OptimizeDeviceConfiguration

[hendchem2024]

I hope to find some help in understanding this part of the "OptimizeDeviceConfiguration" block mentioned in the QATK tutorials .So that I can do the geometric optimization of two-probe system.
Does the " the width of the optimization region " mentioned in the tutorial description refer to the " the optimization region length " mentioned in the illustration within the tutorial, as shown in the screenshot attached to the question for further clarification?
Here is the link to that section of the tutorials for further explanation.

https://docs.quantumatk.com/tutorials/optimize_device_configuration/optimize_device_configuration.html

[Anders Blom]

The optimization region is the part INSIDE the dashed line; the part outside that line cannot be moved, it has to remain exactly the same as the electrode. If you compare your device with the tutorial you see that the example has many more layers inside the scattering region - those are the ones which are optimized.

[hendchem2024]

I would like to thank you for your interest in providing assistance. However, my question is: Is 'the optimization region length' the same as 'the width of the optimization region'?

[Troels-Markussen]

Yes, the 'width of the optimization region' is meant as the same as the 'Optimization region length'. Only the atoms inside this optimization region, defined by the 'Optimization region length' and 'Optimization region center' will be relaxed. This is indicated by the red box in this image https://docs.quantumatk.com/_images/before_after_default.png from the tutorial.

[hendchem2024]

Thank you for your interest in providing assistance with my study. I am currently facing a challenge regarding the optimization of the organic molecule situated between the gold electrodes.

The molecule's length is 12 angstroms. When using the OptimizeDeviceConfiguration block, I have observed that if I set the "optimization region length" above 10 angstroms, a break appears between the molecule and the electrode, as shown in the attached image (2a). I tested various settings between 10 and 30 angstroms, and consistently encountered this issue. However, when I set the "optimization region length" to exactly 10 angstroms, no break occurred, as illustrated in the attached image (2b).

I would appreciate any insights you might have regarding this behavior.