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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 999 by chrisfen, Fri Jan 30 15:01:09 2004 UTC vs.
Revision 1127 by tim, Tue Apr 20 16:56:40 2004 UTC

# Line 31 | Line 31 | template<typename T> Integrator<T>::Integrator(SimInfo
31    }
32  
33    nAtoms = info->n_atoms;
34 +  integrableObjects = info->integrableObjects;
35  
36    // check for constraints
37  
# Line 68 | Line 69 | template<typename T> void Integrator<T>::checkConstrai
69  
70    SRI** theArray;
71    for (int i = 0; i < nMols; i++){
72 <    theArray = (SRI * *) molecules[i].getMyBonds();
72 >
73 >          theArray = (SRI * *) molecules[i].getMyBonds();
74      for (int j = 0; j < molecules[i].getNBonds(); j++){
75        constrained = theArray[j]->is_constrained();
76  
# Line 114 | Line 116 | template<typename T> void Integrator<T>::checkConstrai
116      }
117    }
118  
119 +
120    if (nConstrained > 0){
121      isConstrained = 1;
122  
# Line 176 | Line 179 | template<typename T> void Integrator<T>::integrate(voi
179  
180    readyCheck();
181  
182 +  // remove center of mass drift velocity (in case we passed in a configuration
183 +  // that was drifting
184 +  tStats->removeCOMdrift();
185 +
186    // initialize the forces before the first step
187  
188    calcForce(1, 1);
189 <
189 >  
190    if (nConstrained){
191      preMove();
192      constrainA();
# Line 207 | Line 214 | template<typename T> void Integrator<T>::integrate(voi
214    MPIcheckPoint();
215   #endif // is_mpi
216  
217 <  while (info->getTime() < runTime){
217 >  while (info->getTime() < runTime && !stopIntegrator()){
218      if ((info->getTime() + dt) >= currStatus){
219        calcPot = 1;
220        calcStress = 1;
# Line 329 | Line 336 | template<typename T> void Integrator<T>::moveA(void){
336  
337  
338   template<typename T> void Integrator<T>::moveA(void){
339 <  int i, j;
339 >  size_t i, j;
340    DirectionalAtom* dAtom;
341    double Tb[3], ji[3];
342    double vel[3], pos[3], frc[3];
343    double mass;
344 <
345 <  for (i = 0; i < nAtoms; i++){
346 <    atoms[i]->getVel(vel);
347 <    atoms[i]->getPos(pos);
348 <    atoms[i]->getFrc(frc);
344 >
345 >  for (i = 0; i < integrableObjects.size() ; i++){
346 >    integrableObjects[i]->getVel(vel);
347 >    integrableObjects[i]->getPos(pos);
348 >    integrableObjects[i]->getFrc(frc);
349 >    
350 >    mass = integrableObjects[i]->getMass();
351  
343 –    mass = atoms[i]->getMass();
344 –
352      for (j = 0; j < 3; j++){
353        // velocity half step
354        vel[j] += (dt2 * frc[j] / mass) * eConvert;
# Line 349 | Line 356 | template<typename T> void Integrator<T>::moveA(void){
356        pos[j] += dt * vel[j];
357      }
358  
359 <    atoms[i]->setVel(vel);
360 <    atoms[i]->setPos(pos);
359 >    integrableObjects[i]->setVel(vel);
360 >    integrableObjects[i]->setPos(pos);
361  
362 <    if (atoms[i]->isDirectional()){
356 <      dAtom = (DirectionalAtom *) atoms[i];
362 >    if (integrableObjects[i]->isDirectional()){
363  
364        // get and convert the torque to body frame
365  
366 <      dAtom->getTrq(Tb);
367 <      dAtom->lab2Body(Tb);
366 >      integrableObjects[i]->getTrq(Tb);
367 >      integrableObjects[i]->lab2Body(Tb);
368  
369        // get the angular momentum, and propagate a half step
370  
371 <      dAtom->getJ(ji);
371 >      integrableObjects[i]->getJ(ji);
372  
373        for (j = 0; j < 3; j++)
374          ji[j] += (dt2 * Tb[j]) * eConvert;
375  
376 <      this->rotationPropagation( dAtom, ji );
376 >      this->rotationPropagation( integrableObjects[i], ji );
377  
378 <      dAtom->setJ(ji);
378 >      integrableObjects[i]->setJ(ji);
379      }
380    }
381  
# Line 381 | Line 387 | template<typename T> void Integrator<T>::moveB(void){
387  
