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root/OpenMD/trunk/src/primitives/RigidBody.cpp
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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 641 by tim, Mon Oct 3 14:31:31 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
166 >    // Moment of Inertia calculation
167      Mat3x3d Itmp(0.0);
168    
169      for (std::size_t i = 0; i < atoms_.size(); i++) {
170 <        mtmp = atoms_[i]->getMass();
171 <        Itmp -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
172 <        double r2 = refCoords_[i].lengthSquare();
173 <        Itmp(0, 0) += mtmp * r2;
174 <        Itmp(1, 1) += mtmp * r2;
175 <        Itmp(2, 2) += mtmp * r2;
170 >      mtmp = atoms_[i]->getMass();
171 >      Itmp -= outProduct(refCoords_[i], refCoords_[i]) * mtmp;
172 >      double r2 = refCoords_[i].lengthSquare();
173 >      Itmp(0, 0) += mtmp * r2;
174 >      Itmp(1, 1) += mtmp * r2;
175 >      Itmp(2, 2) += mtmp * r2;
176      }
177  
178      //project the inertial moment of directional atoms into this rigid body
179      for (std::size_t i = 0; i < atoms_.size(); i++) {
180 <        if (atoms_[i]->isDirectional()) {
181 <            RectMatrix<double, 3, 3> Iproject = refOrients_[i].transpose() * atoms_[i]->getI();
182 <            Itmp(0, 0) += Iproject(0, 0);
182 <            Itmp(1, 1) += Iproject(1, 1);
183 <            Itmp(2, 2) += Iproject(2, 2);
184 <        }
180 >      if (atoms_[i]->isDirectional()) {
181 >            Itmp += refOrients_[i].transpose() * atoms_[i]->getI() * refOrients_[i];
182 >      }
183      }
184  
185      //diagonalize
# Line 195 | Line 193 | void  RigidBody::calcRefCoords() {
193          
194      int nLinearAxis = 0;
195      for (int i = 0; i < 3; i++) {    
196 <        if (fabs(evals[i]) < oopse::epsilon) {
197 <            linear_ = true;
198 <            linearAxis_ = i;
199 <            ++ nLinearAxis;
200 <        }
196 >      if (fabs(evals[i]) < oopse::epsilon) {
197 >        linear_ = true;
198 >        linearAxis_ = i;
199 >        ++ nLinearAxis;
200 >      }
201      }
202  
203      if (nLinearAxis > 1) {
204 <        sprintf( painCave.errMsg,
205 <            "RigidBody error.\n"
206 <            "\tOOPSE found more than one axis in this rigid body with a vanishing \n"
207 <            "\tmoment of inertia.  This can happen in one of three ways:\n"
208 <            "\t 1) Only one atom was specified, or \n"
209 <            "\t 2) All atoms were specified at the same location, or\n"
210 <            "\t 3) The programmers did something stupid.\n"
211 <            "\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
212 <            );
213 <        painCave.isFatal = 1;
214 <        simError();
204 >      sprintf( painCave.errMsg,
205 >               "RigidBody error.\n"
206 >               "\tOOPSE found more than one axis in this rigid body with a vanishing \n"
207 >               "\tmoment of inertia.  This can happen in one of three ways:\n"
208 >               "\t 1) Only one atom was specified, or \n"
209 >               "\t 2) All atoms were specified at the same location, or\n"
210 >               "\t 3) The programmers did something stupid.\n"
211 >               "\tIt is silly to use a rigid body to describe this situation.  Be smarter.\n"
212 >               );
213 >      painCave.isFatal = 1;
214 >      simError();
215      }
216    
217 < }
217 >  }
218  
219 < void  RigidBody::calcForcesAndTorques() {
219 >  void  RigidBody::calcForcesAndTorques() {
220      Vector3d afrc;
221      Vector3d atrq;
222      Vector3d apos;
# Line 228 | Line 226 | void  RigidBody::calcForcesAndTorques() {
226      Vector3d pos = this->getPos();
227      for (int i = 0; i < atoms_.size(); i++) {
228  
229 <        afrc = atoms_[i]->getFrc();
230 <        apos = atoms_[i]->getPos();
231 <        rpos = apos - pos;
229 >      afrc = atoms_[i]->getFrc();
230 >      apos = atoms_[i]->getPos();
231 >      rpos = apos - pos;
232          
233 <        frc += afrc;
233 >      frc += afrc;
234  
235 <        trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
236 <        trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
237 <        trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];
235 >      trq[0] += rpos[1]*afrc[2] - rpos[2]*afrc[1];
236 >      trq[1] += rpos[2]*afrc[0] - rpos[0]*afrc[2];
