[CP2K-user] [CP2K:20583] fluctuations in DOS calculations

Muhammad Saleh captainmozak at gmail.com
Mon Aug 19 11:48:53 UTC 2024
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Hi Arka

You dont need to change the code at all. You simply run the script, let say

python cp2k_pdos.py Pyrr-Ace-O1-PDOS-after-k1-1.pdos -o out-3.dat

then just plot your interest orbital using xmgrace, gnuplot, or whatever
you like. Here I attach the output from your PDOS data.

Best
MuS

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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>>>>>>> .
>>>>>>>
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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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>>>> <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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