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


License
GPL-3.0
Install
pip install Cathub==0.1.7

Documentation

Introduction

CatHub provides an interface to the Surface Reactions database on 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 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>