amorphgen 1.0.0rc3

AmorphGen: Amorphous structure generation via melt-quench MD and random placement.

Documentation: smtg-bham.github.io/AmorphGen

---

Pipeline overview

AmorphGen exposes three workflows. Pick the one that matches your starting point:

#	Workflow	CLI flag	Starting point
1	Random generation	--random-gen	Composition only
2	Melt-quench (MQ)	(default) or --mq-ensemble	Crystalline input
3	Hybrid	--hybrid-ensemble	Directory of disordered structures

1. Random generation (--random-gen)

Composition  (e.g. "In2O3*16"  or  In=32,O=48)
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Auto-derive  minsep, density, target CN       │
   │  from Shannon ionic / metallic radii           │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Random / coordination-aware placement         │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Optional relax  (--relax)                     │
   └─────┬──────────────────────────────────────────┘
         │
   N amorphous structures  (.xyz / .vasp / .cif)

2. Melt-quench (MQ)

Crystalline input  (POSCAR / .xyz / .cif / .extxyz)
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 1  Structure optimisation               │
   │           optimizer + cell_filter              │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 2  Pre-melt equilibration at T-low      │
   │           NVT/NPT                              │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 3  Melt  –  NPT/NVT heat ramp           │
   │           T-low → T_melt                       │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 4  High-T equilibration   T_melt        │
   │           NVT/NPT                              │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 5  Quench  –  NVT cooling ramp          │
   │           T_melt → T-low                       │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 6  Low-T equilibration   T-low          │
   │           NVT/NPT                              │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 7  Final optimisation (amorphous)       │
   │           optimizer + cell_filter              │
   └─────┬──────────────────────────────────────────┘
         │
   stage7_opt.cif  +  stage7_opt.xyz

--mq-ensemble extends MQ: stages 1–4 run once, then N independent quenches (stages 5–6–7) are launched from snapshots of the stage-4 trajectory.

3. Hybrid: random → MQ stages 4-7 (--hybrid-ensemble)

Directory of disordered structures  (e.g. --random-gen outputs)
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 4  High-T equilibration   T_melt        │
   │           NVT/NPT,  20+ ps                     │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 5  Quench  –  NVT cooling ramp          │
   │           T_melt → T-low                       │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 6  Low-T equilibration   T-low          │
   └─────┬──────────────────────────────────────────┘
         │
   ┌─────▼──────────────────────────────────────────┐
   │  Stage 7  Final optimisation (amorphous)       │
   └─────┬──────────────────────────────────────────┘
         │
   N amorphous structures  (one per input)

Hybrid is cheaper than full MQ: it skips the slow heat ramp (Stage 3) by starting from a disordered structure.

---

Supported backends

AmorphGen supports multiple calculator backends:

Backend	Install	Model name(s)
MACE	pip install amorphgen[mace]	mace-mpa-0, mace-mpa-0-medium, mace-omat-0-medium, ... (20+ variants)
CHGNet	pip install amorphgen[chgnet]	chgnet
SevenNet	pip install amorphgen[sevennet]	sevennet, 7net-mf-ompa, 7net-l3i5, 7net-omat, 7net-0, ...
Classical	built-in (no extra install)	lennard-jones, buckingham

Only install the backend(s) you need. Classical potentials (Lennard-Jones, Buckingham+Coulomb) are built-in and require no GPU. Use amorphgen --list-models to see all available models.

ASE pass-through. AmorphGen wraps each backend's upstream ASE calculator without modifying unit conventions, stress signs, or PBC handling; this energies (eV), forces (eV/Å), stress (eV/ų), and atoms.pbc are inherited directly from the upstream MLIP package. See docs/guides/backends for details.

---

Installation

Tasks	Install	Size
generate random structures, analyse trajectories (RDF, CN, S(q), plots), run classical LJ/Buckingham pipelines	pip install -e .	~80 MB, no PyTorch
+ MLIP relaxation & melt-quench MD	pip install -e ".[mace]" or ".[chgnet]"	+ PyTorch
+ everything (MACE + CHGNet)	pip install -e ".[all]"	+ PyTorch

With pip, from source (once AmorphGen is on PyPI, pip install "amorphgen[mace,chgnet]" replaces the clone):

git clone https://github.com/SMTG-Bham/AmorphGen.git
cd AmorphGen
pip install -e ".[mace,chgnet]"      # example: MACE + CHGNet
pip install -e ".[all,dev]"          # everything + pytest