237 >      trq[2] += rpos[0]*afrc[1] - rpos[1]*afrc[0];
238  
239 <        // If the atom has a torque associated with it, then we also need to
240 <        // migrate the torques onto the center of mass:
239 >      // If the atom has a torque associated with it, then we also need to
240 >      // migrate the torques onto the center of mass:
241  
242 <        if (atoms_[i]->isDirectional()) {
243 <            atrq = atoms_[i]->getTrq();
244 <            trq += atrq;
245 <        }
242 >      if (atoms_[i]->isDirectional()) {
243 >        atrq = atoms_[i]->getTrq();
244 >        trq += atrq;
245 >      }
246          
247      }
248      
249      setFrc(frc);
250      setTrq(trq);
251      
252 < }
252 >  }
253  
254 < void  RigidBody::updateAtoms() {
254 >  void  RigidBody::updateAtoms() {
255      unsigned int i;
256      Vector3d ref;
257      Vector3d apos;
# Line 263 | Line 261 | void  RigidBody::updateAtoms() {
261      
262      for (i = 0; i < atoms_.size(); i++) {
263      
264 <        ref = body2Lab(refCoords_[i]);
264 >      ref = body2Lab(refCoords_[i]);
265  
266 <        apos = pos + ref;
266 >      apos = pos + ref;
267  
268 <        atoms_[i]->setPos(apos);
268 >      atoms_[i]->setPos(apos);
269  
270 <        if (atoms_[i]->isDirectional()) {
270 >      if (atoms_[i]->isDirectional()) {
271            
272 <          dAtom = (DirectionalAtom *) atoms_[i];
273 <          dAtom->setA(a * refOrients_[i]);
274 <          //dAtom->rotateBy( A );      
277 <        }
272 >        dAtom = (DirectionalAtom *) atoms_[i];
273 >        dAtom->setA(refOrients_[i] * a);
274 >      }
275  
276      }
277    
278 < }
278 >  }
279  
280  
281 < bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
282 <    if (index < atoms_.size()) {
281 >  void  RigidBody::updateAtoms(int frame) {
282 >    unsigned int i;
283 >    Vector3d ref;
284 >    Vector3d apos;
285 >    DirectionalAtom* dAtom;
286 >    Vector3d pos = getPos(frame);
287 >    RotMat3x3d a = getA(frame);
288 >    
289 >    for (i = 0; i < atoms_.size(); i++) {
290 >    
291 >      ref = body2Lab(refCoords_[i], frame);
292  
293 <        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 < }
293 >      apos = pos + ref;
294  
295 < bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
296 <    std::vector<Atom*>::iterator i;
297 <    i = std::find(atoms_.begin(), atoms_.end(), atom);
298 <    if (i != atoms_.end()) {
299 <        //RigidBody class makes sure refCoords_ and atoms_ match each other
300 <        Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
301 <        pos = getPos() + ref;
302 <        return true;
305 <    } else {
306 <        std::cerr << "Atom " << atom->getGlobalIndex()
307 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
308 <        return false;
295 >      atoms_[i]->setPos(apos, frame);
296 >
297 >      if (atoms_[i]->isDirectional()) {
298 >          
299 >        dAtom = (DirectionalAtom *) atoms_[i];
300 >        dAtom->setA(refOrients_[i] * a, frame);
301 >      }
302 >
303      }
304 < }
305 < bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
304 >  
305 >  }
306  
307 <    //velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
307 >  void RigidBody::updateAtomVel() {
308 >    Mat3x3d skewMat;;
309  
310 <    if (index < atoms_.size()) {
310 >    Vector3d ji = getJ();
311 >    Mat3x3d I =  getI();
312  
313 <        Vector3d velRot;
314 <        Mat3x3d skewMat;;
315 <        Vector3d ref = refCoords_[index];
320 <        Vector3d ji = getJ();
321 <        Mat3x3d I =  getI();
313 >    skewMat(0, 0) =0;
314 >    skewMat(0, 1) = ji[2] /I(2, 2);
315 >    skewMat(0, 2) = -ji[1] /I(1, 1);
316  
317 <        skewMat(0, 0) =0;
318 <        skewMat(0, 1) = ji[2] /I(2, 2);
319 <        skewMat(0, 2) = -ji[1] /I(1, 1);
317 >    skewMat(1, 0) = -ji[2] /I(2, 2);
318 >    skewMat(1, 1) = 0;
319 >    skewMat(1, 2) = ji[0]/I(0, 0);
320  
321 <        skewMat(1, 0) = -ji[2] /I(2, 2);
322 <        skewMat(1, 1) = 0;
323 <        skewMat(1, 2) = ji[0]/I(0, 0);
321 >    skewMat(2, 0) =ji[1] /I(1, 1);
322 >    skewMat(2, 1) = -ji[0]/I(0, 0);
323 >    skewMat(2, 2) = 0;
324  
325 <        skewMat(2, 0) =ji[1] /I(1, 1);
326 <        skewMat(2, 1) = -ji[0]/I(0, 0);
333 <        skewMat(2, 2) = 0;
325 >    Mat3x3d mat = (getA() * skewMat).transpose();
326 >    Vector3d rbVel = getVel();
327  
335 –        velRot = (getA() * skewMat).transpose() * ref;
