Changeset 39986b for tests/Python/AllActions

Timestamp:

Aug 9, 2013, 2:20:18 PM (11 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:

0afe00

Parents:

9c1324

git-author:

Frederik Heber <heber@…> (07/11/13 21:39:59)

git-committer:

Frederik Heber <heber@…> (08/09/13 14:20:18)

Message:

Added new MakroAction MolecularDynamicsAction.

• this resides within fragmentation, as we perform the four steps ...
  • verlet-integration
  • fragmentation
  • fragmentation-automation
  • analyse-fragmentation-results ... for a given number of times, using ActionSequence::loop with steps.
• outputs after every time integration step, controlled via DoOutput option.
• action only instantiated if HAVE_JOBMARKET.

File:

• tests/Python/AllActions/options.dat (modified) (3 diffs)

tests/Python/AllActions/options.dat

@@ -102 +102 @@
 offset  "1"
 order   "2"
+output-as       "store.conf"
+output-as       "store.data"
+output-as       "store.pdb"
+output-as       "store.xyz"
+output-as       "test.in"
+output-every-step       "1"
 output-file     "emptybox_values.dat"
 output-file     "hydrogenbox_values.dat"
@@ -110 +116 @@
 output-file     "waterbox-mirrored_values.dat"
 output-file     "waterbox_values.dat"
-output-as       "store.conf"
-output-as       "store.data"
-output-as       "store.pdb"
-output-as       "store.xyz"
-output-as       "test.in"
 output-types    "xyz"
 output-types    "xyz mpqc"
@@ -199 +200 @@
 skiplines       "2"
 start-step      "0"
+steps   "5"
 store-saturated-fragment        "BondFragment"
 stretch-bond    "1.5"