References

Some of pymatgen’s functionality is based on scientific advances / principles developed by various scientists. If you use some of these functionality in your research, you may wish to consider citing the following works:

pymatgen.analysis.path_finder

The path finder code, which finds diffusion paths through a structure based on a given potential field, is written by the Ceder group at UC Berkeley.

Rong, Z., Kitchaev, D., Canepa, P., Huang, W., & Ceder, G. (2016).
An efficient algorithm for finding the minimum energy path for cation
migration in ionic materials. The Journal of Chemical Physics, 145(7),
74112. doi:10.1063/1.4960790

pymatgen.core.surface and pymatgen.analysis.wulff

The surface generation code, which can automatically generate surfaces based on any crystal, and the Wulff code, which plots the Wulff shape given a crystal and surface energies, are written by the Materials Virtual Lab.

Tran, R.; Xu, Z.; Radhakrishnan, B.; Winston, D.; Sun, W.; Persson, K. A.;
Ong, S. P. Surface energies of elemental crystals, Sci. Data, 2016, 3,
160080, doi:10.1038/sdata.2016.80.

and contains elements from the following publication.

Sun, W.; Ceder, G. Efficient creation and convergence of surface slabs,
Surface Science, 2013, 617, 53–59, doi:10.1016/j.susc.2013.05.016.

pymatgen.io.vasp.sets

The MIT parameter sets, which are optimized for high-throughput computing, are outlined the following work.

Jain, A.; Hautier, G.; Moore, C. J.; Ong, S. P.; Fischer, C. C.;
Mueller, T.; Persson, K. A.; Ceder, G. A high-throughput infrastructure for
density functional theory calculations, Comput. Mater. Sci., 2011, 50,
2295–2310, doi:10.1016/j.commatsci.2011.02.023.

pymatgen.analysis.phase_diagram

The phase diagram code, in particular the grand canonical phase diagram analysis, is based on the work of Ong et al. and are used in following works.

Ong, S. P.; Wang, L.; Kang, B.; Ceder, G. Li−Fe−P−O2 Phase Diagram from
First Principles Calculations, Chem. Mater., 2008, 20, 1798–1807,
doi:10.1021/cm702327g.

Ong, S. P.; Jain, A.; Hautier, G.; Kang, B.; Ceder, G. Thermal stabilities
of delithiated olivine MPO4 (M=Fe, Mn) cathodes investigated using first
principles calculations, Electrochem. commun., 2010, 12, 427–430,
doi:10.1016/j.elecom.2010.01.010.

pymatgen.entries.compatibility

The compatibility processing, which allows mixing of GGA and GGA+U runs that have been calculated using the MaterialsProjectVaspInputSet or MITVaspInputSet, is based on the following work.

Jain, A.; Hautier, G.; Ong, S. P.; Moore, C. J.; Fischer, C. C.;
Persson, K. A.; Ceder, G. Formation enthalpies by mixing GGA and GGA+U
calculations, Phys. Rev. B, 2011, 84, 45115, doi:10.1103/PhysRevB.84.045115.

pymatgen.ext.matproj

The matproj package contains an interface to the Materials Project REST API (Materials API). If you use data from the Materials Project, please cite the following works.

Jain, A.; Ong, S. P.; Hautier, G.; Chen, W.; Richards, W. D.; Dacek,
S.; Cholia, S.; Gunter, D.; Skinner, D.; Ceder, G.; Persson, K. A.
Commentary: The Materials Project: A materials genome approach to
accelerating materials innovation, APL Mater., 2013, 1, 11002,
doi:10.1063/1.4812323.

Ong, S. P.; Cholia, S.; Jain, A.; Brafman, M.; Gunter, D.; Ceder, G.;
Persson, K. a. The Materials Application Programming Interface (API): A
simple, flexible and efficient API for materials data based on
REpresentational State Transfer (REST) principles, Comput. Mater. Sci.,
2015, 97, 209–215, doi:10.1016/j.commatsci.2014.10.037.

pymatgen.symmetry

The symmetry package is based on the excellent spglib developed by Atz Togo. For more information, please refer to Atz Togo’s site.

pymatgen.command_line.bader_caller

This module implements an interface to the Henkelmann et al.’s excellent Fortran code for calculating a Bader charge analysis. Please cite the following.

Henkelman, G., Arnaldsson, A., & Jónsson, H. (2006). A fast and robust
algorithm for Bader decomposition of charge density. Computational
Materials Science, 36(3), 354–360. doi:10.1016/j.commatsci.2005.04.010

pymatgen.io.feff

This module implements an io interface for FEFF calculations. Please acknowledge the contribution of Alan Dozier, UKY.

pymatgen.io.zeo

This implements an interface to the excellent Zeo++ code base. Please consider citing the following publications.

T.F. Willems, C.H. Rycroft, M. Kazi, J.C. Meza, and M. Haranczyk,
Algorithms and tools for high-throughput geometry- based analysis of
crystalline porous materials, Microporous and Mesoporous Materials,
149 (2012) 134-141, doi:10.1016/j.micromeso.2011.08.020.

R.L. Martin, B. Smit, and M. Haranczyk, Addressing challenges of
identifying geometrically diverse sets of crystalline porous materials,
J. Chem. Information and Modelling, doi:10.1021/ci200386x.