Index

_

__init__() (amorphgen.analysis.StructureAnalyser method)

A

amorphgen.analysis.energy module amorphgen.analysis.validate module amorphgen.cli module amorphgen.configs.default_config module amorphgen.pipeline.batch_quench module amorphgen.pipeline.equilibrate module amorphgen.pipeline.final_opt module amorphgen.pipeline.melt_cell module amorphgen.pipeline.opt_cell module amorphgen.pipeline.quench module

amorphgen.pipeline.random_gen module amorphgen.utils.common module amorphgen.utils.convert module amorphgen.utils.equilibration module amorphgen.utils.radii module analyser() (amorphgen.analysis.EnsembleSpec method) angle_distribution() (amorphgen.analysis.StructureAnalyser method) anion_elements() (in module amorphgen.utils.radii) assert_finite() (in module amorphgen.utils.common) attach_outputs() (in module amorphgen.utils.common) auto_target_cn() (in module amorphgen.utils.radii) available_backends() (in module amorphgen.utils.calculators) averaged_cn() (amorphgen.analysis.StructureAnalyser method) averaged_rdf() (amorphgen.analysis.StructureAnalyser method)

B

backend_available() (in module amorphgen.utils.calculators) batch_optimize() (in module amorphgen.pipeline.opt_cell) batch_random() (in module amorphgen.pipeline.random_gen) block_average_test() (in module amorphgen.utils.equilibration)

bond_angles() (amorphgen.analysis.StructureAnalyser method) bond_distances() (amorphgen.analysis.StructureAnalyser method) bond_order() (amorphgen.analysis.StructureAnalyser method) BuckinghamCalculator (class in amorphgen.utils.classical) build_md_dynamics() (in module amorphgen.utils.common)

C

calculate() (amorphgen.utils.classical.BuckinghamCalculator method) (amorphgen.utils.classical.LennardJonesCalculator method) calculator_supports_stress() (in module amorphgen.utils.common) cation_nonmetals() (in module amorphgen.utils.radii) classify_bond() (in module amorphgen.utils.radii) close() (amorphgen.utils.common.MDLogger method) (amorphgen.utils.common.TrajectoryWriter method) color (amorphgen.analysis.EnsembleSpec attribute) compare_ensembles() (in module amorphgen.analysis) compare_experiment() (amorphgen.analysis.StructureAnalyser method) (in module amorphgen.analysis) compute_bond_order() (in module amorphgen.analysis) compute_cn_vs_time() (in module amorphgen.utils.equilibration) compute_density_gcm3() (in module amorphgen.utils.common) compute_elastic_moduli() (in module amorphgen.analysis)

compute_energy_ranking() (in module amorphgen.analysis.energy) compute_melt_memory() (in module amorphgen.analysis) compute_msd() (in module amorphgen.utils.equilibration) compute_oxygen_speciation() (in module amorphgen.analysis) compute_vibrational_dos() (in module amorphgen.analysis) compute_void_distribution() (in module amorphgen.analysis) compute_xrd_pattern() (in module amorphgen.analysis) convergence_report() (amorphgen.analysis.StructureAnalyser method) (in module amorphgen.analysis) (in module amorphgen.utils.equilibration) convert() (in module amorphgen.utils.convert) coordination() (amorphgen.analysis.StructureAnalyser method) cubic_cell_filter() (in module amorphgen.utils.common) cutoff (amorphgen.analysis.EnsembleSpec attribute) cutoff_robustness() (amorphgen.analysis.StructureAnalyser method)

D

default_minsep() (in module amorphgen.utils.radii) density() (amorphgen.analysis.StructureAnalyser method)

dimer_report() (amorphgen.analysis.StructureAnalyser method) DivergenceError

E

elastic_moduli() (amorphgen.analysis.StructureAnalyser method) energy_ranking() (amorphgen.analysis.StructureAnalyser method) EnsembleSpec (class in amorphgen.analysis)

estimate_cell_length() (in module amorphgen.utils.radii) estimate_density() (in module amorphgen.utils.radii) extract_energies() (in module amorphgen.utils.equilibration) extract_snapshots() (in module amorphgen.utils.common)

F

files (amorphgen.analysis.EnsembleSpec attribute) format_auto_derive_summary() (in module amorphgen.utils.radii) format_convergence_report() (in module amorphgen.analysis) format_cutoff_robustness() (in module amorphgen.analysis) format_experiment_report() (in module amorphgen.analysis)

format_log_ranking() (in module amorphgen.analysis.energy) format_melt_memory() (in module amorphgen.analysis) format_screening_report() (in module amorphgen.analysis) format_validation_report() (in module amorphgen.analysis.validate) from_analyser() (amorphgen.analysis.EnsembleSpec class method)

G

generate_random() (in module amorphgen.pipeline.random_gen) get_calculator() (in module amorphgen.utils.calculators) get_effective_radius() (in module amorphgen.utils.radii)

get_ionic_radius() (in module amorphgen.utils.radii) get_mace_calculator() (in module amorphgen.utils.calculators) get_metallic_radius() (in module amorphgen.utils.radii) get_packing_factor() (in module amorphgen.utils.radii)

I

implemented_properties (amorphgen.utils.classical.BuckinghamCalculator attribute) (amorphgen.utils.classical.LennardJonesCalculator attribute)

infer_oxidation_state() (in module amorphgen.utils.radii)

