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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 1452 by tim, Mon Aug 23 15:11:36 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 >                     &quat);
40    }
41    else{
42      sprintf( painCave.errMsg,
# Line 48 | Line 48 | void DirectionalAtom::setCoords(void){
48  
49    hasCoords = true;
50  
51 –  *mu = myMu;
52 –
51   }
52  
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 –
53   void DirectionalAtom::setA( double the_A[3][3] ){
54  
55    if( hasCoords ){
# Line 92 | Line 69 | void DirectionalAtom::setA( double the_A[3][3] ){
69    }
70   }
71  
72 < void DirectionalAtom::setI( double the_I[3][3] ){
72 > void DirectionalAtom::setI( double the_I[3][3] ){  
73    
74    Ixx = the_I[0][0]; Ixy = the_I[0][1]; Ixz = the_I[0][2];
75    Iyx = the_I[1][0]; Iyy = the_I[1][1]; Iyz = the_I[1][2];
# Line 182 | Line 159 | void DirectionalAtom::getU( double the_u[3] ){
159  
160   void DirectionalAtom::getU( double the_u[3] ){
161    
162 <  the_u[0] = sux;
163 <  the_u[1] = suy;
164 <  the_u[2] = suz;
165 <
162 >  the_u[0] = sU[2][0];
163 >  the_u[1] = sU[2][1];
164 >  the_u[2] = sU[2][2];
165 >  
166    this->body2Lab( the_u );
167   }
168  
# Line 247 | Line 224 | void DirectionalAtom::getQ( double q[4] ){
224    }
225   }
226  
227 + void DirectionalAtom::setUnitFrameFromEuler(double phi,
228 +                                            double theta,
229 +                                            double psi) {
230  
231 +  double myA[3][3];
232 +  double uFrame[3][3];
233 +  double len;
234 +  int i, j;
235 +  
236 +  myA[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
237 +  myA[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
238 +  myA[0][2] = sin(theta) * sin(psi);
239 +  
240 +  myA[1][0] = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
241 +  myA[1][1] = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
242 +  myA[1][2] = sin(theta) * cos(psi);
243 +  
244 +  myA[2][0] = sin(phi) * sin(theta);
245 +  myA[2][1] = -cos(phi) * sin(theta);
246 +  myA[2][2] = cos(theta);
247 +  
248 +  // Make the unit Frame:
249 +
250 +  for (i=0; i < 3; i++)
251 +    for (j=0; j < 3; j++)
252 +      uFrame[i][j] = 0.0;
253 +
254 +  for (i=0; i < 3; i++)
255 +    uFrame[i][i] = 1.0;
256 +
257 +  // rotate by the given rotation matrix:
258 +
259 +  matMul3(myA, uFrame, sU);
260 +
261 +  // renormalize column vectors:
262 +
263 +  for (i=0; i < 3; i++) {
264 +    len = 0.0;
265 +    for (j = 0; j < 3; j++) {
266 +      len += sU[i][j]*sU[i][j];
267 +    }
268 +    len = sqrt(len);
269 +    for (j = 0; j < 3; j++) {
270 +      sU[i][j] /= len;    
271 +    }
272 +  }
273 +  
274 +  // sU now contains the coordinates of the 'special' frame;
275 +    
276 + }
277 +
278   void DirectionalAtom::setEuler( double phi, double theta, double psi ){
279    
280    if( hasCoords ){
# Line 293 | Line 320 | void DirectionalAtom::lab2Body( double r[3] ){
320      
321      sprintf( painCave.errMsg,
322               "Attempt to convert lab2body for atom %d before coords set.\n",
323 +             index );
324 +    painCave.isFatal = 1;
325 +    simError();
326 +  }
327 +
328 + }
329 +
330 + void DirectionalAtom::rotateBy( double by_A[3][3]) {
331 +
332 +  // Check this
333 +  
334 +  double r00, r01, r02, r10, r11, r12, r20, r21, r22;
335 +
336 +  if( hasCoords ){
337 +
338 +    r00 = by_A[0][0]*Amat[Axx] + by_A[0][1]*Amat[Ayx] + by_A[0][2]*Amat[Azx];
339 +    r01 = by_A[0][0]*Amat[Axy] + by_A[0][1]*Amat[Ayy] + by_A[0][2]*Amat[Azy];
340 +    r02 = by_A[0][0]*Amat[Axz] + by_A[0][1]*Amat[Ayz] + by_A[0][2]*Amat[Azz];
341 +    
342 +    r10 = by_A[1][0]*Amat[Axx] + by_A[1][1]*Amat[Ayx] + by_A[1][2]*Amat[Azx];
343 +    r11 = by_A[1][0]*Amat[Axy] + by_A[1][1]*Amat[Ayy] + by_A[1][2]*Amat[Azy];
344 +    r12 = by_A[1][0]*Amat[Axz] + by_A[1][1]*Amat[Ayz] + by_A[1][2]*Amat[Azz];
345 +    
346 +    r20 = by_A[2][0]*Amat[Axx] + by_A[2][1]*Amat[Ayx] + by_A[2][2]*Amat[Azx];
