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

Post by skm »

HI
can any one help how to do the following?

1. I have a hybrid supercell strucuture. I have done bader files written ACF, BVF and Atomic volumes files. Also did '-p atom_index' tag with "CHGCAR -ref CHGCAR_sum". What i wish to plot is the 3D picture view of Bader volume boundaries, where the division of one atom with another is demarked with Zero flux region, as per definition.


A) PLease let me know which output file will give me such data to plot this 3D figure?
B) From this plot, can I pickup only the data that correspond a small part or slab of the cell? That means How to know from the data files, that which correspond to which atom?
C) If i know how the data files are configured with their corresponding unit or definition of each values, would help me picking up desired data and then plot only such sliced picture.

May please help me, and thanks in advance.

Regards
skm

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

Post by graeme »

The -p atom_index tag will give you a CHGCAR-like file with an integer indicating the locations of the atomic volumes. You can use any visualizer of CHGCAR files to see the surfaces between the atomic volumes. Vesta is a good option. I don't understand questions B or C; we provide the partitioning of space between the atoms according to the Bader definition, what you do with it is up to you.

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

Post by skm »

Thank you Dr Graeme.

My query regarding B and C are summarised as below:

May I know how the data in the output file you mentioned as "....a CHGCAR-like file with an integer indicating the locations of the atomic volumes..."?

As i wish to draw the 3D contour plot (for only a part of the crystal- i.e. say a small slab from big crystal) using these above data of bader volumes Boundaries. So, if i know how these data is arranged and if i can segregate the data according to the desired atoms in that part slab, then i can only plot that part.

Kindly help in understanding the output file.

Regards
SKM

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

Post by graeme »

If you use the -p atom_index flag, you will get a CHGCAR-like with integers indicating the locations of the atomic volumes. So then if you want to see the spatial location of the Bader volume around atom 1, you can load this file in a viewer and set your min and max contour values to only include the number 1.

An alternative methods is to use the -p sel_atom which will print a file which has charge density values only in the Bader volume of the selected atom. Then you can use a visualizer and plot a contour above a low value of the charge density.

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 »

Thank you Dr Graeme.
This is quite interesting.

1. Referring to your reply " you can load this file in a viewer and set your min and max contour values to only include the number 1."
When a checked the resulted file from the command 'bader -p atom_index CHGCAR -ref CHGCAR_sum'
i.e this 'AtIndex.dat' file. But I cannot see which values are related to which atom. by the way is this you were referring to, for the above reply?

2. Also, referring to the following commands:

[ -p all_atom | all_bader ]
[ -p sel_atom | sel_bader ] [volume list or range ]
[ -p sum_atom | sum_bader ] [ volume list or range ]
[ -p atom_index | bader_index ]

Kindly give an example command for each above how to select a list of specific atoms?
what is the volume list or range, means?

This might help is isolating the data we need to focus on.
Regards

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

Post by graeme »

The AtIndex.dat file will contain an integer for each grid point indicating the atom to which that grid point belongs. If you plot the region containing the value 1, that is the region associated with atom 1.

Another way to plot that volume is to use the "-p sel_atom 1" which will give you a CHGCAR-like file containing the charge density only in the Bader volume around atom 1. If you plot that using an isosurface with a charge density value close to zero, you will see the volume around atom 1. Obviously you can select any atom in this method, or a combination of atoms using the related flags.

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 »

Thank you Dr Graeme.

i sure try the method and get back if there are any issues.

Meanwhile kindly let me have your response on the 2nd question, i asked.

Regards
SKM

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

Post by graeme »

you can do:
-p sel_atom 1,2,3
or
-p sel_atom 1-3
...
the term 'volume' means an atomic volume or a Bader volume. If you have core charge included, these should typically be identical.

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

Post by skm »

Fantastic Dr Graeme.

I will try my best to work on it :)

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 »

Dear Dr Graeme

1. i run the command as
bader -p sel_bader 1-3 CHGCAR -ref CHGCAR_sum

generated the files as below. And not able to open them, neither able to change its name.
147940795 Jan 22 18:34 '('$'\020''>'$'\001'
4524 Jan 22 18:34 ACF.dat
113895 Jan 22 18:34 AVF.dat
1670777 Jan 22 18:34 BCF.dat
147940795 Jan 22 18:28 '('$'\360\020\002'

2. If i run the command, as
bader -p sel_bader 1,2,3 CHGCAR -ref CHGCAR_sum

GRID BASED BADER ANALYSIS (Version 1.03 11/13/17)
1,2,3 does not exist

gives above error.

May kindly suggest.

Regards

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

Post by graeme »

Something is not right. If you post your CHGCAR and CHGCAR_sum files, I'll take a look. There does seem to be a problem with our code - it should not be printing files with strange file names.

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

Post by skm »

Dr Graeme,

i have attached the two files you asked for, in .tar file.

Regards
Attachments
bader.tar
(288.43 MiB) Downloaded 217 times

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

Post by graeme »

I ran the following:

bader CHGCAR -ref CHGCAR_sum -p sum_atom 1

and the code prints an output file called BvAt_summed.dat, which contains the charge density only in the Bader volume around Atom 1. I read this as a CHGCAR file into VESTA, and you can then see the Bader volume around atom 1 (attached).
Screen Shot 2020-01-23 at  10.34.52 AM.png
Screen Shot 2020-01-23 at 10.34.52 AM.png (218.71 KiB) Viewed 5936 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 »

Dear Dr Graeme

sorry to say, what i asked was different.
the 'sel_bader' or 'sel_atom' tags are not working as expected.

If i use the command
bader-v1-0 CHGCAR -ref CHGCAR_sum -p sel_bader 1-3

its giving the output file as
147940795 Jan 24 18:53 '(@'$'\323\002'

If i use
bader CHGCAR -ref CHGCAR_sum -p sel_bader 1,2,3

it says,
GRID BASED BADER ANALYSIS (Version 1.03 11/13/17)
Option "1,2,3" is not valid

Usage:
bader [ -c bader | voronoi ]
[ -n bader | voronoi ]
-----
-----

Then i changed the command without using 'comma' in between
then it accepts the command, but the output again a weird file name.

bader-v1-0 CHGCAR -ref CHGCAR_sum -p sel_bader 1 2 3

the outputfile name again as
147940795 Jan 24 19:00 '8@'$'\276\002'

Hope you got my query.

Regards

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

Post by graeme »

I get it. I was responding to what 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.

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