skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis

Abstract

We present the Python Materials Genomics (pymatgen) library, a robust, open-source Python library for materials analysis. A key enabler in high-throughput computational materials science efforts is a robust set of software tools to perform initial setup for the calculations (e.g., generation of structures and necessary input files) and post-calculation analysis to derive useful material properties from raw calculated data. The pymatgen library aims to meet these needs by (1) defining core Python objects for materials data representation, (2) providing a well-tested set of structure and thermodynamic analyses relevant to many applications, and (3) establishing an open platform for researchers to collaboratively develop sophisticated analyses of materials data obtained both from first principles calculations and experiments. The pymatgen library also provides convenient tools to obtain useful materials data via the Materials Project's REpresentational State Transfer (REST) Application Programming Interface (API). As an example, using pymatgen's interface to the Materials Project's RESTful API and phasediagram package, we demonstrate how the phase and electrochemical stability of a recently synthesized material, Li 4SnS 4, can be analyzed using a minimum of computing resources. Here, we find that Li 4SnS 4 is a stable phase in the Li-Sn-S phase diagram (consistent with the fact thatmore » it can be synthesized), but the narrow range of lithium chemical potentials for which it is predicted to be stable would suggest that it is not intrinsically stable against typical electrodes used in lithium-ion batteries.« less

Authors:
 [1];  [1];  [2];  [3];  [2];  [2];  [2];  [4];  [2];  [1]
  1. Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)
  2. Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
  3. Univ. catholique de Louvain, Louvain-La-Neuve (Belgium)
  4. 3M, St. Paul, MN (United States)
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES)
OSTI Identifier:
1511345
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Computational Materials Science
Additional Journal Information:
Journal Volume: 68; Journal Issue: C; Journal ID: ISSN 0927-0256
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
36 MATERIALS SCIENCE; Materials; Project; Design; Thermodynamics; High-throughput

Citation Formats

Ong, Shyue Ping, Richards, William Davidson, Jain, Anubhav, Hautier, Geoffroy, Kocher, Michael, Cholia, Shreyas, Gunter, Dan, Chevrier, Vincent L., Persson, Kristin A., and Ceder, Gerbrand. Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis. United States: N. p., 2012. Web. doi:10.1016/j.commatsci.2012.10.028.
Ong, Shyue Ping, Richards, William Davidson, Jain, Anubhav, Hautier, Geoffroy, Kocher, Michael, Cholia, Shreyas, Gunter, Dan, Chevrier, Vincent L., Persson, Kristin A., & Ceder, Gerbrand. Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis. United States. https://doi.org/10.1016/j.commatsci.2012.10.028
Ong, Shyue Ping, Richards, William Davidson, Jain, Anubhav, Hautier, Geoffroy, Kocher, Michael, Cholia, Shreyas, Gunter, Dan, Chevrier, Vincent L., Persson, Kristin A., and Ceder, Gerbrand. Sat . "Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis". United States. https://doi.org/10.1016/j.commatsci.2012.10.028. https://www.osti.gov/servlets/purl/1511345.
@article{osti_1511345,
title = {Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis},
author = {Ong, Shyue Ping and Richards, William Davidson and Jain, Anubhav and Hautier, Geoffroy and Kocher, Michael and Cholia, Shreyas and Gunter, Dan and Chevrier, Vincent L. and Persson, Kristin A. and Ceder, Gerbrand},
abstractNote = {We present the Python Materials Genomics (pymatgen) library, a robust, open-source Python library for materials analysis. A key enabler in high-throughput computational materials science efforts is a robust set of software tools to perform initial setup for the calculations (e.g., generation of structures and necessary input files) and post-calculation analysis to derive useful material properties from raw calculated data. The pymatgen library aims to meet these needs by (1) defining core Python objects for materials data representation, (2) providing a well-tested set of structure and thermodynamic analyses relevant to many applications, and (3) establishing an open platform for researchers to collaboratively develop sophisticated analyses of materials data obtained both from first principles calculations and experiments. The pymatgen library also provides convenient tools to obtain useful materials data via the Materials Project's REpresentational State Transfer (REST) Application Programming Interface (API). As an example, using pymatgen's interface to the Materials Project's RESTful API and phasediagram package, we demonstrate how the phase and electrochemical stability of a recently synthesized material, Li4SnS4, can be analyzed using a minimum of computing resources. Here, we find that Li4SnS4 is a stable phase in the Li-Sn-S phase diagram (consistent with the fact that it can be synthesized), but the narrow range of lithium chemical potentials for which it is predicted to be stable would suggest that it is not intrinsically stable against typical electrodes used in lithium-ion batteries.},
doi = {10.1016/j.commatsci.2012.10.028},
url = {https://www.osti.gov/biblio/1511345}, journal = {Computational Materials Science},
issn = {0927-0256},
number = C,
volume = 68,
place = {United States},
year = {2012},
month = {12}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 662 works
Citation information provided by
Web of Science

Figures / Tables:

Fig. 1 Fig. 1: Overview of the pymatgen library. Text in italics represent names of Python packages, modules or classes.

Save / Share:

Works referencing / citing this record:

Database-Driven Materials Selection for Semiconductor Heterojunction Design
journal, August 2018


The Ternary Post-transition Metal Carbodiimide SrZn(NCN) 2 : The Ternary Post-transition Metal Carbodiimide SrZn(NCN)
journal, September 2017


First Full Structural Characterization of Chloro Formamidinium Salts: First Full Structural Characterization of Chloro Formamidinium Salts
journal, May 2018


Insightful classification of crystal structures using deep learning
journal, July 2018


Deep neural networks for accurate predictions of crystal stability
journal, September 2018


Towards general network architecture design criteria for negative gas adsorption transitions in ultraporous frameworks
journal, August 2019


High-throughput prediction of the ground-state collinear magnetic order of inorganic materials using Density Functional Theory
journal, June 2019


Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds
journal, February 2018


Unsupervised word embeddings capture latent knowledge from materials science literature
journal, July 2019


A database to enable discovery and design of piezoelectric materials
journal, September 2015


Charting the complete elastic properties of inorganic crystalline compounds
journal, March 2015


A polymer dataset for accelerated property prediction and design
journal, March 2016


Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface
journal, January 2017


High-throughput screening of inorganic compounds for the discovery of novel dielectric and optical materials
journal, January 2017


High-throughput ab-initio dilute solute diffusion database
journal, July 2016


Surface energies of elemental crystals
journal, September 2016


A hybrid organic-inorganic perovskite dataset
journal, May 2017


An ab initio electronic transport database for inorganic materials
journal, July 2017


Large scale in silico screening of materials for carbon capture through chemical looping
journal, January 2017


Elastic Properties of Alkali Superionic Conductor Electrolytes from First Principles Calculations
journal, November 2015


Stability, composition and properties of Li2FeSiO4 surfaces studied by DFT
journal, August 2013


Evaluation of thermodynamic equations of state across chemistry and structure in the materials project
journal, July 2018


High-throughput computational discovery of In2Mn2O7 as a high Curie temperature ferromagnetic semiconductor for spintronics
journal, July 2019


Recent advances and applications of machine learning in solid-state materials science
journal, August 2019


Machine-learned and codified synthesis parameters of oxide materials
journal, September 2017


High-throughput density-functional perturbation theory phonons for inorganic materials
journal, May 2018


Computational screening of high-performance optoelectronic materials using OptB88vdW and TB-mBJ formalisms
journal, May 2018


Room-Temperature All-solid-state Rechargeable Sodium-ion Batteries with a Cl-doped Na3PS4 Superionic Conductor
journal, September 2016


Enumeration of de novo inorganic complexes for chemical discovery and machine learning
journal, January 2020


A quantitative uncertainty metric controls error in neural network-driven chemical discovery
journal, January 2019


crystal-torture: A crystal tortuosity module
journal, June 2019


Database-Driven Materials Selection for Semiconductor Heterojunction Design
journal, August 2018


Electride: from computational characterization to theoretical design: Electride: from computational characterization to theoretical design
journal, March 2016


The Ternary Post-transition Metal Carbodiimide SrZn(NCN) 2 : The Ternary Post-transition Metal Carbodiimide SrZn(NCN)
journal, September 2017


First Full Structural Characterization of Chloro Formamidinium Salts: First Full Structural Characterization of Chloro Formamidinium Salts
journal, May 2018


Stability, composition and properties of Li2FeSiO4 surfaces studied by DFT
journal, August 2013


Insightful classification of crystal structures using deep learning
journal, July 2018


Deep neural networks for accurate predictions of crystal stability
journal, September 2018


Towards general network architecture design criteria for negative gas adsorption transitions in ultraporous frameworks
journal, August 2019


Evaluation of thermodynamic equations of state across chemistry and structure in the materials project
journal, July 2018


High-throughput prediction of the ground-state collinear magnetic order of inorganic materials using Density Functional Theory
journal, June 2019


High-throughput computational discovery of In2Mn2O7 as a high Curie temperature ferromagnetic semiconductor for spintronics
journal, July 2019


Recent advances and applications of machine learning in solid-state materials science
journal, August 2019


Two-dimensional materials from high-throughput computational exfoliation of experimentally known compounds
journal, February 2018


Unsupervised word embeddings capture latent knowledge from materials science literature
journal, July 2019


