aiida_castep package

Subpackages

• aiida_castep.calculations package
  • Subpackages
    • aiida_castep.calculations.helper package
      • Submodules
      • aiida_castep.calculations.helper.generate module
      • Module contents
  • Submodules
  • aiida_castep.calculations.castep module
    • CastepCalculation
      • CastepCalculation._DEFAULTS
      • CastepCalculation.__abstractmethods__
      • CastepCalculation.__module__
      • CastepCalculation._abc_impl
      • CastepCalculation._acceptable_tasks
      • CastepCalculation._cell_links
      • CastepCalculation._copied_attributes
      • CastepCalculation._default_retrieve_list
      • CastepCalculation._extra_kpoints
      • CastepCalculation._generate_header_lines()
      • CastepCalculation._param_links
      • CastepCalculation._prepare_cell_file()
      • CastepCalculation._write_headers
      • CastepCalculation.check_restart()
      • CastepCalculation.define()
      • CastepCalculation.dryrun_test()
      • CastepCalculation.get_castep_input_summary()
      • CastepCalculation.prepare_for_submission()
      • CastepCalculation.retrieve_dict
      • CastepCalculation.submit_test()
      • CastepCalculation.update_paraemters()
      • CastepCalculation.use_pseudos_from_family()
    • submit_test()
  • aiida_castep.calculations.datastructure module
    • CastepInputFile
      • CastepInputFile.__init__()
      • CastepInputFile.__module__
      • CastepInputFile.get_file_lines()
      • CastepInputFile.get_string()
    • CellFile
      • CellFile.__module__
    • ParamFile
      • ParamFile.__module__
  • aiida_castep.calculations.inpgen module
    • CastepInputGenerator
      • CastepInputGenerator.__dict__
      • CastepInputGenerator.__init__()
      • CastepInputGenerator.__module__
      • CastepInputGenerator.__weakref__
      • CastepInputGenerator._include_extra_kpoints()
      • CastepInputGenerator._prepare_cell_file()
      • CastepInputGenerator._prepare_param_file()
      • CastepInputGenerator._prepare_pseudo_potentials()
      • CastepInputGenerator.prepare_inputs()
  • aiida_castep.calculations.tools module
    • CastepCalcTools
      • CastepCalcTools.__module__
      • CastepCalcTools.compare_with()
      • CastepCalcTools.create_restart()
      • CastepCalcTools.get_castep_input_summary()
    • castep_input_summary()
    • create_restart()
    • update_parameters()
    • use_pseudos_from_family()
  • aiida_castep.calculations.utils module
    • _lowercase_dict()
    • _uppercase_dict()
    • get_castep_ion_line()
  • Module contents
• aiida_castep.cmdline package
  • Submodules
  • aiida_castep.cmdline.helper_cmd module
    • dot_proc()
    • get_helper()
    • progress()
  • aiida_castep.cmdline.mock_castep module
    • data_path()
    • output_file()
    • stop_and_return()
  • aiida_castep.cmdline.otfg_cmd module
  • Module contents
• aiida_castep.data package
  • Submodules
  • aiida_castep.data.otfg module
    • OTFGData
      • OTFGData.__abstractmethods__
      • OTFGData.__init__()
      • OTFGData.__module__
      • OTFGData.__parameters__
      • OTFGData._abc_impl
      • OTFGData._logger
      • OTFGData._plugin_type_string
      • OTFGData._query_type_string
      • OTFGData._validate()
      • OTFGData.element
      • OTFGData.entry
      • OTFGData.from_entry()
      • OTFGData.get_or_create()
      • OTFGData.get_otfg_group()
      • OTFGData.get_otfg_groups()
      • OTFGData.otfg_family_type_string
      • OTFGData.set_element()
      • OTFGData.set_string()
      • OTFGData.store()
      • OTFGData.string
    • OTFGGroup
      • OTFGGroup.__abstractmethods__
      • OTFGGroup.__module__
      • OTFGGroup.__parameters__
      • OTFGGroup._abc_impl
      • OTFGGroup._type_string
    • migrate_otfg_family()
    • upload_otfg_family()
  • aiida_castep.data.usp module
    • UspData
      • UspData.__abstractmethods__
      • UspData.__init__()
      • UspData.__module__
      • UspData.__parameters__
      • UspData._abc_impl
