Ignore:
Timestamp:
Apr 27, 2010, 2:25:42 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:
632bc3
Parents:
13d5a9 (diff), c695c9 (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.
Message:

Merge branch 'Analysis_PairCorrelation' into StructureRefactoring

Conflicts:

molecuilder/src/Makefile.am
molecuilder/src/World.cpp
molecuilder/src/World.hpp
molecuilder/src/boundary.cpp
molecuilder/src/builder.cpp
molecuilder/src/log.cpp
molecuilder/src/moleculelist.cpp
molecuilder/src/periodentafel.cpp
molecuilder/src/tesselation.cpp
molecuilder/src/unittests/AnalysisCorrelationToSurfaceUnitTest.cpp
molecuilder/src/unittests/Makefile.am
molecuilder/src/unittests/bondgraphunittest.cpp
molecuilder/src/unittests/gslvectorunittest.cpp
molecuilder/src/unittests/logunittest.cpp
molecuilder/src/unittests/tesselation_boundarytriangleunittest.hpp
molecuilder/src/vector.cpp
molecuilder/tests/Tesselations/defs.in

Conflicts have been many and too numerous to listen here, just the few general cases

  • new molecule() replaced by World::getInstance().createMolecule()
  • new atom() replaced by World::getInstance().createAtom() where appropriate.
  • Some DoLog()s added interfered with changes to the message produced by Log() << Verbose(.) << ...
  • DoLog() has been erroneously added to TestRunner.cpp as well, there cout is appropriate
  • ...

Additionally, there was a bug in atom::clone(), sort was set to atom::nr of the atom to clone not of the clone itself. This caused a failure of the fragmentation.

This merge has been fully checked from a clean build directory with subsequent configure,make all install and make check.
It configures, compiles and runs all test cases and the test suite without errors.

Signed-off-by: Frederik Heber <heber@…>

File:
1 edited

Legend:

Unmodified
Added
Removed

  • src/unittests/Makefile.am

    r13d5a9 r5f612ee  
    44AM_CXXFLAGS = $(CPPUNIT_CFLAGS)
    55
    6 MENUTESTS = ActionSequenceTest
     6MENUTESTS = \
     7  ActionSequenceTest
    78
    89TESTS = \
    … …  
    1617  BondGraphUnitTest \
    1718  CacheableTest \
     19  CountBondsUnitTest \
    1820  GSLMatrixSymmetricUnitTest \
    1921  GSLMatrixUnitTest \
    … …  
    2123  InfoUnitTest \
    2224  LinearSystemOfEquationsUnitTest \
     25  LinkedCellUnitTest \
    2326  ListOfBondsUnitTest \
    2427  LogUnitTest \
    … …  
    3639  ${MENUTESTS}
    3740 
    38 
    39      
    4041 
    4142check_PROGRAMS = $(TESTS)
    … …  
    5657  bondgraphunittest.cpp \
    5758  CacheableTest.cpp \
     59  CountBondsUnitTest.cpp \
    5860  gslmatrixsymmetricunittest.cpp \
    5961  gslmatrixunittest.cpp \
    … …  
    6163  infounittest.cpp \
    6264  linearsystemofequationsunittest.cpp \
     65  LinkedCellUnitTest.cpp \
    6366  listofbondsunittest.cpp \
    6467  logunittest.cpp \
    … …  
    7679
    7780TESTHEADERS = \
    78   analysis_correlation.hpp
     81  ActOnAllUnitTest.hpp \
     82  ActionSequenceTest.hpp \
     83  analysisbondsunittest.hpp \
     84  AnalysisCorrelationToPointUnitTest.hpp \
     85  AnalysisCorrelationToSurfaceUnitTest.hpp  \
     86  AnalysisPairCorrelationUnitTest.hpp \
     87  AtomDescriptorTest.hpp \
     88  atomsCalculationTest.hpp \
     89  bondgraphunittest.hpp \
     90  CacheableTest.hpp \
     91  CountBondsUnitTest.hpp \
     92  gslmatrixsymmetricunittest.hpp \
     93  gslmatrixunittest.hpp \
     94  gslvectorunittest.hpp \
     95  infounittest.hpp \
     96  linearsystemofequationsunittest.hpp \
     97  LinkedCellUnitTest.hpp \
     98  listofbondsunittest.hpp \
     99  logunittest.hpp \
     100  manipulateAtomsTest.hpp \
     101  memoryallocatorunittest.hpp  \
     102  memoryusageobserverunittest.hpp \
     103  MoleculeDescriptorTest.hpp \
     104  ObserverTest.hpp \
     105  SingletonTest.hpp \
     106  stackclassunittest.hpp \
     107  tesselationunittest.hpp \
     108  tesselation_boundarytriangleunittest.hpp \
     109  tesselation_insideoutsideunittest.hpp \
     110  vectorunittest.hpp
     111 
    79112
    80113ActOnAllUnitTest_SOURCES = UnitTestMain.cpp ../test/ActOnAllTest.hpp ActOnAllUnitTest.cpp ActOnAllUnitTest.hpp
    … …  
    99132BondGraphUnitTest_LDADD = ${ALLLIBS}
    100133
     134CountBondsUnitTest_SOURCES = UnitTestMain.cpp CountBondsUnitTest.cpp CountBondsUnitTest.hpp
     135CountBondsUnitTest_LDADD = ${ALLLIBS}
     136
    101137GSLMatrixSymmetricUnitTest_SOURCES = UnitTestMain.cpp gslmatrixsymmetricunittest.cpp gslmatrixsymmetricunittest.hpp
    102138GSLMatrixSymmetricUnitTest_LDADD = ${GSLLIBS}
    … …  
    114150LinearSystemOfEquationsUnitTest_LDADD = ${ALLLIBS}
    115151
     152LinkedCellUnitTest_SOURCES = UnitTestMain.cpp LinkedCellUnitTest.cpp LinkedCellUnitTest.hpp
     153LinkedCellUnitTest_LDADD = ${ALLLIBS}
     154
    116155ListOfBondsUnitTest_SOURCES = UnitTestMain.cpp listofbondsunittest.cpp listofbondsunittest.hpp
    117156ListOfBondsUnitTest_LDADD = ${ALLLIBS}
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