aiida-aimall 0.6.12

A plugin to interface AIMAll with AiiDA

!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. 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. 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 Actions configuration
  • workflows/
    • 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
  • 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
    • profile.yaml config file for localhost computer
    • profile.yaml setup file for localhost computer
• aiida_aimall/: The main source code of the plugin package
  • data/: A new AimqbParameters data class, used as input to the AimqbCalculation CalcJob class
  • calculations.py: A new AimqbCalculation CalcJob class, and GaussianWFXCalculation, a modified version of GaussianCalculation from AiiDA Gaussian
  • parsers.py: A new Parser for the AimqbCalculation, and GaussianWFXParser, a modified version of GaussianBaseParser from AiiDA Gaussian
  • 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
    • 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
• 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
• examples/: An example of how to link the four controllers in an overall workflow
• 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)
  

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

(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:

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

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 for more information.

License

MIT

Contact

[e-mail]