
35                       &trq,
36                       &Amat,
37                       &mu,  
38 <                     &ul );
38 >                     &ul,
39 >                 &rc,
40 >                     &massRatio);
41    }
42    else{
43      sprintf( painCave.errMsg,
# Line 48 | Line 49 | void DirectionalAtom::setCoords(void){
49  
50    hasCoords = true;
51  
51 –  *mu = myMu;
52 –
52   }
53  
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 –
54   void DirectionalAtom::setA( double the_A[3][3] ){
55  
56    if( hasCoords ){
# Line 92 | Line 70 | void DirectionalAtom::setI( double the_I[3][3] ){
70    }
71   }
72  
73 < void DirectionalAtom::setI( double the_I[3][3] ){
73 > void DirectionalAtom::setI( double the_I[3][3] ){  
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];
# Line 182 | Line 160 | void DirectionalAtom::getU( double the_u[3] ){
160  
161   void DirectionalAtom::getU( double the_u[3] ){
162    
163 <  the_u[0] = sux;
164 <  the_u[1] = suy;
165 <  the_u[2] = suz;
166 <
163 >  the_u[0] = sU[2][0];
164 >  the_u[1] = sU[2][1];
165 >  the_u[2] = sU[2][2];
166 >  
167    this->body2Lab( the_u );
168   }
169  
# Line 246 | Line 224 | void DirectionalAtom::getQ( double q[4] ){
224      simError();
225    }
226   }
227 +
228 + void DirectionalAtom::setUnitFrameFromEuler(double phi,
229 +                                            double theta,
230 +                                            double psi) {
231 +
232 +  double myA[3][3];
233 +  double uFrame[3][3];
234 +  double len;
235 +  int i, j;
236 +  
237 +  myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
238 +  myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
239 +  myA[0][2] = sin(theta) * sin(psi);
240 +  
241 +  myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
242 +  myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
243 +  myA[1][2] = sin(theta) * cos(psi);
244 +  
245 +  myA[2][0] = sin(phi) * sin(theta);
246 +  myA[2][1] = -cos(phi) * sin(theta);
247 +  myA[2][2] = cos(theta);
248 +  
249 +  // Make the unit Frame:
250 +
251 +  for (i=0; i < 3; i++)
252 +    for (j=0; j < 3; j++)
253 +      uFrame[i][j] = 0.0;
254  
255 +  for (i=0; i < 3; i++)
256 +    uFrame[i][i] = 1.0;
257  
258 +  // rotate by the given rotation matrix:
259 +
260 +  matMul3(myA, uFrame, sU);
261 +
262 +  // renormalize column vectors:
263 +
264 +  for (i=0; i < 3; i++) {
265 +    len = 0.0;
266 +    for (j = 0; j < 3; j++) {
267 +      len += sU[i][j]*sU[i][j];
268 +    }
269 +    len = sqrt(len);
270 +    for (j = 0; j < 3; j++) {
271 +      sU[i][j] /= len;    
272 +    }
273 +  }
274 +  
275 +  // sU now contains the coordinates of the 'special' frame;
276 +    
277 + }
278 +
279   void DirectionalAtom::setEuler( double phi, double theta, double psi ){
280    
281    if( hasCoords ){
# Line 293 | Line 321 | void DirectionalAtom::lab2Body( double r[3] ){
321      
322      sprintf( painCave.errMsg,
323               "Attempt to convert lab2body for atom %d before coords set.\n",
324 +             index );
325 +    painCave.isFatal = 1;
326 +    simError();
327 +  }
328 +
329 + }
330 +
331 + void DirectionalAtom::rotateBy( double by_A[3][3]) {
332 +
333 +  // Check this
334 +  
335 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
336 +
337 +  if( hasCoords ){
338 +
339 +    r00 = by_A[0][0]*Amat[Axx] + by_A[0][1]*Amat[Ayx] + by_A[0][2]*Amat[Azx];
340 +    r01 = by_A[0][0]*Amat[Axy] + by_A[0][1]*Amat[Ayy] + by_A[0][2]*Amat[Azy];
341 +    r02 = by_A[0][0]*Amat[Axz] + by_A[0][1]*Amat[Ayz] + by_A[0][2]*Amat[Azz];
342 +    
343 +    r10 = by_A[1][0]*Amat[Axx] + by_A[1][1]*Amat[Ayx] + by_A[1][2]*Amat[Azx];
344 +    r11 = by_A[1][0]*Amat[Axy] + by_A[1][1]*Amat[Ayy] + by_A[1][2]*Amat[Azy];
345 +    r12 = by_A[1][0]*Amat[Axz] + by_A[1][1]*Amat[Ayz] + by_A[1][2]*Amat[Azz];
346 +    
347 +    r20 = by_A[2][0]*Amat[Axx] + by_A[2][1]*Amat[Ayx] + by_A[2][2]*Amat[Azx];
348 +    r21 = by_A[2][0]*Amat[Axy] + by_A[2][1]*Amat[Ayy] + by_A[2][2]*Amat[Azy];
349 +    r22 = by_A[2][0]*Amat[Axz] + by_A[2][1]*Amat[Ayz] + by_A[2][2]*Amat[Azz];
350 +    
351 +    Amat[Axx] = r00; Amat[Axy] = r01; Amat[Axz] = r02;
352 +    Amat[Ayx] = r10; Amat[Ayy] = r11; Amat[Ayz] = r12;
353 +    Amat[Azx] = r20; Amat[Azy] = r21; Amat[Azz] = r22;
354 +
355 +  }
356 +  else{
357 +    
358 +    sprintf( painCave.errMsg,
359 +             "Attempt to rotate frame for atom %d before coords set.\n",
360               index );
361      painCave.isFatal = 1;
362      simError();
# Line 300 | Line 364 | void DirectionalAtom::body2Lab( double r[3] ){
364  
365   }
366  
367 +
368   void DirectionalAtom::body2Lab( double r[3] ){
369  
370    double rb[3]; // the body frame vector
# Line 326 | Line 391 | void DirectionalAtom::updateU( void ){
391   void DirectionalAtom::updateU( void ){
392  
393    if( hasCoords ){
394 <    ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz);
395 <    ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz);
396 <    ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz);
394 >    ul[offsetX] = (Amat[Axx] * sU[2][0]) +
395 >      (Amat[Ayx] * sU[2][1]) + (Amat[Azx] * sU[2][2]);
396 >    ul[offsetY] = (Amat[Axy] * sU[2][0]) +
397 >      (Amat[Ayy] * sU[2][1]) + (Amat[Azy] * sU[2][2]);
398 >    ul[offsetZ] = (Amat[Axz] * sU[2][0]) +
399 >      (Amat[Ayz] * sU[2][1]) + (Amat[Azz] * sU[2][2]);
400    }
401    else{
402      

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines