Index

Symbols

---no-recursive advance command line option restart command line option --archive-mode harvest command line option --atomic harvest command line option --auto-restart restart command line option --blacklist harvest command line option --buffer run command line option --calc-mod restart command line option --carry-over restart command line option --config advance command line option new command line option restart command line option --dest coordinator command line option harvest command line option new command line option --file-size-limit advance command line option restart command line option --frequency run command line option --name-template advance command line option new command line option restart command line option --no-auto-restart restart command line option --no-sort config-gen command line option --no-submit advance command line option restart command line option --no-time-stamp harvest command line option --no-use-cache harvest command line option --path advance command line option harvest command line option restart command line option --recursive advance command line option restart command line option --relaxed harvest command line option restart command line option --sched-mod restart command line option --sort config-gen command line option

--stem harvest command line option --strict harvest command line option restart command line option --submit advance command line option restart command line option --template-dir coordinator command line option --time run command line option --time-source run command line option --time-stamp harvest command line option --type new command line option --use-cache harvest command line option --verbose advance command line option new command line option restart command line option --whitelist harvest command line option -a restart command line option -b run command line option -c restart command line option -d new command line option -f run command line option -L restart command line option -n new command line option -p advance command line option restart command line option -R advance command line option restart command line option -S advance command line option restart command line option -T run command line option -t run command line option -v advance command line option new command line option restart command line option

A

a0 (autojob.tasks.scan.BondScanParams attribute) a1 (autojob.tasks.scan.BondScanParams attribute) ABCEnumMeta (class in autojob.coordinator.classification) ABINIT (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) account (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) (autojob.hpc.SchedulerInputs attribute) ACE (autojob.coordinator.parameters.CalculatorType attribute) add_calc_params() (autojob.coordinator.gui.summary.JobSummaryFrame method) add_children() (autojob.coordinator.gui.submission_configuration.SpecButton method) add_from_listbox() (autojob.coordinator.gui.submission_configuration.SpecButton method) add_from_treeview() (autojob.coordinator.gui.submission_configuration.SpecButton method) add_item_to_parent() (in module autojob.next) add_parameter_values() (autojob.coordinator.gui.parameter_selection.ParameterPanel method) add_partitions() (autojob.coordinator.gui.job_submission.PartitionPanel method) add_spec() (autojob.coordinator.gui.submission_configuration.SpecButton method) add_specs_to_group() (autojob.coordinator.gui.submission_configuration.AddToGroupFrame method) add_structures() (autojob.coordinator.gui.groups.StructureGroup method) (autojob.coordinator.gui.structure_selection.StructureSelectionFrame method) add_structures_to_group() (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) add_subm_params() (autojob.coordinator.gui.summary.JobSummaryFrame method) add_tabs_to_notebook() (autojob.coordinator.gui.gui.GUI method) add_values() (autojob.coordinator.gui.groups.CalculationParameterGroup method) AddToGroupFrame (class in autojob.coordinator.gui.submission_configuration) adsorbates (autojob.coordinator.coordinator.Coordinator property) ADSORPTION (autojob.coordinator.classification.StudyType attribute) (autojob.legacy.StudyType attribute) adsorption_groups (autojob.coordinator.coordinator.Coordinator property) adsorption_jobs (autojob.coordinator.coordinator.Coordinator property) advance command line option ---no-recursive --config --file-size-limit --name-template --no-submit --path --recursive --submit --verbose -p -R -S -v advance() (in module autojob.next.advance) aggregate_mechanism_data() (in module autojob.harvest.mechanism) AIMS (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) allowed_types (autojob.coordinator.job.CalculationParameter property) (autojob.coordinator.parameters.CalculatorParameter property) alpha1 (autojob.tasks.mh.MHInitParams attribute) alpha2 (autojob.tasks.mh.MHInitParams attribute) alphanum_key() (in module autojob.coordinator.validation) (in module autojob.utils) alphanum_sort() (in module autojob.coordinator.validation) (in module autojob.utils) AMBER (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) analyses (autojob.tasks.calculation.CalculationInputs attribute) analysis_results (autojob.tasks.calculation.CalculationOutputs attribute) AnalysisBase (class in autojob.bases.analysis_base) app (autojob.coordinator.gui.job_submission.JobSubmissionTab attribute) (autojob.coordinator.gui.summary.SummaryTab attribute) append_trajectory (autojob.tasks.md.MDInitParams attribute) apply() (autojob.coordinator.filters.Filter method) (autojob.harvest.patch.Patch method) apply_comp_hydrogen_model() (autojob.harvest.mechanism.ElectrochemicalState method) ar_panel (autojob.coordinator.gui.job_submission.JobSubmissionPanels attribute) archive() (in module autojob.harvest.archive) archive_csv() (in module autojob.harvest.archive) ARCHIVE_FILE (autojob.settings.AutojobSettings attribute) archive_json() (in module autojob.harvest.archive) as_dict() (autojob.coordinator.job.Job method) (autojob.coordinator.job.JobStats method) (autojob.coordinator.parameters.MappingParameter method) (autojob.coordinator.parameters.NumberMappingParameter method) (autojob.coordinator.parameters.NumberParameter method) (autojob.coordinator.parameters.NumberSequenceParameter method) (autojob.coordinator.parameters.SequenceParameter method) as_flat_dict() (autojob.coordinator.job.Job method) ASAP (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) atomic_volume (autojob.harvest.harvesters.bader.BaderAnalysis attribute) atoms (autojob.tasks.vibration.VibrationOutputs attribute) atoms_as_dict() (in module autojob.utils.schemas) atoms_filename (autojob.bases.task_base.TaskInputsBase attribute) (autojob.tasks.task.TaskInputs attribute) atoms_from_dict() (in module autojob.utils.schemas) AtomsAnnotation (class in autojob.utils.schemas) auto_restart (autojob.bases.task_base.TaskInputsBase attribute) (autojob.tasks.task.TaskInputs attribute) autojob module autojob.bases module autojob.bases.analysis_base module autojob.bases.harvester_base module autojob.bases.task_base module autojob.coordinator module autojob.coordinator.classification module autojob.coordinator.coordinator module autojob.coordinator.espresso module autojob.coordinator.filters module autojob.coordinator.gaussian module

autojob.coordinator.gui module autojob.coordinator.gui.groups module autojob.coordinator.gui.gui module autojob.coordinator.gui.job_submission module autojob.coordinator.gui.parameter_selection module autojob.coordinator.gui.structure_selection module autojob.coordinator.gui.study_configuration module autojob.coordinator.gui.submission_configuration module autojob.coordinator.gui.summary module autojob.coordinator.gui.widgets module autojob.coordinator.job module autojob.coordinator.parameters module autojob.coordinator.validation module autojob.coordinator.vasp module autojob.harvest module autojob.harvest.archive module autojob.harvest.harvest module autojob.harvest.harvesters module autojob.harvest.harvesters.bader module autojob.harvest.harvesters.ddec6 module autojob.harvest.harvesters.default module autojob.harvest.harvesters.espresso module autojob.harvest.harvesters.gaussian module autojob.harvest.harvesters.gpaw module autojob.harvest.harvesters.vasp module autojob.harvest.mechanism module autojob.harvest.patch module autojob.hpc module autojob.legacy module autojob.next module autojob.next.advance module autojob.next.restart module autojob.parametrizations module autojob.plugins module autojob.settings module autojob.study module autojob.study_group module autojob.tasks module autojob.tasks.calculation module autojob.tasks.md module autojob.tasks.mh module autojob.tasks.scan module autojob.tasks.task module autojob.tasks.vibration module autojob.utils module autojob.utils.atoms module autojob.utils.cli module autojob.utils.files module autojob.utils.optimize module autojob.utils.parsing module autojob.utils.schemas module autojob.utils.templates module autojob.utils.vasp module autojob.workflow module AutojobSettings (class in autojob.settings) AutoRestartPanel (class in autojob.coordinator.gui.job_submission)

