Changeset 949953


Ignore:
Timestamp:
Nov 7, 2011, 12:23:52 PM (13 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:
c20b35
Parents:
071243
git-author:
Frederik Heber <heber@…> (09/26/11 12:59:25)
git-committer:
Frederik Heber <heber@…> (11/07/11 12:23:52)
Message:

pyMoleCuilder now has full functionality.

  • For each header file there is a COMMAND_stringargs() function defined.
  • boost python module exports all Action's COMMAND_stringargs() that are present in GlobalListOfActions.hpp.
  • new source file AllActionPython.hpp is created in Actions/Makefile.am that enlists all the headers.
  • New implemenations:
    • Action_impl_python.hpp: defines COMMAND_stringargs() via some boost:: preprocessor magic.
    • Action_impl_undef.hpp: contains undefs to the Action's .def files.
  • also docstrings are working, both for module and for each exported function.
  • so far, all arguments have a (in NODEFAULT case empty) default value. This is because we cannot perform string comparisons with the preprocessor only numeric ones (i.e. NODEFAULT would have to be 0 or alike).
  • Extracted cleanUp() from builder_init.cpp and placed into own module.
  • cleanUp() is now also registered atexit() for pyMoleCuilder where it is needed as well.
  • AddStaticEntitiestoIgnoreList() has likewise been extracted.
Location:
src
Files:
4 added
5 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/Makefile.am

    r071243 r949953  
    407407libMolecuilderActionPrototypes_la_includedir = $(includedir)/MoleCuilder/Actions/
    408408
    409 BUILT_SOURCES += AllActionHeaders.hpp
     409BUILT_SOURCES += AllActionHeaders.hpp AllActionPython.hpp
    410410
    411411#       UIElements/libMolecuilderUI.la
    … …  
    459459        echo "#endif /* ALLACTIONHEADERS_HPP_ */" >>$@;
    460460
     461AllActionPython.hpp: $(ACTIONPROTOTYPESHEADER)
     462        echo "#ifndef ALLACTIONPYTHON_HPP_" >$@; \
     463        echo "#define ALLACTIONPYTHON_HPP_" >>$@; \
     464        for file in $(ACTIONPROTOTYPESHEADER); do \
     465                echo "#include \"`echo $$file | sed -e 's/hpp/def/'`\"" >>$@; \
     466                echo "#include \"Actions/Action_impl_python.hpp\"" >>$@; \
     467                echo "#include \"Actions/Action_impl_undef.hpp\"" >>$@; \
     468        done; \
     469        echo "#endif /* ALLACTIONPYTHON_HPP_ */" >>$@;
     470
     471
    461472MOSTLYCLEANFILES += \
    462         AllActionHeaders.hpp
     473        AllActionHeaders.hpp \
     474        AllActionPython.hpp

  • src/Actions/pyMoleCuilder.cpp

    r071243 r949953  
    1818#endif
    1919
    20 #include <boost/python/def.hpp>
     20#include <boost/python.hpp>
    2121#include <boost/python/module.hpp>
    2222#include <boost/python/args.hpp>
    … …  
    2424#include "CodePatterns/MemDebug.hpp"
    2525
    26 #include "Actions/CommandAction/HelpAction.hpp"
     26//!> define all present actions
     27#include "GlobalListOfActions.hpp"
     28
     29//!> python wrapping for all of these actions
     30#include "AllActionPython.hpp"
     31
     32#include "cleanUp.hpp"
     33#include "Actions/ActionHistory.hpp"
     34
    2735
    2836BOOST_PYTHON_MODULE(pyMoleCuilder)
    2937{
    30   boost::python::def(
    31       "CommandHelp",
    32       MoleCuilder::CommandHelp,
    33       boost::python::args("actionname"),
    34       "this gives a list of all Actions."
    35       );
     38  // need to init the history before any action is created
     39  MoleCuilder::ActionHistory::init();
     40
     41  // from this moment on, we need to be sure to deeinitialize in the correct order
     42  // this is handled by the cleanup function
     43  atexit(cleanUp);
     44
     45  // set the docstring of the current module scope
     46  boost::python::scope().attr("__doc__") = "pyMolecuilder are the python bindings to all Actions of the program suite MoleCuilder.\n\nMoleCuilder is a program to build molecular (dynamics) worlds, allowing you indefinite manipulation, control and analysis over the atoms and molecules within a simulation domain.";
     47
     48#define export_print(z,n,list) \
     49        BOOST_PP_CAT(export_, BOOST_PP_SEQ_ELEM(n, list))();
     50#define BOOST_PP_LOCAL_MACRO(n) export_print(~, n, GLOBALLISTOFACTIONS)
     51#define BOOST_PP_LOCAL_LIMITS  (0, BOOST_PP_DEC(BOOST_PP_SEQ_SIZE(GLOBALLISTOFACTIONS)))
     52#include BOOST_PP_LOCAL_ITERATE()
     53#undef instance_print 
    3654}

