Changeset 1259df for src/Actions


Ignore:
Timestamp:
Jul 24, 2015, 4:44:34 PM (10 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
Children:
f01769
Parents:
63fb7a
git-author:
Frederik Heber <heber@…> (06/01/15 08:56:36)
git-committer:
Frederik Heber <heber@…> (07/24/15 16:44:34)
Message:

Replaced World::getAllMolecules() wherever possible by const version.

Location:
src/Actions
Files:
16 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/FillAction/FillVolumeAction.cpp

    r63fb7a r1259df  
    7878  }
    7979  molecule *filler = *(molecules.begin());
    80   for(molecule::const_iterator iter = filler->begin(); iter != filler->end(); ++iter)
     80  for(molecule::const_iterator iter = const_cast<const molecule *>(filler)->begin();
     81      iter != const_cast<const molecule *>(filler)->end();
     82      ++iter)
    8183    movedatoms.push_back( AtomicInfo(*(*iter)) );
    8284  LOG(1, "INFO: Chosen molecule has " << filler->size() << " atoms.");

  • src/Actions/FillAction/SuspendInMoleculeAction.cpp

    r63fb7a r1259df  
    141141  double clustervolume = 0.;
    142142  std::vector<double> GreatestDiameter(NDIM, 0.);
    143   for (std::vector<molecule *>::iterator iter = molecules.begin();
     143  for (std::vector<molecule *>::const_iterator iter = molecules.begin();
    144144      iter != molecules.end(); ++iter)
    145145  {

  • src/Actions/GraphAction/CreateAdjacencyAction.cpp

    r63fb7a r1259df  
    109109  // give info
    110110  size_t BondCount = 0;
    111   std::vector<molecule *> molecules = World::getInstance().getAllMolecules();
    112   for (std::vector<molecule *>::const_iterator iter = molecules.begin();
     111  std::vector<const molecule *> molecules = const_cast<const World &>(World::getInstance()).
     112      getAllMolecules();
     113  for (std::vector<const molecule *>::const_iterator iter = molecules.begin();
    113114      iter != molecules.end(); ++iter)
    114115    BondCount += (*iter)->getBondCount();

  • src/Actions/GraphAction/UpdateMoleculesAction.cpp

    r63fb7a r1259df  
    6767  LOG(0, "STATUS: Creating undo state.");
    6868  MolAtomList moleculelist;
    69   vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
    70   for (vector<molecule *>::const_iterator moliter = allmolecules.begin(); moliter != allmolecules.end(); ++moliter) {
    71     std::vector<atomId_t> atomlist;
    72     atomlist.resize((*moliter)->size());
    73     for (molecule::const_iterator atomiter = (*moliter)->begin(); atomiter != (*moliter)->end(); ++atomiter) {
    74       atomlist.push_back((*atomiter)->getId());
     69  {
     70    vector<const molecule *> allmolecules = const_cast<const World &>(World::getInstance()).
     71        getAllMolecules();
     72    for (vector<const molecule *>::const_iterator moliter = allmolecules.begin(); moliter != allmolecules.end(); ++moliter) {
     73      std::vector<atomId_t> atomlist;
     74      atomlist.resize((*moliter)->size());
     75      for (molecule::const_iterator atomiter = (*moliter)->begin(); atomiter != (*moliter)->end(); ++atomiter) {
     76        atomlist.push_back((*atomiter)->getId());
     77      }
     78      moleculelist.insert( std::pair< moleculeId_t, std::vector<atomId_t> > ((*moliter)->getId(), atomlist));
    7579    }
    76     moleculelist.insert( std::pair< moleculeId_t, std::vector<atomId_t> > ((*moliter)->getId(), atomlist));
    7780  }
    7881  GraphUpdateMoleculesState *UndoState = new GraphUpdateMoleculesState(moleculelist, params);
    … …  
    8184  LOG(0, "STATUS: Removing all present molecules.");
    8285  MoleculeListClass *molecules = World::getInstance().getMolecules();
     86  vector<molecule *> allmolecules = World::getInstance().getAllMolecules();
    8387  for (vector<molecule *>::iterator MolRunner = allmolecules.begin(); MolRunner != allmolecules.end(); ++MolRunner) {
    8488    molecules->erase(*MolRunner);
    … …  
    9094  DFS();
    9195  DFS.UpdateMoleculeStructure();
    92   if (World::getInstance().numMolecules() == 0) {
     96  const size_t numMolecules =
     97      const_cast<const World &>(World::getInstance()).numMolecules();
     98  if (numMolecules == 0) {
    9399    //World::getInstance().destroyMolecule(mol);
    94100    STATUS("There are no molecules.");
    … …  
    96102  }
    97103
    98   LOG(1, "I scanned " << World::getInstance().numMolecules() << " molecules.");
     104  LOG(1, "I scanned " << numMolecules << " molecules.");
    99105
    100106  return ActionState::ptr(UndoState);

