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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 1125 by gezelter, Mon Apr 19 22:13:01 2004 UTC vs.
Revision 1234 by tim, Fri Jun 4 03:15:31 2004 UTC

# Line 14 | Line 14 | using namespace std;
14  
15   #include "MatVec3.h"
16  
17 + #include "ConstraintManager.hpp"
18 +
19   #ifdef IS_MPI
20   #include "mpiSimulation.hpp"
21   #endif
# Line 42 | Line 44 | SimInfo::SimInfo(){
44    thermalTime = 0.0;
45    currentTime = 0.0;
46    rCut = 0.0;
47 <  ecr = 0.0;
46 <  est = 0.0;
47 >  rSw = 0.0;
48  
49    haveRcut = 0;
50 <  haveEcr = 0;
50 >  haveRsw = 0;
51    boxIsInit = 0;
52    
53    resetTime = 1e99;
# Line 63 | Line 64 | SimInfo::SimInfo(){
64    useReactionField = 0;
65    useGB = 0;
66    useEAM = 0;
67 +  useSolidThermInt = 0;
68 +  useLiquidThermInt = 0;
69  
70 +  haveCutoffGroups = false;
71 +
72    excludes = Exclude::Instance();
73  
74    myConfiguration = new SimState();
# Line 71 | Line 76 | SimInfo::SimInfo(){
76    has_minimizer = false;
77    the_minimizer =NULL;
78  
79 +  ngroup = 0;
80 +
81 +  consMan = NULL;
82 +  
83    wrapMeSimInfo( this );
84   }
85  
# Line 83 | Line 92 | SimInfo::~SimInfo(){
92    
93    for(i = properties.begin(); i != properties.end(); i++)
94      delete (*i).second;
95 <    
95 >
96 >  if (!consMan)
97 >    delete consMan;  
98   }
99  
100   void SimInfo::setBox(double newBox[3]) {
# Line 186 | Line 197 | void SimInfo::calcHmatInv( void ) {
197  
198    if( oldOrtho != orthoRhombic ){
199      
200 <    if( orthoRhombic ){
200 >    if( orthoRhombic ) {
201        sprintf( painCave.errMsg,
202                 "OOPSE is switching from the default Non-Orthorhombic\n"
203                 "\tto the faster Orthorhombic periodic boundary computations.\n"
# Line 194 | Line 205 | void SimInfo::calcHmatInv( void ) {
205                 "\tNon-Orthorhombic computations, make the orthoBoxTolerance\n"
206                 "\tvariable ( currently set to %G ) smaller.\n",
207                 orthoTolerance);
208 +      painCave.severity = OOPSE_INFO;
209        simError();
210      }
211      else {
# Line 205 | Line 217 | void SimInfo::calcHmatInv( void ) {
217                 "\tthe Orthorhombic computations, make the orthoBoxTolerance\n"
218                 "\tvariable ( currently set to %G ) larger.\n",
219                 orthoTolerance);
220 +      painCave.severity = OOPSE_WARNING;
221        simError();
222      }
223    }
# Line 349 | Line 362 | int SimInfo::getNDF(){
362  
363    ndf = ndf - 3 - nZconstraints;
364  
352 –  std::cerr << "ndf = " << ndf;
353 –
365    return ndf;
366   }
367  
# Line 441 | Line 452 | void SimInfo::refreshSim(){
452  
453    n_exclude = excludes->getSize();
454    excl = excludes->getFortranArray();
455 <
455 >  
456   #ifdef IS_MPI
457 <  n_global = mpiSim->getTotAtoms();
457 >  n_global = mpiSim->getNAtomsGlobal();
458   #else
459    n_global = n_atoms;
460   #endif
461 <
461 >  
462    isError = 0;
463 <
463 >  
464 >  getFortranGroupArrays(this, FglobalGroupMembership, mfact);
465 >  //it may not be a good idea to pass the address of first element in vector
466 >  //since c++ standard does not require vector to be stored continuously in meomory
467 >  //Most of the compilers will organize the memory of vector continuously
468    setFsimulation( &fInfo, &n_global, &n_atoms, identArray, &n_exclude, excl,
469 <                  &nGlobalExcludes, globalExcludes, molMembershipArray,
470 <                  &isError );
469 >                  &nGlobalExcludes, globalExcludes, molMembershipArray,
470 >                  &mfact[0], &ngroup, &FglobalGroupMembership[0], &isError);
471  
472    if( isError ){
473 <
474 <    sprintf( painCave.errMsg,
475 <             "There was an error setting the simulation information in fortran.\n" );
473 >    
474 >    sprintf( painCave.errMsg,
475 >             "There was an error setting the simulation information in fortran.\n" );
476      painCave.isFatal = 1;
477 +    painCave.severity = OOPSE_ERROR;
478      simError();
479    }
480 <
480 >  
481   #ifdef IS_MPI
482    sprintf( checkPointMsg,
483             "succesfully sent the simulation information to fortran.\n");
484    MPIcheckPoint();
485   #endif // is_mpi
486 <
486 >  
487    this->ndf = this->getNDF();
488    this->ndfRaw = this->getNDFraw();
489    this->ndfTrans = this->getNDFtranslational();
490   }
491  
492   void SimInfo::setDefaultRcut( double theRcut ){
493 <
493 >  
494    haveRcut = 1;
495    rCut = theRcut;
496 <
481 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
482 <
483 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
484 < }
485 <
486 < void SimInfo::setDefaultEcr( double theEcr ){
487 <
488 <  haveEcr = 1;
