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Comparing trunk/src/primitives/RigidBody.cpp (file contents):
Revision 273 by tim, Tue Jan 25 17:45:23 2005 UTC vs.
Revision 646 by tim, Wed Oct 5 19:12:02 2005 UTC

# Line 1 | Line 1
1 < /*
1 > /*
2   * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3   *
4   * The University of Notre Dame grants you ("Licensee") a
# Line 42 | Line 42
42   #include <math.h>
43   #include "primitives/RigidBody.hpp"
44   #include "utils/simError.h"
45 + #include "utils/NumericConstant.hpp"
46   namespace oopse {
47  
48 < RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){
48 >  RigidBody::RigidBody() : StuntDouble(otRigidBody, &Snapshot::rigidbodyData), inertiaTensor_(0.0){
49  
50 < }
50 >  }
51  
52 < void RigidBody::setPrevA(const RotMat3x3d& a) {
52 >  void RigidBody::setPrevA(const RotMat3x3d& a) {
53      ((snapshotMan_->getPrevSnapshot())->*storage_).aMat[localIndex_] = a;
54      //((snapshotMan_->getPrevSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;
55  
56      for (int i =0 ; i < atoms_.size(); ++i){
57 <        if (atoms_[i]->isDirectional()) {
58 <            atoms_[i]->setPrevA(a * refOrients_[i]);
59 <        }
57 >      if (atoms_[i]->isDirectional()) {
58 >        atoms_[i]->setPrevA(a * refOrients_[i]);
59 >      }
60      }
61  
62 < }
62 >  }
63  
64        
65 < void RigidBody::setA(const RotMat3x3d& a) {
65 >  void RigidBody::setA(const RotMat3x3d& a) {
66      ((snapshotMan_->getCurrentSnapshot())->*storage_).aMat[localIndex_] = a;
67      //((snapshotMan_->getCurrentSnapshot())->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;
68  
69      for (int i =0 ; i < atoms_.size(); ++i){
70 <        if (atoms_[i]->isDirectional()) {
71 <            atoms_[i]->setA(a * refOrients_[i]);
72 <        }
70 >      if (atoms_[i]->isDirectional()) {
71 >        atoms_[i]->setA(a * refOrients_[i]);
72 >      }
73      }
74 < }    
74 >  }    
75      
76 < void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
76 >  void RigidBody::setA(const RotMat3x3d& a, int snapshotNo) {
77      ((snapshotMan_->getSnapshot(snapshotNo))->*storage_).aMat[localIndex_] = a;
78      //((snapshotMan_->getSnapshot(snapshotNo))->*storage_).electroFrame[localIndex_] = a.transpose() * sU_;    
79  
80      for (int i =0 ; i < atoms_.size(); ++i){
81 <        if (atoms_[i]->isDirectional()) {
82 <            atoms_[i]->setA(a * refOrients_[i], snapshotNo);
83 <        }
81 >      if (atoms_[i]->isDirectional()) {
82 >        atoms_[i]->setA(a * refOrients_[i], snapshotNo);
83 >      }
84      }
85  
86 < }  
86 >  }  
87  
88 < Mat3x3d RigidBody::getI() {
88 >  Mat3x3d RigidBody::getI() {
89      return inertiaTensor_;
90 < }    
90 >  }    
91  
92 < std::vector<double> RigidBody::getGrad() {
93 <     std::vector<double> grad(6, 0.0);
92 >  std::vector<double> RigidBody::getGrad() {
93 >    std::vector<double> grad(6, 0.0);
94      Vector3d force;
95      Vector3d torque;
96      Vector3d myEuler;
# Line 128 | Line 129 | std::vector<double> RigidBody::getGrad() {
129  
130      //gradient is equal to -force
131      for (int j = 0 ; j<3; j++)
132 <        grad[j] = -force[j];
132 >      grad[j] = -force[j];
133  
134      for (int j = 0; j < 3; j++ ) {
135  
136 <        grad[3] += torque[j]*ephi[j];
137 <        grad[4] += torque[j]*etheta[j];
138 <        grad[5] += torque[j]*epsi[j];
136 >      grad[3] += torque[j]*ephi[j];
137 >      grad[4] += torque[j]*etheta[j];
138 >      grad[5] += torque[j]*epsi[j];
139  
140      }
141      
142      return grad;
143 < }    
143 >  }    
144  
145 < void RigidBody::accept(BaseVisitor* v) {
145 >  void RigidBody::accept(BaseVisitor* v) {
146      v->visit(this);
147 < }    
147 >  }    
148  