B

BaderAnalysis (class in autojob.harvest.harvesters.bader) beta1 (autojob.tasks.mh.MHInitParams attribute) beta2 (autojob.tasks.mh.MHInitParams attribute) beta3 (autojob.tasks.mh.MHInitParams attribute) BIGMEM (autojob.hpc.Partition attribute) bond_lims (autojob.tasks.scan.BondScanParams attribute) bond_order (autojob.harvest.harvesters.ddec6.BondedToDict attribute) bond_order_dict (autojob.harvest.harvesters.ddec6.DDEC6Analysis attribute) bond_order_sum (autojob.harvest.harvesters.ddec6.BondOrders attribute) bond_scan_inputs (autojob.tasks.scan.BondScan attribute) bond_scan_outputs (autojob.tasks.scan.BondScan attribute) bond_scan_params (autojob.tasks.scan.BondScanInputs attribute) bond_scan_results (autojob.tasks.scan.BondScanOutputs attribute)

bonded_to (autojob.harvest.harvesters.ddec6.BondOrders attribute) BondedToDict (class in autojob.harvest.harvesters.ddec6) BondOrders (class in autojob.harvest.harvesters.ddec6) bonds (autojob.tasks.scan.BondScanOutputs property) BondScan (class in autojob.tasks.scan) BondScanInputs (class in autojob.tasks.scan) BondScanOutputs (class in autojob.tasks.scan) BondScanParams (class in autojob.tasks.scan) BOOT_FAIL (autojob.hpc.JobState attribute) build_job_graph() (in module autojob.harvest.mechanism) build_metadata_patches() (in module autojob.harvest.patch) button_frame (autojob.coordinator.gui.job_submission.PartitionPanel attribute) ButtonFrame (class in autojob.coordinator.gui.submission_configuration)

C

calc_param_from() (autojob.coordinator.coordinator.Coordinator method) calc_param_values_for() (autojob.coordinator.coordinator.Coordinator method) calc_params (autojob.coordinator.coordinator.Coordinator property) (autojob.coordinator.gui.parameter_selection.ParameterSelectionTab property) (autojob.tasks.calculation.CalculationInputs attribute) calc_params_for() (autojob.coordinator.coordinator.Coordinator method) Calculation (class in autojob.tasks.calculation) calculation_inputs (autojob.tasks.calculation.Calculation attribute) calculation_outputs (autojob.tasks.calculation.Calculation attribute) calculation_script (autojob.tasks.calculation.CalculationInputs attribute) CALCULATION_SCRIPT_TEMPLATE (autojob.settings.AutojobSettings attribute) calculation_script_template (autojob.tasks.calculation.CalculationInputs attribute) calculation_summary (autojob.coordinator.gui.summary.SummaryFrames attribute) calculation_type (autojob.coordinator.coordinator.Coordinator property) CalculationInputs (class in autojob.tasks.calculation) CalculationOutputs (class in autojob.tasks.calculation) CalculationPanel (class in autojob.coordinator.gui.study_configuration) CalculationParameter (class in autojob.coordinator.job) CalculationParameterGroup (class in autojob.coordinator.gui.groups) CalculationSummaryFrame (class in autojob.coordinator.gui.summary) CalculationType (class in autojob.coordinator.classification) calculator (autojob.coordinator.coordinator.Coordinator property) (autojob.tasks.calculation.CalculationInputs attribute) calculator_results (autojob.tasks.calculation.CalculationOutputs attribute) calculator_summary (autojob.coordinator.gui.summary.SummaryFrames attribute) calculator_type (autojob.coordinator.coordinator.Coordinator property) CalculatorPanel (class in autojob.coordinator.gui.study_configuration) CalculatorParameter (class in autojob.coordinator.parameters) CalculatorSummaryFrame (class in autojob.coordinator.gui.summary) CalculatorType (class in autojob.coordinator.classification) (class in autojob.coordinator.parameters) CANCELLED (autojob.hpc.JobState attribute) carry_over_files() (in module autojob.next) CASTEP (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) change_parameter_panel() (autojob.coordinator.gui.parameter_selection.ParameterSelectionCombobox method) charge (autojob.harvest.harvesters.bader.BaderAnalysis attribute) charge_transfer (autojob.harvest.harvesters.bader.BaderAnalysis attribute) check_inputs() (autojob.hpc.SchedulerInputs method) check_job_status() (in module autojob.utils.files) clean_up_task() (in module autojob.next) clear_items() (autojob.coordinator.gui.submission_configuration.ButtonFrame method) clear_listbox() (autojob.coordinator.gui.widgets.ListboxFrame method) clear_parameter_values() (autojob.coordinator.gui.parameter_selection.ParameterPanel method) clear_partitions() (autojob.coordinator.gui.job_submission.PartitionPanel method) clear_structures() (autojob.coordinator.gui.structure_selection.StructureSelectionFrame method) clear_structures_from_group() (autojob.coordinator.gui.structure_selection.GroupViewFrame method) clear_treeview() (autojob.coordinator.gui.widgets.TreeviewFrame method) cluster_name (autojob.hpc.Partition property) COMMAND run command line option COMPLETED (autojob.hpc.JobState attribute) completion (autojob.coordinator.gui.summary.SummaryFrames attribute) complexes (autojob.coordinator.coordinator.Coordinator property) config-gen command line option --no-sort --sort configure_logging() (autojob.settings.AutojobSettings method) configure_optimizer() (in module autojob.utils.optimize) configure_rbs() (autojob.coordinator.gui.parameter_selection.ParameterPanel method) configure_root() (in module autojob.coordinator.gui.gui) configure_settings() (in module autojob.utils.cli) construct_cli_call() (in module autojob.utils.cli) converged (autojob.tasks.calculation.CalculationOutputs attribute) convert() (autojob.utils.cli.MemoryFloat method) (in module autojob.utils.parsing) convert_mem() (autojob.coordinator.gui.job_submission.MemoryPanel method) coordinator (autojob.coordinator.gui.gui.GUI attribute) Coordinator (class in autojob.coordinator.coordinator) coordinator command line option --dest --template-dir TEMPLATE

CoordinatorTabs (class in autojob.coordinator.gui.gui) copy_atom_metadata() (in module autojob.utils.atoms) copy_permissions_and_ownership() (in module autojob.utils.files) cores (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) (autojob.coordinator.job.JobStats attribute) CP2K (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) CPU2013 (autojob.hpc.Partition attribute) CPU2017_BF05 (autojob.hpc.Partition attribute) CPU2019 (autojob.hpc.Partition attribute) CPU2019_BF05 (autojob.hpc.Partition attribute) CPU2021 (autojob.hpc.Partition attribute) CPU2021_BF05 (autojob.hpc.Partition attribute) CPU2021_BF24 (autojob.hpc.Partition attribute) CPU2022 (autojob.hpc.Partition attribute) CPU2022_BF24 (autojob.hpc.Partition attribute) CPU2023 (autojob.hpc.Partition attribute) cpus_per_node (autojob.hpc.Partition property) cpus_per_task (autojob.hpc.SchedulerInputs attribute) create() (autojob.coordinator.gui.job_submission.MemoryPanel method) (autojob.coordinator.gui.job_submission.ParallelizationPanel method) (autojob.coordinator.gui.job_submission.RunTimePanel method) (autojob.coordinator.gui.summary.SummaryTab method) create_add_group() (autojob.coordinator.gui.submission_configuration.AddToGroupFrame method) create_add_to_group() (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) create_auto_restart_limit() (autojob.coordinator.gui.job_submission.AutoRestartPanel method) create_button_frame() (autojob.coordinator.gui.job_submission.PartitionPanel method) (autojob.coordinator.gui.parameter_selection.ParameterPanel method) (autojob.coordinator.gui.structure_selection.GroupViewFrame method) (autojob.coordinator.gui.structure_selection.StructureSelectionFrame method) create_buttons() (autojob.coordinator.gui.submission_configuration.ButtonFrame method) create_combobox() (autojob.coordinator.gui.job_submission.PartitionPanel method) (autojob.coordinator.gui.parameter_selection.ParameterInputFrame method) create_create_group() (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method) create_default_button() (autojob.coordinator.gui.parameter_selection.ParameterPanel method) create_del_group() (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method) create_entry() (autojob.coordinator.gui.parameter_selection.ParameterInputFrame method) create_group() (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method) create_input_frames() (autojob.coordinator.gui.parameter_selection.ParameterInputSection method) create_job_stats_file() (in module autojob.utils.files) create_label() (autojob.coordinator.gui.parameter_selection.ParameterInputFrame method) create_listbox() (autojob.coordinator.gui.job_submission.PartitionPanel method) (autojob.coordinator.gui.widgets.ListboxFrame method) create_next_step() (in module autojob.next) create_panels() (autojob.coordinator.gui.job_submission.JobSubmissionTab method) (autojob.coordinator.gui.submission_configuration.SubmissionConfigurationTab method) create_param_panels() (autojob.coordinator.gui.parameter_selection.ParameterSelectionTab method) create_parametrization() (in module autojob.parametrizations) create_radio_buttons() (autojob.coordinator.gui.parameter_selection.ParameterRadiobuttonFrame method) create_rbs() (autojob.coordinator.gui.job_submission.MemoryPanel method) create_spinbox() (autojob.coordinator.gui.parameter_selection.ParameterInputFrame method) create_structure_tasks() (autojob.coordinator.coordinator.Coordinator method) create_study_group() (autojob.coordinator.coordinator.Coordinator method) create_tabs() (autojob.coordinator.gui.gui.GUI method) create_task_group_tree() (in module autojob.next) create_task_tree() (in module autojob.next) create_tasks() (autojob.coordinator.coordinator.Coordinator method) create_templated_dir_name() (in module autojob.utils.files) create_treeview() (autojob.coordinator.gui.widgets.TreeviewFrame method) create_unlimited_restart_prompt() (autojob.coordinator.gui.job_submission.AutoRestartPanel method) create_view_group() (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method) create_widg() (autojob.coordinator.gui.parameter_selection.ParameterInputFrame method) create_xscrollbar() (autojob.coordinator.gui.widgets.ListboxFrame method) (autojob.coordinator.gui.widgets.TreeviewFrame method) create_yscrollbar() (autojob.coordinator.gui.widgets.ListboxFrame method) (autojob.coordinator.gui.widgets.TreeviewFrame method) CreateJobsFrame (class in autojob.coordinator.gui.summary) creation() (autojob.coordinator.gui.widgets.RadiobuttonPanel method) CRYSTAL (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute)

