Changeset d6a7b9 for src/Fragmentation/Automation

Timestamp:

Jul 13, 2014, 6:04:51 PM (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:

99692c

Parents:

18ed8c

git-author:

Frederik Heber <heber@…> (07/12/14 23:05:27)

git-committer:

Frederik Heber <heber@…> (07/13/14 18:04:51)

Message:

Specifying executable and suffix in SystemCommandJob with MPQCCommandFragmentController.

• now requiring JobMarket 1.1.5 (if given) for updated SystemCommandJob.
• SystemCommandJob allows specifying a suffix to the temporary file.
• this allows adding ".in" to MPQCCommandJob's temporary file name.

Location:

src/Fragmentation/Automation

Files:

• MPQCCommandFragmentController.cpp (modified) (2 diffs)
• MPQCCommandFragmentController.hpp (modified) (1 diff)

src/Fragmentation/Automation/MPQCCommandFragmentController.cpp

@@ -61 +61 @@
 bool MPQCCommandFragmentController::addJobsFromQueue(
     const MPQCData::DoLongrange_t _DoLongrange,
-    const MPQCData::DoValenceOnly_t _DoValenceOnly
+    const MPQCData::DoValenceOnly_t _DoValenceOnly,
+    const std::string &_executable
     )
 {
@@ -74 +75 @@
 #ifndef HAVE_JOBMARKET
     job->setId(getAvailableId());
+    if (!_executable.empty())
+      job->setCommand(_executable);
+    job->setSuffix(".in");
 #endif /* cause we don't inherit from FragmentController */
     // add the jobs

src/Fragmentation/Automation/MPQCCommandFragmentController.hpp

@@ -44 +44 @@
    * \param _DoSampleDensity whether to actually sample the resulting electronic density
    * \param _DoValenceOnly whether to sample just the valence or the total elctron and nuclei density
+   * \param _command command to pass to jobs for execution
    * \return true - jobs obtained, false - queue empty
    */
   bool addJobsFromQueue(
       const MPQCData::DoLongrange_t _DoLongrange,
-      const MPQCData::DoValenceOnly_t _DoValenceOnly
+      const MPQCData::DoValenceOnly_t _DoValenceOnly,
+      const std::string &_command
       );