janus-core 0.6.6

Tools for machine learnt interatomic potentials

janus-core

Tools for machine learnt interatomic potentials

Getting started

Dependencies

janus-core dependencies currently include:

• Python >= 3.9
• ASE >= 3.23
• mace-torch = 0.3.8
• chgnet = 0.3.8 (optional)
• matgl = 1.1.3 (optional)
• sevenn = 0.10.0 (optional)
• alignn = 2024.5.27 (optional)

All required and optional dependencies can be found in pyproject.toml.

[!NOTE] Where possible, we expect to update pinned MLIP dependencies to match their latest releases, subject to any required API fixes.

Installation

The latest stable release of janus-core, including its dependencies, can be installed from PyPI by running:

python3 -m pip install janus-core

To get all the latest changes, janus-core can also be installed from GitHub:

python3 -m pip install git+https://github.com/stfc/janus-core.git

By default, MACE is the only MLIP installed.

Other MLIPs can be installed as extras. For example, to install CHGNet and M3GNet, run:

python3 -m pip install janus-core[chgnet,m3gnet]

or to install all supported MLIPs:

python3 -m pip install janus-core[all]

Individual extras are listed in Getting Started, as well as in pyproject.toml under [tool.poetry.extras].

Further help

Please see Getting Started, as well as guides for janus-core's Python and command line interfaces, for additional information, or open an issue if something doesn't seem right.

Features

Unless stated otherwise, MLIP calculators and calculations rely heavily on ASE.

Current and planned features include:

• Support for multiple MLIPs
  • MACE
  • M3GNet
  • CHGNet
  • ALIGNN (experimental)
  • SevenNet (experimental)
• 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
  • Phonopy
• Equation of State
• Training ML potentials
  • MACE
• Fine-tuning MLIPs
  • MACE
• MLIP descriptors
  • MACE
• Data preprocessing
  • MACE
• Rare events simulations
  • PLUMED

Command line interface

All supported MLIP calculations are accessible through subcommands of the janus command line tool, which is installed with the package:

janus singlepoint
janus geomopt
janus md
janus phonons
janus eos
janus train
janus descriptors
janus preprocess

For example, a single point calcuation (using the MACE-MP "small" force-field) can be performed by running:

janus singlepoint --struct tests/data/NaCl.cif --arch mace_mp --model-path small

A description of each subcommand, as well as valid options, can be listed using the --help option. For example,

janus singlepoint --help

prints the following:

Usage: janus singlepoint [OPTIONS]

  Perform single point calculations and save to file.

Options:
  --struct PATH        Path of structure to simulate.  [required]
  --arch TEXT          MLIP architecture to use for calculations.  [default:
                       mace_mp]
  --device TEXT        Device to run calculations on.  [default: cpu]
  --model-path TEXT    Path to MLIP model.  [default: None]
  --properties TEXT    Properties to calculate. If not specified, 'energy',
                       'forces' and 'stress' will be returned.
  --out PATH           Path to save structure with calculated results. Default
                       is inferred from name of structure file.
  --read-kwargs DICT   Keyword arguments to pass to ase.io.read. Must be
                       passed as a dictionary wrapped in quotes, e.g. "{'key'
                       : value}".  [default: "{}"]
  --calc-kwargs DICT   Keyword arguments to pass to selected calculator. Must
                       be passed as a dictionary wrapped in quotes, e.g.
                       "{'key' : value}". For the default architecture
                       ('mace_mp'), "{'model':'small'}" is set unless
                       overwritten.
  --write-kwargs DICT  Keyword arguments to pass to ase.io.write when saving
                       results. Must be passed as a dictionary wrapped in
                       quotes, e.g. "{'key' : value}".  [default: "{}"]
  --log PATH           Path to save logs to. Default is inferred from the name
                       of the structure file.
  --summary PATH       Path to save summary of inputs, start/end time, and
                       carbon emissions. Default is inferred from the name of
                       the structure file.
  --config TEXT        Configuration file.
  --help               Show this message and exit.

