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root/group/trunk/OOPSE/libmdtools/Integrator.cpp
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Comparing trunk/OOPSE/libmdtools/Integrator.cpp (file contents):
Revision 1180 by chrisfen, Thu May 20 20:24:07 2004 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

# Line 1 | Line 1
1   #include <iostream>
2   #include <stdlib.h>
3   #include <math.h>
4 <
4 > #include "Rattle.hpp"
5   #ifdef IS_MPI
6   #include "mpiSimulation.hpp"
7   #include <unistd.h>
# Line 32 | Line 32 | template<typename T> Integrator<T>::Integrator(SimInfo
32  
33    nAtoms = info->n_atoms;
34    integrableObjects = info->integrableObjects;
35 <
35 >
36 >  rattle = new RattleFramework(info);
37 >
38 >  if(rattle == NULL){
39 >    sprintf(painCave.errMsg,
40 >      "Integrator::Intergrator() Error: Memory allocation error for RattleFramework" );
41 >    painCave.isFatal = 1;
42 >    simError();
43 >  }
44 >  
45 > /*
46    // check for constraints
47  
48    constrainedA = NULL;
# Line 45 | Line 55 | template<typename T> Integrator<T>::Integrator(SimInfo
55    nConstrained = 0;
56  
57    checkConstraints();
58 <
49 <  for (i=0; i<nMols; i++)
50 <    zAngle[i] = 0.0;
58 > */
59   }
60  
61   template<typename T> Integrator<T>::~Integrator(){
62 +  if (rattle != NULL)
63 +    delete rattle;
64 + /*
65    if (nConstrained){
66      delete[] constrainedA;
67      delete[] constrainedB;
# Line 59 | Line 70 | template<typename T> Integrator<T>::~Integrator(){
70      delete[] moved;
71      delete[] oldPos;
72    }
73 + */
74   }
75  
76 + /*
77   template<typename T> void Integrator<T>::checkConstraints(void){
78    isConstrained = 0;
79  
# Line 153 | Line 166 | template<typename T> void Integrator<T>::checkConstrai
166  
167    delete[] temp_con;
168   }
169 + */
170  
157 –
171   template<typename T> void Integrator<T>::integrate(void){
172  
173    double runTime = info->run_time;
# Line 187 | Line 200 | template<typename T> void Integrator<T>::integrate(voi
200    tStats->removeCOMdrift();
201  
202    // initialize the retraints if necessary
203 <  if (info->useThermInt) {
203 >  if (info->useSolidThermInt && !info->useLiquidThermInt) {
204      myFF->initRestraints();
205    }
206  
207    // initialize the forces before the first step
208  
209    calcForce(1, 1);
210 <  
211 <  if (nConstrained){
212 <    preMove();
213 <    constrainA();
214 <    calcForce(1, 1);
215 <    constrainB();
203 <  }
210 >
211 >  //execute constraint algorithm to make sure at the very beginning the system is constrained  
212 >  rattle->doPreConstraint();
213 >  rattle->doRattleA();
214 >  calcForce(1, 1);
215 >  rattle->doRattleB();
216    
217    if (info->setTemp){
218      thermalize();
# Line 257 | Line 269 | template<typename T> void Integrator<T>::integrate(voi
269  
270      if (info->getTime() >= currStatus){
271        statOut->writeStat(info->getTime());
260 –      statOut->writeRaw(info->getTime());
272        calcPot = 0;
273        calcStress = 0;
274        currStatus += statusTime;
# Line 281 | Line 292 | template<typename T> void Integrator<T>::integrate(voi
292    }
293  
294    // dump out a file containing the omega values for the final configuration
295 <  if (info->useThermInt)
295 >  if (info->useSolidThermInt && !info->useLiquidThermInt)
296      myFF->dumpzAngle();
297    
298  
# Line 297 | Line 308 | template<typename T> void Integrator<T>::integrateStep
308    startProfile(pro3);
309   #endif //profile
310  
311 <  preMove();
311 >  //save old state (position, velocity etc)
312 >  rattle->doPreConstraint();
313  
314   #ifdef PROFILE
315    endProfile(pro3);
# Line 319 | Line 331 | template<typename T> void Integrator<T>::integrateStep
331    MPIcheckPoint();
332   #endif // is_mpi
333  
322 –
334    // calc forces
324 –
335    calcForce(calcPot, calcStress);
336  
337   #ifdef IS_MPI
# Line 356 | Line 366 | template<typename T> void Integrator<T>::moveA(void){
366    double Tb[3], ji[3];
367    double vel[3], pos[3], frc[3];
368    double mass;
369 +  double omega;
370  
371    for (i = 0; i < integrableObjects.size() ; i++){
372      integrableObjects[i]->getVel(vel);
# Line 394 | Line 405 | template<typename T> void Integrator<T>::moveA(void){
405      }
406    }
407  
408 <  if (nConstrained){
398 <    constrainA();
399 <  }
408 >  rattle->doRattleA();
409   }
410  
411  
# Line 437 | Line 446 | template<typename T> void Integrator<T>::moveB(void){
446      }
447    }
448  
449 <  if (nConstrained){
441 <    constrainB();
442 <  }
449 >  rattle->doRattleB();
450   }
451  
452 + /*
453   template<typename T> void Integrator<T>::preMove(void){
454    int i, j;
455    double pos[3];
# Line 700 | Line 708 | template<typename T> void Integrator<T>::constrainB(vo
708      simError();
709    }
710   }
711 <
711 > */
712   template<typename T> void Integrator<T>::rotationPropagation
713   ( StuntDouble* sd, double ji[3] ){
714  
# Line 739 | Line 747 | template<typename T> void Integrator<T>::rotationPropa
747      
748      // rotate about the z-axis
749      angle = dt * ji[2] / I[2][2];
750 +    sd->addZangle(angle);
751      this->rotate( 0, 1, angle, ji, A);
752      
753      // rotate about the y-axis

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