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root/group/trunk/OOPSE/libmdtools/SimInfo.cpp
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Comparing trunk/OOPSE/libmdtools/SimInfo.cpp (file contents):
Revision 1150 by gezelter, Fri May 7 21:35:05 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 <  useMolecularCutoffs = 0;
67 >  useSolidThermInt = 0;
68 >  useLiquidThermInt = 0;
69 >
70 >  haveCutoffGroups = false;
71  
72    excludes = Exclude::Instance();
73  
# Line 74 | Line 78 | SimInfo::SimInfo(){
78  
79    ngroup = 0;
80  
81 +  consMan = NULL;
82 +  
83    wrapMeSimInfo( this );
84   }
85  
# Line 86 | 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 189 | 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 197 | 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 208 | 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 444 | Line 454 | void SimInfo::refreshSim(){
454    excl = excludes->getFortranArray();
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    
462    isError = 0;
463    
464 <  getFortranGroupArray(this, mfact, ngroup, groupList, groupStart);
465 <  
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 <                  &mfact[0], &ngroup, &groupList[0], &groupStart[0], &isError);
471 <  
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" );
476      painCave.isFatal = 1;
477 +    painCave.severity = OOPSE_ERROR;
478      simError();
479    }
480    
# Line 480 | Line 493 | void SimInfo::setDefaultRcut( double theRcut ){
493    
494    haveRcut = 1;
495    rCut = theRcut;
496 +  rList = rCut + 1.0;
497    
498 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
485 <  
486 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
498 >  notifyFortranCutOffs( &rCut, &rSw, &rList );
499   }
500  
501 < void SimInfo::setDefaultEcr( double theEcr ){
490 <
491 <  haveEcr = 1;
492 <  ecr = theEcr;
493 <  
494 <  ( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0;
501 > void SimInfo::setDefaultRcut( double theRcut, double theRsw ){
502  
503 <  notifyFortranCutOffs( &rCut, &rList, &ecr, &est );
503 >  rSw = theRsw;
504 >  setDefaultRcut( theRcut );
505   }
506  
499 – void SimInfo::setDefaultEcr( double theEcr, double theEst ){
507  
501 –  est = theEst;
502 –  setDefaultEcr( theEcr );
503 – }
504 –
505 –
508   void SimInfo::checkCutOffs( void ){
509    
510    if( boxIsInit ){
# Line 511 | 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"
# Line 523 | Line 525 | void SimInfo::checkCutOffs( void ){
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 <    }
529 <    
530 <    if( haveEcr ){
531 <      if( ecr > maxCutoff ){
532 <        sprintf( painCave.errMsg,
533 <                 "electrostaticCutoffRadius is too large for the current\n"
534 <                 "\tperiodic box.\n\n"
535 <                 "\tCurrent Value of ECR = %G at time %G\n "
536 <                 "\tThis is larger than half of at least one of the\n"
537 <                 "\tperiodic box vectors.  Right now, the Box matrix is:\n"
538 <                 "\n"
539 <                 "\t[ %G %G %G ]\n"
540 <                 "\t[ %G %G %G ]\n"
541 <                 "\t[ %G %G %G ]\n",
542 <                 ecr, currentTime,
543 <                 Hmat[0][0], Hmat[0][1], Hmat[0][2],
544 <                 Hmat[1][0], Hmat[1][1], Hmat[1][2],
545 <                 Hmat[2][0], Hmat[2][1], Hmat[2][2]);
546 <        painCave.isFatal = 1;
547 <        simError();
548 <      }
549 <    }
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 595 | Line 578 | GenericData* SimInfo::getProperty(const string& propNa
578   }
579  
580  
581 < void getFortranGroupArray(SimInfo* info, vector<double>& mfact, int& ngroup,
582 <                          vector<int>& groupList, vector<int>& groupStart){
583 <  Molecule* mol;
581 > void SimInfo::getFortranGroupArrays(SimInfo* info,
582 >                                    vector<int>& FglobalGroupMembership,
583 >                                    vector<double>& mfact){
584 >  
585 >  Molecule* myMols;
586    Atom** myAtoms;
587    int numAtom;
603 –  int curIndex;
588    double mtot;
589 <
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 <  groupList.clear();
608 <  groupStart.clear();
599 >  FglobalGroupMembership.clear();
600    
601 <  //Be careful, fortran array begin at 1
602 <  curIndex = 1;
612 <  
613 <  if(info->useMolecularCutoffs){
614 <    
601 >
602 >  // Fix the silly fortran indexing problem
603   #ifdef IS_MPI
604 <    ngroup = mpiSim->getMyNMol();
604 >  numAtom = mpiSim->getNAtomsGlobal();
605   #else
606 <    ngroup = info->n_mol;
606 >  numAtom = n_atoms;
607   #endif
608 <    
609 <    for(int i = 0; i < ngroup; i ++){
610 <      mol = &(info->molecules[i]);
623 <      numAtom = mol->getNAtoms();
624 <      myAtoms = mol->getMyAtoms();
625 <      mtot = 0.0;
608 >  for (int i = 0; i < numAtom; i++)
609 >    FglobalGroupMembership.push_back(globalGroupMembership[i] + 1);
610 >  
611  
612 <      for(int j=0; j < numAtom; j++)
613 <        mtot += myAtoms[j]->getMass();                
614 <      
615 <      for(int j=0; j < numAtom; j++){
616 <              
617 <        // We want the local Index:
618 <        groupList.push_back(myAtoms[j]->getIndex() + 1);
634 <        mfact.push_back(myAtoms[j]->getMass() / mtot);
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 <      }
620 >      totalMass = myCutoffGroup->getMass();
621        
622 <      groupStart.push_back(curIndex);
623 <      curIndex += numAtom;
624 <      
625 <    } //end for(int i =0 ; i < ngroup; i++)    
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 <  else{
644 <    //using atomic cutoff, every single atom is just a group
645 <    
646 < #ifdef IS_MPI
647 <    ngroup = mpiSim->getMyNlocal();
648 < #else
649 <    ngroup = info->n_atoms;
650 < #endif
651 <    
652 <    for(int i =0 ; i < ngroup; i++){
653 <      groupStart.push_back(curIndex++);      
654 <      groupList.push_back((info->atoms[i])->getIndex() + 1);
655 <      mfact.push_back(1.0);
656 <      
657 <    }//end for(int i =0 ; i < ngroup; i++)
658 <    
659 <  }//end if (info->useMolecularCutoffs)
660 <  
629 >
630   }

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