wfl.generate.optimizewfl.generate.phonopyAtoms", "First Example", "Welcome to Workflow\u2019s documentation!", "wfl", "Operations", "Fitting ACE", "Calculators in Workflow", "Descriptors", "Fitting potentials", "Fitting GAP", "Generating Atomic Structures", "Multistage GAP fitting", "Selecting Configs", "Overview", "Input and output of atomic structures", "Overall design", "Automatic parallelization of tasks", "Functions as independently queued jobs", "wfl package", "wfl.autoparallelize package", "wfl.calculators package", "wfl.calculators.orca package", "wfl.cli package", "wfl.cli.commands package", "wfl.descriptors package", "wfl.fit package", "wfl.fit.gap package", "wfl.fit.modify_database package", "wfl.generate package", "wfl.generate.md package", "wfl.select package", "wfl.utils package", "How to do GAP-RSS"], "terms": {"descript": [0, 5, 18], "all": [0, 2, 5, 6, 7, 8, 9, 12, 13, 14, 15, 17, 18, 22, 26, 27, 28, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45, 47, 48], "cli": 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"step": 48, "dft": 48, "set": 48}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "nbsphinx": 4, "sphinx": 57}, "alltitles": {"Command line interface": [[0, "command-line-interface"]], "Calculators": [[0, "calculators"]], "ORCA (outdated)": [[0, "orca-outdated"]], "CASTEP": [[0, "castep"]], "VASP": [[0, "vasp"]], "Utility functions": [[1, "utility-functions"]], "Find Voids": [[1, "find-voids"]], "e0 from GAP XML": [[1, "e0-from-gap-xml"]], "wfl": [[2, "wfl"], [19, "wfl"]], "descriptor": [[2, "wfl-descriptor"]], "quippy": [[2, "wfl-descriptor-quippy"]], "error": [[2, "wfl-error"]], "eval": [[2, "wfl-eval"]], "ace": [[2, "wfl-eval-ace"]], "atomization-energy": [[2, "wfl-eval-atomization-energy"]], "gap": [[2, "wfl-eval-gap"]], "mace": [[2, "wfl-eval-mace"]], "generate": [[2, "wfl-generate"]], "buildcell": [[2, "wfl-generate-buildcell"]], "smiles": [[2, "wfl-generate-smiles"]], "select": [[2, "wfl-select"]], "cur": [[2, "wfl-select-cur"]], "lambda": [[2, "wfl-select-lambda"]], "Examples": [[3, "examples"]], "Contents:": [[3, null], [20, null], [24, null]], "Random Structures via buildcell": [[4, "Random-Structures-via-buildcell"]], "Contributing Examples": [[5, "contributing-examples"]], "Preparing the Example": [[5, "preparing-the-example"]], "Hiding Tests in the Online Documentation": [[5, "hiding-tests-in-the-online-documentation"]], "Updating Related Files": [[5, "updating-related-files"]], "GAP fit workflow with many wfl use-case examples": [[6, "GAP-fit-workflow-with-many-wfl-use-case-examples"]], "Imports": [[6, "Imports"]], "Reference calculator": [[6, "Reference-calculator"]], "Prepare isolated atoms": [[6, "Prepare-isolated-atoms"]], "Generate initial structures": [[6, "Generate-initial-structures"]], "Run Molecular Dynamics simulation": [[6, "Run-Molecular-Dynamics-simulation"]], "Filter structures": [[6, "Filter-structures"]], "Calculate SOAP descriptor": [[6, "Calculate-SOAP-descriptor"]], "Sub-select with CUR": [[6, "Sub-select-with-CUR"]], "Fit GAP": [[6, "Fit-GAP"]], "Evaluate structures with GAP": [[6, "Evaluate-structures-with-GAP"]], "Evaluate error & plot correlation": [[6, "Evaluate-error-&-plot-correlation"]], "Generating Dimer Structures": [[7, "Generating-Dimer-Structures"]], "FHI-Aims Calculator": [[8, "FHI-Aims-Calculator"]], "Index": [[9, "index"]], "Evaluate structures with a calculator": [[9, "evaluate-structures-with-a-calculator"]], "Generate structures": [[9, "generate-structures"]], "Run MD": [[9, "run-md"]], "Remote execution": [[9, "remote-execution"]], "Get descriptors": [[9, "get-descriptors"]], "Sampling structures": [[9, "sampling-structures"]], "Fit a potential": [[9, "fit-a-potential"]], "Iterative training": [[9, "iterative-training"]], "Command line": [[9, "command-line"], [16, "command-line"]], "Miscellaneous": [[9, "miscellaneous"]], "Parallelize MACE calculator": [[10, "parallelize-mace-calculator"]], "Complete example": [[10, "complete-example"]], "Molecular Dynamics": [[11, "molecular-dynamics"], [26, "molecular-dynamics"]], "Iterative GAP fitting": [[12, "iterative-gap-fitting"]], "Table of contents": [[12, "table-of-contents"]], "General workflow and setup": [[12, "general-workflow-and-setup"]], "Getting started: Parallelization and Imports": [[12, "getting-started-parallelization-and-imports"]], "Fitting