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Python API for the Surface Reactions database on

Project description

## Introduction

CatHub provides an interface to the Surface Reactions database on [](

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 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>

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