D

date_created (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.study.Study attribute) (autojob.study_group.StudyGroup attribute) (autojob.tasks.task.TaskMetadata attribute) days (autojob.coordinator.gui.job_submission.RunTimeDict attribute) (autojob.utils.parsing.TimedeltaTuple attribute) DDEC6Analysis (class in autojob.harvest.harvesters.ddec6) DEADLINE (autojob.hpc.JobState attribute) default (autojob.coordinator.job.CalculationParameter property) (autojob.coordinator.parameters.CalculatorParameter property) DEFAULT (autojob.coordinator.parameters.CalculatorType attribute) (autojob.legacy.StudyType attribute) DEFAULT_CALCULATION_SCRIPT_FILE (autojob.settings.AutojobSettings attribute) DEFAULT_TASK (autojob.settings.AutojobSettings attribute) DEFAULT_TASK_SCRIPT_FILE (autojob.settings.AutojobSettings attribute) defined_calculation_parameters (autojob.coordinator.gui.groups.CalculationParameterGroup property) defined_values (autojob.coordinator.gui.groups.CalculationParameterGroup property) del_group() (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method)

delta (autojob.tasks.vibration.VibrationInputs attribute) DEMON (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) DEMON_NANO (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) description (autojob.coordinator.job.CalculationParameter property) DFTB (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) DFTD3 (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) dipoles (autojob.harvest.harvesters.ddec6.DDEC6Analysis attribute) direction (autojob.harvest.harvesters.ddec6.BondedToDict attribute) discover_analysis_plugins() (in module autojob.plugins) discover_harvester_plugins() (in module autojob.plugins) discover_task_plugins() (in module autojob.plugins) display_autorestart_options() (autojob.coordinator.gui.job_submission.AutoRestartPanel method) DMOL3 (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) DOS (autojob.coordinator.classification.CalculationType attribute)

E

EAM (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) Ediff0 (autojob.tasks.mh.MHInitParams attribute) elapsed (autojob.hpc.SchedulerOutputs attribute) ElectrochemicalState (class in autojob.harvest.mechanism) element (autojob.harvest.harvesters.ddec6.BondedToDict attribute) (autojob.harvest.harvesters.ddec6.BondOrders attribute) elementary_step (autojob.harvest.mechanism.MechanisticEntry attribute) ELK (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) EMT (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) end_time (autojob.coordinator.job.JobStats attribute) energy (autojob.harvest.mechanism.MechanisticEntry attribute) (autojob.tasks.calculation.CalculationOutputs attribute)

enforce_partition_limits() (autojob.coordinator.gui.job_submission.PartitionPanel method) enforce_time_limit() (autojob.coordinator.gui.job_submission.RunTimePanel method) entry (autojob.bases.task_base.TaskOutputsBase attribute) (autojob.tasks.task.TaskOutputs attribute) EOS (autojob.coordinator.classification.CalculationType attribute) ESPRESSO (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) EspressoJob (class in autojob.coordinator.espresso) evaluate() (autojob.parametrizations.VariableReference method) EXCITING (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) explicit_values (autojob.coordinator.job.CalculationParameter property) extract_scheduler_inputs() (autojob.hpc.SchedulerInputs static method) ExtrasPanel (class in autojob.coordinator.gui.job_submission)

F

FAILED (autojob.bases.task_base.TaskOutcome attribute) (autojob.hpc.JobState attribute) FILES (autojob.coordinator.espresso.EspressoJob attribute) (autojob.coordinator.gaussian.GaussianJob attribute) (autojob.coordinator.vasp.VaspJob attribute) files_to_carry_over (autojob.bases.task_base.TaskInputsBase attribute) (autojob.tasks.task.TaskInputs attribute) files_to_copy (autojob.bases.task_base.TaskInputsBase attribute) (autojob.tasks.task.TaskInputs attribute) files_to_delete (autojob.bases.task_base.TaskInputsBase attribute) (autojob.tasks.task.TaskInputs attribute) Filter (class in autojob.coordinator.filters) finalize_task() (in module autojob.next) find_ancestor() (in module autojob.harvest.mechanism) find_ancestors() (in module autojob.harvest.mechanism) find_finished_jobs() (in module autojob.utils.files) find_last_submitted_jobs() (in module autojob.utils.files) find_study_dirs() (in module autojob.utils.files) find_study_group_dirs() (in module autojob.utils.files) find_task_dirs() (in module autojob.utils.files) find_task_group_dirs() (in module autojob.utils.files) fix (autojob.tasks.scan.BondScanParams attribute) flatten_calculations() (in module autojob.harvest.archive) FLEUR (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) fmax (autojob.tasks.mh.MHInitParams attribute) FORCE_FIELD (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) forces (autojob.tasks.calculation.CalculationOutputs attribute) format_partitions() (autojob.coordinator.gui.job_submission.PartitionPanel method) format_time() (autojob.utils.parsing.TimedeltaTuple static method) frame_titles() (autojob.coordinator.gui.parameter_selection.ParameterInputSection method)

freeze_atoms() (in module autojob.tasks.vibration) from_dict() (autojob.coordinator.job.Job class method) (autojob.coordinator.job.JobStats class method) (autojob.coordinator.parameters.MappingParameter class method) (autojob.coordinator.parameters.NumberMappingParameter class method) (autojob.coordinator.parameters.NumberParameter class method) (autojob.coordinator.parameters.NumberSequenceParameter class method) (autojob.coordinator.parameters.SequenceParameter class method) from_directory() (autojob.bases.task_base.PathLoadable class method) (autojob.bases.task_base.TaskBase class method) (autojob.bases.task_base.TaskMetadataBase class method) (autojob.hpc.SchedulerInputs class method) (autojob.hpc.SchedulerOutputs class method) (autojob.study.Study class method) (autojob.study_group.StudyGroup class method) (autojob.tasks.calculation.Calculation class method) (autojob.tasks.calculation.CalculationOutputs class method) (autojob.tasks.md.MDOutputs class method) (autojob.tasks.md.MolecularDynamics class method) (autojob.tasks.mh.MHOutputs class method) (autojob.tasks.mh.MinimaHopping class method) (autojob.tasks.scan.BondScan class method) (autojob.tasks.scan.BondScanOutputs class method) (autojob.tasks.task.Task class method) (autojob.tasks.task.TaskInputs class method) (autojob.tasks.task.TaskMetadata class method) (autojob.tasks.task.TaskOutputs class method) (autojob.tasks.vibration.Vibration class method) (autojob.tasks.vibration.VibrationOutputs class method) (autojob.workflow.Workflow class method) from_slurm_time() (autojob.utils.parsing.TimedeltaTuple class method) from_string() (autojob.utils.parsing.TimedeltaTuple class method) from_timedelta() (autojob.utils.parsing.TimedeltaTuple class method)

