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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 1212 by chrisfen, Tue Jun 1 17:15:43 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 241 | Line 255 | template<typename T> void Integrator<T>::integrate(voi
255  
256      if (info->getTime() >= currStatus){
257        statOut->writeStat(info->getTime());
258 +      if (info->useSolidThermInt || info->useLiquidThermInt)
259 +        statOut->writeRaw(info->getTime());
260        calcPot = 0;
261        calcStress = 0;
262        currStatus += statusTime;
# Line 263 | Line 279 | template<typename T> void Integrator<T>::integrate(voi
279   #endif // is_mpi
280    }
281  
282 +  // dump out a file containing the omega values for the final configuration
283 +  if (info->useSolidThermInt && !info->useLiquidThermInt)
284 +    myFF->dumpzAngle();
285 +  
286 +
287    delete dumpOut;
288    delete statOut;
289   }
# Line 297 | Line 318 | template<typename T> void Integrator<T>::integrateStep
318    MPIcheckPoint();
319   #endif // is_mpi
320  
300 –
321    // calc forces
302 –
322    calcForce(calcPot, calcStress);
323  
324   #ifdef IS_MPI
# Line 329 | Line 348 | template<typename T> void Integrator<T>::moveA(void){
348  
349  
350   template<typename T> void Integrator<T>::moveA(void){
351 <  int i, j;
351 >  size_t i, j;
352    DirectionalAtom* dAtom;
353    double Tb[3], ji[3];
354    double vel[3], pos[3], frc[3];
355    double mass;
356 <
357 <  for (i = 0; i < nAtoms; i++){
358 <    atoms[i]->getVel(vel);
359 <    atoms[i]->getPos(pos);
360 <    atoms[i]->getFrc(frc);
361 <
362 <    mass = atoms[i]->getMass();
356 >  double omega;
357 >
358 >  for (i = 0; i < integrableObjects.size() ; i++){
359 >    integrableObjects[i]->getVel(vel);
360 >    integrableObjects[i]->getPos(pos);
361 >    integrableObjects[i]->getFrc(frc);
362 >    
363 >    mass = integrableObjects[i]->getMass();
364  
365      for (j = 0; j < 3; j++){
366        // velocity half step
# Line 349 | Line 369 | template<typename T> void Integrator<T>::moveA(void){
369        pos[j] += dt * vel[j];
370      }
371  
372 <    atoms[i]->setVel(vel);
373 <    atoms[i]->setPos(pos);
372 >    integrableObjects[i]->setVel(vel);
373 >    integrableObjects[i]->setPos(pos);
374  
375 <    if (atoms[i]->isDirectional()){
356 <      dAtom = (DirectionalAtom *) atoms[i];
375 >    if (integrableObjects[i]->isDirectional()){
376  
377        // get and convert the torque to body frame
378  
379 <      dAtom->getTrq(Tb);
380 <      dAtom->lab2Body(Tb);
379 >      integrableObjects[i]->getTrq(Tb);
380 >      integrableObjects[i]->lab2Body(Tb);
381  
382        // get the angular momentum, and propagate a half step
383  
384 <      dAtom->getJ(ji);
384 >      integrableObjects[i]->getJ(ji);
385  
386        for (j = 0; j < 3; j++)
387          ji[j] += (dt2 * Tb[j]) * eConvert;
388  
389 <      this->rotationPropagation( dAtom, ji );
389 >      this->rotationPropagation( integrableObjects[i], ji );
390  
391 <      dAtom->setJ(ji);
391 >      integrableObjects[i]->setJ(ji);
392      }
393    }
394  
# Line 381 | Line 400 | template<typename T> void Integrator<T>::moveB(void){
400  
401   template<typename T> void Integrator<T>::moveB(void){
402    int i, j;
384 –  DirectionalAtom* dAtom;
403    double Tb[3], ji[3];
404    double vel[3], frc[3];
405    double mass;
406  
407 <  for (i = 0; i < nAtoms; i++){
