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root/group/trunk/OOPSE/libmdtools/RigidBody.cpp
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Comparing trunk/OOPSE/libmdtools/RigidBody.cpp (file contents):
Revision 1112 by gezelter, Mon Apr 12 21:02:01 2004 UTC vs.
Revision 1113 by tim, Thu Apr 15 16:18:26 2004 UTC

# Line 6 | Line 6 | RigidBody::RigidBody() : StuntDouble() {
6  
7   RigidBody::RigidBody() : StuntDouble() {
8    objType = OT_RIGIDBODY;
9 –  com_good = false;
10 –  precalc_done = false;
9   }
10  
11   RigidBody::~RigidBody() {
# Line 97 | Line 95 | void RigidBody::zeroForces() {
95      trq[i] = 0.0;
96    }
97  
100 –  forces_good = false;
101 –
98   }
99  
100 < void RigidBody::setEulerAngles( double phi, double theta, double psi ){
100 > void RigidBody::setEuler( double phi, double theta, double psi ){
101    
102      A[0][0] = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
103      A[0][1] = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
# Line 191 | Line 187 | void RigidBody::getA( double the_A[3][3] ){
187    
188    for (int i = 0; i < 3; i++)
189      for (int j = 0; j < 3; j++)
190 <      the_A[i][j] = the_A[i][j];
190 >      the_A[i][j] = A[i][j];
191  
192   }
193  
# Line 229 | Line 225 | void RigidBody::getI( double the_I[3][3] ){  
225  
226   void RigidBody::getI( double the_I[3][3] ){  
227  
232 –  if (precalc_done) {
233 –
228      for (int i = 0; i < 3; i++)
229        for (int j = 0; j < 3; j++)
230          the_I[i][j] = I[i][j];
231  
238 –  } else {
239 –
240 –  }
232   }
233  
234   void RigidBody::lab2Body( double r[3] ){
# Line 270 | Line 261 | void RigidBody::calcRefCoords( ) {
261  
262   void RigidBody::calcRefCoords( ) {
263  
264 <  int i,j,k;
264 >  int i,j,k, it;
265    double mtmp;
266    vec3 apos;
267    double refCOM[3];
268 +  vec3 ptmp;
269 +  double Itmp[3][3];
270 +  double evals[3];
271 +  double evects[3][3];
272 +  double r, r2, len;
273  
274 +  // First, find the center of mass:
275 +  
276    mass = 0.0;
277    for (j=0; j<3; j++)
278      refCOM[j] = 0.0;
# Line 293 | Line 291 | void RigidBody::calcRefCoords( ) {
291    for(j = 0; j < 3; j++)
292      refCOM[j] /= mass;
293  
294 + // Next, move the origin of the reference coordinate system to the COM:
295 +
296    for (i = 0; i < myAtoms.size(); i++) {
297      apos = refCoords[i];
298      for (j=0; j < 3; j++) {
299        apos[j] = apos[j] - refCOM[j];
300      }
301      refCoords[i] = apos;
302 +  }
303 +
304 + // Moment of Inertia calculation
305 +
306 +  for (i = 0; i < 3; i++)
307 +    for (j = 0; j < 3; j++)
308 +      Itmp[i][j] = 0.0;  
309 +  
310 +  for (it = 0; it < myAtoms.size(); it++) {
311 +
312 +    mtmp = myAtoms[it]->getMass();
313 +    ptmp = refCoords[it];
314 +    r= norm3(ptmp.vec);
315 +    r2 = r*r;
316 +    
317 +    for (i = 0; i < 3; i++) {
318 +      for (j = 0; j < 3; j++) {
319 +        
320 +        if (i==j) Itmp[i][j] += mtmp * r2;
321 +
322 +        Itmp[i][j] -= mtmp * ptmp.vec[i]*ptmp.vec[j];
323 +      }
324 +    }
325    }
326 +  
327 +  diagonalize3x3(Itmp, evals, sU);
328 +  
329 +  // zero out I and then fill the diagonals with the moments of inertia:
330  
331 +  for (i = 0; i < 3; i++) {
332 +    for (j = 0; j < 3; j++) {
333 +      I[i][j] = 0.0;  
334 +    }
335 +    I[i][i] = evals[i];
336 +  }
337 +  
338 +  // renormalize column vectors:
339 +  
340 +  for (i=0; i < 3; i++) {
341 +    len = 0.0;
342 +    for (j = 0; j < 3; j++) {
343 +      len += sU[i][j]*sU[i][j];
344 +    }
345 +    len = sqrt(len);
346 +    for (j = 0; j < 3; j++) {
347 +      sU[i][j] /= len;
348 +    }
349 +  }
350   }
351  
352   void RigidBody::doEulerToRotMat(vec3 &euler, mat3x3 &myA ){
# Line 366 | Line 412 | void RigidBody::calcForcesAndTorques() {
412    // (Actually, on second thought, don't.  Integrator does this now.)
413    // lab2Body(trq);
414  
369 –  forces_good = true;
370 –
415   }
416  
417   void RigidBody::updateAtoms() {
# Line 556 | Line 600 | void RigidBody::findCOM() {
600      vel[j] /= mass;
601    }
602  
559 –  com_good = true;
603   }
561 –  
562 – void RigidBody::findOrient() {
563 –  
564 –  size_t it;
565 –  int i, j;
566 –  double ptmp[3];
567 –  double Itmp[3][3];
568 –  double evals[3];
569 –  double evects[3][3];
570 –  double r2, mtmp, len;
571 –
572 –  if (!com_good) findCOM();
573 –
574 –  // Calculate inertial tensor matrix elements:
575 –
576 –  for (i = 0; i < 3; i++)
577 –    for (j = 0; j < 3; j++)
578 –      Itmp[i][j] = 0.0;  
579 –  
580 –  for (it = 0; it < myAtoms.size(); it++) {
581 –    
582 –    mtmp = myAtoms[it]->getMass();    
583 –    myAtoms[it]->getPos(ptmp);
584 –
585 –    for (j = 0; j < 3; j++)
586 –      ptmp[j] = pos[j] - ptmp[j];
587 –
588 –    r2 = norm3(ptmp);
589 –    
590 –    for (i = 0; i < 3; i++) {
591 –      for (j = 0; j < 3; j++) {
592 –        
593 –        if (i==j) Itmp[i][j] = mtmp * r2;
594 –
595 –        Itmp[i][j] -= mtmp * ptmp[i]*ptmp[j];
596 –      }
597 –    }
598 –  }
599 –  
600 –  diagonalize3x3(Itmp, evals, sU);
601 –  
602 –  // zero out I and then fill the diagonals with the moments of inertia:
603 –
604 –  for (i = 0; i < 3; i++) {
605 –    for (j = 0; j < 3; j++) {
606 –      I[i][j] = 0.0;  
607 –    }
608 –    I[i][i] = evals[i];
609 –  }
610 –  
611 –  // renormalize column vectors:
612 –  
613 –  for (i=0; i < 3; i++) {
614 –    len = 0.0;
615 –    for (j = 0; j < 3; j++) {
616 –      len += sU[i][j]*sU[i][j];
617 –    }
618 –    len = sqrt(len);
619 –    for (j = 0; j < 3; j++) {
620 –      sU[i][j] /= len;
621 –    }
622 –  }
623 –  
624 –  // sU now contains the coordinates of the 'special' frame;
625 –  
626 –  orient_good = true;
627 –
628 – }

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