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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 1113 by tim, Thu Apr 15 16:18:26 2004 UTC vs.
Revision 1207 by chrisfen, Thu May 27 20:06:38 2004 UTC

# Line 32 | Line 32 | template<typename T> Integrator<T>::Integrator(SimInfo
32  
33    nAtoms = info->n_atoms;
34    integrableObjects = info->integrableObjects;
35 <
35 >
36    // check for constraints
37  
38    constrainedA = NULL;
# Line 45 | 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 160 | 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 179 | template<typename T> void Integrator<T>::integrate(voi
179    dt2 = 0.5 * dt;
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  
# Line 211 | Line 221 | template<typename T> void Integrator<T>::integrate(voi
221   #endif // is_mpi
222  
223    while (info->getTime() < runTime && !stopIntegrator()){
224 <    if ((info->getTime() + dt) >= currStatus){
224 >    difference = info->getTime() + dt - currStatus;
225 >    if (difference > 0 || fabs(difference) < 1e-4 ){
226        calcPot = 1;
227        calcStress = 1;
228      }
# Line 244 | Line 255 | template<typename T> void Integrator<T>::integrate(voi
255  
256      if (info->getTime() >= currStatus){
257        statOut->writeStat(info->getTime());
258 +      if (info->useThermInt)
259 +        statOut->writeRaw(info->getTime());
260        calcPot = 0;
261        calcStress = 0;
262        currStatus += statusTime;
# Line 265 | Line 278 | template<typename T> void Integrator<T>::integrate(voi
278      MPIcheckPoint();
279   #endif // is_mpi
280    }
281 +
282 +  // dump out a file containing the omega values for the final configuration
283 +  if (info->useThermInt)
284 +    myFF->dumpzAngle();
285 +  
286  
287    delete dumpOut;
288    delete statOut;
# Line 300 | Line 318 | template<typename T> void Integrator<T>::integrateStep
318    MPIcheckPoint();
319   #endif // is_mpi
320  
303 –
321    // calc forces
305 –
322    calcForce(calcPot, calcStress);
323  
324   #ifdef IS_MPI
# Line 337 | Line 353 | template<typename T> void Integrator<T>::moveA(void){
353    double Tb[3], ji[3];
354    double vel[3], pos[3], frc[3];
355    double mass;
356 +  double omega;
357  
358    for (i = 0; i < integrableObjects.size() ; i++){
359      integrableObjects[i]->getVel(vel);
# Line 687 | Line 704 | template<typename T> void Integrator<T>::rotationPropa
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
# Line 694 | Line 712 | template<typename T> void Integrator<T>::rotationPropa
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 <
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  

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