# Open SourceMolecular Dynamics

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exercises:2017_uzh_cmest:stm

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# Simulation of STM images for a graphene nanoribbon adsorbed on a metallic substrate

In this exercise we are going to see how we can generate Scanning Tunneling Microscope (STM) images from simulations. While this is a more elaborate example where we need additional scripts and techniques, the basic idea is simple: Imagine a STM cantilever scanning the surface in the constant current mode, the current is then proportional to the electron density, which is something we get from our simulation (remember the cube files?). Therefore, all we have to do is to find an isosurface of the electron density and plot this isosurfaces z-coordinate.

This exercise is based on ideas and material by Daniele Passerone.

## Preparation

• On the server is a package for you to unpack: tar xf /…, afterwards you should get a number of files in your current directory.
• The scripts are contained in yet another python package: pip install –user https://github.com/ltalirz/asetk/archive/master.zip, and since you have setup the path variable in a previous exercise, you should now have the following commands available: