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root/group/trunk/OOPSE/libmdtools/DirectionalAtom.cpp
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Comparing trunk/OOPSE/libmdtools/DirectionalAtom.cpp (file contents):
Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 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 <    frc[offsetX] = 0.0;
11 <    frc[offsetY] = 0.0;
10 <    frc[offsetZ] = 0.0;
10 >
11 >    Atom::zeroForces();
12      
13      trq[offsetX] = 0.0;
14      trq[offsetY] = 0.0;
# Line 34 | Line 35 | void DirectionalAtom::setCoords(void){
35                       &trq,
36                       &Amat,
37                       &mu,  
38 <                     &ul );
38 >                     &ul);
39    }
40    else{
41      sprintf( painCave.errMsg,
42               "Attempted to set Atom %d  coordinates with an unallocated "
43 <             "SimState object.\n" );
43 >             "SimState object.\n", index );
44      painCave.isFatal = 1;
45      simError();
46    }
47  
48    hasCoords = true;
49  
49 –  mu[index] = myMu;
50 –
50   }
51  
53 – double DirectionalAtom::getMu( void ) {
54 –
55 –  if( hasCoords ){
56 –    return mu[index];
57 –  }
58 –  else{
59 –    return myMu;
60 –  }
61 –  return 0;
62 – }
63 –
64 – void DirectionalAtom::setMu( double the_mu ) {
65 –
66 –  if( hasCoords ){
67 –    mu[index] = the_mu;
68 –    myMu = the_mu;
69 –  }
70 –  else{
71 –    myMu = the_mu;
72 –  }
73 – }
74 –
52   void DirectionalAtom::setA( double the_A[3][3] ){
53  
54    if( hasCoords ){
# Line 91 | 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 181 | 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 245 | 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 299 | 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 325 | 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      
# Line 401 | Line 468 | void DirectionalAtom::getI( double the_I[3][3] ){
468    the_I[2][0] = Izx;
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::getZangle( ){
589 +  
590 +  if( hasCoords ){
591 +    return zAngle;
592 +  }
593 +  else{
594 +    
595 +    sprintf( painCave.errMsg,
596 +             "Attempt to get zAngle for atom %d before coords set.\n",
597 +             index );
598 +    painCave.isFatal = 1;
599 +    simError();
600 +    return 0;
601 +  }
602 + }
603 +
604 + void DirectionalAtom::setZangle( double zAng ){
605 +  
606 +  if( hasCoords ){
607 +    zAngle = zAng;
608 +  }
609 +  else{
610 +    
611 +    sprintf( painCave.errMsg,
612 +             "Attempt to set zAngle for atom %d before coords set.\n",
613 +             index );
614 +    painCave.isFatal = 1;
615 +    simError();
616 +  }
617 + }
618 +
619 + void DirectionalAtom::addZangle( double zAng ){
620 +  
621 +  if( hasCoords ){
622 +    zAngle += zAng;
623 +  }
624 +  else{
625 +    
626 +    sprintf( painCave.errMsg,
627 +             "Attempt to add zAngle to atom %d before coords set.\n",
628 +             index );
629 +    painCave.isFatal = 1;
630 +    simError();
631 +  }
632 + }
633 +
634 + double DirectionalAtom::max(double x, double  y) {  
635 +  return (x > y) ? x : y;
636 + }
637 +
638 + double DirectionalAtom::min(double x, double  y) {  
639 +  return (x > y) ? y : x;
640 + }

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