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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 1284 by tim, Mon Jun 21 18:52:21 2004 UTC

# Line 1 | Line 1
1   #include <iostream>
2   #include <stdlib.h>
3   #include <math.h>
4 <
4 > #include "Rattle.hpp"
5 > #include "Roll.hpp"
6   #ifdef IS_MPI
7   #include "mpiSimulation.hpp"
8   #include <unistd.h>
# Line 32 | Line 33 | template<typename T> Integrator<T>::Integrator(SimInfo
33  
34    nAtoms = info->n_atoms;
35    integrableObjects = info->integrableObjects;
36 <
36 >
37 >  consFramework = new RattleFramework(info);
38 >
39 >  if(consFramework == NULL){
40 >    sprintf(painCave.errMsg,
41 >      "Integrator::Intergrator() Error: Memory allocation error for RattleFramework" );
42 >    painCave.isFatal = 1;
43 >    simError();
44 >  }
45 >  
46 > /*
47    // check for constraints
48  
49    constrainedA = NULL;
# Line 45 | Line 56 | template<typename T> Integrator<T>::Integrator(SimInfo
56    nConstrained = 0;
57  
58    checkConstraints();
59 <
49 <  for (i=0; i<nMols; i++)
50 <    zAngle[i] = 0.0;
59 > */
60   }
61  
62   template<typename T> Integrator<T>::~Integrator(){
63 +  if (consFramework != NULL)
64 +    delete consFramework;
65 + /*
66    if (nConstrained){
67      delete[] constrainedA;
68      delete[] constrainedB;
# Line 59 | Line 71 | template<typename T> Integrator<T>::~Integrator(){
71      delete[] moved;
72      delete[] oldPos;
73    }
74 + */
75   }
76  
77 + /*
78   template<typename T> void Integrator<T>::checkConstraints(void){
79    isConstrained = 0;
80  
# Line 95 | Line 109 | template<typename T> void Integrator<T>::checkConstrai
109        if (constrained){
110          dummy_plug = theArray[j]->get_constraint();
111          temp_con[nConstrained].set_a(dummy_plug->get_a());
112 <        temp_con[nConstrained].set_b(dummy_plug->get_b());
112 >        temp_con[nConstrained].set_b(Dummy_plug->get_b());
113          temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr());
114  
115          nConstrained++;
# Line 153 | Line 167 | template<typename T> void Integrator<T>::checkConstrai
167  
168    delete[] temp_con;
169   }
170 + */
171  
157 –
172   template<typename T> void Integrator<T>::integrate(void){
173  
174    double runTime = info->run_time;
# Line 187 | Line 201 | template<typename T> void Integrator<T>::integrate(voi
201    tStats->removeCOMdrift();
202  
203    // initialize the retraints if necessary
204 <  if (info->useThermInt) {
204 >  if (info->useSolidThermInt && !info->useLiquidThermInt) {
205      myFF->initRestraints();
206    }
207  
208    // initialize the forces before the first step
209  
210    calcForce(1, 1);
211 <  
212 <  if (nConstrained){
213 <    preMove();
214 <    constrainA();
215 <    calcForce(1, 1);
216 <    constrainB();
203 <  }
211 >
212 >  //execute constraint algorithm to make sure at the very beginning the system is constrained  
213 >  //consFramework->doPreConstraint();
214 >  //consFramework->doConstrainA();
215 >  //calcForce(1, 1);
216 >  //consFramework->doConstrainB();
217    
218    if (info->setTemp){
219      thermalize();
# Line 257 | Line 270 | template<typename T> void Integrator<T>::integrate(voi
270  
271      if (info->getTime() >= currStatus){
272        statOut->writeStat(info->getTime());
260 –      statOut->writeRaw(info->getTime());
273        calcPot = 0;
274        calcStress = 0;
275        currStatus += statusTime;
# Line 281 | Line 293 | template<typename T> void Integrator<T>::integrate(voi
293    }
294  
295    // dump out a file containing the omega values for the final configuration
296 <  if (info->useThermInt)
296 >  if (info->useSolidThermInt && !info->useLiquidThermInt)
297      myFF->dumpzAngle();
298    
299  
# Line 297 | Line 309 | template<typename T> void Integrator<T>::integrateStep
309    startProfile(pro3);
310   #endif //profile
311  
312 <  preMove();
312 >  //save old state (position, velocity etc)
313 >  consFramework->doPreConstraint();
314  
315   #ifdef PROFILE
316    endProfile(pro3);
# Line 319 | Line 332 | template<typename T> void Integrator<T>::integrateStep
332    MPIcheckPoint();
333   #endif // is_mpi
334  
322 –
335    // calc forces
324 –
336    calcForce(calcPot, calcStress);
337  
338   #ifdef IS_MPI
# Line 356 | Line 367 | template<typename T> void Integrator<T>::moveA(void){
367    double Tb[3], ji[3];
368    double vel[3], pos[3], frc[3];
369    double mass;
370 +  double omega;
371  
372    for (i = 0; i < integrableObjects.size() ; i++){
373      integrableObjects[i]->getVel(vel);
# Line 394 | Line 406 | template<typename T> void Integrator<T>::moveA(void){
406      }
407    }
408  
409 <  if (nConstrained){
398 <    constrainA();
399 <  }
409 >  consFramework->doConstrainA();
410   }
411  
412  
# Line 437 | Line 447 | template<typename T> void Integrator<T>::moveB(void){
447      }
448    }
449  
450 <  if (nConstrained){
441 <    constrainB();
442 <  }
450 >  consFramework->doConstrainB();
451   }
452  
453 + /*
454   template<typename T> void Integrator<T>::preMove(void){
455    int i, j;
456    double pos[3];
# Line 700 | Line 709 | template<typename T> void Integrator<T>::constrainB(vo
709      simError();
710    }
711   }
712 <
712 > */
713   template<typename T> void Integrator<T>::rotationPropagation
714   ( StuntDouble* sd, double ji[3] ){
715  
# Line 739 | Line 748 | template<typename T> void Integrator<T>::rotationPropa
748      
749      // rotate about the z-axis
750      angle = dt * ji[2] / I[2][2];
751 +    sd->addZangle(angle);
752      this->rotate( 0, 1, angle, ji, A);
753      
754      // rotate about the y-axis

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