[CP2K-user] [CP2K:20585] fluctuations in DOS calculations

Muhammad Saleh captainmozak at gmail.com
Mon Aug 19 12:06:15 UTC 2024
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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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>>>>>>>> <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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>>>>>>> .
>>>>>>>
>>>>>> --
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>>>>>> 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>
>>>>>
>>>>> --
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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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>>> .
>>>
>> --
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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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> "cp2k" group.
> To unsubscribe from this group and stop receiving emails from it, send an
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> .
>

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