  • src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.cpp

    r63fb7a r1259df  
    5656ActionState::ptr SelectionMoleculeByFormulaAction::performCall() {
    5757  LOG(1, "Selecting molecules with chemical formula " << params.formula.get() << ":");
    58 //  std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula.get()));
    59   std::vector<molecule *> selectedMolecules =
    60       World::getInstance().getAllMolecules(MoleculesBySelection() && MoleculeByFormula(params.formula.get()));
     58  std::vector<const molecule *> selectedMolecules =
     59      const_cast<const World &>(World::getInstance()).
     60      getAllMolecules(MoleculesBySelection() && MoleculeByFormula(params.formula.get()));
    6161//  BOOST_FOREACH(molecule *mol, matchingMolecules)
    6262//    LOG(1, "\t" << mol->getId() << ", " << mol->getName() << ".");
    … …  
    7070
    7171  World::getInstance().unselectAllMolecules(MoleculeByFormula(state->params.formula.get()));
    72   BOOST_FOREACH( molecule *mol, state->selectedMolecules)
     72  BOOST_FOREACH( const molecule *mol, state->selectedMolecules)
    7373    World::getInstance().selectMolecule(mol);
    7474

  • src/Actions/SelectionAction/Molecules/MoleculeByFormulaAction.def

    r63fb7a r1259df  
    2222(FormulaValidator())
    2323
    24 #define statetypes (std::vector<molecule*>)
     24#define statetypes (std::vector<const molecule*>)
    2525#define statereferences (selectedMolecules)
    2626

  • src/Actions/SelectionAction/Molecules/MoleculeByNameAction.cpp

    r63fb7a r1259df  
    5656ActionState::ptr SelectionMoleculeByNameAction::performCall() {
    5757  LOG(1, "Selecting all molecules called " << params.molname.get());
    58   std::vector<molecule *> selectedMolecules =
    59       World::getInstance().getAllMolecules(MoleculesBySelection() && MoleculeByName(params.molname.get()));
     58  std::vector<const molecule *> selectedMolecules =
     59      const_cast<const World &>(World::getInstance()).
     60      getAllMolecules(MoleculesBySelection() && MoleculeByName(params.molname.get()));
    6061  World::getInstance().selectAllMolecules(MoleculeByName(params.molname.get()));
    6162  LOG(0, World::getInstance().countSelectedMolecules() << " molecules selected.");
    … …  
    6869
    6970  World::getInstance().unselectAllMolecules(MoleculeByName(state->params.molname.get()));
    70   BOOST_FOREACH( molecule *mol, state->selectedMolecules)
     71  BOOST_FOREACH( const molecule *mol, state->selectedMolecules)
    7172    World::getInstance().selectMolecule(mol);
    7273

  • src/Actions/SelectionAction/Molecules/MoleculeByNameAction.def

    r63fb7a r1259df  
    2424(DummyValidator< std::string >())
    2525
    26 #define statetypes (std::vector<molecule *>)
     26#define statetypes (std::vector<const molecule *>)
    2727#define statereferences (selectedMolecules)
    2828

  • src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.cpp

    r63fb7a r1259df  
    5656ActionState::ptr SelectionNotMoleculeByFormulaAction::performCall() {
    5757  LOG(1, "Unselecting molecules with chemical formula " << params.formula.get() << ":");
    58   std::vector<molecule *> matchingMolecules = World::getInstance().getAllMolecules(MoleculeByFormula(params.formula.get()));
    59   std::vector<molecule *> unselectedMolecules = World::getInstance().getAllMolecules(!MoleculesBySelection());
     58  std::vector<const molecule *> matchingMolecules =
     59      const_cast<const World &>(World::getInstance()).
     60      getAllMolecules(MoleculeByFormula(params.formula.get()));
     61  std::vector<const molecule *> unselectedMolecules =
     62      const_cast<const World &>(World::getInstance()).
     63      getAllMolecules(!MoleculesBySelection());
    6064  World::getInstance().unselectAllMolecules(MoleculeByFormula(params.formula.get()));
    6165  LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
    … …  
    6771
    6872  World::getInstance().selectAllMolecules(MoleculeByFormula(state->params.formula.get()));
    69   BOOST_FOREACH( molecule *mol, state->unselectedMolecules)
     73  BOOST_FOREACH( const molecule *mol, state->unselectedMolecules)
    7074    World::getInstance().unselectMolecule(mol);
    7175

