| Name | aiida-aimall JSON |
| Version |
0.6.12
JSON |
| download |
| home_page | None |
| Summary | A plugin to interface AIMAll with AiiDA |
| upload_time | 2024-04-23 17:39:54 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | None |
| keywords |
aiida
plugin
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
[](https://github.com/kmlefran/aiida-aimall/actions/workflows/ci.yml)
[](https://coveralls.io/github/kmlefran/aiida-aimall?branch=main)
[](https://aiida-aimall.readthedocs.io/en/latest/?badge=latest)
[](https://badge.fury.io/py/aiida-aimall)
!This README and all documentation is a work in progress!
# Copyright notice
This repository contains modified versions of the calculations and parsers presented in [Aiida-Gaussian](https://github.com/nanotech-empa/aiida-gaussian). Copyright (c) 2020 Kristjan Eimre. The modifications basically amount to adding the wfx file to the retrieved nodes and adding some groups/extras to calculation output.
Also, the (incomplete) testing 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))
# 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 builds documentation 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/workflows/config/code-aim.yaml) config file for building precommit and test envs
* [`code-gwfx.yaml`](.github/workflows/config/code-gwfx.yaml) config file for building precommit and test envs
* [`profile.yaml`](.github/workflows/config/profile.yaml) config file for aiida profile
* [`profile.yaml`](.github/workflows/config/localhost-config.yaml) config file for localhost computer
* [`profile.yaml`](.github/workflows/config/localhost-setup.yaml) setup file for localhost computer
* [`aiida_aimall/`](aiida_aimall/): The main source code of the plugin package
* [`data/`](aiida_aimall/data/): A new `AimqbParameters` data class, used as input to the `AimqbCalculation` `CalcJob` class
* [`calculations.py`](aiida_aimall/calculations.py): A new `AimqbCalculation` `CalcJob` class, and `GaussianWFXCalculation`, a modified version of `GaussianCalculation` from [AiiDA Gaussian](https://github.com/nanotech-empa/aiida-gaussian)
* [`parsers.py`](aiida_aimall/parsers.py): A new `Parser` for the `AimqbCalculation`, and `GaussianWFXParser`, a modified version of `GaussianBaseParser` from [AiiDA Gaussian](https://github.com/nanotech-empa/aiida-gaussian)
* [`workchains.py`](aiida_aimall/workchains.py): New `WorkChains`.
* `MultiFragmentWorkChain` to fragment molecules using cml files from the Retrievium database and submit Gaussian calculations for the fragments using functions in `frag_functions` from [subproptools Github](https:github.com/kmlefran/group_decomposition)
* `G16OptWorkchain` to take output from `MultiFragmentWorkChain` and submit Gaussian optimization calculations
* `AimAllReorWorkChain` to run `AimqbCalculation` on output from `GaussianWFXCalculations`, then reorient to coordinate systems defined in `subreor` from [subproptools Github](https:github.com/kmlefran/subproptools)
* [`controllers.py`](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/)
* [`examples/`](examples/): An example of how to link the four controllers in an overall workflow
* [`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`](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`](setup.json): 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)
```
*
## Installation
The aiida-dataframe dependency tables requires h5 headers on your system. You may already have this, or not. One easy way that allows installation of the headers using the h5py package
```shell
(conda-env) conda install h5py
(conda-env) pip install aiida-aimall
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:
```shell
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
```
## 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 [developer guide](http://aiida-aimall.readthedocs.io/en/latest/developer_guide/index.html) for more information.