G

GAMESS_US (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) GAUSSIAN (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) GaussianJob (class in autojob.coordinator.gaussian) get_analysis() (in module autojob.plugins) get_ddec6_index_map() (in module autojob.harvest.harvesters.ddec6) get_harvester() (in module autojob.plugins) get_iid_in_dest() (autojob.coordinator.gui.submission_configuration.SpecButton method) get_last_updated() (in module autojob.utils.files) get_loader() (in module autojob.utils.files) get_next_steps() (autojob.workflow.Workflow method) (in module autojob.next.advance) get_output_atoms() (in module autojob.harvest.harvesters.vasp) get_predecessors() (autojob.workflow.Workflow method) get_scheduler_command() (in module autojob.hpc) get_sets() (autojob.coordinator.gui.groups.CalculationParameterGroup method) get_slurm_job_id() (in module autojob.utils) (in module autojob.utils.files)

get_task_class() (in module autojob.plugins) get_uri() (in module autojob.utils) (in module autojob.utils.files) getattrpath() (in module autojob.parametrizations) GPAW (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) gpu (autojob.hpc.Partition property) GPU_V100 (autojob.hpc.Partition attribute) GROMACS (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) GroupButtonFrame (class in autojob.coordinator.gui.structure_selection) (class in autojob.coordinator.gui.submission_configuration) GroupSelectionCombobox (class in autojob.coordinator.gui.job_submission) (class in autojob.coordinator.gui.parameter_selection) GroupSummary (class in autojob.coordinator.gui.submission_configuration) GroupViewFrame (class in autojob.coordinator.gui.structure_selection) GUI (class in autojob.coordinator.gui.gui) GULP (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute)

H

harvest command line option --archive-mode --atomic --blacklist --dest --no-time-stamp --no-use-cache --path --relaxed --stem --strict --time-stamp --use-cache --whitelist

harvest() (in module autojob.harvest.harvest) harvest_bader_results() (in module autojob.harvest.harvesters.bader) harvest_ddec6_results() (in module autojob.harvest.harvesters.ddec6) harvest_default_calculator_results() (in module autojob.harvest.harvesters.default) harvest_espresso_results() (in module autojob.harvest.harvesters.espresso) harvest_gaussian_results() (in module autojob.harvest.harvesters.gaussian) harvest_gpaw_results() (in module autojob.harvest.harvesters.gpaw) harvest_vasp_results() (in module autojob.harvest.harvesters.vasp) HarvesterBase (class in autojob.bases.harvester_base) hessian (autojob.tasks.vibration.VibrationOutputs attribute) HOTBIT (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) hours (autojob.coordinator.gui.job_submission.RunTimeDict attribute) (autojob.utils.parsing.TimedeltaTuple attribute) hyphenate() (in module autojob.utils.schemas)

I

id_factory() (in module autojob.utils.schemas) IDLE (autojob.bases.task_base.TaskOutcome attribute) idle_time (autojob.hpc.SchedulerOutputs attribute) images (autojob.tasks.scan.BondScanOutputs attribute) ImplementableEnum (class in autojob.coordinator.classification) index (autojob.harvest.harvesters.ddec6.BondedToDict attribute) indices (autojob.tasks.scan.BondScanParams attribute) (autojob.tasks.vibration.VibrationInputs attribute) (autojob.tasks.vibration.VibrationOutputs attribute) initialize_submission_parameters() (autojob.coordinator.gui.job_submission.JobSubmissionTab method) initialize_task() (in module autojob.next) initialize_values() (autojob.coordinator.gui.groups.CalculationParameterGroup static method) INPUT_ATOMS_FILE (autojob.settings.AutojobSettings attribute) input_parameters() (autojob.coordinator.espresso.EspressoJob static method) (autojob.coordinator.gaussian.GaussianJob static method) (autojob.coordinator.job.Job static method) (autojob.coordinator.vasp.VaspJob static method)

INPUTS_FILE (autojob.settings.AutojobSettings attribute) InputWriter (class in autojob.bases.task_base) is_default() (autojob.coordinator.classification.CalculationType method) (autojob.coordinator.classification.CalculatorType method) (autojob.coordinator.classification.ImplementableEnum method) (autojob.coordinator.classification.StudyType method) is_finite_int_range() (autojob.coordinator.job.CalculationParameter method) is_implemented() (autojob.coordinator.classification.CalculationType method) (autojob.coordinator.classification.CalculatorType method) (autojob.coordinator.classification.ImplementableEnum method) (autojob.coordinator.classification.StudyType method) (autojob.coordinator.parameters.CalculatorType method) (autojob.legacy.StudyType method) items (autojob.coordinator.gui.submission_configuration.SelectionFrame property) (autojob.coordinator.gui.widgets.ListboxFrame property) (autojob.coordinator.gui.widgets.TreeviewFrame property) iter_to_native() (in module autojob.coordinator.validation) (in module autojob.utils)

J

Job (class in autojob.coordinator.job) job_id (autojob.hpc.SchedulerOutputs attribute) job_name (autojob.hpc.SchedulerInputs attribute) job_stats (autojob.coordinator.job.Job attribute) job_submission (autojob.coordinator.gui.gui.CoordinatorTabs attribute) job_summary (autojob.coordinator.gui.summary.SummaryFrames attribute) JobError (class in autojob.coordinator.job)

jobs (autojob.coordinator.coordinator.Coordinator property) JobState (class in autojob.hpc) JobStats (class in autojob.coordinator.job) JobSubmissionPanels (class in autojob.coordinator.gui.job_submission) JobSubmissionParameters (class in autojob.coordinator.gui.job_submission) JobSubmissionTab (class in autojob.coordinator.gui.job_submission) JobSummaryFrame (class in autojob.coordinator.gui.summary)

K

KIM (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute)

L

label (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.tasks.task.TaskMetadata attribute) LAMMPS (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) LAMMPS_LIB (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) last_updated (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.tasks.task.TaskMetadata attribute) LATTICE (autojob.hpc.Partition attribute) LEGACY_MODE (autojob.settings.AutojobSettings attribute) LENNARD_JONES (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) ListboxFrame (class in autojob.coordinator.gui.widgets) load() (autojob.coordinator.gui.gui.GUI method) (autojob.coordinator.gui.job_submission.AutoRestartPanel method) (autojob.coordinator.gui.job_submission.ExtrasPanel method) (autojob.coordinator.gui.job_submission.GroupSelectionCombobox method) (autojob.coordinator.gui.job_submission.JobSubmissionTab method) (autojob.coordinator.gui.job_submission.MemoryPanel method) (autojob.coordinator.gui.job_submission.ParallelizationPanel method) (autojob.coordinator.gui.job_submission.PartitionPanel method) (autojob.coordinator.gui.job_submission.RunTimePanel method) (autojob.coordinator.gui.parameter_selection.GroupSelectionCombobox method) (autojob.coordinator.gui.parameter_selection.ParameterPanel method) (autojob.coordinator.gui.parameter_selection.ParameterSelectionCombobox method) (autojob.coordinator.gui.parameter_selection.ParameterSelectionTab method) (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) (autojob.coordinator.gui.structure_selection.GroupViewFrame method) (autojob.coordinator.gui.structure_selection.StructureSelectionFrame method) (autojob.coordinator.gui.structure_selection.StructureSelectionPanel method) (autojob.coordinator.gui.structure_selection.StructureSelectionTab method) (autojob.coordinator.gui.study_configuration.StudyConfigurationTab method) (autojob.coordinator.gui.submission_configuration.AddToGroupFrame method) (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method) (autojob.coordinator.gui.submission_configuration.GroupSummary method) (autojob.coordinator.gui.submission_configuration.SelectionFrame method) (autojob.coordinator.gui.submission_configuration.SelectionPanel method) (autojob.coordinator.gui.submission_configuration.SubmissionConfigurationTab method) (autojob.coordinator.gui.submission_configuration.ViewFrame method) (autojob.coordinator.gui.summary.CreateJobsFrame method) (autojob.coordinator.gui.summary.JobSummaryFrame method) (autojob.coordinator.gui.summary.SummaryFrame method) (autojob.coordinator.gui.summary.SummaryTab method) (autojob.coordinator.gui.summary.WarningsFrame method)

load_calc_params() (autojob.coordinator.gui.parameter_selection.ParameterSelectionTab method) load_magic() (autojob.tasks.task.Task class method) load_panels() (autojob.coordinator.gui.parameter_selection.ParameterSelectionTab method) load_parameter_list() (autojob.coordinator.gui.parameter_selection.ParameterSelectionTab method) load_partitions() (autojob.coordinator.gui.job_submission.PartitionPanel method) LOG_FILE (autojob.settings.AutojobSettings attribute) LOG_LEVEL (autojob.settings.AutojobSettings attribute) logfile (autojob.tasks.md.MDInitParams attribute) (autojob.tasks.mh.MHInitParams attribute) loginterval (autojob.tasks.md.MDInitParams attribute)

