API Reference

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

• Supercell
  • Supercell.from_atoms()
  • Supercell.generate()
  • Supercell.refine_initial_orientations()
  • Supercell.refine_grains()
  • Supercell.refine_grains_coarse_to_fine()
  • Supercell.shell_relax()
  • Supercell.bond_relax()
  • Supercell.enforce_hard_core()
  • Supercell.thermal_relax()
  • Supercell.measure_g3()
  • Supercell.sync_g3()
  • Supercell.view_structure()
  • Supercell.plot_structure()
  • Supercell.plot_g2()
  • Supercell.plot_g3()
  • Supercell.plot_g3_compare()
  • Supercell.plot_shell_relax()
  • Supercell.plot_thermal_relax()
  • Supercell.plot_thermal_before_after()
  • Supercell.plot_monte_carlo()
  • Supercell.export_trajectory_html()
  • Supercell.export_g3_html()
  • Supercell.export_g2_html()
  • Supercell.PRESETS
  • Presets
• CoordinationShellTarget
  • CoordinationShellTarget.from_atoms()
  • CoordinationShellTarget.from_targets()
  • CoordinationShellTarget.with_cross_species_bonds_only()
  • CoordinationShellTarget.with_bonded_species_pairs()
  • CoordinationShellTarget.with_angle_triplets()
  • CoordinationShellTarget.without_angle_triplets()
  • CoordinationShellTarget.pair_labels
  • CoordinationShellTarget.angle_labels
  • Restricting the bond graph
  • Masking angle springs (multi-modal shells)
  • Blending two reference crystals
• G3Distribution
  • G3Distribution.measure_g3()
  • G3Distribution.target_g3()
  • G3Distribution.plot_g3()
• Module-level exporters
  • Multi-cell overview
  • g(r) comparison across supercells

Public module surface

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 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 tricor as tc
from ase.build import bulk

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

cell = tc.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, **tc.Supercell.PRESETS["MRO"])
cell.measure_g3()

After 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 measure_g3()).

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