Changeset 310445

Timestamp:

Jun 22, 2017, 10:28:16 PM (8 years ago)

Author:

Frederik Heber <frederik.heber@…>

Branches:

Action_Thermostats, Add_AtomRandomPerturbation, Add_SelectAtomByNameAction, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_StructOpt_integration_tests, AutomationFragmentation_failures, Candidate_v1.6.1, ChangeBugEmailaddress, ChemicalSpaceEvaluator, EmpiricalPotential_contain_HomologyGraph_documentation, Enhance_userguide, 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, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, StoppableMakroAction, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps

Children:

8e9217

Parents:

78ea3c

git-author:

Frederik Heber <heber@…> (04/02/17 19:23:15)

git-committer:

Frederik Heber <frederik.heber@…> (06/22/17 22:28:16)

Message:

Added RandomPerturbationAction.

• this should be when doing structural optimization for getting given configurations out of ambivalent states, e.g. a water molecule whose three atoms define a straight line.
• note that we need to use a sensible random number distribution, the default is not doing what's expected. Added to docu.
• TESTS: Added regression test with undo/redo.
• DOCU: Added documentation to userguide.

Files:

• doc/userguide/userguide.xml (modified) (1 diff)
• src/Actions/AtomAction/RandomPerturbationAction.cpp (added)
• src/Actions/AtomAction/RandomPerturbationAction.def (added)
• src/Actions/AtomAction/RandomPerturbationAction.hpp (added)
• src/Actions/GlobalListOfActions.hpp (modified) (1 diff)
• src/Actions/Makefile.am (modified) (3 diffs)
• tests/Python/AllActions/options.dat (modified) (1 diff)
• tests/regression/Atoms/RandomPerturbation/post/water.xyz (added)
• tests/regression/Atoms/RandomPerturbation/pre/water.xyz (added)
• tests/regression/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at (added)
• tests/regression/Atoms/testsuite-atoms.at (modified) (1 diff)
• tests/regression/Makefile.am (modified) (1 diff)

doc/userguide/userguide.xml

@@ -879 +879 @@
         <link linkend='geometry'>Geometry</link>.</para>
         </section>
+        <section xml:id="atoms.random-perturbation">
+          <title xml:id="atoms.random-perturbation.title">Randomly perturb atoms</title>
+          <para>The positions of a set of selected atom(s) can be randomly 
+          perturbed by giving a maximum noise level..</para>
+          <programlisting>
+          ... --random-number-distribution "uniform_01"
+      --random-perturbation 0.1</programlisting>
+          <para>This will perturb all atomic positions by adding a vector
+          with components chosen randomly from the interval [-level, level].</para>
+          <para>Note that the manner these random numbers are picked depends
+          on the current random number distribution (and also on the engine),
+          see <link linkend='randomization'>Randomization</link>. The default
+          one will not give good results, therefore the example uses the 
+          uniform_01 distribution</para>
+        </section>
         <section xml:id="atoms.remove-atom">
           <title xml:id="atoms.remove-atom.title">Removing atoms</title>

src/Actions/GlobalListOfActions.hpp

@@ -33 +33 @@
   (AtomChangeElement) \
   (AtomMirror) \
+  (AtomRandomPerturbation) \
   (AtomRemove) \
   (AtomRotateAroundOriginByAngle) \

src/Actions/Makefile.am

@@ -152 +152 @@
   Actions/AtomAction/ChangeElementAction.cpp \
   Actions/AtomAction/MirrorAction.cpp \
+  Actions/AtomAction/RandomPerturbationAction.cpp \
   Actions/AtomAction/RemoveAction.cpp \
   Actions/AtomAction/RotateAroundOriginByAngleAction.cpp \
@@ -163 +164 @@
   Actions/AtomAction/MirrorAction.hpp \
   Actions/AtomAction/RemoveAction.hpp \
+  Actions/AtomAction/RandomPerturbationAction.hpp \
   Actions/AtomAction/RotateAroundOriginByAngleAction.hpp \
   Actions/AtomAction/SaturateAction.hpp \
@@ -172 +174 @@
   Actions/AtomAction/ChangeElementAction.def \
   Actions/AtomAction/MirrorAction.def \
+  Actions/AtomAction/RandomPerturbationAction.def \
   Actions/AtomAction/RemoveAction.def \
   Actions/AtomAction/RotateAroundOriginByAngleAction.def \

tests/Python/AllActions/options.dat

@@ -163 +163 @@
 random-number-distribution-parameters   "max=20;"
 random-number-engine-parameters "seed=2;"
+random-perturbation     "0.1"
 remove-geometry "named_vector"
 repeat-box      "1 1 1"

tests/regression/Atoms/testsuite-atoms.at

@@ -49 +49 @@
 m4_include([Atoms/Saturate/testsuite-atoms-saturate-atoms-nitrogen.at])
 m4_include([Atoms/Saturate/testsuite-atoms-saturate-atoms-bonded_atoms.at])
+
+# mirror atoms
+m4_include([Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at])

tests/regression/Makefile.am

@@ -60 +60 @@
         $(srcdir)/Atoms/ChangeElement/testsuite-atoms-change-element.at \
         $(srcdir)/Atoms/Mirror/testsuite-atoms-mirror.at \
+        $(srcdir)/Atoms/RandomPerturbation/testsuite-atoms-random-perturbation.at \
         $(srcdir)/Atoms/Remove/testsuite-atoms-remove.at \
         $(srcdir)/Atoms/RemoveCuboid/testsuite-atoms-remove-cuboid.at \