aiida-aimall 1.0.5
A plugin to interface AIMAll with AiiDA
Requires Python: >=3.10
Keywords: aiida, plugin

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# aiida-aimall

A plugin to interface AIMAll with AiiDA

## Repository contents

* [`.github/`](.github/): [Github Actions](https://github.com/features/actions) configuration
  * [`workflows/`](.github/workflows/)
    * [`ci.yml`](.github/workflows/ci.yml): runs tests, checks test coverage and continuous integration at every new commit
    * [`publish-on-pypi.yml`](.github/workflows/publish-on-pypi.yml): automatically deploy git tags to PyPI - just generate a [PyPI API token](https://pypi.org/help/#apitoken) for your PyPI account and add it to the `pypi_token` secret of your github repository
  * [`config/`](.github/config) config files for testing/docs environment
    * [`code-aim.yaml`](.github/config/code-aim.yaml) config file for building precommit and test envs
    * [`code-gwfx.yaml`](.github/config/code-gwfx.yaml) config file for building precommit and test envs
    * [`profile.yaml`](.github/config/profile.yaml) config file for aiida profile
    * [`localhost-config.yaml`](.github/config/localhost-config.yaml) config file for localhost computer
    * [`localhost-setup.yaml`](.github/config/localhost-setup.yaml) setup file for localhost computer
* [`aiida_aimall/`](src/aiida_aimall/): The main source code of the plugin package
  * [`data.py`](src/aiida_aimall/data.py): A new `AimqbParameters` data class, used as input to the `AimqbCalculation` `CalcJob` class
  * [`calculations.py`](src/aiida_aimall/calculations.py): A new `AimqbCalculation` `CalcJob` class
  * [`parsers.py`](src/aiida_aimall/parsers.py): Two parsers (`AimqbBaseParser` and `AimqbGroupParser`) for `AimqbCalculation` results
  * [`workchains/`](src/aiida_aimall/workchains/): New `WorkChains`.
    * [`calcfunctions.py`](src/aiida_aimall/workchains/calcfunctions.py): `calcfunction`s that are used in the workchains
    * [`input.py`](src/aiida_aimall/workchains/input.py): `BaseInputWorkChain` that is used in other workchains to validate multiple input options
    * [`param_parts.py`](src/aiida_aimall/workchains/param_parts.py): `SmilesToGaussianWorkChain` and `AIMAllReorWorkChain`: two workchains representing individual steps of the `SubstituentParameterWorkchain`
    * [`qc_programs.py`](src/aiida_aimall/workchains/qc_programs.py): `QMToAIMWorkChain` and `GaussianToAIMWorkChain` linking quantum chemical software output to an AIMQB calculation
    * [`subparam.py`](src/aiida_aimall/workchains/subparam.py): `SubstituentParameterWorkchain` to automate calculation substituent properties in a multistep calculation.
* [`controllers.py`](src/aiida_aimall/controllers.py): Workflow controllers to limit number of running jobs on localhost computers.
  * `AimReorSubmissionController` to control `AimReorWorkChain`s. These use `parent_group_label` for the wavefunction file nodes from `GaussianWFXCalculation`s
  * `AimAllSubmissionController` to control `AimqbCalculations``. These use `parent_group_label` for the wavefunction file nodes from `GaussianWFXCalculation`s
  * `GaussianSubmissionController` to control `GaussianWFXCalculations`. This is mostly intended to have a arbitrarily large number of max concurrents and scan for output structures of `AimReorWorkchain`s to submit to a remote cluster
* [`docs/`](docs/): Source code of documentation for [Read the Docs](http://aiida-diff.readthedocs.io/en/latest/)
* [`tests/`](tests/): Basic regression tests using the [pytest](https://docs.pytest.org/en/latest/) framework (submitting a calculation, ...). Install `pip install -e .[testing]` and run `pytest`.
  * [`conftest.py`](tests/conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)
* [`.gitignore`](.gitignore): Telling git which files to ignore
* [`.pre-commit-config.yaml`](.pre-commit-config.yaml): Configuration of [pre-commit hooks](https://pre-commit.com/) that sanitize coding style and check for syntax errors. Enable via `pip install -e .[pre-commit] && pre-commit install`
* [`.readthedocs.yml`](.readthedocs.yml): Configuration of documentation build for [Read the Docs](https://readthedocs.org/)
* [`.isort.cfg`](.isort.cfg): Configuration to make isort and black precommit actions compatible
* [`LICENSE`](LICENSE): License for your plugin
* [`README.md`](README.md): This file
* [`pyproject.toml`](pyproject.toml): Python package metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)

