Changeset 2d1280


Ignore:
Timestamp:
Nov 4, 2016, 9:37:48 AM (8 years ago)
Author:
Frederik Heber <heber@…>
Branches:
Action_Thermostats, Add_AtomRandomPerturbation, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, 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_ChronosMutex, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, GeometryObjects, Gui_displays_atomic_force_velocity, IndependentFragmentGrids_IntegrationTest, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, RotateToPrincipalAxisSystem_UndoRedo, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, ThirdParty_MPQC_rebuilt_buildsystem, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, Ubuntu_1604_changes, stable
Children:
f946b2
Parents:
3400bb
git-author:
Frederik Heber <heber@…> (10/01/16 17:56:45)
git-committer:
Frederik Heber <heber@…> (11/04/16 09:37:48)
Message:

Added BondSetDegreeAction for manipulating bond degrees.

Files:
15 added
6 edited

Legend:

Unmodified
Added
Removed

  • doc/userguide/userguide.xml

    r3400bb r2d1280  
    939939   found between any pair of these is removed.</para>
    940940        </section>
     941        <section xml:id="bond.set-bond-degree">
     942          <title xml:id="bond.set-bond-degree.title">Setting the bond degree manually </title>
     943          <para>The bond degrees are usually automatically set to fulfill the
     944          valency constraints of each bond partner. However, degrees can also be
     945          set manually for a set of selected atoms. Note that the degree is set
     946          to the given value for all bonds in between any pair of atoms within
     947          the set.</para>
     948          <programlisting>... --set-bond-degree 2</programlisting>
     949          <para>Similarly, if more than two atoms are selected, then all bonds
     950   found between any pair of these are modified.</para>
     951        </section>
    941952        <section xml:id="bond.save-bonds">
    942953          <title xml:id="bond.save-bonds.title">Saving bond information </title>

  • src/Actions/GlobalListOfActions.hpp

    r3400bb r2d1280  
    4141  (BondAdd) \
    4242  (BondRemove) \
     43  (BondSetDegree) \
    4344  (CommandDryRun) \
    4445  (CommandElementDb) \

  • src/Actions/Makefile.am

    r3400bb r2d1280  
    178178BONDACTIONSOURCE = \
    179179  Actions/BondAction/BondAddAction.cpp \
    180   Actions/BondAction/BondRemoveAction.cpp
     180  Actions/BondAction/BondRemoveAction.cpp \
     181  Actions/BondAction/BondSetDegreeAction.cpp
    181182BONDACTIONHEADER = \
    182183  Actions/BondAction/BondAddAction.hpp \
    183   Actions/BondAction/BondRemoveAction.hpp
     184  Actions/BondAction/BondRemoveAction.hpp \
     185  Actions/BondAction/BondSetDegreeAction.hpp
    184186BONDACTIONDEFS = \
    185187  Actions/BondAction/BondAddAction.def \
    186   Actions/BondAction/BondRemoveAction.def
     188  Actions/BondAction/BondRemoveAction.def \
     189  Actions/BondAction/BondSetDegreeAction.def
    187190
    188191CMDACTIONSOURCE = \

  • tests/Python/AllActions/options.dat

    r3400bb r2d1280  
    205205server-port     "1026"
    206206session-type    "cli"
     207set-bond-degree "1"
    207208set-boundary-conditions "Wrap, Wrap, Wrap"
    208209set-max-iterations      "10"

  • tests/regression/Bond/testsuite-bond.at

    r3400bb r2d1280  
    2828# adjacency matcher
    2929m4_include([Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at])
     30
     31# set degree
     32m4_include([Bond/SetDegree/testsuite-bond-set-degree.at])
     33m4_include([Bond/SetDegree/testsuite-bond-set-degree_multiple.at])
     34

  • tests/regression/Makefile.am

    r3400bb r2d1280  
    4949        $(srcdir)/Bond/Add/testsuite-bond-add.at \
    5050        $(srcdir)/Bond/Add/testsuite-bond-add_multiple.at \
     51        $(srcdir)/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at \
    5152        $(srcdir)/Bond/Remove/testsuite-bond-remove.at \
    5253        $(srcdir)/Bond/Remove/testsuite-bond-remove_multiple.at \
    53         $(srcdir)/Bond/AdjacencyMatcher/testsuite-bond-adjacencymatcher.at \
     54        $(srcdir)/Bond/SetDegree/testsuite-bond-set-degree.at \
     55        $(srcdir)/Bond/SetDegree/testsuite-bond-set-degree_multiple.at \
    5456        $(srcdir)/Analysis/testsuite-analysis.at \
    5557        $(srcdir)/Analysis/DipoleAngularCorrelation/testsuite-analysis-dipole-angular-correlation.at \
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