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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 1057 by tim, Tue Feb 17 19:23:44 2004 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 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 159 | 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 178 | 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->useThermInt) {
189 +    myFF->initRestraints();
190 +  }
191 +
192    // initialize the forces before the first step
193  
194    calcForce(1, 1);
184 –
185 –  //temp test
186 –  tStats->getPotential();
195    
196    if (nConstrained){
197      preMove();
# Line 212 | 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 246 | Line 255 | template<typename T> void Integrator<T>::integrate(voi
255  
256      if (info->getTime() >= currStatus){
257        statOut->writeStat(info->getTime());
258 +      statOut->writeRaw(info->getTime());
259        calcPot = 0;
260        calcStress = 0;
261        currStatus += statusTime;
# Line 268 | Line 278 | template<typename T> void Integrator<T>::integrate(voi
278   #endif // is_mpi
279    }
280  
281 +  // dump out a file containing the omega values for the final configuration
282 +  if (info->useThermInt)
283 +    myFF->dumpzAngle();
284 +  
285 +
286    delete dumpOut;
287    delete statOut;
288   }
# Line 302 | Line 317 | template<typename T> void Integrator<T>::integrateStep
317    MPIcheckPoint();
318   #endif // is_mpi
319  
305 –
320    // calc forces
307 –
321    calcForce(calcPot, calcStress);
322  
323   #ifdef IS_MPI
# Line 334 | Line 347 | template<typename T> void Integrator<T>::moveA(void){
347  
348  
349   template<typename T> void Integrator<T>::moveA(void){
350 <  int i, j;
350 >  size_t i, j;
351    DirectionalAtom* dAtom;
352    double Tb[3], ji[3];
353    double vel[3], pos[3], frc[3];
354    double mass;
355 <
356 <  for (i = 0; i < nAtoms; i++){
357 <    atoms[i]->getVel(vel);
358 <    atoms[i]->getPos(pos);
359 <    atoms[i]->getFrc(frc);
360 <
361 <    mass = atoms[i]->getMass();
355 >  double omega;
356 >
357 >  for (i = 0; i < integrableObjects.size() ; i++){
358 >    integrableObjects[i]->getVel(vel);
359 >    integrableObjects[i]->getPos(pos);
360 >    integrableObjects[i]->getFrc(frc);
361 >    
362 >    mass = integrableObjects[i]->getMass();
363  
364      for (j = 0; j < 3; j++){
365        // velocity half step
# Line 354 | Line 368 | template<typename T> void Integrator<T>::moveA(void){
368        pos[j] += dt * vel[j];
369      }
370  
371 <    atoms[i]->setVel(vel);
372 <    atoms[i]->setPos(pos);
371 >    integrableObjects[i]->setVel(vel);
372 >    integrableObjects[i]->setPos(pos);
373  
374 <    if (atoms[i]->isDirectional()){
361 <      dAtom = (DirectionalAtom *) atoms[i];
374 >    if (integrableObjects[i]->isDirectional()){
375  
376        // get and convert the torque to body frame
377  
378 <      dAtom->getTrq(Tb);
379 <      dAtom->lab2Body(Tb);
378 >      integrableObjects[i]->getTrq(Tb);
379 >      integrableObjects[i]->lab2Body(Tb);
380  
381        // get the angular momentum, and propagate a half step
382  
383 <      dAtom->getJ(ji);
383 >      integrableObjects[i]->getJ(ji);
384  
385        for (j = 0; j < 3; j++)
386          ji[j] += (dt2 * Tb[j]) * eConvert;
387  
388 <      this->rotationPropagation( dAtom, ji );
388 >      this->rotationPropagation( integrableObjects[i], ji );
389  
390 <      dAtom->setJ(ji);
390 >      integrableObjects[i]->setJ(ji);
391      }
392    }
393  
# Line 386 | Line 399 | template<typename T> void Integrator<T>::moveB(void){
399  
400   template<typename T> void Integrator<T>::moveB(void){
401    int i, j;