## Features

### Feature specificity
Many of the workflows provided are specific to my field of study, but the calculations and parsers should be widely useful. Again, as many things designed here were specific to my usage, there are some quirks that must be used at this time, but as I progress with this, I'll endeavour to replace them as optional parts.

  * Many calculations and parsers store results in groups. I have used this, due to my usage of the FromGroupSubmissionController from aiida-submission-controller. I wrote for wfx files to be stored in a group in a Gaussian calculation because then a submission controller looks for wfx files in that group.
    * What this means for the general user is that currently, some nodes are going to be stored in groups, and some group labels are to be provided to certain CalcJobs
  * For similar reasons as above, many Parsers/CalcJobs add extras to the node, typically SMILES in my case
    * Some calculations then, require an extra label (frag_label or fragment_label) to be provided as input to tag the output

### Feature List

 * AimqbParameters Data class to validate command line parameters used to run AIMAll calculations
    ```python
    AimqbParameters = DataFactory('aimall.aimqb')
    aim_params = AimqbParameters(parameter_dict={"naat": 2, "nproc": 2, "atlaprhocps": True})
    ```
    * will check for instance, that the value supplied for naat (number of atoms at a time) is an integer.
    * Most of the options provided at [AIMQB Command Line](https://aim.tkgristmill.com/manual/aimqb/aimqb.html#AIMQBCommandLine) are defined and validated


 * Run an AIMQB calculation using a valid starting file format (WFN/WFX/FCHK as SinglefileData)
   ```python
   AimqbCalculation = CalculationFactory('aimall.aimqb')
   builder = AimqbCalculation.get_builder()
   builder.parameters = aim_params
   builder.file = SinglefileData('/absolute/path/to/file')
   # Alternatively, if you have file stored as a string:
   # builder.file = SinglefileData(io.BytesIO(wfx_file_string.encode()))
   submit(builder)
   ```

## Documentation

Documentation is hosted at [ReadTheDocs](http://aiida-aimall.readthedocs.io/).

## Installation


```shell
(env) pip install aiida-aimall
(env) verdi quicksetup  # better to set up a new profile
(env) verdi plugin list aiida.calculations  # should now show your calclulation plugins
```

If you are using `WorkChain`s that run `GaussianCalculation`s on some computers like Apple M1s, the current release v1.8.1 may result in an error in due to a space in the computer name. The master branch of cclib has been updated to fix this bug. The direct dependency is not allowed on PyPi. If you are in the situation, you can fix it by installing the current version of cclib from the master branch.

```shell
(env) pip install git+https://github.com/cclib/cclib
```

## Development

```shell
git clone https://github.com/kmlefran/aiida-aimall .
cd aiida-aimall
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 [guidelines for contributing](CONTRIBUTING.md) for more information.

## Copyright notice

The testing and documentation framework is heavily influenced by the infrastructure presented in [aiida-quantumespresso](https://github.com/aiidateam/aiida-quantumespresso).  Copyright (c), 2015-2020, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for
Computational Design and Discovery of Novel Materials (NCCR MARVEL))

## License

MIT

## Contact

kgagnon@lakeheadu.ca


[ci-badge]: https://github.com/kmlefran/aiida-aimall/workflows/ci/badge.svg?branch=master
[ci-link]: https://github.com/kmlefran/aiida-aimall/actions
[cov-badge]: https://coveralls.io/repos/github/kmlefran/aiida-aimall/badge.svg?branch=master
[cov-link]: https://coveralls.io/github/kmlefran/aiida-aimall?branch=master
[docs-badge]: https://readthedocs.org/projects/aiida-aimall/badge
[docs-link]: http://aiida-aimall.readthedocs.io/
[pypi-badge]: https://badge.fury.io/py/aiida-aimall.svg
[pypi-link]: https://badge.fury.io/py/aiida-aimall