408 <    atoms[i]->getVel(vel);
409 <    atoms[i]->getFrc(frc);
407 >  for (i = 0; i < integrableObjects.size(); i++){
408 >    integrableObjects[i]->getVel(vel);
409 >    integrableObjects[i]->getFrc(frc);
410  
411 <    mass = atoms[i]->getMass();
411 >    mass = integrableObjects[i]->getMass();
412  
413      // velocity half step
414      for (j = 0; j < 3; j++)
415        vel[j] += (dt2 * frc[j] / mass) * eConvert;
416  
417 <    atoms[i]->setVel(vel);
417 >    integrableObjects[i]->setVel(vel);
418  
419 <    if (atoms[i]->isDirectional()){
402 <      dAtom = (DirectionalAtom *) atoms[i];
419 >    if (integrableObjects[i]->isDirectional()){
420  
421        // get and convert the torque to body frame
422  
423 <      dAtom->getTrq(Tb);
424 <      dAtom->lab2Body(Tb);
423 >      integrableObjects[i]->getTrq(Tb);
424 >      integrableObjects[i]->lab2Body(Tb);
425  
426        // get the angular momentum, and propagate a half step
427  
428 <      dAtom->getJ(ji);
428 >      integrableObjects[i]->getJ(ji);
429  
430        for (j = 0; j < 3; j++)
431          ji[j] += (dt2 * Tb[j]) * eConvert;
432  
433  
434 <      dAtom->setJ(ji);
434 >      integrableObjects[i]->setJ(ji);
435      }
436    }
437  
# Line 683 | Line 700 | template<typename T> void Integrator<T>::rotationPropa
700   }
701  
702   template<typename T> void Integrator<T>::rotationPropagation
703 < ( DirectionalAtom* dAtom, double ji[3] ){
703 > ( StuntDouble* sd, double ji[3] ){
704  
705    double angle;
706    double A[3][3], I[3][3];
707 +  int i, j, k;
708  
709    // use the angular velocities to propagate the rotation matrix a
710    // full time step
711  
712 <  dAtom->getA(A);
713 <  dAtom->getI(I);
712 >  sd->getA(A);
713 >  sd->getI(I);
714  
715 <  // rotate about the x-axis
716 <  angle = dt2 * ji[0] / I[0][0];
717 <  this->rotate( 1, 2, angle, ji, A );
715 >  if (sd->isLinear()) {
716 >    i = sd->linearAxis();
717 >    j = (i+1)%3;
718 >    k = (i+2)%3;
719 >    
720 >    angle = dt2 * ji[j] / I[j][j];
721 >    this->rotate( k, i, angle, ji, A );
722  
723 <  // rotate about the y-axis
724 <  angle = dt2 * ji[1] / I[1][1];
703 <  this->rotate( 2, 0, angle, ji, A );
723 >    angle = dt * ji[k] / I[k][k];
724 >    this->rotate( i, j, angle, ji, A);
725  
726 <  // rotate about the z-axis
727 <  angle = dt * ji[2] / I[2][2];
707 <  this->rotate( 0, 1, angle, ji, A);
726 >    angle = dt2 * ji[j] / I[j][j];
727 >    this->rotate( k, i, 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 <  dAtom->setA( A  );
729 >  } else {
730 >    // rotate about the x-axis
731 >    angle = dt2 * ji[0] / I[0][0];
732 >    this->rotate( 1, 2, angle, ji, A );
733 >    
734 >    // rotate about the y-axis
735 >    angle = dt2 * ji[1] / I[1][1];
736 >    this->rotate( 2, 0, angle, ji, A );
737 >    
738 >    // rotate about the z-axis
739 >    angle = dt * ji[2] / I[2][2];
740 >    sd->addZangle(angle);
741 >    this->rotate( 0, 1, angle, ji, A);
742 >    
743 >    // rotate about the y-axis
744 >    angle = dt2 * ji[1] / I[1][1];
745 >    this->rotate( 2, 0, angle, ji, A );
746 >    
747 >    // rotate about the x-axis
748 >    angle = dt2 * ji[0] / I[0][0];
749 >    this->rotate( 1, 2, angle, ji, A );
750 >    
751 >  }
752 >  sd->setA( A  );
753   }
754  
755   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,

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