Index

Symbols

--add-to-known matflow-demo-workflow-go command line option matflow-go command line option matflow-workflow-WORKFLOW_REF-submit command line option --all matflow-config-get command line option matflow-demo-data-cache command line option --backup matflow-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option matflow-workflow-WORKFLOW_REF-rechunk-runs command line option --cancel matflow-demo-workflow-go command line option matflow-go command line option matflow-workflow-WORKFLOW_REF-submit command line option --chunk-size matflow-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option matflow-workflow-WORKFLOW_REF-rechunk-runs command line option --config-dir matflow command line option matflow-manage-get-config-path command line option matflow-manage-reset-config command line option --config-key matflow command line option --defaults matflow-config-add-scheduler command line option matflow-config-add-shell command line option matflow-config-add-shell-wsl command line option --doc matflow-demo-workflow-copy command line option matflow-demo-workflow-show command line option --element matflow-workflow-WORKFLOW_REF-abort-run command line option --env-source-file matflow-configure-env command line option --exclude-os matflow-submission-shell-info command line option --file matflow-config-get command line option matflow-helper-pid command line option --format matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option --full matflow-show command line option --help matflow command line option --hostname matflow-manage-clear-cache command line option --hpcflow-version matflow command line option --include-execute matflow-workflow-WORKFLOW_REF-zip command line option matflow-zip command line option --include-rechunk-backups matflow-workflow-WORKFLOW_REF-zip command line option matflow-zip command line option --infile1 matflow-demo-software-doSomething command line option --infile2 matflow-demo-software-doSomething command line option --jobscripts matflow-workflow-WORKFLOW_REF-wait command line option --js-parallelism matflow-demo-workflow-go command line option matflow-go command line option matflow-workflow-WORKFLOW_REF-submit command line option --json matflow-config-append command line option matflow-config-prepend command line option matflow-config-set command line option matflow-config-update command line option matflow-submission-get-known command line option --legend matflow-show command line option --list matflow-demo-data command line option matflow-demo-workflow command line option --log matflow-unzip command line option matflow-workflow-WORKFLOW_REF-unzip command line option matflow-workflow-WORKFLOW_REF-zip command line option matflow-zip command line option --max-recent matflow-show command line option --metadata matflow-config-get command line option --name matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option matflow-open-env-source command line option --new matflow-config-import command line option --no-add-to-known matflow-demo-workflow-go command line option matflow-go command line option matflow-workflow-WORKFLOW_REF-submit command line option --no-backup matflow-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option matflow-workflow-WORKFLOW_REF-rechunk-runs command line option --no-callback matflow-config command line option --no-doc matflow-demo-workflow-copy command line option matflow-demo-workflow-show command line option --no-rename matflow-config-import command line option --no-status matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option matflow-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option matflow-workflow-WORKFLOW_REF-rechunk-runs command line option matflow-workflow-WORKFLOW_REF-submit command line option --no-syntax matflow-demo-workflow-show command line option --no-update matflow-show command line option --os-info matflow-submission command line option --out matflow-demo-software-doSomething command line option --overwrite matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option matflow-workflow-WORKFLOW_REF-zip command line option matflow-zip command line option

--path matflow-config-init command line option matflow-config-open command line option matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option matflow-open-config command line option matflow-open-demo-data-cache-dir command line option matflow-open-env-source command line option matflow-open-known-subs command line option matflow-open-log command line option matflow-open-user-cache-dir command line option matflow-open-user-cache-hostname-dir command line option matflow-open-user-data-dir command line option matflow-open-user-data-hostname-dir command line option matflow-open-user-runtime-dir command line option matflow-open-workflow command line option matflow-unzip command line option matflow-workflow-WORKFLOW_REF-unzip command line option matflow-workflow-WORKFLOW_REF-zip command line option matflow-zip command line option --print-idx matflow-demo-workflow-go command line option matflow-go command line option matflow-workflow-WORKFLOW_REF-submit command line option --ref-type matflow-cancel command line option matflow-open-workflow command line option matflow-rechunk command line option matflow-workflow command line option matflow-zip command line option --rename matflow-config-import command line option --run-time-info matflow command line option --setup matflow-configure-env command line option --status matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option matflow-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk command line option matflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option matflow-workflow-WORKFLOW_REF-rechunk-runs command line option matflow-workflow-WORKFLOW_REF-submit command line option --stderr matflow-internal-workflow-PATH-save-parameter command line option --store matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option --string matflow-go command line option matflow-make command line option --submission matflow-workflow-WORKFLOW_REF-abort-run command line option --syntax matflow-demo-workflow-show command line option --task matflow-workflow-WORKFLOW_REF-abort-run command line option --tasks matflow-demo-workflow-go command line option matflow-go command line option matflow-workflow-WORKFLOW_REF-submit command line option --timeit matflow command line option --timeit-file matflow command line option --timeout matflow-helper-restart command line option matflow-helper-run command line option matflow-helper-start command line option --timeout-check-interval matflow-helper-restart command line option matflow-helper-run command line option matflow-helper-start command line option --ts-fmt matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option --ts-name-fmt matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option --use-current-env matflow-configure-env command line option --value matflow-demo-software-doSomething command line option --var matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option --version matflow command line option --wait matflow-demo-workflow-go command line option matflow-go command line option matflow-workflow-WORKFLOW_REF-submit command line option --watch-interval matflow-helper-restart command line option matflow-helper-run command line option matflow-helper-start command line option --with-config matflow command line option -f matflow-helper-pid command line option matflow-show command line option -i1 matflow-demo-software-doSomething command line option -i2 matflow-demo-software-doSomething command line option -j matflow-workflow-WORKFLOW_REF-wait command line option -l matflow-demo-data command line option matflow-demo-workflow command line option -o matflow-demo-software-doSomething command line option -r matflow-cancel command line option matflow-open-workflow command line option matflow-rechunk command line option matflow-show command line option matflow-workflow command line option matflow-zip command line option -v matflow-demo-software-doSomething command line option matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-go command line option matflow-make command line option

A

A (matflow.param_classes.orientations.LatticeDirection attribute) A_STAR (matflow.param_classes.orientations.LatticeDirection attribute) abort_EARs_file_name (matflow.Submission property) abort_EARs_file_path (matflow.Submission property) abort_run() (matflow.Workflow method) abortable (matflow.InputFileGenerator attribute) (matflow.OutputFileParser attribute) Action (class in matflow) action (matflow.ElementAction property) (matflow.ElementActionRun property) action_idx (matflow.ElementAction property) action_runs (matflow.Element property) (matflow.ElementIteration property) ActionEnvironment (class in matflow) ActionRule (class in matflow) actions (matflow.Element property) (matflow.ElementIteration property) ActionScope (class in matflow) ActionScopeType (class in matflow) add_elements() (matflow.WorkflowTask method) add_group() (matflow.Task method) add_iteration() (matflow.WorkflowLoop method) add_loop() (matflow.Workflow method) add_object() (matflow.CommandFilesList method) (matflow.EnvironmentsList method) (matflow.ExecutablesList method) (matflow.GroupList method) (matflow.ParametersList method) (matflow.ResourceList method) (matflow.TaskList method) (matflow.TaskSchemasList method) (matflow.TaskTemplateList method) (matflow.WorkflowLoopList method) (matflow.WorkflowTaskList method) add_objects() (matflow.CommandFilesList method) (matflow.EnvironmentsList method) (matflow.ExecutablesList method) (matflow.GroupList method) (matflow.ParametersList method) (matflow.TaskList method) (matflow.TaskSchemasList method) (matflow.TaskTemplateList method) (matflow.WorkflowLoopList method) (matflow.WorkflowTaskList method) add_submission() (matflow.Workflow method) add_task() (matflow.Workflow method) add_task_after() (matflow.Workflow method) add_task_before() (matflow.Workflow method) additive_factor (matflow.ValuePerturbation attribute) address (matflow.SubParameter attribute) all_EAR_IDs (matflow.Jobscript property) (matflow.Submission property) all_EARs (matflow.Jobscript property) (matflow.Submission property) all_labelled_types (matflow.SchemaInput property) all_schema_actions() (matflow.Task method) all_schema_input_normalised_paths (matflow.Task property) all_schema_input_types (matflow.Task property) all_schema_inputs (matflow.Task property) all_schema_output_types (matflow.Task property) all_schema_outputs (matflow.Task property) all_sourced_normalised_paths (matflow.Task property) ALLOWED_PARAMETERS (matflow.ResourceSpec attribute)