389 –  DirectionalAtom* dAtom;
402    double Tb[3], ji[3];
403    double vel[3], frc[3];
404    double mass;
405  
406 <  for (i = 0; i < nAtoms; i++){
407 <    atoms[i]->getVel(vel);
408 <    atoms[i]->getFrc(frc);
406 >  for (i = 0; i < integrableObjects.size(); i++){
407 >    integrableObjects[i]->getVel(vel);
408 >    integrableObjects[i]->getFrc(frc);
409  
410 <    mass = atoms[i]->getMass();
410 >    mass = integrableObjects[i]->getMass();
411  
412      // velocity half step
413      for (j = 0; j < 3; j++)
414        vel[j] += (dt2 * frc[j] / mass) * eConvert;
415  
416 <    atoms[i]->setVel(vel);
416 >    integrableObjects[i]->setVel(vel);
417  
418 <    if (atoms[i]->isDirectional()){
407 <      dAtom = (DirectionalAtom *) atoms[i];
418 >    if (integrableObjects[i]->isDirectional()){
419  
420        // get and convert the torque to body frame
421  
422 <      dAtom->getTrq(Tb);
423 <      dAtom->lab2Body(Tb);
422 >      integrableObjects[i]->getTrq(Tb);
423 >      integrableObjects[i]->lab2Body(Tb);
424  
425        // get the angular momentum, and propagate a half step
426  
427 <      dAtom->getJ(ji);
427 >      integrableObjects[i]->getJ(ji);
428  
429        for (j = 0; j < 3; j++)
430          ji[j] += (dt2 * Tb[j]) * eConvert;
431  
432  
433 <      dAtom->setJ(ji);
433 >      integrableObjects[i]->setJ(ji);
434      }
435    }
436  
# Line 688 | Line 699 | template<typename T> void Integrator<T>::rotationPropa
699   }
700  
701   template<typename T> void Integrator<T>::rotationPropagation
702 < ( DirectionalAtom* dAtom, double ji[3] ){
702 > ( StuntDouble* sd, double ji[3] ){
703  
704    double angle;
705    double A[3][3], I[3][3];
706 +  int i, j, k;
707  
708    // use the angular velocities to propagate the rotation matrix a
709    // full time step
710  
711 <  dAtom->getA(A);
712 <  dAtom->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 );
711 >  sd->getA(A);
712 >  sd->getI(I);
713  
714 <  // rotate about the y-axis
715 <  angle = dt2 * ji[1] / I[1][1];
716 <  this->rotate( 2, 0, angle, ji, A );
714 >  if (sd->isLinear()) {
715 >    i = sd->linearAxis();
716 >    j = (i+1)%3;
717 >    k = (i+2)%3;
718 >    
719 >    angle = dt2 * ji[j] / I[j][j];
720 >    this->rotate( k, i, angle, ji, A );
721  
722 <  // rotate about the z-axis
723 <  angle = dt * ji[2] / I[2][2];
724 <  this->rotate( 0, 1, angle, ji, A);
722 >    angle = dt * ji[k] / I[k][k];
723 >    this->rotate( i, j, angle, ji, A);
724 >
725 >    angle = dt2 * ji[j] / I[j][j];
726 >    this->rotate( k, i, angle, ji, A );
727  
728 <  // rotate about the y-axis
729 <  angle = dt2 * ji[1] / I[1][1];
730 <  this->rotate( 2, 0, angle, ji, A );
731 <
732 <  // rotate about the x-axis
733 <  angle = dt2 * ji[0] / I[0][0];
734 <  this->rotate( 1, 2, angle, ji, A );
735 <
736 <  dAtom->setA( A  );
728 >  } else {
729 >    // rotate about the x-axis
730 >    angle = dt2 * ji[0] / I[0][0];
731 >    this->rotate( 1, 2, angle, ji, A );
732 >    
733 >    // rotate about the y-axis
734 >    angle = dt2 * ji[1] / I[1][1];
735 >    this->rotate( 2, 0, angle, ji, A );
736 >    
737 >    // rotate about the z-axis
738 >    angle = dt * ji[2] / I[2][2];
739 >    sd->addZangle(angle);
740 >    this->rotate( 0, 1, angle, ji, A);
741 >    
742 >    // rotate about the y-axis
743 >    angle = dt2 * ji[1] / I[1][1];
744 >    this->rotate( 2, 0, angle, ji, A );
745 >    
746 >    // rotate about the x-axis
747 >    angle = dt2 * ji[0] / I[0][0];
748 >    this->rotate( 1, 2, angle, ji, A );
749 >    
750 >  }
751 >  sd->setA( A  );
752   }
753  
754   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,

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