Atomic boundary trace or contours in a slice of a super-cell

Bader charge density analysis

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skm
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Joined: Thu Nov 28, 2019 12:26 pm

Re: Atomic boundary trace or contours in a slice of a super-cell

Post by skm »

Dr Graeme,

could anything done on this issue to update the code? i am waiting for this please.

Or please tell me if there is any alternative to calculate and draw contours for Zero flux region in the crystal-hybrid for the selected atoms (to form a plane in crystal)

Regards

graeme
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Re: Atomic boundary trace or contours in a slice of a super-cell

Post by graeme »

I'm just not sure what you are asking for. I explained how to write the charge density in a Bader volume around a single atom. If you want to see a contour plot of the charge density inside that sphere, you can do that with a visualizer (see attached). But I don't really understand the words "draw contours for Zero flux region".
Screen Shot 2020-02-06 at  3.13.50 PM.png
Screen Shot 2020-02-06 at 3.13.50 PM.png (414.91 KiB) Viewed 1885 times

skm
Posts: 15
Joined: Thu Nov 28, 2019 12:26 pm

Re: Atomic boundary trace or contours in a slice of a super-cell

Post by skm »

Dr Graeme,

sorry for troubling you.
May be i could not ask in clear terminology.

1. First thing i am asking about update of code as per your reply to my query dated - Fri Jan 24, 2020 7:23 pm. To which you replied on Sat Jan 25, 2020 3:51 am. that "....I thought was the larger question about how to plot a Bader volume. But yes, I see that we do have a bug in the code and I will try to fix it as soon as I can."

So, my point is if i am able to run the command for the 'sel_bader' or 'sel_atom' tags for selected group of atoms, successfully, without getting weird file names as output. then i think the issue is resolved.

2. If that code updating, takes time, i am asking alternative way, if any, to get the Bader volumes of all selected atoms. In my system, i have to get the Bader volumes for about 15 atoms selected from a total of 500 atoms. So, the above code really helps.

And, what i meant "Zero flux region" is nothing but Bader volume. As by definition (as i understand), wherever there is lowest or almost Zero electron density (Zero-flux density) in a molecule/compound, that region in 3D space is the Bader volume. Correct me if my understanding is wrong.

Kind Regards

graeme
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Re: Atomic boundary trace or contours in a slice of a super-cell

Post by graeme »

I've updated the code to v1.04 with a bug fix for printing the Bader volumes.

skm
Posts: 15
Joined: Thu Nov 28, 2019 12:26 pm

Re: Atomic boundary trace or contours in a slice of a super-cell

Post by skm »

Thank you Dr Graeme.

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