Direct thermal neutron detection by the 2D semiconductor 6LiInP2Se6
journal, January 2020


A database to enable discovery and design of piezoelectric materials
journal, September 2015


Charting the complete elastic properties of inorganic crystalline compounds
journal, March 2015


A polymer dataset for accelerated property prediction and design
journal, March 2016


Evaluation and comparison of classical interatomic potentials through a user-friendly interactive web-interface
journal, January 2017


High-throughput screening of inorganic compounds for the discovery of novel dielectric and optical materials
journal, January 2017


High-throughput ab-initio dilute solute diffusion database
journal, July 2016


Surface energies of elemental crystals
journal, September 2016


Machine-learned and codified synthesis parameters of oxide materials
journal, September 2017


A hybrid organic-inorganic perovskite dataset
journal, May 2017


An ab initio electronic transport database for inorganic materials
journal, July 2017


High-throughput density-functional perturbation theory phonons for inorganic materials
journal, May 2018


Computational screening of high-performance optoelectronic materials using OptB88vdW and TB-mBJ formalisms
journal, May 2018


Room-Temperature All-solid-state Rechargeable Sodium-ion Batteries with a Cl-doped Na3PS4 Superionic Conductor
journal, September 2016


Large scale in silico screening of materials for carbon capture through chemical looping
journal, January 2017


Structural and Na-ion conduction characteristics of Na 3 PS x Se 4−x
journal, January 2016


Enumeration of de novo inorganic complexes for chemical discovery and machine learning
journal, January 2020


A quantitative uncertainty metric controls error in neural network-driven chemical discovery
journal, January 2019


Rationalizing accurate structure prediction in the meta-GGA SCAN functional
journal, July 2019


Tuning the magnetocaloric response in half-Heusler/Heusler MnNi 1 + x Sb solid solutions
journal, December 2017


Elastic Properties of Alkali Superionic Conductor Electrolytes from First Principles Calculations
journal, November 2015


crystal-torture: A crystal tortuosity module
journal, June 2019


Investigation of Alkali‐Ion (Li, Na, and K) Intercalation in K x VPO 4 F ( x ∼ 0) Cathode
journal, June 2019


VI 3 —a New Layered Ferromagnetic Semiconductor
journal, March 2019


Are Cu 2 Te‐Based Compounds Excellent Thermoelectric Materials?
journal, October 2019


Data‐Driven Materials Science: Status, Challenges, and Perspectives
journal, September 2019


Fluorination of Lithium-Excess Transition Metal Oxide Cathode Materials
journal, October 2017


Material Discovery and Design Principles for Stable, High Activity Perovskite Cathodes for Solid Oxide Fuel Cells
journal, January 2018


User applications driven by the community contribution framework MPContribs in the Materials Project: MPCONTRIBS-DRIVEN USER APPLICATIONS
journal, October 2015


Reversible High Capacity and Reaction Mechanism of Cr 2 (NCN) 3 Negative Electrodes for Li‐Ion Batteries
journal, December 2019


PyDEF 2.0: An Easy to Use Post‐treatment Software for Publishable Charts Featuring a Graphical User Interface
journal, October 2018


Crystal structure representations for machine learning models of formation energies
journal, April 2015


P y SCF: the Python-based simulations of chemistry framework : The PySCF program
journal, September 2017

  • Sun, Qiming; Berkelbach, Timothy C.; Blunt, Nick S.
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 8, Issue 1
  • https://doi.org/10.1002/wcms.1340

Theoretical study of phase stability, crystal and electronic structure of MeMgN2 (Me = Ti, Zr, Hf) compounds
journal, November 2017


Visualizing non-equilibrium lithiation of spinel oxide via in situ transmission electron microscopy
journal, May 2016


Computational understanding of Li-ion batteries
journal, March 2016


Computational prediction of new auxetic materials
journal, August 2017


Pulsed axial epitaxy of colloidal quantum dots in nanowires enables facet-selective passivation
journal, November 2018


Effective mass and Fermi surface complexity factor from ab initio band structure calculations
journal, February 2017


Efficient first-principles prediction of solid stability: Towards chemical accuracy
journal, March 2018


Automated generation and ensemble-learned matching of X-ray absorption spectra
journal, March 2018


Materials structure genealogy and high-throughput topological classification of surfaces and 2D materials
journal, September 2018


An electrostatic spectral neighbor analysis potential for lithium nitride
journal, July 2019


Exploring the bottlenecks of anionic redox in Li-rich layered sulfides
journal, November 2019


A map of the inorganic ternary metal nitrides
journal, June 2019


High-throughput computation and evaluation of raman spectra
journal, July 2019


An automatically curated first-principles database of ferroelectrics
journal, March 2020


