Changeset bbf6dc


Ignore:
Timestamp:
Sep 18, 2014, 11:32:23 PM (10 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:
2ed3bf
Parents:
9bce96
git-author:
Frederik Heber <heber@…> (09/09/14 23:55:39)
git-committer:
Frederik Heber <heber@…> (09/18/14 23:32:23)
Message:

Added AtomMirrorAction.

  • also added regression tests.
Files:
7 added
6 edited

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    r9bce96 rbbf6dc  
    955955          domain.</para>
    956956        </section>
     957
     958        <section xml:id='atoms.mirror-atoms'>
     959          <title xml:id='atoms.mirror-atoms.title'>Mirroring atoms</title>
     960
     961          <para>Present (and selected) atoms can be mirrored with respect to
     962          a certain plane. You have to specify the normal vector of the plane
     963          and the offset with respect to the origin as follows</para>
     964
     965          <programlisting>
     966                ... --mirror-atoms "1,0,0" \
     967                    --plane-offset 10.1 \
     968                    --periodic 0
     969          </programlisting>
     970        </section>
    957971
    958972        <section xml:id='atoms.change-element'>

  • src/Actions/GlobalListOfActions.hpp

    r9bce96 rbbf6dc  
    3131  (AtomAdd) \
    3232  (AtomChangeElement) \
     33  (AtomMirror) \
    3334  (AtomRemove) \
    3435  (AtomRotateAroundOriginByAngle) \

  • src/Actions/Makefile.am

    r9bce96 rbbf6dc  
    144144  Actions/AtomAction/AddAction.cpp \
    145145  Actions/AtomAction/ChangeElementAction.cpp \
     146  Actions/AtomAction/MirrorAction.cpp \
    146147  Actions/AtomAction/RemoveAction.cpp \
    147148  Actions/AtomAction/RotateAroundOriginByAngleAction.cpp \
    … …  
    151152  Actions/AtomAction/AddAction.hpp \
    152153  Actions/AtomAction/ChangeElementAction.hpp \
     154  Actions/AtomAction/MirrorAction.hpp \
    153155  Actions/AtomAction/RemoveAction.hpp \
    154156  Actions/AtomAction/RotateAroundOriginByAngleAction.hpp \
    … …  
    158160  Actions/AtomAction/AddAction.def \
    159161  Actions/AtomAction/ChangeElementAction.def \
     162  Actions/AtomAction/MirrorAction.def \
    160163  Actions/AtomAction/RemoveAction.def \
    161164  Actions/AtomAction/RotateAroundOriginByAngleAction.def \

  • tests/Python/AllActions/options.dat

    r9bce96 rbbf6dc  
    9999mesh-size       "10,10,10"
    100100min-distance    "1."
     101mirror-atoms    "1.,1.,1."
    101102molecule-by-id  "0"
    102103near-field-cells        "3"
    … …  
    129130parser-parameters       "psi3"
    130131periodic        "0"
     132plane-offset    "5."
    131133position        "0 0 0"
    132134position        "0 0 1"

  • tests/regression/Atoms/testsuite-atoms.at

    r9bce96 rbbf6dc  
    3838# Undo and redo a translation
    3939m4_include([Atoms/Translation/testsuite-atoms-translation.at])
     40
     41# mirror atoms
     42m4_include([Atoms/Mirror/testsuite-atoms-mirror.at])

  • tests/regression/Makefile.am

    r9bce96 rbbf6dc  
    3535        $(srcdir)/Atoms/Add/testsuite-atoms-add.at \
    3636        $(srcdir)/Atoms/ChangeElement/testsuite-atoms-change-element.at \
     37        $(srcdir)/Atoms/Mirror/testsuite-atoms-mirror.at \
    3738        $(srcdir)/Atoms/Remove/testsuite-atoms-remove.at \
    3839        $(srcdir)/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at \
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