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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 1221 by chrisfen, Wed Jun 2 14:56:18 2004 UTC

# Line 31 | Line 31 | template<typename T> Integrator<T>::Integrator(SimInfo
31    }
32  
33    nAtoms = info->n_atoms;
34 <
34 >  integrableObjects = info->integrableObjects;
35 >
36    // check for constraints
37  
38    constrainedA = NULL;
# Line 44 | Line 45 | template<typename T> Integrator<T>::Integrator(SimInfo
45    nConstrained = 0;
46  
47    checkConstraints();
48 +
49   }
50  
51   template<typename T> Integrator<T>::~Integrator(){
# Line 68 | Line 70 | template<typename T> void Integrator<T>::checkConstrai
70  
71    SRI** theArray;
72    for (int i = 0; i < nMols; i++){
73 <    theArray = (SRI * *) molecules[i].getMyBonds();
73 >
74 >          theArray = (SRI * *) molecules[i].getMyBonds();
75      for (int j = 0; j < molecules[i].getNBonds(); j++){
76        constrained = theArray[j]->is_constrained();
77  
# Line 114 | Line 117 | template<typename T> void Integrator<T>::checkConstrai
117      }
118    }
119  
120 +
121    if (nConstrained > 0){
122      isConstrained = 1;
123  
# Line 157 | Line 161 | template<typename T> void Integrator<T>::integrate(voi
161    double thermalTime = info->thermalTime;
162    double resetTime = info->resetTime;
163  
164 <
164 >  double difference;
165    double currSample;
166    double currThermal;
167    double currStatus;
# Line 176 | Line 180 | template<typename T> void Integrator<T>::integrate(voi
180  
181    readyCheck();
182  
183 +  // remove center of mass drift velocity (in case we passed in a configuration
184 +  // that was drifting
185 +  tStats->removeCOMdrift();
186 +
187 +  // initialize the retraints if necessary
188 +  if (info->useSolidThermInt && !info->useLiquidThermInt) {
189 +    myFF->initRestraints();
190 +  }
191 +
192    // initialize the forces before the first step
193  
194    calcForce(1, 1);
195 <
195 >  
196    if (nConstrained){
197      preMove();
198      constrainA();
# Line 207 | Line 220 | template<typename T> void Integrator<T>::integrate(voi
220    MPIcheckPoint();
221   #endif // is_mpi
222  
223 <  while (info->getTime() < runTime){
224 <    if ((info->getTime() + dt) >= currStatus){
223 >  while (info->getTime() < runTime && !stopIntegrator()){
224 >    difference = info->getTime() + dt - currStatus;
225 >    if (difference > 0 || fabs(difference) < 1e-4 ){
226        calcPot = 1;
227        calcStress = 1;
228      }
# Line 263 | Line 277 | template<typename T> void Integrator<T>::integrate(voi
277   #endif // is_mpi
278    }
279  
280 +  // dump out a file containing the omega values for the final configuration
281 +  if (info->useSolidThermInt && !info->useLiquidThermInt)
282 +    myFF->dumpzAngle();
283 +  
284 +
285    delete dumpOut;
286    delete statOut;
287   }
# Line 297 | Line 316 | template<typename T> void Integrator<T>::integrateStep
316    MPIcheckPoint();
317   #endif // is_mpi
318  
300 –
319    // calc forces
302 –
320    calcForce(calcPot, calcStress);
321  
322   #ifdef IS_MPI
# Line 329 | Line 346 | template<typename T> void Integrator<T>::moveA(void){
346  
347  
348   template<typename T> void Integrator<T>::moveA(void){
349 <  int i, j;
349 >  size_t i, j;
350    DirectionalAtom* dAtom;
351    double Tb[3], ji[3];
352    double vel[3], pos[3], frc[3];
353    double mass;
354 <
355 <  for (i = 0; i < nAtoms; i++){
356 <    atoms[i]->getVel(vel);
357 <    atoms[i]->getPos(pos);
358 <    atoms[i]->getFrc(frc);
359 <
360 <    mass = atoms[i]->getMass();
354 >  double omega;
355 >
356 >  for (i = 0; i < integrableObjects.size() ; i++){
357 >    integrableObjects[i]->getVel(vel);
358 >    integrableObjects[i]->getPos(pos);
359 >    integrableObjects[i]->getFrc(frc);
360 >    
361 >    mass = integrableObjects[i]->getMass();
362  
363      for (j = 0; j < 3; j++){
364        // velocity half step
# Line 349 | Line 367 | template<typename T> void Integrator<T>::moveA(void){
367        pos[j] += dt * vel[j];
368      }
369  
370 <    atoms[i]->setVel(vel);
371 <    atoms[i]->setPos(pos);
370 >    integrableObjects[i]->setVel(vel);
371 >    integrableObjects[i]->setPos(pos);
372  
373 <    if (atoms[i]->isDirectional()){
356 <      dAtom = (DirectionalAtom *) atoms[i];
373 >    if (integrableObjects[i]->isDirectional()){
374  
375        // get and convert the torque to body frame
376  
377 <      dAtom->getTrq(Tb);
378 <      dAtom->lab2Body(Tb);
