Band Structure Sets with cp2k_bs2csv.py

[Brian Day]

Could anybody explain to me the difference between all of the different 'material.bs-setN.csv' files generated by the cp2k_bs2csv.py code?

My understanding is that there is typically one per K-point set, but I'm a bit confused as to how I should be plotting the csv files. Should I only be plotting set 1? Or should I be plotting all the sets in a concatenated fashion, or taking the range between the k-points of that set, etc.?

Any clarification would be hugely appreciated - Thanks!

-Brian

[Brian Day]

Answering my own question:

Each 'material.bs-setN.csv' file is the set of energies for all points between the corresponding set of k points, so in order to plot the full band structure between all k-point sets, each file needs to be loaded. 

One could make the argument for returning a single CSV file rather than multiple, but in the case of disjointed paths, distinct files is preferred. Hopefully this answers any questions future users might have.

-Brian

[Dmitry Ryndyk]

Dear all,

as far as I can see, the format of the output file is changed in the developing version (or maybe earlier).

The cp2k_bs2csv.py script does not work anymore.

Did somebody modify it?

Best wishes,

Dmitry

[Krack Matthias (PSI)]

Hi Dmitry

 

the BS output in the development version was changed by me. I have been working on a python script to plot band structures based on the new output, but this work is delayed.

 

Matthias

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[Tiziano Müller]

Dear Dmitry,

you can find an updated version of the cp2k_bs2csv.py in the
cp2k-output-tools project here:


https://github.com/cp2k/cp2k-output-tools/blob/develop/cp2k_output_tools/scripts/bandstructure.py

Installation via pip is best:

pip install cp2k-output-tools

It should then be available as cp2k_bs2csv
Depending on your system you may have to use `pip3` instead of `pip` to
use Python 3, or call `pip` with `--user`: `pip install --user
cp2k-output-tools`, and/or add the directory `$HOME/.local/bin` to your
`$PATH`.

Best regards,
Tiziano

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[Dmitry Ryndyk]

Dear Matthias and Tiziano,

thank you. I will have a look.

Dima

[Dmitry Ryndyk]

It is an old version in

https://github.com/cp2k/cp2k-output-tools/blob/develop/cp2k_output_tools
and does not work with new output .bs files.

That is what I asked.

So, what we plan to do?

Dima

[Tiziano Müller]

Hi Dima,

I've updated the script there to work with CP2K as on May 5th and there
were no changes to the relevant output since then as far as I see?

Can you please test whether it works and if not make a bugreport on
https://github.com/cp2k/cp2k-output-tools/issues ?

Best,
Tiziano

On 12/10/20 10:21 AM, 'Dmitry Ryndyk' via cp2k wrote:
> It is an old version in
> https://github.com/cp2k/cp2k-output-tools/blob/develop/cp2k_output_tools

> <https://github.com/cp2k/cp2k-output-tools/blob/develop/cp2k_output_tools/scripts/bandstructure.py>

> <https://groups.google.com/d/msgid/cp2k/817b82bf-95a0-4dd3-b6fc-0d1740eea246n%40googlegroups.com?utm_medium=email&utm_source=footer

> <https://groups.google.com/d/msgid/cp2k/817b82bf-95a0-4dd3-b6fc-0d1740eea246n%40googlegroups.com?utm_medium=email&utm_source=footer>>.
>
>
> --
> Tiziano Müller
> University of Zurich
> Department of Chemistry
> Winterthurerstrasse 190
> CH-8057 Zürich
>
> Tel: +41 44 63 54234

> www.chem.uzh.ch <http://www.chem.uzh.ch>
> tiziano...@chem.uzh.ch

>
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[Dmitry Ryndyk]

Sorry, I found changes now! Should work!

[Dmitry Ryndyk]

So. Finally, it really works.

But I was not able to find it quickly without your help. And the script in exercises is outdated.

I think it is a good idea to make tools like it more visible at cp2k.org.

Dima 

[Alexander Kramarenko]

Hello, Dmitry

Could you please provide the working script? or give an idea how you found a solution for the problem.

thank you in advance.

Best regards, Alexander 

[Dmitry Ryndyk]

Hi Alexander,

first of all install 

https://github.com/cp2k/cp2k-output-tools

it will transfer .bs file to .csv file ready for figure.

If you get .csv, I can try my second script to make a figure.

But you need to edit this script by hand, I hope to make better script later.

Ask me for details.

[Alexander Kramarenko]

Hi Dmitry

Thank you so much for your reply!

But the problem is that script from the link you provided doesn't work for me and i don't understand why.

it just does nothing. I thought you did some corrections in the code.   

[Dmitry Ryndyk]

If you write "cp2k_bs2csv" do you see:

$ cp2k_bs2csv

usage: cp2k_bs2csv [-h] [-p OUTPUT_PATTERN] <bandstructure-file>

cp2k_bs2csv: error: the following arguments are required: <bandstructure-file>

[Alexander Kramarenko]

Yeah! it works! i did some mistakes

thank you for your help

[Anjali ganai]

Dear all,

as far as I can see, the format of the output file is changed in the developing version (or maybe earlier).

The  https://github.com/ltalirz/cp2k-output-tools/blob/develop/cp2k_output_tools/scripts/bandstructure.py  script does not work for me now.

Can anyone suggest me something please? (.bs attached)

Best wishes,

Anjali

[Krack Matthias (PSI)]

Hi Anjali

 

You refer to a forked cp2k-output-tools repository which is not up-to-date. Try the original master https://github.com/cp2k/cp2k-output-tools instead of that fork.

 

Best

 

Matthias

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[Anjali ganai]

Thank you for the reply but I'm quite confused about which script you are talking of. I went to this page 

https://github.com/cp2k/cp2k-output-tools/tree/develop/cp2k_output_tools 

and I'm quite confused about which python script to use. Should I use cli.py or bandstructure_parser.py? Could you please guide me through this

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[Krack Matthias (PSI)]

You can use pip to install the cp2k-output-tools like the cp2k-input-tools: pip install cp2k-output-tools

Alternatively, you can run in the folder cp2k-output-tools “pip install .”

After a successful installation (note the requirements) the command “cp2k_bs2csv” should be available.

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[Anjali ganai]

Thank you very much. It worked.

Regards

Anjali