aiida-amber

AiiDA plugin that wraps amber molecular dynamics executables

This plugin is the default output of the AiiDA plugin cutter, intended to help developers get started with their AiiDA plugins.

Repository contents

• .github/: Github Actions configuration
  • ci.yml: runs tests, checks test coverage and builds documentation at every new commit
  • publish-on-pypi.yml: automatically deploy git tags to PyPI - just generate a PyPI API token for your PyPI account and add it to the pypi_token secret of your github repository
• aiida_amber/: The main source code of the plugin package
  • data/: A new DiffParameters data class, used as input to the DiffCalculation CalcJob class
  • calculations.py: A new DiffCalculation CalcJob class
  • cli.py: Extensions of the verdi data command line interface for the DiffParameters class
  • helpers.py: Helpers for setting up an AiiDA code for diff automatically
  • parsers.py: A new Parser for the DiffCalculation
• docs/: A documentation template ready for publication on Read the Docs
• examples/: An example of how to submit a calculation using this plugin
• tests/: Basic regression tests using the pytest framework (submitting a calculation, ...). Install pip install -e .[testing] and run pytest.
• .gitignore: Telling git which files to ignore
• .pre-commit-config.yaml: Configuration of pre-commit hooks that sanitize coding style and check for syntax errors. Enable via pip install -e .[pre-commit] && pre-commit install
• .readthedocs.yml: Configuration of documentation build for Read the Docs
• LICENSE: License for your plugin
• README.md: This file
• conftest.py: Configuration of fixtures for pytest
• pyproject.toml: Python package metadata for registration on PyPI and the AiiDA plugin registry (including entry points)

See also the following video sequences from the 2019-05 AiiDA tutorial:

• run aiida-diff example calculation
• aiida-diff CalcJob plugin
• aiida-diff Parser plugin
• aiida-diff computer/code helpers
• aiida-diff input data (with validation)
• aiida-diff cli
• aiida-diff tests
• Adding your plugin to the registry
• pre-commit hooks

For more information, see the developer guide of your plugin.

Features

• Add input files using SinglefileData:

  SinglefileData = DataFactory('singlefile')
  inputs['file1'] = SinglefileData(file='/path/to/file1')
  inputs['file2'] = SinglefileData(file='/path/to/file2')

• Specify command line options via a python dictionary and DiffParameters:

  d = { 'ignore-case': True }
  DiffParameters = DataFactory('amber')
  inputs['parameters'] = DiffParameters(dict=d)

• DiffParameters dictionaries are validated using voluptuous. Find out about supported options:

  DiffParameters = DataFactory('amber')
  print(DiffParameters.schema.schema)

Installation

pip install aiida-amber
verdi quicksetup  # better to set up a new profile
verdi plugin list aiida.calculations  # should now show your calclulation plugins

Usage

Here goes a complete example of how to submit a test calculation using this plugin.

A quick demo of how to submit a calculation:

verdi daemon start     # make sure the daemon is running
cd examples
./example_01.py        # run test calculation
verdi process list -a  # check record of calculation

The plugin also includes verdi commands to inspect its data types:

verdi data amber list
verdi data amber export <PK>

Development

git clone https://github.com/PSDI-UK/aiida-amber .
cd aiida-amber
pip install --upgrade pip
pip install -e .[pre-commit,testing]  # install extra dependencies
pre-commit install  # install pre-commit hooks
pytest -v  # discover and run all tests

See the developer guide for more information.

License

MIT

Contact

jas.kalayan@stfc.ac.uk