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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 2004 UTC

# Line 42 | Line 42 | SimInfo::SimInfo(){
42    thermalTime = 0.0;
43    currentTime = 0.0;
44    rCut = 0.0;
45 <  ecr = 0.0;
46 <  est = 0.0;
45 >  rSw = 0.0;
46  
47    haveRcut = 0;
48 <  haveEcr = 0;
48 >  haveRsw = 0;
49    boxIsInit = 0;
50    
51    resetTime = 1e99;
# Line 63 | Line 62 | SimInfo::SimInfo(){
62    useReactionField = 0;
63    useGB = 0;
64    useEAM = 0;
65 +  useSolidThermInt = 0;
66 +  useLiquidThermInt = 0;
67  
68 +  haveCutoffGroups = false;
69 +
70    excludes = Exclude::Instance();
71  
72    myConfiguration = new SimState();
73  
74    has_minimizer = false;
75    the_minimizer =NULL;
76 +
77 +  ngroup = 0;
78  
79    wrapMeSimInfo( this );
80   }
# Line 83 | Line 88 | SimInfo::~SimInfo(){
88    
89    for(i = properties.begin(); i != properties.end(); i++)
90      delete (*i).second;
91 <    
91 >  
92   }
93  
94   void SimInfo::setBox(double newBox[3]) {
# Line 322 | Line 327 | int SimInfo::getNDF(){
327   int SimInfo::getNDF(){
328    int ndf_local;
329  
330 +  ndf_local = 0;
331 +  
332    for(int i = 0; i < integrableObjects.size(); i++){
333      ndf_local += 3;
334 <    if (integrableObjects[i]->isDirectional())
335 <      ndf_local += 3;
334 >    if (integrableObjects[i]->isDirectional()) {
335 >      if (integrableObjects[i]->isLinear())
336 >        ndf_local += 2;
337 >      else
338 >        ndf_local += 3;
339 >    }
340    }
341  
342    // n_constraints is local, so subtract them on each processor:
# Line 350 | Line 361 | int SimInfo::getNDFraw() {
361    int ndfRaw_local;
362  
363    // Raw degrees of freedom that we have to set
364 +  ndfRaw_local = 0;
365  
366    for(int i = 0; i < integrableObjects.size(); i++){
367      ndfRaw_local += 3;
368 <    if (integrableObjects[i]->isDirectional())
369 <      ndfRaw_local += 3;
368 >    if (integrableObjects[i]->isDirectional()) {
369 >       if (integrableObjects[i]->isLinear())
370 >        ndfRaw_local += 2;
371 >      else
372 >        ndfRaw_local += 3;
373 >    }
374    }
375      
376   #ifdef IS_MPI
# Line 383 | Line 399 | int SimInfo::getNDFtranslational() {
399    return ndfTrans;
400   }
401  
402 + int SimInfo::getTotIntegrableObjects() {
403 +  int nObjs_local;
404 +  int nObjs;
405 +
406 +  nObjs_local =  integrableObjects.size();
407 +
408 +
409 + #ifdef IS_MPI
410 +  MPI_Allreduce(&nObjs_local,&nObjs,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD);
411 + #else
412 +  nObjs = nObjs_local;
413 + #endif
414 +
415 +
416 +  return nObjs;
417 + }
418 +
419   void SimInfo::refreshSim(){
420  
421    simtype fInfo;
# Line 411 | Line 444 | void SimInfo::refreshSim(){
444  
445    n_exclude = excludes->getSize();
446    excl = excludes->getFortranArray();
447 <
447 >  
448   #ifdef IS_MPI
449 <  n_global = mpiSim->getTotAtoms();
449 >  n_global = mpiSim->getNAtomsGlobal();
450   #else
451    n_global = n_atoms;
452   #endif
453 <
453 >  
454    isError = 0;
455 <
455 >  
456 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
457 >  //it may not be a good idea to pass the address of first element in vector
458 >  //since c++ standard does not require vector to be stored continuously in meomory
459 >  //Most of the compilers will organize the memory of vector continuously
460    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
461 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
462 <                  &isError );
463 <
461 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
462 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
463 >  
464    if( isError ){
465 <
465 >    
466      sprintf( painCave.errMsg,
467 <             "There was an error setting the simulation information in fortran.\n" );
467 >             "There was an error setting the simulation information in fortran.\n" );
468      painCave.isFatal = 1;
469      simError();
470    }
471 <
471 >  
472   #ifdef IS_MPI
473    sprintf( checkPointMsg,
474             "succesfully sent the simulation information to fortran.\n");
475    MPIcheckPoint();
476   #endif // is_mpi
477 <
477 >  
478    this->ndf = this->getNDF();
479    this->ndfRaw = this->getNDFraw();
480    this->ndfTrans = this->getNDFtranslational();
481   }
482  
483   void SimInfo::setDefaultRcut( double theRcut ){
484 <
484 >  
485    haveRcut = 1;
486    rCut = theRcut;
487 <
451 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
452 <
453 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
454 < }
455 <
456 < void SimInfo::setDefaultEcr( double theEcr ){
457 <
458 <  haveEcr = 1;
459 <  ecr = theEcr;
487 >  rList = rCut + 1.0;
488    
489 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
462 <
463 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
