matador

matador is an aggregator, manipulator and runner of first-principles calculations, written with a bent towards battery electrode materials. The source can be found on Bitbucket and online documentation is hosted on ReadTheDocs.

Written by Matthew Evans (2016-).

Core functionality

The core functionality can be summarised by the various sub-commands of the command-line interface. The API has many more features that can be explored in the examples and API documentation.

1. The scraping of CASTEP/Quantum Espresso output files into flexible Python dictionaries with a sensible schema via matador import.
2. The transferal of the scraped dictionaries into a MongoDB database.
3. Powerful CLI querying of the database, with a focus on energy storage applications using matador query.
4. Calculation and presentation of binary and ternary phase diagrams with matador hull.
5. 0K voltage curves for binary and ternary systems, as well as arbitrary intercalation electrodes, using matador voltage.
6. Atomic species swapping and polishing from previous calculations using matador swaps.
7. Automated high-throughput geometry optimisations, electronic and vibrational properties, plus convergence tests, using CASTEP or Quantum Espresso, with the run3 entrypoint. Tested on several supercomputers.
8. Refinement of structural and chemical data, and symmetries powered by spglib, via matador refine.

Usage

For basic command-line usage, please explore the help system for each sub-command. Common workflows can be found inside examples/ and in the `online docs <http://matador-db.readthedocs.io/en/develop/examples_index.html`_.

Please consult the full `Python API documentation <http://matador-db.readthedocs.io/en/develop/modules.html`_ for programmatic usage.

usage: matador [-h] [--version]
               {stats,query,import,hull,voltage,changes,hulldiff,swaps,refine}
               ...

MATerial and Atomic Database Of Refined structures.

optional arguments:
  -h, --help            show this help message and exit
  --version             show program's version number and exit

subcommands:
  valid sub-commands

  {stats,query,import,hull,voltage,changes,hulldiff,swaps,refine}
    stats               print some stats about the database.
    query               query and extract structures from the database
    import              import new structures in folder into database
    hull                create a convex hull from query results (currently
                        limited to binaries and ternaries)
    voltage             plot a voltage curve from query results (currently
                        limited to binaries and ternaries)
    changes             view database changelog or undo additions to database
                        (NB: not deletions!)
    hulldiff            diff two convex hulls with the --compare flag.
    swaps               perform atomic swaps on query results
    refine              update structures in the database according to
                        specified --task

License

matador is available under the MIT License.