  • src/Makefile.am

    r071243 r949953  
    271271
    272272pyexec_LTLIBRARIES += pyMoleCuilder.la
    273 pyMoleCuilder_la_SOURCES = Actions/pyMoleCuilder.cpp
     273pyMoleCuilder_la_SOURCES = \
     274        cleanUp.cpp \
     275        cleanUp.hpp \
     276        Actions/pyMoleCuilder.cpp
    274277pyMoleCuilder_la_CPPFLAGS = ${BOOST_CPPFLAGS} ${CodePatterns_CFLAGS} -I$(PYTHON_INCLUDE_DIR)
    275278pyMoleCuilder_la_LDFLAGS = -module -avoid-version -shared
    … …  
    284287#molecuilder_CXXFLAGS += -DNO_CACHING
    285288molecuilder_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_RANDOM_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)
    286 molecuilder_SOURCES = builder.cpp builder_init.cpp builder_init.hpp
     289molecuilder_SOURCES = \
     290        builder.cpp \
     291        builder_init.cpp \
     292        builder_init.hpp \
     293        cleanUp.cpp \
     294        cleanUp.hpp
    287295molecuilder_LDADD = \
    288296        libMolecuilderUI.la \
    … …  
    296304
    297305#Stuff for building the GUI using Qt
    298 molecuildergui_SOURCES = builder.cpp builder_init.cpp builder_init.hpp
     306molecuildergui_SOURCES = \
     307        builder.cpp \
     308        builder_init.cpp \
     309        builder_init.hpp \
     310        cleanUp.cpp \
     311        cleanUp.hpp
    299312molecuildergui_CXXFLAGS = $(AM_CPPFLAGS) -DUSE_GUI_QT
    300313molecuildergui_LDFLAGS = $(AM_LDFLAGS) $(BOOST_FILESYSTEM_LDFLAGS) $(BOOST_PROGRAM_OPTIONS_LDFLAGS) $(BOOST_SYSTEM_LDFLAGS) $(BOOST_THREAD_LDFLAGS)

