AiiDAlab DL_POLY Application

This is an AiiDAlab application plugin for running and managing DL_POLY molecular dynamics simulations, maintained by the Ada Lovelace Centre (ALC). It provides a guided, wizard-style interface for configuring, submitting and inspecting DL_POLY calculations from within the AiiDA/AiiDAlab environment, building on the aiida-dlpoly plugin which supplies the underlying AiiDA calculation and parser.

The app is still in an early development stage and any input or contributions are welcome. Full documentation can be found at https://stfc.github.io/aiidalab-dlpoly/.

Features

The application guides the user through a molecular dynamics calculation as a sequence of wizard steps:

• Select Structure — provide the simulation cell either by uploading a DL_POLY CONFIG file or by querying an existing structure from the AiiDA database, with an integrated structure viewer.
• Configure Workflow — supply the force field (FIELD) file, either by upload or by searching the AiiDA database, and define the simulation control either as a pre-formatted DL_POLY CONTROL file or through basic control parameters. Note: Some DL_POLY features are only available through a pre-configured CONTROL file.
• Configure Computational Resources — select the registered DL_POLY code and set the resources (e.g. number of CPUs) for the run.
• Results — browse the submitted process, its provenance and outputs through an interactive node tree and viewer.

A dedicated history page lists previously submitted DL_POLY calculations, and a resources page provides computational resource setup.

Usage

This plugin is hosted on the AiiDAlab plugin registry and can therefore be installed via the AiiDAlab plugin management UI page from within the AiiDAlab application interface. Instructions for how to run AiiDAlab itself can be found in its documentation and are also included in the documentation associated with this project at https://stfc.github.io/aiidalab-dlpoly/. It is generally recommended to run AiiDAlab through a container engine such as Docker or Apptainer. In general the core docker image applicable to most use cases is aiidalab/full-stack:latest, however many other options exist for more tailored startup environments.

Once installed in an AiiDAlab environment, the app appears on the AiiDAlab home page. Launch it to open main.ipynb and step through the wizard.

Alternatively, the package can be installed directly from source for development:

pip install .

For Developers

Style Checking

This package uses pre-commit hooks (running Ruff for linting and formatting) to enforce a consistent style. Install the development dependencies,

pip install .[dev]

then enable the hooks in the repository root,

pre-commit install

Style and formatting checks will now run on every commit.

Testing

This package uses pytest for its unit tests, included in the [dev] optional dependencies. From the project root the tests, together with a coverage report, can be run via,

pytest --cov=aiidalab_dlpoly

The CI workflows are configured to ensure all tests pass before a pull request can be accepted into the main repository. It is important that any new additions to the code base are accompanied by appropriate testing, maintaining a high code coverage.

Documentation

The documentation, including a User Guide and an API reference, is built using Sphinx. The source is contained in the docs/ directory. All required packages can be installed alongside the core package via,

pip install .[docs]

and the documentation can then be built with,

sphinx-build -b html docs/source/ docs/build/html

from the root directory.

See CONTRIBUTING and CODING_STYLE for further guidance on contributing to the project.

Citation

If you use this software, please cite it as described in the CITATION.cff file.

License

BSD 3-Clause License

Author

Dr. Benjamin T. Speake (ORCID: 0000-0002-5690-9470).

Funding

Contributors to this project were funded by the Ada Lovelace Centre (ALC).