Changeset eee1b7 for src/documentation/constructs

Timestamp:

Feb 24, 2013, 12:59:34 PM (12 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:

dd966f

Parents:

c91572

git-author:

Frederik Heber <heber@…> (02/19/13 12:51:53)

git-committer:

Frederik Heber <heber@…> (02/24/13 12:59:34)

Message:

DOCU: Documentation on ShapeRegistry, QtUI changes, validators, and parameters.

Location:

src/documentation/constructs

Files:

• actions.dox (modified) (3 diffs)
• constructs.dox (modified) (2 diffs)
• parameters.dox (added)
• qt-gui.dox (modified) (2 diffs)
• queries.dox (added)
• shaperegistry.dox (added)
• shapes.dox (modified) (2 diffs)
• validators.dox (added)

src/documentation/constructs/actions.dox

@@ -22 +22 @@
  *  have to create three files of which only one actually contains more than a
  *  few lines, namely the code of the Action itself.
+ *  Each Action also derives a specific ActionState and ActionParameters for
+ *  containing the undo/redo state information and the parameters steering what
+ *  the Action does.
  *
- *  Each Action has thus three types of functionalty: do, undo, and redo.
+ *  Each Action has thus three types of functionality: do, undo, and redo.
  *
  *  The ActionRegistry contains a prototype of each Action under its token
  *  such that an instance can be retrieved by knowing this token.
  *
- *  Each Action obtains its options from a central ValueStorage such that
- *  they are independent of where the option originated from: a command line
- *  parameter, a value entered in a graphical dialog or given via the keyboard
- *  in a terminal. That's why each begins with a function call to
- *  getParametersfromValueStorage() to fill its internal Action::params
- *  structure.
+ *  Each Action can contain multiple \ref parameters in its specific ActionParameters
+ *  structure that represent the options. Executing call() first fills a dialog
+ *  with \ref queries, one for each option. The UI then tries to obtain the
+ *  values from the user. Depending on the type of the UI in use that could mean
+ *  parsing stored command line parameters or displaying a real dialog box with widgets.
  *
  *  Also there is a regression test (\ref regression-test) for each Action to
@@ -53 +55 @@
  * has to be implemented in two more functions beside the "do".
  *
- * Note that undoing means to get everything back to its original state and by
- * whatever means seem appropriate, e.g. just remvoing all inserted atoms.
+ * Note that undoing means to get everything back to its original state and by whatever
+ * means seem appropriate, e.g. remvoing all just inserted atoms.
  * To make this more elaborate it is usually very useful to store extra information
  * in the Action's state such that undo and redo can be accomplished more quickly.
@@ -70 +72 @@
  *
  *
- *  \date 2012-12-04
+ *  \date 2013-02-07
  *
  */

src/documentation/constructs/constructs.dox

@@ -30 +30 @@
  *  \li \ref molecules
  *  \li \ref observers
+ *  \li \ref parameters
  *  \li \ref parsers
  *  \li \ref qt-gui
+ *  \li \ref queries
  *  \li \ref randomnumbers
  *  \li \ref serialization
  *  \li \ref shapes
+ *  \li \ref shaperegistry
  *  \li \ref tesselation
- *  \li \ref values
+ *  \li \ref validators
  *  \li \ref world
  *
@@ -43 +46 @@
  *
  *
- * \date 2012-01-16
+ * \date 2013-02-07
  *
  */

src/documentation/constructs/qt-gui.dox

@@ -22 +22 @@
  * \section qt-gui-qt3d Qt3D and the way to get atoms and bonds displayed
  *
- * Atoms and Bonds have to displayed, the widget for this is GLWorldView. This
+ * Atoms and Bonds have to displayed, the widget for this is GLWorldView. To
  * this class belongs GLWorldScene that contains lots of GLMoleculeObject's or
- * nodes in the speak of Qt3D. We have two derived class for these kind of
+ * nodes in the speak of Qt3D. We have four derived class for these kind of
  * objects:
  * -# GLMoleculeObject_atom: for each atom,
- * -# GLMoleculeObject_bond: for each "side" of the bond.
+ * -# GLMoleculeObject_bond: for each "side" of the bond (each represents half of
+ *     the bond that join in the middle between the two atoms),
+ * -# GLMoleculeObject_molecule: for each molecule (shows a box is selected),
+ * -# GLMoleculeObject_shape: shows the shapes in the ShapeRegistry.
  *
  * We can only add new nodes to the Qt3D scene at the level of GLWorldScene,
@@ -72 +75 @@
  * Additionally, we use GLWorldScene to do some bookkeeping about all bond nodes.
  * This is not strictly required but might in general be useful. Hence, signals
- * notify GLWorldScene also about GLWorldScene::BondRemoved that are emitted by
+ * notify GLWorldScene also about GLWorldScene::bondRemoved that are emitted by
  * the node itself.
  *
- * \date 2012-01-05
+ * \section QtElementList
+ *
+ * Lists for each element how often it occures in the world. Selecting an entry
+ * calls SelectionAtomByElementAction to select all atoms of that particular
+ * element.
+ *
+ * It observes the World and performs a complete refill on any message. To reduce
+ * performance issues it marks the list as dirty and refills it the next time the
+ * GUI is idle. This way many successive changes to the world only lead to a
+ * single refill.
+ *
+ * \section QtMoleculeList
+ *
+ * Lists all the molecules currently in the world grouped by their formula.
+ * Selecting an entry calls the SelectionMoleculeByIdAction.
+ *
+ * It observes the World the same way QtElementList does.
+ *
+ * \section QtShapeController
+ *
+ * This is the interface for the ShapeRegistry. It lists all the shapes in the
+ * registry and lets the user select them. It also features buttons to call
+ * actions creating and manipulating the selected shapes.
+ *
+ * As an Observer it handles the following messages from ShapeRegistry:
+ *  - ShapeRegistry::ShapeInserted
+ *  - ShapeRegistry::ShapeRemoved
+ *  - ShapeRegistry::SelectionChanged
+ *
+ * \section QtInfoBox
+ *
+ * Shows information about the atom and molecule the cursor is currently hovering over.
+ *
+ * The info pages are Observers of the respective atom/molecule. When receiving
+ * e.g. QtAtomInfoPage::subjectKilled() they automatically clear the info box.
+ *
+ * \date 2013-02-07
  */

src/documentation/constructs/shapes.dox

@@ -16 +16 @@
  *
  * Shapes are present for denoting a specific region of the simulation domain.
- * There are three types present:
+ * There are four primitive types present:
  *  - Sphere
  *  - Ellipsoid
  *  - Cuboid
+ *  - Cylinder
  *
- * Note that both may be modified (shrink/grow, rotate, morph) via an arbitrary
+ * Note that all may be modified (shrink/grow, rotate, morph) via an arbitrary
  * matrix.
  *
@@ -43 +44 @@
  * Cuboid(Vector(0,0,0), Vector(2,2,2)) && !Sphere(Vector(1,1,1), 1.)
  * \endcode
- * which would be match any object within the cuboid from (0,0,0) to (2,2,2)
+ * which would match any object within the cuboid from (0,0,0) to (2,2,2)
  * that is not in the unit sphere at (1,1,1).
  *
  *
- * \date 2011-10-31
+ * \date 2013-02-07
  *
  */