Index

_

__call__() (Collater method) (ExtractVaspFiles method) __getitem__() (LoadDataset method) __init__() (AddAtoms method) (AgatCalculator method) (AgatCalculator_deprecat method) (AgatCalculatorAseGraphTorch method) (AgatCalculatorAseGraphTorchNumpy method) (AgatEnsembleCalculator method) (AseGraphTorch method) (BuildDatabase method) (Collater method) (CrystalGraph method) (DataGenerator method) (Dataset method) (EarlyStopping method) (ExtractVaspFiles method) (Fit method) (HtDftAds method) (Layer method) (ModifiedNPT method) (OnTheFlyCalculator method) (PotentialModel method) (ReadGraphs method)

__len__() (LoadDataset method) __repr__() _support_sites (AddAtoms property)

A

AddAtoms (built-in class) ads_aimd() (HtDftAds method) ads_opt() (HtDftAds method) adsorbate_poscar (built-in variable) AgatCalculator (built-in class) AgatCalculator_deprecat (built-in class) AgatCalculatorAseGraphTorch (built-in class)

AgatCalculatorAseGraphTorchNumpy (built-in class) AgatEnsembleCalculator (built-in class) aimd() (DataGenerator method) all_elements (built-in variable) apply_perturbation() (DataGenerator method) apply_strain() (DataGenerator method) AseGraphTorch (built-in class)

B

best_score (EarlyStopping property) build() (AseGraphTorch method) (BuildDatabase method) BuildDatabase (built-in class) built-in function concat_dataset(), [1] concat_graphs(), [1] config_parser() file_exit() find_adsorption_site() generate_file_name() get_ase_atom_from_formula() get_ase_atom_from_formula_template() get_atomic_feature_onehot() get_atomic_features() get_concentration_from_ase_formula() get_v_per_atom() HtAds.__init__() HtAds.ads_calc() HtAds.geo_opt() HtAds.run() increase_vacuum() load_graph_build_method() load_model() load_state_dict() modify_INCAR() PearsonR() perturb_positions() run_vasp() save_dataset(), [1] save_model() save_state_dict() scale_atoms() select_graphs_from_dataset_random(), [1] select_graphs_random(), [1] volcano_2e() volcano_plot()

bulk_aimd() (HtDftAds method) bulk_opt() (HtDftAds method)

C

calculate() (AgatCalculator method) (AgatCalculator_deprecat method) (AgatCalculatorAseGraphTorch method) (AgatCalculatorAseGraphTorchNumpy method) (AgatEnsembleCalculator method) (OnTheFlyCalculator method) cartesian2fractional() (AddAtoms method) classname (ModifiedNPT attribute) Collater (built-in class) concat_dataset() built-in function, [1]

concat_graphs() built-in function, [1] config_parser() built-in function converged() (Optimizable method) counter (EarlyStopping property) create_species_vacancy() (DataGenerator method) create_vacancy() (DataGenerator method) CrystalGraph (built-in class)

D

DataGenerator (built-in class) Dataset (built-in class) default_parameters (AgatCalculator attribute) (AgatCalculator_deprecat attribute) (AgatCalculatorAseGraphTorch attribute) (AgatCalculatorAseGraphTorchNumpy attribute) (AgatEnsembleCalculator attribute) (OnTheFlyCalculator attribute)

div() (PotentialModel method)

E

early_stop (EarlyStopping property) EarlyStopping (built-in class)

elements (built-in variable) Elements_used (built-in variable) ExtractVaspFiles (built-in class)

F

file_exit() built-in function FileExit (built-in class) find_adsorption_site() built-in function

Fit (built-in class) fit() (Fit method) forward() (Layer method) (PotentialModel method) fractional2cartesian() (AddAtoms method) (AseGraphTorch method)