328  
329 <        vel =getVel() + velRot;
330 <        return true;
329 >    Vector3d velRot;        
330 >    for (int i =0 ; i < refCoords_.size(); ++i) {
331 >      atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
332 >    }
333 >
334 >  }
335 >
336 >  void RigidBody::updateAtomVel(int frame) {
337 >    Mat3x3d skewMat;;
338 >
339 >    Vector3d ji = getJ(frame);
340 >    Mat3x3d I =  getI();
341 >
342 >    skewMat(0, 0) =0;
343 >    skewMat(0, 1) = ji[2] /I(2, 2);
344 >    skewMat(0, 2) = -ji[1] /I(1, 1);
345 >
346 >    skewMat(1, 0) = -ji[2] /I(2, 2);
347 >    skewMat(1, 1) = 0;
348 >    skewMat(1, 2) = ji[0]/I(0, 0);
349 >
350 >    skewMat(2, 0) =ji[1] /I(1, 1);
351 >    skewMat(2, 1) = -ji[0]/I(0, 0);
352 >    skewMat(2, 2) = 0;
353 >
354 >    Mat3x3d mat = (getA(frame) * skewMat).transpose();
355 >    Vector3d rbVel = getVel(frame);
356 >
357 >
358 >    Vector3d velRot;        
359 >    for (int i =0 ; i < refCoords_.size(); ++i) {
360 >      atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
361 >    }
362 >
363 >  }
364 >
365          
366 +
367 +  bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
368 +    if (index < atoms_.size()) {
369 +
370 +      Vector3d ref = body2Lab(refCoords_[index]);
371 +      pos = getPos() + ref;
372 +      return true;
373      } else {
374 <        std::cerr << index << " is an invalid index, current rigid body contains "
375 <                      << atoms_.size() << "atoms" << std::endl;
376 <        return false;
374 >      std::cerr << index << " is an invalid index, current rigid body contains "
375 >                << atoms_.size() << "atoms" << std::endl;
376 >      return false;
377 >    }    
378 >  }
379 >
380 >  bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
381 >    std::vector<Atom*>::iterator i;
382 >    i = std::find(atoms_.begin(), atoms_.end(), atom);
383 >    if (i != atoms_.end()) {
384 >      //RigidBody class makes sure refCoords_ and atoms_ match each other
385 >      Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
386 >      pos = getPos() + ref;
387 >      return true;
388 >    } else {
389 >      std::cerr << "Atom " << atom->getGlobalIndex()
390 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
391 >      return false;
392      }
393 < }
393 >  }
394 >  bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
395  
396 < bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
396 >    //velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
397  
398 +    if (index < atoms_.size()) {
399 +
400 +      Vector3d velRot;
401 +      Mat3x3d skewMat;;
402 +      Vector3d ref = refCoords_[index];
403 +      Vector3d ji = getJ();
404 +      Mat3x3d I =  getI();
405 +
406 +      skewMat(0, 0) =0;
407 +      skewMat(0, 1) = ji[2] /I(2, 2);
408 +      skewMat(0, 2) = -ji[1] /I(1, 1);
409 +
410 +      skewMat(1, 0) = -ji[2] /I(2, 2);
411 +      skewMat(1, 1) = 0;
412 +      skewMat(1, 2) = ji[0]/I(0, 0);
413 +
414 +      skewMat(2, 0) =ji[1] /I(1, 1);
415 +      skewMat(2, 1) = -ji[0]/I(0, 0);
416 +      skewMat(2, 2) = 0;
417 +
418 +      velRot = (getA() * skewMat).transpose() * ref;
419 +
420 +      vel =getVel() + velRot;
421 +      return true;
422 +        
423 +    } else {
424 +      std::cerr << index << " is an invalid index, current rigid body contains "
425 +                << atoms_.size() << "atoms" << std::endl;
426 +      return false;
427 +    }
428 +  }
429 +
430 +  bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
431 +
432      std::vector<Atom*>::iterator i;
433      i = std::find(atoms_.begin(), atoms_.end(), atom);
434      if (i != atoms_.end()) {
435 <        return getAtomVel(vel, i - atoms_.begin());
435 >      return getAtomVel(vel, i - atoms_.begin());
436      } else {
437 <        std::cerr << "Atom " << atom->getGlobalIndex()
438 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
439 <        return false;
437 >      std::cerr << "Atom " << atom->getGlobalIndex()
438 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
439 >      return false;
440      }    
441 < }
441 >  }
442  
443 < bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
443 >  bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
444      if (index < atoms_.size()) {
445  
446 <        coor = refCoords_[index];
447 <        return true;
446 >      coor = refCoords_[index];
447 >      return true;
448      } else {
