Changeset 415ddd for utils/Python/boxmaker.py.in

Timestamp:

May 20, 2014, 9:14:56 AM (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:

74459a

Parents:

975b83

git-author:

Frederik Heber <heber@…> (08/26/13 22:56:36)

git-committer:

Frederik Heber <heber@…> (05/20/14 09:14:56)

Message:

ActionQueue now contains a run thread.

• otherwise the progress bar of the QtMainWindow cannot be seen as waitForResults() takes up all of the executing thread.
• added mutex for operations modifying the queue.
• added ActionQueue::run() and ::stop(), used by friend stopQueue().
• insertAction() now makes use of a tempqueue that is added to true queue during run() instead of calling the actions directly.
• new stopQueue() in cleanUp.hpp is used by module_exit in pyMoleCuilder and in main() before saveAll().
• cleanup: printTiming() requires now list of action tokens and added new stopAndPurgeQueue() to place waiting for Actions to end into extra function.
• added ActionQueue::wait() which allows for synchronization in python scripts, is ignored in session python scripts. Otherwise we wait for ActionQueue's queue to empty during execution of load-session which hangs.
• DOCU: added note to python documentation.
• added waitQueue() also to purgeStaticInstances().
• static UIFactory::isFactoryPresent() added that allows checking whether we have a UI or are executed within a python script (i.e. pyMoleCuilder).
• DOCU: Extended docu on threads and who this affects python scripts.
• TESTFIX: changed regression tests on storing python sessions.

File:

• utils/Python/boxmaker.py.in (modified) (4 diffs)

utils/Python/boxmaker.py.in

@@ -151 +151 @@
 def GetSourceMolareMass(opt, units):
     mol.SelectionAllAtoms()
+    mol.wait()
     mass_sum = mol.getSelectedMolarMass()
     have = ("%f atomicmassunit" % mass_sum)
@@ -279 +280 @@
 def GetSourceBBabs(opt):
     mol.WorldCenterOnEdge()
+    mol.wait()
     bb = mol.getBoundingBox()
     bbmin = [bb[0], bb[2], bb[4]]
@@ -299 +301 @@
         mol.SelectAllAtoms()
         mol.RotateToPrincipalAxisSystem("0 1 0")
+    mol.wait()
 
 # Global options with sensible default parameters
@@ -341 +344 @@
 mol.WorldOutputAs(opt.outfilename + '.data')
 mol.WorldOutputAs(opt.outfilename + '.xyz')
+mol.wait()
 
 domain = [0.0]*3