M

mail_panel (autojob.coordinator.gui.job_submission.JobSubmissionPanels attribute) mail_type (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) (autojob.hpc.SchedulerInputs attribute) mail_user (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) (autojob.hpc.SchedulerInputs attribute) MappingParameter (class in autojob.coordinator.parameters) mask (autojob.tasks.scan.BondScanParams attribute) match_path (autojob.harvest.patch.Patch attribute) match_value (autojob.harvest.patch.Patch attribute) max_mem_per_node (autojob.hpc.Partition property) max_rss (autojob.hpc.SchedulerOutputs attribute) maxtemp (autojob.tasks.mh.MHRunParams attribute) MD (autojob.coordinator.classification.CalculationType attribute) md_init_params (autojob.tasks.md.MDInputs attribute) md_inputs (autojob.tasks.md.MolecularDynamics attribute) md_outputs (autojob.tasks.md.MolecularDynamics attribute) md_params_to_inputs() (autojob.tasks.md.MDInputs method) (autojob.tasks.mh.MHInputs method) md_run_params (autojob.tasks.md.MDInputs attribute) md_traj_pattern (autojob.tasks.mh.MHInputs attribute) md_trajectories (autojob.tasks.mh.MHOutputs attribute) md_trajectory (autojob.tasks.md.MDOutputs attribute) md_trajectory_results (autojob.tasks.md.MDOutputs attribute) (autojob.tasks.mh.MHOutputs attribute) MDInitParams (class in autojob.tasks.md) MDInputs (class in autojob.tasks.md) mdmin (autojob.tasks.mh.MHInitParams attribute) MDOutputs (class in autojob.tasks.md) MDRunParams (class in autojob.tasks.md) MECHANISM (autojob.coordinator.classification.StudyType attribute) (autojob.legacy.StudyType attribute) MechanisticEntry (class in autojob.harvest.mechanism) mem (autojob.hpc.SchedulerInputs attribute) mem_panel (autojob.coordinator.gui.job_submission.JobSubmissionPanels attribute) mem_per_cpu (autojob.hpc.SchedulerInputs attribute) member_types (autojob.coordinator.parameters.MappingParameter property) (autojob.coordinator.parameters.SequenceParameter property) memory (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) (autojob.coordinator.job.JobStats attribute) MEMORY_LIMIT (autojob.coordinator.job.JobError attribute) MemoryFloat (class in autojob.utils.cli) MemoryPanel (class in autojob.coordinator.gui.job_submission) mh_init_params (autojob.tasks.mh.MHInputs attribute) mh_inputs (autojob.tasks.mh.MinimaHopping attribute) mh_outputs (autojob.tasks.mh.MinimaHopping attribute) mh_run_params (autojob.tasks.mh.MHInputs attribute) MHInitParams (class in autojob.tasks.mh) MHInputs (class in autojob.tasks.mh) MHOutputs (class in autojob.tasks.mh) MHRunParams (class in autojob.tasks.mh) min_dist (autojob.harvest.harvesters.bader.BaderAnalysis attribute) minima (autojob.tasks.mh.MHOutputs attribute) minima_results (autojob.tasks.mh.MHOutputs attribute) minima_threshold (autojob.tasks.mh.MHInitParams attribute) minima_traj (autojob.tasks.mh.MHInitParams attribute) MinimaHopping (class in autojob.tasks.mh) minutes (autojob.coordinator.gui.job_submission.RunTimeDict attribute) (autojob.utils.parsing.TimedeltaTuple attribute) model_config (autojob.bases.task_base.TaskBase attribute) (autojob.bases.task_base.TaskInputsBase attribute) (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.bases.task_base.TaskOutputsBase attribute) (autojob.hpc.SchedulerInputs attribute) (autojob.hpc.SchedulerOutputs attribute) (autojob.settings.AutojobSettings attribute) (autojob.study.Study attribute) (autojob.study_group.StudyGroup attribute) (autojob.tasks.calculation.Calculation attribute) (autojob.tasks.calculation.CalculationInputs attribute) (autojob.tasks.calculation.CalculationOutputs attribute) (autojob.tasks.md.MDInputs attribute) (autojob.tasks.md.MDOutputs attribute) (autojob.tasks.md.MolecularDynamics attribute) (autojob.tasks.mh.MHInputs attribute) (autojob.tasks.mh.MHOutputs attribute) (autojob.tasks.mh.MinimaHopping attribute) (autojob.tasks.scan.BondScan attribute) (autojob.tasks.scan.BondScanInputs attribute) (autojob.tasks.scan.BondScanOutputs attribute) (autojob.tasks.task.Task attribute) (autojob.tasks.task.TaskInputs attribute) (autojob.tasks.task.TaskMetadata attribute) (autojob.tasks.task.TaskOutputs attribute) (autojob.tasks.vibration.Vibration attribute) (autojob.tasks.vibration.VibrationInputs attribute) (autojob.tasks.vibration.VibrationOutputs attribute) (autojob.utils.schemas.AtomsAnnotation attribute) (autojob.workflow.Step attribute)

mods_to_dict() (in module autojob.utils.cli) module autojob autojob.bases autojob.bases.analysis_base autojob.bases.harvester_base autojob.bases.task_base autojob.coordinator autojob.coordinator.classification autojob.coordinator.coordinator autojob.coordinator.espresso autojob.coordinator.filters autojob.coordinator.gaussian autojob.coordinator.gui autojob.coordinator.gui.groups autojob.coordinator.gui.gui autojob.coordinator.gui.job_submission autojob.coordinator.gui.parameter_selection autojob.coordinator.gui.structure_selection autojob.coordinator.gui.study_configuration autojob.coordinator.gui.submission_configuration autojob.coordinator.gui.summary autojob.coordinator.gui.widgets autojob.coordinator.job autojob.coordinator.parameters autojob.coordinator.validation autojob.coordinator.vasp autojob.harvest autojob.harvest.archive autojob.harvest.harvest autojob.harvest.harvesters autojob.harvest.harvesters.bader autojob.harvest.harvesters.ddec6 autojob.harvest.harvesters.default autojob.harvest.harvesters.espresso autojob.harvest.harvesters.gaussian autojob.harvest.harvesters.gpaw autojob.harvest.harvesters.vasp autojob.harvest.mechanism autojob.harvest.patch autojob.hpc autojob.legacy autojob.next autojob.next.advance autojob.next.restart autojob.parametrizations autojob.plugins autojob.settings autojob.study autojob.study_group autojob.tasks autojob.tasks.calculation autojob.tasks.md autojob.tasks.mh autojob.tasks.scan autojob.tasks.task autojob.tasks.vibration autojob.utils autojob.utils.atoms autojob.utils.cli autojob.utils.files autojob.utils.optimize autojob.utils.parsing autojob.utils.schemas autojob.utils.templates autojob.utils.vasp autojob.workflow MolecularDynamics (class in autojob.tasks.md) MOPAC (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) MORSE_POTENTIAL (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute)