ANY (matflow.ActionScopeType attribute) (matflow.TaskSourceType attribute) any() (matflow.ActionScope class method) app (in module matflow) (matflow.Action attribute) (matflow.ActionEnvironment attribute) (matflow.ActionRule attribute) (matflow.ActionScope attribute) (matflow.Command attribute) (matflow.DirectPosix attribute) (matflow.DirectWindows attribute) (matflow.Element attribute) (matflow.ElementAction attribute) (matflow.ElementActionRun attribute) (matflow.ElementFilter attribute) (matflow.ElementGroup attribute) (matflow.ElementIteration attribute) (matflow.ElementParameter attribute) (matflow.ElementPropagation attribute) (matflow.ElementResources attribute) (matflow.ElementSet attribute) (matflow.Environment attribute) (matflow.Executable attribute) (matflow.ExecutableInstance attribute) (matflow.FileNameExt attribute) (matflow.FileNameSpec attribute) (matflow.FileNameStem attribute) (matflow.FileSpec attribute) (matflow.InputFile attribute) (matflow.InputFileGenerator attribute) (matflow.InputFileGeneratorSource attribute) (matflow.InputSource attribute) (matflow.InputValue attribute) (matflow.Jobscript attribute) (matflow.Loop attribute) (matflow.NumCores attribute) (matflow.OutputFileParser attribute) (matflow.OutputFileParserSource attribute) (matflow.OutputLabel attribute) (matflow.Parameter attribute) (matflow.ParameterPath attribute) (matflow.ResourceSpec attribute) (matflow.Rule attribute) (matflow.RunDirAppFiles attribute) (matflow.SchemaInput attribute) (matflow.SchemaOutput attribute) (matflow.SchemaParameter attribute) (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) (matflow.Submission attribute) (matflow.Task attribute) (matflow.TaskObjective attribute) (matflow.TaskSchema attribute) (matflow.ValuePerturbation attribute) (matflow.ValueSequence attribute) (matflow.Workflow attribute) (matflow.WorkflowLoop attribute) (matflow.WorkflowLoopList attribute) (matflow.WorkflowTask attribute) (matflow.WorkflowTaskList attribute) (matflow.WorkflowTemplate attribute) arguments (matflow.Command attribute) artifacts_path (matflow.Workflow property) as_base() (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters method)

B

B (matflow.param_classes.orientations.LatticeDirection attribute) B_STAR (matflow.param_classes.orientations.LatticeDirection attribute) base (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters property) basic_info (matflow.TaskSchema property)

batch_update() (matflow.Workflow method) biaxial() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) box_size (matflow.param_classes.seeds.MicrostructureSeeds attribute) BUNGE (matflow.param_classes.orientations.EulerDefinition attribute)

C

C (matflow.param_classes.orientations.LatticeDirection attribute) C_STAR (matflow.param_classes.orientations.LatticeDirection attribute) cancel() (in module matflow) (matflow.Jobscript method) (matflow.Submission method) (matflow.Workflow method) cancel_jobs() (matflow.DirectPosix method) (matflow.DirectWindows method) (matflow.SGEPosix method) (matflow.SlurmPosix method) check_exists() (matflow.ActionRule class method) check_loop_termination() (matflow.Workflow method) check_missing() (matflow.ActionRule class method) check_parameters_exist() (matflow.Workflow method) clean_up (matflow.OutputFileParser attribute) CMD_FILES_RE_PATTERN (matflow.RunDirAppFiles attribute) CMD_IDX matflow-internal-workflow-PATH-save-parameter command line option

Command (class in matflow) command (matflow.Command attribute) (matflow.ExecutableInstance attribute) CommandFilesList (class in matflow) commands_idx (matflow.ElementActionRun property) compose_commands() (matflow.ElementActionRun method) compose_jobscript() (matflow.Jobscript method) compose_source() (matflow.Action method) (matflow.InputFileGenerator method) (matflow.OutputFileParser method) contents (matflow.InputFile property) (matflow.InputFileGeneratorSource property) (matflow.OutputFileParserSource property) copy() (matflow.Workflow method) copy_non_persistent() (matflow.ResourceSpec method) creation_info (matflow.Workflow property)

D

data (matflow.param_classes.orientations.Orientations attribute) data_idx (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.ElementParameter property) data_idx_is_set (matflow.ElementParameter property) DEF_GRAD_RATE (matflow.param_classes.load.StrainRateMode attribute) DEFAULT (matflow.InputSourceType attribute) default (matflow.Parameters attribute) default() (matflow.InputSource class method) DEFAULT_ARRAY_ITEM_VAR (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) DEFAULT_ARRAY_SWITCH (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) DEFAULT_CWD_SWITCH (matflow.SGEPosix attribute) DEFAULT_DEL_CMD (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) DEFAULT_JS_CMD (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) DEFAULT_LOGIN_NODE_MATCH (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) DEFAULT_LOGIN_NODES_CMD (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) DEFAULT_SHEBANG_ARGS (matflow.DirectPosix attribute) (matflow.DirectWindows attribute) (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) DEFAULT_SHELL_ARGS (matflow.DirectPosix attribute) (matflow.DirectWindows attribute) (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) DEFAULT_SHELL_EXECUTABLE (matflow.DirectPosix attribute) (matflow.DirectWindows attribute) (matflow.SlurmPosix attribute) DEFAULT_SHOW_CMD (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute)

DEFAULT_SUBMIT_CMD (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) default_value (matflow.SchemaInput property) defined_input_types (matflow.ElementSet property) (matflow.Task property) delete() (matflow.Workflow method) dependencies (matflow.Jobscript property) DESTINATION matflow-demo-data-copy command line option matflow-demo-workflow-copy command line option dir_diff (matflow.ElementActionRun property) dir_name (matflow.Element property) (matflow.Task property) (matflow.WorkflowTask property) direct_stderr_file_name (matflow.Jobscript property) direct_stderr_path (matflow.Jobscript property) direct_stdout_file_name (matflow.Jobscript property) direct_stdout_path (matflow.Jobscript property) direct_win_pid_file_name (matflow.Jobscript property) direct_win_pid_file_path (matflow.Jobscript property) DirectPosix (class in matflow) DirectWindows (class in matflow) doc (matflow.WorkflowTemplate attribute) downstream_tasks (matflow.WorkflowLoop property) (matflow.WorkflowTask property) dump_to_HDF5_group() (matflow.param_classes.load.LoadCase method) (matflow.param_classes.load.LoadStep method) (matflow.param_classes.orientations.OrientationRepresentation method) (matflow.param_classes.orientations.Orientations method) (matflow.param_classes.orientations.UnitCellAlignment method) (matflow.param_classes.seeds.MicrostructureSeeds method) (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters method) (matflow.ParameterValue method)

E

EAR_ID matflow-internal-workflow-PATH-check-loop command line option matflow-internal-workflow-PATH-get-ear-skipped command line option matflow-internal-workflow-PATH-save-parameter command line option matflow-internal-workflow-PATH-set-ear-end command line option matflow-internal-workflow-PATH-set-ear-skip command line option matflow-internal-workflow-PATH-set-ear-start command line option matflow-internal-workflow-PATH-write-commands command line option EAR_ID (matflow.Jobscript property) EAR_ID_file_name (matflow.Jobscript property) EAR_ID_file_path (matflow.Jobscript property) EAR_IDs (matflow.ElementIteration property) EAR_IDs_flat (matflow.ElementIteration property) EARs_by_elements (matflow.Submission property) EARs_initialised (matflow.ElementIteration property) elem_iter_IDs (matflow.ElementSet property) Element (class in matflow) element (matflow.ElementAction property) (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.ElementParameter attribute) element_action (matflow.ElementActionRun property) element_IDs (matflow.WorkflowTask property) element_iteration (matflow.ElementAction property) (matflow.ElementActionRun property) element_iterations (matflow.ElementSet property) element_local_idx_range (matflow.ElementSet property) element_run_dir_file_name (matflow.Jobscript property) element_run_dir_file_path (matflow.Jobscript property) element_set (matflow.Element property) (matflow.ElementPropagation property) (matflow.ResourceList property) (matflow.ResourceSpec property) element_set_idx (matflow.Element property) element_sets (matflow.Task property) ElementAction (class in matflow) ElementActionRun (class in matflow) ElementFilter (class in matflow) ElementGroup (class in matflow) ElementInputFiles (class in matflow) ElementInputs (class in matflow) ElementIteration (class in matflow) ElementOutputFiles (class in matflow) ElementOutputs (class in matflow) ElementParameter (class in matflow) ElementPropagation (class in matflow)

