PyCDT: A Python toolkit for modeling point defects in semiconductors and insulators

Author(s): Broberg, D; Medasani, B; Zimmermann, NER; Yu, G; Canning, A; Haranczyk, M; Asta, M; Hautier, G | Abstract: © 2018 Point defects have a strong impact on the performance of semiconductor and insulator materials used in technological applications, spanning microelectronics to energy conversion and storage. The nature of the dominant defect types, how they vary with processing conditions, and their impact on materials properties are central aspects that determine the performance of a material in a certain application. This information is, however, difficult to access directly from experimental measurements. Consequently, computational methods, based on electronic density functional theory (DFT), have found widespread use in the calculation of point-defect properties. Here we have developed the Python Charged Defect Toolkit (PyCDT) to expedite the setup and post-processing of defect calculations with widely used DFT software. PyCDT has a user-friendly command-line interface and provides a direct interface with the Materials Project database. This allows for setting up many charged defect calculations for any material of interest, as well as post-processing and applying state-of-the-art electrostatic correction terms. Our paper serves as a documentation for PyCDT, and demonstrates its use in an application to the well-studied GaAs compound semiconductor. We anticipate that the PyCDT code will be useful as a framework for undertaking readily reproducible calculations of charged point-defect properties, and that it will provide a foundation for automated, high-throughput calculations. Program summary: Program title: PyCDT Program Files doi: http://dx.doi.org/10.17632/7vzk5gxzh3.1 Licensing Provisions: MIT License. Programming language: Python External routines/libraries: NumPy [1], matplotlib [2], and Pymatgen [3], Nature of problem: Computing the formation energies and stable point defects with finite size supercell error corrections for charged defects in semiconductors and insulators. Solution method: Automated setup, and parsing of defect calculations, combined with local use of finite size supercell corrections. All combined into a code with a standard user-friendly command line interface that leverages a core set of tools with a wide range of applicability. Additional comments: This article describes version 1.0.0. Program obtainable from https://bitbucket.org/mbkumar/pycdt

[1]  M. G. Medvedev,et al.  Density functional theory is straying from the path toward the exact functional , 2017, Science.

[2]  Wolf Gero Schmidt,et al.  Group-VII point defects in ZnSe , 2011 .

[3]  John D. Hunter,et al.  Matplotlib: A 2D Graphics Environment , 2007, Computing in Science & Engineering.

[4]  Kristin A. Persson,et al.  Commentary: The Materials Project: A materials genome approach to accelerating materials innovation , 2013 .

[5]  Alex Zunger,et al.  Assessment of correction methods for the band-gap problem and for finite-size effects in supercell defect calculations: Case studies for ZnO and GaAs , 2008 .

[6]  Anubhav Jain,et al.  Accuracy of density functional theory in predicting formation energies of ternary oxides from binary oxides and its implication on phase stability , 2012 .

[7]  Alfredo Pasquarello,et al.  Assessing the accuracy of hybrid functionals in the determination of defect levels: Application to the As antisite in GaAs , 2011 .

[8]  P. Rodnyi.  Physical Processes in Inorganic Scintillators , 2020 .

[9]  Normand Mousseau,et al.  Self-vacancies in gallium arsenide: An ab initio calculation , 2005 .

[10]  David Quigley,et al.  Nucleation of NaCl from Aqueous Solution: Critical Sizes, Ion-Attachment Kinetics, and Rates. , 2015, Journal of the American Chemical Society.

[11]  Guohong Liu,et al.  Native point defects in ZnS: First-principles studies based on LDA, LDA + U and an extrapolation scheme , 2012 .

[12]  Jianwei Sun,et al.  Accurate first-principles structures and energies of diversely bonded systems from an efficient density functional. , 2016, Nature chemistry.

[13]  Hafner,et al.  Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium. , 1994, Physical review. B, Condensed matter.