N

name (autojob.coordinator.job.CalculationParameter property) (autojob.harvest.mechanism.MechanisticEntry attribute) (autojob.study.Study attribute) (autojob.study_group.StudyGroup attribute) (autojob.tasks.vibration.VibrationInputs attribute) (autojob.utils.cli.MemoryFloat attribute) nelectrons (autojob.harvest.harvesters.bader.BaderAnalysis attribute) net_electrons (autojob.harvest.mechanism.ElectrochemicalState attribute) net_hydrogens (autojob.harvest.mechanism.ElectrochemicalState attribute) net_water_lost (autojob.harvest.mechanism.ElectrochemicalState attribute) new command line option --config --dest --name-template --type --verbose -d -n -v new_parameter_warning() (autojob.coordinator.gui.summary.WarningsFrame method)

new_structure_warning() (autojob.coordinator.gui.summary.WarningsFrame method) new_submission_parameters() (autojob.coordinator.gui.job_submission.JobSubmissionTab method) nfree (autojob.tasks.vibration.VibrationInputs attribute) NODE_FAIL (autojob.hpc.JobState attribute) nodes (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) (autojob.coordinator.job.JobStats attribute) (autojob.hpc.Partition property) (autojob.hpc.SchedulerInputs attribute) (autojob.hpc.SchedulerOutputs attribute) notebook (autojob.coordinator.gui.gui.GUI attribute) notes (autojob.study.Study attribute) (autojob.study_group.StudyGroup attribute) ntasks_per_node (autojob.hpc.SchedulerInputs attribute) number_range (autojob.coordinator.parameters.NumberParameter property) NumberMappingParameter (class in autojob.coordinator.parameters) NumberParameter (class in autojob.coordinator.parameters) NumberRange (class in autojob.coordinator.parameters) NumberSequenceParameter (class in autojob.coordinator.parameters) NWCHEM (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute)

O

OCTOPUS (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) on_close() (autojob.coordinator.gui.submission_configuration.GroupSummary method) ONETEP (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) OPENMX (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) opt_params (autojob.tasks.calculation.CalculationInputs attribute) opt_traj_pattern (autojob.tasks.mh.MHInputs attribute) opt_trajectories (autojob.tasks.mh.MHOutputs attribute) opt_trajectory_results (autojob.tasks.mh.MHOutputs attribute) optimizer (autojob.tasks.calculation.CalculationInputs attribute) (autojob.tasks.mh.MHInitParams attribute) optimizer_results (autojob.tasks.calculation.CalculationOutputs attribute) ORCA (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) organize() (autojob.coordinator.gui.gui.GUI method) (autojob.coordinator.gui.job_submission.AutoRestartPanel method) (autojob.coordinator.gui.job_submission.MemoryPanel method) (autojob.coordinator.gui.job_submission.ParallelizationPanel method) (autojob.coordinator.gui.job_submission.PartitionPanel method) (autojob.coordinator.gui.job_submission.RunTimePanel method) (autojob.coordinator.gui.parameter_selection.ParameterPanel method) (autojob.coordinator.gui.parameter_selection.ParameterSelectionTab method) (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) (autojob.coordinator.gui.structure_selection.GroupViewFrame method) (autojob.coordinator.gui.structure_selection.StructureSelectionFrame method) (autojob.coordinator.gui.structure_selection.StructureSelectionPanel method) (autojob.coordinator.gui.structure_selection.StructureSelectionTab method) (autojob.coordinator.gui.submission_configuration.AddToGroupFrame method) (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method) (autojob.coordinator.gui.submission_configuration.SelectionFrame method) (autojob.coordinator.gui.submission_configuration.SelectionPanel method) (autojob.coordinator.gui.submission_configuration.SubmissionConfigurationTab method) (autojob.coordinator.gui.submission_configuration.ViewFrame method) (autojob.coordinator.gui.summary.SummaryFrame method) (autojob.coordinator.gui.summary.SummaryTab method) (autojob.coordinator.gui.widgets.ListboxFrame method) (autojob.coordinator.gui.widgets.TreeviewFrame method)

OUT_OF_MEMORY (autojob.hpc.JobState attribute) outcome (autojob.bases.task_base.TaskOutputsBase attribute) (autojob.tasks.task.TaskOutputs attribute) OUTPUT_ATOMS_FILE (autojob.settings.AutojobSettings attribute)

P

pack_panels() (autojob.coordinator.gui.job_submission.JobSubmissionTab method) panels (autojob.coordinator.gui.job_submission.JobSubmissionTab attribute) para_panel (autojob.coordinator.gui.job_submission.JobSubmissionPanels attribute) PARALLEL (autojob.hpc.Partition attribute) ParallelizationPanel (class in autojob.coordinator.gui.job_submission) parameter_selection (autojob.coordinator.gui.gui.CoordinatorTabs attribute) ParameterInputFrame (class in autojob.coordinator.gui.parameter_selection) ParameterInputSection (class in autojob.coordinator.gui.parameter_selection) ParameterPanel (class in autojob.coordinator.gui.parameter_selection) ParameterRadiobuttonFrame (class in autojob.coordinator.gui.parameter_selection) ParameterSelectionCombobox (class in autojob.coordinator.gui.parameter_selection) ParameterSelectionTab (class in autojob.coordinator.gui.parameter_selection) PARAMETRIZATION_FILE (autojob.settings.AutojobSettings attribute) parametrizations (autojob.workflow.Step attribute) params (autojob.coordinator.gui.parameter_selection.ParameterSelectionTab property) parent (autojob.coordinator.gui.gui.GUI attribute) (autojob.coordinator.gui.job_submission.JobSubmissionTab attribute) (autojob.coordinator.gui.job_submission.MemoryPanel attribute) (autojob.coordinator.gui.job_submission.ParallelizationPanel attribute) (autojob.coordinator.gui.job_submission.PartitionPanel attribute) (autojob.coordinator.gui.job_submission.RunTimePanel attribute) (autojob.coordinator.gui.summary.SummaryTab attribute) parse_acf() (in module autojob.harvest.harvesters.bader) parse_job_stats_file() (in module autojob.utils) (in module autojob.utils.parsing) parse_max_rss() (autojob.coordinator.job.JobStats static method) parse_time_from_slurm_script() (in module autojob.utils.parsing)

part_panel (autojob.coordinator.gui.job_submission.JobSubmissionPanels attribute) partial_charges (autojob.harvest.harvesters.ddec6.DDEC6Analysis attribute) partition (autojob.hpc.SchedulerOutputs attribute) Partition (class in autojob.hpc) partition_enforcement() (autojob.coordinator.gui.job_submission.JobSubmissionTab method) PartitionPanel (class in autojob.coordinator.gui.job_submission) partitions (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) (autojob.coordinator.gui.job_submission.PartitionPanel attribute) (autojob.hpc.SchedulerInputs attribute) Patch (class in autojob.harvest.patch) patch_path (autojob.harvest.patch.Patch attribute) patch_task() (autojob.tasks.calculation.Calculation static method) patch_tasks() (in module autojob.harvest.patch) patch_value (autojob.harvest.patch.Patch attribute) PathLoadable (class in autojob.bases.task_base) PENDING (autojob.hpc.JobState attribute) place_input_sections() (autojob.coordinator.gui.parameter_selection.ParameterInputSection method) place_radio_buttons() (autojob.coordinator.gui.parameter_selection.ParameterRadiobuttonFrame method) placement() (autojob.coordinator.gui.widgets.RadiobuttonPanel method) populate() (autojob.coordinator.gui.submission_configuration.GroupSummary method) (autojob.coordinator.gui.summary.JobSummaryFrame method) positions (autojob.harvest.harvesters.bader.BaderAnalysis attribute) PREEMPTED (autojob.hpc.JobState attribute) prepare_input_atoms() (autojob.tasks.calculation.Calculation method) progression (autojob.workflow.Step attribute) PSI4 (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute)

Q

QCHEM (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute)

queued_time (autojob.coordinator.job.JobStats property)

