janus-core 0.1.0b4

Tools for machine learnt interatomic potentials

janus-core

Tools for machine learnt interatomic potentials

Features in development

• Support for multiple MLIPs
  • MACE
  • M3GNET
  • CHGNET
• Single point calculations
• Geometry optimisation
• Molecular Dynamics
  • NVE
  • NVT (Langevin(Eijnden/Ciccotti flavour) and Nosé-Hoover (Melchionna flavour))
  • NPT (Nosé-Hoover (Melchiona flavour))
• Nudge Elastic Band
• Phonons
  • vibroscopy
• Training ML potentials
  • MACE
• Fine tunning MLIPs
  • MACE
• Rare events simulations
  • PLUMED

The code relies heavily on ASE, unless something else is mentioned.

Development

1. Install poetry
2. (Optional) Create a virtual environment
3. Install janus-core with dependencies:

git clone https://github.com/stfc/janus-core
cd janus-core
pip install --upgrade pip
poetry install --with pre-commit,dev,docs  # install extra dependencies
pre-commit install  # install pre-commit hooks
pytest -v  # discover and run all tests

Manually updating ASE via https://gitlab.com/ase/ase is strongly recommended, as tags are no longer regularly published. For example:

pip install git+https://gitlab.com/ase/ase.git@b31569210d739bd12c8ad2b6ec0290108e049eea

To prevent poetry downgrading ASE when installing in future, add the commit to pyproject.toml:

poetry add git+https://gitlab.com:ase/ase.git#b31569210d739bd12c8ad2b6ec0290108e049eea

Examples

Single Point Calculations

Perform a single point calcuation (using the MACE-MP "small" force-field):

janus singlepoint --struct tests/data/NaCl.cif --arch mace_mp --calc-kwargs "{'model' : 'small'}"

This will calculate the energy, stress and forces and save this in NaCl-results.xyz, in addition to generating a log file, singlepoint.log.

Additional options may be specified. For example:

janus singlepoint --struct tests/data/NaCl.cif --arch mace --calc-kwargs "{'model' : '/path/to/your/ml.model'}" --property energy --log './example.log' --write-kwargs "{'filename': './example.xyz'}"

This defines the MLIP architecture and path to your locally saved model, as well as changing where the log and results files are saved.

Note: the MACE calculator currently returns energy, forces and stress together, so in this case the choice of property will not change the output.

For all options, run janus singlepoint --help.

Geometry optimization

Perform geometry optimization (using the MACE-MP "small" force-field):

janus geomopt --struct tests/data/H2O.cif --arch mace_mp --calc-kwargs "{'model' : 'small'}"

This will calculate optimize the atomic positions and save the resulting structure in H2O-opt.xyz, in addition to generating a log file, geomopt.log.

Additional options may be specified. This shares most options with singlepoint, as well as a few additional options, such as:

janus geomopt --struct tests/data/NaCl.cif --arch mace_mp --calc-kwargs "{'model' : 'small'}" --fully-opt --vectors-only --traj 'NaCl-traj.xyz'

This allows the cell to be optimised, allowing only hydrostatic deformation, and saves the optimization trajector in addition to the final structure and log.

For all options, run janus geomopt --help.

License

BSD 3-Clause License

Funding

Contributors to this project were funded by