ElementRepeats (class in matflow) ElementResources (class in matflow) Elements (class in matflow) elements (matflow.ElementSet property) (matflow.WorkflowTask property) elements() (matflow.Workflow method) ElementSet (class in matflow) end_time (matflow.ElementActionRun property) (matflow.Jobscript property) (matflow.Submission property) ensure_element_sets() (matflow.ElementSet class method) ensure_input_sources() (matflow.WorkflowTask method) env_presets (matflow.WorkflowTemplate attribute) env_spec (matflow.ElementActionRun property) Environment (class in matflow) environment (matflow.ActionEnvironment attribute) (matflow.Executable property) (matflow.ExecutablesList attribute) (matflow.InputFileGenerator attribute) (matflow.OutputFileParser attribute) environments (matflow.ElementResources attribute) (matflow.ResourceSpec property) (matflow.Submission property) (matflow.WorkflowTemplate attribute) EnvironmentsList (class in matflow) EULER (matflow.param_classes.orientations.OrientationRepresentationType attribute) euler_definition (matflow.param_classes.orientations.OrientationRepresentation attribute) euler_is_degrees (matflow.param_classes.orientations.OrientationRepresentation attribute) EulerDefinition (class in matflow.param_classes.orientations) example_uniaxial() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) Executable (class in matflow) executable (matflow.Command attribute) ExecutableInstance (class in matflow) ExecutablesList (class in matflow) execution_path (matflow.Workflow property) EXIT_CODE matflow-internal-workflow-PATH-set-ear-end command line option exit_code (matflow.ElementActionRun property) expand() (matflow.Action method) EXPLICIT (matflow.ParameterPropagationMode attribute) ext (matflow.FileNameSpec property) (matflow.FileSpec property) extension (matflow.InputFile property) (matflow.InputFileGeneratorSource property) (matflow.OutputFileParserSource property)

F

FILE_NAME matflow-demo-data-cache command line option matflow-demo-data-copy command line option file_name (matflow.FileNameExt attribute) (matflow.FileNameStem attribute) FILE_PATH matflow-config-import command line option FileNameExt (class in matflow) FileNameSpec (class in matflow) FileNameStem (class in matflow) FileSpec (class in matflow) filter() (matflow.ElementFilter method) filter_instances() (matflow.Executable method) format_array_request() (matflow.SGEPosix method) (matflow.SlurmPosix method) format_core_request_lines() (matflow.SGEPosix method) (matflow.SlurmPosix method) format_options() (matflow.SGEPosix method) (matflow.SlurmPosix method) format_std_stream_file_option_lines() (matflow.SGEPosix method) (matflow.SlurmPosix method) format_switch() (matflow.SGEPosix method) (matflow.SlurmPosix method) from_file() (matflow.param_classes.orientations.Orientations class method) (matflow.param_classes.seeds.MicrostructureSeeds class method) (matflow.ValueSequence class method) (matflow.Workflow class method) (matflow.WorkflowTemplate class method) from_geometric_space() (matflow.ValueSequence class method) from_hex_convention_DAMASK() (matflow.param_classes.orientations.UnitCellAlignment class method) from_hex_convention_MTEX() (matflow.param_classes.orientations.UnitCellAlignment class method) from_JSON_file() (matflow.Workflow class method) (matflow.WorkflowTemplate class method) from_json_like() (matflow.Action class method) (matflow.ActionEnvironment class method) (matflow.ActionRule class method) (matflow.ActionScope class method) (matflow.Command class method) (matflow.CommandFilesList class method) (matflow.ElementFilter class method) (matflow.ElementGroup class method) (matflow.ElementResources class method) (matflow.ElementSet class method) (matflow.Environment class method) (matflow.EnvironmentsList class method) (matflow.Executable class method) (matflow.ExecutableInstance class method) (matflow.ExecutablesList class method) (matflow.FileNameExt class method) (matflow.FileNameSpec class method) (matflow.FileNameStem class method) (matflow.FileSpec class method) (matflow.GroupList class method) (matflow.InputFile class method) (matflow.InputFileGenerator class method) (matflow.InputFileGeneratorSource class method) (matflow.InputSource class method) (matflow.InputValue class method) (matflow.Jobscript class method) (matflow.Loop class method) (matflow.NumCores class method) (matflow.OutputFileParser class method) (matflow.OutputFileParserSource class method) (matflow.OutputLabel class method)

from_JSON_like() (matflow.param_classes.orientations.Orientations class method) (matflow.param_classes.seeds.MicrostructureSeeds class method) from_json_like() (matflow.Parameter class method) (matflow.ParameterPath class method) (matflow.ParametersList class method) (matflow.ResourceList class method) (matflow.ResourceSpec class method) (matflow.Rule class method) (matflow.SchemaInput class method) (matflow.SchemaOutput class method) (matflow.SchemaParameter class method) (matflow.Submission class method) (matflow.Task class method) (matflow.TaskList class method) (matflow.TaskObjective class method) (matflow.TaskSchema class method) (matflow.TaskSchemasList class method) (matflow.TaskTemplateList class method) (matflow.ValuePerturbation class method) (matflow.ValueSequence class method) (matflow.WorkflowLoopList class method) (matflow.WorkflowTaskList class method) (matflow.WorkflowTemplate class method) from_JSON_string() (matflow.Workflow class method) (matflow.WorkflowTemplate class method) from_linear_space() (matflow.ValueSequence class method) from_log_space() (matflow.ValueSequence class method) from_random() (matflow.param_classes.orientations.Orientations class method) (matflow.param_classes.seeds.MicrostructureSeeds class method) from_random_uniform() (matflow.ValueSequence class method) from_range() (matflow.ValueSequence class method) from_rectangle() (matflow.ValueSequence class method) from_spec() (matflow.ExecutableInstance class method) (matflow.ValuePerturbation class method) from_string() (matflow.InputSource class method) from_template() (matflow.Workflow class method) from_template_data() (matflow.Workflow class method) from_YAML_file() (matflow.Workflow class method) (matflow.WorkflowTemplate class method) from_YAML_string() (matflow.Workflow class method) (matflow.WorkflowTemplate class method)

G

generate_data_index() (matflow.Action method) generate_new_elements() (matflow.WorkflowTask method) get() (matflow.CommandFilesList method) (matflow.Element method) (matflow.ElementAction method) (matflow.ElementActionRun method) (matflow.ElementIteration method) (matflow.EnvironmentsList method) (matflow.ExecutablesList method) (matflow.GroupList method) (matflow.ParametersList method) (matflow.ResourceList method) (matflow.TaskList method) (matflow.TaskSchemasList method) (matflow.TaskTemplateList method) (matflow.WorkflowLoopList method) (matflow.WorkflowTask method) (matflow.WorkflowTaskList method) get_action_rules() (matflow.InputFileGenerator method) (matflow.OutputFileParser method) get_active_jobscripts() (matflow.Submission method) get_active_states() (matflow.Jobscript method) get_all() (matflow.CommandFilesList method) (matflow.EnvironmentsList method) (matflow.ExecutablesList method) (matflow.GroupList method) (matflow.ParametersList method) (matflow.ResourceList method) (matflow.TaskList method) (matflow.TaskSchemasList method) (matflow.TaskTemplateList method) (matflow.WorkflowLoopList method) (matflow.WorkflowTaskList method) get_all_EARs() (matflow.Workflow method) get_all_element_iterations() (matflow.Workflow method) (matflow.WorkflowTask method) get_all_elements() (matflow.Workflow method) get_all_parameter_data() (matflow.Workflow method) get_all_parameter_sources() (matflow.Workflow method) get_all_parameters() (matflow.Workflow method) get_all_previous_iteration_runs() (matflow.ElementActionRun method) get_all_submission_run_IDs() (matflow.Workflow method) get_available_task_input_sources() (matflow.Task method) get_by_key() (matflow.TaskSchema class method) get_child_loops() (matflow.WorkflowLoop method) get_command_input_file_labels() (matflow.Action method) get_command_input_types() (matflow.Action method) get_command_line() (matflow.Command method) get_command_output_types() (matflow.Action method) get_commands_action_env() (matflow.Action method) get_commands_file_name() (matflow.Jobscript method) (matflow.RunDirAppFiles class method) get_data_idx() (matflow.Element method) (matflow.ElementAction method) (matflow.ElementActionRun method) (matflow.ElementIteration method) get_default_os_name() (matflow.ElementResources static method) get_default_scheduler() (matflow.ElementResources class method) get_default_shell() (matflow.ElementResources class method) get_defined_parameter_types() (matflow.ElementSet method) get_defined_sub_parameter_types() (matflow.ElementSet method) get_dependent_EARs() (matflow.Element method) (matflow.ElementActionRun method) (matflow.ElementIteration method) get_dependent_element_iterations() (matflow.Element method) (matflow.ElementIteration method) get_dependent_elements() (matflow.Element method) (matflow.ElementIteration method) (matflow.WorkflowTask method) get_dependent_elements_recursively() (matflow.Element method) get_dependent_tasks() (matflow.Element method) (matflow.ElementIteration method) (matflow.WorkflowTask method) get_dir_name() (matflow.WorkflowTask method) get_EAR_dependencies() (matflow.Element method) (matflow.ElementActionRun method) (matflow.ElementIteration method) get_EAR_IDs_of_tasks() (matflow.Workflow method) get_EAR_skipped() (matflow.Workflow method) get_EARs_from_IDs() (matflow.Workflow method) get_EARs_of_tasks() (matflow.Workflow method) get_element_dependencies() (matflow.Element method) (matflow.ElementIteration method) (matflow.WorkflowTask method) get_element_IDs_from_EAR_IDs() (matflow.Workflow method) get_element_iteration_dependencies() (matflow.Element method) (matflow.ElementIteration method) get_element_iteration_IDs_from_EAR_IDs() (matflow.Workflow method) get_element_iterations_from_IDs() (matflow.Workflow method) get_element_iterations_of_tasks() (matflow.Workflow method) get_elements_from_IDs() (matflow.Workflow method) get_end_time() (matflow.Submission method) get_env_instance_filterable_attributes() (matflow.ElementResources static method) get_environment() (matflow.Action method) (matflow.ElementActionRun method) get_environment_name() (matflow.Action method) get_environment_spec() (matflow.Action method) (matflow.ElementActionRun method) get_IFG_input_values() (matflow.ElementActionRun method) get_info_html() (matflow.TaskSchema method) get_input_dependencies() (matflow.Element method) (matflow.ElementActionRun method) (matflow.ElementIteration method) get_input_file_generator_action_env() (matflow.Action method)

