[CP2K-user] [CP2K:20588] fluctuations in DOS calculations
Arka Prava Sarkar
sarkar.arkaprava200 at gmail.com
Mon Aug 19 12:26:59 UTC 2024
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>
>>>>>>>>>>>>
>>>>>>>>>>>> --
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>>>>>>>>>>>> .
>>>>>>>>>>>>
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>>>>>>>>>>> .
>>>>>>>>>>>
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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>
>>>>>>>>
>>>>>>>> --
>>>>>>>> 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.
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>>>>>>>> <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>
>>>>>>
>>>>>> --
>>>>>> 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.
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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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>>>>> an email to cp2k+unsubscribe at googlegroups.com.
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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.
>>>> To view this discussion on the web visit
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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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>> .
>>
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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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