Skip to main content

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

  • Chapter
  • First Online:
Materials Discovery and Design

Part of the book series: Springer Series in Materials Science ((SSMATERIALS,volume 280))

  • 1531 Accesses

Abstract

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.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 199.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. A.R. West, Basic Solid State Chemistry, 2nd edn. (Wiley, West Sussex, England, 1999)

    Google Scholar 

  2. R.C. Smith, Uncertainty Quantification: Theory, Implementation, and Applications (Society for Industrial and Applied Mathematics, Philadelphia, 2014)

    MATH  Google Scholar 

  3. C.M. Fancher, Z. Han, I. Levin, K. Page, B.J. Reich, R.C. Smith, A.G. Wilson, J.L. Jones, Sci. Rep. 6, 31625 (2016)

    Article  ADS  Google Scholar 

  4. P.S. Bandyopadhyay, M.R. Forster, Philosophy of Statistics, vol. 7 (Elsevier B.V., Oxford, 2011)

    MATH  Google Scholar 

  5. J.C. Nino, W. Qiu, J.L. Jones, Thin Solid Films 517, 4325 (2009)

    Article  ADS  Google Scholar 

  6. H.M. Rietveld, J. Appl. Crystallogr. 2, 65 (1969)

    Article  Google Scholar 

  7. H.M. Rietveld, Acta Crystallogr. 22, 151 (1967)

    Article  Google Scholar 

  8. H.M. Rietveld, Zeitschrift Für Krist. 225, 545 (2010)

    Article  ADS  Google Scholar 

  9. B.H. Toby, R.B. Von Dreele, J. Appl. Crystallogr. 46, 544 (2013)

    Article  Google Scholar 

  10. M.J. Cooper, Acta Crystallogr. Sect. A 38, 264 (1982)

    Article  ADS  Google Scholar 

  11. M. Sakata, M.J. Cooper, J. Appl. Crystallogr. 12, 554 (1979)

    Article  Google Scholar 

  12. H.G. Scott, J. Appl. Crystallogr. 16, 159 (1983)

    Article  Google Scholar 

  13. P. Tian, S.J.L. Billinge, Zeitschrift Fur Krist. 226, 898 (2011)

    Article  ADS  Google Scholar 

  14. R.A. Young, The Rietveld Method (Oxford University Press, 1995)

    Google Scholar 

  15. G. Will, Powder Diffraction: The Rietveld Method and the Two Stage Method to Determine and Refine Crystal Structures from Powder Diffraction Data (Springer, Berlin/Heidelberg, 2006)

    Google Scholar 

  16. E. Prince, J. Appl. Crystallogr. 14, 157 (1981)

    Article  Google Scholar 

  17. B.S. Everitt, The Cambridge Dictionary of Statistics, 2nd edn. (Cambridge University Press, Cambridge, 2002)

    MATH  Google Scholar 

  18. R. Hoekstra, R.D. Morey, J.N. Rouder, E.-J. Wagenmakers, Psychon. Bull. Rev. 21, 1157 (2014)

    Article  Google Scholar 

  19. A. Gelman, J.B. Carlin, H.S. Stern, D.B. Dunson, A. Vehtari, D.B. Rubin, Bayesian Data Analysis, 3rd edn. (CRC Press, 2014)

    Google Scholar 

  20. T. Iamsasri, J. Guerrier, G. Esteves, C.M. Fancher, A.G. Wilson, R.C. Smith, E.A. Paisley, R. Johnson-Wilke, J.F. Ihlefeld, N. Bassiri-Gharb, J.L. Jones, J. Appl. Crystallogr. 50, 211 (2017)

    Article  Google Scholar 

  21. C. Yuan, M.J. Druzdzel, Math. Comput. Model. 43, 1189 (2006)

    Article  Google Scholar 

  22. S. Chib, E. Greenberg, Am. Stat. 49, 327 (1995)

    Google Scholar 

  23. Data-Enabled Science and Engineering of Atomic Structure at North Carolina State University. https://youtu.be/S_ItC4ytT60 (2016)

