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
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Last change
on this file since 936a02 was 750cff, checked in by Frederik Heber <heber@…>, 13 years ago |
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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.
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Property mode
set to
100644
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File size:
1.6 KB
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| 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2010 University of Bonn. All rights reserved.
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| 5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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| 6 | */
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| 7 |
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| 8 | /**
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| 9 | * \file molecules.dox
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| 10 | *
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| 11 | * Created on: Oct 31, 2011
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| 12 | * Author: heber
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| 13 | */
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| 14 |
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| 15 | /**
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| 16 | * \page molecules Molecules
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| 17 | *
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| 18 | * Molecule is the next important structure to atom.
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| 19 | *
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| 20 | * Molecule are especially important for \ref fragmentation and lots of
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| 21 | * their (old) code comes from this theme.
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| 22 | *
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| 23 | * Basically, a molecule is just a conglomerate of atoms whose nodes form a
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| 24 | * connected subgraph of the entire molecular system.
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| 25 | *
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| 26 | * A molecule has its own internal array of atoms that may be traversed.
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| 27 | * Similar concepts as with the World with regards to const and non-const
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| 28 | * traversal, the former involving an Observer mechanism, come into play here
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| 29 | * as well.
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| 30 | *
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| 31 | * \section molecules-formula Formula
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| 32 | *
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| 33 | * One important concept of molecules is the associated Formula. It, as well
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| 34 | * as the AtomCount, are implemented as Cachables, i.e. they are aware of
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| 35 | * changes to the contained atoms via the Observer mechanism but update
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| 36 | * themselves only when requested.
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| 37 | *
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| 38 | * Formulas are very powerful because they can also be used as a Descriptor
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| 39 | * (\ref descriptors) to access only a certain subsets of molecules, e.g.
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| 40 | * "H2O" selects all water molecules.
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| 41 | *
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| 42 | * \section molecules-bondgraph Notes on the BondGraph
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| 43 | *
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| 44 | * Note that molecules are very volatile: Changing the bond graph also changes
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| 45 | * most of the present molecules at this time as so far there is no update
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| 46 | * mechanism. Hence, be aware of it.
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| 47 | *
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| 48 | *
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| 49 | * \date 2011-10-31
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| 50 | *
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| 51 | */
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