  • src/Actions/SelectionAction/Molecules/NotMoleculeByFormulaAction.def

    r63fb7a r1259df  
    2222(FormulaValidator())
    2323
    24 #define statetypes (std::vector<molecule*>)
     24#define statetypes (std::vector<const molecule*>)
    2525#define statereferences (unselectedMolecules)
    2626

  • src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.cpp

    r63fb7a r1259df  
    5656ActionState::ptr SelectionNotMoleculeByNameAction::performCall() {
    5757  LOG(1, "Unselecting all molecule called " << params.molname.get());
    58   std::vector<molecule *> unselectedMolecules =
    59       World::getInstance().getAllMolecules((!MoleculesBySelection()) && MoleculeByName(params.molname.get()));
     58  std::vector<const molecule *> unselectedMolecules =
     59      const_cast<const World &>(World::getInstance()).
     60        getAllMolecules((!MoleculesBySelection()) && MoleculeByName(params.molname.get()));
    6061  World::getInstance().unselectAllMolecules(MoleculeByName(params.molname.get()));
    6162  LOG(0, World::getInstance().countSelectedMolecules() << " molecules remain selected.");
    … …  
    6869
    6970  World::getInstance().selectAllMolecules(MoleculeByName(state->params.molname.get()));
    70   BOOST_FOREACH( molecule *mol, state->unselectedMolecules)
     71  BOOST_FOREACH( const molecule *mol, state->unselectedMolecules)
    7172    World::getInstance().unselectMolecule(mol);
    7273

  • src/Actions/SelectionAction/Molecules/NotMoleculeByNameAction.def

    r63fb7a r1259df  
    2222(DummyValidator< std::string >())
    2323
    24 #define statetypes (std::vector<molecule *>)
     24#define statetypes (std::vector<const molecule *>)
    2525#define statereferences (unselectedMolecules)
    2626

  • src/Actions/WorldAction/BoundInBoxAction.cpp

    r63fb7a r1259df  
    5656  // create undo state
    5757  std::vector< boost::shared_ptr<Vector> > OldPositions;
    58   std::vector<molecule*> AllMolecules = World::getInstance().getAllMolecules();
    59   for (vector<molecule*>::iterator MolRunner = AllMolecules.begin();
    60       MolRunner != AllMolecules.end();
    61       ++MolRunner) {
    62     for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
    63         AtomRunner != (*MolRunner)->end();
    64         ++AtomRunner) {
    65       OldPositions.push_back(
    66           boost::shared_ptr<Vector>(new Vector(
    67               (*AtomRunner)->getPosition()
    68               ))
    69           );
     58  {
     59    std::vector<const molecule*> AllMolecules = const_cast<const World &>(World::getInstance()).
     60        getAllMolecules();
     61    for (vector<const molecule*>::iterator MolRunner = AllMolecules.begin();
     62        MolRunner != AllMolecules.end();
     63        ++MolRunner) {
     64      for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
     65          AtomRunner != (*MolRunner)->end();
     66          ++AtomRunner) {
     67        OldPositions.push_back(
     68            boost::shared_ptr<Vector>(new Vector(
     69                (*AtomRunner)->getPosition()
     70                ))
     71            );
     72      }
    7073    }
    7174  }
    … …  
    7376
    7477  // center
     78  std::vector<molecule*> AllMolecules = World::getInstance().getAllMolecules();
    7579  for (std::vector<molecule*>::iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
    7680    (*MolRunner)->BoundInBox();

