Skip to main content

Python API for the Surface Reactions database on Catalysis-Hub.org

Project description

## Introduction

CatHub provides an interface to the Surface Reactions database on [Catalysis-Hub.org](http://www.catalysis-hub.org).

The module includes a command line interface that can be used to access and upload data. A short guide is given below. We refer to the [catalysis-hub documentation](http://docs.catalysis-hub.org/en/latest/tutorials/upload.html) for details on how to submit data.

## Using the cathub cli

Run cathub from the command line:

cathub –help

or with any of its sub-commands:

cathub reactions –help

## Examples

Querying the Surface Reactions database in Python:

from cathub.cathubsql import CathubSQL

# To get data on catalysis-hub.org db = CathubSQL()

# Data from local cathub .db file db = CathubSQL(‘filename.db’)

Get reactions in pandas dataframe:

dataframe = db.get_dataframe(pub_id=’PengRole2020’,
include_atoms=False, include_atoms=True, # include atoms in dataframe #include_atoms=’PengRole2020.db’, # save atoms to local db reactants=[‘COgas’], products=[‘COstar’], elements=[‘Cu’, ‘Al’], #surface_composition=’Cu’, # match specific composition facet = ‘100’ )

Get atomic structure seperately:

# Get atoms for one reaction_id taken from dataframe atoms_list = db.get_atoms_for_reaction(reaction_id)

# Get atoms for entire dataset atoms_list = db.get_atoms_for_publication(pub_id=’PengRole2020’)

Quick view of atomic structures on Catalysis Hub with ase db CLI:

cathub ase ‘CuAg pub_id=PengRole2020’

## Uploading data

Organizing a general folder into a structured folder:

cathub organize <folderame> -a <ads1,ads2> -c <dft-code> -x <xc-functional> -f <facet> -S <crystal structure>

As an alternative to cathub organize, create an empty organized folderstructure for dropping files yourself. First create a template and edit it, then create the folders.

cathub make_folders –create-template <template> cathub make_folders <template>

Reading folders into a local .db file:

cathub folder2db <foldername>

Sending the data to the Catalysis Hub server:

cathub db2server <dbfile>

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Files for Cathub, version 0.1.7
Filename, size File type Python version Upload date Hashes
Filename, size Cathub-0.1.7-py3-none-any.whl (82.5 kB) File type Wheel Python version py3 Upload date Hashes View
Filename, size Cathub-0.1.7.tar.gz (63.6 kB) File type Source Python version None Upload date Hashes View

Supported by

AWS AWS Cloud computing Datadog Datadog Monitoring DigiCert DigiCert EV certificate Facebook / Instagram Facebook / Instagram PSF Sponsor Fastly Fastly CDN Google Google Object Storage and Download Analytics Pingdom Pingdom Monitoring Salesforce Salesforce PSF Sponsor Sentry Sentry Error logging StatusPage StatusPage Status page