With conda, which keeps the install isolated and on HPC provides the CUDA toolchain. Create the environment with conda, then install into it with pip:

conda create -n amorphgen python=3.11
conda activate amorphgen

# from source (current):
git clone https://github.com/SMTG-Bham/AmorphGen.git
cd AmorphGen
pip install -e ".[mace,chgnet]"

# or, once released on PyPI:
pip install "amorphgen[mace,chgnet]"

MLIPs are optional. The base package is deliberately torch-free. Install an MLIP extra only when you need MACE/CHGNet/SevenNet relaxation or melt-quench MD; with no torch present, --device auto resolves to CPU, and calculator-requiring commands fail fast with the exact install line. amorphgen --list-models shows every model with installed/missing markers.

SevenNet needs its own environment. SevenNet depends on e3nn>=0.5, while MACE foundation-model files (mace-mpa-0, ...) were pickled with e3nn==0.4.x and fail to load against the newer e3nn. The [all] extra therefore intentionally excludes SevenNet. To use SevenNet, create a separate conda env:

conda create -n amorphgen-sevennet python=3.11
conda activate amorphgen-sevennet
pip install -e ".[sevennet,chgnet]"

The [full] extra installs MACE+CHGNet+SevenNet in one env but loading MACE foundation models will then fail unless you upgrade mace-torch to a release that supports e3nn 0.5+.

GPU strongly recommended. Use --device cuda or "device": "auto". Device auto-detection only runs when a job starts. On a login node with no GPU, no device message will appear until a stage is launched.

---

Quick start

Command line

# -- Random generation (no crystal input needed) --
# Generate 10 random In2O3 structures (80 atoms each) and relax with MACE
amorphgen --random-gen --composition "In2O3*16" --relax --device cpu

# Same thing with explicit atom counts
amorphgen --random-gen --composition In=32,O=48 --relax --device cpu

# -- Melt-quench pipeline (from crystalline input) --
# Full 7-stage pipeline with MACE (default)
amorphgen POSCAR --device cuda

# Use CHGNet (faster on CPU)
amorphgen POSCAR --model chgnet --device cpu

# List all available models
amorphgen --list-models

--composition accepts two formats:

• Formula: In2O3*16 (16 formula units = 80 atoms)
• Atom counts: In=32,O=48 (explicit)

Typical sizes: 40-100 atoms for random generation, 100-500 for melt-quench.

Python API

from amorphgen import MeltQuenchPipeline

# MACE (default)
pipe = MeltQuenchPipeline(
    input_file="POSCAR",
    work_dir="InO_run",
    cfg_override={
        "model":  "mace-mpa-0",
        "device": "cuda",
    },
)
atoms = pipe.run()                  # all 7 stages

# CHGNet
pipe = MeltQuenchPipeline(
    input_file="POSCAR",
    cfg_override={"model": "chgnet"},
)

# SevenNet
pipe = MeltQuenchPipeline(
    input_file="POSCAR",
    cfg_override={"model": "7net-mf-ompa"},
)

# Custom fine-tuned MACE model
pipe = MeltQuenchPipeline(
    input_file="POSCAR",
    cfg_override={"model_path": "/data/models/InO_finetuned.model"},
)

# Run specific stages
pipe.run(stages=[5, 6, 7], input_file="stage4_eq_high.xyz")

---

YAML configuration

Instead of passing many CLI flags, you can define settings in a YAML file:

# config.yaml
model: mace-mpa-0
device: cuda
default_dtype: float64

opt:
  fmax: 0.01
  max_steps: 1000
  optimizer: LBFGS

melt:
  T_start: 300
  T_end: 3000
  T_step: 100

quench:
  T_start: 3000
  T_end: 300
  T_step: -100
  steps_per_T: 2000

# Use YAML config
amorphgen POSCAR --config config.yaml

# CLI args override YAML values
amorphgen POSCAR --config config.yaml --fmax 0.05 --device cpu

from amorphgen.configs import load_yaml_config
from amorphgen import MeltQuenchPipeline

cfg = load_yaml_config("config.yaml")
pipe = MeltQuenchPipeline(input_file="POSCAR", cfg_override=cfg)
atoms = pipe.run()

Precedence: CLI arguments > YAML config > built-in defaults.

