ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/primitives/RigidBody.cpp
(Generate patch)

Comparing trunk/src/primitives/RigidBody.cpp (file contents):
Revision 253 by tim, Thu Jan 13 19:40:37 2005 UTC vs.
Revision 507 by gezelter, Fri Apr 15 22:04:00 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);
183 +        Itmp(1, 1) += Iproject(1, 1);
184 +        Itmp(2, 2) += Iproject(2, 2);
185 +      }
186 +    }
187 +
188      //diagonalize
189      Vector3d evals;
190      Mat3x3d::diagonalize(Itmp, evals, sU_);
# Line 185 | 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 218 | 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 253 | 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 );      
278 <        }
275 >        dAtom = (DirectionalAtom *) atoms_[i];
276 >        dAtom->setA(a * refOrients_[i]);
277 >        //dAtom->rotateBy( A );      
278 >      }
279  
280      }
281    
282 < }
282 >  }
283  
284  
285 < bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
286 <    if (index < atoms_.size()) {
285 >  void  RigidBody::updateAtoms(int frame) {
286 >    unsigned int i;
287 >    Vector3d ref;
288 >    Vector3d apos;
289 >    DirectionalAtom* dAtom;
290 >    Vector3d pos = getPos(frame);
291 >    RotMat3x3d a = getA(frame);
292 >    
293 >    for (i = 0; i < atoms_.size(); i++) {
294 >    
295 >      ref = body2Lab(refCoords_[i], frame);
296  
297 <        Vector3d ref = body2Lab(refCoords_[index]);
278 <        pos = getPos() + ref;
279 <        return true;
280 <    } else {
281 <        std::cerr << index << " is an invalid index, current rigid body contains "
282 <                      << atoms_.size() << "atoms" << std::endl;
283 <        return false;
284 <    }    
285 < }
297 >      apos = pos + ref;
298  
299 < bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
300 <    std::vector<Atom*>::iterator i;
301 <    i = std::find(atoms_.begin(), atoms_.end(), atom);
302 <    if (i != atoms_.end()) {
303 <        //RigidBody class makes sure refCoords_ and atoms_ match each other
304 <        Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
305 <        pos = getPos() + ref;
306 <        return true;
295 <    } else {
296 <        std::cerr << "Atom " << atom->getGlobalIndex()
297 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
298 <        return false;
299 >      atoms_[i]->setPos(apos, frame);
300 >
301 >      if (atoms_[i]->isDirectional()) {
302 >          
303 >        dAtom = (DirectionalAtom *) atoms_[i];
304 >        dAtom->setA(a * refOrients_[i], frame);
305 >      }
306 >
307      }
308 < }
309 < bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
308 >  
309 >  }
310  
311 <    //velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
311 >  void RigidBody::updateAtomVel() {
312 >    Mat3x3d skewMat;;
313  
314 <    if (index < atoms_.size()) {
314 >    Vector3d ji = getJ();
315 >    Mat3x3d I =  getI();
316  
317 <        Vector3d velRot;
318 <        Mat3x3d skewMat;;
319 <        Vector3d ref = refCoords_[index];
310 <        Vector3d ji = getJ();
311 <        Mat3x3d I =  getI();
317 >    skewMat(0, 0) =0;
318 >    skewMat(0, 1) = ji[2] /I(2, 2);
319 >    skewMat(0, 2) = -ji[1] /I(1, 1);
320  
321 <        skewMat(0, 0) =0;
322 <        skewMat(0, 1) = ji[2] /I(2, 2);
323 <        skewMat(0, 2) = -ji[1] /I(1, 1);
321 >    skewMat(1, 0) = -ji[2] /I(2, 2);
322 >    skewMat(1, 1) = 0;
323 >    skewMat(1, 2) = ji[0]/I(0, 0);
324  
325 <        skewMat(1, 0) = -ji[2] /I(2, 2);
326 <        skewMat(1, 1) = 0;
327 <        skewMat(1, 2) = ji[0]/I(0, 0);
325 >    skewMat(2, 0) =ji[1] /I(1, 1);
326 >    skewMat(2, 1) = -ji[0]/I(0, 0);
327 >    skewMat(2, 2) = 0;
328  
329 <        skewMat(2, 0) =ji[1] /I(1, 1);
330 <        skewMat(2, 1) = -ji[0]/I(0, 0);
323 <        skewMat(2, 2) = 0;
329 >    Mat3x3d mat = (getA() * skewMat).transpose();
330 >    Vector3d rbVel = getVel();
331  
325 –        velRot = (getA() * skewMat).transpose() * ref;
332  
333 <        vel =getVel() + velRot;
334 <        return true;
333 >    Vector3d velRot;        
334 >    for (int i =0 ; i < refCoords_.size(); ++i) {
335 >      atoms_[i]->setVel(rbVel + mat * refCoords_[i]);
336 >    }
337 >
338 >  }
339 >
340 >  void RigidBody::updateAtomVel(int frame) {
341 >    Mat3x3d skewMat;;
