ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
(Generate patch)

Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 1131 by tim, Thu Apr 22 21:33:55 2004 UTC vs.
Revision 1201 by tim, Thu May 27 15:31:36 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 +  useThermInt = 0;
66  
67 +  haveCutoffGroups = false;
68 +
69    excludes = Exclude::Instance();
70  
71    myConfiguration = new SimState();
# Line 71 | Line 73 | SimInfo::SimInfo(){
73    has_minimizer = false;
74    the_minimizer =NULL;
75  
76 +  ngroup = 0;
77 +
78    wrapMeSimInfo( this );
79   }
80  
# Line 83 | Line 87 | SimInfo::~SimInfo(){
87    
88    for(i = properties.begin(); i != properties.end(); i++)
89      delete (*i).second;
90 <    
90 >  
91   }
92  
93   void SimInfo::setBox(double newBox[3]) {
# Line 439 | Line 443 | void SimInfo::refreshSim(){
443  
444    n_exclude = excludes->getSize();
445    excl = excludes->getFortranArray();
446 <
446 >  
447   #ifdef IS_MPI
448    n_global = mpiSim->getTotAtoms();
449   #else
450    n_global = n_atoms;
451   #endif
452 <
452 >  
453    isError = 0;
454 <
455 <  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
456 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
457 <                  &isError );
458 <
454 >  
455 >  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
456 >  //it may not be a good idea to pass the address of first element in vector
457 >  //since c++ standard does not require vector to be stored continuously in meomory
458 >  //Most of the compilers will organize the memory of vector continuously
459 >  setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
460 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
461 >                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
462 >  
463    if( isError ){
464 <
464 >    
465      sprintf( painCave.errMsg,
466 <             "There was an error setting the simulation information in fortran.\n" );
466 >             "There was an error setting the simulation information in fortran.\n" );
467      painCave.isFatal = 1;
468      simError();
469    }
470 <
470 >  
471   #ifdef IS_MPI
472    sprintf( checkPointMsg,
473             "succesfully sent the simulation information to fortran.\n");
474    MPIcheckPoint();
475   #endif // is_mpi
476 <
476 >  
477    this->ndf = this->getNDF();
478    this->ndfRaw = this->getNDFraw();
479    this->ndfTrans = this->getNDFtranslational();
480   }
481  
482   void SimInfo::setDefaultRcut( double theRcut ){
483 <
483 >  
484    haveRcut = 1;
485    rCut = theRcut;
486 <
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;
486 >  rList = rCut + 1.0;
487    
488 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
490 <
491 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
488 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
489   }
490  
491 < void SimInfo::setDefaultEcr( double theEcr, double theEst ){
491 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
492  
493 <  est = theEst;
494 <  setDefaultEcr( theEcr );
493 >  rSw = theRsw;
494 >  setDefaultRcut( theRcut );
495   }
496  
497  
# Line 506 | Line 503 | void SimInfo::checkCutOffs( void ){
503      
504      if( rCut > maxCutoff ){
505        sprintf( painCave.errMsg,
506 <               "LJrcut is too large for the current periodic box.\n"
507 <               "\tCurrent Value of LJrcut = %G at time %G\n "
506 >               "cutoffRadius is too large for the current periodic box.\n"
507 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
508                 "\tThis is larger than half of at least one of the\n"
509                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
510                 "\n"
# Line 520 | Line 517 | void SimInfo::checkCutOffs( void ){
517                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
518        painCave.isFatal = 1;
519        simError();
520 <    }
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 <    }
520 >    }    
521    } else {
522      // initialize this stuff before using it, OK?
523      sprintf( painCave.errMsg,
# Line 589 | Line 565 | GenericData* SimInfo::getProperty(const string& propNa
565      return NULL;  
566   }
567  
568 +
569 + void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
570 +                          vector<int>& groupList, vector<int>& groupStart){
571 +  Molecule* myMols;
572 +  Atom** myAtoms;
573 +  int numAtom;
574 +  int curIndex;
575 +  double mtot;
576 +  int numMol;
577 +  int numCutoffGroups;
578 +  CutoffGroup* myCutoffGroup;
579 +  vector<CutoffGroup*>::iterator iterCutoff;
580 +  Atom* cutoffAtom;
581 +  vector<Atom*>::iterator iterAtom;
582 +  int atomIndex;
583 +  double totalMass;
584 +  
585 +  mfact.clear();
586 +  groupList.clear();
587 +  groupStart.clear();
588 +  
589 +  //Be careful, fortran array begin at 1
590 +  curIndex = 1;
591 +
592 +  myMols = info->molecules;
593 +  numMol = info->n_mol;
594 +  for(int i  = 0; i < numMol; i++){
595 +    numCutoffGroups = myMols[i].getNCutoffGroups();
596 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff); myCutoffGroup != NULL;
597 +                                                  myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
598 +
599 +      totalMass = myCutoffGroup->getMass();
600 +      
601 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom); cutoffAtom != NULL;
602 +                                           cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
603 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
604 + #ifdef IS_MPI        
605 +        groupList.push_back(cutoffAtom->getGlobalIndex() + 1);
606 + #else
607 +        groupList.push_back(cutoffAtom->getIndex() + 1);
608 + #endif
609 +      }  
610 +                              
611 +      groupStart.push_back(curIndex);
612 +      curIndex += myCutoffGroup->getNumAtom();
613 +
614 +    }//end for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff))
615 +
616 +  }//end for(int i  = 0; i < numMol; i++)
617 +
618 +
619 +  //The last cutoff group need more element to indicate the end of the cutoff
620 +  ngroup = groupStart.size();
621 + }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines