Voilà/Jupyter client for searching through OPTIMADE databases.
Project description
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
Default
To use the OPTIMADE structure importer in your own AiiDAlab application write the following:
from optimade_client 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 in App Mode
_ = 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.
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 -U numpy
$ pip install --no-binary :all: scipy
$ pip install optimade-client
or
$ pip install optimade-client
$ pip uninstall -y scipy
$ pip install --no-binary :all: scipy
GitHub
$ git clone https://github.com/CasperWA/voila-optimade-client.git
$ cd voila-optimade-client
voila-optimade-client$ pip install -r requirements.txt
voila-optimade-client$ pip install .
Note, both of these methods install scipy by rebuilding the binaries based on the local numpy installation. This can take a considerable time, but will result in a more stable application, especially concerning converting structures to other data formats for download.
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 at the URL.
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] Voila is running at:
http://localhost:8866/
...
For a list of all options that can be passed to optimade-client use the -h/--help option.
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.jsonis automatically copied over asvoila.jsonwhen running the application using theoptimade-clientcommand.
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] Voila 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.
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