optimade-client 2020.10.29

Voilà/Jupyter client for searching through OPTIMADE databases.

OPTIMADE client (in Voilà)

Query for and import structures from OPTIMADE providers (COD, Materials Cloud, NoMaD, Materials Project, ODBX, OQMD, and more ...).

Current supported OPTIMADE API versions: 1.0.0, 1.0.0-rc.2, 1.0.0-rc.1, 0.10.1

Run the client

This Jupyter-based app is intended to run either:

• In AiiDAlab as well as inside a Quantum Mobile Virtual Machine;
• As a Materials Cloud tool;
• As a standalone MyBinder application; or
• As a standalone local application (see more information about this below).

For AiiDAlab, use the App Store in the Home App to install it.

Usage

AiiDAlab

To use the OPTIMADE structure importer in your own AiiDAlab application write the following:

from aiidalab_widget_base import OptimadeQueryWidget
from aiidalab_widgets_base.viewers import StructureDataViewer
from ipywidgets import dlink

structure_query = OptimadeQueryWidget()
structure_viewer = StructureDataViewer()

# Save to `_` in order to suppress output
_ = dlink((structure_query, 'structure'), (structure_viewer, 'structure'))

display(structure_query)
display(structure_viewer)

This will immediately display a query widget with a dropdown of current structure databases that implements the OPTIMADE API.

Then you can filter to find a family of structures according to elements, number of elements, chemical formula, and more. See the OPTIMADE API specification for the full list of filter options and their description.

In order to delve deeper into the details of a particular structure, you can also import and display OptimadeResultsWidget.
See the notebook OPTIMADE-Client.ipynb for an example of how to set up a general purpose OPTIMADE importer.

Embedded

The query widget may also be embedded into another app.
For this a more "minimalistic" version of the widget can be used by passing embedded=True upon initiating the widget, i.e., structure_query = OptimadeQueryWidget(embedded=True).

Everything else works the same - so you would still have to link up the query widget to the rest of your app.

General Jupyter notebook

The package's widgets can be used in any general Jupyter notebook as well as AiiDAlab. Example:

from optimade_client import
    OptimadeQueryProviderWidget,
    OptimadeQueryFilterWidget,
    OptimadeSummaryWidget
from ipywidgets import dlink

database_selector = OptimadeQueryProviderWidget()
structure_query = OptimadeQueryFilterWidget()
structure_viewer = OptimadeSummaryWidget()

# Save to `_` in order to suppress output
_ = dlink((database_selector, 'database'), (structure_query, 'database'))
_ = dlink((structure_query, 'structure'), (structure_viewer, 'entity'))

display(database_selector, structure_query, structure_viewer)

This will use the package's own structure viewer and summary widget.

Note, the OptimadeQueryWidget mentioned above is a special wrapper widget in AiiDAlab for the OptimadeQueryProviderWidget and OptimadeQueryFilterWidget widgets.

Running application locally

First, you will need to install the package either from PyPI or by retrieving the git repository hosted on GitHub.

PyPI

$ pip install optimade-client[server]

GitHub

$ git clone https://github.com/CasperWA/voila-optimade-client.git
$ cd voila-optimade-client
voila-optimade-client$ pip install .[server]

Note, it is important to install the server extra in order to also install the voila package (and the ase package for a wider variety of download formats).

To now run the application (notebook) OPTIMADE-Client.ipynb you can simply run the command optimade-client in a terminal and go to the printed URL (usually http://localhost:8866) or pass the --open-browser option to let the program try to automatically open your default browser.

The application will be run in Voilà using Voilà's own tornado-based server. The configuration will automatically be copied to Jupyter's configuration directory before starting the server.

$ optimade-client
...
[Voila] Voilà is running at:
http://localhost:8866/
...

For a list of all options that can be passed to optimade-client use the -h/--help option.

Contribute

If you wish to contribute to the application, you can install it in "editable" mode by using the -e flag: pip install -e .[dev]. It is recommended that you use the GitHub-route mentioned above.

You should also install pre-commit in the cloned git repository by running:

voila-optimade-client$ pre-commit install

To start making contributions, fork the repository and create PRs.

Configuration (Voilà)

For running the application (in Voilà) on Binder, the configuration file jupyter_config.json can be used.
If you wish to start the Voilà server locally with the same configuration, either copy the jupyter_config.json file to your Jupyter config directory, renaming it to voila.json or pass the configurations when you start the server using the CLI.

Note: jupyter_config.json is automatically copied over as voila.json when running the application using the optimade-client command.

Locate your Jupyter config directory:

$ jupyter --config-dir
/path/to/jupyter/config/dir

Example of passing configurations when you start the Voilà server using the CLI:

$ voila --enable_nbextensions=True --VoilaExecutePreprocessor.timeout=180 "OPTIMADE-Client.ipynb"
...
[Voila] Voilà is running at:
http://localhost:8866/
...

To see the full list of configurations you can call voila and pass --help-all.

License

MIT. The terms of the license can be found in the LICENSE file.

Contact

[e-mail]
[e-mail]