149 < /**@todo need modification */
150 < void  RigidBody::calcRefCoords() {
149 >  /**@todo need modification */
150 >  void  RigidBody::calcRefCoords() {
151      double mtmp;
152      Vector3d refCOM(0.0);
153      mass_ = 0.0;
154      for (std::size_t i = 0; i < atoms_.size(); ++i) {
155 <        mtmp = atoms_[i]->getMass();
156 <        mass_ += mtmp;
157 <        refCOM += refCoords_[i]*mtmp;
155 >      mtmp = atoms_[i]->getMass();
156 >      mass_ += mtmp;
157 >      refCOM += refCoords_[i]*mtmp;
158      }
159      refCOM /= mass_;
160  
161      // Next, move the origin of the reference coordinate system to the COM:
162      for (std::size_t i = 0; i < atoms_.size(); ++i) {
163 <        refCoords_[i] -= refCOM;
163 >      refCoords_[i] -= refCOM;
164      }
165  
166 < // Moment of Inertia calculation
167 <    Mat3x3d Itmp(0.0);
167 <  
166 >    // Moment of Inertia calculation
167 >    Mat3x3d Itmp(0.0);    
168      for (std::size_t i = 0; i < atoms_.size(); i++) {
169 <        mtmp = atoms_[i]->getMass();
170 <        Itmp -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
171 <        double r2 = refCoords_[i].lengthSquare();
172 <        Itmp(0, 0) += mtmp * r2;
173 <        Itmp(1, 1) += mtmp * r2;
174 <        Itmp(2, 2) += mtmp * r2;
175 <    }
169 >      Mat3x3d IAtom(0.0);  
170 >      mtmp = atoms_[i]->getMass();
171 >      IAtom -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
172 >      double r2 = refCoords_[i].lengthSquare();
173 >      IAtom(0, 0) += mtmp * r2;
174 >      IAtom(1, 1) += mtmp * r2;
175 >      IAtom(2, 2) += mtmp * r2;
176  
177 <    //project the inertial moment of directional atoms into this rigid body
178 <    for (std::size_t i = 0; i < atoms_.size(); i++) {
179 <        if (atoms_[i]->isDirectional()) {
180 <            RectMatrix<double, 3, 3> Iproject = refOrients_[i].transpose() * atoms_[i]->getI();
181 <            Itmp(0, 0) += Iproject(0, 0);
182 <            Itmp(1, 1) += Iproject(1, 1);
183 <            Itmp(2, 2) += Iproject(2, 2);
184 <        }
177 >      //project the inertial moment of directional atoms into this rigid body
178 >      if (atoms_[i]->isDirectional()) {
179 >        //IAtom += atoms_[i]->getI();
180 >        Itmp += IAtom;
181 >        Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
182 >      } else {
183 >        Itmp += IAtom;
184 >      }
185      }
186  
187 +    std::cout << Itmp <<std::endl;
188      //diagonalize
189      Vector3d evals;
190      Mat3x3d::diagonalize(Itmp, evals, sU_);
# Line 195 | Line 196 | void  RigidBody::calcRefCoords() {
196          
197      int nLinearAxis = 0;
198      for (int i = 0; i < 3; i++) {    
199 <        if (fabs(evals[i]) < oopse::epsilon) {
200 <            linear_ = true;
201 <            linearAxis_ = i;
202 <            ++ nLinearAxis;
203 <        }
199 >      if (fabs(evals[i]) < oopse::epsilon) {
200 >        linear_ = true;
201 >        linearAxis_ = i;
202 >        ++ nLinearAxis;
203 >      }
204      }
205  
206      if (nLinearAxis > 1) {
207 <        sprintf( painCave.errMsg,
208 <            "RigidBody error.\n"
209 <            "\tOOPSE found more than one axis in this rigid body with a vanishing \n"
210 <            "\tmoment of inertia.  This can happen in one of three ways:\n"
211 <            "\t 1) Only one atom was specified, or \n"
212 <            "\t 2) All atoms were specified at the same location, or\n"
213 <            "\t 3) The programmers did something stupid.\n"
214 <            "\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
215 <            );
216 <        painCave.isFatal = 1;
217 <        simError();
207 >      sprintf( painCave.errMsg,
208 >               "RigidBody error.\n"
