refnx: neutron and X-ray reflectometry analysis in Python

Journal of Applied Crystallography - Tập 52 Số 1 - Trang 193-200 - 2019
Andrew Nelson1, Stuart W. Prescott2
1ANSTO, Locked Bag 2001 Kirrawee DC NSW, 2232, Australia
2School of Chemical Engineering, University of New South Wales, Sydney, NSW 2052, Australia

Tóm tắt

refnxis 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 aJupyternotebook. 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 moleculeetc.). 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 distribution of the model parameters. The Bayesian approach is useful for examining parameter covariances, model selection and variability in the resulting scattering length density profiles. The package is designed to facilitate reproducible research; its use inJupyternotebooks, and subsequent distribution of those notebooks as supporting information, permits straightforward reproduction of analyses.

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Journal of Applied Crystallography

Tập 52 Số 1

193-200

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