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.
Run cathub from the command line:
cathub --help
or with any of its sub-commands:
cathub reactions --help
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='filename.db')
Get reactions in pandas dataframe:
dataframe = db.get_dataframe(pub_id='PengRole2020',
include_atoms=False,
reactants={'COgas': 1},
products={'COstar': 1},
elements=['Cu', 'Al'],
#surface_composition='Cu', # match specific composition
facet = '100'
)
Get atomic structure separately:
# 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'
Organizing a general folder into a structured folder:
cathub organize <foldername> -a <ads1,ads2> -c <dft-code> -x <xc-functional> -f <facet> -S <crystal structure>
New: organize in interactive manner to update adsorbate name, site and facet on the run:
cathub organize <foldername> -I ...
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>
Inspecting local local .db file:
cathub show-reactions <dbfile>
Sending the data to the Catalysis Hub server:
cathub db2server <dbfile>