Melt-and-quench pipeline

The melt-and-quench pipeline is a 7-stage molecular dynamics workflow that transforms a crystalline input into a realistic amorphous structure.

Overview

┌───────────┐    ┌───────────┐    ┌───────┐    ┌──────────┐    ┌─────────┐    ┌──────────┐    ┌───────────┐
│ 1. Opt    │───▶│ 2. Pre-eq │───▶│ 3.Melt│───▶│ 4. Hi-eq │───▶│ 5.Quench│───▶│ 6. Lo-eq │───▶│ 7. Opt    │
│  300 K    │    │  300 K    │    │ →3000K│    │  3000 K  │    │ →300 K  │    │  300 K   │    │  final    │
└───────────┘    └───────────┘    └───────┘    └──────────┘    └─────────┘    └──────────┘    └───────────┘

Stage descriptions

Stage 1: Structure optimisation

Relaxes the input structure (cell + atomic positions) to remove any initial stress. Uses LBFGS with UnitCellFilter by default.

Stage 2: Pre-melt equilibration

Short NVT equilibration at 300 K. Thermalises the system before the rapid heating stage, improving trajectory stability.

Stage 3: Melt (heat ramp)

Linear temperature ramp from 300 K to the target melt temperature (default 3000 K). Uses NPT with the Berendsen weak-coupling barostat by default — the cell expands physically as the system heats.

Stage 4: High-temperature equilibration

Holds the system at the melt temperature to ensure thorough melting and loss of crystalline memory. Uses NPT with the Martyna-Tobias-Klein (MTK) Nose-Hoover-chain integrator by default, giving true canonical fluctuations around the equilibrium melt volume. Users who want the legacy constant-volume behaviour can set eq_high.ensemble: NVT.

Stage 5: Quench (cooling ramp)

Linear cooling from the melt temperature back to 300 K. The quench rate controls the degree of structural disorder. Uses NVT by default.

Stage 6: Low-temperature equilibration

Equilibrates the quenched structure at 300 K to relax any residual thermal stress.

Stage 7: Final optimisation

Final cell + position relaxation of the amorphous structure. Produces the output file.

NPT integrators

AmorphGen exposes three NPT integrators via the per-stage npt_method YAML key:

`npt_method`	ASE class	Use case
`berendsen` (default)	`NPTBerendsen`	Robust during the 300 K → 3000 K melt ramp; does not produce true canonical fluctuations (averages are correct, fluctuation-derived quantities like heat capacity are not).
`mtk`	`IsotropicMTKNPT`	Martyna-Tobias-Klein Nose-Hoover-chain NPT. True canonical fluctuations. Recommended for equilibration plateaux; may become unstable during rapid temperature ramps.
`parrinello-rahman`	`MelchionnaNPT`	Nose-Hoover + Parrinello-Rahman flexible-cell NPT. Allows the cell shape (not just volume) to change; useful for anisotropic glasses. Requires upper-triangular cell.

Stability knobs

Two parameters tune the Berendsen barostat for stiffer/slower volume control during the heating ramp:

Key	Default	What it does
`taup_factor`	10.0	Ratio of barostat coupling time to thermostat coupling time (`taup = taup_factor * ttime`). Larger → slower, more stable barostat. Applied to Berendsen `taup` and MTK `pdamp`.
`compressibility_GPa`	100.0	Reference compressibility for the Berendsen barostat. The default (100 GPa) is liquid-like; oxides with bulk modulus 150–300 GPa benefit from 200 GPa for less aggressive volume control.

Example: tighten the melt ramp for a-In₂O₃ / a-Ga₂O₃ / a-HfO₂

melt:
  ensemble: NPT
  npt_method: berendsen
  taup_factor: 30.0              # slower barostat (3× default)
  compressibility_GPa: 200.0     # stiffer, oxide-realistic

On a Cu/EMT benchmark at 1500 K over 300 fs, these settings reduce the maximum volume excursion from 6.7 % (defaults) to 1.8 % — a 74 % reduction.

Example: true canonical fluctuations at the equilibration plateau

eq_high:
  ensemble: NPT
  npt_method: mtk

This is the new default for eq_high; the legacy NVT behaviour is restored by setting ensemble: NVT.

Running specific stages

You can run a subset of stages using the --stages flag:

# Only quench and post-process (e.g. after restarting from a snapshot)
amorphgen POSCAR --model mace-mpa-0 --stages 5 6 7

Customising parameters

See the Configuration page for all available configuration keys.