L

label (amorphgen.analysis.EnsembleSpec attribute) LennardJonesCalculator (class in amorphgen.utils.classical)

list_models() (in module amorphgen.utils.calculators) load_experiment() (in module amorphgen.analysis) log() (amorphgen.utils.common.MDLogger method)

M

main() (in module amorphgen.cli) make_cubic() (in module amorphgen.utils.common) mark_screening_analysed() (in module amorphgen.analysis) MDLogger (class in amorphgen.utils.common) MeltQuenchPipeline (class in amorphgen.pipeline.run_pipeline) merge_config() (in module amorphgen.utils.common) module amorphgen.analysis.energy amorphgen.analysis.validate amorphgen.cli amorphgen.configs.default_config amorphgen.pipeline.batch_quench amorphgen.pipeline.equilibrate amorphgen.pipeline.final_opt amorphgen.pipeline.melt_cell amorphgen.pipeline.opt_cell amorphgen.pipeline.quench amorphgen.pipeline.random_gen amorphgen.utils.common amorphgen.utils.convert amorphgen.utils.equilibration amorphgen.utils.radii

N

needs_velocity_init() (in module amorphgen.utils.common)

O

oxygen_speciation() (amorphgen.analysis.StructureAnalyser method)

P

parse_args() (in module amorphgen.cli) parse_index_spec() (in module amorphgen.utils.common) parse_md_log() (in module amorphgen.utils.equilibration) per_structure_summary() (amorphgen.analysis.StructureAnalyser method) plot() (amorphgen.analysis.StructureAnalyser method) plot_block_averages() (in module amorphgen.utils.equilibration)

plot_cn_vs_time() (in module amorphgen.utils.equilibration) plot_energy_convergence() (in module amorphgen.utils.equilibration) plot_msd() (in module amorphgen.utils.equilibration) plot_rdf_time_windows() (in module amorphgen.utils.equilibration) plot_temperature() (in module amorphgen.utils.equilibration) polyhedral_connectivity() (amorphgen.analysis.StructureAnalyser method)

R

ramp_resume_position() (in module amorphgen.utils.common) random_gen_dir_hint() (in module amorphgen.pipeline.random_gen) rank_from_log() (in module amorphgen.analysis.energy) rdf() (amorphgen.analysis.StructureAnalyser method) read_md_checkpoint() (in module amorphgen.utils.common) require_backend() (in module amorphgen.utils.calculators) require_stress() (in module amorphgen.utils.common) resolve_device() (in module amorphgen.utils.common) resolve_files() (amorphgen.analysis.EnsembleSpec method) resolve_ramp() (in module amorphgen.utils.common) resume_md_stage() (in module amorphgen.utils.common)

ring_statistics() (amorphgen.analysis.StructureAnalyser method) run() (amorphgen.pipeline.run_pipeline.MeltQuenchPipeline method) (in module amorphgen.pipeline.batch_quench) (in module amorphgen.pipeline.equilibrate) (in module amorphgen.pipeline.final_opt) (in module amorphgen.pipeline.melt_cell) (in module amorphgen.pipeline.opt_cell) (in module amorphgen.pipeline.quench) run_index_for() (in module amorphgen.utils.common) run_index_from_cwd() (in module amorphgen.utils.common) run_torchsim() (in module amorphgen.pipeline.batch_quench) running_average() (in module amorphgen.utils.equilibration)

S

save_convergence_report() (in module amorphgen.analysis) save_cutoff_robustness() (in module amorphgen.analysis) save_experiment_comparison() (in module amorphgen.analysis) save_report() (amorphgen.analysis.StructureAnalyser method) save_xrd_pattern() (in module amorphgen.analysis) scoped_run_index() (in module amorphgen.utils.common) screen() (amorphgen.analysis.StructureAnalyser method) screen_structures() (in module amorphgen.analysis) screened() (amorphgen.analysis.StructureAnalyser method)

set_md_temperature() (in module amorphgen.utils.common) STAGE_CHECKPOINTS (amorphgen.pipeline.run_pipeline.MeltQuenchPipeline attribute) stage_file() (in module amorphgen.utils.common) STAGE_NAMES (amorphgen.pipeline.run_pipeline.MeltQuenchPipeline attribute) stage_rng() (in module amorphgen.utils.common) structure_factor() (amorphgen.analysis.StructureAnalyser method) structure_factor_direct() (amorphgen.analysis.StructureAnalyser method) StructureAnalyser (class in amorphgen.analysis) summary() (amorphgen.analysis.StructureAnalyser method)

T

total_coordination() (amorphgen.analysis.StructureAnalyser method)

total_correlation() (amorphgen.analysis.StructureAnalyser method) TrajectoryWriter (class in amorphgen.utils.common)

V

validate_against_reference() (in module amorphgen.analysis.validate) validate_screening_config() (in module amorphgen.analysis)

vibrational_dos() (amorphgen.analysis.StructureAnalyser method) void_distribution() (amorphgen.analysis.StructureAnalyser method) voronoi() (amorphgen.analysis.StructureAnalyser method)

W

write() (amorphgen.utils.common.TrajectoryWriter method)

write_screening_outputs() (in module amorphgen.analysis)

X

xrd_pattern() (amorphgen.analysis.StructureAnalyser method)