449 <        std::cerr << index << " is an invalid index, current rigid body contains "
450 <                      << atoms_.size() << "atoms" << std::endl;
451 <        return false;
449 >      std::cerr << index << " is an invalid index, current rigid body contains "
450 >                << atoms_.size() << "atoms" << std::endl;
451 >      return false;
452      }
453  
454 < }
454 >  }
455  
456 < bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
456 >  bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
457      std::vector<Atom*>::iterator i;
458      i = std::find(atoms_.begin(), atoms_.end(), atom);
459      if (i != atoms_.end()) {
460 <        //RigidBody class makes sure refCoords_ and atoms_ match each other
461 <        coor = refCoords_[i - atoms_.begin()];
462 <        return true;
460 >      //RigidBody class makes sure refCoords_ and atoms_ match each other
461 >      coor = refCoords_[i - atoms_.begin()];
462 >      return true;
463      } else {
464 <        std::cerr << "Atom " << atom->getGlobalIndex()
465 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
466 <        return false;
464 >      std::cerr << "Atom " << atom->getGlobalIndex()
465 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
466 >      return false;
467      }
468  
469 < }
469 >  }
470  
471  
472 < void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
472 >  void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
473  
474 <  Vector3d coords;
475 <  Vector3d euler;
474 >    Vector3d coords;
475 >    Vector3d euler;
476    
477  
478 <  atoms_.push_back(at);
478 >    atoms_.push_back(at);
479  
480 <  if( !ats->havePosition() ){
481 <    sprintf( painCave.errMsg,
482 <             "RigidBody error.\n"
483 <             "\tAtom %s does not have a position specified.\n"
484 <             "\tThis means RigidBody cannot set up reference coordinates.\n",
485 <             ats->getType() );
486 <    painCave.isFatal = 1;
487 <    simError();
488 <  }
480 >    if( !ats->havePosition() ){
481 >      sprintf( painCave.errMsg,
482 >               "RigidBody error.\n"
483 >               "\tAtom %s does not have a position specified.\n"
484 >               "\tThis means RigidBody cannot set up reference coordinates.\n",
485 >               ats->getType() );
486 >      painCave.isFatal = 1;
487 >      simError();
488 >    }
489    
490 <  coords[0] = ats->getPosX();
491 <  coords[1] = ats->getPosY();
492 <  coords[2] = ats->getPosZ();
490 >    coords[0] = ats->getPosX();
491 >    coords[1] = ats->getPosY();
492 >    coords[2] = ats->getPosZ();
493  
494 <  refCoords_.push_back(coords);
494 >    refCoords_.push_back(coords);
495  
496 <  RotMat3x3d identMat = RotMat3x3d::identity();
496 >    RotMat3x3d identMat = RotMat3x3d::identity();
497    
498 <  if (at->isDirectional()) {  
498 >    if (at->isDirectional()) {  
499  
500 <    if( !ats->haveOrientation() ){
501 <      sprintf( painCave.errMsg,
502 <               "RigidBody error.\n"
503 <               "\tAtom %s does not have an orientation specified.\n"
504 <               "\tThis means RigidBody cannot set up reference orientations.\n",
505 <               ats->getType() );
506 <      painCave.isFatal = 1;
507 <      simError();
508 <    }    
500 >      if( !ats->haveOrientation() ){
501 >        sprintf( painCave.errMsg,
502 >                 "RigidBody error.\n"
503 >                 "\tAtom %s does not have an orientation specified.\n"
504 >                 "\tThis means RigidBody cannot set up reference orientations.\n",
505 >                 ats->getType() );
506 >        painCave.isFatal = 1;
507 >        simError();
508 >      }    
509      
510 <    euler[0] = ats->getEulerPhi();
511 <    euler[1] = ats->getEulerTheta();
512 <    euler[2] = ats->getEulerPsi();
510 >      euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
511 >      euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
512 >      euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;
513  
514 <    RotMat3x3d Atmp(euler);
515 <    refOrients_.push_back(Atmp);
514 >      RotMat3x3d Atmp(euler);
515 >      refOrients_.push_back(Atmp);
516      
517 <  }else {
518 <    refOrients_.push_back(identMat);
519 <  }
517 >    }else {
518 >      refOrients_.push_back(identMat);
519 >    }
520    
521    
522 < }
522 >  }
523  
524   }
525  

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