get_input_file_labels() (matflow.Action method) get_input_statuses() (matflow.Task method) get_input_types() (matflow.Action method) get_input_values() (matflow.ElementActionRun method) get_input_values_direct() (matflow.ElementActionRun method) get_iteration_final_run_IDs() (matflow.Workflow method) get_iteration_task_pathway() (matflow.Workflow method) get_job_state_info() (matflow.DirectPosix method) (matflow.DirectWindows method) (matflow.SGEPosix method) (matflow.SlurmPosix method) get_job_statuses() (matflow.SGEPosix method) get_jobscript_hash() (matflow.ElementResources method) get_key() (matflow.TaskSchema method) get_known_submissions() (in module matflow) get_locally_defined_inputs() (matflow.ElementSet method) get_log_file_name() (matflow.RunDirAppFiles class method) get_login_nodes() (matflow.SGEPosix method) get_loop_map() (matflow.Workflow method) get_OFP_inputs() (matflow.ElementActionRun method) get_OFP_output_files() (matflow.ElementActionRun method) get_OFP_outputs() (matflow.ElementActionRun method) get_OS_info() (in module matflow) get_output_file_labels() (matflow.Action method) get_output_file_parser_action_env() (matflow.Action method) get_output_types() (matflow.Action method) (matflow.Command method) get_param_dump_file_path_HDF5() (matflow.Action method) get_param_dump_file_path_JSON() (matflow.Action method) get_param_dump_file_stem() (matflow.Action static method) get_param_load_file_path_HDF5() (matflow.Action method) get_param_load_file_path_JSON() (matflow.Action method) get_param_load_file_stem() (matflow.Action static method) get_param_provided_element_sets() (matflow.Task method) get_parameter() (matflow.Workflow method) get_parameter_data() (matflow.Workflow method) get_parameter_dependence() (matflow.Action method) (matflow.TaskSchema method) get_parameter_names() (matflow.Action method) (matflow.ElementAction method) (matflow.ElementActionRun method) (matflow.ElementIteration method) get_parameter_set_statuses() (matflow.Workflow method) get_parameter_source() (matflow.Workflow method) get_parameter_sources() (matflow.Element method) (matflow.ElementAction method) (matflow.ElementActionRun method) (matflow.ElementIteration method) (matflow.Workflow method) get_parameters() (matflow.Workflow method) get_parent_loops() (matflow.WorkflowLoop method) get_possible_scopes() (matflow.Action method) get_precise_scope() (matflow.Action method) get_required_executables() (matflow.Action method) (matflow.Command method) get_resolved_action_env() (matflow.Action method) get_resources() (matflow.ElementActionRun method) (matflow.ElementIteration method) get_resources_obj() (matflow.ElementIteration method) get_run_file_prefix() (matflow.RunDirAppFiles static method) get_run_param_dump_file_prefix() (matflow.RunDirAppFiles class method) get_run_param_load_file_prefix() (matflow.RunDirAppFiles class method) get_running_elements() (matflow.Workflow method) get_running_runs() (matflow.Workflow method) get_schema_action() (matflow.Task method) get_scopes() (matflow.ResourceList method) get_script_name() (matflow.Action class method) get_sequence_by_path() (matflow.ElementSet method) get_sequence_from_path() (matflow.ElementSet method) get_sequence_value() (matflow.Element method) get_shell_info() (in module matflow) get_size() (matflow.ElementParameter method) get_snippet_script_path() (matflow.Action class method) get_snippet_script_str() (matflow.Action class method) get_start_time() (matflow.Submission method) get_std_file_name() (matflow.RunDirAppFiles class method) get_store_EARs() (matflow.Workflow method) get_store_element_iterations() (matflow.Workflow method) get_store_elements() (matflow.Workflow method) get_store_tasks() (matflow.Workflow method) get_submit_command() (matflow.DirectPosix method) (matflow.DirectWindows method) (matflow.SGEPosix method) (matflow.SlurmPosix method) get_task() (matflow.InputSource method) get_task_dependencies() (matflow.Element method) (matflow.ElementIteration method) (matflow.ElementSet method) (matflow.WorkflowTask method) get_task_elements() (matflow.Workflow method) get_task_IDs_from_element_IDs() (matflow.Workflow method) get_task_loop_idx_array() (matflow.Jobscript method) get_task_unique_names() (matflow.Task static method) (matflow.Workflow method) get_template_resources() (matflow.ElementIteration method) get_unique_schedulers() (matflow.Submission method) get_unique_schedulers_of_jobscripts() (matflow.Submission static method) get_unique_shells() (matflow.Submission method) get_version_info() (matflow.DirectPosix method) (matflow.DirectWindows method) (matflow.SGEPosix method) (matflow.SlurmPosix method) group_by_distinct (matflow.ElementGroup attribute) GroupList (class in matflow)

I

id_ (matflow.Element property) (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.Workflow property) ignore_invalid_actions() (matflow.TaskSchema class method) IMPLICIT (matflow.ParameterPropagationMode attribute) IMPORT (matflow.InputSourceType attribute) import_() (matflow.InputSource class method) INDEX matflow-config-pop command line option matflow-workflow-WORKFLOW_REF-get-param command line option matflow-workflow-WORKFLOW_REF-get-param-source command line option matflow-workflow-WORKFLOW_REF-is-param-set command line option index (matflow.Element property) (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.ElementSet property) (matflow.Jobscript property) (matflow.Submission property) (matflow.Task property) (matflow.WorkflowLoop property) (matflow.WorkflowTask property) info (matflow.TaskSchema property) init_loop_index() (matflow.Element method) initialise_EARs() (matflow.WorkflowTask method) INPUT (matflow.TaskSourceType attribute) input_file (matflow.InputFileGenerator attribute) INPUT_FILE_GENERATOR (matflow.ActionScopeType attribute) input_file_generator() (matflow.ActionScope class method) input_files (matflow.Element property) (matflow.ElementAction property) (matflow.ElementActionRun property) (matflow.ElementIteration property) input_files_path (matflow.Workflow property) input_or_output (matflow.SchemaInput property) (matflow.SchemaOutput property) input_path (matflow.ValueSequence property) input_source_idx (matflow.Element property) input_sources (matflow.Element property) (matflow.ElementPropagation attribute) input_type (matflow.ValueSequence property) input_types (matflow.ElementSet property) (matflow.TaskSchema property)

InputFile (class in matflow) InputFileGenerator (class in matflow) InputFileGeneratorSource (class in matflow) inputs (matflow.Element property) (matflow.ElementAction property) (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.InputFileGenerator attribute) (matflow.OutputFileParser attribute) (matflow.WorkflowTask property) InputSource (class in matflow) InputSourceType (class in matflow) InputValue (class in matflow) insert_ID (matflow.Task property) (matflow.WorkflowTask property) is_array (matflow.Jobscript property) is_file (matflow.Parameter attribute) is_in() (matflow.InputSource method) is_input_type_provided() (matflow.ElementSet method) is_input_type_required() (matflow.Action method) (matflow.Task method) is_jobscript_active() (matflow.DirectPosix method) (matflow.DirectWindows method) (matflow.SGEPosix method) (matflow.SlurmPosix method) is_num_cores_supported() (matflow.DirectPosix static method) (matflow.DirectWindows static method) (matflow.SGEPosix static method) (matflow.SlurmPosix static method) is_parallel (matflow.ElementResources property) is_parameter_set() (matflow.Workflow method) is_pending (matflow.Element property) (matflow.ElementActionRun property) (matflow.ElementIteration property) is_set (matflow.ElementParameter property) is_snippet_script() (matflow.Action static method) is_sub_value (matflow.InputValue property) (matflow.ValueSequence property) is_submitted (matflow.Jobscript property) iterable_parameters (matflow.WorkflowLoop property) iteration_IDs (matflow.Element property) iterations (matflow.Element property)