[14]  H. Overhof,et al.  Point Defects in Semiconductors and Insulators: Determination of Atomic and Electronic Structure from Paramagnetic Hyperfine Interactions , 2012 .

[15]  P. Dorenbos.  Scintillation mechanisms in Ce3+ doped halide scintillators , 2005 .

[16]  G. G. Stokes.  "J." , 1890, The New Yale Book of Quotations.

[17]  J. Zaanen,et al.  Density-functional theory and strong interactions: Orbital ordering in Mott-Hubbard insulators. , 1995, Physical review. B, Condensed matter.

[18]  Bálint Aradi,et al.  Calculation ofthe transitions and migration of nitrogen and vacancy related defects,with implications on the formation of NV centers in bulk diamond , 2013, 1311.6598.

[19]  Andreas Höglund,et al.  Density functional theory calculations of defect energies using supercells , 2009 .

[20]  Roger Grimes,et al.  Vacancies and defect levels in III-V semiconductors , 2013 .

[21]  Anubhav Jain,et al.  Computational and experimental investigation of TmAgTe2 and XYZ2 compounds, a new group of thermoelectric materials identified by first-principles high-throughput screening , 2015 .

[22]  Fabien Bruneval,et al.  Understanding and correcting the spurious interactions in charged supercells , 2011 .

[23]  Hyo Sug Lee,et al.  Property database for single-element doping in ZnO obtained by automated first-principles calculations , 2017, Scientific Reports.

[24]  Thomas M Henderson,et al.  Screened hybrid density functionals for solid-state chemistry and physics. , 2009, Physical chemistry chemical physics : PCCP.

[25]  Guido Petretto,et al.  Systematic defect donor levels in III-V and II-VI semiconductors revealed by hybrid functional density-functional theory , 2015 .

[26]  Angela N. Fioretti,et al.  Defect Tolerant Semiconductors for Solar Energy Conversion. , 2014, The journal of physical chemistry letters.

[27]  Alex Zunger,et al.  Accurate prediction of defect properties in density functional supercell calculations , 2009 .

[28]  B. Peters.  Competing nucleation pathways in a mixture of oppositely charged colloids: out-of-equilibrium nucleation revisited. , 2009, The Journal of chemical physics.

[29]  Ulrich Wahl,et al.  Lattice location study of ion implanted Sn and Sn-related defects in Ge , 2010 .

[30]  G. J. Snyder,et al.  Defect-controlled electronic properties in AZn₂Sb₂ Zintl phases. , 2014, Angewandte Chemie.

[31]  Vladan Stevanovic,et al.  A Computational Framework for Automation of Point Defect Calculations , 2016, 1611.00825.

[32]  Ulrich Wahl,et al.  Lattice position and thermal stability of diluted As in Ge , 2012 .

[33]  Fabiano Corsetti,et al.  System-size convergence of point defect properties: The case of the silicon vacancy , 2010, 1010.3921.

[34]  L M Amorim,et al.  A versatile apparatus for on-line emission channeling experiments. , 2013, The Review of scientific instruments.

[35]  G. Kresse,et al.  Ab initio molecular dynamics for liquid metals. , 1993 .

[36]  Ulrich Wahl,et al.  Lattice location and thermal stability of implanted nickel in silicon studied by on-line emission channeling , 2014 .

[37]  S. Ong,et al.  Design principles for solid-state lithium superionic conductors. , 2015, Nature materials.

[38]  Jeff W. Doak,et al.  Determining dilute-limit solvus boundaries in multi-component systems using defect energetics: Na in PbTe and PbS , 2015 .

[39]  Niels Grønbech-Jensen,et al.  First-principles study of luminescence in Ce-doped inorganic scintillators , 2010, 1008.2627.

[40]  Ulrich Wahl,et al.  Lattice location study of implanted In in Ge , 2009 .

[41]  S. Ong,et al.  The thermodynamic scale of inorganic crystalline metastability , 2016, Science Advances.

