Changeset 127a8e for src/World.hpp


Ignore:
Timestamp:
Jul 8, 2010, 4:04:11 PM (14 years ago)
Author:
Tillmann Crueger <crueger@…>
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:
4d7462
Parents:
40f928
Message:

Improved managing of Ids in the World

  • Improved algorithm for managing ids to use less time and space
  • Made the moleculeIds managed
File:
1 edited

Legend:

Unmodified
Added
Removed
  • src/World.hpp

    r40f928 r127a8e  
    288288  void releaseAtomId(atomId_t);
    289289  bool reserveAtomId(atomId_t);
     290  void defragAtomIdPool();
     291
     292  moleculeId_t getNextMoleculeId();
     293  void releaseMoleculeId(moleculeId_t);
     294  bool reserveMoleculeId(moleculeId_t);
     295  void defragMoleculeIdPool();
    290296
    291297  periodentafel *periode;
     
    298304  AtomSet atoms;
    299305private:
    300   std::set<atomId_t> atomIdPool; //<!stores the pool for all available AtomIds below currAtomId
     306  typedef std::set<std::pair<atomId_t, atomId_t> > atomIdPool_t;
     307
     308  /**
     309   * stores the pool for all available AtomIds below currAtomId
     310   *
     311   * The pool contains ranges of free ids in the form [bottom,top).
     312   */
     313  atomIdPool_t atomIdPool;
    301314  atomId_t currAtomId; //!< stores the next available Id for atoms
     315  size_t lastAtomPoolSize; //!< size of the pool after last defrag, to skip some defrags
     316  unsigned int numAtomDefragSkips;
     317
    302318  MoleculeSet molecules;
     319  typedef std::set<std::pair<moleculeId_t, moleculeId_t> > moleculeIdPool_t;
     320  moleculeIdPool_t moleculeIdPool;
    303321  moleculeId_t currMoleculeId;
     322  size_t lastMoleculePoolSize; //!< size of the pool after last defrag, to skip some defrags
     323  unsigned int numMoleculeDefragSkips;
    304324private:
    305325  /**
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