the initial GAP": [[12, "fitting-the-initial-gap"]], "Preparing the iterative process": [[12, "preparing-the-iterative-process"]], "The Iterative Process": [[12, "the-iterative-process"]], "Keeping track of training and test errors": [[12, "keeping-track-of-training-and-test-errors"]], "Normal Modes of molecules": [[13, "normal-modes-of-molecules"]], "Generate": [[13, "generate"]], "Visualize": [[13, "visualize"]], "Sample": [[13, "sample"]], "ORCA via Python script": [[14, "orca-via-python-script"]], "Selection or Sampling of Structures": [[15, "Selection-or-Sampling-of-Structures"]], "SMILES to Atoms": [[16, "smiles-to-atoms"], [26, "smiles-to-atoms"]], "Python script": [[16, "python-script"]], "First Example": [[17, "first-example"]], "Complete script": [[17, "complete-script"], [17, "id2"]], "With remote execution": [[17, "with-remote-execution"]], "Welcome to Workflow\u2019s documentation!": [[18, "welcome-to-workflow-s-documentation"]], "Installation": [[18, "installation"]], "Repository": [[18, "repository"]], "Contents": [[18, "contents"]], "Operations": [[20, "operations"]], "Fitting ACE": [[21, "fitting-ace"]], "Calculators in Workflow": [[22, "calculators-in-workflow"]], "Parallelize with generic.calculate()": [[22, "parallelize-with-generic-calculate"]], "File-based calculators": [[22, "file-based-calculators"]], "Special calculators": [[22, "special-calculators"]], "Descriptors": [[23, "descriptors"]], "Fitting potentials": [[24, "fitting-potentials"]], "Fitting GAP": [[25, "fitting-gap"]], "Generating Atomic Structures": [[26, "generating-atomic-structures"]], "Atoms and Dimers": [[26, "atoms-and-dimers"]], "BuildCell": [[26, "buildcell"]], "Super Cells": [[26, "super-cells"]], "Geometry Optimization": [[26, "geometry-optimization"]], "Minima Hopping": [[26, "minima-hopping"]], "Structures for phonons": [[26, "structures-for-phonons"]], "Normal Modes of Molecules": [[26, "normal-modes-of-molecules"]], "Multistage GAP fitting": [[27, "multistage-gap-fitting"]], "Procedure": [[27, "procedure"]], "Configuration file": [[27, "configuration-file"]], "Creating configuration file": [[27, "creating-configuration-file"]], "Selecting Configs": [[28, "selecting-configs"]], "CUR on global descriptor": [[28, "cur-on-global-descriptor"]], "Furthest point sampling": [[28, "furthest-point-sampling"]], "Flat histogram": [[28, "flat-histogram"]], "Convex hull": [[28, "convex-hull"]], "Simple select": [[28, "simple-select"]], "Overview": [[29, "overview"]], "This section outlines:": [[29, null]], "Input and output of atomic structures": [[30, "input-and-output-of-atomic-structures"]], "Internals, for developers": [[30, "internals-for-developers"]], "Overall design": [[31, "overall-design"]], "Automatic parallelization of tasks": [[32, "automatic-parallelization-of-tasks"]], "Programming script that use parallelized operations": [[32, "programming-script-that-use-parallelized-operations"]], "MPI with WFL_MPIPOOL": [[32, "mpi-with-wfl-mpipool"]], "Runtime control over parallelization": [[32, "runtime-control-over-parallelization"]], "Single node using python subprocesses": [[32, "single-node-using-python-subprocesses"]], "Multiple nodes using MPI": [[32, "multiple-nodes-using-mpi"]], "Creating auto-parallelized functions": [[32, "creating-auto-parallelized-functions"]], "Functions as independently queued jobs": [[33, "functions-as-independently-queued-jobs"]], 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"flat_histo_then_by_desc() (in module wfl.cli.gap_rss_iter_fit)": [[38, "wfl.cli.gap_rss_iter_fit.flat_histo_then_by_desc"]], "get_buildcell_input_files() (in module wfl.cli.gap_rss_iter_fit)": [[38, "wfl.cli.gap_rss_iter_fit.get_buildcell_input_files"]], "get_old_fitting_files() (in module wfl.cli.gap_rss_iter_fit)": [[38, "wfl.cli.gap_rss_iter_fit.get_old_fitting_files"]], "increment_active_iter() (in module wfl.cli.gap_rss_iter_fit)": [[38, "wfl.cli.gap_rss_iter_fit.increment_active_iter"]], "inputs() (in module wfl.cli.cli_options)": [[38, "wfl.cli.cli_options.inputs"]], "is_elemental() (in module wfl.cli.gap_rss_iter_fit)": [[38, "wfl.cli.gap_rss_iter_fit.is_elemental"]], "load_old_descriptors_arrays() (in module wfl.cli.gap_rss_iter_fit)": [[38, "wfl.cli.gap_rss_iter_fit.load_old_descriptors_arrays"]], "num_inputs_per_python_subprocess() (in module