[42]  A. Canning,et al.  First-principles study of luminescence in Eu$^{2+}$-doped inorganic scintillators , 2014 .

[43]  Stefano de Gironcoli,et al.  Reproducibility in density functional theory calculations of solids , 2016, Science.

[44]  Ulrich Wahl,et al.  Experimental evidence of tetrahedral interstitial and bond-centered Er in Ge , 2008 .

[45]  P. Papoulias,et al.  First-principles study of As interstitials in GaAs: Convergence, relaxation, and formation energy , 2002, 1101.1413.

[46]  Steven G. Louie,et al.  GW study of the metal-insulator transition of bcc hydrogen , 2002 .

[47]  G. Rignanese,et al.  Electronic properties of interfaces and defects from many‐body perturbation theory: Recent developments and applications , 2011 .

[48]  Maciej Haranczyk,et al.  Assessing Local Structure Motifs Using Order Parameters for Motif Recognition, Interstitial Identification, and Diffusion Path Characterization , 2017, Front. Mater..

[49]  Gibson,et al.  Stability of vacancy defects in MgO: The role of charge neutrality. , 1994, Physical review. B, Condensed matter.

[50]  A. Zunger,et al.  Dopability, intrinsic conductivity, and nonstoichiometry of transparent conducting oxides. , 2007, Physical review letters.

[51]  H Emmerich,et al.  Transition metal impurities on the bond-centered site in germanium. , 2009, Physical review letters.

[52]  Aron Walsh,et al.  Self-Regulation Mechanism for Charged Point Defects in Hybrid Halide Perovskites** , 2015, Angewandte Chemie.

[53]  Roger Grimes,et al.  Antisites in III-V semiconductors: Density functional theory calculations , 2014 .

[55]  Wei Chen,et al.  FireWorks: a dynamic workflow system designed for high‐throughput applications , 2015, Concurr. Comput. Pract. Exp..

[56]  Hans Hofsäss,et al.  Emission channeling and blocking , 1991 .

[57]  Anubhav Jain,et al.  Computational and experimental investigation of TmAgTe 2 and XYZ 2 compounds , a new group of thermoelectric materials identified by first-principles high-throughput screening † , 2015 .

[58]  Ulrich Wahl,et al.  Direct identification of interstitial Mn in heavily p-type doped GaAs and evidence of its high thermal stability , 2011 .

[59]  Tsuyoshi Murata,et al.  {m , 1934, ACML.

[60]  Geoffroy Hautier,et al.  Electronic structure and defect properties of B6O from hybrid functional and many-body perturbation theory calculations: A possible ambipolar transparent conductor , 2014 .

[61]  Andrew G. Glen,et al.  APPL , 2001 .

[62]  Risto M. Nieminen,et al.  Intrinsic n-type behavior in transparent conducting oxides: a comparative hybrid-functional study of In2O3, SnO2, and ZnO. , 2009 .

[63]  E. Seebauer,et al.  Charged point defects in semiconductors , 2006 .

[64]  Vladan Stevanović,et al.  Convergence of density and hybrid functional defect calculations for compound semiconductors , 2013 .

[65]  Payne,et al.  Periodic boundary conditions in ab initio calculations. , 1995, Physical review. B, Condensed matter.

[66]  G. L. Dirichlet.  Über die Reduction der positiven quadratischen Formen mit drei unbestimmten ganzen Zahlen. , 1850 .

[67]  Annabella Selloni,et al.  Excess electron states in reduced bulk anatase TiO2: comparison of standard GGA, GGA+U, and hybrid DFT calculations. , 2008, The Journal of chemical physics.

[68]  Alessandro. De Vita,et al.  The energetics of defects and impurities in metals and ionic materials from first principles. , 1992 .

[69]  Anubhav Jain,et al.  Materials Design Rules for Multivalent Ion Mobility in Intercalation Structures , 2015 .

