API Reference - atomode

Top-level overview of every public symbol exported from atomode, with full signatures, parameter docs, and return types pulled straight from the source docstrings.

Public module surface¶

.. currentmodule:: atomode

Symbol	Kind	Purpose
`Supercell`	class	Central disorder-generator with visualisation + export helpers.
`CoordinationShellTarget`	class	First-shell coordination + angle targets extracted from a reference crystal. Composable via `CoordinationShellTarget.from_targets` into phase blends (e.g. sp²/sp³ carbon).
`G3Distribution`	class	Stand-alone three-body g3 measurement + pairwise g2 byproduct.
`export_overview_html`	function	Rotating multi-panel 3D grid of finished supercells.
`export_g2_compare_html`	function	Overlaid g(r) across multiple supercells, stacked y-offset, species-pair dropdown.
`plot_g2_compare`	function	Inline-Jupyter wrapper around `export_g2_compare_html`.

Pipeline summary¶

A typical end-to-end build chains four calls:

import atomode as am
from ase.build import bulk

atoms_ref = bulk("Si", "diamond", a=5.431)
shell = am.CoordinationShellTarget.from_atoms(atoms_ref, phi_num_bins=90)

cell = am.Supercell.from_atoms(
    atoms_ref,
    cell_dim_angstroms=(40, 40, 40),
    r_max=10, r_step=0.1, phi_num_bins=90,
    rng_seed=42,
)
cell.generate(shell, **am.Supercell.PRESETS["MRO"])
cell.measure_g3()

After Supercell.generate the cell carries:

cell.atoms: the ASE Atoms object with periodic positions.
cell.shell_relax_history: per-step bond / angle / repulsion losses, FIRE trajectory, and (optionally) per-atom cost vectors.
cell.refine_initial_orientations_history: only populated when refine_orientations=True is passed; one entry per accepted rotation.
cell.current_distribution: the most recently measured G3Distribution (set by Supercell.measure_g3).

From there the visualisation methods (Supercell.plot_g3, Supercell.view_structure, Supercell.plot_shell_relax) render inline in Jupyter, and the export methods (Supercell.export_trajectory_html, Supercell.export_g3_html, Supercell.export_g2_html) write self-contained HTML for embedding in static sites or sharing as standalone files.