## 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
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"description": "[](https://github.com/kmlefran/aiida-aimall/actions/workflows/ci.yml)\n[](https://coveralls.io/github/kmlefran/aiida-aimall?branch=main)\n[](https://aiida-aimall.readthedocs.io/en/latest/?badge=latest)\n[](https://badge.fury.io/py/aiida-aimall)\n\n!This README and all documentation is a work in progress!\n\n# Copyright notice\n\nThis repository contains modified versions of the calculations and parsers presented in [Aiida-Gaussian](https://github.com/nanotech-empa/aiida-gaussian). Copyright (c) 2020 Kristjan Eimre. The modifications basically amount to adding the wfx file to the retrieved nodes and adding some groups/extras to calculation output.\n\nAlso, the (incomplete) testing 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\n(Theory and Simulation of Materials (THEOS) and National Centre for\nComputational Design and Discovery of Novel Materials (NCCR MARVEL))\n\n# aiida-aimall\n\nA plugin to interface AIMAll with AiiDA\n\n## Repository contents\n\n* [`.github/`](.github/): [Github Actions](https://github.com/features/actions) configuration\n * [`workflows/`](.github/workflows/)\n * [`ci.yml`](.github/workflows/ci.yml): runs tests, checks test coverage and builds documentation at every new commit\n * [`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\n * [`config/`](.github/config) config files for testing/docs environment\n * [`code-aim.yaml`](.github/workflows/config/code-aim.yaml) config file for building precommit and test envs\n * [`code-gwfx.yaml`](.github/workflows/config/code-gwfx.yaml) config file for building precommit and test envs\n * [`profile.yaml`](.github/workflows/config/profile.yaml) config file for aiida profile\n * [`profile.yaml`](.github/workflows/config/localhost-config.yaml) config file for localhost computer\n * [`profile.yaml`](.github/workflows/config/localhost-setup.yaml) setup file for localhost computer\n* [`aiida_aimall/`](aiida_aimall/): The main source code of the plugin package\n * [`data/`](aiida_aimall/data/): A new `AimqbParameters` data class, used as input to the `AimqbCalculation` `CalcJob` class\n * [`calculations.py`](aiida_aimall/calculations.py): A new `AimqbCalculation` `CalcJob` class, and `GaussianWFXCalculation`, a modified version of `GaussianCalculation` from [AiiDA Gaussian](https://github.com/nanotech-empa/aiida-gaussian)\n * [`parsers.py`](aiida_aimall/parsers.py): A new `Parser` for the `AimqbCalculation`, and `GaussianWFXParser`, a modified version of `GaussianBaseParser` from [AiiDA Gaussian](https://github.com/nanotech-empa/aiida-gaussian)\n * [`workchains.py`](aiida_aimall/workchains.py): New `WorkChains`.\n * `MultiFragmentWorkChain` to fragment molecules using cml files from the Retrievium database and submit Gaussian calculations for the fragments using functions in `frag_functions` from [subproptools Github](https:github.com/kmlefran/group_decomposition)\n * `G16OptWorkchain` to take output from `MultiFragmentWorkChain` and submit Gaussian optimization calculations\n * `AimAllReorWorkChain` to run `AimqbCalculation` on output from `GaussianWFXCalculations`, then reorient to coordinate systems defined in `subreor` from [subproptools Github](https:github.com/kmlefran/subproptools)\n* [`controllers.py`](aiida_aimall/controllers.py): Workflow controllers to limit number of running jobs on localhost computers.\n * `AimReorSubmissionController` to control `AimReorWorkChain`s. These use `parent_group_label` for the wavefunction file nodes from `GaussianWFXCalculation`s\n * `AimAllSubmissionController` to control `AimqbCalculations``. These use `parent_group_label` for the wavefunction file nodes from `GaussianWFXCalculation`s\n * `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\n* [`docs/`](docs/): Source code of documentation for [Read the Docs](http://aiida-diff.readthedocs.io/en/latest/)\n* [`examples/`](examples/): An example of how to link the four controllers in an overall workflow\n* [`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`.\n * [`conftest.py`](conftest.py): Configuration of fixtures for [pytest](https://docs.pytest.org/en/latest/)\n* [`.gitignore`](.gitignore): Telling git which files to ignore\n* [`.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`\n* [`.readthedocs.yml`](.readthedocs.yml): Configuration of documentation build for [Read the Docs](https://readthedocs.org/)\n* [`.isort.cfg`](.isort.cfg): Configuration to make isort and black precommit actions compatible\n* [`LICENSE`](LICENSE): License for your plugin\n* [`README.md`](README.md): This file\n* [`pyproject.toml`](setup.json): Python package metadata for registration on [PyPI](https://pypi.org/) and the [AiiDA plugin registry](https://aiidateam.github.io/aiida-registry/) (including entry points)\n\n\n\n## Features\n\n### Feature specificity\nMany 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.\n\n * 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.\n * 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\n * For similar reasons as above, many Parsers/CalcJobs add extras to the node, typically SMILES in my case\n * Some calculations then, require an extra label (frag_label or fragment_label) to be provided as input to tag the output\n\n### Feature List\n\n * AimqbParameters Data class to validate command line parameters used to run AIMAll calculations\n ```python\n AimqbParameters = DataFactory('aimall.aimqb')\n aim_params = AimqbParameters(parameter_dict={\"naat\": 2, \"nproc\": 2, \"atlaprhocps\": True})\n ```\n * will check for instance, that the value supplied for naat (number of atoms at a time) is an integer.\n * Most of the options provided at [AIMQB Command Line](https://aim.tkgristmill.com/manual/aimqb/aimqb.html#AIMQBCommandLine) are defined and validated\n\n\n * Run an AIMQB calculation using a valid starting file format (WFN/WFX/FCHK as SinglefileData)\n ```python\n AimqbCalculation = CalculationFactory('aimall.aimqb')\n builder = AimqbCalculation.get_builder()\n builder.parameters = aim_params\n builder.file = SinglefileData('/absolute/path/to/file')\n # Alternatively, if you have file stored as a string:\n # builder.file = SinglefileData(io.BytesIO(wfx_file_string.encode()))\n submit(builder)\n ```\n\n *\n\n## Installation\n\nThe aiida-dataframe dependency tables requires h5 headers on your system. 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