Changeset e4afb4 for src/Actions/MoleculeAction/FillWithMoleculeAction.def

Timestamp:

Oct 30, 2010, 8:42:44 PM (15 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:

76cec6, c38826

Parents:

23359f

git-author:

Frederik Heber <heber@…> (10/30/10 19:55:54)

git-committer:

Frederik Heber <heber@…> (10/30/10 20:42:44)

Message:

Huge refactoring: Introduction of Traits to Actions.

This change is really big but the introduction of the Trait concept (at least
in its current light form) is so fundamental that lots of pieces had to be
changed in order to get everything working.

The main point why it was necessary to add these traits in the first place was
to comfortably allow for adding extension of Actions information-wise, i.e.
with stuff that is only important for the QtUI, such as icons, or tooltips, ...
This extra information should not be stored with Action itself, as it has
nothing to do with the workings of the Action. And neither should it get
stored with some blown-out-of-proportions MapOfActions class ...

The gist of the change is as follows:

• OptionTrait contains the token, description, shortform and type of an option, such as ("position", "position in space, none, typeid(Vector)).
• ActionTrait is the derived form for actions where additionally MenuPosition and MenuName are stored (and probably more to come for the GUI), also we have a set of OptionTrait instances, one for each option of the Action.
• Action then contains this ActionTrait, specialized for each Action.
• the preprocessor macros have been enhanced to gather all this information from the .def files.
• MapOfActions is gone. Completely. Most of its use was to store this extra information and the ValueStorage part now is just in class ValueStorage.
• ValueStorage is no more an interface to MapOfActions but as the name says a (type-safe) ValueStorage.

Listing the (remaining) changes in alphabetical order of the class:

• Action
  • member value ::name dropped, ::getName() uses ActionTraits::getName()
  • new define NODEFAULT which is used in paramdefaults in .def files
  • all derived actions classes such as Process, Calculations, MakroAction,... have been adapated to use the ActionTrait concept as well.

• ActionHistory
  • extraced RedoAction and UndoAction, shifted implementation into their own object files and they use .def files as well (i.e. streamlined with method used for other actions)

• CommandLineParser
  • CommandLineParser goes through ActionRegistry to get arguments and types to add
  • we use TypeEnumContainer which before was present in MapOfActions, as CommandLineParser::AddOptionsToParser() needs enums in its switch statement, we can't switch on types and types are not known until run-time. Hence, templates won't do either.
  • ShortFormMap is created here now (and used here only)
  • File was moved over to UIElements/CommandLineUI.

• MenuDescription
  • contain information on Menus such as name, ...
  • new unit test checks for consistency

• molecule
  • const member functions: Copy(), Output() and OutputBonds()

• OptionRegistry
  • new registry class for options only
  • we want the same type throughout the code for each token, e.g. "position"
  • the registry containts checks for consistency

• OptionTrait
  • default values are specified in paramdefaults, none are given by NODEFAULT
  • introduced default for translate-atoms, point-correlation, pair-correlation

• Registry pattern
  • new unit test, but only sceleton code so far

• ...Query, also ...Pipe
  • atoms, molecule and elements are now all const
  • also ValueStorage's signatures all have const therein

• ValueStorage
  • set/queryCurrentValue from MapOfActions
  • at times VectorValue has been in .def files where Vector was in the signature. This is cleared. Such stuff is only present for e.g. BoxVector being queried as a Vector. But this is a feature and intended.

• World
  • most of the (un)selection functions now work on const atoms and molecules
  • in one case we need a const_cast to remove this, but this is intentional, as the vector of selected atoms stores non-const pointers and this is ok.

There is only one test which had to be changed slightly because a specific
option token as "position" must now have the same type everywhere, e.g. always
Vector.

• TESTFIX: Simple_configuration/2: --position -> --domain-position (and associated to BoxVector)

File:

• src/Actions/MoleculeAction/FillWithMoleculeAction.def (modified) (2 diffs)

src/Actions/MoleculeAction/FillWithMoleculeAction.def

@@ -12 +12 @@
 // i.e. there is an integer with variable name Z that can be found in
 // ValueStorage by the token "Z" -> first column: int, Z, "Z"
-// "undefine" if no parameters are required
-#define paramtypes (std::string)(Vector)(Vector)(double)(bool)
+// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
+#define paramtypes (boost::filesystem::path)(Vector)(Vector)(double)(bool)
 #define paramtokens ("fill-molecule")("distances")("lengths")("MaxDistance")("DoRotate")
-#define paramdescriptions ("fill around molecules' surface with a filler molecule")("list of three of distances in space, one for each axis direction")("list of three of lengths in space, one for each axis direction")("maximum spatial distance")("whether to rotate or not")
+#define paramdescriptions ("name of xyz file of filler molecule")("list of three of distances in space, one for each axis direction")("list of three of lengths in space, one for each axis direction")("maximum spatial distance")("whether to rotate or not")
+#undef paramdefaults
 #define paramreferences (fillername)(distances)(lengths)(MaxDistance)(DoRotate)
 
@@ -30 +31 @@
 
 // finally the information stored in the ActionTrait specialization
-#undef DEFAULTVALUE
 #define DESCRIPTION "fill around molecules' surface with a filler molecule"
 #define SHORTFORM "F"
-#define TYPEINFO &typeid(std::string)
+