Nanocrystalline

Silicon in the nanocrystalline regime: a single ~20 Å grain spans the 40 × 40 × 40 Å supercell (grain_size ≥ min(box_dim) triggers the identity-rotation single-grain path), so the cell reads as a coherent diamond-cubic tile. With the bigger grain + stronger springs compared to LRO, this panel is the most ordered of the six, with sharper first and second g(r) peaks and the clearest tetrahedral g3 signature.

Parameters¶

from ase.build import bulk
import atomode as am

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

cell = am.Supercell.from_atoms(
    atoms,
    cell_dim_angstroms=(40, 40, 40),
    r_max=10, r_step=0.1, phi_num_bins=90,
    rng_seed=42,
)
cell.generate(shell_target, **am.Supercell.PRESETS["nanocrystalline"])

Relaxation trajectory¶

Interactive 3D viewer of the shell-relaxation trajectory (40 × 40 × 40 Å cell). Drag to rotate, scroll to zoom. Controls below the canvas play, scrub, and change playback speed.

g3 distribution¶

Measured from the final (post-relaxation) atoms. The heatmap is the reduced three-body density in units of the uniform random reference, where white = 1.0, blue = depleted, red = enhanced. The lower panel shows the pair profile g(r); the shaded amber band marks the first-neighbour shell used as the root-bond integration window for the g3 slice. For silicon there is a single Si-Si-Si triplet channel.