R

RadiobuttonPanel (class in autojob.coordinator.gui.widgets) RAZI (autojob.hpc.Partition attribute) rcubed_moments (autojob.harvest.harvesters.ddec6.DDEC6Analysis attribute) RECORD_FILE (autojob.settings.AutojobSettings attribute) reference (autojob.harvest.mechanism.ElectrochemicalState attribute) register_plugin() (in module autojob.plugins) RELAXATION (autojob.coordinator.classification.CalculationType attribute) remove_items() (autojob.coordinator.gui.submission_configuration.ButtonFrame method) remove_panels() (autojob.coordinator.gui.job_submission.JobSubmissionTab method) remove_parameter_values() (autojob.coordinator.gui.parameter_selection.ParameterPanel method) remove_partitions() (autojob.coordinator.gui.job_submission.PartitionPanel method) remove_structures() (autojob.coordinator.gui.groups.StructureGroup method) (autojob.coordinator.gui.structure_selection.StructureSelectionFrame method) remove_structures_from_group() (autojob.coordinator.gui.structure_selection.GroupViewFrame method) remove_values() (autojob.coordinator.gui.groups.CalculationParameterGroup method) reorder_vasp_sequence() (in module autojob.utils.vasp) REQUEUED (autojob.hpc.JobState attribute) reset_cbs() (autojob.coordinator.gui.structure_selection.GroupButtonFrame method) RESIZING (autojob.hpc.JobState attribute) restart command line option ---no-recursive --auto-restart --calc-mod --carry-over --config --file-size-limit --name-template --no-auto-restart --no-submit --path --recursive --relaxed --sched-mod --strict --submit --verbose -a -c -L -p -R -S -v

restart() (in module autojob.next.restart) restart_limit (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) REVOKED (autojob.hpc.JobState attribute) rfourth_moments (autojob.harvest.harvesters.ddec6.DDEC6Analysis attribute) rng (autojob.tasks.mh.MHInitParams attribute) rsquared_moments (autojob.harvest.harvesters.ddec6.DDEC6Analysis attribute) rt_panel (autojob.coordinator.gui.job_submission.JobSubmissionPanels attribute) run command line option --buffer --frequency --time --time-source -b -f -T -t COMMAND run() (in module autojob.coordinator.gui.gui) run_jobs() (autojob.coordinator.coordinator.Coordinator method) run_time (autojob.coordinator.gui.job_submission.JobSubmissionParameters attribute) (autojob.coordinator.job.JobStats property) RUNNING (autojob.bases.task_base.TaskOutcome attribute) (autojob.hpc.JobState attribute) RunTimeDict (class in autojob.coordinator.gui.job_submission) RunTimePanel (class in autojob.coordinator.gui.job_submission)

S

scan_step (autojob.tasks.scan.BondScanInputs attribute) ScheduledMixin (class in autojob.hpc) SCHEDULER (autojob.settings.AutojobSettings attribute) scheduler_inputs (autojob.hpc.ScheduledMixin attribute) scheduler_outputs (autojob.hpc.ScheduledMixin attribute) SCHEDULER_STATS_FILE (autojob.settings.AutojobSettings attribute) SchedulerInputs (class in autojob.hpc) SchedulerOutputs (class in autojob.hpc) seconds (autojob.utils.parsing.TimedeltaTuple attribute) SelectionFrame (class in autojob.coordinator.gui.submission_configuration) SelectionPanel (class in autojob.coordinator.gui.submission_configuration) SENSITIVITY (autojob.coordinator.classification.StudyType attribute) (autojob.legacy.StudyType attribute) sensitivity_jobs (autojob.coordinator.coordinator.Coordinator property) SequenceParameter (class in autojob.coordinator.parameters) serialize_bond_scan_results() (autojob.tasks.scan.BondScanOutputs method) serialize_calculator_results() (autojob.tasks.calculation.CalculationOutputs method) serialize_date_created() (autojob.study.Study method) serialize_mail_type() (autojob.hpc.SchedulerInputs method) serialize_md_trajectory_results() (autojob.tasks.md.MDOutputs method) serialize_memory() (in module autojob.hpc) serialize_minima_results() (autojob.tasks.mh.MHOutputs method) serialize_partitions() (autojob.hpc.SchedulerInputs method) serialize_studies() (autojob.study_group.StudyGroup method) serialize_tasks() (autojob.study.Study method) serialize_time() (in module autojob.hpc) serialize_trajectory_results() (autojob.tasks.mh.MHOutputs method) set_input_value() (autojob.parametrizations.VariableReference method) set_parameter_entry_method() (autojob.coordinator.gui.parameter_selection.ParameterPanel method) set_states() (autojob.coordinator.gui.parameter_selection.ParameterPanel method) (autojob.coordinator.gui.widgets.RadiobuttonPanel method) set_task_class() (autojob.bases.task_base.SetTaskClassMixin method) SetTaskClassMixin (class in autojob.bases.task_base) settings_customise_sources() (autojob.settings.AutojobSettings class method) SIESTA (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) SINGLE (autojob.hpc.Partition attribute) source (autojob.coordinator.filters.Filter attribute) space_capitalize() (in module autojob.utils.schemas) SpecButton (class in autojob.coordinator.gui.submission_configuration) special_values (autojob.coordinator.parameters.CalculatorParameter property) specials (autojob.coordinator.job.CalculationParameter property) spin_moments (autojob.harvest.harvesters.ddec6.DDEC6Analysis attribute) spin_polarization (autojob.harvest.harvesters.ddec6.BondedToDict attribute) start_time (autojob.coordinator.job.JobStats attribute) state (autojob.hpc.SchedulerOutputs attribute) Step (class in autojob.workflow) steps (autojob.tasks.md.MDRunParams attribute) stoich (autojob.harvest.mechanism.ElectrochemicalState attribute) STRICT_MODE (autojob.settings.AutojobSettings attribute) structure_groups (autojob.coordinator.coordinator.Coordinator property) (autojob.coordinator.gui.structure_selection.GroupButtonFrame property) structure_groups_with() (autojob.coordinator.coordinator.Coordinator method)

structure_selection (autojob.coordinator.gui.gui.CoordinatorTabs attribute) StructureGroup (class in autojob.coordinator.gui.groups) structures (autojob.coordinator.coordinator.Coordinator property) (autojob.coordinator.gui.groups.StructureGroup property) (autojob.coordinator.gui.structure_selection.StructureSelectionFrame property) (autojob.coordinator.gui.submission_configuration.SelectionFrame property) structures_without_calc_params (autojob.coordinator.coordinator.Coordinator property) structures_without_subm_params (autojob.coordinator.coordinator.Coordinator property) StructureSelectionFrame (class in autojob.coordinator.gui.structure_selection) StructureSelectionPanel (class in autojob.coordinator.gui.structure_selection) (class in autojob.coordinator.gui.submission_configuration) StructureSelectionTab (class in autojob.coordinator.gui.structure_selection) studies (autojob.coordinator.coordinator.Coordinator property) (autojob.study_group.StudyGroup attribute) Study (class in autojob.study) study_configuration (autojob.coordinator.gui.gui.CoordinatorTabs attribute) study_group_id (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.study.Study attribute) (autojob.study_group.StudyGroup attribute) (autojob.tasks.task.TaskMetadata attribute) STUDY_GROUP_METADATA_FILE (autojob.settings.AutojobSettings attribute) study_id (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.study.Study attribute) (autojob.tasks.task.TaskMetadata attribute) STUDY_METADATA_FILE (autojob.settings.AutojobSettings attribute) study_summary (autojob.coordinator.gui.summary.SummaryFrames attribute) study_type (autojob.coordinator.coordinator.Coordinator property) StudyConfigurationTab (class in autojob.coordinator.gui.study_configuration) StudyGroup (class in autojob.study_group) StudyPanel (class in autojob.coordinator.gui.study_configuration) StudySummaryFrame (class in autojob.coordinator.gui.summary) StudyType (class in autojob.coordinator.classification) (class in autojob.legacy) subm_params (autojob.coordinator.coordinator.Coordinator property) subm_params_for() (autojob.coordinator.coordinator.Coordinator method) submission_configuration (autojob.coordinator.gui.gui.CoordinatorTabs attribute) submission_group_to_filters() (in module autojob.coordinator.filters) submission_parameter_groups (autojob.coordinator.coordinator.Coordinator property) (autojob.coordinator.gui.submission_configuration.GroupButtonFrame property) submission_parameters (autojob.coordinator.gui.job_submission.JobSubmissionTab property) submission_parameters_to_scheduler_inputs() (in module autojob.coordinator.coordinator) SubmissionConfigurationTab (class in autojob.coordinator.gui.submission_configuration) SubmissionParameterGroup (class in autojob.coordinator.gui.groups) submit_new_task() (in module autojob.next) submit_time (autojob.coordinator.job.JobStats attribute) substitute_context() (in module autojob.next) substitute_placeholders() (in module autojob.utils.templates) SUCCESS (autojob.bases.task_base.TaskOutcome attribute) summaries (autojob.coordinator.gui.summary.SummaryTab attribute) summary (autojob.coordinator.gui.gui.CoordinatorTabs attribute) SummaryFrame (class in autojob.coordinator.gui.summary) SummaryFrames (class in autojob.coordinator.gui.summary) SummaryTab (class in autojob.coordinator.gui.summary) SUSPENDED (autojob.hpc.JobState attribute)

