[CP2K-user] [CP2K:20590] fluctuations in DOS calculations

Arka Prava Sarkar sarkar.arkaprava200 at gmail.com
Mon Aug 19 12:49:04 UTC 2024


Hi Muhammad,
Thanks for all the help. I think I can now work on this. Extremely grateful
for your kind and patient responses to all my queries. Thank you so much
once again.

On Mon, 19 Aug 2024 at 18:16, Muhammad Saleh <captainmozak at gmail.com> wrote:

> Hi Arka
>
> I think that should be enough, if you somehow wanted to have all the PDOS
> then use
>
>             # print all projected DOS available:
>             NLUMO -1
>             # split the density by quantum number:
>             COMPONENTS
>
> anyway, you can also combine all of the d orbital by evaluate its average,
> which I believe will produce the "total" of the graph  you wanted. For this
> you can use python + matplotlib, or gawk + xmgrace.
>
> Best
> MuS
>
>
>
>
>
>
>
> On Mon, Aug 19, 2024 at 2:27 PM Arka Prava Sarkar <
> sarkar.arkaprava200 at gmail.com> wrote:
>
>> Hi Muhammad,
>> in the below section of cp2k, what should I include extra so that it
>> produces the total of d-orbital?
>>
>>       &PRINT
>>        &PDOS
>>         &EACH
>>            MD  1
>>          &END EACH
>>        &END PDOS
>> This section, in this form, produces an individual magnetic number PDOS
>> of each orbitals, as you mentioned. Thanks.
>>
>> On Mon, 19 Aug 2024 at 17:53, Muhammad Saleh <captainmozak at gmail.com>
>> wrote:
>>
>>> Hi Arka,
>>>
>>> If you want to produce the total of d-orbital, then you just have
>>> assigned it from cp2k, the Python script only does the smoothing and unit
>>> transformation. The output you have specifies the PDOS corresponding to the
>>> magnetic quantum number of the d-orbital. For instance, d0 represents PDOS
>>> along the z-axis, while d+1 represents PDOS along the xz-plane, etc.
>>>
>>> Best
>>> MuS
>>>
>>> On Mon, Aug 19, 2024 at 2:08 PM Arka Prava Sarkar <
>>> sarkar.arkaprava200 at gmail.com> wrote:
>>>
>>>> Hi Muhammed,
>>>> Thank you for the reference. So I guess, there is no way I can combine
>>>> all the columns and plot as one single d orbital. I need to plot it
>>>> separately. Thank you.
>>>>
>>>> On Mon, 19 Aug 2024 at 17:36, Muhammad Saleh <captainmozak at gmail.com>
>>>> wrote:
>>>>
>>>>> Hi Arka
>>>>>
>>>>> If you plot the d orbital from the output, it will be like the figure
>>>>> I attach, collumn 6 to 10, you simply plot it
>>>>>
>>>>> Best
>>>>> MuS
>>>>>
>>>>> On Mon, Aug 19, 2024 at 12:17 PM Arka Prava Sarkar <
>>>>> sarkar.arkaprava200 at gmail.com> wrote:
>>>>>
>>>>>> Hi Arup,
>>>>>> I am stuck on the part of plotting the d orbitals actually, since it
>>>>>> has multiple columns. Also, Xmgrace will not be using convoluted gaussians.
>>>>>>
>>>>>> On Mon, 19 Aug 2024 at 15:44, Arup Sarkar <arupsarkar1398 at gmail.com>
>>>>>> wrote:
>>>>>>
>>>>>>> Hi Arka,
>>>>>>>
>>>>>>> You can use Xmgrace software to plot the PDOS directly.
>>>>>>>
>>>>>>>
>>>>>>> Dr. Arup Sarkar
>>>>>>> Postdoctoral Researcher
>>>>>>> Max Planck Institute for Polymer Research
>>>>>>> Theory (Andrienko Group)
>>>>>>> Ackermannweg 10
>>>>>>> Mainz 55128, Germany
>>>>>>> Webpage: https://arupsarkar91.github.io/
