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OpenChemistry / avogadrolibs

Avogadro libraries provide 3D rendering, visualization, analysis and data processing useful in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
https://two.avogadro.cc/
BSD 3-Clause "New" or "Revised" License
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Opening a VASP CHGCAR file #422

Open alejandrogallo opened 5 years ago

alejandrogallo commented 5 years ago

I wish avogadro could open vasp CHGCAR files, which are volumetric data files. I could work on this, do you have already a .cube format reader and renderer?

welcome[bot] commented 5 years ago

Thanks for opening your first issue here! Please try to include example files and screenshots if possible. If you're looking for support, please post on our forum: https://discuss.avogadro.cc/

cryos commented 5 years ago

We do already have a cube file reader, I would be happy to help you as you develop CHGCAR, we have some VASP readers already.

alejandrogallo commented 5 years ago

Perfect, next week I'll be busy but the week after I'll set out to do it, since there is already a poscar parser and a cube parser, it should be fairly easy to adapt the chgcar parser.

I'm relatively new to avogadro, and I'm used to vesta, and there I can open a .cube file or a CHGCAR for that matter just doing

vesta file.cube

I'm curious how do I do this in avogadro, I tried

./avogadroapp/bin/avogadro2 file.cube

but it did not plot the volumetric data, I'm not sure I'm doing everything correctly. I could compile avogadro and everything with cmake, you have set up a nice building setup, I have to say.

Thanks!

ghutchis commented 5 years ago

Since I use a Mac, I haven't checked the command-line method for opening files. When you add a filename to the command line does it open the structure at least?

alejandrogallo commented 5 years ago

Yes, it does open it, when I do

avogadro molecule.cml

or even with POSCAR

avogadro POSCAR

it works perfectly. However for instance for .cube files it does not work. I think a large fraction of the Quantum chemistry community would like this to be the behaviour, since it is kind of a de facto standard of doing things.

But maybe I'm doing something wrong.

cryos commented 5 years ago

We just haven't added default code to visualize volumetric data, I think this could use some improvement. The cube data is loaded, you need to create a surface. I don't spend a lot of time thinking about cubes, but agree it would be good to show a surface by default whether opened from the command line of the GUI.

You need to create a surface from the dialog in the extensions menu.