      • UspData._logger
      • UspData._plugin_type_string
      • UspData._query_type_string
      • UspData._validate()
      • UspData.element
      • UspData.from_md5()
      • UspData.get_or_create()
      • UspData.get_usp_group()
      • UspData.get_usp_groups()
      • UspData.md5sum
      • UspData.set_element()
      • UspData.set_file()
      • UspData.store()
      • UspData.string
      • UspData.uspfamily_type_string
    • upload_usp_family()
  • aiida_castep.data.utils module
    • get_usp_element()
    • split_otfg_entry()
  • Module contents
    • _get_pseudos_from_aiida_pseudo()
    • get_pseudos_from_structure()
• aiida_castep.parsers package
  • Submodules
  • aiida_castep.parsers.castep module
    • CastepParser
      • CastepParser.__abstractmethods__
      • CastepParser.__module__
      • CastepParser._abc_impl
      • CastepParser._has_empty_bands()
      • CastepParser._setting_key
      • CastepParser.castep_input_parameters
      • CastepParser.castep_task
      • CastepParser.parse()
    • RetrievedFileManager
      • RetrievedFileManager.__dict__
      • RetrievedFileManager.__init__()
      • RetrievedFileManager.__module__
      • RetrievedFileManager.__weakref__
      • RetrievedFileManager.get_object_content()
      • RetrievedFileManager.has_file()
      • RetrievedFileManager.list_object_names()
      • RetrievedFileManager.open()
    • bands_from_castepbin()
    • bands_to_bandsdata()
  • aiida_castep.parsers.castep_bin module
    • CastepbinFile
      • CastepbinFile.__dict__
      • CastepbinFile.__init__()
      • CastepbinFile.__module__
      • CastepbinFile.__weakref__
      • CastepbinFile._reindex2()
      • CastepbinFile._reindex3()
      • CastepbinFile.cell
      • CastepbinFile.eigenvalues
      • CastepbinFile.fermi_energy
      • CastepbinFile.forces
      • CastepbinFile.kpoint_weights
      • CastepbinFile.kpoints
      • CastepbinFile.kpoints_current_cell
      • CastepbinFile.kpoints_indices
      • CastepbinFile.occupancies
      • CastepbinFile.scaled_positions
      • CastepbinFile.total_energy
  • aiida_castep.parsers.constants module
  • aiida_castep.parsers.raw_parser module
    • LineParser
      • LineParser.__dict__
      • LineParser.__init__()
      • LineParser.__module__
      • LineParser.__weakref__
      • LineParser.parse()
    • Matcher
      • Matcher.__dict__
      • Matcher.__init__()
      • Matcher.__module__
      • Matcher.__weakref__
      • Matcher.match_pattern()
    • RawParser
      • RawParser.__dict__
      • RawParser.__init__()
      • RawParser.__module__
      • RawParser.__weakref__
      • RawParser.parse()
      • RawParser.parse_dot_bands()
      • RawParser.parse_dot_castep()
      • RawParser.parse_geom()
    • UnitMatcher
      • UnitMatcher.__module__
      • UnitMatcher.match_pattern()
    • get_iter_parser()
    • parse_castep_text_output()
    • parse_dot_bands()
    • parse_force_box()
    • parse_geom_text_output()
    • parse_popn_box()
    • parse_stress_box()
  • aiida_castep.parsers.test_marcher module
  • aiida_castep.parsers.utils module
    • CASTEPOutputParsingError
      • CASTEPOutputParsingError.__module__
    • add_last_if_exists()
    • desort_structure()
    • get_desort_args()
    • structure_from_input()
  • Module contents
• aiida_castep.utils package
  • Submodules
  • aiida_castep.utils.dos module
    • DOSProcessor
      • DOSProcessor.__dict__
      • DOSProcessor.__init__()
      • DOSProcessor.__module__
      • DOSProcessor.__weakref__
      • DOSProcessor.bin_width
      • DOSProcessor.get_dos()
      • DOSProcessor.has_spin
      • DOSProcessor.max_eigen_value
      • DOSProcessor.min_eigen_value
    • gaussian_kernel()
  • aiida_castep.utils.mock module
    • MockOutput
      • MockOutput.__dict__
      • MockOutput.__init__()
      • MockOutput.__module__
      • MockOutput.__weakref__
      • MockOutput._reg_file
      • MockOutput.calculate_hash()
      • MockOutput.copy_results()
