aiida-aimall

A plugin to interface AIMAll with AiiDA

Repository contents

• .github/: Github Actions configuration
  • workflows/
    • ci.yml: runs tests, checks test coverage and continuous integration 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
  • config/ config files for testing/docs environment
    • code-aim.yaml config file for building precommit and test envs
    • code-gwfx.yaml config file for building precommit and test envs
    • profile.yaml config file for aiida profile
    • localhost-config.yaml config file for localhost computer
    • localhost-setup.yaml setup file for localhost computer
• aiida_aimall/: The main source code of the plugin package
  • data.py: A new AimqbParameters data class, used as input to the AimqbCalculation CalcJob class
  • calculations.py: A new AimqbCalculation CalcJob class
  • parsers.py: Two parsers (AimqbBaseParser and AimqbGroupParser) for AimqbCalculation results
  • workchains/: New WorkChains.
    • calcfunctions.py: calcfunctions that are used in the workchains
    • input.py: BaseInputWorkChain that is used in other workchains to validate multiple input options
    • param_parts.py: SmilesToGaussianWorkChain and AIMAllReorWorkChain: two workchains representing individual steps of the SubstituentParameterWorkchain
    • qc_programs.py: QMToAIMWorkChain and GaussianToAIMWorkChain linking quantum chemical software output to an AIMQB calculation
    • subparam.py: SubstituentParameterWorkchain to automate calculation substituent properties in a multistep calculation.
• controllers.py: Workflow controllers to limit number of running jobs on localhost computers.
  • AimReorSubmissionController to control AimReorWorkChains. These use parent_group_label for the wavefunction file nodes from GaussianWFXCalculations
  • AimAllSubmissionController to control AimqbCalculations``. These use parent_group_labelfor the wavefunction file nodes fromGaussianWFXCalculation`s
  • GaussianSubmissionController to control GaussianWFXCalculations. This is mostly intended to have a arbitrarily large number of max concurrents and scan for output structures of AimReorWorkchains to submit to a remote cluster
• docs/: Source code of documentation for Read the Docs
• tests/: Basic regression tests using the pytest framework (submitting a calculation, ...). Install pip install -e .[testing] and run pytest.
  • conftest.py: Configuration of fixtures for 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
• .isort.cfg: Configuration to make isort and black precommit actions compatible
• LICENSE: License for your plugin
• README.md: This file
• pyproject.toml: Python package metadata for registration on PyPI and the AiiDA plugin 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

  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 are defined and validated

• Run an AIMQB calculation using a valid starting file format (WFN/WFX/FCHK as SinglefileData)

  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.

Installation

(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 WorkChains that run GaussianCalculations 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.

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

Development

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 for more information.

Copyright notice

The testing and documentation framework is heavily influenced by the infrastructure presented in 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