489 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
490   }
491  
492 < void SimInfo::setDefaultEcr( double theEcr, double theEst ){
492 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
493  
494 <  est = theEst;
495 <  setDefaultEcr( theEcr );
494 >  rSw = theRsw;
495 >  setDefaultRcut( theRcut );
496   }
497  
498  
# Line 478 | Line 504 | void SimInfo::checkCutOffs( void ){
504      
505      if( rCut > maxCutoff ){
506        sprintf( painCave.errMsg,
507 <               "LJrcut is too large for the current periodic box.\n"
508 <               "\tCurrent Value of LJrcut = %G at time %G\n "
507 >               "cutoffRadius is too large for the current periodic box.\n"
508 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
509                 "\tThis is larger than half of at least one of the\n"
510                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
511 <               "\n, %G"
511 >               "\n"
512                 "\t[ %G %G %G ]\n"
513                 "\t[ %G %G %G ]\n"
514                 "\t[ %G %G %G ]\n",
515 <               rCut, currentTime, maxCutoff,
515 >               rCut, currentTime,
516                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
517                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
518                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
519        painCave.isFatal = 1;
520        simError();
521 <    }
496 <    
497 <    if( haveEcr ){
498 <      if( ecr > maxCutoff ){
499 <        sprintf( painCave.errMsg,
500 <                 "electrostaticCutoffRadius is too large for the current\n"
501 <                 "\tperiodic box.\n\n"
502 <                 "\tCurrent Value of ECR = %G at time %G\n "
503 <                 "\tThis is larger than half of at least one of the\n"
504 <                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
505 <                 "\n"
506 <                 "\t[ %G %G %G ]\n"
507 <                 "\t[ %G %G %G ]\n"
508 <                 "\t[ %G %G %G ]\n",
509 <                 ecr, currentTime,
510 <                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
511 <                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
512 <                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
513 <        painCave.isFatal = 1;
514 <        simError();
515 <      }
516 <    }
521 >    }    
522    } else {
523      // initialize this stuff before using it, OK?
524      sprintf( painCave.errMsg,
# Line 561 | Line 566 | GenericData* SimInfo::getProperty(const string& propNa
566      return NULL;  
567   }
568  
564 – vector<GenericData*> SimInfo::getProperties(){
569  
570 <  vector<GenericData*> result;
571 <  map<string, GenericData*>::iterator i;
570 > void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
571 >                          vector<int>& groupList, vector<int>& groupStart){
572 >  Molecule* myMols;
573 >  Atom** myAtoms;
574 >  int numAtom;
575 >  int curIndex;
576 >  double mtot;
577 >  int numMol;
578 >  int numCutoffGroups;
579 >  CutoffGroup* myCutoffGroup;
580 >  vector<CutoffGroup*>::iterator iterCutoff;
581 >  Atom* cutoffAtom;
582 >  vector<Atom*>::iterator iterAtom;
583 >  int atomIndex;
584 >  double totalMass;
585    
586 <  for(i = properties.begin(); i != properties.end(); i++)
587 <    result.push_back((*i).second);
588 <    
589 <  return result;
586 >  mfact.clear();
587 >  groupList.clear();
588 >  groupStart.clear();
589 >  
590 >  //Be careful, fortran array begin at 1
591 >  curIndex = 1;
592 >
593 >  myMols = info->molecules;
594 >  numMol = info->n_mol;
595 >  for(int i  = 0; i < numMol; i++){
596 >    numCutoffGroups = myMols[i].getNCutoffGroups();
597 >    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
598 >                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
599 >
600 >      totalMass = myCutoffGroup->getMass();
601 >      
602 >      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
603 >                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
604 >        mfact.push_back(cutoffAtom->getMass()/totalMass);
605 > #ifdef IS_MPI        
606 >        groupList.push_back(cutoffAtom->getGlobalIndex() + 1);
607 > #else
608 >        groupList.push_back(cutoffAtom->getIndex() + 1);
609 > #endif
610 >      }  
611 >                              
612 >      groupStart.push_back(curIndex);
613 >      curIndex += myCutoffGroup->getNumAtom();
614 >
615 >    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
616 >
617 >  }//end for(int i  = 0; i < numMol; i++)
618 >
619 >
620 >  //The last cutoff group need more element to indicate the end of the cutoff
621 >  ngroup = groupStart.size();
622   }

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