209 >               "\tOOPSE found more than one axis in this rigid body with a vanishing \n"
210 >               "\tmoment of inertia.  This can happen in one of three ways:\n"
211 >               "\t 1) Only one atom was specified, or \n"
212 >               "\t 2) All atoms were specified at the same location, or\n"
213 >               "\t 3) The programmers did something stupid.\n"
214 >               "\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
215 >               );
216 >      painCave.isFatal = 1;
217 >      simError();
218      }
219    
220 < }
220 >  }
221  
222 < void  RigidBody::calcForcesAndTorques() {
222 >  void  RigidBody::calcForcesAndTorques() {
223      Vector3d afrc;
224      Vector3d atrq;
225      Vector3d apos;
# Line 228 | Line 229 | void  RigidBody::calcForcesAndTorques() {
229      Vector3d pos = this->getPos();
230      for (int i = 0; i < atoms_.size(); i++) {
231  
232 <        afrc = atoms_[i]->getFrc();
233 <        apos = atoms_[i]->getPos();
234 <        rpos = apos - pos;
232 >      afrc = atoms_[i]->getFrc();
233 >      apos = atoms_[i]->getPos();
234 >      rpos = apos - pos;
235          
236 <        frc += afrc;
236 >      frc += afrc;
237  
238 <        trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
239 <        trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
240 <        trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];
238 >      trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
239 >      trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
240 >      trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];
241  
242 <        // If the atom has a torque associated with it, then we also need to
243 <        // migrate the torques onto the center of mass:
242 >      // If the atom has a torque associated with it, then we also need to
243 >      // migrate the torques onto the center of mass:
244  
245 <        if (atoms_[i]->isDirectional()) {
246 <            atrq = atoms_[i]->getTrq();
247 <            trq += atrq;
248 <        }
245 >      if (atoms_[i]->isDirectional()) {
246 >        atrq = atoms_[i]->getTrq();
247 >        trq += atrq;
248 >      }
249          
250      }
251      
252      setFrc(frc);
253      setTrq(trq);
254      
255 < }
255 >  }
256  
257 < void  RigidBody::updateAtoms() {
257 >  void  RigidBody::updateAtoms() {
258      unsigned int i;
259      Vector3d ref;
260      Vector3d apos;
# Line 263 | Line 264 | void  RigidBody::updateAtoms() {
264      
265      for (i = 0; i < atoms_.size(); i++) {
266      
267 <        ref = body2Lab(refCoords_[i]);
267 >      ref = body2Lab(refCoords_[i]);
268  
269 <        apos = pos + ref;
269 >      apos = pos + ref;
270  
271 <        atoms_[i]->setPos(apos);
271 >      atoms_[i]->setPos(apos);
272  
273 <        if (atoms_[i]->isDirectional()) {
273 >      if (atoms_[i]->isDirectional()) {
274            
275 <          dAtom = (DirectionalAtom *) atoms_[i];
276 <          dAtom->setA(a * refOrients_[i]);
277 <          //dAtom->rotateBy( A );      
277 <        }
275 >        dAtom = (DirectionalAtom *) atoms_[i];
276 >        dAtom->setA(refOrients_[i] * a);
277 >      }
278  
279      }
280    
281 < }
281 >  }
282  
283  
284 < bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
285 <    if (index < atoms_.size()) {
284 >  void  RigidBody::updateAtoms(int frame) {
285 >    unsigned int i;
286 >    Vector3d ref;
287 >    Vector3d apos;
288 >    DirectionalAtom* dAtom;
289 >    Vector3d pos = getPos(frame);
290 >    RotMat3x3d a = getA(frame);
291 >    
292 >    for (i = 0; i < atoms_.size(); i++) {
293 >    
294 >      ref = body2Lab(refCoords_[i], frame);
295  
296 <        Vector3d ref = body2Lab(refCoords_[index]);
288 <        pos = getPos() + ref;
289 <        return true;