>>>>>>>
>>>>>>>
>>>>>>> On Mon, Aug 19, 2024 at 12:10 PM Arka Prava Sarkar <
>>>>>>> sarkar.arkaprava200 at gmail.com> wrote:
>>>>>>>
>>>>>>>> Hi Muhammed,
>>>>>>>> I am attaching one of the PDOS file that I am using here. The file
>>>>>>>> has density columns as s, px, py, pz, d-2, d-1, etc. Now, suppose I want to
>>>>>>>> plot the d orbital only for this file. d orbital will have the columns d-2
>>>>>>>> to d+2. I am trying to implement the code developed by Tiziano (link:
>>>>>>>> https://raw.githubusercontent.com/dev-zero/cp2k-tools/master/scripts/cp2k_pdos.py).
>>>>>>>> In this code, I need to make changes in the "DENSITY_COLUMN". However, it
>>>>>>>> is taking only one value. For multiple columns, how to change the code?
>>>>>>>> Thanks.
>>>>>>>>
>>>>>>>> On Mon, 19 Aug 2024 at 14:42, Muhammad Saleh <
>>>>>>>> captainmozak at gmail.com> wrote:
>>>>>>>>
>>>>>>>>> Hi Arka,
>>>>>>>>>
>>>>>>>>> The output from CP2K if you use the PDOS flag is several PDOS
>>>>>>>>> files that respect the element of your system, which is also applied when
>>>>>>>>> you smooth it. To identify which element is which, simply plot the data
>>>>>>>>> based on the specified column. For instance, if one of your elements had s,
>>>>>>>>> p, and d orbitals, then the output would be
>>>>>>>>>
>>>>>>>>> <Energy>  <s_orbital>  <p_orbital> <d_orbital>
>>>>>>>>> ...                ...                 ...                ...
>>>>>>>>>
>>>>>>>>> If you check your PDOS files, you can see the details of the
>>>>>>>>> orbital of each element in your system.
>>>>>>>>>
>>>>>>>>> Best
>>>>>>>>> MuS
>>>>>>>>>
>>>>>>>>> On Sun, Aug 18, 2024 at 12:53 PM Arka Prava Sarkar <
>>>>>>>>> sarkar.arkaprava200 at gmail.com> wrote:
>>>>>>>>>
>>>>>>>>>> Hi Muahmmed,
>>>>>>>>>> I tried to plot the DOS and PDOS with the python codes, however,
>>>>>>>>>> I can't figure out how to plot the individual PDOS, for example, the d
>>>>>>>>>> orbital of the Pt(111) surface using the code. Any suggestions? Thanks
>>>>>>>>>>
>>>>>>>>>> On Tue, 13 Aug 2024 at 18:37, Muhammad Saleh <
>>>>>>>>>> captainmozak at gmail.com> wrote:
>>>>>>>>>>
>>>>>>>>>>> Hi Arka
>>>>>>>>>>>
>>>>>>>>>>> Ok, then you need to smooth it out. You can use the script from
>>>>>>>>>>> here: https://wiki.wpi.edu/deskinsgroup/Density_of_States.
>>>>>>>>>>> or if you go down on the exercise link I previously sent, then
>>>>>>>>>>> you may find a Python script for the smoothing. Hope it help
>>>>>>>>>>>
>>>>>>>>>>> Best
>>>>>>>>>>> MuS
>>>>>>>>>>>
>>>>>>>>>>> On Tue, Aug 13, 2024 at 1:23 PM Arka Prava Sarkar <
>>>>>>>>>>> sarkar.arkaprava200 at gmail.com> wrote:
>>>>>>>>>>>
>>>>>>>>>>>> Hi Muhammed,
>>>>>>>>>>>> I have calculated PDOS in a separate input file, using the same
>>>>>>>>>>>> flags you have mentioned. My issue is about the fluctuations. Thanks.
>>>>>>>>>>>> Thanks & Regards,
>>>>>>>>>>>> অর্ক প্রভ সরকার
>>>>>>>>>>>> Arka Prava Sarkar
>>>>>>>>>>>> বৃত্তিজীবী বাচম্পত্যাধয়নকারী
>>>>>>>>>>>> Research Scholar (Ph.D.),
>>>>>>>>>>>> গণনা এবং তথ্য বিজ্ঞান কেন্দ্র
>>>>>>>>>>>> Centre for Computational and Data Science (CCDS)
>>>>>>>>>>>> ভারতীয় প্রযুক্তি প্রতিষ্ঠান, খড়গপুর
