Changeset 560bbe for src/documentation

Timestamp:

Feb 17, 2012, 3:24:18 PM (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:

cdaae6

Parents:

ac5c36

git-author:

Frederik Heber <heber@…> (01/06/12 16:49:11)

git-committer:

Frederik Heber <heber@…> (02/17/12 15:24:18)

Message:

AtomicInfo now also (re)stores ParticleInfo::Nr, molecule has own IdPool.

• molecule now also has an internal IdPool to be able to hand out unique ids, according to uniqueId policy.
• new functions: molecule::changeAtomNr(), molecule::setAtomName()
• molecule::erase() and ::insert() release and set the id (and the name).
• molecule::setAtomName() uses getNr() with id increased by one.
• AtomicInfo stores and sets ParticleInfo::Nr.
• atom::changeNr() is similar to changeId() only for the molecule.
• molecule::AddAtom() does not set the name anymore, is done by ::insert().
• simplified molecule::doCountAtoms() a lot, no more naming of atoms.
• SPEEDUP: This speeds up the GUI already a lot.
• TESTFIX: changed regression test Tesselation/BigNonConvex due to different ordering of node ids (due to above), surface is still the same (checked).

File:

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

src/documentation/constructs/molecules.dox

@@ -29 +29 @@
  * as well.
  *
+ * \section molecules-atoms Atoms
+ *
+ * Atoms are added to the molecule via molecule::AddAtom() and removed via
+ * molecule::RemoveAtom(). Therein, the atom receives a unique ParticleInfo::Nr
+ * that is useful only within the molecule and is displayed in the atoms name,
+ * i.e. atom names only vary within the molecule.
+ *
+ * The molecule only stores the atoms global id and uses a boost::transform_iterator
+ * to map the ids to the true refs obtained from the World.
+ *
  * \section molecules-formula Formula
  *