[yt-users] Import of crystallographic charge density data

[Nathan Goldbaum]

Hi Matthew,

First this is the first I've heard of anyone using yt to look at
crystallagraphic charge density data, so I'm glad you were able to get as
far as you were.

Right now yt is mostly used by astrophysicists and there are still plenty
of places where we make assumptions that are only really valid for
astrophysics simulation data. We have long-term goals to improve this
situation. Getting input on places where yt makes poor assumptions for data
from new domains is very valuable for informing our long-term plans for yt
development, so thank you for writing in :)

On Mon, Mar 27, 2017 at 5:50 PM, Matthew Horton <mkhorton at lbl.gov> wrote:

> Hello all,
>
> I’m a new user to yt looking for some general guidance.
>
> 1. I have files describing the charge density in a crystal (CHGCAR files
> for any DFT/VASP users on the mailing list). I can import these with yt as
> generic (periodic) unigrid data, however the axes are not always
> orthogonal… In cubic crystals, `yt.load_uniform_grid` works perfectly, but
> in some crystals this would give a distorted visualization. What would be
> the best way to import this kind of data?
>

Right now yt only supports periodic and isolated boundary conditions.
Adding support for additional boundary conditions is a longstanding issue,
but most of the time we get requests to add e.g. reflecting, inflow, or
diode boundary conditions, not what you're asking about here.

Unfortunately I'm not terribly familiar with crystallography (the last I
thought about this was in a solid state physics course I took in undergrad)
so it would help if you can give a little bit more detail about what sort
of boundary conditions you need.

Unfortunately it's not terribly easy right now to add new boundary
conditions, so it might take some work to get yt fully working for
non-cubic crystal structures. I don't think anyone is working on making it
easier to add new boundary conditions but it's definitely on our long-term
roadmap. If you'd like to work on this I'd be happy to chat further about
what needs to be done in terms of code changes to get this working.

2. Regarding units, the units in my file are nominally fractional electrons
> per grid cell volume, e/Angstrom^3 … importing into yt as a density field,
> what units should I use? Would be good to keep the data in its natural
> units, rather than converting to SI/cgs, because they’d be very very small
> floats otherwise.


> I tried 'unit_system = yt.UnitSystem('custom', 'Angstrom', 'g', 's’)' and
> this works as expected for the length units in my plots, but how do I set
> the custom Charge unit? What ‘units’ string would I then use for the
> density field? It doesn’t seem to want to accept ‘Angstrom’, ‘C’ etc.
>

I *think* this will work:

us = UnitSystem('custom', 'angstrom', 'me', 's',
current_mks_unit='1.6e-19*A')

Here 'me' is the electron mass.


>
> Many thanks for any help!
>
> Best regards,
>
> Matthew
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