VESTA file formatting; Command line capabilities

[Jack Sundberg]

Hi all,

Two quick questions:

(1) Is there documentation on the formatting of *.vesta files? That is, descriptions for file descriptors like STRUC, CELLP, SHAPE, etc... and how to go about making a *.vesta file from scratch (rather than through the GUI or importing of another filetype)?

(2) Are there any current capabilities for scripting visualization of structures (on any OS)? Or possibly work being done towards Python API scripting of visualization?

Thanks in advance,

Jack

[Amund Raniseth]

Hi!

I still can't seem to find any documentation on what you too seem to have struggled with. Did you manage to find out anything?

Best regards

[Samuel Young]

I think users would benefit greatly from an API that allows one to script VESTA. Being able to integrate it into ASE/Pymatgen workflows would speed up exploratory analysis of structures because the default visualizers in those packages don't allow for some commonly used crystallographic visualization features (e.g., polyhedra).

I'm trying to examine the structures of ~160 perovskite structures, and have so far had to manually enable polyhedra/bond length parameters for each one. An API would be quite helpful.

Thanks,

-- Sam

[Lloyd Bumm]

I found a partial work around that avoids needing to recreate all the display settings. The details are a couple posts earlier. If you have a series of similar structures you want to view, you can create a .vesta file and them drop it into the directory for each structure in the series. That ports all the settings to the new structure. Just open the .vesta nd you have it. There are a few tricks in the set up. I am looking at volumetric data, which is automatically linked in the .vesta, however the structure data is embedded in the .vesta be default. You can make that linked, so the structure is pulled from the directory in which the .vest resides, the caveat is that the attributes for the atoms remain embedded in the .vesta. That's not a problem is they are the same for each structure in the series. The fix for that is re-linking the structure data, which recreates that.

You can learn a lot about the .vesta structure using a file compare tool and making small changes in the setting to see what is changed in the .vesta. That was my approach. You can also edit the linked filenames with a text editor, for example. 

I second Jacks request to allow VESTA to be scripted. Even a basic command line capability with standard i/o would be great. I am making some rudimentary animations. This would automate the open, export, close. operation. The parameters of the view could also be changed by modifying the .vesta in the program looping the script command.

--Lloyd

[samu...@umich.edu]

Oh my gosh, this is a lifesaver! Thanks so much!!!