QSTEM

Quantitative TEM/STEM Simulations

Introduction

screenshots

Introduction

QSTEM is a suite of software for quantitative image simulation in electron microscopy, including model building and TEM/STEM/CBED image simulation.  The qstem package contains the following tools:

  • QSTEM: a user interface for setting up STEM/TEM/CBED simulationsimageSim
  • stem3: a multislice code for simulating TEM and STEM images
  • ImageSim: although integral part of QSTEM, this program can also be called independently and may be used to apply various aberrations to complex-valued wave functions. These wave functions can  be the result of a QSTEM simulation or a focal series reconstruction.
  • ShowImage: a simple tool for displaying .img images.
  • QMB: the QSTEM Model Builder. This GUI-based tool lets you build super structures containing arbitrarily many crystalline grains. It also lets you load images (.dm3, .img, .tif, .jpg, etc.) and build the atomic model to match the atomic columns in the image.
  • Convert2CFG: this little tool converts crystal
    structure data in .xtl or .qmbxyz format to the .cfg format that can
  • be read by qstem and the other tools.
  • VirtualGoniometer: a tool for converting unit cell parameters to the structure matrix and then finding the required tilt angles to tilt to a specific zone axis.
  • GBMaker: a command line tool for constructing arbitrary super structure containing crystalline and amorphous phases.

 

QSTEM has been designed with the following in mind:

  1. Potential slicing should work for arbitrary samples (e.g. interfaces, defects, not just perfect crystals in zone axis).
  2. It should be possible to compute images for arbitrary orientations, not just low-index zone axes of single crystals.
  3. Atomic scattering factors should be accurate up to the large angles needed for STEM simulations.
  4. The simulation should be quantitative.
  5. Accuracy over speed, but still try to be as fast as possible.
  6. Allow very large simulations to be run on any computer.

STEM_animationQSTEM was initially written to do HAADF-/ADF-/ABF-STEM simulations, but also offers the possibility to do TEM and CBED calculations, all using the multislice algorithm. Much of how the STEM simulation works, and the particular strengths of the simulation software provided on this website is described in Christoph Koch’s PhD thesis.

For those interested in using this software, there is a short introduction and a tutorial on running the GUI. This tutorial describes mainly how to simulate STEM images. For TEM images you should turn off TDS when simulating electron exit face wave functions and use the ImageSim tool to compute images, focal series, or thickness-defocus maps (see this tutorial).

Since this code was originally intended for the simulation of STEM images of large super-cells (e.g. dislocations, interfaces), it uses a simple version of the .cfg format as it is used by the AtomEye atomistic configuration viewing program for defining unit cell and super-cell atom positions. The software recognizes no other format at the moment, but the convert2cfg tool can help you in converting your non-cfg structures into cfg.

Images generated by QSTEM will be in a binary format, detailed here. They can be displayed using the showimage tool included in QSTEM.  They can also be imported into Gatan Digitalmicrograph using the script readImg.s.

In case any publications result from simulations done using this software, please reference Christoph’s dissertation (until we find time for a regular publication).