wfl.cli.cli_options)": [[38, "wfl.cli.cli_options.num_inputs_per_python_subprocess"]], "outputs() (in module wfl.cli.cli_options)": 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"wfl.cli.commands.descriptor.calculate_descriptor"]], "pyjulip_ace() (in module wfl.cli.commands.eval)": [[39, "wfl.cli.commands.eval.pyjulip_ace"]], "wfl.cli.commands": [[39, "module-wfl.cli.commands"]], "wfl.cli.commands.descriptor": [[39, "module-wfl.cli.commands.descriptor"]], "wfl.cli.commands.error": [[39, "module-wfl.cli.commands.error"]], "wfl.cli.commands.eval": [[39, "module-wfl.cli.commands.eval"]], "wfl.cli.commands.generate": [[39, "module-wfl.cli.commands.generate"]], "wfl.cli.commands.select": [[39, "module-wfl.cli.commands.select"]], "calculate() (in module wfl.descriptors.quippy)": [[40, "wfl.descriptors.quippy.calculate"]], "from_any_to_descriptor() (in module wfl.descriptors.quippy)": [[40, "wfl.descriptors.quippy.from_any_to_Descriptor"]], "wfl.descriptors": [[40, "module-wfl.descriptors"]], "wfl.descriptors.quippy": [[40, "module-wfl.descriptors.quippy"]], "ace_fit_jl_path() (in module wfl.fit.utils)": [[41, "wfl.fit.utils.ace_fit_jl_path"]], "calc() (in module 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"module-wfl.fit"]], "wfl.fit.ace": [[41, "module-wfl.fit.ace"]], "wfl.fit.error": [[41, "module-wfl.fit.error"]], "wfl.fit.utils": [[41, "module-wfl.fit.utils"]], "gap_xml_modify_label() (in module wfl.fit.gap.multistage)": [[42, "wfl.fit.gap.multistage.GAP_xml_modify_label"]], "construct_glue_2b() (in module wfl.fit.gap.glue_2b)": [[42, "wfl.fit.gap.glue_2b.construct_glue_2b"]], "dict_to_gap_fit_string() (in module wfl.fit.gap.simple)": [[42, "wfl.fit.gap.simple.dict_to_gap_fit_string"]], "fit() (in module wfl.fit.gap.multistage)": [[42, "wfl.fit.gap.multistage.fit"]], "gap_relocate() (in module wfl.fit.gap.relocate)": [[42, "wfl.fit.gap.relocate.gap_relocate"]], "max_cutoff() (in module wfl.fit.gap.multistage)": [[42, "wfl.fit.gap.multistage.max_cutoff"]], "prep_params() (in module wfl.fit.gap.multistage)": [[42, "wfl.fit.gap.multistage.prep_params"]], "run_gap_fit() (in module wfl.fit.gap.simple)": [[42, "wfl.fit.gap.simple.run_gap_fit"]], "wfl.fit.gap": [[42, 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"wfl.generate.normal_modes.NormalModes.freqs_to_evals"]], "generate_normal_modes_parallel_atoms() (in module wfl.generate.normal_modes)": [[44, "wfl.generate.normal_modes.generate_normal_modes_parallel_atoms"]], "generate_normal_modes_parallel_hessian() (in module wfl.generate.normal_modes)": [[44, "wfl.generate.normal_modes.generate_normal_modes_parallel_hessian"]], "interstitial() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.interstitial"]], "isolated_atom_from_e0() (in module wfl.generate.atoms_and_dimers)": [[44, "wfl.generate.atoms_and_dimers.isolated_atom_from_e0"]], "largest_bulk() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.largest_bulk"]], "minimahopping() (in module wfl.generate.minimahopping)": [[44, "wfl.generate.minimahopping.minimahopping"]], "modes_to_evecs() (wfl.generate.normal_modes.normalmodes static method)": [[44, "wfl.generate.normal_modes.NormalModes.modes_to_evecs"]], "num_hess_delta (wfl.generate.normal_modes.normalmodes attribute)": [[44, "wfl.generate.normal_modes.NormalModes.num_hess_delta"]], "optimize() (in module wfl.generate.optimize)": [[44, "wfl.generate.optimize.optimize"]], "prepare() (in module wfl.generate.atoms_and_dimers)": [[44, "wfl.generate.atoms_and_dimers.prepare"]], "sample_normal_modes() (in module wfl.generate.normal_modes)": [[44, "wfl.generate.normal_modes.sample_normal_modes"]], "sample_normal_modes() (wfl.generate.normal_modes.normalmodes method)": [[44, "wfl.generate.normal_modes.NormalModes.sample_normal_modes"]], "smi_to_atoms() (in module wfl.generate.smiles)": [[44, "wfl.generate.smiles.smi_to_atoms"]], "smiles() (in module wfl.generate.smiles)": [[44, "wfl.generate.smiles.smiles"]], "subselect_from_traj() (in module wfl.generate.optimize)": [[44, "wfl.generate.optimize.subselect_from_traj"]], "summary() (wfl.generate.normal_modes.normalmodes method)": [[44, "wfl.generate.normal_modes.NormalModes.summary"]], "surface() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.surface"]], "vacancy() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.vacancy"]], "view() (wfl.generate.normal_modes.normalmodes