  24. S. French, Acta Crystallogr. Sect. A 34, 728 (1978)

    Article  ADS  Google Scholar 

  25. C.R. Hogg III, K. Mullen, I. Levin, J. Appl. Crystallogr. 45, 471 (2012)

    Article  Google Scholar 

  26. N. Armstrong, W. Kalceff, J.P. Cline, J.E. Bonevich, J. Res. Natl. Inst. Stand. Technol. 109, 155 (2004)

    Article  Google Scholar 

  27. C.J. Gilmore, Acta Crystallogr. Sect. A: Found. Crystallogr. 52, 561 (1996)

    Article  Google Scholar 

  28. G.P. Bourenkov, A.N. Popov, H.D. Bartunik, Acta Crystallogr. Sect. A: Found. Crystallogr. 52, 797 (1996)

    Article  Google Scholar 

  29. J. Bergmann, T. Monecke, J. Appl. Crystallogr. 44, 13 (2011)

    Article  Google Scholar 

  30. W.I.F. David, D.S. Sivia, J. Appl. Crystallogr. 34, 318 (2001)

    Article  Google Scholar 

  31. A. Mikhalychev, A. Ulyanenkov, J. Appl. Crystallogr. 50, 776 (2017)

    Article  Google Scholar 

  32. J. Clérouin, N. Desbiens, V. Dubois, P. Arnault, Phys. Rev. E 94, 61202 (2016)

    Article  ADS  Google Scholar 

  33. A. Altomare, R. Caliandro, M. Camalli, C. Cuocci, I. Da Silva, C. Giacovazzo, A.G. Giuseppina Moliterni, R. Spagna, J. Appl. Crystallogr. 37, 957 (2004)

    Article  Google Scholar 

  34. M. Wiessner, P. Angerer, J. Appl. Crystallogr. 47, 1819 (2014)

    Article  Google Scholar 

  35. A. Gagin, I. Levin, J. Appl. Crystallogr. 48, 1201 (2015)

    Article  Google Scholar 

  36. M. Wallace, R.L. Johnson-Wilke, G. Esteves, C.M. Fancher, R.H.T. Wilke, J.L. Jones, S. Trolier-McKinstry, J. Appl. Phys. 117, 54103 (2015)

    Article  ADS  Google Scholar 

  37. J.L. Jones, E.B. Slamovich, K.J. Bowman, J. Appl. Phys. 97, 34113 (2005)

    Article  Google Scholar 

  38. G. Esteves, C.M. Fancher, J.L. Jones, J. Mater. Res. 30, 340 (2015)

    Article  ADS  Google Scholar 

  39. G. Tutuncu, D. Damjanovic, J. Chen, J.L. Jones, Phys. Rev. Lett. 108, 177601 (2012)

    Article  ADS  Google Scholar 

  40. D.A. Hall, A. Steuwer, B. Cherdhirunkorn, T. Mori, P.J. Withers, J. Appl. Phys. 96, 4245 (2004)

    Article  ADS  Google Scholar 

  41. V. Anbusathaiah, D. Kan, F.C. Kartawidjaja, R. Mahjoub, M.A. Arredondo, S. Wicks, I. Takeuchi, J. Wang, V. Nagarajan, Adv. Mater. 21, 3497 (2009)

    Article  Google Scholar 

  42. P. Muralt, R.G. Polcawich, S. Trolier-McKinstry, MRS Bull. 34, 658 (2009)

    Article  Google Scholar 

  43. D.R. Black, D. Windover, A. Henins, D. Gil, J. Filliben, J.P. Cline, Powder Diffr. 25, 187 (2010)

    Article  ADS  Google Scholar 

  44. D. Balzar, N. Audebrand, M.R. Daymond, A. Fitch, A. Hewat, J.I. Langford, A. Le Bail, D. Louër, O. Masson, C.N. McCowan, N.C. Popa, P.W. Stephens, B.H. Toby, J. Appl. Crystallogr. 37, 911 (2004)

    Article  Google Scholar 

  45. J.I. Langford, D. Louër, P. Scardi, J. Appl. Crystallogr. 33, 964 (2000)

    Article  Google Scholar 

  46. J.E. Lesniewski, S.M. Disseler, D.J. Quintana, P.A. Kienzle, W.D. Ratcliff, J. Appl. Crystallogr. 49, 2201 (2016)

    Article  Google Scholar 

  47. G. Esteves, K. Ramos, C.M. Fancher, J.L. Jones. https://github.com/SneakySnail/LIPRAS (2017)

Download references

Acknowledgements

The authors acknowledge the support from the National Science Foundation under awards DMR-1409399 and DGE-1633587.

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jacob L. Jones .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Paterson, A.R., Reich, B.J., Smith, R.C., Wilson, A.G., Jones, J.L. (2018). Bayesian Approaches to Uncertainty Quantification and Structure Refinement from X-Ray Diffraction. In: Lookman, T., Eidenbenz, S., Alexander, F., Barnes, C. (eds) Materials Discovery and Design. Springer Series in Materials Science, vol 280. Springer, Cham. https://doi.org/10.1007/978-3-319-99465-9_4

Download citation

Publish with us

Policies and ethics