[CP2K-user] [CP2K:20589] fluctuations in DOS calculations

Muhammad Saleh captainmozak at gmail.com
Mon Aug 19 12:46:40 UTC 2024
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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>
>>>>>>>>>>>>>
>>>>>>>>>>>>> --
>>>>>>>>>>>>> You received this message because you are subscribed to the
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>>>>>>>>>>>>> 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
>>>>>>>>>>>>> https://groups.google.com/d/msgid/cp2k/CAMedUiqoxb3osZEB2iUDAe8SD31TpQ7R3oqmfLkQTk-SR2C_ZA%40mail.gmail.com
>>>>>>>>>>>>> <https://groups.google.com/d/msgid/cp2k/CAMedUiqoxb3osZEB2iUDAe8SD31TpQ7R3oqmfLkQTk-SR2C_ZA%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>>>>>>>>>>>> .
>>>>>>>>>>>>>
>>>>>>>>>>>> --
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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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>>>>>>>>>>> <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
>>>>>>>>>> https://groups.google.com/d/msgid/cp2k/CAPD_w6w8A-vGLy52r9T7nJSditk0%3DsuTzfGEoXLeD9gyZbiBcw%40mail.gmail.com
>>>>>>>>>> <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
>>>>>>>>> https://groups.google.com/d/msgid/cp2k/CAMedUio-wun2xHOnyJ6wSq40hrSAcdNpbHpZHxzuiyGg9biHEw%40mail.gmail.com
>>>>>>>>> <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,
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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>
>>>>>>> .
>>>>>>>
>>>>>> --
>>>>>> 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/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>
>>>
>>> --
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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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