YAML also supports random generation settings:

# random_gen_config.yaml
model: chgnet
device: cpu
default_dtype: float32

opt:
  fmax: 0.05
  max_steps: 500
  cell_filter: cubic

random_gen:
  composition:
    Si: 16
    O: 32
  n_structures: 5
  target_density: 2.2
  target_cn:
    Si: 4
    O: 2
  output_format: vasp

amorphgen --random-gen --config random_gen_config.yaml --work-dir SiO2_sc
amorphgen --batch-opt --input-dir SiO2_sc --work-dir SiO2_sc_opt --config random_gen_config.yaml

See amorphgen/configs/example_config.yaml for all available options.

---

Random structure generation

Generate random amorphous starting structures:

# Generate 20 random In₂O₃ structures (80 atoms each)
amorphgen --random-gen \
    --composition "In2O3*16" \
    --n-structures 20 \
    --work-dir random_structures/

# Same with explicit atom counts and target density
amorphgen --random-gen \
    --composition In=32,O=48 \
    --target-density 5.5 \
    --n-structures 20

# Generate with relaxation
amorphgen --random-gen \
    --composition "TiO2*16" \
    --n-structures 10 \
    --relax --model mace-mpa-0

# Resume after interruption (skips completed structures)
amorphgen --random-gen \
    --composition "Ga2O3*80" -n 20 \
    --relax --device cuda --format vasp --resume

from amorphgen import generate_random, batch_random

# Single structure
atoms = generate_random({"In": 16, "O": 24})

# Batch generation
batch_random(
    composition={"In": 32, "O": 48},   # atom counts (Python API always uses dict)
    n_structures=20,
    output_dir="random_structures",
)

Two-step workflow: generate then optimise separately

You can decouple generation and optimisation into separate steps. This gives more control over optimisation settings (optimizer, cell filter, precision, convergence) and lets you inspect structures before committing to expensive relaxation.

Step 1: Generate (default, no relaxation):

amorphgen --random-gen \
    --composition Ga=16,O=24 \
    --n-structures 5 \
    --work-dir random_Ga2O3

from amorphgen.pipeline.random_gen import batch_random

paths = batch_random(
    composition={"Ga": 16, "O": 24},
    n_structures=5,
    output_dir="random_Ga2O3",
    relax=False,
    seed=42,
)

Step 2: Batch optimise:

amorphgen --batch-opt \
    --input-dir random_Ga2O3 \
    --work-dir random_Ga2O3_opt \
    --model mace-mpa-0 --device cpu --fmax 0.01

from amorphgen.pipeline.opt_cell import batch_optimize
from amorphgen.utils import get_calculator

calc = get_calculator(model="mace-mpa-0", device="cpu", default_dtype="float64")

batch_optimize(
    input_dir="random_Ga2O3",
    output_dir="random_Ga2O3_opt",
    calc=calc,
)

The --batch-opt mode uses the full opt_cell.run() under the hood, giving you proper logging, trajectory files, configurable optimizer/cell filter, and float64 precision.

Coordination-aware placement

For better short-range order, enable coordination-aware placement with --target-cn. New atoms are biased toward existing under-coordinated sites, and placements that would push any neighbour over its target CN are rejected:

# Coordination-aware placement: atoms placed near under-coordinated sites
amorphgen --random-gen \
    --composition "SiO2*16" \
    --target-density 2.2 \
    --target-cn Si=4,O=2 \
    --work-dir random_SiO2

# With explicit bonding shell distances
amorphgen --random-gen \
    --composition Li=16,Zr=8,Cl=48 \
    --target-cn Zr=6,Li=6 \
    --dmax Zr-Cl=3.2,Li-Cl=3.2 \
    --work-dir random_Li2ZrCl6

from amorphgen.pipeline.random_gen import generate_random

atoms = generate_random(
    composition={"Si": 16, "O": 32},
    target_density=2.2,
    target_cn={"Si": 4, "O": 2},
    seed=42,
)

Coordination-aware placement produces structures with correct coordination from the start, requiring less relaxation to reach the correct topology. Disable it with --no-sc (legacy flag name; the placement is enabled by default whenever --target-cn is set or auto-detected).