J

Jobscript (class in matflow) JOBSCRIPT_IDX matflow-internal-workflow-PATH-write-commands command line option jobscript_indices (matflow.Submission property) jobscript_name (matflow.Jobscript property) jobscript_path (matflow.Jobscript property) jobscripts (matflow.Submission property)

JS_ACT_IDX matflow-internal-workflow-PATH-set-ear-end command line option JS_ACTION_IDX matflow-internal-workflow-PATH-write-commands command line option JS_IDX matflow-internal-workflow-PATH-set-ear-end command line option matflow-workflow-WORKFLOW_REF-sub-SUB_IDX-js command line option JS_parallelism (matflow.Submission property)

K

KNOWN_NAME matflow-config-init command line option

L

label (matflow.FileSpec attribute) labelled_info() (matflow.SchemaInput method) labelled_type (matflow.InputValue property) (matflow.ValueSequence property) latest_iteration (matflow.Element property) LatticeDirection (class in matflow.param_classes.orientations) list_attrs() (matflow.CommandFilesList method) (matflow.EnvironmentsList method) (matflow.ExecutablesList method) (matflow.GroupList method) (matflow.ParametersList method) (matflow.ResourceList method) (matflow.TaskList method) (matflow.TaskSchemasList method) (matflow.TaskTemplateList method) (matflow.WorkflowLoopList method) (matflow.WorkflowTaskList method)

LoadCase (class in matflow.param_classes.load) LoadStep (class in matflow.param_classes.load) LOCAL (matflow.InputSourceType attribute) local() (matflow.InputSource class method) Loop (class in matflow) loop_idx (matflow.ElementIteration property) LOOP_NAME matflow-internal-workflow-PATH-check-loop command line option loops (matflow.Workflow property) (matflow.WorkflowTemplate attribute)

M

MAIN (matflow.ActionScopeType attribute) main() (matflow.ActionScope class method) make_and_submit_demo_workflow() (in module matflow) make_and_submit_workflow() (in module matflow) make_artifact_dirs() (matflow.Jobscript method) make_demo_workflow() (in module matflow) make_persistent() (matflow.InputFile method) (matflow.InputFileGeneratorSource method) (matflow.InputValue method) (matflow.OutputFileParserSource method) (matflow.ResourceSpec method) (matflow.TaskSchema method) (matflow.ValuePerturbation method) (matflow.ValueSequence method) make_workflow() (in module matflow) masked_array_from_list() (in module matflow.param_classes.utils) matflow module matflow command line option --config-dir --config-key --help --hpcflow-version --run-time-info --timeit --timeit-file --version --with-config matflow-cancel command line option --ref-type -r WORKFLOW_REF matflow-config command line option --no-callback matflow-config-add-scheduler command line option --defaults NAME matflow-config-add-shell command line option --defaults NAME matflow-config-add-shell-wsl command line option --defaults matflow-config-append command line option --json NAME VALUE matflow-config-get command line option --all --file --metadata NAME matflow-config-import command line option --new --no-rename --rename FILE_PATH matflow-config-init command line option --path KNOWN_NAME matflow-config-open command line option --path matflow-config-pop command line option INDEX NAME matflow-config-prepend command line option --json NAME VALUE matflow-config-set command line option --json NAME VALUE matflow-config-set-github-demo-data-dir command line option SHA matflow-config-unset command line option NAME matflow-config-update command line option --json NAME VALUE matflow-configure-env command line option --env-source-file --setup --use-current-env NAME matflow-demo-data command line option --list -l matflow-demo-data-cache command line option --all FILE_NAME matflow-demo-data-copy command line option DESTINATION FILE_NAME matflow-demo-software-doSomething command line option --infile1 --infile2 --out --value -i1 -i2 -o -v matflow-demo-workflow command line option --list -l matflow-demo-workflow-copy command line option --doc --no-doc DESTINATION WORKFLOW_NAME matflow-demo-workflow-go command line option --add-to-known --cancel --format --js-parallelism --name --no-add-to-known --no-status --overwrite --path --print-idx --status --store --tasks --ts-fmt --ts-name-fmt --var --wait -v WORKFLOW_NAME matflow-demo-workflow-make command line option --format --name --no-status --overwrite --path --status --store --ts-fmt --ts-name-fmt --var -v WORKFLOW_NAME matflow-demo-workflow-show command line option --doc --no-doc --no-syntax --syntax WORKFLOW_NAME matflow-go command line option --add-to-known --cancel --format --js-parallelism --name --no-add-to-known --no-status --overwrite --path --print-idx --status --store --string --tasks --ts-fmt --ts-name-fmt --var --wait -v TEMPLATE_FILE_OR_STR matflow-helper-pid command line option --file -f matflow-helper-restart command line option --timeout --timeout-check-interval --watch-interval matflow-helper-run command line option --timeout --timeout-check-interval --watch-interval matflow-helper-start command line option --timeout --timeout-check-interval --watch-interval matflow-internal-workflow command line option PATH matflow-internal-workflow-PATH-check-loop command line option EAR_ID LOOP_NAME matflow-internal-workflow-PATH-get-ear-skipped command line option EAR_ID matflow-internal-workflow-PATH-save-parameter command line option --stderr CMD_IDX EAR_ID NAME VALUE matflow-internal-workflow-PATH-set-ear-end command line option EAR_ID EXIT_CODE JS_ACT_IDX JS_IDX

matflow-internal-workflow-PATH-set-ear-skip command line option EAR_ID matflow-internal-workflow-PATH-set-ear-start command line option EAR_ID matflow-internal-workflow-PATH-write-commands command line option EAR_ID JOBSCRIPT_IDX JS_ACTION_IDX SUBMISSION_IDX matflow-make command line option --format --name --no-status --overwrite --path --status --store --string --ts-fmt --ts-name-fmt --var -v TEMPLATE_FILE_OR_STR matflow-manage-clear-cache command line option --hostname matflow-manage-get-config-path command line option --config-dir matflow-manage-reset-config command line option --config-dir matflow-open-config command line option --path matflow-open-demo-data-cache-dir command line option --path matflow-open-env-source command line option --name --path matflow-open-known-subs command line option --path matflow-open-log command line option --path matflow-open-user-cache-dir command line option --path matflow-open-user-cache-hostname-dir command line option --path matflow-open-user-data-dir command line option --path matflow-open-user-data-hostname-dir command line option --path matflow-open-user-runtime-dir command line option --path matflow-open-workflow command line option --path --ref-type -r WORKFLOW_REF matflow-rechunk command line option --backup --chunk-size --no-backup --no-status --ref-type --status -r WORKFLOW_REF matflow-show command line option --full --legend --max-recent --no-update -f -r matflow-submission command line option --os-info matflow-submission-get-known command line option --json matflow-submission-scheduler command line option SCHEDULER_NAME matflow-submission-shell-info command line option --exclude-os SHELL_NAME matflow-test command line option PY_TEST_ARGS matflow-test-hpcflow command line option PY_TEST_ARGS matflow-unzip command line option --log --path WORKFLOW_PATH matflow-workflow command line option --ref-type -r WORKFLOW_REF matflow-workflow-WORKFLOW_REF-abort-run command line option --element --submission --task matflow-workflow-WORKFLOW_REF-get-param command line option INDEX matflow-workflow-WORKFLOW_REF-get-param-source command line option INDEX matflow-workflow-WORKFLOW_REF-is-param-set command line option INDEX matflow-workflow-WORKFLOW_REF-rechunk command line option --backup --chunk-size --no-backup --no-status --status matflow-workflow-WORKFLOW_REF-rechunk-parameter-base command line option --backup --chunk-size --no-backup --no-status --status matflow-workflow-WORKFLOW_REF-rechunk-runs command line option --backup --chunk-size --no-backup --no-status --status matflow-workflow-WORKFLOW_REF-sub command line option SUB_IDX matflow-workflow-WORKFLOW_REF-sub-SUB_IDX-js command line option JS_IDX matflow-workflow-WORKFLOW_REF-submit command line option --add-to-known --cancel --js-parallelism --no-add-to-known --no-status --print-idx --status --tasks --wait matflow-workflow-WORKFLOW_REF-unzip command line option --log --path matflow-workflow-WORKFLOW_REF-wait command line option --jobscripts -j matflow-workflow-WORKFLOW_REF-zip command line option --include-execute --include-rechunk-backups --log --overwrite --path matflow-zip command line option --include-execute --include-rechunk-backups --log --overwrite --path --ref-type -r WORKFLOW_REF matflow.cli module matflow.param_classes module matflow.param_classes.load module matflow.param_classes.orientations module matflow.param_classes.seeds module matflow.param_classes.single_crystal_parameters module matflow.param_classes.utils module matflow.tests module matflow.tests.conftest module matflow.tests.test_cli module matflow.tests.test_utils module max_array_items (matflow.ElementResources attribute) (matflow.ResourceSpec property) merge_envs (matflow.WorkflowTemplate attribute) merge_other() (matflow.ResourceList method) merge_resources (matflow.WorkflowTemplate attribute) metadata (matflow.ElementActionRun property) method_args (matflow.param_classes.load.LoadStep property) method_name (matflow.param_classes.load.LoadStep property) MicrostructureSeeds (class in matflow.param_classes.seeds) module matflow matflow.cli matflow.param_classes matflow.param_classes.load matflow.param_classes.orientations matflow.param_classes.seeds matflow.param_classes.single_crystal_parameters matflow.param_classes.utils matflow.tests matflow.tests.conftest matflow.tests.test_cli matflow.tests.test_utils multi_input_types (matflow.TaskSchema property) multiplicative_factor (matflow.ValuePerturbation attribute) multistep() (matflow.param_classes.load.LoadCase class method)

