Amorphous SiO₂

A 30 Å cubic SiO₂ supercell (2052 atoms) built with atomode’s amorphous-like regime, then refined through the four-stage pipeline:

Voronoi tile — Voronoi grain construction at grain_size = 10 Å, displacement_sigma = 0.012.
Orientation refine — per-grain SO(3) coordinate search.
FIRE shell-relax — 150 steps of the spring network via cell.shell_relax.
DFTB+ relax — bond_relax(20) + enforce_hard_core(40) cleanup, then ASE FIRE optimizer to fmax = 1.0 eV/Å with volume-only cell relax (UnitCellFilter(hydrostatic_strain=True)) and maxstep = 0.03 Å. matsci-0-3 SK set, Γ-only, Fermi smearing T = 0.012 Ha, SCC tolerance 1e-2.

To re-generate:

python scripts/regen_dftb_examples.py --regime amorphous --box 30.0

g(r) per stage¶

Pair g(r) for Si-O / O-O / Si-Si at each stage of the amorphous SiO2 refinement

Si–O bond length distribution¶

Si-O bond length histogram for amorphous SiO2 at each refinement stage

stage	Si–O peak (Å)	⟨r⟩ (Å)	σ (Å)	# Si–O bonds
Voronoi	1.61	1.61	0.067	2174
after orient	1.61	1.61	0.067	2174
after FIRE	1.69	1.70	0.092	2415
after DFTB+ (60 steps)	1.67	1.72	0.076	2313

DFTB+ pulls the peak back toward the crystalline 1.61 Å and narrows the distribution by ~17 % (σ 0.092 → 0.076 Å). Residual fmax at step 60 is 9.38 eV/Å — the 60-step cap stops the relax short of the 1.0 eV/Å target, but energy descent is monotonic across all 60 steps.

Angle distributions¶

O-Si-O and Si-O-Si angle histograms for amorphous SiO2 at each refinement stage

Energy ladder¶

stage	E_total (eV)	ΔE vs previous
Voronoi	-139713.26	—
after orient	-139713.26	0
after FIRE	-145516.22	-5803
after DFTB+ relax	-145892.40	-376 (≈ -0.18 eV/atom)

Cell volume change Voronoi → DFTB+: +0.1 %. DFTB+ total at 60 steps is -71.1 eV/atom, matching the SRO and nanocrystalline results at the same cell size and the smaller-cell baselines.

DFTB+ relax wallclock: 12,937 s = 3.6 hr for the seed SP + 60 FIRE+UCF steps (~3 min/step on average — amorphous has more SCC iterations per FIRE step than the ordered regimes).

Reproduction summary¶

knob	value
cell side	30 Å
atoms	2052
grain_size	10 Å
FIRE steps (atomode stage 3)	150
pre-DFTB cleanup	bond_relax(20) + enforce_hard_core(40)
DFTB+ optimizer	ASE FIRE, maxstep = 0.03 Å
DFTB+ cell DOFs	volume only (`hydrostatic_strain=True`)
DFTB+ fmax target	1.0 eV/Å, 60-step cap
charge restart	seed SP + `ReadInitialCharges=Yes`
SK set	matsci-0-3
k-points	(1, 1, 1) Γ-only

Per-stage trajectory (extxyz): docs/figures/dftb/amorphous_traj.xyz