Index

A

add_dft_phonons() (autoplex.auto.phonons.flows.CompleteDFTvsMLBenchmarkWorkflow static method) add_dft_random() (autoplex.auto.phonons.flows.CompleteDFTvsMLBenchmarkWorkflow static method) adjust_forces() (autoplex.data.rss.utils.HookeanRepulsion method) adjust_momenta() (autoplex.data.rss.utils.HookeanRepulsion method) adjust_positions() (autoplex.data.rss.utils.HookeanRepulsion method) adjust_potential_energy() (autoplex.data.rss.utils.HookeanRepulsion method) atomic_numbers (in module autoplex.data.rss.jobs) (in module autoplex.data.rss.utils) autoplex.auto module autoplex.auto.phonons module autoplex.auto.phonons.flows module autoplex.auto.phonons.jobs module autoplex.auto.rss module autoplex.benchmark module autoplex.benchmark.phonons module autoplex.benchmark.phonons.flows module autoplex.benchmark.phonons.jobs module autoplex.benchmark.phonons.utils module autoplex.benchmark.rss module autoplex.data module autoplex.data.common module autoplex.data.common.flows module autoplex.data.common.jobs module autoplex.data.common.utils module

autoplex.data.phonons module autoplex.data.phonons.flows module autoplex.data.phonons.jobs module autoplex.data.phonons.utils module autoplex.data.rss module autoplex.data.rss.flows module autoplex.data.rss.jobs module autoplex.data.rss.utils module autoplex.fitting module autoplex.fitting.common module autoplex.fitting.common.flows module autoplex.fitting.common.jobs module autoplex.fitting.common.regularization module autoplex.fitting.common.utils module autoplex.fitting.phonons module autoplex.fitting.phonons.flows module autoplex.fitting.phonons.jobs module autoplex.fitting.rss module autoplex.fitting.rss.flows module autoplex.fitting.rss.jobs module

B

boltz() (in module autoplex.data.common.utils)

boltzhist_cur() (in module autoplex.data.common.utils)

C

calculate() (autoplex.data.rss.utils.myPotential method) calculate_delta() (in module autoplex.fitting.common.utils) calculate_hull_3D() (in module autoplex.fitting.common.regularization) calculate_hull_ND() (in module autoplex.fitting.common.regularization) check_convergence() (in module autoplex.fitting.common.utils) check_convergence_vasp() (in module autoplex.data.common.jobs) check_distances() (in module autoplex.data.common.utils) check_supercells() (in module autoplex.data.phonons.utils) chemical_symbols (in module autoplex.data.rss.utils) (in module autoplex.fitting.common.utils)

compare_plot() (in module autoplex.benchmark.phonons.utils) complete_benchmark() (in module autoplex.auto.phonons.jobs) CompleteDFTvsMLBenchmarkWorkflow (class in autoplex.auto.phonons.flows) compute_bandstructure_benchmark_metrics() (in module autoplex.benchmark.phonons.utils) compute_pairs_triplets() (in module autoplex.fitting.common.utils) convert_to_extxyz() (in module autoplex.data.common.jobs) convert_xyz_to_structure() (in module autoplex.fitting.common.utils) convexhull_cur() (in module autoplex.data.common.utils) covalent_radii (in module autoplex.data.rss.jobs) create_soap_descriptor() (in module autoplex.data.common.utils) cur_select() (in module autoplex.data.common.utils)

D

data_distillation() (in module autoplex.data.common.utils) Data_preprocessing() (in module autoplex.data.common.jobs) DataPreprocessing (class in autoplex.fitting.common.flows) dft_phonopy_gen_data() (in module autoplex.auto.phonons.jobs) dft_random_gen_data() (in module autoplex.auto.phonons.jobs)

DFTPhononMaker (class in autoplex.data.phonons.flows) DFTStaticMaker (class in autoplex.data.common.flows) DFTSupercellSettingsMaker (class in autoplex.auto.phonons.flows) do_rss() (in module autoplex.data.rss.jobs) do_rss_iterations() (in module autoplex.data.rss.flows)

E

ElementCollection (class in autoplex.data.common.utils) energy_plot() (in module autoplex.data.common.utils) energy_remain() (in module autoplex.fitting.common.utils)

extract_base_name() (in module autoplex.data.common.utils) extract_gap_label() (in module autoplex.fitting.common.utils) extract_pairstyle() (in module autoplex.data.rss.utils)

