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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 1097 by gezelter, Mon Apr 12 20:32:20 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 179 | 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);
185 –
186 –  //temp test
187 –  tStats->getPotential();
195    
196    if (nConstrained){
197      preMove();
# Line 213 | 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 247 | 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 269 | 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->useThermInt)
284 +    myFF->dumpzAngle();
285 +  
286 +
287    delete dumpOut;
288    delete statOut;
289   }
# Line 303 | Line 318 | template<typename T> void Integrator<T>::integrateStep
318    MPIcheckPoint();
319   #endif // is_mpi
320  
306 –
321    // calc forces
308 –
322    calcForce(calcPot, calcStress);
323  
324   #ifdef IS_MPI
# Line 340 | 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 690 | 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 697 | 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 );
718 <
719 <  // rotate about the y-axis
720 <  angle = dt2 * ji[1] / I[1][1];
721 <  this->rotate( 2, 0, angle, ji, A );
707 <
708 <  // rotate about the z-axis
709 <  angle = dt * ji[2] / I[2][2];
710 <  this->rotate( 0, 1, 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];
714 <  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 x-axis
727 <  angle = dt2 * ji[0] / I[0][0];
718 <  this->rotate( 1, 2, angle, ji, A );
726 >    angle = dt2 * ji[j] / I[j][j];
727 >    this->rotate( k, i, angle, ji, A );
728  
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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