[70]  C. Walle,et al.  First-principles calculations for defects and impurities: Applications to III-nitrides , 2004 .

[71]  Gerbrand Ceder,et al.  Interface Stability in Solid-State Batteries , 2016 .

[72]  Zhang,et al.  Chemical potential dependence of defect formation energies in GaAs: Application to Ga self-diffusion. , 1991, Physical review letters.

[73]  Alfredo Pasquarello,et al.  Finite-size supercell correction schemes for charged defect calculations , 2012 .

[74]  A. Gottberg,et al.  Precise lattice location of substitutional and interstitial Mg in AlN , 2013 .

[75]  Van de Walle CG,et al.  Atomic geometry and electronic structure of native defects in GaN. , 1994, Physical review. B, Condensed matter.

[76]  Zhang,et al.  Energetics of the As vacancy in GaAs: The stability of the 3+ charge state. , 1994, Physical review. B, Condensed matter.

[77]  F. Oba,et al.  Electrostatics-based finite-size corrections for first-principles point defect calculations , 2014, 1402.1226.

[78]  Eugene E. Haller,et al.  Dopants and Defects in Semiconductors , 2012 .

[79]  P ? ? ? ? ? ? ? % ? ? ? ? , 1991 .

[80]  K. Rosso,et al.  Vacancies and Vacancy-Mediated Self Diffusion in Cr2O3: A First-Principles Study , 2017 .

[81]  C. Freysoldt,et al.  Fully ab initio finite-size corrections for charged-defect supercell calculations. , 2009, Physical review letters.

[82]  Northrup,et al.  Theory of quasiparticle energies in alkali metals. , 1987, Physical review letters.

[83]  M. O'keefe,et al.  Atom sizes and bond lengths in molecules and crystals , 1991 .

[84]  A. Dick,et al.  The object-oriented DFT program library S/PHI/nX , 2011, Comput. Phys. Commun..

[85]  G. Kresse,et al.  First-principles calculations for point defects in solids , 2014 .

[86]  W. D. Callister,et al.  Materials Science and Engineering: An Introduction, 7th Edition , 2006 .

[87]  Udo Schwingenschlögl,et al.  Formation and Migration of Oxygen Vacancies in SrCoO3 and Their Effect on Oxygen Evolution Reactions , 2016 .

[88]  Anubhav Jain,et al.  Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis , 2012 .

[89]  Anubhav Jain,et al.  Formation enthalpies by mixing GGA and GGA + U calculations , 2011 .

[90]  Alfredo Pasquarello,et al.  Identification of defect levels at InxGa1-xAs/oxide interfaces through hybrid functionals , 2011 .

[91]  O. Anatole von Lilienfeld,et al.  Simple intrinsic defects in gallium arsenide , 2009 .

[92]  Jianwei Zheng,et al.  Study of Native Defects and Transition-Metal (Mn, Fe, Co, and Ni) Doping in a Zinc-Blende CdS Photocatalyst by DFT and Hybrid DFT Calculations , 2011 .

[93]  Ulrich Wahl,et al.  Stability and diffusion of interstitial and substitutional Mn in GaAs of different doping types , 2012 .

[94]  Ulrich Wahl,et al.  Diluted manganese on the bond-centered site in germanium , 2010 .

[95]  David O. Scanlon,et al.  Conductivity Limits in CuAlO2 from Screened-Hybrid Density Functional Theory , 2010 .

[96]  Jörg Neugebauer,et al.  Electrostatic interactions between charged defects in supercells , 2011 .

[97]  Stéphane Jobic,et al.  Presentation of the PyDEF post-treatment Python software to compute publishable charts for defect energy formation , 2017 .

[98]  Front , 2020, 2020 Fourth World Conference on Smart Trends in Systems, Security and Sustainability (WorldS4).

[99]  Burke,et al.  Generalized Gradient Approximation Made Simple. , 1996, Physical review letters.