AiiDA plugin which contains data and methods for atomistic simulations. Up to now, only a prototype of StructureData is implemented, you can inspect it in aiida_atomistic/data/structure/prototype.py; You can run the script to see the "tests" as outputs.
A discussion on the design of the new StructureData is provided here.
This plugin is the default output of the AiiDA plugin cutter, intended to help developers get started with their AiiDA plugins.
.github/
: Github Actions configuration
ci.yml
: runs tests, checks test coverage and builds documentation at every new commitpublish-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 repositoryaiida_atomistic/
: The main source code of the plugin package
data/
: A new DiffParameters
data class, used as input to the DiffCalculation
CalcJob
classcalculations.py
: A new DiffCalculation
CalcJob
classcli.py
: Extensions of the verdi data
command line interface for the DiffParameters
classhelpers.py
: Helpers for setting up an AiiDA code for diff
automaticallyparsers.py
: A new Parser
for the DiffCalculation
docs/
: A documentation template ready for publication on Read the Docsexamples/
: An example of how to submit a calculation using this plugintests/
: 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 DocsLICENSE
: License for your pluginREADME.md
: This fileconftest.py
: Configuration of fixtures for pytestpyproject.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:
For more information, see the developer guide of your plugin.
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('atomistic')
inputs['parameters'] = DiffParameters(dict=d)
DiffParameters
dictionaries are validated using voluptuous.
Find out about supported options:
DiffParameters = DataFactory('atomistic')
print(DiffParameters.schema.schema)
pip install aiida-atomistic
verdi quicksetup # better to set up a new profile
verdi plugin list aiida.calculations # should now show your calclulation plugins
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 atomistic list
verdi data atomistic export <PK>
git clone https://github.com/aiidateam/aiida-atomistic .
cd aiida-atomistic
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.
MIT
mikibonacci@psi.ch