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/chrisjsewell/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

The following will discover and run all unit test:

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

To omit tests which call crystal executable:

>> pytest -v -m "not process_execution"

or alternatively to call the mock_crystal17 executable, first set the global environmental variable:

>> export MOCK_CRY17_EXECUTABLES=true

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.

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.

To use this mock executable when running tests, set the global variable MOCK_CRY17_EXECUTABLES=true.

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

MIT

Contact

chrisj_sewell@hotmail.com