Turn-key Module¶
Coordinating Modules¶
- Augmentor Module
- Abstract Base Class
AugmentorAugmentor.__init__()Augmentor.checkpoint_augmentor()Augmentor.restart_augmentor()Augmentor.identify_novel_environments()Augmentor.extract_and_tag_subcells()Augmentor.score_and_extract_subcells()Augmentor.simple_prune_dataset()Augmentor.estimate_pruning_ratio()Augmentor.iterative_fps_prune()Augmentor.chunked_iterative_fps_prune()
- Abstract Base Class
- Target Property Module
- Analysis sub-module
- Analyze Lammps Log
AnalyzeLammpsLogAnalyzeLammpsLog.__init__()AnalyzeLammpsLog.read_file_to_dict()AnalyzeLammpsLog.flush_dict_and_set_new_keyword()AnalyzeLammpsLog.get()AnalyzeLammpsLog.get_keywords()AnalyzeLammpsLog.to_exdir_group()AnalyzeLammpsLog.get_num_partial_logs()AnalyzeLammpsLog.extract_msd()AnalyzeLammpsLog.extract_density()AnalyzeLammpsLog.extract_q()
- Extract Elastic Compliance
- Analyze Lammps Log
Atomic Modules¶
- Computer Module
- Abstract Base Class
ComputerComputer.OUTPUT_KEYComputer.__init__()Computer.compute()Computer.compute_batch()Computer.get_run_command()Computer.get_batched_run_command()Computer.run()Computer.save_labeled_configs()Computer.write_input()Computer.parse_for_storage()Computer.save_results()Computer.cleanup()Computer.data_from_calc_ids()Computer.get_colabfit_property_definition()Computer.get_colabfit_property_map()
- Abstract Base Class
- Descriptor Module
- Abstract Base Class
DescriptorBaseDescriptorBase.OUTPUT_KEYDescriptorBase.atoms_file_nameDescriptorBase.init_args_file_nameDescriptorBase.init_args_subdirDescriptorBase.compute_args_file_nameDescriptorBase.compute_args_subdirDescriptorBase.script_file_nameDescriptorBase.compute()DescriptorBase.compute_batch()DescriptorBase.get_run_command()DescriptorBase.get_batched_run_command()DescriptorBase.run()DescriptorBase.write_input()DescriptorBase.parse_for_storage()
AtomCenteredDescriptorConfigurationDescriptor
- Concrete Implementations
- Abstract Base Class
- Score Module
- Abstract Base Class
ScoreQuantityScoreBaseScoreBase.OUTPUT_KEYScoreBase.suppported_score_quantitiesScoreBase.data_file_nameScoreBase.output_file_nameScoreBase.init_args_file_nameScoreBase.init_args_subdirScoreBase.compute_args_file_nameScoreBase.compute_args_subdirScoreBase.script_file_nameScoreBase.compute()ScoreBase.compute_batch()ScoreBase.get_run_command()ScoreBase.get_batched_run_command()ScoreBase.run()ScoreBase.write_input()ScoreBase.cleanup()ScoreBase.read_data()ScoreBase.write_data()
AtomCenteredScoreConfigurationScoreDatasetScoreModelScore
- Concrete Implementations
- LTAU
- QUESTS
- FIMTrain
FIMTrainingSetScoreFIMTrainingSetScore.OUTPUT_KEYFIMTrainingSetScore.supported_score_quantitiesFIMTrainingSetScore.supported_potential_typeFIMTrainingSetScore.default_evaluate_kwargsFIMTrainingSetScore.default_derivative_kwargsFIMTrainingSetScore.__init__()FIMTrainingSetScore.compute()FIMTrainingSetScore.compute_batch()FIMTrainingSetScore.get_colabfit_property_definition()
- FIMProperty
FIMPropertyScoreFIMPropertyScore.OUTPUT_KEYFIMPropertyScore.data_file_nameFIMPropertyScore.supported_score_quantitiesFIMPropertyScore.supported_potential_typeFIMPropertyScore.property_output_dirFIMPropertyScore.__init__()FIMPropertyScore.compute()FIMPropertyScore.compute_batch()FIMPropertyScore.compute_fim()FIMPropertyScore.compute_jacobian()FIMPropertyScore.read_data()FIMPropertyScore.write_data()FIMPropertyScore.get_colabfit_property_definition()
- FIMMatching
FIMMatchingScoreFIMMatchingScore.OUTPUT_KEYFIMMatchingScore.supported_score_quantitiesFIMMatchingScore.default_solver_kwargsFIMMatchingScore.default_fim_preconditioning_kwargsFIMMatchingScore.__init__()FIMMatchingScore.compute()FIMMatchingScore.compute_batch()FIMMatchingScore.fim_match()FIMMatchingScore.setup_problem()FIMMatchingScore.get_colabfit_property_definition()
- Abstract Base Class
- Oracle Module
- Abstract Base Class
- AiiDA
- Concrete Implementations
- Espresso