>>>>>>>>>>>> Indian Institute of Technology, Kharagpur
>>>>>>>>>>>> পশ্চিমবঙ্গ-721302
>>>>>>>>>>>> West Bengal -721302
>>>>>>>>>>>> India
>>>>>>>>>>>> Email1 : sarkar.arkaprava200 at gmail.com
>>>>>>>>>>>> Email2 : arkaps.ccds at iitkgp.ac.in
>>>>>>>>>>>>
>>>>>>>>>>>> On Tue, Aug 13, 2024, 4:52 PM Muhammad Saleh <
>>>>>>>>>>>> captainmozak at gmail.com> wrote:
>>>>>>>>>>>>
>>>>>>>>>>>>> Hi Arka
>>>>>>>>>>>>>
>>>>>>>>>>>>> In order to evaluate the PDOS, I believe you should also put
>>>>>>>>>>>>> PDOS on the print section
>>>>>>>>>>>>> ...
>>>>>>>>>>>>>       &PRINT
>>>>>>>>>>>>>        &PDOS
>>>>>>>>>>>>>         &EACH
>>>>>>>>>>>>>            MD  1
>>>>>>>>>>>>>          &END EACH
>>>>>>>>>>>>>        &END PDOS
>>>>>>>>>>>>> .....
>>>>>>>>>>>>>
>>>>>>>>>>>>> you can find the details on the cp2k excercise
>>>>>>>>>>>>> https://www.cp2k.org/exercises:2016_uzh_cmest:calculating_pdos
>>>>>>>>>>>>>
>>>>>>>>>>>>> best
>>>>>>>>>>>>> MuS
>>>>>>>>>>>>>
>>>>>>>>>>>>> On Tue, Aug 13, 2024 at 12:46 PM Arka Prava Sarkar <
>>>>>>>>>>>>> sarkar.arkaprava200 at gmail.com> wrote:
>>>>>>>>>>>>>
>>>>>>>>>>>>>> Dear Users,
>>>>>>>>>>>>>> I am trying to calculate the DOS and PDOS of a Pt(111)-Ionic
>>>>>>>>>>>>>> Liquid interfacial system. Upon calculating, the DOS and PDOS obtained
>>>>>>>>>>>>>> shows a large fluctuation of the Pt(111) system. I am unable to figure out
>>>>>>>>>>>>>> the reason behind this and how to resolve the issue. Any help will
>>>>>>>>>>>>>> be appreciated. I am attaching the DOS and PDOS plot along with the input
>>>>>>>>>>>>>> file. Thanks in advance.
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> *Thanks and Regards,*
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> *অর্ক প্রভ সরকার*
>>>>>>>>>>>>>>  *Arka Prava Sarkar*
>>>>>>>>>>>>>> *বৃত্তিজীবী বাচস্পত্যাধয়নকারী*
>>>>>>>>>>>>>> *Research Scholar (Ph.D.), *
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> *গণনা এবং তথ্য বিজ্ঞান কেন্দ্র *
>>>>>>>>>>>>>> *Centre for Computational and Data Sciences (CCDS)*
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> *ভারতীয় প্রযুক্তি প্রতিষ্ঠান, খড়গপুর*
>>>>>>>>>>>>>> *Indian Institute of Technology, Kharagpur*
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> *পশ্চিমবঙ্গ - ৭২১৩০২ *
>>>>>>>>>>>>>> *West Bengal-721302*
>>>>>>>>>>>>>> *email1 : sarkar.arkaprava200 at gmail.com
>>>>>>>>>>>>>> <sarkar.arkaprava200 at gmail.com>*
>>>>>>>>>>>>>> *email2 : arkaps.ccds at iitkgp.ac.in <arkaps.ccds at iitkgp.ac.in>*
>>>>>>>>>>>>>> <http://www.linkedin.com/in/quantum-arka-phys-497052>
>>>>>>>>>>>>>>
>>>>>>>>>>>>>> --
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>>>>>>>>>>>>>> <https://groups.google.com/d/msgid/cp2k/CAMedUiqoxb3osZEB2iUDAe8SD31TpQ7R3oqmfLkQTk-SR2C_ZA%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>>>>>>>> .
>>>>>>>>>>>>>>
>>>>>>>>>>>>> --
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>>>>>>>>>>>>> .
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>>>>>>>>>>>> .
>>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>> You received this message because you are subscribed to the
