Ignore:
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, 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:
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)
  • 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)
Location:
src/Actions/AnalysisAction
Files:
10 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/AnalysisAction/MolecularVolumeAction.cpp

    r23359f re4afb4  
    8282  return true;
    8383}
    84 
    85 const string AnalysisMolecularVolumeAction::getName() {
    86   return NAME;
    87 }
    8884/** =========== end of function ====================== */

  • src/Actions/AnalysisAction/MolecularVolumeAction.def

    r23359f re4afb4  
    1010// i.e. there is an integer with variable name Z that can be found in
    1111// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    12 // "undefine" if no parameters are required
     12// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1313#undef paramtypes
    1414#undef paramreferences
    1515#undef paramtokens
    1616#undef paramdescriptions
     17#undef paramdefaults
    1718
    1819// some defines for all the names, you may use ACTION, STATE and PARAMS
    … …  
    2425
    2526// finally the information stored in the ActionTrait specialization
    26 #undef DEFAULTVALUE
    2727#define DESCRIPTION "calculate the volume of a given molecule"
    2828#undef SHORTFORM
    29 #define TYPEINFO &typeid(molecule)

  • src/Actions/AnalysisAction/PairCorrelationAction.cpp

    r23359f re4afb4  
    5454
    5555  // execute action
    56   output.open(params.outputname.c_str());
    57   binoutput.open(params.binoutputname.c_str());
     56  output.open(params.outputname.string().c_str());
     57  binoutput.open(params.binoutputname.string().c_str());
    5858  PairCorrelationMap *correlationmap = NULL;
    5959  std::vector<molecule*> molecules = World::getInstance().getSelectedMolecules();
    … …  
    8787  return true;
    8888}
    89 
    90 const string AnalysisPairCorrelationAction::getName() {
    91   return NAME;
    92 }
    9389/** =========== end of function ====================== */

  • src/Actions/AnalysisAction/PairCorrelationAction.def

    r23359f re4afb4  
    1313// i.e. there is an integer with variable name Z that can be found in
    1414// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    15 // "undefine" if no parameters are required
    16 #define paramtypes (std::vector<const element *>)(double)(double)(double)(std::string)(std::string)(bool)
     15// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
     16#define paramtypes (std::vector<const element *>)(double)(double)(double)(boost::filesystem::path)(boost::filesystem::path)(bool)
    1717#define paramreferences (elements)(BinStart)(BinWidth)(BinEnd)(outputname)(binoutputname)(periodic)
    1818#define paramtokens ("elements")("bin-start")("bin-width")("bin-end")("output-file")("bin-output-file")("periodic")
    1919#define paramdescriptions ("set of elements")("start of the first bin")("width of the bins")("start of the last bin")("name of the output file")("name of the bin output file")("system is constraint to periodic boundary conditions")
     20#define paramdefaults (NODEFAULT)(NODEFAULT)("0.5")(NODEFAULT)(NODEFAULT)(NODEFAULT)("0")
    2021
    2122// some defines for all the names, you may use ACTION, STATE and PARAMS
    … …  
    2728
    2829// finally the information stored in the ActionTrait specialization
    29 #undef DEFAULTVALUE
    3030#define DESCRIPTION "pair correlation analysis between two elements"
    3131#define SHORTFORM "C"
    32 #define TYPEINFO &typeid(void)

  • src/Actions/AnalysisAction/PointCorrelationAction.cpp

    r23359f re4afb4  
    5656
    5757  // execute action
    58   output.open(params.outputname.c_str());
    59   binoutput.open(params.binoutputname.c_str());
     58  output.open(params.outputname.string().c_str());
     59  binoutput.open(params.binoutputname.string().c_str());
    6060  cout << "Point to correlate to is  " << params.Point << endl;
    6161  CorrelationToPointMap *correlationmap = NULL;
    … …  
    9292  return true;
    9393}
    94 
    95 const string AnalysisPointCorrelationAction::getName() {
    96   return NAME;
    97 }
    9894/** =========== end of function ====================== */

