pymatgen.ext.cod module

This module provides classes to interface with the Crystallography Open Database. If you use data from the COD, please cite the following works (as stipulated by the COD developers):

Merkys, A., Vaitkus, A., Butkus, J., Okulič-Kazarinas, M., Kairys, V. &
Gražulis, S. (2016) "COD::CIF::Parser: an error-correcting CIF parser for
the Perl language". Journal of Applied Crystallography 49.

Gražulis, S., Merkys, A., Vaitkus, A. & Okulič-Kazarinas, M. (2015)
"Computing stoichiometric molecular composition from crystal structures".
Journal of Applied Crystallography 48, 85-91.

Gražulis, S., Daškevič, A., Merkys, A., Chateigner, D., Lutterotti, L.,
Quirós, M., Serebryanaya, N. R., Moeck, P., Downs, R. T. & LeBail, A.
(2012) "Crystallography Open Database (COD): an open-access collection of
crystal structures and platform for world-wide collaboration". Nucleic
Acids Research 40, D420-D427.

Grazulis, S., Chateigner, D., Downs, R. T., Yokochi, A. T., Quiros, M.,
Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. & Le Bail, A. (2009)
"Crystallography Open Database – an open-access collection of crystal
structures". J. Appl. Cryst. 42, 726-729.

Downs, R. T. & Hall-Wallace, M. (2003) "The American Mineralogist Crystal
Structure Database". American Mineralogist 88, 247-250.
class COD[source]

Bases: object

An interface to the Crystallography Open Database.

get_cod_ids(formula)[source]

Queries the COD for all cod ids associated with a formula. Requires mysql executable to be in the path.

Parameters:formula (str) – Formula.
Returns:List of cod ids.
get_structure_by_formula(formula, **kwargs)[source]

Queries the COD for structures by formula. Requires mysql executable to be in the path.

Parameters:
  • cod_id (int) – COD id.
  • kwargs – All kwargs supported by pymatgen.core.structure.Structure.from_str().
Returns:

A list of dict of the format [{“structure”: Structure, “cod_id”: cod_id, “sg”: “P n m a”}]

get_structure_by_id(cod_id, **kwargs)[source]

Queries the COD for a structure by id.

Parameters:
  • cod_id (int) – COD id.
  • kwargs – All kwargs supported by pymatgen.core.structure.Structure.from_str().
Returns:

A Structure.

query(sql)[source]