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>>>>>>>>>>> <https://groups.google.com/d/msgid/cp2k/CAPD_w6w8A-vGLy52r9T7nJSditk0%3DsuTzfGEoXLeD9gyZbiBcw%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>>>>> .
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>>
>>>>>>>>>> *Thanks and Regards,*
>>>>>>>>>>
>>>>>>>>>> *অর্ক প্রভ সরকার*
>>>>>>>>>>  *Arka Prava Sarkar*
>>>>>>>>>> *বৃত্তিজীবী বাচস্পত্যাধয়নকারী*
>>>>>>>>>> *Research Scholar (Ph.D.), *
>>>>>>>>>>
>>>>>>>>>> *গণনা এবং তথ্য বিজ্ঞান কেন্দ্র *
>>>>>>>>>> *Centre for Computational and Data Sciences (CCDS)*
>>>>>>>>>>
>>>>>>>>>> *ভারতীয় প্রযুক্তি প্রতিষ্ঠান, খড়গপুর*
>>>>>>>>>> *Indian Institute of Technology, Kharagpur*
>>>>>>>>>>
>>>>>>>>>> *পশ্চিমবঙ্গ - ৭২১৩০২ *
>>>>>>>>>> *West Bengal-721302*
>>>>>>>>>> *email1 : sarkar.arkaprava200 at gmail.com
>>>>>>>>>> <sarkar.arkaprava200 at gmail.com>*
>>>>>>>>>> *email2 : arkaps.ccds at iitkgp.ac.in <arkaps.ccds at iitkgp.ac.in>*
>>>>>>>>>> <http://www.linkedin.com/in/quantum-arka-phys-497052>
>>>>>>>>>>
>>>>>>>>>> --
>>>>>>>>>> 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+unsubscribe at googlegroups.com.
>>>>>>>>>> To view this discussion on the web visit
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>>>>>>>>>> <https://groups.google.com/d/msgid/cp2k/CAMedUio-wun2xHOnyJ6wSq40hrSAcdNpbHpZHxzuiyGg9biHEw%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>> --
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>>>>>>>>> <https://groups.google.com/d/msgid/cp2k/CAPD_w6yBN-nkbgcwzmD-1pOYpoxRDE3QrEQV4QgaKYCedrs7BQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>>> .
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> --
>>>>>>>>
>>>>>>>> *Thanks and Regards,*
>>>>>>>>
>>>>>>>> *অর্ক প্রভ সরকার*
>>>>>>>>  *Arka Prava Sarkar*
>>>>>>>> *বৃত্তিজীবী বাচস্পত্যাধয়নকারী*
>>>>>>>> *Research Scholar (Ph.D.), *
>>>>>>>>
>>>>>>>> *গণনা এবং তথ্য বিজ্ঞান কেন্দ্র *
>>>>>>>> *Centre for Computational and Data Sciences (CCDS)*
>>>>>>>>
>>>>>>>> *ভারতীয় প্রযুক্তি প্রতিষ্ঠান, খড়গপুর*
>>>>>>>> *Indian Institute of Technology, Kharagpur*
>>>>>>>>
>>>>>>>> *পশ্চিমবঙ্গ - ৭২১৩০২ *
>>>>>>>> *West Bengal-721302*
>>>>>>>> *email1 : sarkar.arkaprava200 at gmail.com
>>>>>>>> <sarkar.arkaprava200 at gmail.com>*
>>>>>>>> *email2 : arkaps.ccds at iitkgp.ac.in <arkaps.ccds at iitkgp.ac.in>*
>>>>>>>> <http://www.linkedin.com/in/quantum-arka-phys-497052>
>>>>>>>>
>>>>>>>> --
>>>>>>>> You received this message because you are subscribed to the Google
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>>>>>>>> To unsubscribe from this group and stop receiving emails from it,
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>>>>>>>> <https://groups.google.com/d/msgid/cp2k/CAMedUiose5-yFEaNp6tCiuzDB_idti_L%2BfendTpe%2BGgnkhbybg%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>> .
>>>>>>>>
>>>>>>> --
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>>>>>>> .
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>>
>>>>>> *Thanks and Regards,*
>>>>>>
>>>>>> *অর্ক প্রভ সরকার*
>>>>>>  *Arka Prava Sarkar*
>>>>>> *বৃত্তিজীবী বাচস্পত্যাধয়নকারী*
>>>>>> *Research Scholar (Ph.D.), *
>>>>>>
>>>>>> *গণনা এবং তথ্য বিজ্ঞান কেন্দ্র *
>>>>>> *Centre for Computational and Data Sciences (CCDS)*
