API_Docs

default_parameters

• Default parameters
  • default_elements
  • default_build_properties
  • default_data_config
  • default_train_config
  • default_ase_calculator_config.
  • default_high_throughput_config
  • default_hp_dft_config

lib

• lib
  • adsorbate_poscar
    • adsorbate_poscar
  • exceptions
    • FileExit
    • file_exit()
  • file_lib
    • generate_file_name()
    • modify_INCAR()
  • high_throughput_lib
    • perturb_positions()
    • scale_atoms()
    • get_concentration_from_ase_formula()
    • get_v_per_atom()
    • get_ase_atom_from_formula()
    • get_ase_atom_from_formula_template()
    • run_vasp()
  • incar_tag
    • incar_tag
  • model_lib
    • save_model()
    • load_model()
    • save_state_dict()
    • load_state_dict()
    • config_parser()
    • EarlyStopping
      • EarlyStopping.__init__()
      • EarlyStopping.model
      • EarlyStopping.patience
      • EarlyStopping.counter
      • EarlyStopping.best_score
      • EarlyStopping.update
      • EarlyStopping.early_stop
      • EarlyStopping.step()
      • EarlyStopping.save_model()
    • load_graph_build_method()
    • PearsonR()

data

• data
  • atomic_feature
    • all_elements
    • elements
    • selected_elements
    • Elements_used
    • get_atomic_features()
    • get_atomic_feature_onehot()
  • build_graph
    • CrystalGraph
      • CrystalGraph.__init__()
      • CrystalGraph.get_adsorbate_bool()
      • CrystalGraph.get_crystal()
      • CrystalGraph.get_1NN_pairs_voronoi()
      • CrystalGraph.get_1NN_pairs_distance()
      • CrystalGraph.get_1NN_pairs_ase_distance()
      • CrystalGraph.get_ndata()
      • CrystalGraph.get_graph_from_ase()
      • CrystalGraph.get_graph_from_pymatgen()
      • CrystalGraph.get_graph()
    • AseGraphTorch
      • AseGraphTorch.__init__()
      • AseGraphTorch.reset()
      • AseGraphTorch.get_ndata()
      • AseGraphTorch.get_adsorbate_bool()
      • AseGraphTorch.get_scaled_positions_wrap()
      • AseGraphTorch.get_scaled_positions()
      • AseGraphTorch.fractional2cartesian()
      • AseGraphTorch.safe_to_use()
      • AseGraphTorch.get_pair_distances()
      • AseGraphTorch.update_pair_distances()
      • AseGraphTorch.get_all_possible_distances()
      • AseGraphTorch.get_init_connections()
      • AseGraphTorch.update_connections()
      • AseGraphTorch.build()
      • AseGraphTorch.update()
      • AseGraphTorch.get_graph()
  • build_dataset
    • ReadGraphs
      • ReadGraphs.__init__()
      • ReadGraphs.read_batch_graphs()
      • ReadGraphs.read_all_graphs()
    • TrainValTestSplit
    • ExtractVaspFiles
      • ExtractVaspFiles.__init__()
      • ExtractVaspFiles.read_oszicar()
      • ExtractVaspFiles.split_output()
      • ExtractVaspFiles.__call__()
    • BuildDatabase
      • BuildDatabase.__init__()
      • BuildDatabase.build()
    • concat_graphs()
    • concat_dataset()
    • select_graphs_random()
    • select_graphs_from_dataset_random()
    • save_dataset()
  • dataset
    • Dataset
      • Dataset.__init__()
    • __getitem__()
    • __repr__()
    • __len__()
    • save()
    • Collater
      • Collater.__init__()
      • Collater.__call__()
    • concat_graphs()
    • concat_dataset()
    • select_graphs_random()
    • select_graphs_from_dataset_random()
    • save_dataset()
  • generate_database
    • DataGenerator
      • DataGenerator.__init__()
      • DataGenerator.set_structure()
      • DataGenerator.get_INCAR()
      • DataGenerator.get_KPOINTS()
      • DataGenerator.get_POTCAR()
      • DataGenerator.apply_strain()
      • DataGenerator.apply_perturbation()
      • DataGenerator.create_vacancy()
      • DataGenerator.create_species_vacancy()
      • DataGenerator.relocate_atoms()
      • DataGenerator.static()
      • DataGenerator.aimd()
  • load_dataset
    • LoadDataset
      • LoadDataset.__getitem__()
      • LoadDataset.__len__()
  • PymatgenStructureAnalyzer