G

generate_file_name() built-in function get_1NN_cutoff() (AddAtoms method) get_1NN_of_top_layer() (AddAtoms method) get_1NN_pairs_ase_distance() (CrystalGraph method) get_1NN_pairs_distance() (CrystalGraph method) get_1NN_pairs_voronoi() (CrystalGraph method) get_adsorbate_bool() (AseGraphTorch method) (CrystalGraph method) get_all_possible_distances() (AseGraphTorch method) get_ase_atom_from_formula() built-in function get_ase_atom_from_formula_template() built-in function get_atomic_diameter_for_slab() (AddAtoms method) get_atomic_feature_onehot() built-in function get_atomic_features() built-in function get_bridge_sites() (AddAtoms method) get_concentration_from_ase_formula() built-in function

get_crystal() (CrystalGraph method) get_disigma_sites() (AddAtoms method) get_graph() (AseGraphTorch method) (CrystalGraph method) get_graph_from_ase() (CrystalGraph method) get_graph_from_pymatgen() (CrystalGraph method) get_head_mechanism() (PotentialModel method) get_hollow_sites() (AddAtoms method) get_INCAR() (DataGenerator method) get_init_connections() (AseGraphTorch method) get_KPOINTS() (DataGenerator method) get_ndata() (AseGraphTorch method) (CrystalGraph method) get_ontop_sites() (AddAtoms method) get_pair_distances() (AseGraphTorch method) get_POTCAR() (DataGenerator method) get_scaled_positions() (AseGraphTorch method) get_scaled_positions_wrap() (AseGraphTorch method) get_v_per_atom() built-in function

H

HtAds (built-in class) HtAds.__init__() built-in function HtAds.ads_calc() built-in function

HtAds.geo_opt() built-in function HtAds.run() built-in function HtDftAds (built-in class)

I

ignored_changes (AgatCalculator attribute) (AgatCalculatorAseGraphTorch attribute) (AgatCalculatorAseGraphTorchNumpy attribute) (AgatEnsembleCalculator attribute) (OnTheFlyCalculator attribute) implemented_properties (AgatCalculator attribute) (AgatCalculator_deprecat attribute) (AgatCalculatorAseGraphTorch attribute) (AgatCalculatorAseGraphTorchNumpy attribute) (AgatEnsembleCalculator attribute) (OnTheFlyCalculator attribute)

incar_tag (built-in variable) increase_vacuum() built-in function

L

Layer (built-in class) load_graph_build_method() built-in function load_graph_build_scheme() (AgatCalculator method) (AgatCalculator_deprecat method) (AgatCalculatorAseGraphTorch method) (AgatCalculatorAseGraphTorchNumpy method) (AgatEnsembleCalculator method) (OnTheFlyCalculator method)

load_model() built-in function load_state_dict() built-in function LoadDataset (built-in class)

M

MDMinTorch (built-in class) model (EarlyStopping property) ModifiedNPT (built-in class)

modify_INCAR() built-in function mul() (PotentialModel method)

O

OnTheFlyCalculator (built-in class)

Optimizable (built-in class)

P

patience (EarlyStopping property) PearsonR() built-in function

perturb_positions() built-in function PotentialModel (built-in class)

R

read_all_graphs() (ReadGraphs method) read_batch_graphs() (ReadGraphs method) read_oszicar() (ExtractVaspFiles method) ReadGraphs (built-in class) relocate_atoms() (DataGenerator method)

reset() (AseGraphTorch method) root_dir (HtDftAds property) run() (HtDftAds method) (ModifiedNPT method) run_vasp() built-in function

S

safe_to_use() (AseGraphTorch method) save() save_dataset() built-in function, [1] save_model() built-in function save_model() (EarlyStopping method) save_state_dict() built-in function scale_atoms() built-in function

select_graphs_from_dataset_random() built-in function, [1] select_graphs_random() built-in function, [1] selected_elements (built-in variable) set_structure() (DataGenerator method) shift_fcoords() (AddAtoms method) split_output() (ExtractVaspFiles method) static() (DataGenerator method) step() (EarlyStopping method) surf_opt() (HtDftAds method) surface_aimd() (HtDftAds method)

T

TrainValTestSplit (built-in class)

U

update (EarlyStopping property) update() (AseGraphTorch method)

update_connections() (AseGraphTorch method) update_pair_distances() (AseGraphTorch method)

V

volcano_2e() built-in function

volcano_plot() built-in function

W

write_file_with_adsorption_sites() (AddAtoms method)