Changeset 2fcef3


Ignore:
Timestamp:
Feb 13, 2015, 9:17:52 AM (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:
88afc9
Parents:
0241c5
git-author:
Frederik Heber <heber@…> (01/27/15 21:28:27)
git-committer:
Frederik Heber <heber@…> (02/13/15 09:17:52)
Message:

Added SaturateAction that uses SphericalPointDistribution.

  • added saturate-atoms to userguide.
  • added regression test fpr saturate-atoms.
Files:
9 added
5 edited

Legend:

Unmodified
Added
Removed
  • TabularUnified doc/userguide/userguide.xml

    r0241c5 r2fcef3  
    960960
    961961          <programlisting>... --remove-atom</programlisting>
     962        </section>
     963
     964        <section xml:id='atoms.saturate-atom'>
     965          <title xml:id='atoms.saturate-atom.title'>Saturating atoms</title>
     966
     967          <para>Newly instantiated atoms have no bonds to any other atom. If
     968          you want to fill up their valence by a slew of hydrogen atoms
     969          residing on a sphere around this atom, use this action.</para>
     970
     971          <programlisting>
     972                ... --saturate-atoms
     973          </programlisting>
     974
     975          <para>A number of hydrogen atoms is added. The number corrresponding
     976          to the valence of each selected atom. They are placed in the same
     977          distance to this atom and approximately with same distance to their
     978          nearest neighbors.</para>
    962979        </section>
    963980
  • TabularUnified src/Actions/GlobalListOfActions.hpp

    r0241c5 r2fcef3  
    3535  (AtomRemove) \
    3636  (AtomRotateAroundOriginByAngle) \
     37  (AtomSaturate) \
    3738  (AtomSaveSelectedAtoms) \
    3839  (AtomTranslate) \
  • TabularUnified src/Actions/Makefile.am

    r0241c5 r2fcef3  
    150150  Actions/AtomAction/RemoveAction.cpp \
    151151  Actions/AtomAction/RotateAroundOriginByAngleAction.cpp \
     152  Actions/AtomAction/SaturateAction.cpp \
    152153  Actions/AtomAction/SaveSelectedAtomsAction.cpp \
    153154  Actions/AtomAction/TranslateAction.cpp \
     
    159160  Actions/AtomAction/RemoveAction.hpp \
    160161  Actions/AtomAction/RotateAroundOriginByAngleAction.hpp \
     162  Actions/AtomAction/SaturateAction.hpp \
    161163  Actions/AtomAction/SaveSelectedAtomsAction.hpp \
    162164  Actions/AtomAction/TranslateAction.hpp \
     
    168170  Actions/AtomAction/RemoveAction.def \
    169171  Actions/AtomAction/RotateAroundOriginByAngleAction.def \
     172  Actions/AtomAction/SaturateAction.def \
    170173  Actions/AtomAction/SaveSelectedAtomsAction.def \
    171174  Actions/AtomAction/TranslateAction.def \
  • TabularUnified tests/regression/Atoms/testsuite-atoms.at

    r0241c5 r2fcef3  
    4444# mirror atoms
    4545m4_include([Atoms/Mirror/testsuite-atoms-mirror.at])
     46
     47# saturate atoms
     48m4_include([Atoms/Saturate/testsuite-atoms-saturate_carbon.at])
     49m4_include([Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at])
  • TabularUnified tests/regression/Makefile.am

    r0241c5 r2fcef3  
    4040        $(srcdir)/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at \
    4141        $(srcdir)/Atoms/SaveSelectedAtoms/testsuite-atoms-save-selected-atoms.at \
     42        $(srcdir)/Atoms/Saturate/testsuite-atoms-saturate_carbon.at \
     43        $(srcdir)/Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at \
    4244        $(srcdir)/Atoms/Translation/testsuite-atoms-translation.at \
    4345        $(srcdir)/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at \
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