N

NAME matflow-config-add-scheduler command line option matflow-config-add-shell command line option matflow-config-append command line option matflow-config-get command line option matflow-config-pop command line option matflow-config-prepend command line option matflow-config-set command line option matflow-config-unset command line option matflow-config-update command line option matflow-configure-env command line option matflow-internal-workflow-PATH-save-parameter command line option name (matflow.ElementGroup attribute) (matflow.FileSpec attribute) (matflow.Loop property) (matflow.SchemaInput property) (matflow.SchemaOutput property) (matflow.SchemaParameter property) (matflow.Task property) (matflow.TaskObjective attribute) (matflow.TaskSchema property) (matflow.ValuePerturbation attribute) (matflow.Workflow property) (matflow.WorkflowLoop property) (matflow.WorkflowTask property) (matflow.WorkflowTemplate attribute) needs_submit (matflow.Submission property) nesting_order (matflow.ElementPropagation attribute) NEVER (matflow.ParameterPropagationMode attribute) new_empty_loop() (matflow.WorkflowLoop class method) new_empty_task() (matflow.WorkflowTask class method) new_null_config() (in module matflow.tests.conftest) non_iterable_parameters (matflow.Loop property) non_universal_input_types (matflow.Task property) normalise() (matflow.ResourceList class method) normalised_files_path (matflow.InputFile property) normalised_inputs_path (matflow.InputValue property) (matflow.ValueSequence property)

normalised_path (matflow.InputFile property) (matflow.InputValue property) (matflow.ResourceSpec property) (matflow.ValueSequence property) normalised_resources_path (matflow.ResourceSpec property) null_config() (in module matflow.tests.conftest) num_actions (matflow.Jobscript property) (matflow.WorkflowTask property) num_added_iterations (matflow.WorkflowLoop property) num_added_tasks (matflow.Workflow property) num_all_schema_actions (matflow.Task property) num_cores (matflow.ElementResources attribute) (matflow.ExecutableInstance attribute) (matflow.ResourceSpec property) num_cores_per_node (matflow.ElementResources attribute) (matflow.ResourceSpec property) num_EARs (matflow.Workflow property) num_element_iterations (matflow.Workflow property) num_element_sets (matflow.Task property) (matflow.WorkflowTask property) num_elements (matflow.Jobscript property) (matflow.Workflow property) (matflow.WorkflowTask property) num_iterations (matflow.Loop property) (matflow.WorkflowLoop property) num_loops (matflow.Workflow property) num_nodes (matflow.ElementResources attribute) (matflow.ResourceSpec property) num_runs (matflow.ElementAction property) num_seeds (matflow.param_classes.seeds.MicrostructureSeeds property) num_steps (matflow.param_classes.load.LoadCase property) num_submissions (matflow.Workflow property) num_tasks (matflow.Workflow property) num_threads (matflow.ElementResources attribute) (matflow.ResourceSpec property) number (matflow.ElementRepeats attribute) NumCores (class in matflow)

O

objective (matflow.Task property) options (matflow.OutputFileParser attribute) OrientationRepresentation (class in matflow.param_classes.orientations) OrientationRepresentationType (class in matflow.param_classes.orientations) Orientations (class in matflow.param_classes.orientations) orientations (matflow.param_classes.seeds.MicrostructureSeeds attribute) os_name (matflow.ElementResources attribute) (matflow.Jobscript property) (matflow.ResourceSpec property) output (matflow.OutputFileParser attribute) OUTPUT (matflow.TaskSourceType attribute) OUTPUT_FILE_PARSER (matflow.ActionScopeType attribute) output_file_parser() (matflow.ActionScope class method) output_files (matflow.Element property) (matflow.ElementAction property) (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.OutputFileParser attribute)

output_labels (matflow.Task property) output_types (matflow.TaskSchema property) OutputFileParser (class in matflow) OutputFileParserSource (class in matflow) OutputLabel (class in matflow) outputs (matflow.Element property) (matflow.ElementAction property) (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.OutputFileParser attribute) (matflow.WorkflowTask property) outstanding_jobscripts (matflow.Submission property)

P

parallel_mode (matflow.ElementResources attribute) (matflow.ExecutableInstance attribute) (matflow.ResourceSpec property) Parameter (class in matflow) parameter (matflow.SchemaOutput attribute) (matflow.SubParameter attribute) (matflow.ValueSequence property) ParameterPath (class in matflow) ParameterPropagationMode (class in matflow) Parameters (class in matflow) ParametersList (class in matflow) ParameterValue (class in matflow) parent (matflow.ElementParameter attribute) parents (matflow.WorkflowLoop property) parse_submission_output() (matflow.DirectPosix method) (matflow.DirectWindows method) (matflow.SGEPosix method) (matflow.SlurmPosix method) PATH matflow-internal-workflow command line option path (matflow.ElementParameter attribute) (matflow.InputFile property) (matflow.InputFileGeneratorSource property) (matflow.OutputFileParserSource property) (matflow.ParameterPath attribute) (matflow.Parameters attribute) (matflow.Submission property) (matflow.ValuePerturbation attribute) path_split (matflow.ValueSequence property) path_type (matflow.ValueSequence property) perturbations (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters property) phase_label (matflow.param_classes.seeds.MicrostructureSeeds attribute) phases (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters property) planar_2D() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) plane_strain() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) position (matflow.param_classes.seeds.MicrostructureSeeds attribute)

prefixed_names_unlabelled (matflow.ElementInputFiles property) (matflow.ElementInputs property) (matflow.ElementOutputFiles property) (matflow.ElementOutputs property) prefixed_names_unlabelled_str (matflow.ElementInputFiles property) (matflow.ElementInputs property) (matflow.ElementOutputFiles property) (matflow.ElementOutputs property) prepare_element_resolution() (matflow.Task method) prepare_JSON_dump() (matflow.param_classes.load.LoadCase method) (matflow.param_classes.load.LoadStep method) (matflow.param_classes.orientations.OrientationRepresentation method) (matflow.param_classes.orientations.Orientations method) (matflow.param_classes.orientations.UnitCellAlignment method) (matflow.param_classes.seeds.MicrostructureSeeds method) (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters method) (matflow.ParameterValue method) prepare_persistent_copy() (matflow.ElementSet method) process_ID (matflow.Jobscript property) process_resources() (matflow.DirectPosix class method) (matflow.DirectWindows class method) (matflow.SGEPosix class method) (matflow.SlurmPosix class method) process_script_data_formats() (matflow.Action method) process_shell_parameter_output() (matflow.Workflow method) process_std_stream() (matflow.Command method) PROCESSING (matflow.ActionScopeType attribute) processing() (matflow.ActionScope class method) propagation_mode (matflow.SchemaOutput attribute) provides_parameters (matflow.TaskSchema property) provides_parameters() (matflow.Task method) PY_TEST_ARGS matflow-test command line option matflow-test-hpcflow command line option pytest_addoption() (in module matflow.tests.conftest) pytest_collection_modifyitems() (in module matflow.tests.conftest) pytest_configure() (in module matflow.tests.conftest) pytest_unconfigure() (in module matflow.tests.conftest)

Q

quat_order (matflow.param_classes.orientations.OrientationRepresentation attribute) quat_sample_random() (matflow.param_classes.orientations.Orientations static method)

QUATERNION (matflow.param_classes.orientations.OrientationRepresentationType attribute) QuatOrder (class in matflow.param_classes.orientations)