290 <    } else {
291 <        std::cerr << index << " is an invalid index, current rigid body contains "
292 <                      << atoms_.size() << "atoms" << std::endl;
293 <        return false;
294 <    }    
295 < }
296 >      apos = pos + ref;
297  
298 < bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
298 <    std::vector<Atom*>::iterator i;
299 <    i = std::find(atoms_.begin(), atoms_.end(), atom);
300 <    if (i != atoms_.end()) {
301 <        //RigidBody class makes sure refCoords_ and atoms_ match each other
302 <        Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
303 <        pos = getPos() + ref;
304 <        return true;
305 <    } else {
306 <        std::cerr << "Atom " << atom->getGlobalIndex()
307 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
308 <        return false;
309 <    }
310 < }
311 < bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
298 >      atoms_[i]->setPos(apos, frame);
299  
300 <    //velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
300 >      if (atoms_[i]->isDirectional()) {
301 >          
302 >        dAtom = (DirectionalAtom *) atoms_[i];
303 >        dAtom->setA(refOrients_[i] * a, frame);
304 >      }
305  
306 <    if (index < atoms_.size()) {
306 >    }
307 >  
308 >  }
309  
310 <        Vector3d velRot;
311 <        Mat3x3d skewMat;;
319 <        Vector3d ref = refCoords_[index];
320 <        Vector3d ji = getJ();
321 <        Mat3x3d I =  getI();
310 >  void RigidBody::updateAtomVel() {
311 >    Mat3x3d skewMat;;
312  
313 <        skewMat(0, 0) =0;
314 <        skewMat(0, 1) = ji[2] /I(2, 2);
325 <        skewMat(0, 2) = -ji[1] /I(1, 1);
313 >    Vector3d ji = getJ();
314 >    Mat3x3d I =  getI();
315  
316 <        skewMat(1, 0) = -ji[2] /I(2, 2);
317 <        skewMat(1, 1) = 0;
318 <        skewMat(1, 2) = ji[0]/I(0, 0);
316 >    skewMat(0, 0) =0;
317 >    skewMat(0, 1) = ji[2] /I(2, 2);
318 >    skewMat(0, 2) = -ji[1] /I(1, 1);
319  
320 <        skewMat(2, 0) =ji[1] /I(1, 1);
321 <        skewMat(2, 1) = -ji[0]/I(0, 0);
322 <        skewMat(2, 2) = 0;
320 >    skewMat(1, 0) = -ji[2] /I(2, 2);
321 >    skewMat(1, 1) = 0;
322 >    skewMat(1, 2) = ji[0]/I(0, 0);
323  
324 <        velRot = (getA() * skewMat).transpose() * ref;
324 >    skewMat(2, 0) =ji[1] /I(1, 1);
325 >    skewMat(2, 1) = -ji[0]/I(0, 0);
326 >    skewMat(2, 2) = 0;
327  
328 <        vel =getVel() + velRot;
329 <        return true;
328 >    Mat3x3d mat = (getA() * skewMat).transpose();
329 >    Vector3d rbVel = getVel();
330 >
331 >
332 >    Vector3d velRot;        
333 >    for (int i =0 ; i < refCoords_.size(); ++i) {
334 >      atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
335 >    }
336 >
337 >  }
338 >
339 >  void RigidBody::updateAtomVel(int frame) {
340 >    Mat3x3d skewMat;;
341 >
342 >    Vector3d ji = getJ(frame);
343 >    Mat3x3d I =  getI();
344 >
345 >    skewMat(0, 0) =0;
346 >    skewMat(0, 1) = ji[2] /I(2, 2);
347 >    skewMat(0, 2) = -ji[1] /I(1, 1);
348 >
349 >    skewMat(1, 0) = -ji[2] /I(2, 2);
350 >    skewMat(1, 1) = 0;
351 >    skewMat(1, 2) = ji[0]/I(0, 0);
352 >
353 >    skewMat(2, 0) =ji[1] /I(1, 1);
354 >    skewMat(2, 1) = -ji[0]/I(0, 0);
355 >    skewMat(2, 2) = 0;
356 >
357 >    Mat3x3d mat = (getA(frame) * skewMat).transpose();
358 >    Vector3d rbVel = getVel(frame);
359 >
360 >
361 >    Vector3d velRot;        
362 >    for (int i =0 ; i < refCoords_.size(); ++i) {
363 >      atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
364 >    }
365 >
366 >  }
367 >
368          
369 +
370 +  bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
371 +    if (index < atoms_.size()) {
372 +
373 +      Vector3d ref = body2Lab(refCoords_[index]);
374 +      pos = getPos() + ref;