388   template<typename T> void Integrator<T>::moveB(void){
389    int i, j;
384 –  DirectionalAtom* dAtom;
390    double Tb[3], ji[3];
391    double vel[3], frc[3];
392    double mass;
393  
394 <  for (i = 0; i < nAtoms; i++){
395 <    atoms[i]->getVel(vel);
396 <    atoms[i]->getFrc(frc);
394 >  for (i = 0; i < integrableObjects.size(); i++){
395 >    integrableObjects[i]->getVel(vel);
396 >    integrableObjects[i]->getFrc(frc);
397  
398 <    mass = atoms[i]->getMass();
398 >    mass = integrableObjects[i]->getMass();
399  
400      // velocity half step
401      for (j = 0; j < 3; j++)
402        vel[j] += (dt2 * frc[j] / mass) * eConvert;
403  
404 <    atoms[i]->setVel(vel);
404 >    integrableObjects[i]->setVel(vel);
405  
406 <    if (atoms[i]->isDirectional()){
402 <      dAtom = (DirectionalAtom *) atoms[i];
406 >    if (integrableObjects[i]->isDirectional()){
407  
408        // get and convert the torque to body frame
409  
410 <      dAtom->getTrq(Tb);
411 <      dAtom->lab2Body(Tb);
410 >      integrableObjects[i]->getTrq(Tb);
411 >      integrableObjects[i]->lab2Body(Tb);
412  
413        // get the angular momentum, and propagate a half step
414  
415 <      dAtom->getJ(ji);
415 >      integrableObjects[i]->getJ(ji);
416  
417        for (j = 0; j < 3; j++)
418          ji[j] += (dt2 * Tb[j]) * eConvert;
419  
420  
421 <      dAtom->setJ(ji);
421 >      integrableObjects[i]->setJ(ji);
422      }
423    }
424  
# Line 683 | Line 687 | template<typename T> void Integrator<T>::rotationPropa
687   }
688  
689   template<typename T> void Integrator<T>::rotationPropagation
690 < ( DirectionalAtom* dAtom, double ji[3] ){
690 > ( StuntDouble* sd, double ji[3] ){
691  
692    double angle;
693    double A[3][3], I[3][3];
694 +  int i, j, k;
695  
696    // use the angular velocities to propagate the rotation matrix a
697    // full time step
698  
699 <  dAtom->getA(A);
700 <  dAtom->getI(I);
699 >  sd->getA(A);
700 >  sd->getI(I);
701  
702 <  // rotate about the x-axis
703 <  angle = dt2 * ji[0] / I[0][0];
704 <  this->rotate( 1, 2, angle, ji, A );
702 >  if (sd->isLinear()) {
703 >    i = sd->linearAxis();
704 >    j = (i+1)%3;
705 >    k = (i+2)%3;
706 >    
707 >    angle = dt2 * ji[j] / I[j][j];
708 >    this->rotate( k, i, angle, ji, A );
709  
710 <  // rotate about the y-axis
711 <  angle = dt2 * ji[1] / I[1][1];
703 <  this->rotate( 2, 0, angle, ji, A );
710 >    angle = dt * ji[k] / I[k][k];
711 >    this->rotate( i, j, angle, ji, A);
712  
713 <  // rotate about the z-axis
714 <  angle = dt * ji[2] / I[2][2];
707 <  this->rotate( 0, 1, angle, ji, A);
713 >    angle = dt2 * ji[j] / I[j][j];
714 >    this->rotate( k, i, angle, ji, A );
715  
716 <  // rotate about the y-axis
717 <  angle = dt2 * ji[1] / I[1][1];
718 <  this->rotate( 2, 0, angle, ji, A );
719 <
720 <  // rotate about the x-axis
721 <  angle = dt2 * ji[0] / I[0][0];
722 <  this->rotate( 1, 2, angle, ji, A );
723 <
724 <  dAtom->setA( A  );
716 >  } else {
717 >    // rotate about the x-axis
718 >    angle = dt2 * ji[0] / I[0][0];
719 >    this->rotate( 1, 2, angle, ji, A );
720 >    
721 >    // rotate about the y-axis
722 >    angle = dt2 * ji[1] / I[1][1];
723 >    this->rotate( 2, 0, angle, ji, A );
724 >    
725 >    // rotate about the z-axis
726 >    angle = dt * ji[2] / I[2][2];
727 >    this->rotate( 0, 1, angle, ji, A);
728 >    
729 >    // rotate about the y-axis
730 >    angle = dt2 * ji[1] / I[1][1];
731 >    this->rotate( 2, 0, angle, ji, A );
732 >    
733 >    // rotate about the x-axis
734 >    angle = dt2 * ji[0] / I[0][0];
735 >    this->rotate( 1, 2, angle, ji, A );
736 >    
737 >  }
738 >  sd->setA( A  );
739   }
740  
741   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,

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