Not able to visualize atomic volumes

Bader charge density analysis

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silviob
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Joined: Sun Mar 14, 2021 10:03 pm

Not able to visualize atomic volumes

Post by silviob »

Hello everyone,

I'm performing some DFT calculation with vasp, regarding the bader analysis i didn't find any particular trouble and the code worked perfectly, thank you so much!
What i would like to do now is to visualize the atomic volumes obtained with VESTA, after different trials i didn't manage to correctly visualize the AtIndex.dat file generated: in particular i would like to superimpose the chgcar file and the AtIndex zero flux surfaces partitioning in a c-axis (001) visualization (2D).
The only kind of visualization i managed to obtain is, what it looks to be, a 2D visualization of the bader partitioning results, indexed as expected from the atoms order.
Any suggestion on this point would be really appreciated, aybe i'm not using the right visualization tool.
If it's not a problem could someone please help me to understand the physical difference between values reported as bader volumes and atomic volumes ?

Thanks in advance
graeme
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Re: Not able to visualize atomic volumes

Post by graeme »

Hi Silvio,

I don't have a good answer for you in regards to plotting the surfaces of the Bader volumes superimposed upon the charge density. I get what you are after, and I can see why you want to show it that way, but I just don't know of any existing software that allows for that. If you can get Vesta to show two charge densities at the same time, then maybe you show the regular charge density as a contour plot and an isosurface from the AtIndex.dat. But I'm guessing that's what you tried. Sorry I'm not more help.

The difference between the bader and atomic volumes is a subtle one. In our code, every charge density maximum will have an associated Bader volume. There are cases in which the charge density can be rough, such as in a near-vacuum region, or near atomic centers if the core charge is not well reproduced in the charge density file, or in very rare cases, true charge density maxima which are not at any atom. To help with these issues, we also define atomic volumes as the set of bader volumes which are nearest to each atom. Thus, there should always be one atomic volume for each atom, but there could be more Bader volumes. If there are, it is good to check to make sure there is not a problem with the calculation. Ideally the Bader volumes should be identical to the Atomic volumes and there should be one per atom, but things are not always ideal.

Graeme
silviob
Posts: 2
Joined: Sun Mar 14, 2021 10:03 pm

Re: Not able to visualize atomic volumes

Post by silviob »

Hi Graeme,

Thank you for the quick answer and for the clear explanation now i get the difference.
I'm going to try different softwares or maybe with a bunch of python scripting. If ill be able to find a solution i can post it here.

Silvio
songzj
Posts: 1
Joined: Sat Aug 14, 2021 1:41 pm

Re: Not able to visualize atomic volumes

Post by songzj »

Dear Professor,

What is the unit of the atomic volumes?







graeme wrote:
> Hi Silvio,
>
> I don't have a good answer for you in regards to plotting the surfaces of
> the Bader volumes superimposed upon the charge density. I get what you are
> after, and I can see why you want to show it that way, but I just don't
> know of any existing software that allows for that. If you can get Vesta
> to show two charge densities at the same time, then maybe you show the
> regular charge density as a contour plot and an isosurface from the
> AtIndex.dat. But I'm guessing that's what you tried. Sorry I'm not more
> help.
>
> The difference between the bader and atomic volumes is a subtle one. In
> our code, every charge density maximum will have an associated Bader
> volume. There are cases in which the charge density can be rough, such as
> in a near-vacuum region, or near atomic centers if the core charge is not
> well reproduced in the charge density file, or in very rare cases, true
> charge density maxima which are not at any atom. To help with these
> issues, we also define atomic volumes as the set of bader volumes which are
> nearest to each atom. Thus, there should always be one atomic volume for
> each atom, but there could be more Bader volumes. If there are, it is good
> to check to make sure there is not a problem with the calculation. Ideally
> the Bader volumes should be identical to the Atomic volumes and there
> should be one per atom, but things are not always ideal.
>
> Graeme
graeme
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Posts: 2037
Joined: Tue Apr 26, 2005 4:25 am
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Re: Not able to visualize atomic volumes

Post by graeme »

They should be in Ang^3
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