[CP2K-user] [CP2K:17236] Re: Band Structure Sets with cp2k_bs2csv.py

Anjali ganai jk831183 at gmail.com
Tue Jun 28 05:58:34 UTC 2022
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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

On Wednesday, March 17, 2021 at 6:27:52 PM UTC+5:30 king... at gmail.com wrote:

> Yeah! it works! i did some mistakes
> thank you for your help
>
> On Wednesday, 17 March 2021 at 15:50:36 UTC+3 Dmitry Ryndyk wrote:
>
>> 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>
>>
>> king... at gmail.com schrieb am Mittwoch, 17. März 2021 um 13:40:17 UTC+1:
>>
>>> 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.   
>>>
>>>
>>> On Tuesday, 16 March 2021 at 20:09:37 UTC+3 Dmitry Ryndyk wrote:
>>>
>>>> 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.
>>>>
>>>> king... at gmail.com schrieb am Dienstag, 16. März 2021 um 17:42:51 UTC+1:
>>>>
>>>>> 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 
>>>>>
>>>>> On Thursday, 10 December 2020 at 13:22:36 UTC+3 Dmitry Ryndyk wrote:
>>>>>
>>>>>> 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 script in exercises is outdated.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 
>>>>>>
>>>>>> Dmitry Ryndyk schrieb am Donnerstag, 10. Dezember 2020 um 11:02:54 
>>>>>> UTC+1:
>>>>>>
>>>>>>> Sorry, I found changes now! Should work!
>>>>>>>
>>>>>>> tiziano... at chem.uzh.ch schrieb am Donnerstag, 10. Dezember 2020 um 
>>>>>>> 10:41:16 UTC+1:
>>>>>>>
>>>>>>>> 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> 
>>>>>>>>
>>>>>>>> > and does not work with new output .bs files. 
>>>>>>>> > That is what I asked. 
>>>>>>>> > So, what we plan to do? 
>>>>>>>> > 
>>>>>>>> > Dima 
>>>>>>>> > Dmitry Ryndyk schrieb am Donnerstag, 10. Dezember 2020 um 
>>>>>>>> 10:06:58 UTC+1: 
>>>>>>>> > 
>>>>>>>> > Dear Matthias and Tiziano, 
>>>>>>>> > 
>>>>>>>> > thank you. I will have a look. 
>>>>>>>> > 
>>>>>>>> > Dima 
>>>>>>>> > 
>>>>>>>> > tiziano... at chem.uzh.ch schrieb am Donnerstag, 10. Dezember 2020 
>>>>>>>> um 
>>>>>>>> > 09:12:50 UTC+1: 
>>>>>>>> > 
>>>>>>>> > 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 
>>>>>>>> > <
>>>>>>>> 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 
>>>>>>>> > 
>>>>>>>> > On 12/9/20 11:15 PM, 'Dmitry Ryndyk' via cp2k wrote: 
>>>>>>>> > > 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 
>>>>>>>> > > 
>>>>>>>> > > 22b... at gmail.com schrieb am Montag, 22. Juni 2020 um 20:52:41 
>>>>>>>> > UTC+2: 
>>>>>>>> > > 
>>>>>>>> > > 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 
>>>>>>>> > > 
>>>>>>>> > > -- 
>>>>>>>> > > You received this message because you are subscribed to the 
>>>>>>>> > Google 
>>>>>>>> > > Groups "cp2k" group. 
>>>>>>>> > > To unsubscribe from this group and stop receiving emails from 
>>>>>>>> > it, send 
>>>>>>>> > > an email to cp2k+uns... at googlegroups.com 
>>>>>>>> > > <mailto:cp2k+uns... at googlegroups.com>. 
>>>>>>>> > > To view this discussion on the web visit 
>>>>>>>> > > 
>>>>>>>> > 
>>>>>>>> https://groups.google.com/d/msgid/cp2k/817b82bf-95a0-4dd3-b6fc-0d1740eea246n%40googlegroups.com 
>>>>>>>> > <
>>>>>>>> https://groups.google.com/d/msgid/cp2k/817b82bf-95a0-4dd3-b6fc-0d1740eea246n%40googlegroups.com> 
>>>>>>>>
>>>>>>>> > 
>>>>>>>> > > 
>>>>>>>> > <
>>>>>>>> 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... at chem.uzh.ch 
>>>>>>>> > 
>>>>>>>> > -- 
>>>>>>>> > You received this message because you are subscribed to the 
>>>>>>>> Google 
>>>>>>>> > Groups "cp2k" group. 
>>>>>>>> > To unsubscribe from this group and stop receiving emails from it, 
>>>>>>>> send 
>>>>>>>> > an email to cp2k+uns... at googlegroups.com 
>>>>>>>> > <mailto:cp2k+uns... at googlegroups.com>. 
>>>>>>>> > To view this discussion on the web visit 
>>>>>>>> > 
>>>>>>>> https://groups.google.com/d/msgid/cp2k/7a7f08cd-e066-451b-89cc-2fe4621daca6n%40googlegroups.com 
>>>>>>>> > <
>>>>>>>> https://groups.google.com/d/msgid/cp2k/7a7f08cd-e066-451b-89cc-2fe4621daca6n%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 
>>>>>>>> tiziano... at chem.uzh.ch 
>>>>>>>>
>>>>>>>

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