[CP2K-user] [CP2K:20591] fluctuations in DOS calculations

Muhammad Saleh captainmozak at gmail.com
Mon Aug 19 13:12:35 UTC 2024


Hi Arka

No problem, good luck

Best
MuS

On Mon, Aug 19, 2024 at 2:49 PM Arka Prava Sarkar <
sarkar.arkaprava200 at gmail.com> wrote:

> Hi Muhammad,
> Thanks for all the help. I think I can now work on this. Extremely
> grateful for your kind and patient responses to all my queries. Thank you
> so much once again.
>
> On Mon, 19 Aug 2024 at 18:16, Muhammad Saleh <captainmozak at gmail.com>
> wrote:
>
>> Hi Arka
>>
>> I think that should be enough, if you somehow wanted to have all the PDOS
>> then use
>>
>>             # print all projected DOS available:
>>             NLUMO -1
>>             # split the density by quantum number:
>>             COMPONENTS
>>
>> anyway, you can also combine all of the d orbital by evaluate its
>> average, which I believe will produce the "total" of the graph  you wanted.
>> For this you can use python + matplotlib, or gawk + xmgrace.
>>
>> Best
>> MuS
>>
>>
>>
>>
>>
>>
>>
>> On Mon, Aug 19, 2024 at 2:27 PM Arka Prava Sarkar <
>> sarkar.arkaprava200 at gmail.com> wrote:
>>
>>> 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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>>>>>>>>>>>> .
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>> --
>>>>>>>>>>>
>>>>>>>>>>> *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_w6yBN-nkbgcwzmD-1pOYpoxRDE3QrEQV4QgaKYCedrs7BQ%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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>>>>> .
>>>>>
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>>>> To view this discussion on the web visit
>>>> https://groups.google.com/d/msgid/cp2k/CAPD_w6x_7FVFWOee6tFNdk5bSfkFU66uFMCmaNj_2ufwqawHDQ%40mail.gmail.com
>>>> <https://groups.google.com/d/msgid/cp2k/CAPD_w6x_7FVFWOee6tFNdk5bSfkFU66uFMCmaNj_2ufwqawHDQ%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.
>>> To view this discussion on the web visit
>>> https://groups.google.com/d/msgid/cp2k/CAMedUirvZu4Ow-KtdR%2BhsR%3DCvOsebd74ZouWX6VhHVYh%2BkA2XQ%40mail.gmail.com
>>> <https://groups.google.com/d/msgid/cp2k/CAMedUirvZu4Ow-KtdR%2BhsR%3DCvOsebd74ZouWX6VhHVYh%2BkA2XQ%40mail.gmail.com?utm_medium=email&utm_source=footer>
>>> .
>>>
>> --
>> 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.
>> To view this discussion on the web visit
>> https://groups.google.com/d/msgid/cp2k/CAPD_w6yZw5GxEs1eJvH1VtWTTAR6kc%2B6-O-0xDmq%2B9onvd%3Ds%3Dw%40mail.gmail.com
>> <https://groups.google.com/d/msgid/cp2k/CAPD_w6yZw5GxEs1eJvH1VtWTTAR6kc%2B6-O-0xDmq%2B9onvd%3Ds%3Dw%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.
> To view this discussion on the web visit
> https://groups.google.com/d/msgid/cp2k/CAMedUio3EqibB2A8vua58gOAfmtrvpSpKQxAS4HmiQpGA_pgkg%40mail.gmail.com
> <https://groups.google.com/d/msgid/cp2k/CAMedUio3EqibB2A8vua58gOAfmtrvpSpKQxAS4HmiQpGA_pgkg%40mail.gmail.com?utm_medium=email&utm_source=footer>
> .
>

-- 
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