model

• model
  • layer
    • Layer
      • Layer.__init__()
      • Layer.forward()
  • model
    • PotentialModel
      • PotentialModel.__init__()
      • PotentialModel.mul()
      • PotentialModel.div()
      • PotentialModel.get_head_mechanism()
      • PotentialModel.forward()
  • fit
    • Fit
      • Fit.__init__()
      • Fit.fit()

app

• app
  • calculators
    • AgatCalculator
      • AgatCalculator.implemented_properties
      • AgatCalculator.default_parameters
      • AgatCalculator.ignored_changes
      • AgatCalculator.__init__()
      • AgatCalculator.load_graph_build_scheme()
      • AgatCalculator.calculate()
    • AgatCalculatorAseGraphTorch
      • AgatCalculatorAseGraphTorch.implemented_properties
      • AgatCalculatorAseGraphTorch.default_parameters
      • AgatCalculatorAseGraphTorch.ignored_changes
      • AgatCalculatorAseGraphTorch.__init__()
      • AgatCalculatorAseGraphTorch.load_graph_build_scheme()
      • AgatCalculatorAseGraphTorch.calculate()
    • AgatCalculatorAseGraphTorchNumpy
      • AgatCalculatorAseGraphTorchNumpy.implemented_properties
      • AgatCalculatorAseGraphTorchNumpy.default_parameters
      • AgatCalculatorAseGraphTorchNumpy.ignored_changes
      • AgatCalculatorAseGraphTorchNumpy.__init__()
      • AgatCalculatorAseGraphTorchNumpy.load_graph_build_scheme()
      • AgatCalculatorAseGraphTorchNumpy.calculate()
    • AgatEnsembleCalculator
      • AgatEnsembleCalculator.implemented_properties
      • AgatEnsembleCalculator.default_parameters
      • AgatEnsembleCalculator.ignored_changes
      • AgatEnsembleCalculator.__init__()
      • AgatEnsembleCalculator.load_graph_build_scheme()
      • AgatEnsembleCalculator.calculate()
    • OnTheFlyCalculator
      • OnTheFlyCalculator.implemented_properties
      • OnTheFlyCalculator.default_parameters
      • OnTheFlyCalculator.ignored_changes
      • OnTheFlyCalculator.__init__()
      • OnTheFlyCalculator.load_graph_build_scheme()
      • OnTheFlyCalculator.calculate()
  • cata
    • find_adsorption_site
      • find_adsorption_site()
    • generate_adsorption_sites_ase
      • AddAtoms
        • AddAtoms.__init__()
        • AddAtoms._support_sites
        • AddAtoms.shift_fcoords()
        • AddAtoms.get_1NN_cutoff()
        • AddAtoms.get_atomic_diameter_for_slab()
        • AddAtoms.get_1NN_of_top_layer()
        • AddAtoms.get_ontop_sites()
        • AddAtoms.get_bridge_sites()
        • AddAtoms.get_disigma_sites()
        • AddAtoms.get_hollow_sites()
        • AddAtoms.fractional2cartesian()
        • AddAtoms.cartesian2fractional()
        • AddAtoms.write_file_with_adsorption_sites()
    • high_throughput_dft_calculation
      • HtDftAds
        • HtDftAds.root_dir
        • HtDftAds.__init__()
        • HtDftAds.bulk_opt()
        • HtDftAds.surf_opt()
        • HtDftAds.ads_opt()
        • HtDftAds.bulk_aimd()
        • HtDftAds.surface_aimd()
        • HtDftAds.ads_aimd()
        • HtDftAds.run()
    • high_throughput_predict
      • HtAds
        • HtAds.__init__()
        • HtAds.geo_opt()
        • HtAds.ads_calc()
        • HtAds.run()
    • increase_vacuum
      • increase_vacuum()
    • volcano_2e
      • volcano_2e()
    • volcano_plot
      • volcano_plot()
  • ase_torch
    • ase_abc
      • Optimizable
        • Optimizable.converged()
    • ase_dyn
      • MDMinTorch
    • ase_filters
    • bfgs_torch
    • optimize_torch
  • ensembles
    • ModifiedNPT
      • ModifiedNPT.classname
      • ModifiedNPT.__init__()
      • ModifiedNPT.run()
  • optimizers
    • __init__()
  • app_deprecated
    • AgatCalculator_deprecat
      • AgatCalculator_deprecat.implemented_properties
      • AgatCalculator_deprecat.default_parameters
      • AgatCalculator_deprecat.__init__()
      • AgatCalculator_deprecat.load_graph_build_scheme()
      • AgatCalculator_deprecat.calculate()

bin

• bin
  • agat_bayesian_opt
  • bayesian_skopt