This repository contains the scripts and notebooks to reproduce the figures, simulations and numerical data shown in Real-space Imaging of Confined Magnetic Skyrmion Tubes by M. T. Birch, D. Cortés-Ortuño, L. A. Turnbull, M. N. Wilson, F. Groß, N. Träger, A. Laurenson, N. Bukin, S. H. Moody, M. Weigand, G. Schütz, H. Popescu, R. Fan, P. Steadman, J. A. T. Verezhak, G. Balakrishnan, J. C. Loudon, A. C. Twitchett-Harrison, O. Hovorka, H. Fangohr, F. Ogrin, J. Gräfe and P. D. Hatton.
Both simulation and experimental data analysis are performed using Python with the Matplotlib, Jupyter, Scipy, Numpy and h5py libraries.
Jupyter notebooks are provided to process the experimental data and reproduce the STXM, X-Ray Holography and LTEM images, which are shown as Figures 2, 3, 4 and 5 in the paper.
Simulation scripts are based on the finite difference micromagnetic code OOMMF with the extension to simulate DMI for materials with symmetry class T: [oommf-extension-dmi-t](https://github.com/joommf/oommf-extension-dmi-t)
The analysis of OOMMF's output files, which are in the `OMF` format, are processed using the [OOMMFPy](https://github.com/davidcortesortuno/oommfpy) library, which can calculate the topological charge in a 2D slice.
Three-dimensional visualisations of the magnetic states are performed using Paraview. In order to get VTK files for visualisation, convert the `OMF` files into `.vtk` using the `OOMMFPy` library.</span
