Tutorials

In response to user feedback about data analysis needs, we are pleased to offer tutorials for several software packages developed at the SNS and HFIR that are available for data modeling, analysis, and visualization. Tutorials will be provided for Mantid, Mantid with Python, SpinWaveGenie, SASView, and Molecular Dynamics Force Field Refinements for Quasi-Elastic Neutron Scattering on Saturday and Sunday, October 24-25, 2015. Please register for the course when making your user meeting registration. Class sizes are limited to fifteen participants, and registration will be first-come, first-serve.



An Introduction to Mantid using MantidPlot

1 day course October 24, 2015

Instructors: Andrei Savici and Wendou Zhou

Class limit: 15 people

This course will introduce the Mantid Framework, for reducing and analyzing neutron data, using the MantidPlot interface. This course will include loading and manipulating neutron data, using the plotting and fitting tools, and will touch on using the live data analysis features and the multi-dimensional workspaces. No familiarity with Mantid is assumed. The student will need to bring their laptop so they can access analysis.sns.gov to run the exercises.



Mantid and Python

1 Day Course, October 25, 2015

Instructors: Andrei Savici and Garrett Granroth

Class limit: 15 people

Mantid is a framework for interacting with neutron data that can utilized from many interfaces. One extremely powerful interface, due to its extensibility, is through the Python scripting language. This course will introduce interacting with Mantid through Python. A brief introduction to scientific programming in Python will be provided, but some familiarity with Python and numpy is recommended to get the most out of the course1. Also the introduction to Mantid is a prerequisite to this course. The course will be taught as a series of exercises. Some will use the Python interpreter bundled in the MantidPlot interface and others will use a standard command line interface. The student will need to bring their laptop so they can access analysis.sns.gov to run the exercises. The exercises will include examples of scripting repetitive tasks, working with sample environment logs, and extracting workspaces to leverage all the power of Python and Mantid together.


[1] There are many resourced for learning python for scientific computing. Here are a couple of interfaces. A brief introduction is to work through software carpentry’s introduction at http://swcarpentry.github.io/python-novice-inflammation/reference.html a more in depth tutorial can be found at http://scipy-lectures.github.io/index.html

An Introduction to SpinWaveGenie

1/2 day course, Sunday October 25, 2015

Instructors: Steven Hahn and (TBD).

Neutron Data Analysis and Visualization Division, Oak Ridge National Laboratory, USA

Class limit: 15 people

SpinWaveGenie is a C++ software library that simplifies the modeling of collective spin wave excitations, allowing an instrument user to analyze neutron scattering data with sophisticated models faster and more efficiently. Furthermore, one can convolute the four-dimensional scattering function S(Q,E) with the instrumental resolution function and magnetic form factor to directly compare and fit the calculation to experimental measurements. The course will be taught as a series of exercises demonstrating calculations of toy models and real materials. The topics of visualization of S(Q,E) with matplotlib and ParaView and extending SpinWaveGenie with new custom interactions will also be covered. The student will need to bring a laptop to access the computers at http://analysis.sns.gov via ThinLinc to perform the exercises. Some familiarity with C++11 and Python (optional) is recommended to get the most out of the course.



SasView Tutorial

1/2 day course, Sunday October 25, 2015

Instructor: Mathieu Doucet

Neutron Data Analysis and Visualization Division, Oak Ridge National Laboratory, USA

Class limit: 15 people

SasView is an open source project to provide data analysis for small-angle scattering. SasView reads most common 1D data formats and reads reduced 2D formats produced by various reduction packages including Mantid. SasView provides several tools for modeling SANS data. About 90 models are available to fit 1D data. Several of those models can also be used to analyze non-azimuthally symmetric 2D data. Wedges tools can also be applied to 2D data to compute I(Q). Although SasView has mostly been focused on modeling, it also offers other tools such as a P(r) calculator, an SLD calculator and image processing tools. In this tutorial, we will look at the main features of SasView and highlight some of the recent improvements of version 3.1. Participants will need to bring a laptop to run exercises.



Molecular dynamics force-field refinement against quasi elastic neutron scattering data

1/2 day course, Sunday October 25, 2015

Instructor: Jose M. Borreguero Calvo

Neutron Data Analysis and Visualization Division, Oak Ridge National Laboratory, USA

Class limit: 15 people

Quasi elastic neutron scattering (QENS) is one of the few experimental techniques probing dynamics in length and time scales that are the realm of full-atom molecular dynamics (MD) simulations. This intersection enables extension of current force-field fitting methods that use equilibrium measurements to new methods fitting against dynamical data. In the tutorial we will learn how to: (i) run a set of MD simulations; (ii) derive QENS spectra from the atomic trajectories that can be compared to experiment; and (iii) refine a critical parameter of the MD force-field to obtain optimal comparison between simulated and experimental QENS spectra. We will showcase the difficulties inherent to this type of fitting problem, discussing in detail the limitations arising from an incomplete sampling of phase space by the simulation, and how this problem can be overcome. Our hands-on application will consist of obtaining the activation energy for methyl rotations in the octa-methyl polyhedral oligomeric silsesquioxane molecule. Students will need to bring a laptop to perform the exercises.