method)": [[44, "wfl.generate.normal_modes.NormalModes.view"]], "wfl.generate": [[44, "module-wfl.generate"]], "wfl.generate.atoms_and_dimers": [[44, "module-wfl.generate.atoms_and_dimers"]], "wfl.generate.buildcell": [[44, "module-wfl.generate.buildcell"]], "wfl.generate.minimahopping": [[44, "module-wfl.generate.minimahopping"]], "wfl.generate.normal_modes": [[44, "module-wfl.generate.normal_modes"]], "wfl.generate.optimize": [[44, "module-wfl.generate.optimize"]], "wfl.generate.smiles": [[44, "module-wfl.generate.smiles"]], "wfl.generate.supercells": [[44, "module-wfl.generate.supercells"]], "wfl.generate.utils": [[44, "module-wfl.generate.utils"]], "abortoncollision (class in wfl.generate.md.abort)": [[45, "wfl.generate.md.abort.AbortOnCollision"]], "abortsimbase (class in wfl.generate.md.abort_base)": [[45, "wfl.generate.md.abort_base.AbortSimBase"]], "atoms_ok() (wfl.generate.md.abort.abortoncollision method)": [[45, "wfl.generate.md.abort.AbortOnCollision.atoms_ok"]], "atoms_ok() (wfl.generate.md.abort_base.abortsimbase method)": [[45, "wfl.generate.md.abort_base.AbortSimBase.atoms_ok"]], "md() (in module wfl.generate.md)": [[45, "wfl.generate.md.md"]], "stop() (wfl.generate.md.abort_base.abortsimbase method)": [[45, "wfl.generate.md.abort_base.AbortSimBase.stop"]], "wfl.generate.md": [[45, "module-wfl.generate.md"]], "wfl.generate.md.abort": [[45, "module-wfl.generate.md.abort"]], "wfl.generate.md.abort_base": [[45, "module-wfl.generate.md.abort_base"]], "cur() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.CUR"]], "cur_conf_global() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.CUR_conf_global"]], "biased_select_conf() (in module wfl.select.flat_histogram)": [[46, "wfl.select.flat_histogram.biased_select_conf"]], "by_bool_func() (in module wfl.select.simple)": [[46, "wfl.select.simple.by_bool_func"]], "by_index() (in module wfl.select.simple)": [[46, "wfl.select.simple.by_index"]], "compare_manual_minima() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.compare_manual_minima"]], "do_svd() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.do_svd"]], "greedy_fps_conf_global() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.greedy_fps_conf_global"]], "minima_among_neighbors() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.minima_among_neighbors"]], "prep_descs_and_exclude() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.prep_descs_and_exclude"]], "select() (in module wfl.select.convex_hull)": [[46, "wfl.select.convex_hull.select"]], "val_relative_to_nearby_composition_volume_min() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.val_relative_to_nearby_composition_volume_min"]], "wfl.select": [[46, "module-wfl.select"]], "wfl.select.by_descriptor": [[46, "module-wfl.select.by_descriptor"]], "wfl.select.convex_hull": [[46, "module-wfl.select.convex_hull"]], "wfl.select.flat_histogram": [[46, "module-wfl.select.flat_histogram"]], "wfl.select.selection_space": [[46, "module-wfl.select.selection_space"]], "wfl.select.simple": [[46, "module-wfl.select.simple"]], "write_selected_and_clean() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.write_selected_and_clean"]], "params (class in wfl.utils.params)": [[47, "wfl.utils.params.Params"]], "pressurerecursionerror": [[47, "wfl.utils.pressure.PressureRecursionError"]], "at_copy_save_results() (in module wfl.utils.at_copy_save_results)": [[47, "wfl.utils.at_copy_save_results.at_copy_save_results"]], "atomization_energy() (in module wfl.utils.configs)": [[47, "wfl.utils.configs.atomization_energy"]], "atoms_to_list() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.atoms_to_list"]], "calc_list() (in module wfl.utils.ndim_neighbor_list)": [[47, "wfl.utils.ndim_neighbor_list.calc_list"]], "calc_list_cells() (in module wfl.utils.ndim_neighbor_list)": [[47, "wfl.utils.ndim_neighbor_list.calc_list_cells"]], "chunks() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.chunks"]], "clean_dir() (in module wfl.utils.file_utils)": [[47, "wfl.utils.file_utils.clean_dir"]], "composition_space_zs() (in module wfl.utils.vol_composition_space)": [[47, "wfl.utils.vol_composition_space.composition_space_Zs"]], "composition_space_coord() (in module wfl.utils.vol_composition_space)": [[47, "wfl.utils.vol_composition_space.composition_space_coord"]], "construct_calculator_picklesafe() (in module