| Literature DB >> 26089769 |
I Bressler1, B R Pauw2, A F Thünemann1.
Abstract
A user-friendly open-source Monte Carlo regression package (McSAS) is presented, which structures the analysis of small-angle scattering (SAS) using uncorrelated shape-similar particles (or scattering contributions). The underdetermined problem is solvable, provided that sufficient external information is available. Based on this, the user picks a scatterer contribution model (or 'shape') from a comprehensive library and defines variation intervals of its model parameters. A multitude of scattering contribution models are included, including prolate and oblate nanoparticles, core-shell objects, several polymer models, and a model for densely packed spheres. Most importantly, the form-free Monte Carlo nature of McSAS means it is not necessary to provide further restrictions on the mathematical form of the parameter distribution; without prior knowledge, McSAS is able to extract complex multimodal or odd-shaped parameter distributions from SAS data. When provided with data on an absolute scale with reasonable uncertainty estimates, the software outputs model parameter distributions in absolute volume fraction, and provides the modes of the distribution (e.g. mean, variance etc.). In addition to facilitating the evaluation of (series of) SAS curves, McSAS also helps in assessing the significance of the results through the addition of uncertainty estimates to the result. The McSAS software can be integrated as part of an automated reduction and analysis procedure in laboratory instruments or at synchrotron beamlines.Entities:
Keywords: Monte Carlo; data analysis software; disperse samples; small-angle scattering
Year: 2015 PMID: 26089769 PMCID: PMC4453982 DOI: 10.1107/S1600576715007347
Source DB: PubMed Journal: J Appl Crystallogr ISSN: 0021-8898 Impact factor: 3.304
Figure 1The main process of the McSAS software for parameter optimization. In each cycle, an attempt is made to replace one of the model contributions in order to improve the agreement between model and measured data.
Figure 2The main interface of the McSAS software upon startup, showing four configuration panels. The ‘Data Files’ panel allows selection and input of the data of interest, the ‘Algorithm’ panel contains settings to adjust the optimization method behaviour, ‘Model’ contains all parameters and settings relevant to the chosen morphology, and ‘Post-fit Analysis’ holds the settings for histogramming and visualization of the result.
Selected program parameters and their effects on the computation
For the advanced settings and defaults that can be found in the mcsasparameters.json file, only selected values are listed.
| Location | Parameter name | Effect |
|---|---|---|
| GUI Algorithm panel | Convergence criterion | The least-squares value ( |
| Number of repetitions | The number of independent optimizations to be run. Larger values will result in improved uncertainty estimates on the result (and a slightly smoother result), but calculation time increases proportionally. | |
| Number of contributions | The number of individual contributions whose weighted sum comprises the total model intensity. Too few or too many will result in slow optimization times. Most patterns can be fitted using 300 contributions quickly, but times can be optimized using the timing information shown in the result. | |
| Find background level | If selected, a flat background is fitted during matching of model and data. This speeds up the fit with minimal effect on the result, as many scattering patterns contain a flat scattering component as well (due to density variations or incoherent scattering). | |
| GUI Post-fit Analysis panel | Parameter | The parameter to show the distribution of. |
| Lower upper | The distribution will be shown in this parameter range only. This can be used to cut off regions outside the range of interest. Population statistics also apply only to this range. | |
| Number of bins | The number of divisions to use in the distribution display. By increasing this number, more detail | |
|
| Scaling (linear or logarithmic) for the parameter axis of the distribution. Logarithmic recommended for wide parameter ranges. | |
|
| The vertical axis can be shown in volume or number distributions. Volume-weighted distributions recommended; number-weighted distributions can be used for samples with a narrow dispersity. | |
|
| maxIterations | If convergence has not been reached within this number of iterations, the optimization attempt is aborted. Larger values may allow complex calculations to finish successfully, but often nonconvergence can be traced back to poor initialization settings. Increasing this value increases the maximum possible calculation time. |
| compensationExponent | Adjusts internal weighting of scattering pattern contributions. Adjustment between 0.3 and 0.7 may lead to slight speed increases for some samples. | |
| eMin | Minimum uncertainty estimate in fraction of intensity. Default 0.01 sets the uncertainty value to be no less than 1% of the data intensity value. Can be increased or reduced based on best guess estimate for minimum inter-related data point uncertainty. A too low value may prevent reaching convergence. | |
Figure 3McSAS graphical output showing the best fit obtained using the MC method to a scattering pattern obtained from a mixture of dilute particles with certified diameter of 17 (2) nm and 89 (2) nm silica particles. The particle volume ratio of small to large particles is 19:1.
Figure 4McSAS graphical output showing the volume-weighted size distribution associated with the MC fit of dilute silica particles shown in Fig. 3 ▶.
Figure 5Best fit using a classical model (implemented in SASfit) to a scattering pattern obtained from packed silica spheres. Model uses a sphere form factor with a LMA-PY structure factor and a Gaussian size distribution.
Figure 6The best fit obtained using the MC method to a scattering pattern obtained from packed silica spheres. Model using a sphere form factor with a LMA-PY structure factor.
Figure 7McSAS graphical output panel showing volume-weighted size distribution associated with the MC fit of Fig. 6 ▶.