      • MockOutput.register()
      • MockOutput.register_node()
      • MockOutput.registry
      • MockOutput.run()
    • get_hash()
    • test_hash()
  • aiida_castep.utils.mock_code module
    • MockCastep
      • MockCastep.__dict__
      • MockCastep.__init__()
      • MockCastep.__module__
      • MockCastep.__weakref__
      • MockCastep.is_runnable
      • MockCastep.run()
    • MockRegistry
      • MockRegistry.__dict__
      • MockRegistry.__init__()
      • MockRegistry.__module__
      • MockRegistry.__weakref__
      • MockRegistry._register_folder()
      • MockRegistry._setup_logger()
      • MockRegistry.compute_hash()
      • MockRegistry.extract_calc_by_hash()
      • MockRegistry.extract_calc_by_path()
      • MockRegistry.get_path_by_hash()
      • MockRegistry.get_path_by_name()
      • MockRegistry.scan()
      • MockRegistry.upload_aiida_calc()
      • MockRegistry.upload_aiida_work()
      • MockRegistry.upload_calc()
    • copy_from_aiida()
    • get_hash()
  • Module contents
    • ase_to_castep_index()
    • atoms_to_castep()
    • band_array_ensure_ndim()
    • castep_to_atoms()
    • compute_kpoints_spacing()
    • desort_atoms_castep()
    • export_calculation()
    • generate_ionic_fix_cons()
    • generate_rel_fix()
    • get_remote_folder_info()
    • get_remote_folder_size()
    • is_castep_sorted()
    • read_popn()
    • reuse_kpoints_grid()
    • sort_atoms_castep()
    • take_popn()
    • traj_to_atoms()
• aiida_castep.workflows package
  • Submodules
  • aiida_castep.workflows.bands module
    • CastepBandsWorkChain
      • CastepBandsWorkChain.__abstractmethods__
      • CastepBandsWorkChain.__module__
      • CastepBandsWorkChain._abc_impl
      • CastepBandsWorkChain._base_wk_string
      • CastepBandsWorkChain._relax_wk_string
      • CastepBandsWorkChain._task_name
      • CastepBandsWorkChain.define()
      • CastepBandsWorkChain.inspect_bands_dos()
      • CastepBandsWorkChain.on_terminated()
      • CastepBandsWorkChain.run_bands_dos()
      • CastepBandsWorkChain.run_relax()
      • CastepBandsWorkChain.run_scf()
      • CastepBandsWorkChain.run_seekpath()
      • CastepBandsWorkChain.setup()
      • CastepBandsWorkChain.setup_restart_folder()
      • CastepBandsWorkChain.should_do_relax()
      • CastepBandsWorkChain.should_run_scf()
      • CastepBandsWorkChain.should_run_seekpath()
      • CastepBandsWorkChain.verify_relax()
      • CastepBandsWorkChain.verify_scf()
    • compose_labelled_bands()
    • dos_from_bands()
    • ensure_checkpoint()
    • nested_update()
    • nested_update_dict_node()
    • seekpath_structure_analysis()
  • aiida_castep.workflows.base module
    • CastepBaseWorkChain
      • CastepBaseWorkChain.__abstractmethods__
      • CastepBaseWorkChain.__init__()
      • CastepBaseWorkChain.__module__
      • CastepBaseWorkChain._abc_impl
      • CastepBaseWorkChain._calculation_class
      • CastepBaseWorkChain._context_pain_dicts
      • CastepBaseWorkChain._error_handlers
      • CastepBaseWorkChain._handle_calculation_failure()
      • CastepBaseWorkChain._handle_no_empty_bands()
      • CastepBaseWorkChain._handle_scf_failure()
      • CastepBaseWorkChain._handle_stop_by_request()
      • CastepBaseWorkChain._handle_unexpected_failure()
      • CastepBaseWorkChain._handle_walltime_limit()
      • CastepBaseWorkChain._prepare_process_inputs()
      • CastepBaseWorkChain._spec
      • CastepBaseWorkChain._verbose
      • CastepBaseWorkChain.define()
      • CastepBaseWorkChain.inspect_calculation()
      • CastepBaseWorkChain.inspect_dryrun()
      • CastepBaseWorkChain.on_terminated()
      • CastepBaseWorkChain.prepare_calculation()
      • CastepBaseWorkChain.results()
      • CastepBaseWorkChain.run_calculation()
      • CastepBaseWorkChain.run_dry_run()
      • CastepBaseWorkChain.setup()
      • CastepBaseWorkChain.should_dry_run()
      • CastepBaseWorkChain.should_run_calculation()
      • CastepBaseWorkChain.validate_dryrun_inputs()