>>>>>>
>>>>>> *ভারতীয় প্রযুক্তি প্রতিষ্ঠান, খড়গপুর*
>>>>>> *Indian Institute of Technology, Kharagpur*
>>>>>>
>>>>>> *পশ্চিমবঙ্গ - ৭২১৩০২ *
>>>>>> *West Bengal-721302*
>>>>>> *email1 : sarkar.arkaprava200 at gmail.com
>>>>>> <sarkar.arkaprava200 at gmail.com>*
>>>>>> *email2 : arkaps.ccds at iitkgp.ac.in <arkaps.ccds at iitkgp.ac.in>*
>>>>>> <http://www.linkedin.com/in/quantum-arka-phys-497052>
>>>>>>
>>>>>> --
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>>>>>> <https://groups.google.com/d/msgid/cp2k/CAMedUirQhXYLf%2Byxif_zADm%2BT4iUYLLiN%3DEbVcmdHAY_rNf-dA%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>> .
>>>>>>
>>>>> --
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>>>>> <https://groups.google.com/d/msgid/cp2k/CAPD_w6z%2BCH%2BDrN5_8Y-JiSiW0eN0OdZ_VbxhgqvdfsPY1E5MbQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>>
>>>>
>>>>
>>>> --
>>>>
>>>> *Thanks and Regards,*
>>>>
>>>> *অর্ক প্রভ সরকার*
>>>>  *Arka Prava Sarkar*
>>>> *বৃত্তিজীবী বাচস্পত্যাধয়নকারী*
>>>> *Research Scholar (Ph.D.), *
>>>>
>>>> *গণনা এবং তথ্য বিজ্ঞান কেন্দ্র *
>>>> *Centre for Computational and Data Sciences (CCDS)*
>>>>
>>>> *ভারতীয় প্রযুক্তি প্রতিষ্ঠান, খড়গপুর*
>>>> *Indian Institute of Technology, Kharagpur*
>>>>
>>>> *পশ্চিমবঙ্গ - ৭২১৩০২ *
>>>> *West Bengal-721302*
>>>> *email1 : sarkar.arkaprava200 at gmail.com <sarkar.arkaprava200 at gmail.com>*
>>>> *email2 : arkaps.ccds at iitkgp.ac.in <arkaps.ccds at iitkgp.ac.in>*
>>>> <http://www.linkedin.com/in/quantum-arka-phys-497052>
>>>>
>>>> --
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>>>> .
>>>>
>>> --
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>>> .
>>>
>>
>>
>> --
>>
>> *Thanks and Regards,*
>>
>> *অর্ক প্রভ সরকার*
>>  *Arka Prava Sarkar*
>> *বৃত্তিজীবী বাচস্পত্যাধয়নকারী*
>> *Research Scholar (Ph.D.), *
>>
>> *গণনা এবং তথ্য বিজ্ঞান কেন্দ্র *
>> *Centre for Computational and Data Sciences (CCDS)*
>>
>> *ভারতীয় প্রযুক্তি প্রতিষ্ঠান, খড়গপুর*
>> *Indian Institute of Technology, Kharagpur*
>>
>> *পশ্চিমবঙ্গ - ৭২১৩০২ *
>> *West Bengal-721302*
>> *email1 : sarkar.arkaprava200 at gmail.com <sarkar.arkaprava200 at gmail.com>*
>> *email2 : arkaps.ccds at iitkgp.ac.in <arkaps.ccds at iitkgp.ac.in>*
>> <http://www.linkedin.com/in/quantum-arka-phys-497052>
>>
>> --
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>> <https://groups.google.com/d/msgid/cp2k/CAMedUirvZu4Ow-KtdR%2BhsR%3DCvOsebd74ZouWX6VhHVYh%2BkA2XQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>> .
>>
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> .
>


-- 

*Thanks and Regards,*

*অর্ক প্রভ সরকার*
 *Arka Prava Sarkar*
*বৃত্তিজীবী বাচস্পত্যাধয়নকারী*
*Research Scholar (Ph.D.), *

*গণনা এবং তথ্য বিজ্ঞান কেন্দ্র *
*Centre for Computational and Data Sciences (CCDS)*

*ভারতীয় প্রযুক্তি প্রতিষ্ঠান, খড়গপুর*
*Indian Institute of Technology, Kharagpur*

*পশ্চিমবঙ্গ - ৭২১৩০২ *
*West Bengal-721302*
*email1 : sarkar.arkaprava200 at gmail.com <sarkar.arkaprava200 at gmail.com>*
*email2 : arkaps.ccds at iitkgp.ac.in <arkaps.ccds at iitkgp.ac.in>*
<http://www.linkedin.com/in/quantum-arka-phys-497052>

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