Index

_

__init__() (amorphgen.analysis.StructureAnalyser method)

_detect_backend() (in module amorphgen.utils.calculators)

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 attach_outputs() (in module amorphgen.utils.common) auto_target_cn() (in module amorphgen.utils.radii) averaged_cn() (amorphgen.analysis.StructureAnalyser method) averaged_rdf() (amorphgen.analysis.StructureAnalyser method)

B

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) 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) classify_bond() (in module amorphgen.utils.radii) close() (amorphgen.utils.common.MDLogger method) (amorphgen.utils.common.TrajectoryWriter method) compute_cn_vs_time() (in module amorphgen.utils.equilibration)

compute_density_gcm3() (in module amorphgen.utils.common) compute_energy_ranking() (in module amorphgen.analysis.energy) compute_msd() (in module amorphgen.utils.equilibration) convergence_report() (in module amorphgen.utils.equilibration) convert() (in module amorphgen.utils.convert) coordination() (amorphgen.analysis.StructureAnalyser method)

D

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

density() (amorphgen.analysis.StructureAnalyser method)

E

energy_ranking() (amorphgen.analysis.StructureAnalyser method) 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

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

format_log_ranking() (in module amorphgen.analysis.energy) format_validation_report() (in module amorphgen.analysis.validate)

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)

I

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

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

L

LennardJonesCalculator (class in amorphgen.utils.classical)

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

M

main() (in module amorphgen.cli) make_cubic() (in module amorphgen.utils.common) 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

P

parse_args() (in module amorphgen.cli) 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)

R

rank_from_log() (in module amorphgen.analysis.energy) rdf() (amorphgen.analysis.StructureAnalyser method) resolve_ramp() (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)

running_average() (in module amorphgen.utils.equilibration)

S

save_report() (amorphgen.analysis.StructureAnalyser method) STAGE_CHECKPOINTS (amorphgen.pipeline.run_pipeline.MeltQuenchPipeline attribute) STAGE_NAMES (amorphgen.pipeline.run_pipeline.MeltQuenchPipeline attribute)

structure_factor() (amorphgen.analysis.StructureAnalyser method) StructureAnalyser (class in amorphgen.analysis) summary() (amorphgen.analysis.StructureAnalyser method)

T

TrajectoryWriter (class in amorphgen.utils.common)

V

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

voronoi() (amorphgen.analysis.StructureAnalyser method)

W

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