  • src/Actions/AnalysisAction/PointCorrelationAction.def

    r23359f re4afb4  
    1515// i.e. there is an integer with variable name Z that can be found in
    1616// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    17 // "undefine" if no parameters are required
    18 #define paramtypes (std::vector<const element *>)(Vector)(double)(double)(double)(std::string)(std::string)(bool)
     17// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
     18#define paramtypes (std::vector<const element *>)(Vector)(double)(double)(double)(boost::filesystem::path)(boost::filesystem::path)(bool)
    1919#define paramreferences (elements)(Point)(BinStart)(BinWidth)(BinEnd)(outputname)(binoutputname)(periodic)
    2020#define paramtokens ("elements")("position")("bin-start")("bin-width")("bin-end")("output-file")("bin-output-file")("periodic")
    2121#define paramdescriptions ("set of elements")("position in R^3 space")("start of the first bin")("width of the bins")("start of the last bin")("name of the output file")("name of the bin output file")("system is constraint to periodic boundary conditions")
     22#define paramdefaults (NODEFAULT)(NODEFAULT)(NODEFAULT)("0.5")(NODEFAULT)(NODEFAULT)(NODEFAULT)("0")
    2223
    2324// some defines for all the names, you may use ACTION, STATE and PARAMS
    … …  
    2930
    3031// finally the information stored in the ActionTrait specialization
    31 #undef DEFAULTVALUE
    3232#define DESCRIPTION "pair correlation analysis between element and point"
    3333#undef SHORTFORM
    34 #define TYPEINFO &typeid(void)

  • src/Actions/AnalysisAction/PrincipalAxisSystemAction.cpp

    r23359f re4afb4  
    8686  return true;
    8787}
    88 
    89 const string AnalysisPrincipalAxisSystemAction::getName() {
    90   return NAME;
    91 }
    9288/** =========== end of function ====================== */

  • src/Actions/AnalysisAction/PrincipalAxisSystemAction.def

    r23359f re4afb4  
    11#undef paramdescriptions
     2#undef paramdefaults
    23/*
    34 * PrincipalAxisSystemAction.def
    … …  
    1112// i.e. there is an integer with variable name Z that can be found in
    1213// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    13 // "undefine" if no parameters are required
     14// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
    1415#undef paramtypes
    1516#undef paramreferences
    1617#undef paramtokens
    1718#undef paramdescriptions
     19#undef paramdefaults
    1820
    1921// some defines for all the names, you may use ACTION, STATE and PARAMS
    … …  
    2527
    2628// finally the information stored in the ActionTrait specialization
    27 #undef DEFAULTVALUE
    2829#define DESCRIPTION "calculate the principal axis system of the specified molecule"
    2930#undef SHORTFORM
    30 #define TYPEINFO &typeid(void)

  • src/Actions/AnalysisAction/SurfaceCorrelationAction.cpp

    r23359f re4afb4  
    5555
    5656  // execute action
    57   output.open(params.outputname.c_str());
    58   binoutput.open(params.binoutputname.c_str());
     57  output.open(params.outputname.string().c_str());
     58  binoutput.open(params.binoutputname.string().c_str());
    5959  ASSERT(params.Boundary != NULL, "No molecule specified for SurfaceCorrelation.");
    6060  const double radius = 4.;
    … …  
    114114  return true;
    115115}
    116 
    117 const string AnalysisSurfaceCorrelationAction::getName() {
    118   return NAME;
    119 }
    120116/** =========== end of function ====================== */

  • src/Actions/AnalysisAction/SurfaceCorrelationAction.def

    r23359f re4afb4  
    1414// i.e. there is an integer with variable name Z that can be found in
    1515// ValueStorage by the token "Z" -> first column: int, Z, "Z"
    16 // "undefine" if no parameters are required
    17 #define paramtypes (std::vector<const element *>)(molecule *)(double)(double)(double)(std::string)(std::string)(bool)
     16// "undefine" if no parameters are required, use (NODEFAULT) for each (undefined) default value
     17#define paramtypes (std::vector<const element *>)(const molecule *)(double)(double)(double)(boost::filesystem::path)(boost::filesystem::path)(bool)
    1818#define paramreferences (elements)(Boundary)(BinStart)(BinWidth)(BinEnd)(outputname)(binoutputname)(periodic)
    1919#define paramtokens ("elements")("molecule-by-id")("bin-start")("bin-width")("bin-end")("output-file")("bin-output-file")("periodic")
    2020#define paramdescriptions ("set of elements")("index of a molecule")("start of the first bin")("width of the bins")("start of the last bin")("name of the output file")("name of the bin output file")("system is constraint to periodic boundary conditions")
     21#define paramdefaults (NODEFAULT)(NODEFAULT)(NODEFAULT)("0.5")(NODEFAULT)(NODEFAULT)(NODEFAULT)("0")
    2122
    2223// some defines for all the names, you may use ACTION, STATE and PARAMS
    … …  
    2829
    2930// finally the information stored in the ActionTrait specialization
    30 #undef DEFAULTVALUE
    3131#define DESCRIPTION "pair correlation analysis between element and surface"
    3232#undef SHORTFORM
    33 #define TYPEINFO &typeid(void)
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