Changeset 5589e7e


Ignore:
Timestamp:
Mar 22, 2013, 12:03:38 AM (12 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:
4f54b3
Parents:
d5b90b
git-author:
Frederik Heber <heber@…> (02/26/13 21:45:20)
git-committer:
Frederik Heber <heber@…> (03/22/13 00:03:38)
Message:

Added StoreSaturatedFragmentAction to save a set of atoms satured with hydrogen.

  • add regression test on new action with a graphene sheet.
  • the test is deactivated (with respect to diffing the output) as the bond degree correction is far not stable and the output is hence random with respect to the saturated hydrogens.
Files:
6 added
5 edited

Legend:

Unmodified
Added
Removed

  • src/Actions/GlobalListOfActions.hpp

    rd5b90b r5589e7e  
    121121  (SelectionNotShapeByName) \
    122122  (FragmentationFragmentation) \
     123  (FragmentationStoreSaturatedFragment) \
    123124  (FillRegularGrid) \
    124125  (FillSurface) \

  • src/Actions/Makefile.am

    rd5b90b r5589e7e  
    211211
    212212FRAGMENTATIONACTIONSOURCE = \
    213   Actions/FragmentationAction/FragmentationAction.cpp
     213  Actions/FragmentationAction/FragmentationAction.cpp \
     214  Actions/FragmentationAction/StoreSaturatedFragmentAction.cpp
    214215FRAGMENTATIONACTIONHEADER = \
    215   Actions/FragmentationAction/FragmentationAction.hpp
     216  Actions/FragmentationAction/FragmentationAction.hpp \
     217  Actions/FragmentationAction/StoreSaturatedFragmentAction.hpp
    216218FRAGMENTATIONACTIONDEFS = \
    217   Actions/FragmentationAction/FragmentationAction.def
     219  Actions/FragmentationAction/FragmentationAction.def \
     220  Actions/FragmentationAction/StoreSaturatedFragmentAction.def
    218221
    219222if CONDJOBMARKET

  • tests/Python/AllActions/options.dat

    rd5b90b r5589e7e  
    193193skiplines       "2"
    194194start-step      "0"
     195store-saturated-fragment        "BondFragment"
    195196stretch-bond    "1.5"
    196197stretch "1. 1. 1."

  • tests/regression/Fragmentation/testsuite-fragmentation.at

    rd5b90b r5589e7e  
    2323# check whether parsing of BondFragment files and re-rwriting config files is working (exit code is 2 as we don't need to continue wrt to ...OrderAtSite)
    2424m4_include([Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at])
     25
     26# check storing saturated fragment
     27m4_include([Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at])

  • tests/regression/Makefile.am

    rd5b90b r5589e7e  
    7474        $(srcdir)/Fragmentation/FragmentMolecule/testsuite-fragmentation-fragment-molecule.at \
    7575        $(srcdir)/Fragmentation/FragmentMolecule-MaxOrder/testsuite-fragmentation-fragment-molecule-maxorder.at \
     76        $(srcdir)/Fragmentation/StoreSaturatedFragment/testsuite-fragmentation-store-saturated-fragment.at \
    7677        $(srcdir)/Graph/testsuite-graph.at \
    7778        $(srcdir)/Graph/DepthFirstSearch/testsuite-graph-depth-first-search.at \
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