EspressoOracleEspressoOracle.__init__()EspressoOracle.write_atomic_positions()EspressoOracle.write_cell()EspressoOracle.write_input()EspressoOracle.get_run_command()EspressoOracle.parse_for_storage()EspressoOracle.ry_to_metal_units()EspressoOracle.get_pw_parameters()EspressoOracle.translate_universal_parameters()
- VASP
- KIM
- LAMMPS+KIM
- LAMMPS+SNAP
- Espresso
- Oracle Builder
- Potential Module
- Abstract Base Class
PotentialPotential.__init__()Potential.default_wfPotential.checkpoint_potential()Potential.restart_potential()Potential.build_potential()Potential.load_potential()Potential.generate_new_kim_id()Potential.get_potential_files()Potential.save_potential_files()Potential.evaluate()Potential.install_potential_in_kim_api()Potential.uninstall_potential_from_kim_api()Potential.list_saved_potentials()Potential.get_params()Potential.get_metadata()Potential.get_hyperparameters()
- Concrete Implementations
- DNN (Behler-Parrinello)
KliffBPPotentialKliffBPPotential.__init__()KliffBPPotential.checkpoint_potential()KliffBPPotential.restart_potential()KliffBPPotential.build_potential()KliffBPPotential.load_potential()KliffBPPotential.get_potential_files()KliffBPPotential.install_potential_in_kim_api()KliffBPPotential.get_params()KliffBPPotential.get_metadata()KliffBPPotential.get_hyperparameters()KliffBPPotential.evaluate()
- FitSNAP Potential
FitSnapPotentialFitSnapPotential.__init__()FitSnapPotential.checkpoint_potential()FitSnapPotential.restart_potential()FitSnapPotential.build_potential()FitSnapPotential.load_potential()FitSnapPotential.get_potential_files()FitSnapPotential.install_potential_in_kim_api()FitSnapPotential.convert_input_file_to_dict()FitSnapPotential.create_fitsnap_input_file()FitSnapPotential.get_params()FitSnapPotential.get_metadata()FitSnapPotential.get_hyperparameters()
- ChIMES Potential
ChIMESChIMESPotentialChIMESPotential.__init__()ChIMESPotential.checkpoint_potential()ChIMESPotential.restart_potential()ChIMESPotential.build_potential()ChIMESPotential.load_potential()ChIMESPotential.install_potential_in_kim_api()ChIMESPotential.get_params()ChIMESPotential.get_metadata()ChIMESPotential.get_hyperparameters()
- KIM Potential
KIMPotentialKIMPotential.__init__()KIMPotential.checkpoint_potential()KIMPotential.restart_potential()KIMPotential.build_potential()KIMPotential.load_potential()KIMPotential.get_potential_files()KIMPotential.get_params()KIMPotential.get_metadata()KIMPotential.get_hyperparameters()KIMPotential.set_params()
- DNN (Behler-Parrinello)
- Potential Builder
- Abstract Base Class
- Simulator Module
- Trainer Module
Utility Modules¶
- Workflow Module
- Abstract Base Classes
WorkflowWorkflow.__init__()Workflow.make_path_base()Workflow.make_path()Workflow.get_job_status()Workflow.get_job_path()Workflow.get_attached_metadata()Workflow.get_all_statuses()Workflow.job_done_file_present()Workflow.save_job_dict()Workflow.read_job_dict()Workflow.checkpoint_workflow()Workflow.restart_workflow()Workflow.block_until_completed()Workflow.submit_job()
HPCWorkflow
- Concrete Implementations
- Workflow Builder
- Abstract Base Classes
- Job Status
- Storage Module
- Abstract Base Class
- Concrete Implementations
- Local (demo/testing)
- Colabfit (production)
ColabfitStorageColabfitStorage.__init__()ColabfitStorage.check_if_dataset_name_unique()ColabfitStorage.add_data()ColabfitStorage.new_dataset()ColabfitStorage.get_data()ColabfitStorage.update_data()ColabfitStorage.list_data()ColabfitStorage.delete_dataset()ColabfitStorage.delete_items()ColabfitStorage.dataset_intersection_and_differences()ColabfitStorage.define_new_properties()ColabfitStorage.set_property_map()ColabfitStorage.set_default_property_map()ColabfitStorage.check_example_config()ColabfitStorage.add_property_mapping()ColabfitStorage.get_dataset_property_map()ColabfitStorage.get_dataset_name_from_id()ColabfitStorage.get_property_definitions()ColabfitStorage.update_property_definition()ColabfitStorage.setup_tables()ColabfitStorage.sort_configurations()ColabfitStorage.get_dataset_input_parameters()
- Storage Builder
- Restart Module
- General Factory and Builder Interface
- Recorder Module
- Utility Functions