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root/group/trunk/SHAPES/RigidBody.cpp
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Comparing trunk/SHAPES/RigidBody.cpp (file contents):
Revision 1271 by gezelter, Tue Jun 15 20:20:36 2004 UTC vs.
Revision 1285 by chrisfen, Tue Jun 22 18:04:58 2004 UTC

# Line 1 | Line 1
1   #include <math.h>
2 + #include <iostream>
3   #include "RigidBody.hpp"
4   #include "VDWAtom.hpp"
5   #include "MatVec3.h"
# Line 15 | Line 16 | void RigidBody::addAtom(VDWAtom* at) {
16   void RigidBody::addAtom(VDWAtom* at) {
17  
18    vec3 coords;
18 –  vec3 euler;
19 –  mat3x3 Atmp;
19  
20    myAtoms.push_back(at);
21    
# Line 175 | Line 174 | void RigidBody::calcRefCoords( ) {
174  
175   void RigidBody::calcRefCoords( ) {
176  
177 <  int i,j,k, it, n_linear_coords;
177 >  int i, j, it, n_linear_coords, pAxis, maxAxis, midAxis;
178    double mtmp;
179    vec3 apos;
180    double refCOM[3];
181    vec3 ptmp;
182    double Itmp[3][3];
183 +  double pAxisMat[3][3], pAxisRotMat[3][3];
184    double evals[3];
185 –  double evects[3][3];
185    double r, r2, len;
186 <
186 >  double iMat[3][3];
187 >  double test[3];
188 >  
189    // First, find the center of mass:
190    
191    mass = 0.0;
# Line 196 | Line 197 | void RigidBody::calcRefCoords( ) {
197      mass += mtmp;
198  
199      apos = refCoords[i];
199 –    
200      for(j = 0; j < 3; j++) {
201        refCOM[j] += apos[j]*mtmp;    
202      }    
# Line 260 | Line 260 | void RigidBody::calcRefCoords( ) {
260    if (n_linear_coords > 1) {
261            printf(
262                 "RigidBody error.\n"
263 <               "\tOOPSE found more than one axis in this rigid body with a vanishing \n"
263 >               "\tSHAPES found more than one axis in this rigid body with a vanishing \n"
264                 "\tmoment of inertia.  This can happen in one of three ways:\n"
265                 "\t 1) Only one atom was specified, or \n"
266                 "\t 2) All atoms were specified at the same location, or\n"
# Line 269 | Line 269 | void RigidBody::calcRefCoords( ) {
269                 );
270                 exit(-1);    
271    }
272 <  
272 >
273    // renormalize column vectors:
274    
275    for (i=0; i < 3; i++) {
# Line 280 | Line 280 | void RigidBody::calcRefCoords( ) {
280      len = sqrt(len);
281      for (j = 0; j < 3; j++) {
282        sU[i][j] /= len;
283 +    }
284 +  }
285 +  
286 +  //sort and reorder the moment axes
287 +
288 +  // The only problem below is for molecules like C60 with 3 nearly identical
289 +  // non-zero moments of inertia.  In this case it doesn't really matter which is
290 +  // the principal axis, so they get assigned nearly randomly depending on the
291 +  // floating point comparison between eigenvalues
292 +  if (! is_linear) {
293 +    pAxis = 0;
294 +    maxAxis = 0;
295 +  
296 +    for (i = 0; i < 3; i++) {
297 +      if (evals[i] < evals[pAxis]) pAxis = i;
298 +      if (evals[i] > evals[maxAxis]) maxAxis = i;
299      }
300 +  
301 +    midAxis = 0;
302 +    for (i=0; i < 3; i++) {
303 +      if (pAxis != i && maxAxis != i) midAxis = i;
304 +    }
305 +  } else {
306 +    pAxis = linear_axis;
307 +    // linear molecules have one zero moment of inertia and two identical
308 +    // moments of inertia.  In this case, it doesn't matter which is chosen
309 +    // as mid and which is max, so just permute from the pAxis:
310 +    midAxis = (pAxis + 1)%3;
311 +    maxAxis = (pAxis + 2)%3;
312    }
313 +      
314 +  //let z be the smallest and x be the largest eigenvalue axes
315 +  for (i=0; i<3; i++){
316 +    pAxisMat[i][2] = sU[i][pAxis];
317 +    pAxisMat[i][1] = sU[i][midAxis];
318 +    pAxisMat[i][0] = sU[i][maxAxis];
319 +  }
320 +    
321 +  //calculate the proper rotation matrix
322 +  transposeMat3(pAxisMat, pAxisRotMat);
323 +  
324 +  
325 +  //rotate the rigid body to the principle axis frame
326 +  for (i = 0; i < myAtoms.size(); i++) {
327 +    matVecMul3(pAxisRotMat, refCoords[i].vec, refCoords[i].vec);
328 +    myAtoms[i]->setPos(refCoords[i].vec);
329 +  }
330 +  
331 +  identityMat3(iMat);
332 +  setA(iMat);
333   }
334  
335 < void RigidBody::doEulerToRotMat(vec3 &euler, mat3x3 &myA ){
335 > void RigidBody::doEulerToRotMat(double euler[3], double myA[3][3] ){
336  
337    double phi, theta, psi;
338    
# Line 344 | Line 392 | void RigidBody::getEulerAngles(double myEuler[3]) {
392    
393    
394    double phi,theta,psi,eps;
395 <  double pi;
396 <  double cphi,ctheta,cpsi;
397 <  double sphi,stheta,spsi;
350 <  double b[3];
351 <  int flip[3];
352 <  
395 >  double ctheta;
396 >  double stheta;
397 >    
398    // set the tolerance for Euler angles and rotation elements
399    
400    eps = 1.0e-8;
# Line 400 | Line 445 | double RigidBody::min(double x, double  y) {  
445    return (x > y) ? y : x;
446   }
447  
448 + double RigidBody::findMaxExtent(){
449 +        int i;
450 +        double refAtomPos[3];
451 +        double maxExtent;
452 +        double tempExtent;
453 +        
454 +        //zero the extent variables
455 +        maxExtent = 0.0;
456 +        tempExtent = 0.0;
457 +        for (i=0; i<3; i++)
458 +                refAtomPos[i] = 0.0;
459 +        
460 +        //loop over all atoms
461 +        for (i=0; i<myAtoms.size(); i++){
462 +                getAtomRefCoor(refAtomPos, i);
463 +                tempExtent = sqrt(refAtomPos[0]*refAtomPos[0] + refAtomPos[1]*refAtomPos[1]
464 +                                                  + refAtomPos[2]*refAtomPos[2]);
465 +                if (tempExtent > maxExtent)
466 +                        maxExtent = tempExtent;
467 +        }
468 +        return maxExtent;
469 + }
470 +
471   void RigidBody::findCOM() {
472    
473    size_t i;
474    int j;
475    double mtmp;
476    double ptmp[3];
477 <  double vtmp[3];
410 <  
477 >  
478    for(j = 0; j < 3; j++) {
479      pos[j] = 0.0;
480    }
# Line 457 | Line 524 | void RigidBody::getAtomRefCoor(double pos[3], int inde
524    pos[2] = ref[2];
525    
526   }
527 +
528 + double RigidBody::getAtomRpar(int index){
529 +  
530 +  return myAtoms[index]->getRpar();
531 +  
532 + }
533 +
534 + double RigidBody::getAtomEps(int index){
535 +  
536 +  return myAtoms[index]->getEps();
537 +  
538 + }

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