Quick Description: If we have two structures that we wish to compare, one method to use is to take a look at their corrugation. We can look both at the average height of each structure and how much that height varies (corrugation) for each structure. This gives us an idea of what they should appear as individually and relatively when we are using STM. Moreover, we can use the height information to set the tip-sample distances to be the same for between structures, comparing their STS measurements at various tip-sample distances. Keep in mind that an STS measurement at one height for one structure and at another height for the other structure is like "comparing apples and oranges" (as Prof. Bartels would say), so it's important to analyze in this manner that puts each structure in comparable states.
The Point: Comparing two structures using corrugation.
Prerequisites: Optimized jobs of each structures with WAVECAR files and completed STS calculations generated for both.
Notes: Although I discuss several ways of obtaining a simulated STM image, in this section, I describe everything in terms of using Jon's code because it outputs the necessary values that I want.
- We want to use the same scale for each job. Using Jon's ExampleSTM code, we can generate a simulated STM image for one structure. For example, here I have an image of a 2H MoS2 structure on Cu(111). At a certain tip-sample distance, this will output three relevant values for you: scale, lowest point, and highest point. You can think of the difference between the latter two values as your image corrugation.
- Repeat the same process for your second structure, in my case 1T MoS2 on Cu(111). Using the same scale value you just acquired, use this value instead when running "DispSTM" on your second structure. (Both simulated STM images should be generated with the same scale value.) This will move the tip to a location where it experiences a similar current/charge value from your system.
- If you take the average of the corrugation values from each system, you can obtain the average height of each system using the following equation.
- So now you can compare the heights and corrugations of each system at different tip height settings. Additionally, you can compare the difference that this makes in STS measurements. With Jon's ExampleIV Code, we can set the z values ourselves. Disregarding the offset we use in the above equation, we set the z value to be the height of the tip in the STM simulation. This requires the following change in the code.
- Now you can form a table for comparing tip height vs. structure vs. STS (bandgap).
Optional: You may consider using a "more realistic" STM tip by applying median and Gaussian filters to the isosurface data. This involves delving into the molXML code and editing idxTable. Also, you may find that your corrugation and height values become weird at a certain distance away from the surface. I'm still trying to work out what this means, but according to Profesor Bartels, "maybe at the point of inflection (where the first deriv changes sign) we run out of the accuracy of our method".