Please see the user guide for examples of each subcommand.

Using configuration files

Default values for all command line options may be specifed through a Yaml 1.1 formatted configuration file by adding the --config option. If an option is present in both the command line and configuration file, the command line value takes precedence.

For example, with the following configuration file and command:

struct: "NaCl.cif"
properties:
  - "energy"
out: "NaCl-results.extxyz"
arch: mace_mp
model-path: medium
calc-kwargs:
  dispersion: True

janus singlepoint --struct KCl.cif --out KCl-results.cif --config config.yml

This will run a singlepoint energy calculation on KCl.cif using the MACE-MP "medium" force-field, saving the results to KCl-results.cif.

[!NOTE] properties must be passed as a Yaml list, as above, not as a string.

Example configurations for all commands can be found in janus-tutorials

Python interface

Calculations can also be run through the Python interface. For example, running:

from janus_core.calculations.single_point import SinglePoint

single_point = SinglePoint(
    struct_path="tests/data/NaCl.cif",
    arch="mace_mp",
    model_path="tests/models/mace_mp_small.model",
)

results = single_point.run()
print(results)

will read the NaCl structure file and attach the MACE-MP (medium) calculator, before calculating and printing the energy, forces, and stress.

Jupyter Notebook tutorials illustrating the use of currently available calculations can be found in the janus-tutorials repository. This currently includes examples for:

• Single Point
• Geometry Optimization
• Molecular Dynamics
• Equation of State
• Phonons

Calculation outputs

By default, calculations performed will modify the underlying ase.Atoms object to store information in the Atoms.info and Atoms.arrays dictionaries about the MLIP used.

Additional dictionary keys include arch, corresponding to the MLIP architecture used, and model_path, corresponding to the model path, name or label.

Results from the MLIP calculator, which are typically stored in Atoms.calc.results, will also, by default, be copied to these dictionaries, prefixed by the MLIP arch.

For example:

from janus_core.calculations.single_point import SinglePoint

single_point = SinglePoint(
    struct_path="tests/data/NaCl.cif",
    arch="mace_mp",
    model_path="tests/models/mace_mp_small.model",
)

single_point.run()
print(single_point.struct.info)

will return

{
  'spacegroup': Spacegroup(1, setting=1),
  'unit_cell': 'conventional',
  'occupancy': {'0': {'Na': 1.0}, '1': {'Cl': 1.0}, '2': {'Na': 1.0}, '3': {'Cl': 1.0}, '4': {'Na': 1.0}, '5': {'Cl': 1.0}, '6': {'Na': 1.0}, '7': {'Cl': 1.0}},
  'model_path': 'tests/models/mace_mp_small.model',
  'arch': 'mace_mp',
  'mace_mp_energy': -27.035127799332745,
  'mace_mp_stress': array([-4.78327600e-03, -4.78327600e-03, -4.78327600e-03,  1.08000967e-19, -2.74004242e-19, -2.04504710e-19]),
  'system_name': 'NaCl',
}

[!NOTE] If running calculations with multiple MLIPs, arch and mlip_model will be overwritten with the most recent MLIP information. Results labelled by the architecture (e.g. mace_mp_energy) will be saved between MLIPs, unless the same arch is chosen, in which case these values will also be overwritten.

This is also the case the calculations performed using the CLI, with the same information written to extxyz output files.

[!TIP] For complete provenance tracking, calculations and training can be run using the aiida-mlip AiiDA plugin.

Development

We recommend installing poetry for dependency management when developing for janus-core:

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
python3 -m pip install --upgrade pip
poetry install --with pre-commit,dev,docs  # install with useful dev dependencies
pre-commit install  # install pre-commit hooks
pytest -v  # discover and run all tests

License

BSD 3-Clause License

Funding

Contributors to this project were funded by