Installation¶
To install from pypi:
>> pip install --pre aiida-crystal17
To install from Conda:
>> conda install -c conda-forge aiida-crystal17 aiida-core.services
To install the development version:
>> git clone https://github.com/aiidaplugins/aiida-crystal17 .
>> cd aiida-crystal17
and either use the pre-written Conda development environment:
>> conda env create -n aiida_testenv -f conda_dev_env.yml python=3.6
>> conda activate aiida_testenv
>> pip install --no-deps -e .
or install all via pip:
>> pip install -e .
Note
This will not install Postgres and RabbitMQ
To configure aiida see the AiiDA Documentation: Getting Started.
You should then see the crystal17 plugins in verdi:
>> verdi calculation plugins
Then use verdi code setup with a crystal17. input plugin
to set up an AiiDA code for that plugin.
See also
AiiDA documentation: How to run external codes
CRYSTAL17 Executable¶
aiida-crystal17 is designed to directly call the crystal or properties binary executables (or their parallel variants, e.g. Pcrystal).
This is required to be available on the computer that the calculations are being run on.
If the code is called as a serial run (metadata.options.withmpi=False),
then the input file will be piped to the executable via stdout (as required by crystal):
crystal < INPUT > main.out 2>&1
Whereas, if the code is called as a parallel run
(metadata.options.withmpi=True),
then the INPUT file is placed in the directory,
and the executable will read from it (as required by Pcrystal):
mpiexec Pcrystal > main.out 2>&1
Note that, using the standard AiiDA schedulers,
the calculations will run directly in the working directory,
i.e. the files will not be copied to/from a temporary directory.
If this is required, then the prepend_text and append_text
features of the Code node should be utilised.
See also
AiiDA documentation: How to run external codes
For test purposes, mock_crystal17 and mock_properties17 executables
are installed with aiida-crystal17, that will return pre-computed output files,
if parsed specific test input files (based on the contents hash).
When running the test suite, these executable will be used in place of crystal,
unless pytest --cry17-no-mock is used.
Development¶
Testing¶
Using tox is the best way to run the test-suite:
>> cd aiida-crystal17
>> tox -e py37
To omit tests which call external executables (like crystal17):
>> tox -e py37 -- --cry17-skip-exec
To call the actual executables (e.g. crystal17 instead of mock_crystal17):
>> tox -e py37 -- --cry17-no-mock
To output the results of calcjob executions to a specific directory:
>> tox -e py37 -- --cry17-workdir "test_workdir"
Coding Style Requirements¶
The code style is tested using pre-commit, which will ensure these tests are passed by reformatting the code and testing for lint errors before submitting a commit:
>> pip install pre-commit
>> pre-commit run --all
Optionally you can install this to run before all commits:
>> pre-commit install
Documentation¶
The documentation can be created locally by running tox:
>> tox -e py37-docs-clean
>> tox -e py37-docs-update
Or directly:
>> cd aiida-crystal17/docs
>> make clean
>> make # or make debug
Tip
You can sync the notebooks in the docs/source/notebooks/ folder, with Markdown representations (for easier editing), by running:
>> tox -e py37-sync
This will first generate the Markdown files, edit them, then on re-running the sync, the notebooks will be updated.
Run rm docs/source/notebooks/*.md before docs builds.