[CP2K-user] [CP2K:20584] fluctuations in DOS calculations

Arka Prava Sarkar sarkar.arkaprava200 at gmail.com
Mon Aug 19 11:57:47 UTC 2024
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Hi Muhammed,
Thanks for the output file reference. I understood the output generated.
However, if I want to plot the d orbitals, I need to consider all the
columns of the d orbitals. Is there any way to combine all these together?
Or do I need to do it in xmgrace? Thanks.

On Mon, 19 Aug 2024 at 17:19, Muhammad Saleh <captainmozak at gmail.com> wrote:

> 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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>>>>>>> .
>>>>>>>
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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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>> .
>>
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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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