File formats

A STEMsalabim simulation is set-up via input files and its results are stored in an output file. The file for configuring a simulation is described in detail at Parameter files. Here, we describe the format of the crystal file, i.e., the atomic information about the specimen, and the output file, in which the results are stored.

Crystal file format

The crystal file is expected to be in XYZ format.

  1. The first line contains the number of atoms.

  2. The second line contains the cell dimension in x,y,z direction as floating point numbers in units of nm, separated by a space. Optionally, it can contain the x, y, z dimensions in the .exyz format:

    Lattice="lx 0.0 0.0 0.0 ly 0.0 0.0 0.0 lz"
  3. The atomic information is given from the third line onwards, with each line corresponding to a single atom. Each line must have exactly 5 columns:

    • The atomic species as elemental abbreviation (e.g., Ga for gallium)
    • the x,y,z coordinates as floating point numbers in units of nm
    • the mean square displacement for the frozen lattice dislocations in units of \(nm^2\).
    • (optional) The id of the slice this atom belongs to. This can be used to do custom slicing.

Below is a very brief, artificial example (without custom slicing):

1.0 2.0 10.0
Ga  0.0  0.0   0.0   1e-5
P   0.2  0.1   0.0   2e-5
Ga  0.0  0.0   1.0   1e-5
P   1.2  0.1   0.0   2e-5
O   1.0  2.0  10.0   0.0


Atomic coordinates outside of the cell are periodically wrapped in x and y and clipped to the simulation box in z direction!

Output file format

All results of a STEMsalabim simulation are written to a binary NetCDF file. The NetCDF format is based on the Hierarchical Data Format and there are libraries to read the data for many programming languages.

The structure of NetCDF files is hierarchical and organized in groups. The following groups are written by STEMsalabim:


This group contains information about the program and the simulation, such as version, UUID and so on.


This group contains the atomic coordinates, species, displacements, radii, etc. for the complete crystal for each single calculated frozen lattice configuration, as well as for each calculated defocus value. The AMBER group content is compatible with the AMBER specifications. A STEMsalabim NetCDF file can be opened seamlessly with the Ovito crystal viewer.


All simulation parameters are collected in the params group as attributes.


This group contains the simulated ADF intensities, the coordinates of the electron probe beam during scanning, the detector angle grid that is used, and coordinates of the slices as used in the multi-slice algorithm.


This group contains the simulated CBED intensities, the coordinates of the electron probe beam during scanning, k-space grid, and coordinates of the slices as used in the multi-slice algorithm.

Reading NC Files

For a detailed view of the structure, we suggest using the ncdump utility: ncdump -h As the underlying file format of NetCDF is HDF5, you may use any other HDF5 viewer to have a look at the results.

There are NetCDF bindings for most popular programming languages.

  1. In MATLAB, we recommend using h5read() and the other HDF5 functions.
  2. For Python, use the netCDF4 module.