[CP2K-user] [CP2K:20587] fluctuations in DOS calculations

Muhammad Saleh captainmozak at gmail.com
Mon Aug 19 12:23:20 UTC 2024
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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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>>>>>>>>>>> To view this discussion on the web visit
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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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>>>>>>>>>> To view this discussion on the web visit
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>>>>>>>>>> <https://groups.google.com/d/msgid/cp2k/CAPD_w6w4KwkNDnBF%2B8rq0MqiBU_0UdozY%2BCn-Q1b60PrgRq6ew%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>>>> .
>>>>>>>>>>
>>>>>>>>> --
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>>>>>>>>> send an email to cp2k+unsubscribe at googlegroups.com.
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>>>>>>>>> <https://groups.google.com/d/msgid/cp2k/CAMedUip3GBqz0C4BX3X1FmJPUZDL9w%2BMZqnA_HcAdNM4CnLs9Q%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>>> .
>>>>>>>>>
>>>>>>>> --
>>>>>>>> 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/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>
>>>>>>> .
>>>>>>>
>>>>>> --
>>>>>> 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/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
>>>>> 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/CAMedUiose5-yFEaNp6tCiuzDB_idti_L%2BfendTpe%2BGgnkhbybg%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>> .
>>>>>
>>>> --
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>>>> To unsubscribe from this group and stop receiving emails from it, send
>>>> an email to cp2k+unsubscribe at googlegroups.com.
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>>>> <https://groups.google.com/d/msgid/cp2k/CAEYoAgX8%3DX1Cc8s4sc2_2Pq9ohLhXQcgoGciAzNq30Qq8E8Y9Q%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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>>> To unsubscribe from this group and stop receiving emails from it, send
>>> an email to cp2k+unsubscribe at googlegroups.com.
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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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>> To unsubscribe from this group and stop receiving emails from it, send an
>> email to cp2k+unsubscribe at googlegroups.com.
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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>
>
> --
> 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.
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> https://groups.google.com/d/msgid/cp2k/CAMedUirxTFTCh7e3WaJuPWAs_RpegUjBPxeqDm4cdt0heUAKTg%40mail.gmail.com
> <https://groups.google.com/d/msgid/cp2k/CAMedUirxTFTCh7e3WaJuPWAs_RpegUjBPxeqDm4cdt0heUAKTg%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>

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