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Published: May 28 2014
Tags: geometry optimization
In this tutorial, you will learn how to optimize the internal coordinates of the central region in the most efficient way. The primary point to note is that this can be achieved in a single-step process, involving only the two-probe geometry (as opposed to extracting, separately optimizing, and then re-inserting the central region).
One of the most crucial aspects of an atomic-scale calculation is to set up the atomic coordinates properly. This is not as simple as just defining the basic geometry of the system you want to study (if you want a nanotube, naturally you have to insert a nanotube in the system) - one should also take care that the atoms are placed such that the total energy of the system is minimal. The process of finding this minimum, and the corresponding "optimized geometry", can be rather time-consuming, but is a necessary step in order to ensure the quality of the results.
To find the optimized geometry of a two-probe system has traditionally been a rather cumbersome task, involving many different steps, but as of ATK 11.2 this process has been made much easier.
Our test system will be a simple atomic chain of Li atoms, with a hydrogen molecule inserted in the middle. For details on how to set this system up, please refer to the basic ATK Tutorial for Device Configurations. For the purpose of this tutorial, you can just download a pre-defined script with the device geometry. Save the Python file, and drop it on the Viewer to verify that it looks correct.
In this approach for optimizing the two-probe geometry we are neglecting a few things: