Visualization of crystals and results

Now that our simulation finished successfully, we can continue with visualizing the results.

Visualize the supercell with Ovito

The STEMsalabim output files (somewhat) comply with the AMBER specifications to visualize the specimen structure. However, all the dimensions and variables of AMBER live within the NetCDF group /AMBER in the NC file. This means that STEMsalabim output files will not be compatible to visualization programs requiring the pure AMBER specs!

However, the authors of the excellent cross-platform Ovito software, which is a visualization program for atomic structures (and much more), have added support for the /AMBER sub-group, so that STEMsalabim NetCDF result files can be visualized seamlessly in Ovito.

What you will see is the atomic structure of the input specimen. In addition to the positional coordinates of each atom, you find the mean square displacement (msd), the slice ID (slice), the equilibrium coordinates (lattice_coordinates), elements (elements) and atomic radii (radii) as variables. Each frozen lattice configuration is one frame in the AMBER specs, so you can see the atoms wiggling around if you use the frame slider of ovito.

Generate an ADF STEM image

In the examples/Si_001 folder you will find the two files make_haadf.m and Both extract an HAADF image from the simulated file. Please have a look at the code to get an idea of how to work with the NetCDF result files.

  • MATLAB® uses HDF5 for its .mat format for a couple of versions now, and is therefore perfectly capable of reading STEMsalabim result files. For quick analysis and image generation is a great tool.
  • Python with the NetCDF4 module is also a great tool to analyze and visualize STEMsalabim result files, especially combined with numerical libraries such as numpy or pandas.

What now?

You have now completed your first simulation and looked at some of its results. In order to use STEMsalabim for your research you should dig deeper into this documentation and read the following documents: