refnx : neutron and X-ray reflectometry analysis in Python

Journal of Applied Crystallography
Andrew R J Nelson, Stuart W Prescott

Abstract

refnx is a model-based neutron and X-ray reflectometry data analysis package written in Python. It is cross platform and has been tested on Linux, macOS and Windows. Its graphical user interface is browser based, through a Jupyter notebook. Model construction is modular, being composed from a series of components that each describe a subset of the interface, parameterized in terms of physically relevant parameters (volume fraction of a polymer, lipid area per molecule etc.). The model and data are used to create an objective, which is used to calculate the residuals, log-likelihood and log-prior probabilities of the system. Objectives are combined to perform co-refinement of multiple data sets and mixed-area models. Prior knowledge of parameter values is encoded as probability distribution functions or bounds on all parameters in the system. Additional prior probability terms can be defined for sets of components, over and above those available from the parameters alone. Algebraic parameter constraints are available. The software offers a choice of fitting approaches, including least-squares (global and gradient-based optimizers) and a Bayesian approach using a Markov-chain Monte Carlo algorithm to investigate the posterior dis...Continue Reading

References

Oct 28, 2005·Statistics in Medicine·D Karlis, I Ntzoufras
Aug 29, 2009·Langmuir : the ACS Journal of Surfaces and Colloids·Frank HeinrichMathias Lösche
Aug 31, 2013·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Brian Richard Pauw
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May 26, 2018·Nature·Philip B Stark
Jul 22, 2018·Journal of Colloid and Interface Science·Richard A CampbellM Jayne Lawrence

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Citations

Mar 1, 2019·Physical Chemistry Chemical Physics : PCCP·Andrew R McCluskeyThomas Arnold
Feb 13, 2020·Journal of Applied Crystallography·Gennady PospelovJoachim Wuttke
Jul 22, 2021·Langmuir : the ACS Journal of Surfaces and Colloids·Sebastian KöhlerMarco Maccarini
Aug 5, 2021·Langmuir : the ACS Journal of Surfaces and Colloids·Jakob AnderssonIngo Köper
Aug 21, 2019·Langmuir : the ACS Journal of Surfaces and Colloids·Christian AppelBernd Stühn
Oct 28, 2020·Langmuir : the ACS Journal of Surfaces and Colloids·Edwin C JohnsonErica J Wanless
Dec 22, 2020·Langmuir : the ACS Journal of Surfaces and Colloids·Hiroyuki AokiMikihito Takenaka
Sep 14, 2020·Methods : a Companion to Methods in Enzymology·Jakob AnderssonWolfgang Knoll
Nov 13, 2021·Journal of the American Chemical Society·Johannes D BartlBernhard Rieger
Dec 21, 2021·Physical Chemistry Chemical Physics : PCCP·Thomas M McCoyAlexander F Routh
Nov 18, 2020·Journal of Colloid and Interface Science·Hannah BoydJavier Sotres
Jan 5, 2022·ACS Applied Materials & Interfaces·Thomas J FerronDean M DeLongchamp

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Methods Mentioned

BETA
X-ray
neutron reflectometry

Software Mentioned

ipynb
ReflectModel
Python
gui
Data1D
Docker
PyPI
Windows
emcee
GitHub

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