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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 1131 by tim, Thu Apr 22 21:33:55 2004 UTC vs.
Revision 1158 by tim, Tue May 11 21:14:26 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 +  
66 +  haveCutoffGroups = false;
67  
68    excludes = Exclude::Instance();
69  
# Line 71 | Line 72 | SimInfo::SimInfo(){
72    has_minimizer = false;
73    the_minimizer =NULL;
74  
75 +  ngroup = 0;
76 +
77    wrapMeSimInfo( this );
78   }
79  
# Line 83 | Line 86 | SimInfo::~SimInfo(){
86    
87    for(i = properties.begin(); i != properties.end(); i++)
88      delete (*i).second;
89 <    
89 >  
90   }
91  
92   void SimInfo::setBox(double newBox[3]) {
# Line 439 | Line 442 | void SimInfo::refreshSim(){
442  
443    n_exclude = excludes->getSize();
444    excl = excludes->getFortranArray();
445 <
445 >  
446   #ifdef IS_MPI
447    n_global = mpiSim->getTotAtoms();
448   #else
449    n_global = n_atoms;
450   #endif
451 <
451 >  
452    isError = 0;
453 <
454 <  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
455 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
456 <                  &isError );
457 <
458 <  if( isError ){
459 <
453 >  
454 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
455 >  //it may not be a good idea to pass the address of first element in vector
456 >  //since c++ standard does not require vector to be stored continously in meomory
457 >  //Most of the compilers will organize the memory of vector continously
458 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
459 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
460 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
461 >  
462 >  if( isError ){
463 >    
464      sprintf( painCave.errMsg,
465 <             "There was an error setting the simulation information in fortran.\n" );
465 >             "There was an error setting the simulation information in fortran.\n" );
466      painCave.isFatal = 1;
467      simError();
468    }
469 <
469 >  
470   #ifdef IS_MPI
471    sprintf( checkPointMsg,
472             "succesfully sent the simulation information to fortran.\n");
473    MPIcheckPoint();
474   #endif // is_mpi
475 <
475 >  
476    this->ndf = this->getNDF();
477    this->ndfRaw = this->getNDFraw();
478    this->ndfTrans = this->getNDFtranslational();
479   }
480  
481   void SimInfo::setDefaultRcut( double theRcut ){
482 <
482 >  
483    haveRcut = 1;
484    rCut = theRcut;
485 <
479 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
480 <
481 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
482 < }
483 <
484 < void SimInfo::setDefaultEcr( double theEcr ){
485 <
486 <  haveEcr = 1;
487 <  ecr = theEcr;
485 >  rList = rCut + 1.0;
486    
487 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
490 <
491 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
487 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
488   }
489  
490 < void SimInfo::setDefaultEcr( double theEcr, double theEst ){
490 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
491  
492 <  est = theEst;
493 <  setDefaultEcr( theEcr );
492 >  rSw = theRsw;
493 >  setDefaultRcut( theRcut );
494   }
495  
496  
# Line 506 | Line 502 | void SimInfo::checkCutOffs( void ){
502      
503      if( rCut > maxCutoff ){
504        sprintf( painCave.errMsg,
505 <               "LJrcut is too large for the current periodic box.\n"
506 <               "\tCurrent Value of LJrcut = %G at time %G\n "
505 >               "cutoffRadius is too large for the current periodic box.\n"
506 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
507                 "\tThis is larger than half of at least one of the\n"
508                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
509                 "\n"
# Line 520 | Line 516 | void SimInfo::checkCutOffs( void ){
516                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
517        painCave.isFatal = 1;
518        simError();
519 <    }
524 <    
525 <    if( haveEcr ){
526 <      if( ecr > maxCutoff ){
527 <        sprintf( painCave.errMsg,
528 <                 "electrostaticCutoffRadius is too large for the current\n"
529 <                 "\tperiodic box.\n\n"
530 <                 "\tCurrent Value of ECR = %G at time %G\n "
531 <                 "\tThis is larger than half of at least one of the\n"
532 <                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
533 <                 "\n"
534 <                 "\t[ %G %G %G ]\n"
535 <                 "\t[ %G %G %G ]\n"
536 <                 "\t[ %G %G %G ]\n",
537 <                 ecr, currentTime,
538 <                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
539 <                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
540 <                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
541 <        painCave.isFatal = 1;
542 <        simError();
543 <      }
544 <    }
519 >    }    
520    } else {
521      // initialize this stuff before using it, OK?
522      sprintf( painCave.errMsg,
# Line 589 | Line 564 | GenericData* SimInfo::getProperty(const string& propNa
564      return NULL;  
565   }
566  
567 +
568 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
569 +                          vector<int>& groupList, vector<int>& groupStart){
570 +  Molecule* myMols;
571 +  Atom** myAtoms;
572 +  int numAtom;
573 +  int curIndex;
574 +  double mtot;
575 +  int numMol;
576 +  int numCutoffGroups;
577 +  CutoffGroup* myCutoffGroup;
578 +  vector<CutoffGroup*>::iterator iterCutoff;
579 +  Atom* cutoffAtom;
580 +  vector<Atom*>::iterator iterAtom;
581 +  int atomIndex;
582 +  double totalMass;
583 +  
584 +  mfact.clear();
585 +  groupList.clear();
586 +  groupStart.clear();
587 +  
588 +  //Be careful, fortran array begin at 1
589 +  curIndex = 1;
590 +
591 +  myMols = info->molecules;
592 +  numMol = info->n_mol;
593 +  for(int i  = 0; i < numMol; i++){
594 +    numAtom = myMols[i].getNAtoms();
595 +    myAtoms = myMols[i].getMyAtoms();
596 +
597 +    
598 +    for(int j = 0; j < numAtom; j++){
599 +
600 +    
601 + #ifdef IS_MPI      
602 +      atomIndex = myAtoms[j]->getGlobalIndex();
603 + #else
604 +      atomIndex = myAtoms[j]->getIndex();
605 + #endif
606 +
607 +      if(myMols[i].belongToCutoffGroup(atomIndex))
608 +        continue;
609 +      else{
610 +        mfact.push_back(myAtoms[j]->getMass());
611 +        groupList.push_back(myAtoms[j]->getIndex() + 1);
612 +        groupStart.push_back(curIndex++);  
613 +      }
614 +    }
615 +      
616 +    numCutoffGroups = myMols[i].getNCutoffGroups();
617 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
618 +                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
619 +
620 +      totalMass = myCutoffGroup->getMass();
621 +      
622 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
623 +                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
624 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
625 +        groupList.push_back(cutoffAtom->getIndex() + 1);
626 +      }  
627 +                              
628 +      groupStart.push_back(curIndex);
629 +      curIndex += myCutoffGroup->getNumAtom();
630 +
631 +    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
632 +
633 +  }//end for(int i  = 0; i < numMol; i++)
634 +  
635 +  ngroup = groupStart.size();
636 + }

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