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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 1113 by tim, Thu Apr 15 16:18:26 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();
75  
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 326 | Line 339 | int SimInfo::getNDF(){
339    
340    for(int i = 0; i < integrableObjects.size(); i++){
341      ndf_local += 3;
342 <    if (integrableObjects[i]->isDirectional())
343 <      ndf_local += 3;
342 >    if (integrableObjects[i]->isDirectional()) {
343 >      if (integrableObjects[i]->isLinear())
344 >        ndf_local += 2;
345 >      else
346 >        ndf_local += 3;
347 >    }
348    }
349  
350    // n_constraints is local, so subtract them on each processor:
# Line 356 | Line 373 | int SimInfo::getNDFraw() {
373  
374    for(int i = 0; i < integrableObjects.size(); i++){
375      ndfRaw_local += 3;
376 <    if (integrableObjects[i]->isDirectional())
377 <      ndfRaw_local += 3;
376 >    if (integrableObjects[i]->isDirectional()) {
377 >       if (integrableObjects[i]->isLinear())
378 >        ndfRaw_local += 2;
379 >      else
380 >        ndfRaw_local += 3;
381 >    }
382    }
383      
384   #ifdef IS_MPI
# Line 431 | 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 <
473 >    
474      sprintf( painCave.errMsg,
475 <             "There was an error setting the simulation information in fortran.\n" );
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 <
471 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
472 <
473 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
474 < }
475 <
476 < void SimInfo::setDefaultEcr( double theEcr ){
477 <
478 <  haveEcr = 1;
479 <  ecr = theEcr;
496 >  rList = rCut + 1.0;
497    
498 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
482 <
483 <  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 498 | 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 <    }
516 <    
517 <    if( haveEcr ){
518 <      if( ecr > maxCutoff ){
519 <        sprintf( painCave.errMsg,
520 <                 "electrostaticCutoffRadius is too large for the current\n"
521 <                 "\tperiodic box.\n\n"
522 <                 "\tCurrent Value of ECR = %G at time %G\n "
523 <                 "\tThis is larger than half of at least one of the\n"
524 <                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
525 <                 "\n"
526 <                 "\t[ %G %G %G ]\n"
527 <                 "\t[ %G %G %G ]\n"
528 <                 "\t[ %G %G %G ]\n",
529 <                 ecr, currentTime,
530 <                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
531 <                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
532 <                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
533 <        painCave.isFatal = 1;
534 <        simError();
535 <      }
536 <    }
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 581 | Line 577 | GenericData* SimInfo::getProperty(const string& propNa
577      return NULL;  
578   }
579  
584 – vector<GenericData*> SimInfo::getProperties(){
580  
581 <  vector<GenericData*> result;
582 <  map<string, GenericData*>::iterator i;
581 > void SimInfo::getFortranGroupArrays(SimInfo* info,
582 >                                    vector<int>& FglobalGroupMembership,
583 >                                    vector<double>& mfact){
584    
585 <  for(i = properties.begin(); i != properties.end(); i++)
586 <    result.push_back((*i).second);
587 <    
588 <  return result;
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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