R

raise_on_missing (matflow.Parameters attribute) raise_on_unset (matflow.Parameters attribute) random_2D() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) random_3D() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) random_seed (matflow.param_classes.seeds.MicrostructureSeeds attribute) read_contents() (matflow.InputFile method) (matflow.InputFileGeneratorSource method) (matflow.OutputFileParserSource method) rechunk() (matflow.Workflow method) rechunk_parameter_base() (matflow.Workflow method) rechunk_runs() (matflow.Workflow method) reload() (matflow.Workflow method) representation (matflow.param_classes.orientations.Orientations attribute) resolve_element_data_indices() (matflow.WorkflowTask static method) resolve_jobscripts() (matflow.Workflow method)

resource_scope (matflow.ValueSequence property) ResourceList (class in matflow) resources (matflow.ElementActionRun property) (matflow.Jobscript property) (matflow.WorkflowTemplate attribute) ResourceSpec (class in matflow) return_element_parameters (matflow.Parameters attribute) Rule (class in matflow) rules (matflow.Command attribute) (matflow.ElementFilter attribute) (matflow.InputFileGenerator attribute) (matflow.OutputFileParser attribute) run_hostname (matflow.ElementActionRun property) run_hpcflow_tests() (in module matflow) run_tests() (in module matflow) RunDirAppFiles (class in matflow) runs (matflow.ElementAction property)

S

save_files (matflow.OutputFileParser attribute) save_from_HDF5_group() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) (matflow.param_classes.orientations.OrientationRepresentation class method) (matflow.param_classes.orientations.Orientations class method) (matflow.param_classes.orientations.UnitCellAlignment class method) (matflow.param_classes.seeds.MicrostructureSeeds class method) (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters class method) (matflow.ParameterValue class method) save_from_JSON() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) (matflow.param_classes.orientations.OrientationRepresentation class method) (matflow.param_classes.orientations.Orientations class method) (matflow.param_classes.orientations.UnitCellAlignment class method) (matflow.param_classes.seeds.MicrostructureSeeds class method) (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters class method) (matflow.ParameterValue class method) save_parameter() (matflow.Workflow method) SCALAR_VECTOR (matflow.param_classes.orientations.QuatOrder attribute) scheduler (matflow.ElementResources attribute) (matflow.Jobscript property) (matflow.ResourceSpec property) scheduler_args (matflow.ElementResources attribute) (matflow.ResourceSpec property) scheduler_job_ID (matflow.Jobscript property) scheduler_js_ref (matflow.Jobscript property) SCHEDULER_NAME matflow-submission-scheduler command line option scheduler_name (matflow.Jobscript property) scheduler_ref (matflow.Jobscript property) schema (matflow.Task property) schema_parameters (matflow.Element property) (matflow.ElementIteration property) SchemaInput (class in matflow) SchemaOutput (class in matflow) SchemaParameter (class in matflow) schemas (matflow.Task property) scope (matflow.ActionEnvironment attribute) scratch (matflow.ElementResources attribute) (matflow.ResourceSpec property) script (matflow.InputFileGenerator attribute) (matflow.OutputFileParser attribute) script_data_in_grouped (matflow.Action property) script_data_in_has_direct (matflow.Action property) script_data_in_has_files (matflow.Action property) script_data_out_grouped (matflow.Action property) script_data_out_has_direct (matflow.Action property) script_data_out_has_files (matflow.Action property) script_is_python (matflow.Action property) script_pass_env_spec (matflow.InputFileGenerator attribute) (matflow.OutputFileParser attribute) sequence_idx (matflow.Element property) set_defaults() (matflow.ElementResources method) set_EAR_end() (matflow.Workflow method) set_EAR_skip() (matflow.Workflow method) set_EAR_start() (matflow.Workflow method) set_EAR_submission_index() (matflow.Workflow method) set_EARs_initialised() (matflow.Workflow method) set_parameter_value() (matflow.Workflow method) set_sequence_parameters() (matflow.Task method) SGE_parallel_env (matflow.ElementResources attribute) (matflow.ResourceSpec property) SGEPosix (class in matflow) SHA matflow-config-set-github-demo-data-dir command line option shell (matflow.ElementResources attribute) (matflow.Jobscript property) (matflow.ResourceSpec property) shell_args (matflow.ElementResources attribute) (matflow.ResourceSpec property) SHELL_NAME matflow-submission-shell-info command line option

shell_name (matflow.Jobscript property) show() (in module matflow) (matflow.param_classes.seeds.MicrostructureSeeds method) show_all_EAR_statuses() (matflow.Workflow method) show_legend() (in module matflow) single_label (matflow.SchemaInput property) single_labelled_data (matflow.SchemaInput property) single_labelled_type (matflow.SchemaInput property) SingleCrystalParameters (class in matflow.param_classes.single_crystal_parameters) skip (matflow.ElementActionRun property) SLURM_is_parallel (matflow.ElementResources property) SLURM_num_cpus_per_task (matflow.ElementResources attribute) (matflow.ResourceSpec property) SLURM_num_nodes (matflow.ElementResources attribute) (matflow.ResourceSpec property) SLURM_num_tasks (matflow.ElementResources attribute) (matflow.ResourceSpec property) SLURM_num_tasks_per_node (matflow.ElementResources attribute) (matflow.ResourceSpec property) SLURM_partition (matflow.ElementResources attribute) (matflow.ResourceSpec property) SlurmPosix (class in matflow) snapshot_end (matflow.ElementActionRun property) snapshot_start (matflow.ElementActionRun property) source_file (matflow.WorkflowTemplate attribute) start (matflow.NumCores attribute) start_time (matflow.ElementActionRun property) (matflow.Jobscript property) (matflow.Submission property) state_lookup (matflow.SGEPosix attribute) (matflow.SlurmPosix attribute) status (matflow.ElementActionRun property) (matflow.Submission property) stderr (matflow.Command attribute) stdin (matflow.Command attribute) stdout (matflow.Command attribute) stem (matflow.FileNameSpec property) (matflow.FileSpec property) step (matflow.NumCores attribute) steps (matflow.param_classes.load.LoadCase attribute) stop (matflow.NumCores attribute) store_contents (matflow.InputFile property) (matflow.InputFileGeneratorSource property) (matflow.OutputFileParserSource property) store_format (matflow.Workflow property) store_kwargs (matflow.WorkflowTemplate attribute) strain_like_tensor (matflow.param_classes.load.LoadStep property) StrainRateMode (class in matflow.param_classes.load) SUB_IDX matflow-workflow-WORKFLOW_REF-sub command line option sub_parameters (matflow.Parameter attribute) Submission (class in matflow) submission (matflow.Jobscript property) SUBMISSION_IDX matflow-internal-workflow-PATH-write-commands command line option submission_idx (matflow.ElementActionRun property) submission_parts (matflow.Submission property) submissions (matflow.Workflow property) submissions_path (matflow.Workflow property) submit() (matflow.Jobscript method) (matflow.Submission method) (matflow.Workflow method) submit_cmdline (matflow.Jobscript property) submit_hostname (matflow.Jobscript property) submit_machine (matflow.Jobscript property) submit_time (matflow.Jobscript property) submit_workflow() (in module matflow) submitted_jobscripts (matflow.Submission property) SubParameter (class in matflow) success (matflow.ElementActionRun property)

