Changeset d2596b


Ignore:
Timestamp:
Apr 4, 2012, 11:32:30 AM (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:
3d0892
Parents:
613da6
git-author:
Frederik Heber <heber@…> (03/24/12 16:39:43)
git-committer:
Frederik Heber <heber@…> (04/04/12 11:32:30)
Message:

Added XmlParser for parsing configurations for ScaFaCoS generic test code.

  • XML is parsed via pugixml which is placed in subfolder pugixml in src/Parser.
  • NOTE: pugixml does not import/export double with high enough precision. Hence, we always obtain strings and convert them ourselves.
  • also added unit test on the new parser.
  • NOTE: Unit test is failing as charges are not yet written correctly, hence marked as XFAIL.
Files:
8 added
7 edited

Legend:

Unmodified
Added
Removed

  • README

    r613da6 rd2596b  
    2222* GSL (GNU Scientific Library, available at http://www.gnu.org/software/gsl)
    2323* Boost 1.4 or newer
     24* PugiXML (is provided in src/Parser/pugixml)
    2425
    2526LINKS

  • src/Parser/Makefile.am

    r613da6 rd2596b  
    2222  Parser/TremoloParser_ElementKeys.cpp \
    2323  Parser/TremoloAtomInfoContainer.cpp \
     24  Parser/XmlParser.cpp \
    2425  Parser/XyzParser.cpp
    2526
    … …  
    5253  Parser/TremoloParser_ElementKeys.hpp \
    5354  Parser/TremoloAtomInfoContainer.hpp \
     55  Parser/XmlParser.hpp \
    5456  Parser/XyzParser.hpp
    5557
    … …  
    7274        Parser/Parameters/ValueInterface.hpp
    7375
     76PUGIXMLSOURCE = \
     77        Parser/pugixml/pugixml.cpp
     78
     79PUGIXMLHEADER = \
     80        Parser/pugixml/pugixml.hpp \
     81        Parser/pugixml/pugiconfig.hpp
     82
    7483noinst_LTLIBRARIES += libMolecuilderParser.la
    7584libMolecuilderParser_la_includedir = $(includedir)/MoleCuilder/Parser/
    7685
    77 nobase_libMolecuilderParser_la_include_HEADERS = ${PARSERHEADER} ${PARSERPARAMETERSHEADER}
     86nobase_libMolecuilderParser_la_include_HEADERS = ${PARSERHEADER} ${PARSERPARAMETERSHEADER} $(PUGIXMLHEADER)
    7887
    7988## Define the source file list for the "libexample-@MOLECUILDER_API_VERSION@.la"
    … …  
    8594## from each source file.  Note that it is not necessary to list header files
    8695## which are already listed elsewhere in a _HEADERS variable assignment.
    87 libMolecuilderParser_la_SOURCES = ${PARSERSOURCE} ${PARSERPARAMETERSSOURCE}
     96libMolecuilderParser_la_SOURCES = ${PARSERSOURCE} ${PARSERPARAMETERSSOURCE} $(PUGIXMLSOURCE)
    8897
    8998## Instruct libtool to include ABI version information in the generated shared

  • src/Parser/ParserTypes.def

    r613da6 rd2596b  
    11//!> preprocessor sequence of all known parser types. Just add new parser here
    2 #define PARSERSEQUENCE (mpqc)(pcp)(pdb)(psi3)(tremolo)(xyz)
     2#define PARSERSEQUENCE (mpqc)(pcp)(pdb)(psi3)(tremolo)(xml)(xyz)
    33//!> Number of enumerations calculate automatically
    44#define ParserTypes_END BOOST_PP_SEQ_SIZE(PARSERSEQUENCE)

  • src/Parser/unittests/Makefile.am

    r613da6 rd2596b  
    1111        ../Parser/unittests/ParserTremoloUnitTest.cpp \
    1212        ../Parser/unittests/ParserTremolo_ElementKeysUnitTest.cpp \
     13        ../Parser/unittests/ParserXmlUnitTest.cpp \
    1314        ../Parser/unittests/ParserXyzUnitTest.cpp
    1415
    … …  
    2021        ../Parser/unittests/ParserTremoloUnitTest.hpp \
    2122        ../Parser/unittests/ParserTremolo_ElementKeysUnitTest.hpp \
     23        ../Parser/unittests/ParserXmlUnitTest.hpp \
    2224        ../Parser/unittests/ParserXyzUnitTest.hpp
    2325
    … …  
    2931  ParserTremoloUnitTest \
    3032  ParserTremolo_ElementKeysUnitTest \
     33  ParserXmlUnitTest \
    3134  ParserXyzUnitTest
     35
     36XFAIL_TESTS += \
     37        ParserXmlUnitTest
    3238
    3339TESTS += $(PARSERTESTS)
    … …  
    7278ParserTremolo_ElementKeysUnitTest_LDADD = ${PARSERLIBS}
    7379
     80ParserXmlUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
     81        ../Parser/unittests/ParserXmlUnitTest.cpp \
     82        ../Parser/unittests/ParserXmlUnitTest.hpp
     83ParserXmlUnitTest_LDADD = ${PARSERLIBS}
     84
    7485ParserXyzUnitTest_SOURCES = $(top_srcdir)/src/unittests/UnitTestMain.cpp \
    7586        ../Parser/unittests/ParserXyzUnitTest.cpp \

  • tests/CodeChecks/testsuite-config_h.at

    r613da6 rd2596b  
    11AT_SETUP([Checking for present config.h include])
    22AT_KEYWORDS([CodeCheck config_h])
    3 ok="unity.cpp AllActionHeaders.hpp AllActionPython.hpp"
     3ok="unity.cpp AllActionHeaders.hpp AllActionPython.hpp pugiconfig.hpp pugixml.cpp pugixml.hpp"
    44echo `pwd`
    55echo "${#ok[*]} are ok to not contain config.h: ${ok[*]}."

  • tests/CodeChecks/testsuite-memdebug.at

    r613da6 rd2596b  
    11AT_SETUP([Checking for present MemDebug.hpp include])
    22AT_KEYWORDS([CodeCheck MemDebug])
    3 ok="builder.cpp MemDebug.cpp SubspaceFactorizer.cpp TestRunner.cpp unity.cpp"
     3ok="builder.cpp MemDebug.cpp SubspaceFactorizer.cpp TestRunner.cpp unity.cpp pugixml.cpp"
    44echo `pwd`
    55echo "${#ok[*]} are ok to not contain MemDebug.hpp: ${ok[0]} ${ok[1]}."

  • tests/CodeChecks/testsuite-project-disclaimer.at

    r613da6 rd2596b  
    11AT_SETUP([Checking for present project disclaimer])
    22AT_KEYWORDS([CodeCheck disclaimer])
    3 ok="unity.cpp"
     3ok="unity.cpp pugixml.cpp"
    44echo `pwd`
    55echo "${#ok[*]} are ok to not contain config.h: ${ok[*]}."
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