A plugin to interface AIMAll with AiiDA
Project description
!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 configurationworkflows/
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 thepypi_token
secret of your github repository
config/
config files for testing/docs environmentcode-aim.yaml
config file for building precommit and test envscode-gwfx.yaml
config file for building precommit and test envsprofile.yaml
config file for aiida profileprofile.yaml
config file for localhost computerprofile.yaml
setup file for localhost computer
aiida_aimall/
: The main source code of the plugin packagedata/
: A newAimqbParameters
data class, used as input to theAimqbCalculation
CalcJob
classcalculations.py
: A newAimqbCalculation
CalcJob
class, andGaussianWFXCalculation
, a modified version ofGaussianCalculation
from AiiDA Gaussianparsers.py
: A newParser
for theAimqbCalculation
, andGaussianWFXParser
, a modified version ofGaussianBaseParser
from AiiDA Gaussianworkchains.py
: NewWorkChains
.MultiFragmentWorkChain
to fragment molecules using cml files from the Retrievium database and submit Gaussian calculations for the fragments using functions infrag_functions
from subproptools GithubG16OptWorkchain
to take output fromMultiFragmentWorkChain
and submit Gaussian optimization calculationsAimAllReorWorkChain
to runAimqbCalculation
on output fromGaussianWFXCalculations
, then reorient to coordinate systems defined insubreor
from subproptools Github
controllers.py
: Workflow controllers to limit number of running jobs on localhost computers.AimReorSubmissionController
to controlAimReorWorkChain
s. These useparent_group_label
for the wavefunction file nodes fromGaussianWFXCalculation
sAimAllSubmissionController
to controlAimqbCalculations``. These use
parent_group_labelfor the wavefunction file nodes from
GaussianWFXCalculation`sGaussianSubmissionController
to controlGaussianWFXCalculations
. This is mostly intended to have a arbitrarily large number of max concurrents and scan for output structures ofAimReorWorkchain
s to submit to a remote cluster
docs/
: Source code of documentation for Read the Docsexamples/
: An example of how to link the four controllers in an overall workflowtests/
: Basic regression tests using the pytest framework (submitting a calculation, ...). Installpip install -e .[testing]
and runpytest
.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 viapip 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 compatibleLICENSE
: License for your pluginREADME.md
: This filepyproject.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
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