T

take_snapshot() (matflow.RunDirAppFiles class method) Task (class in matflow) task (matflow.Element property) (matflow.ElementAction property) (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.ElementParameter attribute) (matflow.ElementPropagation attribute) (matflow.Elements property) (matflow.ElementSet property) TASK (matflow.InputSourceType attribute) task (matflow.ParameterPath attribute) (matflow.Parameters attribute) (matflow.TaskInputParameters attribute) (matflow.TaskOutputParameters attribute) task() (matflow.InputSource class method) task_actions (matflow.Jobscript property) task_artifacts_path (matflow.Workflow property) task_elements (matflow.Jobscript property) task_indices (matflow.WorkflowLoop property) task_insert_IDs (matflow.Jobscript property) (matflow.Loop property) (matflow.WorkflowLoop property) task_loop_idx (matflow.Jobscript property) task_objects (matflow.Loop property) (matflow.WorkflowLoop property) task_schema (matflow.Action property) (matflow.SchemaInput property) task_template (matflow.ElementSet property) (matflow.TaskSchema property) TaskInputParameters (class in matflow) TaskList (class in matflow) TaskObjective (class in matflow) TaskOutputParameters (class in matflow) tasks (matflow.Workflow property) (matflow.WorkflowTemplate attribute) TaskSchema (class in matflow) TaskSchemasList (class in matflow) TaskSourceType (class in matflow) TaskTemplateList (class in matflow) template (matflow.Workflow property) (matflow.WorkflowLoop property) (matflow.WorkflowTask property) template_components (matflow.Workflow property) TEMPLATE_FILE_OR_STR matflow-go command line option matflow-make command line option temporary_rename() (matflow.Workflow class method) termination (matflow.Loop property) test() (matflow.ActionRule method) (matflow.Rule method) test_hpcflow_version() (in module matflow.tests.test_cli) test_masked_array_from_list_1D() (in module matflow.tests.test_utils) test_masked_array_from_list_1D_masked() (in module matflow.tests.test_utils) test_masked_array_from_list_2D() (in module matflow.tests.test_utils) test_masked_array_from_list_2D_masked() (in module matflow.tests.test_utils) test_rules() (matflow.Action method) test_termination() (matflow.WorkflowLoop method) test_version() (in module matflow.tests.test_cli) time_limit (matflow.ElementResources attribute) (matflow.ResourceSpec property) to_dict() (matflow.Action method) (matflow.ActionEnvironment method) (matflow.ActionRule method) (matflow.ActionScope method) (matflow.Command method) (matflow.CommandFilesList method) (matflow.ElementFilter method) (matflow.ElementGroup method) (matflow.ElementResources method) (matflow.ElementSet method) (matflow.Environment method) (matflow.EnvironmentsList method) (matflow.Executable method) (matflow.ExecutableInstance method) (matflow.ExecutablesList method) (matflow.FileNameExt method) (matflow.FileNameSpec method) (matflow.FileNameStem method) (matflow.FileSpec method) (matflow.GroupList method) (matflow.InputFile method) (matflow.InputFileGenerator method) (matflow.InputFileGeneratorSource method) (matflow.InputSource method) (matflow.InputValue method) (matflow.Jobscript method) (matflow.Loop method) (matflow.NumCores method) (matflow.OutputFileParser method) (matflow.OutputFileParserSource method) (matflow.OutputLabel method) (matflow.param_classes.load.LoadCase method) (matflow.param_classes.load.LoadStep method) (matflow.param_classes.orientations.OrientationRepresentation method) (matflow.param_classes.orientations.Orientations method) (matflow.param_classes.orientations.UnitCellAlignment method) (matflow.param_classes.seeds.MicrostructureSeeds method) (matflow.param_classes.single_crystal_parameters.SingleCrystalParameters method) (matflow.Parameter method) (matflow.ParameterPath method) (matflow.ParametersList method) (matflow.ParameterValue method) (matflow.ResourceList method) (matflow.ResourceSpec method) (matflow.Rule method) (matflow.SchemaInput method) (matflow.SchemaOutput method) (matflow.SchemaParameter method) (matflow.Submission method) (matflow.Task method) (matflow.TaskList method) (matflow.TaskObjective method) (matflow.TaskSchema method) (matflow.TaskSchemasList method) (matflow.TaskTemplateList method) (matflow.ValuePerturbation method) (matflow.ValueSequence method) (matflow.WorkflowLoopList method) (matflow.WorkflowTaskList method) (matflow.WorkflowTemplate method)

to_element_set_data() (matflow.Element method) to_json_like() (matflow.Action method) (matflow.ActionEnvironment method) (matflow.ActionRule method) (matflow.ActionScope method) (matflow.Command method) (matflow.CommandFilesList method) (matflow.ElementFilter method) (matflow.ElementGroup method) (matflow.ElementResources method) (matflow.ElementSet method) (matflow.Environment method) (matflow.EnvironmentsList method) (matflow.Executable method) (matflow.ExecutableInstance method) (matflow.ExecutablesList method) (matflow.FileNameExt method) (matflow.FileNameSpec method) (matflow.FileNameStem method) (matflow.FileSpec method) (matflow.GroupList method) (matflow.InputFile method) (matflow.InputFileGenerator method) (matflow.InputFileGeneratorSource method) (matflow.InputSource method) (matflow.InputValue method) (matflow.Jobscript method) (matflow.Loop method) (matflow.NumCores method) (matflow.OutputFileParser method) (matflow.OutputFileParserSource method) (matflow.OutputLabel method) (matflow.Parameter method) (matflow.ParameterPath method) (matflow.ParametersList method) (matflow.ResourceList method) (matflow.ResourceSpec method) (matflow.Rule method) (matflow.SchemaInput method) (matflow.SchemaOutput method) (matflow.SchemaParameter method) (matflow.Submission method) (matflow.Task method) (matflow.TaskList method) (matflow.TaskObjective method) (matflow.TaskSchema method) (matflow.TaskSchemasList method) (matflow.TaskTemplateList method) (matflow.ValuePerturbation method) (matflow.ValueSequence method) (matflow.WorkflowLoopList method) (matflow.WorkflowTaskList method) (matflow.WorkflowTemplate method) to_persistent() (matflow.Task method) to_string() (matflow.ActionScope method) (matflow.InputSource method) ts_fmt (matflow.Workflow property) ts_name_fmt (matflow.Workflow property) typ (matflow.Parameter attribute) (matflow.SchemaInput property) (matflow.SchemaOutput property) (matflow.SchemaParameter property) type (matflow.param_classes.load.LoadCase property) (matflow.param_classes.load.LoadStep property) (matflow.param_classes.orientations.OrientationRepresentation attribute) types (matflow.param_classes.load.LoadCase property)

U

undefined_input_types (matflow.ElementSet property) (matflow.Task property) undefined_inputs (matflow.Task property) uniaxial() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) uniaxial_cyclic() (matflow.param_classes.load.LoadCase class method) (matflow.param_classes.load.LoadStep class method) unique_name (matflow.WorkflowTask property) unique_properties (matflow.DirectPosix property) (matflow.DirectWindows property) (matflow.SGEPosix property) (matflow.SlurmPosix property)

unit_cell_alignment (matflow.param_classes.orientations.Orientations attribute) UnitCellAlignment (class in matflow.param_classes.orientations) universal_input_types (matflow.Task property) unzip() (matflow.Workflow method) upstream_tasks (matflow.WorkflowLoop property) (matflow.WorkflowTask property) url (matflow.Workflow property) url_slug (matflow.Parameter property) use_job_array (matflow.ElementResources attribute) (matflow.ResourceSpec property)

V

validate_against_machine() (matflow.ElementResources method) VALUE matflow-config-append command line option matflow-config-prepend command line option matflow-config-set command line option matflow-config-update command line option matflow-internal-workflow-PATH-save-parameter command line option value (matflow.ElementParameter property) (matflow.InputValue property) (matflow.ValuePerturbation property) value() (matflow.FileNameExt method) (matflow.FileNameSpec method) (matflow.FileNameStem method) (matflow.FileSpec method)

ValuePerturbation (class in matflow) values (matflow.ValueSequence property) ValueSequence (class in matflow) variables (matflow.Command attribute) VECTOR_SCALAR (matflow.param_classes.orientations.QuatOrder attribute) VEL_GRAD (matflow.param_classes.load.StrainRateMode attribute) VEL_GRAD_APPROX (matflow.param_classes.load.StrainRateMode attribute) version_info (matflow.Jobscript property)

W

wait() (matflow.Workflow method) wait_for_jobscripts() (matflow.DirectPosix class method) (matflow.DirectWindows class method) (matflow.SGEPosix method) (matflow.SlurmPosix method) where (matflow.ElementGroup attribute) (matflow.ElementRepeats attribute) Workflow (class in matflow) workflow (matflow.Element property) (matflow.ElementActionRun property) (matflow.ElementIteration property) (matflow.InputFile property) (matflow.InputFileGeneratorSource property) (matflow.InputValue property) (matflow.Jobscript property) (matflow.OutputFileParserSource property) (matflow.ResourceSpec property) (matflow.Submission property) (matflow.ValuePerturbation property) (matflow.ValueSequence property) (matflow.WorkflowLoop property) (matflow.WorkflowTask property) (matflow.WorkflowTemplate attribute) workflow_app_alias (matflow.Jobscript property) WORKFLOW_NAME matflow-demo-workflow-copy command line option matflow-demo-workflow-go command line option matflow-demo-workflow-make command line option matflow-demo-workflow-show command line option

WORKFLOW_PATH matflow-unzip command line option WORKFLOW_REF matflow-cancel command line option matflow-open-workflow command line option matflow-rechunk command line option matflow-workflow command line option matflow-zip command line option workflow_template (matflow.Loop property) (matflow.ResourceList property) (matflow.ResourceSpec property) (matflow.WorkflowBlueprint attribute) WorkflowBlueprint (class in matflow) WorkflowLoop (class in matflow) WorkflowLoopList (class in matflow) WorkflowTask (class in matflow) WorkflowTaskList (class in matflow) WorkflowTemplate (class in matflow) write_commands() (matflow.Workflow method) write_EAR_ID_file() (matflow.Jobscript method) write_element_run_dir_file() (matflow.Jobscript method) write_jobscript() (matflow.Jobscript method) write_source() (matflow.ElementActionRun method) (matflow.InputFileGenerator method) (matflow.OutputFileParser method)

X

x (matflow.param_classes.orientations.UnitCellAlignment attribute)

Y

y (matflow.param_classes.orientations.UnitCellAlignment attribute)

Z

z (matflow.param_classes.orientations.UnitCellAlignment attribute)

zip() (matflow.Workflow method)