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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 1180 by chrisfen, Thu May 20 20:24:07 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 +  for (i=0; i<nMols; i++)
50 +    zAngle[i] = 0.0;
51   }
52  
53   template<typename T> Integrator<T>::~Integrator(){
# Line 160 | Line 163 | template<typename T> void Integrator<T>::integrate(voi
163    double thermalTime = info->thermalTime;
164    double resetTime = info->resetTime;
165  
166 <
166 >  double difference;
167    double currSample;
168    double currThermal;
169    double currStatus;
# Line 179 | Line 182 | template<typename T> void Integrator<T>::integrate(voi
182  
183    readyCheck();
184  
185 +  // remove center of mass drift velocity (in case we passed in a configuration
186 +  // that was drifting
187 +  tStats->removeCOMdrift();
188 +
189 +  // initialize the retraints if necessary
190 +  if (info->useThermInt) {
191 +    myFF->initRestraints();
192 +  }
193 +
194    // initialize the forces before the first step
195  
196    calcForce(1, 1);
185 –
186 –  //temp test
187 –  tStats->getPotential();
197    
198    if (nConstrained){
199      preMove();
# Line 213 | Line 222 | template<typename T> void Integrator<T>::integrate(voi
222    MPIcheckPoint();
223   #endif // is_mpi
224  
225 <  while (info->getTime() < runTime){
226 <    if ((info->getTime() + dt) >= currStatus){
225 >  while (info->getTime() < runTime && !stopIntegrator()){
226 >    difference = info->getTime() + dt - currStatus;
227 >    if (difference > 0 || fabs(difference) < 1e-4 ){
228        calcPot = 1;
229        calcStress = 1;
230      }
# Line 247 | Line 257 | template<typename T> void Integrator<T>::integrate(voi
257  
258      if (info->getTime() >= currStatus){
259        statOut->writeStat(info->getTime());
260 +      statOut->writeRaw(info->getTime());
261        calcPot = 0;
262        calcStress = 0;
263        currStatus += statusTime;
# Line 268 | Line 279 | template<typename T> void Integrator<T>::integrate(voi
279      MPIcheckPoint();
280   #endif // is_mpi
281    }
282 +
283 +  // dump out a file containing the omega values for the final configuration
284 +  if (info->useThermInt)
285 +    myFF->dumpzAngle();
286 +  
287  
288    delete dumpOut;
289    delete statOut;
# Line 690 | Line 706 | template<typename T> void Integrator<T>::rotationPropa
706  
707    double angle;
708    double A[3][3], I[3][3];
709 +  int i, j, k;
710  
711    // use the angular velocities to propagate the rotation matrix a
712    // full time step
713  
714    sd->getA(A);
715    sd->getI(I);
699 –
700 –  // rotate about the x-axis
701 –  angle = dt2 * ji[0] / I[0][0];
702 –  this->rotate( 1, 2, angle, ji, A );
716  
717 <  // rotate about the y-axis
718 <  angle = dt2 * ji[1] / I[1][1];
719 <  this->rotate( 2, 0, angle, ji, A );
720 <
721 <  // rotate about the z-axis
722 <  angle = dt * ji[2] / I[2][2];
723 <  this->rotate( 0, 1, angle, ji, A);
717 >  if (sd->isLinear()) {
718 >    i = sd->linearAxis();
719 >    j = (i+1)%3;
720 >    k = (i+2)%3;
721 >    
722 >    angle = dt2 * ji[j] / I[j][j];
723 >    this->rotate( k, i, angle, ji, A );
724  
725 <  // rotate about the y-axis
726 <  angle = dt2 * ji[1] / I[1][1];
714 <  this->rotate( 2, 0, angle, ji, A );
725 >    angle = dt * ji[k] / I[k][k];
726 >    this->rotate( i, j, angle, ji, A);
727  
728 <  // rotate about the x-axis
729 <  angle = dt2 * ji[0] / I[0][0];
718 <  this->rotate( 1, 2, angle, ji, A );
728 >    angle = dt2 * ji[j] / I[j][j];
729 >    this->rotate( k, i, angle, ji, A );
730  
731 +  } else {
732 +    // rotate about the x-axis
733 +    angle = dt2 * ji[0] / I[0][0];
734 +    this->rotate( 1, 2, angle, ji, A );
735 +    
736 +    // rotate about the y-axis
737 +    angle = dt2 * ji[1] / I[1][1];
738 +    this->rotate( 2, 0, angle, ji, A );
739 +    
740 +    // rotate about the z-axis
741 +    angle = dt * ji[2] / I[2][2];
742 +    this->rotate( 0, 1, angle, ji, A);
743 +    
744 +    // rotate about the y-axis
745 +    angle = dt2 * ji[1] / I[1][1];
746 +    this->rotate( 2, 0, angle, ji, A );
747 +    
748 +    // rotate about the x-axis
749 +    angle = dt2 * ji[0] / I[0][0];
750 +    this->rotate( 1, 2, angle, ji, A );
751 +    
752 +  }
753    sd->setA( A  );
754   }
755  

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