Tsim documentation

Welcome! This is the documentation of the Tsim toolbox for MATLAB®.

Tsim lets you simulate and fit spin-polarised triplet spectra recorded with time-resolved electron paramagnetic resonance (TREPR) spectroscopy. For simulation capabilities, it relies on the well-proven EasySpin toolbox, fitting is performed using the functionality provided by the MATLAB® Optimization Toolbox™.

Key to Tsim is a fully reproducible and documented workflow resulting in well-formatted reports as well as a command-line interface (CLI) guiding the user through the process of simulating and fitting the data. Thus, even Bachelor students with next to no prior knowledge of EPR spectroscopy and spectral simulations can get sensible results within reasonable time frame and presented in a form that makes life easier for both, them and their supervisors.

Note

If using this program leads to a publication, please mention it in the methods section and cite the following reference:

Deborah L. Meyer, Florian Lombeck, Sven Huettner, Michael Sommer, Till Biskup
Direct S0→T Excitation of a Conjugated Polymer Repeat Unit: Unusual Spin-Forbidden Transitions Probed by Time-Resolved Electron Paramagnetic Resonance Spectroscopy

Features

  • Comfortable command-line interface (CLI) for fit and simulation

  • Modular design

  • Reproducibility: all routines operate on datasets

  • Support for different input file formats

  • Integrated help

  • Automatically generated reports: well-formatted presentation of results

  • Complete simulation and fit history

Where to start?

After installing the toolbox, the best bet is to start MATLAB® and fire up Tsim by simply typing Tsim into the command line and hit “enter”. The Tsim CLI should guide you through all the necessary steps.

Installation

The Tsim toolbox for MATLAB® comes with a dedicated installer. Therefore, it is highly recommended to use this installer to get a properly working installation of the Tsim toolbox.

  • Download the source code (from GitHub).

  • Start MATLAB®

  • Change to the folder you’ve downloaded (and unpacked) the source code to

  • Change to the ‘internal’ subdirectory

  • Call the TsimInstall function

This will add all necessary (and only the necessary) folders to the MATLAB® path and place configuration and templates in their respective folders in your user’s home directory.

Warning

If you don’t use the installer provided with the Tsim toolbox, but simply add the Tsim directory and all subdirectories to the MATLAB® path, you will most certainly run into trouble, as the .git directory contains all sorts of files that you don’t want to be added to the MATLAB® path.

Prerequisites

License

The toolbox is distributed under the GNU Lesser General Public License (LGPL) as published by the Free Software Foundation.

This ensures both, free availability in source-code form and compatibility with the (closed-source and commercial) Matlab® environment.

Indices and tables