  • src/builder_init.cpp

    r071243 r949953  
    2323#include <iostream>
    2424
    25 #include "config.hpp"
    26 #include "molecule.hpp"
    27 #include "World.hpp"
     25#include "Actions/ActionHistory.hpp"
     26#include "Actions/ActionExceptions.hpp"
    2827
    29 #include "Actions/ActionExceptions.hpp"
    30 #include "Actions/ActionHistory.hpp"
    31 #include "Actions/ActionRegistry.hpp"
     28#include "builder_init.hpp"
     29#include "cleanUp.hpp"
    3230
    33 #include "CodePatterns/Chronos.hpp"
    3431#include "CodePatterns/Log.hpp"
    35 #include "Element/periodentafel.hpp"
     32
    3633#include "Graph/BondGraph.hpp"
     34
    3735#include "Parser/ChangeTracker.hpp"
    3836#include "Parser/FormatParserStorage.hpp"
    39 #include "RandomNumbers/RandomNumberDistributionFactory.hpp"
    40 #include "RandomNumbers/RandomNumberEngineFactory.hpp"
    41 #include "RandomNumbers/RandomNumberGeneratorFactory.hpp"
    42 #include "Tesselation/tesselationhelpers.hpp"
     37
     38#include "UIElements/UIFactory.hpp"
     39#include "UIElements/CommandLineUI/CommandLineParser.hpp"
    4340#include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
    44 #include "UIElements/CommandLineUI/CommandLineUIFactory.hpp"
    45 #include "UIElements/CommandLineUI/CommandLineParser.hpp"
    46 #include "UIElements/Dialog.hpp"
    47 #include "UIElements/MainWindow.hpp"
    48 #include "UIElements/Menu/MenuDescription.hpp"
    4941#ifdef USE_GUI_QT
    5042#include "UIElements/Qt4/QtUIFactory.hpp"
    5143#endif
    5244#include "UIElements/TextUI/TextUIFactory.hpp"
    53 #include "UIElements/UIFactory.hpp"
     45#include "UIElements/MainWindow.hpp"
    5446
    5547#include "version.h"
    5648
    57 #include "builder_init.hpp"
     49#include "World.hpp"
     50
    5851
    5952/** Print some initial information output the program.
    … …  
    148141}
    149142
    150 
    151 /** In this function all dynamicly allocated member variables to static/global
    152  * variables are added to the ignore list of Memory/MemDebug.
    153  *
    154  * Use this to prevent their listing in the Memory::getState() at the end of the
    155  * program. Check with valgrind that truely no memory leak occurs!
    156  */
    157 void AddStaticEntitiestoIgnoreList()
    158 {
    159   // zeroVec and unitVec are global variables (on the stack) but vectorContent
    160   // within is situated on the heap and has to be ignored
    161   Memory::ignore(zeroVec.get());
    162   Memory::ignore(unitVec[0].get());
    163   Memory::ignore(unitVec[1].get());
    164   Memory::ignore(unitVec[2].get());
    165 }
    166 
    167 /** We give a list of all times per action and a total time.
    168  *
    169  */
    170 void printTimings()
    171 {
    172   const MoleCuilder::ActionRegistry &AR = MoleCuilder::ActionRegistry::getInstance();
    173   const Chronos &Chron = Chronos::getInstance();
    174   std::cout << "(Non-zero) Times used per Action [seconds]:" << std::endl;
    175   for (MoleCuilder::ActionRegistry::const_iterator iter = AR.getBeginIter(); iter != AR.getEndIter(); ++iter)
    176     if (Chron.getTime(iter->first) != 0.) { // dont give if action has not been used
    177       std::cout << "  " << setiosflags(ios::left) << setw(24) << setfill('.') << iter->first;
    178       std::cout << setiosflags(ios::left) << setprecision(6) << fixed << Chron.getTime(iter->first) << std::endl;
    179     }
    180   std::cout << "Total Time: " << Chron.SumUpTotalTime() << " seconds" << std::endl;
    181   std::cout << "Total Actions called: " << Chron.SumUpTotalFunctions() << std::endl;
    182 }
    183 
    184 /** Cleans all singleton instances in an orderly fashion.
    185  * C++ does not guarantee any specific sequence of removal of single instances
    186  * which have static/global variables. Some singletons depend on others hence we
    187  * acertain a specific ordering here, which is is used via the atexit() hook.
    188  */
    189 void cleanUp()
    190 {
    191   printTimings();
    192   Chronos::purgeInstance();
    193 
    194   RandomNumberDistributionFactory::purgeInstance();
    195   RandomNumberEngineFactory::purgeInstance();
    196   RandomNumberGeneratorFactory::purgeInstance();
    197   FormatParserStorage::purgeInstance();
    198   ChangeTracker::purgeInstance();
    199   World::purgeInstance();
    200   MenuDescription::purgeInstance();
    201   UIFactory::purgeInstance();
    202   ValueStorage::purgeInstance();
    203   CommandLineParser::purgeInstance();
    204   MoleCuilder::ActionRegistry::purgeInstance();
    205   MoleCuilder::OptionRegistry::purgeInstance();
    206   MoleCuilder::ActionHistory::purgeInstance();
    207   // we have to remove these two static as otherwise their boost::shared_ptrs are still present
    208   MoleCuilder::Action::removeStaticStateEntities();
    209   // put some static variables' dynamic contents on the Memory::ignore map to avoid their
    210   // admonishing lateron
    211   AddStaticEntitiestoIgnoreList();
    212   logger::purgeInstance();
    213   errorLogger::purgeInstance();
    214 #ifdef LOG_OBSERVER
    215   cout << observerLog().getLog();
    216 #endif
    217   Memory::getState();
    218 }
    219 
    220143/** Dump current memory chunks.
    221144 *

  • src/builder_init.hpp

    r071243 r949953  
    2020void doUI();
    2121
    22 void AddStaticEntitiestoIgnoreList();
    23 void cleanUp();
    2422void dumpMemory();
    2523
Note: See TracChangeset for help on using the changeset viewer.