      • CastepBaseWorkChain.validate_inputs()
    • _compute_castep_gam_offset()
    • _get_castep_output_file()
    • _handle_no_empty_bands()
    • _handle_scf_failure()
    • _handle_stop_by_request()
    • _handle_walltime_limit()
  • aiida_castep.workflows.common module
    • ErrorHandler
      • ErrorHandler.__getnewargs__()
      • ErrorHandler.__module__
      • ErrorHandler.__new__()
      • ErrorHandler.__repr__()
      • ErrorHandler.__slots__
      • ErrorHandler._asdict()
      • ErrorHandler._field_defaults
      • ErrorHandler._fields
      • ErrorHandler._fields_defaults
      • ErrorHandler._make()
      • ErrorHandler._replace()
      • ErrorHandler.method
      • ErrorHandler.priority
    • ErrorHandlerReport
      • ErrorHandlerReport.__getnewargs__()
      • ErrorHandlerReport.__module__
      • ErrorHandlerReport.__new__()
      • ErrorHandlerReport.__repr__()
      • ErrorHandlerReport.__slots__
      • ErrorHandlerReport._asdict()
      • ErrorHandlerReport._field_defaults
      • ErrorHandlerReport._fields
      • ErrorHandlerReport._fields_defaults
      • ErrorHandlerReport._make()
      • ErrorHandlerReport._replace()
      • ErrorHandlerReport.do_break
      • ErrorHandlerReport.exit_code
      • ErrorHandlerReport.is_handled
    • UnexpectedCalculationFailure
      • UnexpectedCalculationFailure.__module__
    • register_error_handler()
  • aiida_castep.workflows.relax module
    • CastepAlterRelaxWorkChain
      • CastepAlterRelaxWorkChain.__abstractmethods__
      • CastepAlterRelaxWorkChain.__module__
      • CastepAlterRelaxWorkChain._abc_impl
      • CastepAlterRelaxWorkChain._default_fix_cell_iter_max
      • CastepAlterRelaxWorkChain._default_var_cell_iter_max
      • CastepAlterRelaxWorkChain._max_meta_iterations
      • CastepAlterRelaxWorkChain.define()
      • CastepAlterRelaxWorkChain.inspect_relax()
      • CastepAlterRelaxWorkChain.set_cons_and_imax()
      • CastepAlterRelaxWorkChain.setup()
    • CastepRelaxWorkChain
      • CastepRelaxWorkChain.__abstractmethods__
      • CastepRelaxWorkChain.__module__
      • CastepRelaxWorkChain._abc_impl
      • CastepRelaxWorkChain._max_meta_iterations
      • CastepRelaxWorkChain._push_parameters()
      • CastepRelaxWorkChain._spec
      • CastepRelaxWorkChain.define()
      • CastepRelaxWorkChain.finalize()
      • CastepRelaxWorkChain.inspect_relax()
      • CastepRelaxWorkChain.result()
      • CastepRelaxWorkChain.run_relax()
      • CastepRelaxWorkChain.setup()
      • CastepRelaxWorkChain.should_run_relax()
  • Module contents

Submodules

aiida_castep._version module

This module stores a single version for calculation-parser.

A single version number is used here so whenever any change to parser or calculation modules, the version number should be increased.This avoids falsely matching nodes via hashes.

CHANGELOG

• 0.2.3 FIX a typo psedu_pots, should be pseudo_pots

• 0.2.4 Sort the bands and parsed kpoints from .bands file using the index given

• 1.0.0 initial version for plugin version 1.0. Changed the warning messages to EXIT_CODE style

• 1.0.1 Revision to include error messages. Added parsing of the .err file and put the content in the field ‘error_messages’ of the returned Dict. The order of error is also adjusted. Fixed a bug where if the .err files are present the returned code would be same as when end of the calculation is not found. This fix allows the internal crash of CASTEP (usually with the .err files) to be differentiated with the calculation being killed (by scheduler).

• 1.0.2 Fix a bug of parsing cons’d forces

• 1.0.3 Fix a bug where the forces are not reorderred as for the case of StructureData

• 1.1.0 Enabled parsing of castep_bin files and return error codes when there is no empty band in at least one kpoint.

• 1.1.1 Fixed a bug where the kpoints fro castep_bin can be incompatible with the band structure calculation

aiida_castep.common module

Store common stuff

Module contents

Top level module