347 +    r21 = by_A[2][0]*Amat[Axy] + by_A[2][1]*Amat[Ayy] + by_A[2][2]*Amat[Azy];
348 +    r22 = by_A[2][0]*Amat[Axz] + by_A[2][1]*Amat[Ayz] + by_A[2][2]*Amat[Azz];
349 +    
350 +    Amat[Axx] = r00; Amat[Axy] = r01; Amat[Axz] = r02;
351 +    Amat[Ayx] = r10; Amat[Ayy] = r11; Amat[Ayz] = r12;
352 +    Amat[Azx] = r20; Amat[Azy] = r21; Amat[Azz] = r22;
353 +
354 +  }
355 +  else{
356 +    
357 +    sprintf( painCave.errMsg,
358 +             "Attempt to rotate frame for atom %d before coords set.\n",
359               index );
360      painCave.isFatal = 1;
361      simError();
# Line 300 | Line 363 | void DirectionalAtom::lab2Body( double r[3] ){
363  
364   }
365  
366 +
367   void DirectionalAtom::body2Lab( double r[3] ){
368  
369    double rb[3]; // the body frame vector
# Line 326 | Line 390 | void DirectionalAtom::updateU( void ){
390   void DirectionalAtom::updateU( void ){
391  
392    if( hasCoords ){
393 <    ul[offsetX] = (Amat[Axx] * sux) + (Amat[Ayx] * suy) + (Amat[Azx] * suz);
394 <    ul[offsetY] = (Amat[Axy] * sux) + (Amat[Ayy] * suy) + (Amat[Azy] * suz);
395 <    ul[offsetZ] = (Amat[Axz] * sux) + (Amat[Ayz] * suy) + (Amat[Azz] * suz);
393 >    ul[offsetX] = (Amat[Axx] * sU[2][0]) +
394 >      (Amat[Ayx] * sU[2][1]) + (Amat[Azx] * sU[2][2]);
395 >    ul[offsetY] = (Amat[Axy] * sU[2][0]) +
396 >      (Amat[Ayy] * sU[2][1]) + (Amat[Azy] * sU[2][2]);
397 >    ul[offsetZ] = (Amat[Axz] * sU[2][0]) +
398 >      (Amat[Ayz] * sU[2][1]) + (Amat[Azz] * sU[2][2]);
399    }
400    else{
401      
# Line 365 | Line 432 | void DirectionalAtom::getTrq( double theT[3] ){
432      
433      sprintf( painCave.errMsg,
434               "Attempt to get Trq for atom %d before coords set.\n",
435 +             index );
436 +    painCave.isFatal = 1;
437 +    simError();
438 +  }
439 + }
440 +
441 + void DirectionalAtom::setTrq( double theT[3] ){
442 +  
443 +  if( hasCoords ){
444 +    trq[offsetX] = theT[0];
445 +    trq[offsetY] = theT[1];
446 +    trq[offsetZ] = theT[2];
447 +  }
448 +  else{
449 +    
450 +    sprintf( painCave.errMsg,
451 +             "Attempt to add Trq for atom %d before coords set.\n",
452               index );
453      painCave.isFatal = 1;
454      simError();
# Line 473 | Line 557 | void DirectionalAtom::getEulerAngles(double myEuler[3]
557    
558    
559    double phi,theta,psi,eps;
560 <  double pi;
477 <  double cphi,ctheta,cpsi;
478 <  double sphi,stheta,spsi;
479 <  double b[3];
480 <  int flip[3];
560 >  double ctheta,stheta;
561  
562    // set the tolerance for Euler angles and rotation elements
563    
# Line 519 | Line 599 | void DirectionalAtom::getEulerAngles(double myEuler[3]
599    return;
600   }
601  
602 + double DirectionalAtom::getZangle( ){
603 +  
604 +  if( hasCoords ){
605 +    return zAngle;
606 +  }
607 +  else{
608 +    
609 +    sprintf( painCave.errMsg,
610 +             "Attempt to get zAngle for atom %d before coords set.\n",
611 +             index );
612 +    painCave.isFatal = 1;
613 +    simError();
614 +    return 0;
615 +  }
616 + }
617 +
618 + void DirectionalAtom::setZangle( double zAng ){
619 +  
620 +  if( hasCoords ){
621 +    zAngle = zAng;
622 +  }
623 +  else{
624 +    
625 +    sprintf( painCave.errMsg,
626 +             "Attempt to set zAngle for atom %d before coords set.\n",
627 +             index );
628 +    painCave.isFatal = 1;
629 +    simError();
630 +  }
631 + }
632 +
633 + void DirectionalAtom::addZangle( double zAng ){
634 +  
635 +  if( hasCoords ){
636 +    zAngle += zAng;
637 +  }
638 +  else{
639 +    
640 +    sprintf( painCave.errMsg,
641 +             "Attempt to add zAngle to atom %d before coords set.\n",
642 +             index );
643 +    painCave.isFatal = 1;
644 +    simError();
645 +  }
646 + }
647 +
648   double DirectionalAtom::max(double x, double  y) {  
649    return (x > y) ? x : y;
650   }

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