Bayesian Approaches to Uncertainty Quantification and Structure Refinement from X-Ray Diffraction

This chapter introduces classical frequentist and Bayesian inference applied to analyzing diffraction profiles, and the methods are compared and contrasted. The methods are applied to both the modelling of single diffraction profiles and the full profile refinement of crystallographic structures. In the Bayesian method, Markov chain Monte Carlo algorithms are used to sample the distribution of model parameters, allowing for the construction of posterior probability distributions, which provide both parameter estimates and quantifiable uncertainties. We present the application of this method to single peak fitting in lead zirconate titanate, and the crystal structure refinement of a National Institute of Standards and Technology silicon standard reference material.

[1]  David B. Dunson,et al.  Bayesian Data Analysis , 2010 .

[2]  Alyson G. Wilson,et al.  Use of Bayesian Inference in Crystallographic Structure Refinement via Full Diffraction Profile Analysis , 2016, Scientific Reports.

[3]  Changhe Yuan,et al.  Importance sampling algorithms for Bayesian networks: Principles and performance , 2006, Math. Comput. Model..

[4]  Paul Muralt,et al.  Piezoelectric Thin Films for Sensors, Actuators, and Energy Harvesting , 2009 .

[5]  P. Scardi,et al.  Effect of a crystallite size distribution on X‐ray diffraction line profiles and whole‐powder‐pattern fitting , 2000 .

[6]  M. J. Cooper Analysis of powder diffraction data , 1982 .

[7]  Jacob L. Jones,et al.  Domain texture distributions in tetragonal lead zirconate titanate by x-ray and neutron diffraction , 2005 .

[8]  Jacob L. Jones,et al.  In situ measurement of increased ferroelectric/ferroelastic domain wall motion in declamped tetragonal lead zirconate titanate thin films , 2015 .

[9]  Jacob L. Jones,et al.  Strain state of bismuth zinc niobate pyrochlore thin films , 2009 .

[10]  G. Will Powder Diffraction: The Rietveld Method and the Two Stage Method to Determine and Refine Crystal Structures from Powder Diffraction Data , 2005 .

[11]  Bayesian inference of x-ray diffraction spectra from warm dense matter with the one-component-plasma model. , 2016, Physical review. E.

[12]  L. J. Anthony,et al.  The Cambridge Dictionary of Statistics (2nd ed.) , 2003 .

[13]  P. Angerer,et al.  Bayesian approach applied to the Rietveld method , 2014 .

[14]  Igor Levin,et al.  Accounting for unknown systematic errors in Rietveld refinements: a Bayesian statistics approach , 2015 .

[15]  A. Steuwer,et al.  A high energy synchrotron x-ray study of crystallographic texture and lattice strain in soft lead zirconate titanate ceramics , 2004 .

[16]  R. Young,et al.  The Rietveld method , 2006 .

[17]  C. Giacovazzo,et al.  Space-group determination from powder diffraction data: a probabilistic approach , 2004 .

[18]  M. Sakata,et al.  An analysis of the Rietveld refinement method , 1979 .

[19]  Jacob L. Jones,et al.  In situ characterization of polycrystalline ferroelectrics using x-ray and neutron diffraction , 2015 .

[20]  Jeffrey N. Rouder,et al.  Robust misinterpretation of confidence intervals , 2013, Psychonomic bulletin & review.

[21]  Jacob L. Jones,et al.  Deaging and asymmetric energy landscapes in electrically biased ferroelectrics. , 2012, Physical review letters.

[22]  Steven Disseler,et al.  Bayesian method for the analysis of diffraction patterns using BLAND , 2016 .

[23]  I. Levin,et al.  A Bayesian approach for denoising one-dimensional data , 2012 .

[24]  A. Mikhalychev,et al.  Bayesian approach to powder phase identification , 2017 .

[25]  H. Rietveld Line profiles of neutron powder-diffraction peaks for structure refinement , 1967 .

[26]  E. Prince Comparison of profile and integrated‐intensity methods in powder refinement , 1981 .

[27]  H. Rietveld A profile refinement method for nuclear and magnetic structures , 1969 .

[28]  H. Scott The Estimation of Standard Deviations in Powder Diffraction Rietveld Refinements , 1983 .

[29]  D. Balzar,et al.  Size–strain line-broadening analysis of the ceria round-robin sample , 2004 .

[30]  Brian H. Toby,et al.  GSAS‐II: the genesis of a modern open‐source all purpose crystallography software package , 2013 .

[31]  J. Filliben,et al.  Certification of NIST Standard Reference Material 640d , 2010, Powder Diffraction.

[32]  Gleb Bourenkov,et al.  A Bayesian Approach to Laue Diffraction Analysis and its Potential for Time‐Resolved Protein Crystallography , 1996 .

[33]  S. Chib,et al.  Understanding the Metropolis-Hastings Algorithm , 1995 .

[34]  D. S. Sivia,et al.  Background estimation using a robust Bayesian analysis , 2001 .

[35]  S. Billinge,et al.  Testing different methods for estimating uncertainties on Rietveld refined parameters using SrRietveld , 2011 .

[36]  Christopher J. Gilmore,et al.  Maximum Entropy and Bayesian Statistics in Crystallography: a Review of Practical Applications , 1996 .

[37]  H. Rietveld The Rietveld Method: A Retrospection , 2010 .

[38]  S. French,et al.  A Bayesian three-stage model in crystallography , 1978 .

[39]  Alyson G. Wilson,et al.  A Bayesian approach to modeling diffraction profiles and application to ferroelectric materials , 2017 .

[40]  I. Takeuchi,et al.  Labile Ferroelastic Nanodomains in Bilayered Ferroelectric Thin Films , 2009 .