Spinel compounds as multivalent battery cathodes: a systematic evaluation based on ab initio calculations
journal, January 2015


Li-ion conductivity in Li 9 S 3 N
journal, January 2015


Alloying ZnS in the hexagonal phase to create high-performing transparent conducting materials
journal, January 2016


Reduced overpotentials for electrocatalytic water splitting over Fe- and Ni-modified BaTiO 3
journal, January 2016


A first-principles study of the preventive effects of Al and Mg doping on the degradation in LiNi 0.8 Co 0.1 Mn 0.1 O 2 cathode materials
journal, January 2017


Materials informatics: a journey towards material design and synthesis
journal, January 2016


Anti-perovskite cathodes for lithium batteries
journal, January 2018


Exploring new approaches towards the formability of mixed-ion perovskites by DFT and machine learning
journal, January 2019


Materials discovery by chemical analogy: role of oxidation states in structure prediction
journal, January 2018


Atomic layer deposition and first principles modeling of glassy Li 3 BO 3 –Li 2 CO 3 electrolytes for solid-state Li metal batteries
journal, January 2018


Origins of ultralow thermal conductivity in 1-2-1-4 quaternary selenides
journal, January 2019


Rational synthesis and electrochemical performance of LiVOPO 4 polymorphs
journal, January 2019


Unveiling new stable manganese based photoanode materials via theoretical high-throughput screening and experiments
journal, January 2019


LiAl 5 O 8 as a potential coating material in lithium-ion batteries: a first principles study
journal, January 2019


Bulk and surface DFT investigations of inorganic halide perovskites screened using machine learning and materials property databases
journal, January 2019


Efficient Pourbaix diagrams of many-element compounds
journal, January 2019


Electronic properties of heterogenized Ru( ii ) polypyridyl photoredox complexes on covalent triazine frameworks
journal, January 2019


A Li 2 CuPS 4 superionic conductor: a new sulfide-based solid-state electrolyte
journal, January 2019


Depth-dependent oxygen redox activity in lithium-rich layered oxide cathodes
journal, January 2019


Revealing cooperative Li-ion migration in Li 1+x Al x Ti 2−x (PO 4 ) 3 solid state electrolytes with high Al doping
journal, January 2020


Constructing first-principles phase diagrams of amorphous Li x Si using machine-learning-assisted sampling with an evolutionary algorithm
journal, June 2018


Predicting the stability of ternary intermetallics with density functional theory and machine learning
journal, June 2018


Nonlinear elastic behavior and anisotropic electronic properties of two-dimensional borophene
journal, April 2019


Machine learning reveals orbital interaction in materials
journal, January 2017


Computational methods for 2D materials: discovery, property characterization, and application design
journal, November 2017


Carbon diffusion in molten uranium: an ab initio molecular dynamics study
journal, March 2018


Transferability of interatomic potentials for molybdenum and silicon
journal, January 2019


Rare-earth magnetic nitride perovskites
journal, March 2019


From DFT to machine learning: recent approaches to materials science–a review
journal, May 2019


Modeling the structural distortion and magnetic ground state of the polar lacunar spinel GaV 4 Se 8
journal, July 2019


Ab initio insight into the formation of small polarons: A study across four metal peroxides
journal, November 2019


Computational screening of Fe-Ta hard magnetic phases
journal, January 2020


Mapping skyrmion stability in uniaxial lacunar spinel magnets from first principles
journal, February 2020


Dynamic instabilities in strongly correlated VSe 2 monolayers and bilayers
journal, December 2017


Electronic-Structure Origin of Cation Disorder in Transition-Metal Oxides
journal, October 2017


Accurate force field for molybdenum by machine learning large materials data
journal, September 2017


Crystal structure prediction accelerated by Bayesian optimization
journal, January 2018


High-density electron doping of SmNiO 3 from first principles
journal, November 2019


COD::CIF::Parser : an error-correcting CIF parser for the Perl language
journal, February 2016


The thermodynamic scale of inorganic crystalline metastability
journal, November 2016


Atomistic Structure and Ab Initio Electrochemical Properties of Li 4 Ti 5 O 12 Defect Spinel for Li Ion Batteries
journal, December 2013


A Combinatorial Investigation of Fe-Si-Zn Thin Film Negative Electrodes for Li-Ion Batteries
journal, November 2014


A data ecosystem to support machine learning in materials science
journal, October 2019


Robocrystallographer: automated crystal structure text descriptions and analysis
journal, July 2019


SMACT: Semiconducting Materials by Analogy and Chemical Theory
journal, June 2019


WulffPack: A Python package for Wulff constructions
journal, January 2020


Computational Screening of New Perovskite Materials Using Transfer Learning and Deep Learning
journal, December 2019


    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.