matador-db 0.9.1

MATerial and Atomic Databases Of Refined structures.

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 GitHub and online documentation is hosted on ReadTheDocs.

Example Jupyter notebooks and tutorials can be found online or in the examples/ folder of the matador source code.

Written & maintained by Matthew Evans (2016-).

Installation

In the simplest case, pip install matador-db is sufficient to get up and running, preferably in a fresh virtual environment. More detailed instructions can be found in the Installation instructions.

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.

Please consult the full Python API documentation 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

Core functionality

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

• Scraping of CASTEP (and Quantum Espresso) input/output files into flexible Python dictionaries/models.

• The creation and curation of MongoDB collections of geometry optimisation, calculations, with a powerful querying CLI/API.

• Customisable, publication-ready plots for all models, e.g. phase diagrams, PDF, PXRD, voltage profiles, electronic/vibrational bandstructures etc.

• Automated high-throughput geometry optimisations, electronic and vibrational properties using CASTEP (and Quantum Espresso) with run3. Tested on several supercomputers.

• Creation of phase diagrams and electrochemical voltage profiles from the results of DFT calculations.