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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 1118 by tim, Mon Apr 19 03:52:27 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 178 | Line 181 | template<typename T> void Integrator<T>::integrate(voi
181    dt2 = 0.5 * dt;
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  
# Line 211 | Line 223 | template<typename T> void Integrator<T>::integrate(voi
223   #endif // is_mpi
224  
225    while (info->getTime() < runTime && !stopIntegrator()){
226 <    if ((info->getTime() + dt) >= currStatus){
226 >    difference = info->getTime() + dt - currStatus;
227 >    if (difference > 0 || fabs(difference) < 1e-4 ){
228        calcPot = 1;
229        calcStress = 1;
230      }
# Line 244 | 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 265 | 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 710 | Line 729 | template<typename T> void Integrator<T>::rotationPropa
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 <
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   }

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