source: src/documentation/constructs/atoms.dox@ ab26c3

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 Candidate_v1.7.0 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 ab26c3 was 750cff, checked in by Frederik Heber <heber@…>, 14 years ago

HUGE: Update on documenation.

  • a general skeleton of the documentation is now in place with all the major components of MoleCuilder explained to some extent.
  • some information has been transfered from TRAC (e.g. install procecure) into this doxygen documentation where it is general and not specific to the situation at our institute.
  • 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 atoms.dox
10 *
11 * Created on: Oct 31, 2011
12 * Author: heber
13 */
14
15/**
16 * \page atoms Atoms
17 *
18 * Atoms are the central ingredient. They store the following information:
19 * - position, velocity, and force (over multiple time steps)
20 * - element
21 * - bond neighbours (over multiple time steps)
22 * - id
23 *
24 * \section atoms-structure
25 *
26 * The atom class has quite a complicated structure because an atoms has to
27 * fulfill various roles within this code:
28 * - atom
29 * - TesselPoint for Tesselation
30 * - Graph node for BondGraph
31 * - bonded particle
32 *
33 * There is an onion structure where additional information has been added
34 * as the layers of an onion via inheritance.
35 *
36 * We briefly want to explain the various elements of the inheritance
37 * - AtomObservable - contains notification channels enumeration and also all
38 * interface function required by the Observable pattern.
39 * - AtomInfo - contains position, element and so on.
40 * - ParticleInfo - contains name and number of the atom
41 * - BondedParticle - contains all functions related to bonds
42 * - BondedParticleInfo - contains all member variables related to storing bond
43 * information
44 * - GraphNode - contains all functions related to graphs
45 * - GraphNodeInfo - contains all member variables for graph information
46 * - TesselPoint - contains functions for considering the atom as a TesselPoint
47 * in Tesselation (\ref tesselation)
48 *
49 * Member variables and functions have been split into class with and without
50 * added \a ...Info. ...Info classes that are required multiple times are
51 * inherited as virtual to guarantee that their members are unique (exist
52 * only once) within an instance.
53 *
54 * \note Atoms have a sort-of early serialization concept (\ref serialization)
55 * as AtomicInfo. \todo This could be refactored into a full serialization
56 * compatible implementation.
57 *
58 *
59 * \date 2011-10-31
60 */
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