377 >      integrableObjects[i]->getTrq(Tb);
378 >      integrableObjects[i]->lab2Body(Tb);
379  
380        // get the angular momentum, and propagate a half step
381  
382 <      dAtom->getJ(ji);
382 >      integrableObjects[i]->getJ(ji);
383  
384        for (j = 0; j < 3; j++)
385          ji[j] += (dt2 * Tb[j]) * eConvert;
386  
387 <      this->rotationPropagation( dAtom, ji );
387 >      this->rotationPropagation( integrableObjects[i], ji );
388  
389 <      dAtom->setJ(ji);
389 >      integrableObjects[i]->setJ(ji);
390      }
391    }
392  
# Line 381 | Line 398 | template<typename T> void Integrator<T>::moveB(void){
398  
399   template<typename T> void Integrator<T>::moveB(void){
400    int i, j;
384 –  DirectionalAtom* dAtom;
401    double Tb[3], ji[3];
402    double vel[3], frc[3];
403    double mass;
404  
405 <  for (i = 0; i < nAtoms; i++){
406 <    atoms[i]->getVel(vel);
407 <    atoms[i]->getFrc(frc);
405 >  for (i = 0; i < integrableObjects.size(); i++){
406 >    integrableObjects[i]->getVel(vel);
407 >    integrableObjects[i]->getFrc(frc);
408  
409 <    mass = atoms[i]->getMass();
409 >    mass = integrableObjects[i]->getMass();
410  
411      // velocity half step
412      for (j = 0; j < 3; j++)
413        vel[j] += (dt2 * frc[j] / mass) * eConvert;
414  
415 <    atoms[i]->setVel(vel);
415 >    integrableObjects[i]->setVel(vel);
416  
417 <    if (atoms[i]->isDirectional()){
402 <      dAtom = (DirectionalAtom *) atoms[i];
417 >    if (integrableObjects[i]->isDirectional()){
418  
419        // get and convert the torque to body frame
420  
421 <      dAtom->getTrq(Tb);
422 <      dAtom->lab2Body(Tb);
421 >      integrableObjects[i]->getTrq(Tb);
422 >      integrableObjects[i]->lab2Body(Tb);
423  
424        // get the angular momentum, and propagate a half step
425  
426 <      dAtom->getJ(ji);
426 >      integrableObjects[i]->getJ(ji);
427  
428        for (j = 0; j < 3; j++)
429          ji[j] += (dt2 * Tb[j]) * eConvert;
430  
431  
432 <      dAtom->setJ(ji);
432 >      integrableObjects[i]->setJ(ji);
433      }
434    }
435  
# Line 683 | Line 698 | template<typename T> void Integrator<T>::rotationPropa
698   }
699  
700   template<typename T> void Integrator<T>::rotationPropagation
701 < ( DirectionalAtom* dAtom, double ji[3] ){
701 > ( StuntDouble* sd, double ji[3] ){
702  
703    double angle;
704    double A[3][3], I[3][3];
705 +  int i, j, k;
706  
707    // use the angular velocities to propagate the rotation matrix a
708    // full time step
693 –
694 –  dAtom->getA(A);
695 –  dAtom->getI(I);
709  
710 <  // rotate about the x-axis
711 <  angle = dt2 * ji[0] / I[0][0];
699 <  this->rotate( 1, 2, angle, ji, A );
710 >  sd->getA(A);
711 >  sd->getI(I);
712  
713 <  // rotate about the y-axis
714 <  angle = dt2 * ji[1] / I[1][1];
715 <  this->rotate( 2, 0, angle, ji, A );
713 >  if (sd->isLinear()) {
714 >    i = sd->linearAxis();
715 >    j = (i+1)%3;
716 >    k = (i+2)%3;
717 >    
718 >    angle = dt2 * ji[j] / I[j][j];
719 >    this->rotate( k, i, angle, ji, A );
720  
721 <  // rotate about the z-axis
722 <  angle = dt * ji[2] / I[2][2];
723 <  this->rotate( 0, 1, angle, ji, A);
721 >    angle = dt * ji[k] / I[k][k];
722 >    this->rotate( i, j, angle, ji, A);
723 >
724 >    angle = dt2 * ji[j] / I[j][j];
725 >    this->rotate( k, i, angle, ji, A );
726  
727 <  // rotate about the y-axis
728 <  angle = dt2 * ji[1] / I[1][1];
729 <  this->rotate( 2, 0, angle, ji, A );
730 <
731 <  // rotate about the x-axis
732 <  angle = dt2 * ji[0] / I[0][0];
733 <  this->rotate( 1, 2, angle, ji, A );
734 <
735 <  dAtom->setA( A  );
727 >  } else {
728 >    // rotate about the x-axis
729 >    angle = dt2 * ji[0] / I[0][0];
730 >    this->rotate( 1, 2, angle, ji, A );
731 >    
732 >    // rotate about the y-axis
733 >    angle = dt2 * ji[1] / I[1][1];
734 >    this->rotate( 2, 0, angle, ji, A );
735 >    
736 >    // rotate about the z-axis
737 >    angle = dt * ji[2] / I[2][2];
738 >    sd->addZangle(angle);
739 >    this->rotate( 0, 1, angle, ji, A);
740 >    
741 >    // rotate about the y-axis
742 >    angle = dt2 * ji[1] / I[1][1];
743 >    this->rotate( 2, 0, angle, ji, A );
744 >    
745 >    // rotate about the x-axis
746 >    angle = dt2 * ji[0] / I[0][0];
747 >    this->rotate( 1, 2, angle, ji, A );
748 >    
749 >  }
750 >  sd->setA( A  );
751   }
752  
753   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,

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