T

T0 (autojob.tasks.mh.MHInitParams attribute) tabs (autojob.coordinator.gui.gui.GUI attribute) tags (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.tasks.task.TaskMetadata attribute) Task (class in autojob.tasks.task) task_class (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.tasks.task.TaskMetadata attribute) (autojob.workflow.Step attribute) task_group_id (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.tasks.task.TaskMetadata attribute) TASK_GROUP_METADATA_FILE (autojob.settings.AutojobSettings attribute) task_id (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.tasks.task.TaskMetadata attribute) task_inputs (autojob.bases.task_base.TaskBase attribute) (autojob.tasks.task.Task attribute) task_metadata (autojob.bases.task_base.TaskBase attribute) (autojob.tasks.task.Task attribute) TASK_METADATA_FILE (autojob.settings.AutojobSettings attribute) task_outputs (autojob.bases.task_base.TaskBase attribute) (autojob.tasks.task.Task attribute) task_script (autojob.bases.task_base.TaskInputsBase attribute) (autojob.tasks.task.TaskInputs attribute) task_script_template (autojob.bases.task_base.TaskInputsBase attribute) TASK_SCRIPT_TEMPLATE (autojob.settings.AutojobSettings attribute) task_script_template (autojob.tasks.task.TaskInputs attribute) TaskBase (class in autojob.bases.task_base) TaskInputs (class in autojob.tasks.task) TaskInputsBase (class in autojob.bases.task_base) TaskMetadata (class in autojob.tasks.task)

TaskMetadataBase (class in autojob.bases.task_base) TaskOutcome (class in autojob.bases.task_base) TaskOutputs (class in autojob.tasks.task) TaskOutputsBase (class in autojob.bases.task_base) tasks (autojob.study.Study attribute) TEMPLATE coordinator command line option TEMPLATE_DIR (autojob.settings.AutojobSettings attribute) template_script() (in module autojob.utils.files) time (autojob.hpc.SchedulerInputs attribute) TIME_LIMIT (autojob.coordinator.job.JobError attribute) time_limit (autojob.hpc.Partition property) TimedeltaTuple (class in autojob.utils.parsing) TIMEOUT (autojob.hpc.JobState attribute) timestep (autojob.tasks.md.MDInitParams attribute) (autojob.tasks.mh.MHInitParams attribute) TIP3P (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) TIP4P (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) to_directory() (autojob.study.Study method) (autojob.study_group.StudyGroup method) to_slurm_time() (autojob.utils.parsing.TimedeltaTuple method) to_timedelta() (autojob.utils.parsing.TimedeltaTuple method) totalsteps (autojob.tasks.mh.MHRunParams attribute) traj_template (autojob.tasks.scan.BondScanInputs attribute) trajectory (autojob.tasks.md.MDInitParams attribute) TreeviewFrame (class in autojob.coordinator.gui.widgets) TURBOMOLE (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute)

U

UNKNOWN (autojob.bases.task_base.TaskOutcome attribute) (autojob.hpc.JobState attribute) update() (autojob.coordinator.gui.groups.SubmissionParameterGroup method) update_groups() (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method) update_limit() (autojob.coordinator.gui.job_submission.AutoRestartPanel method) update_panels() (autojob.coordinator.gui.job_submission.JobSubmissionTab method)

update_parallelization() (autojob.coordinator.gui.job_submission.ParallelizationPanel method) update_parameters() (autojob.coordinator.gui.job_submission.JobSubmissionTab method) update_values() (autojob.hpc.SchedulerInputs static method) uri (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.tasks.task.TaskMetadata attribute) use_default() (autojob.coordinator.gui.parameter_selection.ParameterPanel method)

V

vacuum_charge (autojob.harvest.harvesters.bader.BaderAnalysis attribute) vacuum_volume (autojob.harvest.harvesters.bader.BaderAnalysis attribute) val_to_native() (in module autojob.coordinator.validation) (in module autojob.utils) validate() (autojob.coordinator.job.CalculationParameter method) (autojob.coordinator.parameters.CalculatorParameter method) (autojob.coordinator.parameters.MappingParameter method) (autojob.coordinator.parameters.NumberMappingParameter method) (autojob.coordinator.parameters.NumberParameter method) (autojob.coordinator.parameters.NumberSequenceParameter method) (autojob.coordinator.parameters.SequenceParameter method) validate_bond_scan_params() (autojob.tasks.scan.BondScanInputs class method) validate_ids() (autojob.tasks.task.TaskMetadata class method) validate_job_state() (autojob.hpc.SchedulerOutputs class method) validate_log_level() (autojob.settings.AutojobSettings class method) validate_mail_type() (autojob.hpc.SchedulerInputs class method) validate_memory() (autojob.coordinator.gui.job_submission.MemoryPanel method) (in module autojob.hpc) validate_number() (autojob.coordinator.parameters.NumberRange method) validate_partitions() (autojob.hpc.SchedulerInputs class method) validate_structures() (autojob.coordinator.gui.groups.StructureGroup static method) validate_time() (in module autojob.hpc)

validated_structures() (autojob.coordinator.gui.groups.StructureGroup method) values (autojob.coordinator.filters.Filter attribute) (autojob.coordinator.gui.groups.CalculationParameterGroup property) (autojob.coordinator.gui.groups.SubmissionParameterGroup property) (autojob.coordinator.gui.submission_configuration.SelectionFrame property) (autojob.coordinator.job.CalculationParameter property) ValueSelectionPanel (class in autojob.coordinator.gui.submission_configuration) VariableReference (class in autojob.parametrizations) VASP (autojob.coordinator.classification.CalculatorType attribute) (autojob.coordinator.parameters.CalculatorType attribute) VASP_KEEP_DOS (autojob.settings.AutojobSettings attribute) VaspError VaspJob (class in autojob.coordinator.vasp) VIB (autojob.coordinator.classification.CalculationType attribute) vib_energies (autojob.tasks.vibration.VibrationOutputs attribute) Vibration (class in autojob.tasks.vibration) vibration_inputs (autojob.tasks.vibration.Vibration attribute) vibration_outputs (autojob.tasks.vibration.Vibration attribute) VibrationInputs (class in autojob.tasks.vibration) VibrationOutputs (class in autojob.tasks.vibration) view_groups() (autojob.coordinator.gui.submission_configuration.GroupButtonFrame method) ViewFrame (class in autojob.coordinator.gui.submission_configuration)

W

wall_time (autojob.coordinator.job.JobStats property) warnings (autojob.coordinator.gui.summary.SummaryFrames attribute) (autojob.coordinator.gui.summary.WarningsFrame attribute) WarningsFrame (class in autojob.coordinator.gui.summary) Workflow (class in autojob.workflow) WORKFLOW_FILE (autojob.settings.AutojobSettings attribute) workflow_step_id (autojob.bases.task_base.TaskMetadataBase attribute) (autojob.tasks.task.TaskMetadata attribute) (autojob.workflow.Step attribute) write_calculation_script() (autojob.tasks.calculation.Calculation method) write_input_atoms() (autojob.tasks.calculation.Calculation method) (autojob.tasks.task.Task method) write_inputs() (autojob.bases.task_base.InputWriter method) (autojob.bases.task_base.TaskBase method) (autojob.tasks.calculation.Calculation method) (autojob.tasks.task.Task method)

write_inputs_json() (autojob.tasks.calculation.Calculation method) (autojob.tasks.md.MolecularDynamics method) (autojob.tasks.mh.MinimaHopping method) (autojob.tasks.scan.BondScan method) (autojob.tasks.task.Task method) (autojob.tasks.vibration.Vibration method) write_metadata() (autojob.tasks.task.Task method) write_task_script() (autojob.tasks.calculation.Calculation method) (autojob.tasks.task.Task method) write_traj (autojob.tasks.scan.BondScanInputs attribute)

Z

zero_point_energy (autojob.tasks.vibration.VibrationOutputs attribute)