---

Structure analysis

Analyse optimised structures for density, coordination, bond distances, angles, and RDF:

# Auto cutoff (default)
amorphgen --analyse --input-dir optimised_structures/

# Save report and plots
amorphgen --analyse --input-dir optimised_structures/ \
    --save-report report.txt --save-plot plots/

# RDF-based auto cutoff
amorphgen --analyse --input-dir optimised_structures/ --cutoff auto-rdf

from amorphgen.utils.analysis import StructureAnalyser

sa = StructureAnalyser("optimised_structures/", cutoff="auto")
sa.summary()
sa.save_report("report.txt")
sa.plot(output_dir="plots/", angle_style="line")

---

Generating multiple independent structures (batch quench)

Step 1: Run Stages 1–4 with snapshot sampling

amorphgen POSCAR \
    --stages 1 2 3 4 \
    --eq-high-steps 100000 \
    --work-dir melt_run/

Step 2: Batch quench N independent runs from snapshots

amorphgen --batch-quench \
    --snapshot-dir snapshots/ \
    --n-runs 20 --select uniform \
    --batch-stages 5 6 7 \
    --work-dir batch_run/

from amorphgen.pipeline import batch_quench

results = batch_quench.run(
    snapshot_files=snapshot_paths,
    n_runs=20,
    select="uniform",
    work_dir="batch_run",
)

Each run gets its own subdirectory: batch_run/run_0000/, batch_run/run_0001/, …

Resuming an interrupted batch

If a batch job times out, resubmit with --resume; already-completed runs are skipped:

amorphgen --batch-quench \
    --snapshot-dir snapshots/ \
    --n-runs 20 --select uniform \
    --resume \
    --work-dir batch_run/

Hybrid workflow: random generation → high-T equilibration → batch quench

An alternative approach combines random structure generation with high-temperature equilibration to skip the slow heating stage:

Random structure (target density)
    │
    ▼
Optimise (positions only - preserves density)
    │
    ▼
Equilibrate at T_melt (NVT, 20+ ps)
    │
    ├── snapshot 0 ──→ Quench → Low-T eq → Opt → amorphous_0
    ├── snapshot 1 ──→ Quench → Low-T eq → Opt → amorphous_1
    └── ...

from amorphgen.pipeline.random_gen import generate_random
from amorphgen.pipeline.opt_cell import run as opt_run
from amorphgen.pipeline.equilibrate import run as eq_run
from amorphgen import MeltQuenchPipeline

# Step 1: Generate random structure (auto minsep from Shannon radii)
atoms = generate_random(
    composition={"Ti": 8, "O": 16},
    target_density=3.2,       # optional, auto-estimated if omitted
    target_cn={"Ti": 6},      # optional, enables coordination-aware placement + CN-aware radii
)

# Step 2: Optimise (positions only)
calc = get_calculator(model="chgnet", device="cpu")
optimised = opt_run(atoms, cfg_override={"opt": {"fmax": 0.1}}, calc=calc)

# Step 3: Equilibrate at 2000 K
liquid = eq_run(optimised, cfg_override={
    "eq_high": {"ensemble": "NVT", "T": 2000, "steps": 10000, "timestep": 0.5},
}, calc=calc, stage="high")

# Step 4: Extract snapshots and batch quench (Stages 5 → 6 → 7)
for snap_file in snapshot_files:
    pipe = MeltQuenchPipeline(input_file=snap_file, work_dir=run_dir,
        cfg_override={"model": "chgnet", "device": "cpu"})
    pipe.run(stages=[5, 6, 7])

See Tutorial 5 for a complete working example.

---

Ensemble choice

Stage	Default	Override flag
Stage 2 pre-melt eq	NVT	--eq-premelt-ensemble NPT
Stage 3 melt	NPT	--melt-ensemble NVT
Stage 4 high-T eq	NVT	--eq-high-ensemble NPT
Stage 5 quench	NVT	--quench-ensemble NPT
Stage 6 low-T eq	NVT	--eq-low-ensemble NPT

---

Heating / cooling rate

amorphgen POSCAR \
    --melt-T-step 100 --melt-steps-per-T 1000     # 100 K/ps heating
    --quench-T-step -50 --quench-steps-per-T 2000  # 25 K/ps cooling

Common cooling rates:

Rate	--quench-steps-per-T	Time (3000 → 300 K)
200 K/ps	500	~13 ps
100 K/ps (default)	1000	~27 ps
10 K/ps	10000	~270 ps
1 K/ps	100000	~2700 ps

---

Trajectory format

Format	Extension	Notes
extxyz	.xyz	Default. ASE extended XYZ (cell + energy + forces). Readable by OVITO, VESTA, ASE.
xyz	.xyz	Plain XYZ (positions only)
traj	.traj	ASE binary
lammps-dump	.dump	LAMMPS text dump

