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root/group/trunk/OOPSE/libmdtools/DirectionalAtom.cpp
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Comparing trunk/OOPSE/libmdtools/DirectionalAtom.cpp (file contents):
Revision 1046 by tim, Tue Feb 10 21:33:44 2004 UTC vs.
Revision 1167 by tim, Wed May 12 16:38:45 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    }
40    else{
41      sprintf( painCave.errMsg,
# Line 48 | Line 47 | void DirectionalAtom::setCoords(void){
47  
48    hasCoords = true;
49  
51 –  *mu = myMu;
52 –
50   }
51  
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 –
52   void DirectionalAtom::setA( double the_A[3][3] ){
53  
54    if( hasCoords ){
# Line 92 | Line 68 | void DirectionalAtom::setA( double the_A[3][3] ){
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 182 | Line 158 | void DirectionalAtom::getU( double the_u[3] ){
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 246 | Line 222 | void DirectionalAtom::getQ( double q[4] ){
222      simError();
223    }
224   }
225 +
226 + void DirectionalAtom::setUnitFrameFromEuler(double phi,
227 +                                            double theta,
228 +                                            double psi) {
229 +
230 +  double myA[3][3];
231 +  double uFrame[3][3];
232 +  double len;
233 +  int i, j;
234 +  
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 +  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 +  for (i=0; i < 3; i++)
250 +    for (j=0; j < 3; j++)
251 +      uFrame[i][j] = 0.0;
252  
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 ){
# Line 300 | Line 326 | void DirectionalAtom::lab2Body( double r[3] ){
326  
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
# Line 326 | Line 389 | void DirectionalAtom::updateU( void ){
389   void DirectionalAtom::updateU( void ){
390  
391    if( hasCoords ){
392 <    ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz);
393 <    ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz);
394 <    ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz);
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      

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