wfl.utils.parallel)": [[47, "wfl.utils.parallel.construct_calculator_picklesafe"]], "cur_iter (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.cur_iter"]], "dft_code (wfl.utils.params.params property)": [[47, 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"wfl.utils.params.Params.implemented_calculators"]], "increment_active_iter() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.increment_active_iter"]], "julia_exec_path() (in module wfl.utils.julia)": [[47, "wfl.utils.julia.julia_exec_path"]], "print_log() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.print_log"]], "process_active_iter() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.process_active_iter"]], "random_three_vector() (in module wfl.utils.vector_utils)": [[47, "wfl.utils.vector_utils.random_three_vector"]], "replace_eval_in_strs() (in module wfl.utils.replace_eval_in_strs)": [[47, "wfl.utils.replace_eval_in_strs.replace_eval_in_strs"]], "round_sig_figs() (in module wfl.utils.round_sig_figs)": [[47, "wfl.utils.round_sig_figs.round_sig_figs"]], "sample_pressure() (in module wfl.utils.pressure)": [[47, "wfl.utils.pressure.sample_pressure"]], "vertical_dist_from_hull() (in module wfl.utils.convex_hull)": [[47, 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\ No newline at end of file
+Search.setIndex({"docnames": ["attic/command_line", "attic/operations.utils", "command_line.automatic_docs", "examples", "examples.buildcell", "examples.contributions", "examples.daisy_chain_mlip_fitting", "examples.dimers", "examples.fhiaims_calculator", "examples.index", "examples.mace", "examples.md", "examples.mlip_fitting", "examples.normal_modes", "examples.orca_python", "examples.select_fps", "examples.smiles", "first_example", "index", "modules", "operations", "operations.ace_fitting", "operations.calculators", "operations.descriptors", "operations.fitting", "operations.gap_fitting", "operations.generate", "operations.multistage_gap_fitting", "operations.select", "overview", "overview.configset", "overview.overall_design", "overview.parallelisation", "overview.queued", "wfl", "wfl.autoparallelize", "wfl.calculators", "wfl.calculators.orca", "wfl.cli", "wfl.cli.commands", "wfl.descriptors", "wfl.fit", "wfl.fit.gap", "wfl.fit.modify_database", "wfl.generate", "wfl.generate.md_PROTECT", "wfl.select", "wfl.utils", "workflows.rss"], "filenames": ["attic/command_line.rst", "attic/operations.utils.md", "command_line.automatic_docs.rst", "examples.rst", "examples.buildcell.ipynb", "examples.contributions.md", "examples.daisy_chain_mlip_fitting.ipynb", "examples.dimers.ipynb", "examples.fhiaims_calculator.ipynb", "examples.index.md", "examples.mace.md", "examples.md.md", "examples.mlip_fitting.md", "examples.normal_modes.md", "examples.orca_python.md", "examples.select_fps.ipynb", "examples.smiles.md", "first_example.md", "index.rst", "modules.rst", "operations.rst", "operations.ace_fitting.md", "operations.calculators.md", "operations.descriptors.md", "operations.fitting.rst", "operations.gap_fitting.md", "operations.generate.md", "operations.multistage_gap_fitting.rst", "operations.select.md", "overview.rst", "overview.configset.rst", "overview.overall_design.rst", "overview.parallelisation.rst", "overview.queued.md", "wfl.rst", "wfl.autoparallelize.rst", "wfl.calculators.rst", "wfl.calculators.orca.rst", "wfl.cli.rst", "wfl.cli.commands.rst", "wfl.descriptors.rst", "wfl.fit.rst", "wfl.fit.gap.rst", "wfl.fit.modify_database.rst", "wfl.generate.rst", "wfl.generate.md_PROTECT.rst", "wfl.select.rst", "wfl.utils.rst", "workflows.rss.rst"], "titles": ["Command line interface", "Utility functions", "wfl", "Examples", "Random Structures via buildcell", "Contributing Examples", "GAP fit workflow with many wfl use-case examples", "Generating Dimer Structures", "FHI-Aims Calculator", "Index", "Parallelize MACE calculator", "Molecular Dynamics", "Iterative GAP fitting", "Normal Modes of molecules", "ORCA via Python script", "Selection or Sampling of Structures", "SMILES to Atoms", "First Example", "Welcome to Workflow\u2019s documentation!", "wfl", "Operations", "Fitting ACE", "Calculators in Workflow", "Descriptors", "Fitting potentials", "Fitting GAP", "Generating Atomic Structures", "Multistage GAP fitting", "Selecting Configs", "Overview", "Input and output of atomic structures", "Overall design", "Automatic parallelization of tasks", "Functions as independently