375 +      return true;
376      } else {
377 <        std::cerr << index << " is an invalid index, current rigid body contains "
378 <                      << atoms_.size() << "atoms" << std::endl;
379 <        return false;
377 >      std::cerr << index << " is an invalid index, current rigid body contains "
378 >                << atoms_.size() << "atoms" << std::endl;
379 >      return false;
380 >    }    
381 >  }
382 >
383 >  bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
384 >    std::vector<Atom*>::iterator i;
385 >    i = std::find(atoms_.begin(), atoms_.end(), atom);
386 >    if (i != atoms_.end()) {
387 >      //RigidBody class makes sure refCoords_ and atoms_ match each other
388 >      Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
389 >      pos = getPos() + ref;
390 >      return true;
391 >    } else {
392 >      std::cerr << "Atom " << atom->getGlobalIndex()
393 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
394 >      return false;
395      }
396 < }
396 >  }
397 >  bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
398  
399 < bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
399 >    //velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
400  
401 +    if (index < atoms_.size()) {
402 +
403 +      Vector3d velRot;
404 +      Mat3x3d skewMat;;
405 +      Vector3d ref = refCoords_[index];
406 +      Vector3d ji = getJ();
407 +      Mat3x3d I =  getI();
408 +
409 +      skewMat(0, 0) =0;
410 +      skewMat(0, 1) = ji[2] /I(2, 2);
411 +      skewMat(0, 2) = -ji[1] /I(1, 1);
412 +
413 +      skewMat(1, 0) = -ji[2] /I(2, 2);
414 +      skewMat(1, 1) = 0;
415 +      skewMat(1, 2) = ji[0]/I(0, 0);
416 +
417 +      skewMat(2, 0) =ji[1] /I(1, 1);
418 +      skewMat(2, 1) = -ji[0]/I(0, 0);
419 +      skewMat(2, 2) = 0;
420 +
421 +      velRot = (getA() * skewMat).transpose() * ref;
422 +
423 +      vel =getVel() + velRot;
424 +      return true;
425 +        
426 +    } else {
427 +      std::cerr << index << " is an invalid index, current rigid body contains "
428 +                << atoms_.size() << "atoms" << std::endl;
429 +      return false;
430 +    }
431 +  }
432 +
433 +  bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
434 +
435      std::vector<Atom*>::iterator i;
436      i = std::find(atoms_.begin(), atoms_.end(), atom);
437      if (i != atoms_.end()) {
438 <        return getAtomVel(vel, i - atoms_.begin());
438 >      return getAtomVel(vel, i - atoms_.begin());
439      } else {
440 <        std::cerr << "Atom " << atom->getGlobalIndex()
441 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
442 <        return false;
440 >      std::cerr << "Atom " << atom->getGlobalIndex()
441 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
442 >      return false;
443      }    
444 < }
444 >  }
445  
446 < bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
446 >  bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
447      if (index < atoms_.size()) {
448  
449 <        coor = refCoords_[index];
450 <        return true;
449 >      coor = refCoords_[index];
450 >      return true;
451      } else {
452 <        std::cerr << index << " is an invalid index, current rigid body contains "
453 <                      << atoms_.size() << "atoms" << std::endl;
454 <        return false;
452 >      std::cerr << index << " is an invalid index, current rigid body contains "
453 >                << atoms_.size() << "atoms" << std::endl;
454 >      return false;
455      }
456  
457 < }
457 >  }
458  
459 < bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
459 >  bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
460      std::vector<Atom*>::iterator i;
461      i = std::find(atoms_.begin(), atoms_.end(), atom);
462      if (i != atoms_.end()) {
