Changeset 750cff for src/documentation/constructs/parsers.dox

Timestamp:

Oct 31, 2011, 5:13:52 PM (14 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, 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

Children:

5982c5

Parents:

19bc74

Message:

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.

File:

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

src/documentation/constructs/parsers.dox

@@ -12 +12 @@
  *    Author: heber
  */
+
+/** \page parsers Format Parsers
+ *
+ *  Format Parsers load or save information about the World (i.e. all atoms,
+ *  contained bonds, ...) in a specific file format.
+ *
+ *  All parsers derive from FormatParser and all available instances of
+ *  FormatParser's are stored in a FormatParserStorage such that they can be
+ *  retrieved with simply knowing the associated token.
+ *
+ *  We have this storage as the FormatParser may also contain extra information
+ *  per atom (...AtomDataContainer or alikes) which should be copied when an
+ *  atom is copied. Hence, as soon as a FormatParser is accessed once it sits
+ *  in the Storage and accumulates all information. Therefore, every parser
+ *  instance is unique per type throughout the run of the program.
+ *
+ *  A specific parser can be obtained from the FormatParserStorage just by
+ *  knowing the correct keyword such as this:
+ *  \code
+ *  ParserTypes type = FormatParserStorage::getInstance().getTypeFromName("xyz");
+ *  FormatParserInterface &parser = FormatParserStorage::getInstance().get(type);
+ *  \endcode
+ *
+ *  Associated to the FormatParser's is also the ChangeTracker (\ref observers)
+ *  that observers the World and tells all parsers on program exit whether
+ *  to save or not (i.e. whether any changes occurred). FormatParser_common
+ *  makes sure that each FormatParser signUp()s to this ChangeTracker.
+ *
+ *  Important is also the concept of a Parameter here. A Parameter is a value
+ *  of a certain type with a given valid range or set of valid values. There
+ *  ContinuousValue and DiscreteValue template classes that are subsequently
+ *  joined with a name to give a ContinuousParameter and DiscreteParameter to
+ *  be stored via a unifying ParameterInterface into a ParameterStorage. Such
+ *  an instance each of the FormatParser's contains. Therein extra information
+ *  such as a basis set, unit length, energy cutoff or other parser-specific
+ *  parameters are stored.
+ *
+ *  Various actions (WorldInputAction, WorldOuputAction, AtomSaveSelectedAtomsAction,
+ *  MoleculeSaveSelectedAction) use the parser to load or store atoms or to
+ *  control the behavior of storage (ParserSetOutputFormatAction, ...)
+ *
+ * \section parsers-add To add a new parser ...
+ *
+ *  The following tasks are necessary:
+ *  -# think of unique brief name for your parser, e.g. "xyz" and add to
+ *  \b ParserTypes.def. This will inform FormatParserStorage of your new parser.
+ *  (Again there is some preprocessor magic for instanting all ...)
+ *  -# Implement a FormatParserTraits specialization with some common stuff to
+ *    your parsers
+ *  \code
+ *  template<>
+ *  struct FormatParserTrait<name>
+ *  {
+ *    //!> Name of the parser
+ *    static const std::string name;
+ *    //!> suffix of the files the parser understands to read and write
+ *    static const std::string suffix;
+ *    //!> ParserTypes enumeration for the parser
+ *    static const enum ParserTypes type;
+ *  };
+ *  \endcode
+ *  where \a name is the name unique name of your parser, e.g. \a xyz.
+ *  -# Create all these static variables with matching contents.
+ *  -# Implement a FormatParser specialization
+ *  \code
+ *  template <>
+ *  class FormatParser< name >  : virtual public FormatParserInterface, public FormatParser_common
+ *  {
+ *  ...
+ *  };
+ *  \endcode
+ *  where \a name is again the name of your parser. FormatParser_common
+ *  contains some functionality common to all Parsers where FormatParserInterface
+ *  is the interface where load() and save() are defined. This allows for storage
+ *  in FormatParserRegistry.
+ *  -# implement FormatParserInterface::load() and FormatParserInterface::save().
+ *  -# implement FormatParser_common::AtomInserted() and
+ *    FormatParser_common::AtomRemoved()
+ *
+ *
+ * \date 2011-10-31
+ */