---

Available models

Name	Backend	Notes
mace-mpa-0	MACE	default (MPTrj + sAlex)
mace-omat-0-medium	MACE	OMAT, excellent phonons (ASL license)
mace-matpes-r2scan	MACE	MATPES, r²SCAN functional (ASL license)
chgnet	CHGNet	Charge-informed, good CPU speed
7net-mf-ompa	SevenNet	Multi-fidelity foundation, OMat+MPtrj+Alexandria
lennard-jones	Classical	Pair potential, no GPU needed
buckingham	Classical	Buckingham + Coulomb (Wolf summation), no GPU needed

amorphgen --list-models   # full table of all models grouped by backend

---

Full configuration reference

All defaults are in amorphgen/configs/default_config.py. Override any value via cfg_override:

pipe = MeltQuenchPipeline(
    input_file="POSCAR",
    work_dir="my_run",
    cfg_override={
        "model":       "mace-mpa-0",  # or "chgnet", "7net-mf-ompa", "buckingham", etc.
        "model_path":  None,           # path to local .model file (overrides model)
        "device":      "auto",         # "cuda", "cpu", or "auto"
        "traj_format": "extxyz",       # "extxyz", "xyz", "traj", "lammps-dump"

        "opt": {
            "fmax": 0.01,
            "max_steps": 1000,
        },
        "eq_premelt": {
            "ensemble": "NVT",
            "T": 300,
            "steps": 100000,       # 50 ps at 0.5 fs timestep
            "timestep": 0.5,
            "friction": 0.01,
        },
        "melt": {
            "ensemble": "NPT",
            "T_start": 300, "T_end": 3000,
            "T_step": 100, "steps_per_T": 1000,
            "timestep": 0.5,
            "friction": 0.01, "ttime": 25.0,
        },
        "eq_high": {
            "ensemble": "NVT",
            "T": 3000,
            "steps": 10000,
            "timestep": 0.5,
            "friction": 0.01,
        },
        "quench": {
            "ensemble": "NVT",
            "T_start": 3000, "T_end": 300,
            "T_step": -100, "steps_per_T": 1000,
            "timestep": 0.5,
            "friction": 0.01, "ttime": 25.0,
        },
        "eq_low": {
            "ensemble": "NVT",
            "T": 300,
            "steps": 10000,
            "timestep": 0.5,
            "friction": 0.01,
        },
    },
)

---

Output files

Stage	Trajectory	Final structure	Log
1	stage1_opt.traj	stage1_opt.cif + stage1_opt.xyz	stage1_opt.log
2	stage2_eq_traj.xyz	stage2_eq.xyz	stage2_eq.log
3	stage3_melt_traj.xyz	stage3_melted.xyz	stage3_melt.log
4	stage4_eq_traj.xyz	stage4_eq.xyz	stage4_eq.log
5	stage5_quench_traj.xyz	stage5_quenched.xyz	stage5_quench.log
6	stage6_eq_traj.xyz	stage6_eq.xyz	stage6_eq.log
7	stage7_opt.traj	stage7_opt.cif + stage7_opt.xyz	stage7_opt.log

---

Tutorials

Start here:

Tutorial	Description
Tutorial 1	Quick-start tutorial: orientation: what it does, the three workflows, decision tree, one live demo (random + CHGNet relax on a-SiO₂)

Workflow tutorials (each reports the wall time measured on the CPU it was validated on):

Tutorial	Description
Tutorial 2	Zero-config random gen: composition is the only input; auto-derive minsep, density, target CN, oxidation state across 8 material classes (Si, SiO₂, In₂O₃, CdTe, AlN, LiCl, TiO₂, Cu). Each structure is CHGNet-relaxed and saved to output_T2/
Tutorial 3	Explicit control + ensemble analysis: the opposite end of T2: hand-picked minsep (from crystalline bond lengths) and target density (from cited amorphous-thin-film references), 5-structure ensembles per system, quantitative RDF / energy / CN / bond-angle analysis vs the crystalline reference (In₂O₃, TiO₂, Al₂O₃, Ga₂O₃; MACE-MPA-0)
Tutorial 4	Full 7-stage melt-quench from crystalline SiO₂ (CHGNet on CPU; flip the backend toggle for MACE on GPU)
Tutorial 5	Hybrid workflow: random gen → high-T equilibration → batch quench (TiO₂)
Tutorial 6	Classical potential (Buckingham+Coulomb) relaxation, no GPU needed (SiO₂, Al₂O₃, TiO₂)

