Query for and import structures from OPTIMADE providers (COD, MaterialsCloud, 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
This Jupyter-based app is intended to run either:
For AiiDAlab, use the App Store in the Home App to install it.
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.
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.
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.
First, you will need to install the package either from PyPI or by retrieving the git repository hosted on GitHub.
pip install optimade-client[server]
git clone https://github.com/CasperWA/voila-optimade-client.git
cd 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
For a list of all options that can be passed to optimade-client
use the -h/--help
option.
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:
pre-commit install
To start making contributions, fork the repository and create PRs.
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 asvoila.json
when running the application using theoptimade-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"
To see the full list of configurations you can call voila
and pass --help-all
.
Set the environment variable OPTIMADE_CLIENT_DEVELOPMENT_MODE
to 1
(the integer version for True
(1
) or False
(0
)) in order to force the use of development servers for providers (currently only relevant for Materials Cloud).
MIT. The terms of the license can be found in the LICENSE file.
BIG-MAP; This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 957189. The project is part of BATTERY 2030+, the large-scale European research initiative for inventing the sustainable batteries of the future. |
casper+github@welzel.nu
aiidalab@materialscloud.org