# Amorphous
Cu, 40 × 40 × 40 Å, regime preset `"amorphous"` with build-time
orientation refinement enabled.
## Orientation-refinement movie
Each frame is one accepted grain rotation; the schedule walks
30° → 15° → 5° → 2° and accepts the best of 50 trials per (amplitude,
grain). Discrete steps, no FIRE between accepts.
## FIRE quench movie
Continuous atomic relaxation after rotation refinement. The starting
state is whatever the rotation search settled on; FIRE then converges
all atoms into the basin.
## Cost trace: refinement + FIRE
Total / bond / angle / repulsion components. Left of the dashed
line: rotation refinement (one point per accepted rotation). Right:
FIRE convergence (downsampled).
## g3 distribution: initial · after refine · after FIRE
Three rooted three-body distributions captured at three points along
the pipeline so the algorithmic effect of each stage is visible.
**Initial** (post-build, post-retile): grain interiors are perfect
crystal slabs at random orientations.
**After refinement** (pre-FIRE): SO(3) coordinate descent has
walked each grain into a better-aligned basin against its
neighbours. Differences from the initial g3 are concentrated at
grain boundaries.
**After FIRE** (final): all atoms relaxed. A small post-FIRE
thermal jitter (σ scaled by regime grain density) is applied
before measurement so the peaks have realistic finite-T width
rather than the perfectly sharp 0K-FIRE-quench result.
## Code
```python
from ase.build import bulk
import tricor as tc
atoms = bulk("Si", "diamond", a=5.431) # use the right reference for Cu
shell_target = tc.CoordinationShellTarget.from_atoms(atoms, phi_num_bins=90)
cell = tc.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,
**tc.Supercell.PRESETS["amorphous"],
refine_orientations=True,
refine_orientations_kwargs=dict(
amplitudes_deg=(30.0, 15.0, 5.0, 2.0),
trials_per_amplitude_per_grain=50,
max_rounds_per_amplitude=2,
cost_function="pair_distance",
score_cutoff_factor=1.5,
time_budget_sec=180.0,
capture_trajectory=True,
),
capture_trajectory=True,
)
```