aiida-crystal17

aiida-crystal17

AiiDA plugin for running the CRYSTAL17 code. The code is principally tested against CRYSTAL17, but the output parsing has also been tested against CRYSTAL14.

Documentation: https://readthedocs.org/projects/aiida-crystal17

Installation

To install from Conda (recommended)::

>> conda install -c conda-forge aiida-crystal17 aiida-core.services

To install from pypi::

>> pip install aiida-crystal17

To install the development version:

>> git clone https://github.com/aiidaplugins/aiida-crystal17 .
>> cd aiida-crystal17
>> pip install -e .  # also installs aiida, if missing (but not postgres)
>> #pip install -e .[pre-commit,testing] # install extras for more features
>> verdi quicksetup  # set up a new profile
>> verdi calculation plugins  # should now show the calclulation plugins (with prefix crystal17.)

Development

Testing against mock CRYSTAL17 executables

Because CRYSTAL17 is a licensed software, it is not possible to source a copy of the executable on Travis CI. Therefore, a mock executable (mock_runcry17) has been created for testing purposes (which also speeds up test runs).

This executable computes the md5 hash of the supplied input file and tries to match it against a dictionary of precomputed hashes. If found, the executable will write the matching output (from test/output_files) to stdout.

The following will discover and run all unit test:

>> pip install -e .[testing]
>> reentry scan -r aiida
>> pytest -v

To omit tests which call external executables (like crystal17):

>> pytest --cry17-skip-exec

To call the actual executables (e.g. crystal17 instead of mock_crystal17):

>> pytest --cry17-no-mock

To output the results of calcjob executions to a specific directory:

>> pytest --cry17-workdir "test_workdir"

Coding Style Requirements

The code style is tested using flake8, with the configuration set in .flake8, and code should be formatted with yapf (configuration set in .style.yapf).

Installing with aiida-crystal17[code_style] makes the pre-commit package available, which will ensure these tests are passed by reformatting the code and testing for lint errors before submitting a commit. It can be setup by:

>> cd aiida-crystal17
>> pre-commit install

Optionally you can run yapf and flake8 separately:

>> yapf -r -i .  # recrusively find and format files in-place
>> flake8

Editors like VS Code also have automatic code reformat utilities, which can adhere to this standard.

Setting up CRYSTAL17 locally

To set up local version of CRYSTAL17 on a mac (after downloading a copy from the distributor), I had to:

1. Remove the quarantine from the executable permissions:

   xattr -c crystal
   xattr -c properties
   

2. Create versions of the lapack/blas libraries in the expected folders:

   sudo port install lapack
   sudo cp /opt/local/lib/lapack/liblapack.3.dylib /usr/local/opt/lapack/lib/liblapack.3.dylib
   sudo cp /opt/local/lib/lapack/libblas.3.dylib /usr/local/opt/lapack/lib/libblas.3.dylib
   

3. Define environmental variables in ~/.bashrc, as detailed in cry17_scripts/cry17.bashrc

4. Copy or symlink the cry17_scripts/runcry17 script into /usr/local/bin/

License

See LICENSE file

Contact

chrisj_sewell@hotmail.com