From Motofit

Motofit and Reflectometry(scattering) resources Wiki.

This Wiki describes the use of Motofit to analyse X-ray and neutron reflectometry data, although there is some information on other scattering techniques.

Contents 1 Motofit 1.1 Features 1.2 Software available 1.3 Download address 1.4 Publications 1.5 Screenshots 1.6 Acknowledging Motofit 1.7 Benchmarking Motofit 1.8 Motofit manual 1.9 Frequently asked questions 1.10 Other scattering resources

Motofit

Motofit is a package that aids the simultaneous least squares fitting of multiple-contrast specular X-ray and neutron reflectivity data, using an Abeles Matrix formalism or Parratts recursion formula. Motofit provides robust and fast optimisation, with a choice between Genetic Optimization (Differential Evolution) and Levenberg-Marquardt.

The aim is to provide maximal functionality, with easiest interaction. Limit the time between collection and publication.

Motofit is licensed using the GNU General Public Licence.

It works within the analysis package IGOR Pro (Wavemetrics, OR). You don't need to purchase IGOR in order to use the functions, a free demo version is available from their website. Motofit will work just as well in the demo version, as the full version.

The development of the Motofit package has been sponsored by the Australian Nuclear Science and Technology Organisation (ANSTO).

Features

• Fits neutron and X-ray reflectivity data using Parratt recursion or Abeles matrix.
• Easy co-refinement of multiple contrast reflectometry data (X-rays and neutrons)
• Genetic Algorithm or Levenberg-Marquardt for minimisation
• Point by point Resolution smearing, roughness (Nevot+Croce) and background included
• Fitting as log R vs Q, RQ4 vs Q and R vs Q.
• Fit to normalised Fresnel Reflectivities.
• Absorption effects through imaginary scattering length density
• Publication quality graphs, with no further manipulation required
• Provides a graphical interface to assist fitting
• Fitting with complex interparameter constraints
• Fitting of multilayer stacks
• Estimation of layer thicknesses from Fourier transform of datasets
• Estimation of layer thicknesses from fringe spacing
• Simultaneous co-refinement of multiple contrast datasets, with arbitrary linkages.
• Analytic scattering length density profiles (user specified functional form).
• Fits as many layers as you like (or can fit on the screen).
• Batch fitting of multiple datasets, e.g. Kinetic data.
• 3D data plotting with OpenGL
• OPEN SOURCE CODE

Motofit isn't a black box, you find something you don't like, you can change it (within the license conditions)

Software available

1. Motofit - this is when you want to parametrise solvent (subphase) penetration in your layers.
2. Motofit_imag - this version uses imaginary scattering length densities, to account for absorption effects. Unfortunately solvent penetration is not available in this version. The coefficient files used in Motofit will not work in Motofit_imag.
3. lsGex - this file fits a generalised distribution of exponentials to dynamic light scattering data.
4. Gencurvefit is a plugin for IGOR Pro. It is a pre-compiled plugin, which allows anyone to use genetic optimisation to fit any user-defined fitfunction. It is designed to complement and follow the same syntax as IGOR's curvefit operation.

Please note that the Motofit package now installs Gencurvefit.xop and Abeles.xop when you use the Win32/Mac installer programs

Download address

You can download all the Motofit software, and manuals from the sourceforge website.

Publications

A list of publications that have used the Motofit program to analyse data.

Screenshots

Graphical examples of the Motofit program. All graphical output is fully customisable, and publication quality. Jump straight from collection to publication: no messy, timewasting replotting via Excel.

Acknowledging Motofit

If you use Motofit to analyse reflectometry data, please cite Motofit in the references. This is so I can justify spending the time writing it to my bosses. Cite:

Nelson, A. (2006). "Co-refinement of multiple contrast neutron / X-ray reflectivity data using MOTOFIT." Journal of Applied Crystallography 39: 273-276.

doi:10.1107/S0021889806005073

Benchmarking Motofit

Motofit has been benchmarked against other reflectometry software, to investigate it's accuracy.

Motofit manual

You can examine the Motofit manual on the wiki.

Frequently asked questions

Please read the list of frequently asked questions (FAQ) before emailing for support.

Other scattering resources

A list of other reflectivity software:

• http://www.ill.fr/lss/data_treatment/REF_analysis.html

Some tutorials:

• http://www.mrl.ucsb.edu/~pynn/
• http://users.ox.ac.uk/~dgbuck/people/bucknall/research/NR.htm
• http://en.wikipedia.org/wiki/Neutron_reflectometry
• http://en.wikipedia.org/wiki/X-ray_reflectivity
• http://en.wikipedia.org/wiki/Abeles_matrix_formalism

Other tools for IGOR users

• http://wavemetrics.com
• http://www.wavemetrics.com/users/tools.htm
• http://www.igorexchange.com

An expanding list of other scattering resources.