342 >
343 >    Vector3d ji = getJ(frame);
344 >    Mat3x3d I =  getI();
345 >
346 >    skewMat(0, 0) =0;
347 >    skewMat(0, 1) = ji[2] /I(2, 2);
348 >    skewMat(0, 2) = -ji[1] /I(1, 1);
349 >
350 >    skewMat(1, 0) = -ji[2] /I(2, 2);
351 >    skewMat(1, 1) = 0;
352 >    skewMat(1, 2) = ji[0]/I(0, 0);
353 >
354 >    skewMat(2, 0) =ji[1] /I(1, 1);
355 >    skewMat(2, 1) = -ji[0]/I(0, 0);
356 >    skewMat(2, 2) = 0;
357 >
358 >    Mat3x3d mat = (getA(frame) * skewMat).transpose();
359 >    Vector3d rbVel = getVel(frame);
360 >
361 >
362 >    Vector3d velRot;        
363 >    for (int i =0 ; i < refCoords_.size(); ++i) {
364 >      atoms_[i]->setVel(rbVel + mat * refCoords_[i], frame);
365 >    }
366 >
367 >  }
368 >
369          
370 +
371 +  bool RigidBody::getAtomPos(Vector3d& pos, unsigned int index) {
372 +    if (index < atoms_.size()) {
373 +
374 +      Vector3d ref = body2Lab(refCoords_[index]);
375 +      pos = getPos() + ref;
376 +      return true;
377      } else {
378 <        std::cerr << index << " is an invalid index, current rigid body contains "
379 <                      << atoms_.size() << "atoms" << std::endl;
380 <        return false;
378 >      std::cerr << index << " is an invalid index, current rigid body contains "
379 >                << atoms_.size() << "atoms" << std::endl;
380 >      return false;
381 >    }    
382 >  }
383 >
384 >  bool RigidBody::getAtomPos(Vector3d& pos, Atom* atom) {
385 >    std::vector<Atom*>::iterator i;
386 >    i = std::find(atoms_.begin(), atoms_.end(), atom);
387 >    if (i != atoms_.end()) {
388 >      //RigidBody class makes sure refCoords_ and atoms_ match each other
389 >      Vector3d ref = body2Lab(refCoords_[i - atoms_.begin()]);
390 >      pos = getPos() + ref;
391 >      return true;
392 >    } else {
393 >      std::cerr << "Atom " << atom->getGlobalIndex()
394 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;
395 >      return false;
396      }
397 < }
397 >  }
398 >  bool RigidBody::getAtomVel(Vector3d& vel, unsigned int index) {
399  
400 < bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
400 >    //velRot = $(A\cdot skew(I^{-1}j))^{T}refCoor$
401  
402 +    if (index < atoms_.size()) {
403 +
404 +      Vector3d velRot;
405 +      Mat3x3d skewMat;;
406 +      Vector3d ref = refCoords_[index];
407 +      Vector3d ji = getJ();
408 +      Mat3x3d I =  getI();
409 +
410 +      skewMat(0, 0) =0;
411 +      skewMat(0, 1) = ji[2] /I(2, 2);
412 +      skewMat(0, 2) = -ji[1] /I(1, 1);
413 +
414 +      skewMat(1, 0) = -ji[2] /I(2, 2);
415 +      skewMat(1, 1) = 0;
416 +      skewMat(1, 2) = ji[0]/I(0, 0);
417 +
418 +      skewMat(2, 0) =ji[1] /I(1, 1);
419 +      skewMat(2, 1) = -ji[0]/I(0, 0);
420 +      skewMat(2, 2) = 0;
421 +
422 +      velRot = (getA() * skewMat).transpose() * ref;
423 +
424 +      vel =getVel() + velRot;
425 +      return true;
426 +        
427 +    } else {
428 +      std::cerr << index << " is an invalid index, current rigid body contains "
429 +                << atoms_.size() << "atoms" << std::endl;
430 +      return false;
431 +    }
432 +  }
433 +
434 +  bool RigidBody::getAtomVel(Vector3d& vel, Atom* atom) {
435 +
436      std::vector<Atom*>::iterator i;
437      i = std::find(atoms_.begin(), atoms_.end(), atom);
438      if (i != atoms_.end()) {
439 <        return getAtomVel(vel, i - atoms_.begin());
439 >      return getAtomVel(vel, i - atoms_.begin());
440      } else {
441 <        std::cerr << "Atom " << atom->getGlobalIndex()
442 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
443 <        return false;
441 >      std::cerr << "Atom " << atom->getGlobalIndex()
442 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
443 >      return false;
444      }    
445 < }
445 >  }
446  
447 < bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
447 >  bool RigidBody::getAtomRefCoor(Vector3d& coor, unsigned int index) {
448      if (index < atoms_.size()) {
449  
450 <        coor = refCoords_[index];
451 <        return true;
450 >      coor = refCoords_[index];
451 >      return true;
452      } else {
453 <        std::cerr << index << " is an invalid index, current rigid body contains "
454 <                      << atoms_.size() << "atoms" << std::endl;
455 <        return false;
