[CP2K-user] [CP2K:20586] fluctuations in DOS calculations

Arka Prava Sarkar sarkar.arkaprava200 at gmail.com
Mon Aug 19 12:08:09 UTC 2024
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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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>>>>>>>>> <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>
>>>>>>>> .
>>>>>>>>
>>>>>>> --
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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>
>>>>>>
>>>>>> --
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>>>>>> 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>
>>>>>> .
>>>>>>
>>>>> --
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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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>>>> 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/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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> .
>


-- 

*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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