Changeset ea7a50 for src/documentation/constructs

Timestamp:

Feb 22, 2012, 11:26:49 AM (13 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:

3dfd9c

Parents:

52ed5b

git-author:

Frederik Heber <heber@…> (01/06/12 17:53:45)

git-committer:

Frederik Heber <heber@…> (02/22/12 11:26:49)

Message:

Rewrote some of the descriptors such that they access World's AtomSet and MoleculeSet directly.

• this is the way they are intended. They are friends of the World and may use the sets directly without causing update()s although they return non- const references. This is because here we need not be careful as no atoms are destroyed or added.
• In most cases we had implemented both predicate() and new find() and findAll() that were not necessary (default find..() would do the job better).
• This concerned: AtomOfMoleculeSelectionDescriptor, MoleculeNameDescriptor, MoleculeOfAtomSelectionDescriptor, MoleculeOrderDescriptor, and MoleculePtrDescriptor.
• We left the specific implementation for AtomIdDescriptor and MoleculeIdDescriptor as they directly access World's Atom- and MoleculeSet and may thus find ids significantly faster.
• NOTE: so far some tests are broken and this needs to be fixed yet.

File:

• src/documentation/constructs/descriptors.dox (modified) (1 diff)

src/documentation/constructs/descriptors.dox

@@ -73 +73 @@
  *  - currently selected molecules: MoleculesBySelection()
  *
+ * \subsection descriptors-world Descriptors and the World
  *
- * \date 2011-10-31
+ *  In the World we make heavy use of descriptors. However, the World is also
+ *  responsibly of informing connected Observers about removal or insertion of
+ *  atoms or molecules.
+ *  That's why its containers are protectedly constructed as ObservedContainers.
+ *  Whenever you walk through them with a normal iterator, afterwards an update()
+ *  is initiated. Only if you use a const_interator, this is prevented. But this
+ *  at the natural disadvantage that the reference may only be used in constant
+ *  environment.
+ *  Descriptors however may return non-const reference. And we rely heavily on
+ *  these to cheaply give us the correct reference for a given id, element type,
+ *  and so on. So how do we do this?
+ *
+ *  Some of the descriptors are friends of the World and may use its internal
+ *  containers directly, see AtomSelectionDescriptor_impl. Thus it can quickly
+ *  walk through the atoms and find the correct one without causing huge delays
+ *  by unnecessarily calling forth an update().
+ *
+ *
+ * \date 2012-01-06
  *
  */