queued jobs", "wfl package", "wfl.autoparallelize package", "wfl.calculators package", "wfl.calculators.orca package", "wfl.cli package", "wfl.cli.commands package", "wfl.descriptors package", "wfl.fit package", "wfl.fit.gap package", "wfl.fit.modify_database package", "wfl.generate package", "wfl.generate.md package", "wfl.select package", "wfl.utils package", "How to do GAP-RSS"], "terms": {"descript": [0, 5, 18], "all": [0, 2, 5, 6, 7, 8, 9, 12, 13, 14, 15, 17, 18, 22, 26, 27, 28, 30, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 44, 45, 47, 48], "cli": [0, 19, 34, 47, 48], "tool": [0, 47], "automat": [0, 15, 17, 18, 21, 29, 33, 34, 36, 40, 41, 44, 45, 46, 48], "gener": [0, 3, 4, 8, 10, 11, 14, 15, 16, 17, 18, 19, 20, 23, 31, 32, 34, 35, 37, 38, 41, 42, 46, 47, 48], "documment": [0, 17, 21], "function": [0, 2, 4, 6, 7, 8, 9, 12, 13, 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"-f": [[2, "cmdoption-wfl-error-f"]], "-i": [[2, "cmdoption-wfl-descriptor-quippy-i"], [2, "cmdoption-wfl-error-i"], [2, "cmdoption-wfl-eval-ace-i"], [2, "cmdoption-wfl-eval-atomization-energy-i"], [2, "cmdoption-wfl-eval-gap-i"], [2, "cmdoption-wfl-eval-mace-i"], [2, "cmdoption-wfl-select-cur-i"], [2, "cmdoption-wfl-select-lambda-i"]], "-k": [[2, "cmdoption-wfl-eval-atomization-energy-k"]], "-o": [[2, "cmdoption-wfl-descriptor-quippy-o"], [2, "cmdoption-wfl-eval-ace-o"], [2, "cmdoption-wfl-eval-atomization-energy-o"], [2, "cmdoption-wfl-eval-gap-o"], [2, "cmdoption-wfl-eval-mace-o"], [2, "cmdoption-wfl-generate-buildcell-o"], [2, "cmdoption-wfl-generate-smiles-o"], [2, "cmdoption-wfl-select-cur-o"], [2, "cmdoption-wfl-select-lambda-o"]], "-p": [[2, "cmdoption-wfl-error-p"]], "-pf": [[2, "cmdoption-wfl-eval-ace-pf"], [2, "cmdoption-wfl-eval-gap-pf"], [2, "cmdoption-wfl-eval-mace-pf"]], "-pp": [[2, "cmdoption-wfl-eval-ace-pp"], [2, "cmdoption-wfl-eval-atomization-energy-pp"], [2, 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"wfl.generate.normal_modes.NormalModes.freqs_to_evals"]], "generate_normal_modes_parallel_atoms() (in module wfl.generate.normal_modes)": [[44, "wfl.generate.normal_modes.generate_normal_modes_parallel_atoms"]], "generate_normal_modes_parallel_hessian() (in module wfl.generate.normal_modes)": [[44, "wfl.generate.normal_modes.generate_normal_modes_parallel_hessian"]], "interstitial() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.interstitial"]], "isolated_atom_from_e0() (in module wfl.generate.atoms_and_dimers)": [[44, "wfl.generate.atoms_and_dimers.isolated_atom_from_e0"]], "largest_bulk() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.largest_bulk"]], "minimahopping() (in module wfl.generate.minimahopping)": [[44, "wfl.generate.minimahopping.minimahopping"]], "modes_to_evecs() (wfl.generate.normal_modes.normalmodes static method)": [[44, "wfl.generate.normal_modes.NormalModes.modes_to_evecs"]], "num_hess_delta (wfl.generate.normal_modes.normalmodes attribute)": [[44, "wfl.generate.normal_modes.NormalModes.num_hess_delta"]], "optimize() (in module wfl.generate.optimize)": [[44, "wfl.generate.optimize.optimize"]], "phonopy() (in module wfl.generate.phonopy)": [[44, "wfl.generate.phonopy.phonopy"]], "prepare() (in module wfl.generate.atoms_and_dimers)": [[44, "wfl.generate.atoms_and_dimers.prepare"]], "sample_normal_modes() (in module wfl.generate.normal_modes)": [[44, "wfl.generate.normal_modes.sample_normal_modes"]], "sample_normal_modes() (wfl.generate.normal_modes.normalmodes method)": [[44, "wfl.generate.normal_modes.NormalModes.sample_normal_modes"]], "smi_to_atoms() (in module wfl.generate.smiles)": [[44, "wfl.generate.smiles.smi_to_atoms"]], "smiles() (in module wfl.generate.smiles)": [[44, "wfl.generate.smiles.smiles"]], "subselect_from_traj() (in module wfl.generate.optimize)": [[44, "wfl.generate.optimize.subselect_from_traj"]], "summary() (wfl.generate.normal_modes.normalmodes method)": [[44, "wfl.generate.normal_modes.NormalModes.summary"]], "surface() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.surface"]], "vacancy() (in module wfl.generate.supercells)": [[44, "wfl.generate.supercells.vacancy"]], "view() (wfl.generate.normal_modes.normalmodes