453 >      std::cerr << index << " is an invalid index, current rigid body contains "
454 >                << atoms_.size() << "atoms" << std::endl;
455 >      return false;
456      }
457  
458 < }
458 >  }
459  
460 < bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
460 >  bool RigidBody::getAtomRefCoor(Vector3d& coor, Atom* atom) {
461      std::vector<Atom*>::iterator i;
462      i = std::find(atoms_.begin(), atoms_.end(), atom);
463      if (i != atoms_.end()) {
464 <        //RigidBody class makes sure refCoords_ and atoms_ match each other
465 <        coor = refCoords_[i - atoms_.begin()];
466 <        return true;
464 >      //RigidBody class makes sure refCoords_ and atoms_ match each other
465 >      coor = refCoords_[i - atoms_.begin()];
466 >      return true;
467      } else {
468 <        std::cerr << "Atom " << atom->getGlobalIndex()
469 <                      <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
470 <        return false;
468 >      std::cerr << "Atom " << atom->getGlobalIndex()
469 >                <<" does not belong to Rigid body "<< getGlobalIndex() << std::endl;    
470 >      return false;
471      }
472  
473 < }
473 >  }
474  
475  
476 < void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
476 >  void RigidBody::addAtom(Atom* at, AtomStamp* ats) {
477  
478 <  Vector3d coords;
479 <  Vector3d euler;
478 >    Vector3d coords;
479 >    Vector3d euler;
480    
481  
482 <  atoms_.push_back(at);
482 >    atoms_.push_back(at);
483  
484 <  if( !ats->havePosition() ){
485 <    sprintf( painCave.errMsg,
486 <             "RigidBody error.\n"
487 <             "\tAtom %s does not have a position specified.\n"
488 <             "\tThis means RigidBody cannot set up reference coordinates.\n",
489 <             ats->getType() );
490 <    painCave.isFatal = 1;
491 <    simError();
492 <  }
484 >    if( !ats->havePosition() ){
485 >      sprintf( painCave.errMsg,
486 >               "RigidBody error.\n"
487 >               "\tAtom %s does not have a position specified.\n"
488 >               "\tThis means RigidBody cannot set up reference coordinates.\n",
489 >               ats->getType() );
490 >      painCave.isFatal = 1;
491 >      simError();
492 >    }
493    
494 <  coords[0] = ats->getPosX();
495 <  coords[1] = ats->getPosY();
496 <  coords[2] = ats->getPosZ();
494 >    coords[0] = ats->getPosX();
495 >    coords[1] = ats->getPosY();
496 >    coords[2] = ats->getPosZ();
497  
498 <  refCoords_.push_back(coords);
498 >    refCoords_.push_back(coords);
499  
500 <  RotMat3x3d identMat = RotMat3x3d::identity();
500 >    RotMat3x3d identMat = RotMat3x3d::identity();
501    
502 <  if (at->isDirectional()) {  
502 >    if (at->isDirectional()) {  
503  
504 <    if( !ats->haveOrientation() ){
505 <      sprintf( painCave.errMsg,
506 <               "RigidBody error.\n"
507 <               "\tAtom %s does not have an orientation specified.\n"
508 <               "\tThis means RigidBody cannot set up reference orientations.\n",
509 <               ats->getType() );
510 <      painCave.isFatal = 1;
511 <      simError();
512 <    }    
504 >      if( !ats->haveOrientation() ){
505 >        sprintf( painCave.errMsg,
506 >                 "RigidBody error.\n"
507 >                 "\tAtom %s does not have an orientation specified.\n"
508 >                 "\tThis means RigidBody cannot set up reference orientations.\n",
509 >                 ats->getType() );
510 >        painCave.isFatal = 1;
511 >        simError();
512 >      }    
513      
514 <    euler[0] = ats->getEulerPhi();
515 <    euler[1] = ats->getEulerTheta();
516 <    euler[2] = ats->getEulerPsi();
514 >      euler[0] = ats->getEulerPhi() * NumericConstant::PI /180.0;
515 >      euler[1] = ats->getEulerTheta() * NumericConstant::PI /180.0;
516 >      euler[2] = ats->getEulerPsi() * NumericConstant::PI /180.0;
517  
518 <    RotMat3x3d Atmp(euler);
519 <    refOrients_.push_back(Atmp);
518 >      RotMat3x3d Atmp(euler);
519 >      refOrients_.push_back(Atmp);
520      
521 <  }else {
522 <    refOrients_.push_back(identMat);
523 <  }
521 >    }else {
522 >      refOrients_.push_back(identMat);
523 >    }
524    
525    
526 < }
526 >  }
527  
528   }
529  

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines