Changeset 3f6aac


Ignore:
Timestamp:
Jul 3, 2017, 3:06:31 PM (8 years ago)
Author:
Frederik Heber <frederik.heber@…>
Branches:
Action_Thermostats, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChemicalSpaceEvaluator, EmpiricalPotential_contain_HomologyGraph_documentation, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, Fix_Verbose_Codepatterns, ForceAnnealing_oldresults, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, PythonUI_with_named_parameters, Recreated_GuiChecks, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps
Children:
8f2f4e
Parents:
9a4772
git-author:
Frederik Heber <frederik.heber@…> (05/12/17 20:09:49)
git-committer:
Frederik Heber <frederik.heber@…> (07/03/17 15:06:31)
Message:

Added (Un)selectAtomByName.

  • Descriptor for AtomByName was already present.
  • TESTS: also added regression test.
Files:
10 added
6 edited

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    r9a4772 r3f6aac  
    498498              </listitem>
    499499              <listitem>
    500                 <para>By Element (all hydrogen atoms, all sulphur atoms,
    501                 ...)</para>
     500                <para>By Element (all hydrogen atoms, all sulphur atoms, ...)</para>
    502501                <programlisting>
    503502                ... --select-atom-by-element 1
    … …  
    505504                <programlisting>
    506505                ... --unselect-atom-by-element 1
     506                </programlisting>
     507              </listitem>
     508              <listitem>
     509                <para>By name (atom with molecule internal name "H1", e.g.
     510                this will select all "H1" atoms in every present water molecule)</para>
     511                <programlisting>
     512                ... --select-atom-by-name "H1"
     513                </programlisting>
     514                <programlisting>
     515                ... --unselect-atom-by-name "H1"
    507516                </programlisting>
    508517              </listitem>

  • src/Actions/GlobalListOfActions.hpp

    r9a4772 r3f6aac  
    120120  (SelectionAtomByElement) \
    121121  (SelectionAtomById) \
     122  (SelectionAtomByName) \
    122123  (SelectionAtomByOrder) \
    123124  (SelectionClearAllAtoms) \
    … …  
    135136  (SelectionNotAllMolecules) \
    136137  (SelectionNotAllShapes) \
     138  (SelectionNotAtomByElement) \
    137139  (SelectionNotAtomById) \
    138   (SelectionNotAtomByElement) \
     140  (SelectionNotAtomByName) \
    139141  (SelectionNotAtomByOrder) \
    140142  (SelectionNotMoleculeOfAtom) \

  • src/Actions/Makefile.am

    r9a4772 r3f6aac  
    466466  Actions/SelectionAction/Atoms/AtomByElementAction.cpp \
    467467  Actions/SelectionAction/Atoms/AtomByIdAction.cpp \
     468  Actions/SelectionAction/Atoms/AtomByNameAction.cpp \
    468469  Actions/SelectionAction/Atoms/AtomByOrderAction.cpp \
    469470  Actions/SelectionAction/Atoms/ClearAllAtomsAction.cpp \
    … …  
    474475  Actions/SelectionAction/Atoms/NotAtomByElementAction.cpp \
    475476  Actions/SelectionAction/Atoms/NotAtomByIdAction.cpp \
     477  Actions/SelectionAction/Atoms/NotAtomByNameAction.cpp \
    476478  Actions/SelectionAction/Atoms/NotAtomByOrderAction.cpp \
    477479  Actions/SelectionAction/Atoms/PopAtomsAction.cpp \
    … …  
    483485  Actions/SelectionAction/Atoms/AtomByElementAction.hpp \
    484486  Actions/SelectionAction/Atoms/AtomByIdAction.hpp \
     487  Actions/SelectionAction/Atoms/AtomByNameAction.hpp \
    485488  Actions/SelectionAction/Atoms/AtomByOrderAction.hpp \
    486489  Actions/SelectionAction/Atoms/ClearAllAtomsAction.hpp \
    … …  
    491494  Actions/SelectionAction/Atoms/NotAtomByElementAction.hpp \
    492495  Actions/SelectionAction/Atoms/NotAtomByIdAction.hpp \
     496  Actions/SelectionAction/Atoms/NotAtomByNameAction.hpp \
    493497  Actions/SelectionAction/Atoms/NotAtomByOrderAction.hpp \
    494498  Actions/SelectionAction/Atoms/PopAtomsAction.hpp \
    … …  
    500504  Actions/SelectionAction/Atoms/AtomByElementAction.def \
    501505  Actions/SelectionAction/Atoms/AtomByIdAction.def \
     506  Actions/SelectionAction/Atoms/AtomByNameAction.def \
    502507  Actions/SelectionAction/Atoms/AtomByOrderAction.def \
    503508  Actions/SelectionAction/Atoms/ClearAllAtomsAction.def \
    … …  
    508513  Actions/SelectionAction/Atoms/NotAtomByElementAction.def \
    509514  Actions/SelectionAction/Atoms/NotAtomByIdAction.def \
     515  Actions/SelectionAction/Atoms/NotAtomByNameAction.def \
    510516  Actions/SelectionAction/Atoms/NotAtomByOrderAction.def \
    511517  Actions/SelectionAction/Atoms/PopAtomsAction.def \

  • tests/Python/AllActions/options.dat

    r9a4772 r3f6aac  
    194194select-atom-by-element  "4"
    195195select-atom-by-id       "0"
     196select-atom-by-name     "H1"
    196197select-atom-by-order    "1"
    197198select-atoms-inside-cuboid      "10 10 10"
    … …  
    254255unselect-atom-by-element        "4"
    255256unselect-atom-by-id     "0"
     257unselect-atom-by-name   "H1"
    256258unselect-atom-by-order  "1"
    257259unselect-atoms-inside-cuboid    "10 10 10"

  • tests/regression/Makefile.am

    r9a4772 r3f6aac  
    237237        $(srcdir)/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id.at \
    238238        $(srcdir)/Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id-multiple.at \
     239        $(srcdir)/Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at \
     240        $(srcdir)/Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at \
    239241        $(srcdir)/Selection/Atoms/AtomByOrder/testsuite-selection-select-atom-by-order.at \
    240242        $(srcdir)/Selection/Atoms/AtomByOrder/testsuite-selection-unselect-atom-by-order.at \

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

    r9a4772 r3f6aac  
    3838m4_include(Selection/Atoms/AtomById/testsuite-selection-unselect-atom-by-id-multiple.at)
    3939
     40# (un)select atoms by name
     41m4_include(Selection/Atoms/AtomByName/testsuite-selection-select-atoms-by-name.at)
     42m4_include(Selection/Atoms/AtomByName/testsuite-selection-unselect-atoms-by-name.at)
     43
    4044# (un)select atom by order
    4145m4_include(Selection/Atoms/AtomByOrder/testsuite-selection-select-atom-by-order.at)
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