  • src/Actions/WorldAction/CenterInBoxAction.cpp

    r63fb7a r1259df  
    6868  oa << matrix;
    6969  std::vector< boost::shared_ptr<Vector> > OldPositions;
    70   std::vector<molecule*> AllMolecules = World::getInstance().getAllMolecules();
    71   for (std::vector<molecule*>::iterator MolRunner = AllMolecules.begin();
    72       MolRunner != AllMolecules.end();
    73       ++MolRunner) {
    74     for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
    75         AtomRunner != (*MolRunner)->end();
    76         ++AtomRunner) {
    77       OldPositions.push_back(
    78           boost::shared_ptr<Vector>(new Vector(
    79               (*AtomRunner)->getPosition()
    80               ))
    81           );
     70  {
     71    std::vector<const molecule*> AllMolecules = const_cast<const World &>(World::getInstance()).
     72        getAllMolecules();
     73    for (std::vector<const molecule*>::iterator MolRunner = AllMolecules.begin();
     74        MolRunner != AllMolecules.end();
     75        ++MolRunner) {
     76      for(molecule::const_iterator AtomRunner = (*MolRunner)->begin();
     77          AtomRunner != (*MolRunner)->end();
     78          ++AtomRunner) {
     79        OldPositions.push_back(
     80            boost::shared_ptr<Vector>(new Vector(
     81                (*AtomRunner)->getPosition()
     82                ))
     83            );
     84      }
    8285    }
    8386  }
    … …  
    8790
    8891  // center atoms
     92  std::vector<molecule*> AllMolecules = World::getInstance().getAllMolecules();
    8993  for (std::vector<molecule*>::iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
    9094    (*MolRunner)->CenterInBox();

  • src/Actions/WorldAction/RepeatBoxAction.cpp

    r63fb7a r1259df  
    6363void repeatMoleculesinDomain(
    6464    std::vector< unsigned int > Repeater,
    65     const std::vector<molecule *> &AllMolecules)
     65    const std::vector<const molecule *> &AllMolecules)
    6666{
    6767  LOG(0, "STATUS: Repeating box " << Repeater << " times for (x,y,z) axis.");
    … …  
    8585
    8686  // add molecules in each repeated domain part
    87   molecule *newmol = NULL;
    8887  std::vector<Vector> vectors;
    8988  MoleculeListClass *molecules = World::getInstance().getMolecules();
    … …  
    9695        if ((n[0] == 0) && (n[1] == 0) && (n[2] == 0))
    9796          continue;
    98         for (vector<molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
    99           molecule * const mol = *MolRunner;
     97        for (vector<const molecule *>::const_iterator MolRunner = AllMolecules.begin(); MolRunner != AllMolecules.end(); ++MolRunner) {
     98          const molecule * const mol = *MolRunner;
    10099          LOG(2, "DEBUG: Current mol is " << mol->name << "." << endl);
    101           newmol = mol->CopyMolecule();
     100          molecule * const newmol = mol->CopyMolecule();
    102101          // TODO: remove this when World does not have MoleculeListClass anymore.
    103102          molecules->insert(newmol);
    … …  
    114113
    115114ActionState::ptr WorldRepeatBoxAction::performCall() {
    116   std::vector<molecule *> AllMolecules;
    117115  DoLog(0) && (Log() << Verbose(0) << "Using all molecules." << endl);
    118   AllMolecules = World::getInstance().getAllMolecules();
     116  std::vector<const molecule *> AllMolecules =
     117      const_cast<const World &>(World::getInstance()).getAllMolecules();
    119118
    120119  // prepare undo state
    121120  RealSpaceMatrix olddomain = World::getInstance().getDomain().getM();
    122   std::set<molecule *> oldmolecules;
    123   for(std::vector<molecule *>::const_iterator iter = AllMolecules.begin();
     121  std::set<const molecule *> oldmolecules;
     122  for(std::vector<const molecule *>::const_iterator iter = AllMolecules.begin();
    124123      iter != AllMolecules.end();
    125124      ++iter)
    … …  
    160159  WorldRepeatBoxState *state = assert_cast<WorldRepeatBoxState*>(_state.get());
    161160
    162   std::vector<molecule *> originalmolecules;
    163   for(std::set<molecule *>::const_iterator iter = state->oldmolecules.begin();
     161  std::vector<const molecule *> originalmolecules;
     162  for(std::set<const molecule *>::const_iterator iter = state->oldmolecules.begin();
    164163      iter != state->oldmolecules.end();
    165164      ++iter)

  • src/Actions/WorldAction/RepeatBoxAction.def

    r63fb7a r1259df  
    2828(STLVectorValidator< std::vector< unsigned int > >(NDIM, NDIM))
    2929
    30 #define statetypes (RealSpaceMatrix)(std::set< molecule *>)
     30#define statetypes (RealSpaceMatrix)(std::set< const molecule *>)
    3131#define statereferences (olddomain)(oldmolecules)
    3232
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