463 <        //RigidBody class makes sure refCoords_ and atoms_ match each other
464 <        coor = refCoords_[i - atoms_.begin()];
465 <        return true;
463 >      //RigidBody class makes sure refCoords_ and atoms_ match each other
464 >      coor = refCoords_[i - atoms_.begin()];
465 >      return true;
466      } else {
467 <        std::cerr << "Atom " << atom->getGlobalIndex()
468 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
469 <        return false;
467 >      std::cerr << "Atom " << atom->getGlobalIndex()
468 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
469 >      return false;
470      }
471  
472 < }
472 >  }
473  
474  
475 < void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
475 >  void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
476  
477 <  Vector3d coords;
478 <  Vector3d euler;
477 >    Vector3d coords;
478 >    Vector3d euler;
479    
480  
481 <  atoms_.push_back(at);
481 >    atoms_.push_back(at);
482  
483 <  if( !ats->havePosition() ){
484 <    sprintf( painCave.errMsg,
485 <             "RigidBody error.\n"
486 <             "\tAtom %s does not have a position specified.\n"
487 <             "\tThis means RigidBody cannot set up reference coordinates.\n",
488 <             ats->getType() );
489 <    painCave.isFatal = 1;
490 <    simError();
491 <  }
483 >    if( !ats->havePosition() ){
484 >      sprintf( painCave.errMsg,
485 >               "RigidBody error.\n"
486 >               "\tAtom %s does not have a position specified.\n"
487 >               "\tThis means RigidBody cannot set up reference coordinates.\n",
488 >               ats->getType() );
489 >      painCave.isFatal = 1;
490 >      simError();
491 >    }
492    
493 <  coords[0] = ats->getPosX();
494 <  coords[1] = ats->getPosY();
495 <  coords[2] = ats->getPosZ();
493 >    coords[0] = ats->getPosX();
494 >    coords[1] = ats->getPosY();
495 >    coords[2] = ats->getPosZ();
496  
497 <  refCoords_.push_back(coords);
497 >    refCoords_.push_back(coords);
498  
499 <  RotMat3x3d identMat = RotMat3x3d::identity();
499 >    RotMat3x3d identMat = RotMat3x3d::identity();
500    
501 <  if (at->isDirectional()) {  
501 >    if (at->isDirectional()) {  
502  
503 <    if( !ats->haveOrientation() ){
504 <      sprintf( painCave.errMsg,
505 <               "RigidBody error.\n"
506 <               "\tAtom %s does not have an orientation specified.\n"
507 <               "\tThis means RigidBody cannot set up reference orientations.\n",
508 <               ats->getType() );
509 <      painCave.isFatal = 1;
510 <      simError();
511 <    }    
503 >      if( !ats->haveOrientation() ){
504 >        sprintf( painCave.errMsg,
505 >                 "RigidBody error.\n"
506 >                 "\tAtom %s does not have an orientation specified.\n"
507 >                 "\tThis means RigidBody cannot set up reference orientations.\n",
508 >                 ats->getType() );
509 >        painCave.isFatal = 1;
510 >        simError();
511 >      }    
512      
513 <    euler[0] = ats->getEulerPhi();
514 <    euler[1] = ats->getEulerTheta();
515 <    euler[2] = ats->getEulerPsi();
513 >      euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
514 >      euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
515 >      euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;
516  
517 <    RotMat3x3d Atmp(euler);
518 <    refOrients_.push_back(Atmp);
517 >      RotMat3x3d Atmp(euler);
518 >      refOrients_.push_back(Atmp);
519      
520 <  }else {
521 <    refOrients_.push_back(identMat);
522 <  }
520 >    }else {
521 >      refOrients_.push_back(identMat);
522 >    }
523    
524    
525 < }
525 >  }
526  
527   }
528  

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