source: src/documentation/constructs/molecules.dox@ cdaae6

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
Last change on this file since cdaae6 was 560bbe, checked in by Frederik Heber <heber@…>, 13 years ago

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).
  • Property mode set to 100644
File size: 2.1 KB
Line 
1/*
2 * Project: MoleCuilder
3 * Description: creates and alters molecular systems
4 * Copyright (C) 2010 University of Bonn. All rights reserved.
5 * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
6 */
7
8/**
9 * \file molecules.dox
10 *
11 * Created on: Oct 31, 2011
12 * Author: heber
13 */
14
15/**
16 * \page molecules Molecules
17 *
18 * Molecule is the next important structure to atom.
19 *
20 * Molecule are especially important for \ref fragmentation and lots of
21 * their (old) code comes from this theme.
22 *
23 * Basically, a molecule is just a conglomerate of atoms whose nodes form a
24 * connected subgraph of the entire molecular system.
25 *
26 * A molecule has its own internal array of atoms that may be traversed.
27 * Similar concepts as with the World with regards to const and non-const
28 * traversal, the former involving an Observer mechanism, come into play here
29 * as well.
30 *
31 * \section molecules-atoms Atoms
32 *
33 * Atoms are added to the molecule via molecule::AddAtom() and removed via
34 * molecule::RemoveAtom(). Therein, the atom receives a unique ParticleInfo::Nr
35 * that is useful only within the molecule and is displayed in the atoms name,
36 * i.e. atom names only vary within the molecule.
37 *
38 * The molecule only stores the atoms global id and uses a boost::transform_iterator
39 * to map the ids to the true refs obtained from the World.
40 *
41 * \section molecules-formula Formula
42 *
43 * One important concept of molecules is the associated Formula. It, as well
44 * as the AtomCount, are implemented as Cachables, i.e. they are aware of
45 * changes to the contained atoms via the Observer mechanism but update
46 * themselves only when requested.
47 *
48 * Formulas are very powerful because they can also be used as a Descriptor
49 * (\ref descriptors) to access only a certain subsets of molecules, e.g.
50 * "H2O" selects all water molecules.
51 *
52 * \section molecules-bondgraph Notes on the BondGraph
53 *
54 * Note that molecules are very volatile: Changing the bond graph also changes
55 * most of the present molecules at this time as so far there is no update
56 * mechanism. Hence, be aware of it.
57 *
58 *
59 * \date 2011-10-31
60 *
61 */
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