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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 1097 by gezelter, Mon Apr 12 20:32:20 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 113 | Line 115 | template<typename T> void Integrator<T>::checkConstrai
115        }
116      }
117    }
118 +
119  
120    if (nConstrained > 0){
121      isConstrained = 1;
# Line 180 | Line 183 | template<typename T> void Integrator<T>::integrate(voi
183  
184    calcForce(1, 1);
185  
186 +  //temp test
187 +  tStats->getPotential();
188 +  
189    if (nConstrained){
190      preMove();
191      constrainA();
# Line 329 | Line 335 | template<typename T> void Integrator<T>::moveA(void){
335  
336  
337   template<typename T> void Integrator<T>::moveA(void){
338 <  int i, j;
338 >  size_t i, j;
339    DirectionalAtom* dAtom;
340    double Tb[3], ji[3];
341    double vel[3], pos[3], frc[3];
342    double mass;
343 <
344 <  for (i = 0; i < nAtoms; i++){
345 <    atoms[i]->getVel(vel);
346 <    atoms[i]->getPos(pos);
347 <    atoms[i]->getFrc(frc);
348 <
349 <    mass = atoms[i]->getMass();
343 >
344 >  for (i = 0; i < integrableObjects.size() ; i++){
345 >    integrableObjects[i]->getVel(vel);
346 >    integrableObjects[i]->getPos(pos);
347 >    integrableObjects[i]->getFrc(frc);
348 >    
349 >    mass = integrableObjects[i]->getMass();
350  
351      for (j = 0; j < 3; j++){
352        // velocity half step
# Line 349 | Line 355 | template<typename T> void Integrator<T>::moveA(void){
355        pos[j] += dt * vel[j];
356      }
357  
358 <    atoms[i]->setVel(vel);
359 <    atoms[i]->setPos(pos);
358 >    integrableObjects[i]->setVel(vel);
359 >    integrableObjects[i]->setPos(pos);
360  
361 <    if (atoms[i]->isDirectional()){
356 <      dAtom = (DirectionalAtom *) atoms[i];
361 >    if (integrableObjects[i]->isDirectional()){
362  
363        // get and convert the torque to body frame
364  
365 <      dAtom->getTrq(Tb);
366 <      dAtom->lab2Body(Tb);
365 >      integrableObjects[i]->getTrq(Tb);
366 >      integrableObjects[i]->lab2Body(Tb);
367  
368        // get the angular momentum, and propagate a half step
369  
370 <      dAtom->getJ(ji);
370 >      integrableObjects[i]->getJ(ji);
371  
372        for (j = 0; j < 3; j++)
373          ji[j] += (dt2 * Tb[j]) * eConvert;
374  
375 <      this->rotationPropagation( dAtom, ji );
375 >      this->rotationPropagation( integrableObjects[i], ji );
376  
377 <      dAtom->setJ(ji);
377 >      integrableObjects[i]->setJ(ji);
378      }
379    }
380  
# Line 381 | Line 386 | template<typename T> void Integrator<T>::moveB(void){
386  
387   template<typename T> void Integrator<T>::moveB(void){
388    int i, j;
384 –  DirectionalAtom* dAtom;
389    double Tb[3], ji[3];
390    double vel[3], frc[3];
391    double mass;
392  
393 <  for (i = 0; i < nAtoms; i++){
394 <    atoms[i]->getVel(vel);
395 <    atoms[i]->getFrc(frc);
393 >  for (i = 0; i < integrableObjects.size(); i++){
394 >    integrableObjects[i]->getVel(vel);
395 >    integrableObjects[i]->getFrc(frc);
396  
397 <    mass = atoms[i]->getMass();
397 >    mass = integrableObjects[i]->getMass();
398  
399      // velocity half step
400      for (j = 0; j < 3; j++)
401        vel[j] += (dt2 * frc[j] / mass) * eConvert;
402  
403 <    atoms[i]->setVel(vel);
403 >    integrableObjects[i]->setVel(vel);
404  
405 <    if (atoms[i]->isDirectional()){
402 <      dAtom = (DirectionalAtom *) atoms[i];
405 >    if (integrableObjects[i]->isDirectional()){
406  
407        // get and convert the torque to body frame
408  
409 <      dAtom->getTrq(Tb);
410 <      dAtom->lab2Body(Tb);
409 >      integrableObjects[i]->getTrq(Tb);
410 >      integrableObjects[i]->lab2Body(Tb);
411  
412        // get the angular momentum, and propagate a half step
413  
414 <      dAtom->getJ(ji);
414 >      integrableObjects[i]->getJ(ji);
415  
416        for (j = 0; j < 3; j++)
417          ji[j] += (dt2 * Tb[j]) * eConvert;
418  
419  
420 <      dAtom->setJ(ji);
420 >      integrableObjects[i]->setJ(ji);
421      }
422    }
423  
# Line 683 | Line 686 | template<typename T> void Integrator<T>::rotationPropa
686   }
687  
688   template<typename T> void Integrator<T>::rotationPropagation
689 < ( DirectionalAtom* dAtom, double ji[3] ){
689 > ( StuntDouble* sd, double ji[3] ){
690  
691    double angle;
692    double A[3][3], I[3][3];
# Line 691 | Line 694 | template<typename T> void Integrator<T>::rotationPropa
694    // use the angular velocities to propagate the rotation matrix a
695    // full time step
696  
697 <  dAtom->getA(A);
698 <  dAtom->getI(I);
697 >  sd->getA(A);
698 >  sd->getI(I);
699  
700    // rotate about the x-axis
701    angle = dt2 * ji[0] / I[0][0];
# Line 714 | Line 717 | template<typename T> void Integrator<T>::rotationPropa
717    angle = dt2 * ji[0] / I[0][0];
718    this->rotate( 1, 2, angle, ji, A );
719  
720 <  dAtom->setA( A  );
720 >  sd->setA( A  );
721   }
722  
723   template<typename T> void Integrator<T>::rotate(int axes1, int axes2,

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