489 <  ecr = theEcr;
496 >  rList = rCut + 1.0;
497    
498 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
492 <
493 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
498 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
499   }
500  
501 < void SimInfo::setDefaultEcr( double theEcr, double theEst ){
501 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
502  
503 <  est = theEst;
504 <  setDefaultEcr( theEcr );
503 >  rSw = theRsw;
504 >  setDefaultRcut( theRcut );
505   }
506  
507  
# Line 508 | Line 513 | void SimInfo::checkCutOffs( void ){
513      
514      if( rCut > maxCutoff ){
515        sprintf( painCave.errMsg,
516 <               "LJrcut is too large for the current periodic box.\n"
517 <               "\tCurrent Value of LJrcut = %G at time %G\n "
516 >               "cutoffRadius is too large for the current periodic box.\n"
517 >               "\tCurrent Value of cutoffRadius = %G at time %G\n "
518                 "\tThis is larger than half of at least one of the\n"
519                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
520 <               "\n, %G"
520 >               "\n"
521                 "\t[ %G %G %G ]\n"
522                 "\t[ %G %G %G ]\n"
523                 "\t[ %G %G %G ]\n",
524 <               rCut, currentTime, maxCutoff,
524 >               rCut, currentTime,
525                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
526                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
527                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
528 +      painCave.severity = OOPSE_ERROR;
529        painCave.isFatal = 1;
530        simError();
531 <    }
526 <    
527 <    if( haveEcr ){
528 <      if( ecr > maxCutoff ){
529 <        sprintf( painCave.errMsg,
530 <                 "electrostaticCutoffRadius is too large for the current\n"
531 <                 "\tperiodic box.\n\n"
532 <                 "\tCurrent Value of ECR = %G at time %G\n "
533 <                 "\tThis is larger than half of at least one of the\n"
534 <                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
535 <                 "\n"
536 <                 "\t[ %G %G %G ]\n"
537 <                 "\t[ %G %G %G ]\n"
538 <                 "\t[ %G %G %G ]\n",
539 <                 ecr, currentTime,
540 <                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
541 <                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
542 <                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
543 <        painCave.isFatal = 1;
544 <        simError();
545 <      }
546 <    }
531 >    }    
532    } else {
533      // initialize this stuff before using it, OK?
534      sprintf( painCave.errMsg,
535               "Trying to check cutoffs without a box.\n"
536               "\tOOPSE should have better programmers than that.\n" );
537 +    painCave.severity = OOPSE_ERROR;
538      painCave.isFatal = 1;
539      simError();      
540    }
# Line 591 | Line 577 | GenericData* SimInfo::getProperty(const string& propNa
577      return NULL;  
578   }
579  
580 +
581 + void SimInfo::getFortranGroupArrays(SimInfo* info,
582 +                                    vector<int>& FglobalGroupMembership,
583 +                                    vector<double>& mfact){
584 +  
585 +  Molecule* myMols;
586 +  Atom** myAtoms;
587 +  int numAtom;
588 +  double mtot;
589 +  int numMol;
590 +  int numCutoffGroups;
591 +  CutoffGroup* myCutoffGroup;
592 +  vector<CutoffGroup*>::iterator iterCutoff;
593 +  Atom* cutoffAtom;
594 +  vector<Atom*>::iterator iterAtom;
595 +  int atomIndex;
596 +  double totalMass;
597 +  
598 +  mfact.clear();
599 +  FglobalGroupMembership.clear();
600 +  
601 +
602 +  // Fix the silly fortran indexing problem
603 + #ifdef IS_MPI
604 +  numAtom = mpiSim->getNAtomsGlobal();
605 + #else
606 +  numAtom = n_atoms;
607 + #endif
608 +  for (int i = 0; i < numAtom; i++)
609 +    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
610 +  
611 +
612 +  myMols = info->molecules;
613 +  numMol = info->n_mol;
614 +  for(int i  = 0; i < numMol; i++){
615 +    numCutoffGroups = myMols[i].getNCutoffGroups();
616 +    for(myCutoffGroup =myMols[i].beginCutoffGroup(iterCutoff);
617 +        myCutoffGroup != NULL;
618 +        myCutoffGroup =myMols[i].nextCutoffGroup(iterCutoff)){
619 +
620 +      totalMass = myCutoffGroup->getMass();
621 +      
622 +      for(cutoffAtom = myCutoffGroup->beginAtom(iterAtom);
623 +          cutoffAtom != NULL;
624 +          cutoffAtom = myCutoffGroup->nextAtom(iterAtom)){
625 +        mfact.push_back(cutoffAtom->getMass()/totalMass);
626 +      }  
627 +    }
628 +  }
629 +
630 + }

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