method)": [[44, "wfl.generate.normal_modes.NormalModes.view"]], "wfl.generate": [[44, "module-wfl.generate"]], "wfl.generate.atoms_and_dimers": [[44, "module-wfl.generate.atoms_and_dimers"]], "wfl.generate.buildcell": [[44, "module-wfl.generate.buildcell"]], "wfl.generate.minimahopping": [[44, "module-wfl.generate.minimahopping"]], "wfl.generate.normal_modes": [[44, "module-wfl.generate.normal_modes"]], "wfl.generate.optimize": [[44, "module-wfl.generate.optimize"]], "wfl.generate.phonopy": [[44, "module-wfl.generate.phonopy"]], "wfl.generate.smiles": [[44, "module-wfl.generate.smiles"]], "wfl.generate.supercells": [[44, "module-wfl.generate.supercells"]], "wfl.generate.utils": [[44, "module-wfl.generate.utils"]], "abortoncollision (class in wfl.generate.md.abort)": [[45, "wfl.generate.md.abort.AbortOnCollision"]], "abortsimbase (class in wfl.generate.md.abort_base)": [[45, "wfl.generate.md.abort_base.AbortSimBase"]], "atoms_ok() (wfl.generate.md.abort.abortoncollision method)": [[45, "wfl.generate.md.abort.AbortOnCollision.atoms_ok"]], "atoms_ok() (wfl.generate.md.abort_base.abortsimbase method)": [[45, "wfl.generate.md.abort_base.AbortSimBase.atoms_ok"]], "md() (in module wfl.generate.md)": [[45, "wfl.generate.md.md"]], "stop() (wfl.generate.md.abort_base.abortsimbase method)": [[45, "wfl.generate.md.abort_base.AbortSimBase.stop"]], "wfl.generate.md": [[45, "module-wfl.generate.md"]], "wfl.generate.md.abort": [[45, "module-wfl.generate.md.abort"]], "wfl.generate.md.abort_base": [[45, "module-wfl.generate.md.abort_base"]], "cur() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.CUR"]], "cur_conf_global() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.CUR_conf_global"]], "biased_select_conf() (in module wfl.select.flat_histogram)": [[46, "wfl.select.flat_histogram.biased_select_conf"]], "by_bool_func() (in module wfl.select.simple)": [[46, "wfl.select.simple.by_bool_func"]], "by_index() (in module wfl.select.simple)": [[46, "wfl.select.simple.by_index"]], "compare_manual_minima() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.compare_manual_minima"]], "do_svd() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.do_svd"]], "greedy_fps_conf_global() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.greedy_fps_conf_global"]], "minima_among_neighbors() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.minima_among_neighbors"]], "prep_descs_and_exclude() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.prep_descs_and_exclude"]], "select() (in module wfl.select.convex_hull)": [[46, "wfl.select.convex_hull.select"]], "val_relative_to_nearby_composition_volume_min() (in module wfl.select.selection_space)": [[46, "wfl.select.selection_space.val_relative_to_nearby_composition_volume_min"]], "wfl.select": [[46, "module-wfl.select"]], "wfl.select.by_descriptor": [[46, "module-wfl.select.by_descriptor"]], "wfl.select.convex_hull": [[46, "module-wfl.select.convex_hull"]], "wfl.select.flat_histogram": [[46, "module-wfl.select.flat_histogram"]], "wfl.select.selection_space": [[46, "module-wfl.select.selection_space"]], "wfl.select.simple": [[46, "module-wfl.select.simple"]], "write_selected_and_clean() (in module wfl.select.by_descriptor)": [[46, "wfl.select.by_descriptor.write_selected_and_clean"]], "params (class in wfl.utils.params)": [[47, "wfl.utils.params.Params"]], "pressurerecursionerror": [[47, "wfl.utils.pressure.PressureRecursionError"]], "at_copy_save_results() (in module wfl.utils.at_copy_save_results)": [[47, "wfl.utils.at_copy_save_results.at_copy_save_results"]], "atomization_energy() (in module wfl.utils.configs)": [[47, "wfl.utils.configs.atomization_energy"]], "atoms_to_list() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.atoms_to_list"]], "calc_list() (in module wfl.utils.ndim_neighbor_list)": [[47, "wfl.utils.ndim_neighbor_list.calc_list"]], "calc_list_cells() (in module wfl.utils.ndim_neighbor_list)": [[47, "wfl.utils.ndim_neighbor_list.calc_list_cells"]], "chunks() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.chunks"]], "clean_dir() (in module wfl.utils.file_utils)": [[47, "wfl.utils.file_utils.clean_dir"]], "composition_space_zs() (in module wfl.utils.vol_composition_space)": [[47, "wfl.utils.vol_composition_space.composition_space_Zs"]], "composition_space_coord() (in module wfl.utils.vol_composition_space)": [[47, "wfl.utils.vol_composition_space.composition_space_coord"]], "construct_calculator_picklesafe() (in module wfl.utils.parallel)": [[47, "wfl.utils.parallel.construct_calculator_picklesafe"]], "cur_iter (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.cur_iter"]], "dft_code (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.dft_code"]], "dft_params (wfl.utils.params.params property)": [[47, "wfl.utils.params.Params.dft_params"]], "dict_to_quip_str() (in module wfl.utils.quip_cli_strings)": [[47, "wfl.utils.quip_cli_strings.dict_to_quip_str"]], "dict_tuple_keys_to_str() (in module wfl.utils.misc)": [[47, "wfl.utils.misc.dict_tuple_keys_to_str"]], "extract_e0() (in module wfl.utils.gap_xml_tools)": [[47, "wfl.utils.gap_xml_tools.extract_e0"]], "find_hull() (in module wfl.utils.convex_hull)": [[47, "wfl.utils.convex_hull.find_hull"]], "find_isolated_atoms() (in module wfl.utils.configs)": [[47, "wfl.utils.configs.find_isolated_atoms"]], "find_voids() (in module wfl.utils.find_voids)": [[47, "wfl.utils.find_voids.find_voids"]], "get() (wfl.utils.params.params method)": [[47, "wfl.utils.params.Params.get"]], "get_wfl_version() (in module wfl.utils.version)": [[47, "wfl.utils.version.get_wfl_version"]], "implemented_calculators (wfl.utils.params.params attribute)": [[47, "wfl.utils.params.Params.implemented_calculators"]], "increment_active_iter() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.increment_active_iter"]], "julia_exec_path() (in module wfl.utils.julia)": [[47, "wfl.utils.julia.julia_exec_path"]], "print_log() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.print_log"]], "process_active_iter() (in module wfl.utils.logging)": [[47, "wfl.utils.logging.process_active_iter"]], "random_three_vector() (in module wfl.utils.vector_utils)": [[47, "wfl.utils.vector_utils.random_three_vector"]], "replace_eval_in_strs() (in module wfl.utils.replace_eval_in_strs)": [[47, "wfl.utils.replace_eval_in_strs.replace_eval_in_strs"]], "round_sig_figs() (in module wfl.utils.round_sig_figs)": [[47, "wfl.utils.round_sig_figs.round_sig_figs"]], "sample_pressure() (in module wfl.utils.pressure)": [[47, "wfl.utils.pressure.sample_pressure"]], "vertical_dist_from_hull() (in module wfl.utils.convex_hull)": [[47, "wfl.utils.convex_hull.vertical_dist_from_hull"]], "wfl.utils": [[47, "module-wfl.utils"]], "wfl.utils.at_copy_save_results": [[47, "module-wfl.utils.at_copy_save_results"]], "wfl.utils.configs": [[47, "module-wfl.utils.configs"]], "wfl.utils.convex_hull": [[47, "module-wfl.utils.convex_hull"]], "wfl.utils.file_utils": [[47, "module-wfl.utils.file_utils"]], "wfl.utils.find_voids": [[47, "module-wfl.utils.find_voids"]], "wfl.utils.gap_xml_tools": [[47, "module-wfl.utils.gap_xml_tools"]], "wfl.utils.julia": [[47, "module-wfl.utils.julia"]], "wfl.utils.logging": [[47, "module-wfl.utils.logging"]], "wfl.utils.misc": [[47, "module-wfl.utils.misc"]], "wfl.utils.ndim_neighbor_list": [[47, "module-wfl.utils.ndim_neighbor_list"]], "wfl.utils.parallel": [[47, "module-wfl.utils.parallel"]], "wfl.utils.params": [[47, "module-wfl.utils.params"]], "wfl.utils.pressure": [[47, "module-wfl.utils.pressure"]], "wfl.utils.quip_cli_strings": [[47, "module-wfl.utils.quip_cli_strings"]], "wfl.utils.replace_eval_in_strs": [[47, "module-wfl.utils.replace_eval_in_strs"]], "wfl.utils.round_sig_figs": [[47, "module-wfl.utils.round_sig_figs"]], "wfl.utils.vector_utils": [[47, "module-wfl.utils.vector_utils"]], "wfl.utils.version": [[47, "module-wfl.utils.version"]], "wfl.utils.vol_composition_space": [[47, "module-wfl.utils.vol_composition_space"]]}})
\ No newline at end of file
diff --git a/wfl.autoparallelize.html b/wfl.autoparallelize.html
index 960515e0..0c4e6350 100644
--- a/wfl.autoparallelize.html
+++ b/wfl.autoparallelize.html
@@ -407,7 +407,6 @@ remote_label (str, default None) – string label to match to keys in remote_info dict
run tasks as series of remote jobs
remote_info (RemoteInfo) – object with all information on remote job, including system, resources, job num_inputs_per_python_subprocess, -etc, or dict of kwargs for its constructor
autopara_info (AutoparaInfo) – object with all information on autoparallelizing remote job, including autopara_info.remote_info +which contains RemoteInfo with information on remote job, including system, resources, job +num_inputs_per_python_subprocess, etc, or dict of kwargs for its constructor
quiet (bool, default False) – do not output (to stderr) progress info
args (See autoparallelize.autoparallelize() for other) –
Bases: object
Create a RemoteInfo object
subselect_from_traj()