Application case studies (these assume you have done the workflow tutorials):

Tutorial	Description
Tutorial 7	Defect chemistry: O–O peroxide dimer dissociation kinetics in amorphous In₂O₃, with Arrhenius temperature scan

---

Package layout

AmorphGen/
├── .github/workflows/
│   └── test.yml                    ← CI (pytest on 3.10/3.11/3.12)
├── amorphgen/
│   ├── __init__.py                 ← v1.0.0rc3
│   ├── cli.py                      ← CLI entry point (amorphgen command)
│   ├── configs/
│   │   ├── default_config.py       ← all default parameters
│   │   ├── yaml_config.py          ← YAML config loader
│   │   └── example_config.yaml     ← example YAML with all options
│   ├── pipeline/
│   │   ├── run_pipeline.py         ← MeltQuenchPipeline orchestrator
│   │   ├── opt_cell.py             ← Stages 1 & 7 (optimisation) + batch_optimize()
│   │   ├── equilibrate.py          ← Stages 2, 4, 6 (constant-T equilibration)
│   │   ├── melt_cell.py            ← Stage 3 (heat ramp)
│   │   ├── quench.py               ← Stage 5 (cool ramp)
│   │   ├── batch_quench.py         ← batch runner: Stages 5 → 6 → 7 on N snapshots
│   │   └── random_gen.py           ← random + coordination-aware placement
│   └── utils/
│       ├── analysis.py             ← StructureAnalyser (density, CN, RDF, angles)
│       ├── calculators.py          ← multi-backend calculator factory
│       ├── radii.py                ← Shannon/metallic radii, minsep, density estimation
│       └── common.py               ← dynamics builder, logger, trajectory writer
├── paper/
│   ├── paper.md                    ← JOSS draft
│   └── paper.bib
├── test/                           ← 114 tests (4 skipped without --run-mace)
├── pyproject.toml
├── LICENSE                         ← MIT
└── README.md

---

HPC (SLURM) example

#!/bin/bash
#SBATCH --job-name=amorphgen
#SBATCH --gres=gpu:1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=32G
#SBATCH --time=4:00:00

source /path/to/conda/env/bin/activate

amorphgen /abs/path/to/In2O3_POSCAR \
    --model mace-mpa-0 \
    --device cuda \
    --work-dir /scratch/InO_amorphous \
    --melt-T-end 2500 \
    --quench-T-start 2500

---

Dependencies

Package	Purpose
ase	MD engine, optimisers, I/O
numpy	Array operations
scipy	Vectorized erfc for Coulomb (classical)
torch	GPU backend (MLIP + optional classical GPU)
mace-torch	MACE calculator (optional)
chgnet	CHGNet calculator (optional)
sevenn	SevenNet calculator (optional)

---

Citation

If you use AmorphGen in your research, please cite the package and the foundation model(s) you used.

AmorphGen:

@misc{amorphgen,
  author = {Kaewmeechai, Chaiyawat and Scanlon, David O.},
  title  = {AmorphGen: A Python package for amorphous structure generation
            with machine-learning and classical interatomic potentials},
  year   = {2026},
  url    = {https://github.com/SMTG-Bham/AmorphGen}
}

A Zenodo DOI for tagged releases will be added on first stable release.

Foundation potentials (cite the one you used):

MACE-MP:

@article{batatia2023foundation,
  title   = {A foundation model for atomistic materials chemistry},
  author  = {Ilyes Batatia and others},
  year    = {2023},
  eprint  = {2401.00096},
  archivePrefix = {arXiv},
}

CHGNet:

@article{deng2023chgnet,
  title   = {CHGNet as a pretrained universal neural network potential for charge-informed atomistic modelling},
  author  = {Bowen Deng and others},
  journal = {Nature Machine Intelligence},
  year    = {2023},
}

SevenNet:

@article{park2024sevennet,
  title   = {Scalable parallel algorithm for graph neural network interatomic potentials in molecular dynamics simulations},
  author  = {Park, Yutack and Kim, Jaesun and Hwang, Seungwoo and Han, Seungwu},
  journal = {Journal of Chemical Theory and Computation},
  year    = {2024},
}

---

License

MIT

Development notes

Parts of this codebase were developed with assistance from an AI tool, Anthropic's Claude (Opus 4.8), for code drafting, refactoring, and documentation. All AI-assisted code was reviewed, tested, and validated by the authors, who take full responsibility for the contents of this repository.