F

filter_outlier_energy() (in module autoplex.data.common.utils) filter_outlier_forces() (in module autoplex.data.common.utils) find_element_pairs() (autoplex.data.common.utils.ElementCollection method)

flatten() (in module autoplex.data.common.utils) (in module autoplex.fitting.common.utils) force_plot() (in module autoplex.data.common.utils)

G

gap_fitting() (in module autoplex.fitting.common.utils) gap_hyperparameter_constructor() (in module autoplex.fitting.common.utils) gcm3_to_Vm() (in module autoplex.fitting.common.utils) generate_randomized_structures() (in module autoplex.data.common.jobs) generate_supercells() (in module autoplex.auto.phonons.jobs) GenerateTrainingDataForTesting (class in autoplex.data.common.flows) generic type get_atomic_numbers() (in module autoplex.fitting.common.utils) get_convex_hull() (in module autoplex.fitting.common.regularization) get_e_distance_to_hull() (in module autoplex.fitting.common.regularization) get_e_distance_to_hull_3D() (in module autoplex.fitting.common.regularization) get_indices() (autoplex.data.rss.utils.HookeanRepulsion method)

get_intersect() (in module autoplex.fitting.common.regularization) get_iso_atom() (in module autoplex.auto.phonons.jobs) get_list_of_vasp_calc_dirs() (in module autoplex.fitting.common.utils) get_mole_frac() (in module autoplex.fitting.common.regularization) get_number_of_species() (autoplex.data.common.utils.ElementCollection method) get_removed_dof() (autoplex.data.rss.utils.HookeanRepulsion method) get_rmse() (in module autoplex.benchmark.phonons.utils) get_species() (autoplex.data.common.utils.ElementCollection method) get_species_Z() (autoplex.data.common.utils.ElementCollection method) get_supercell_job() (in module autoplex.data.common.jobs) GPa (in module autoplex.data.common.utils) (in module autoplex.data.rss.utils)

H

HookeanRepulsion (class in autoplex.data.rss.utils)

I

index_shuffle() (autoplex.data.rss.utils.HookeanRepulsion method) initial_rss() (in module autoplex.data.rss.flows)

IsoAtomMaker (class in autoplex.data.phonons.flows) IsoAtomStaticMaker (class in autoplex.data.phonons.flows)

J

jace_fitting() (in module autoplex.fitting.common.utils)

L

label_stoichiometry_volume() (in module autoplex.fitting.common.regularization)

load_mlip_hyperparameter_defaults() (in module autoplex.fitting.common.utils)

M

m3gnet_fitting() (in module autoplex.fitting.common.utils) mace_fitting() (in module autoplex.fitting.common.utils) mace_virial_format_conversion() (in module autoplex.fitting.common.utils) machine_learning_fit() (in module autoplex.fitting.common.jobs) make() (autoplex.auto.phonons.flows.CompleteDFTvsMLBenchmarkWorkflow method) (autoplex.auto.phonons.flows.DFTSupercellSettingsMaker method) (autoplex.benchmark.phonons.flows.PhononBenchmarkMaker method) (autoplex.data.common.flows.DFTStaticMaker method) (autoplex.data.common.flows.GenerateTrainingDataForTesting method) (autoplex.data.phonons.flows.IsoAtomMaker method) (autoplex.data.phonons.flows.RandomStructuresDataGenerator method) (autoplex.data.rss.jobs.RandomizedStructure method) (autoplex.fitting.common.flows.DataPreprocessing method) (autoplex.fitting.common.flows.MLIPFitMaker method) make_from_ml_model() (autoplex.data.phonons.flows.MLPhononMaker method) mc_rattle() (in module autoplex.data.common.utils) minimize_structures() (in module autoplex.data.rss.utils) ml_phonon_maker_preparation() (in module autoplex.data.phonons.utils) MLIPFitMaker (class in autoplex.fitting.common.flows) MLPhononMaker (class in autoplex.data.phonons.flows) module autoplex.auto autoplex.auto.phonons autoplex.auto.phonons.flows autoplex.auto.phonons.jobs autoplex.auto.rss autoplex.benchmark autoplex.benchmark.phonons autoplex.benchmark.phonons.flows autoplex.benchmark.phonons.jobs autoplex.benchmark.phonons.utils autoplex.benchmark.rss autoplex.data autoplex.data.common autoplex.data.common.flows autoplex.data.common.jobs autoplex.data.common.utils autoplex.data.phonons autoplex.data.phonons.flows autoplex.data.phonons.jobs autoplex.data.phonons.utils autoplex.data.rss autoplex.data.rss.flows autoplex.data.rss.jobs autoplex.data.rss.utils autoplex.fitting autoplex.fitting.common autoplex.fitting.common.flows autoplex.fitting.common.jobs autoplex.fitting.common.regularization autoplex.fitting.common.utils autoplex.fitting.phonons autoplex.fitting.phonons.flows autoplex.fitting.phonons.jobs autoplex.fitting.rss autoplex.fitting.rss.flows autoplex.fitting.rss.jobs

