AdvancedPhotonSource/GSAS-II

GSAS-II Fourier map use/export confusing

Opened this issue · 1 comments

briantoby commented

(from user) I was recently stumped when someone here recently asked me to help extract Fourier electron difference maps from a GSAS-II X-ray fit.

The student claimed it was not possible. Some people online seem to feel the same:

https://www.researchgate.net/post/How_to_generate_electron_density_map_in_GSAS_II

https://www.researchgate.net/post/How_to_generate_electron_density_map_in_GSAS_II_software

Within the GUI, the setup and menu items are rather clear - and it's discussed tangentially in some tutorials, for example -- Charge Flipping tutorial:

Nevertheless, it took me some time to solve this for the student.

I think the confusion is twofold:

  1. In the GSAS-II structure viewing window, immediately after doing Compute/Fourier map, you don’t see much - maybe a green dot. But the Contour level slider option in Draw Options tab (described in the tutorial) has vanished from the menu in a past update. So it's not immediately clear now how to see anything in the structure viewing window

  2. TOPAS and FullProf users are accustomed to an *.FCF type map export file, for which one needs to import and compute the Fourier map in widely used software like VESTA. Confusingly, VESTA lets you equally import and “compute” GSAS-II exported Fox type *.GRD files. But the result is of course nonsense. Instead, there is a different second way to open and view these files in VESTA. It took me some time to review file formats to understand the problem. That might be a bit much for the causal user.

In the end - I proved to this student here that it works, by fitting a quick recent LaB6 lab-XRD scans without the B sites, and showing that they are in fact clearly visible (say with VESTA) when the *.GRD file is correctly exported and viewed.

briantoby commented
  • Need a *.FCF map exporter
  • Perhaps a small pop-up window with simple map controls might be useful when a map is present and the openGL window is selected
  • Think through the workflow a bit -- perhaps after computing a map, the data window tab should switch to Atoms so that the map is visible