atomchain 0.3.2

A library to chain the atomic models with applications

atomchain

AtomChain provides CLI tools and Python APIs for atomic structure manipulation, ML-potential calculations, phonon/DDB workflows, and ABINIT HIST/MULTIBINIT training artifact preparation.

CLI Tools

AtomChain includes several command-line tools for common atomistic workflows:

• mlrelax - Relax atomic structures using ML potentials
• mlphonon - Calculate phonon properties and band structures
• mlgap - Predict band gap using ML potentials
• mlsinglepoint - Single point energy/forces/stress calculations
• mlsupercell - Generate supercells with various transformation matrices
• mlrattle - Generate rattled structure datasets for training
• mlbatch - Batch process trajectories with ML potentials
• mlcompare - Compare calculated properties between two trajectories
• mlneb - Nudged elastic band calculations for reaction pathways
• mlcollect - Collect structures from many files into one trajectory
• mlconvert - Convert structures between ASE-supported file formats
• mlmetastable - Explore symmetry-mode metastable structures
• mlddb - Write ABINIT-style DDB files from phonopy and ML finite-difference workflows
• mlhist - Convert between ABINIT HIST.nc and ASE trajectory files
• mltraining - Generate MULTIBINIT training trajectories/artifacts and delegate training to pymultibinit

Installation

AtomChain requires Python 3.10 or newer.

For development from this repository, use uv:

uv sync

For an editable installation with pip, use this from the repository root:

pip install -e .

MACE calculators are optional. To install AtomChain with MACE support, use:

pip install -e '.[mace]'

or with uv:

uv sync --extra mace

The mace-r2scan calculator uses the MACE-MH-1 model. When the model file is missing, AtomChain tries to download it automatically from Hugging Face to ~/.config/mace/mace-mh-1.model. If automatic download fails, download it manually from:

https://huggingface.co/mace-foundations/mace-mh-1/resolve/main/mace-mh-1.model

and save it as:

~/.config/mace/mace-mh-1.model

Quick Start

Single Point Calculation

mlsinglepoint input.vasp --model chgnet --output_file results.yaml

Generate Supercell

mlsupercell input.vasp --size 2 --output supercell.vasp

Generate Training Dataset

mlrattle input.vasp --stdev 0.05 --nstruct 100 --output structures.traj

Batch Process Trajectory

mlbatch structures.traj --calculator chgnet --output results.traj

Compare Trajectories

mlcompare dft.traj ml.traj --labels "DFT" "CHGNet" --output comparison.png

Relax Structure

mlrelax input.vasp --model chgnet --output_file relaxed.vasp

Calculate Phonons

mlphonon input.vasp --model chgnet --ndim 2 2 2

Write DDB From Phonopy

mlddb BaTiO3.vasp --phonopy-yaml phonon_save/phonopy_params.yaml --output BaTiO3.ddb --validate

Write ABINIT HIST From Trajectory

mlhist training.traj training_HIST.nc --to hist

Generate Training Trajectory

mltraining generate BaTiO3.vasp --sources md phonon_modes --model mace-r2scan --output training.traj

Documentation

Detailed documentation for each tool is available in the docs/ directory:

• docs/singlepoint.md - Single point calculations
• docs/supercell.md - Supercell generation
• docs/rattle.md - Dataset generation
• docs/batch.md - Batch trajectory processing
• docs/compare.md - Trajectory comparison
• docs/metastable.md - Metastable state exploration from imaginary phonon modes
• docs/relax.md - Structure relaxation
• docs/phonon.md - Phonon calculations
• docs/md.md - Molecular dynamics
• docs/multibinit.md - MULTIBINIT calculator usage through pymultibinit
• docs/ddb.md - ABINIT-style DDB writer
• docs/hist_training.md - ABINIT HIST and MULTIBINIT training artifacts

Python API

All CLI tools have corresponding Python APIs for programmatic use:

from ase.io import read
from atomchain import (
    calculate_single_point,
    calculate_trajectory_batch,
    calculate_neb,
    compare_trajectories,
    explore_metastable_states,
    generate_multibinit_training_artifacts,
    generate_rattle_dataset,
    generate_training_trajectory,
    init_calc,
    make_supercell_structure,
    phonon_with_ml,
    read_abinit_hist,
    relax_with_ml,
    write_ddb_from_finite_difference,
    write_ddb_from_phonopy,
    write_abinit_hist,
)

atoms = read("structure.vasp")

# Relax structure
relaxed_atoms = relax_with_ml(atoms, calc="chgnet")

# Calculate phonons
phonon_with_ml(atoms, calc="chgnet", ndim=[[2, 0, 0], [0, 2, 0], [0, 0, 2]])

# Single point calculation
results = calculate_single_point(atoms, calc="chgnet")

# Generate supercell
supercell = make_supercell_structure(atoms, 2)

# Generate dataset
generate_rattle_dataset(
    atoms,
    stdev=0.05,
    n_struct=100,
    output="dataset.traj"
)

# Batch process trajectory
results = calculate_trajectory_batch(
    "dataset.traj",
    calculator="chgnet",
    output="results.traj"
)

# Compare trajectories
compare_trajectories("dft.traj", "ml.traj", labels=["DFT", "CHGNet"])

# NEB calculation
initial = read("initial.vasp")
final = read("final.vasp")
calculate_neb(initial, final, calculator="chgnet")

# HIST conversion and training trajectory generation
frames = generate_training_trajectory(atoms, sources=["phonon_modes"], evaluate=False)
write_abinit_hist(frames, "training_HIST.nc", strict=False)
loaded_frames = read_abinit_hist("training_HIST.nc")

Requirements

• Python 3.10+
• ASE (Atomic Simulation Environment)
• Phonopy 3.0.0
• Optional: CHGNet, M3GNet, matgl, MACE (pip install -e '.[mace]'), DeePMD-kit, atomic_potential_xq, and pymultibinit depending on selected calculator/workflow

License

BSD-2-Clause