myPotential (class in autoplex.data.rss.utils)

N

nequip_fitting() (in module autoplex.fitting.common.utils)

P

parallel_calc_descriptor_vec() (in module autoplex.data.common.utils) PhononBenchmarkMaker (class in autoplex.benchmark.phonons.flows) piecewise_linear() (in module autoplex.fitting.common.regularization) plot_convex_hull() (in module autoplex.fitting.common.utils) plot_energy_forces() (in module autoplex.data.common.utils)

plot_force_distribution() (in module autoplex.data.common.jobs) point_in_triangle_2D() (in module autoplex.fitting.common.regularization) point_in_triangle_ND() (in module autoplex.fitting.common.regularization) prepare_fit_environment() (in module autoplex.fitting.common.utils) process_rss() (in module autoplex.data.rss.utils)

R

random_vary_angle() (in module autoplex.data.common.utils) RandomizedStructure (class in autoplex.data.rss.jobs) RandomStructuresDataGenerator (class in autoplex.data.phonons.flows) reduce_supercell_size() (in module autoplex.data.phonons.utils) reduce_supercell_size_job() (in module autoplex.data.phonons.jobs) rms_dict() (in module autoplex.data.common.utils)

rmse_qdep_plot() (in module autoplex.benchmark.phonons.utils) run_ace() (in module autoplex.fitting.common.utils) run_gap() (in module autoplex.fitting.common.utils) run_mace() (in module autoplex.fitting.common.utils) run_nequip() (in module autoplex.fitting.common.utils) run_quip() (in module autoplex.fitting.common.utils) run_supercells() (in module autoplex.auto.phonons.jobs)

S

safe_strip_hostname() (in module autoplex.data.common.jobs) sampling() (in module autoplex.data.common.jobs) scale_cell() (in module autoplex.data.common.utils)

set_sigma() (in module autoplex.fitting.common.regularization) static_run_and_convert() (autoplex.data.common.flows.GenerateTrainingDataForTesting method) std_rattle() (in module autoplex.data.common.utils) stratified_dataset_split() (in module autoplex.data.common.utils)

T

TightDFTStaticMaker (class in autoplex.data.phonons.flows) to_ase_trajectory() (in module autoplex.data.common.utils) todict (autoplex.data.rss.utils.HookeanRepulsion property) TYPE_CHECKING (in module autoplex.auto.phonons.flows) (in module autoplex.auto.phonons.jobs) (in module autoplex.benchmark.phonons.flows) (in module autoplex.benchmark.phonons.utils) (in module autoplex.data.common.flows) (in module autoplex.data.common.jobs) (in module autoplex.data.common.utils) (in module autoplex.data.phonons.flows) (in module autoplex.data.phonons.jobs) (in module autoplex.data.phonons.utils) (in module autoplex.data.rss.jobs) (in module autoplex.fitting.common.regularization) (in module autoplex.fitting.common.utils)

U

update_phonon_displacement_maker() (in module autoplex.data.phonons.utils)

V

VASP_collect_data() (in module autoplex.data.common.jobs)

vaspoutput_2_extended_xyz() (in module autoplex.fitting.common.utils)

W

write_after_distillation_data_split() (in module autoplex.fitting.common.utils)

write_benchmark_metrics() (in module autoplex.benchmark.phonons.jobs)