Changeset 2fcef3
- Timestamp:
- Feb 13, 2015, 9:17:52 AM (10 years ago)
- 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)
- Files:
-
- 9 added
- 5 edited
Legend:
- Unmodified
- Added
- Removed
-
TabularUnified doc/userguide/userguide.xml ¶
r0241c5 r2fcef3 960 960 961 961 <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> 962 979 </section> 963 980 -
TabularUnified src/Actions/GlobalListOfActions.hpp ¶
r0241c5 r2fcef3 35 35 (AtomRemove) \ 36 36 (AtomRotateAroundOriginByAngle) \ 37 (AtomSaturate) \ 37 38 (AtomSaveSelectedAtoms) \ 38 39 (AtomTranslate) \ -
TabularUnified src/Actions/Makefile.am ¶
r0241c5 r2fcef3 150 150 Actions/AtomAction/RemoveAction.cpp \ 151 151 Actions/AtomAction/RotateAroundOriginByAngleAction.cpp \ 152 Actions/AtomAction/SaturateAction.cpp \ 152 153 Actions/AtomAction/SaveSelectedAtomsAction.cpp \ 153 154 Actions/AtomAction/TranslateAction.cpp \ … … 159 160 Actions/AtomAction/RemoveAction.hpp \ 160 161 Actions/AtomAction/RotateAroundOriginByAngleAction.hpp \ 162 Actions/AtomAction/SaturateAction.hpp \ 161 163 Actions/AtomAction/SaveSelectedAtomsAction.hpp \ 162 164 Actions/AtomAction/TranslateAction.hpp \ … … 168 170 Actions/AtomAction/RemoveAction.def \ 169 171 Actions/AtomAction/RotateAroundOriginByAngleAction.def \ 172 Actions/AtomAction/SaturateAction.def \ 170 173 Actions/AtomAction/SaveSelectedAtomsAction.def \ 171 174 Actions/AtomAction/TranslateAction.def \ -
TabularUnified tests/regression/Atoms/testsuite-atoms.at ¶
r0241c5 r2fcef3 44 44 # mirror atoms 45 45 m4_include([Atoms/Mirror/testsuite-atoms-mirror.at]) 46 47 # saturate atoms 48 m4_include([Atoms/Saturate/testsuite-atoms-saturate_carbon.at]) 49 m4_include([Atoms/Saturate/testsuite-atoms-saturate_nitrogen.at]) -
TabularUnified tests/regression/Makefile.am ¶
r0241c5 r2fcef3 40 40 $(srcdir)/Atoms/RemoveSphere/testsuite-atoms-remove-sphere.at \ 41 41 $(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 \ 42 44 $(srcdir)/Atoms/Translation/testsuite-atoms-translation.at \ 43 45 $(srcdir)/Atoms/TranslationToOrigin/testsuite-atoms-translation-to-origin.at \
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