[Pw_forum] dos
Gabriele Sclauzero
sclauzer at sissa.it
Tue May 5 09:26:34 CEST 2009
Stefano Baroni wrote:
> Jonas: I am afraid that what you want to obtain does not make much
> sense. The angular character of any molecular (or Bloch) state depends
> on the origin of your reference system. What is "s-like" with respect to
> one point has an infinite number of angular components with respect to a
> different point. Are you sure you want to add "what is s-like in Iowa"
> with "what is s-like in Italy" ??? ;-)
> Stefano
I agree with what you say, Stefano, about taking the expectation value of the angular
momentum in a periodic system, but summing the PDOS of selected atoms can lead to
meaningful and sometimes very useful results, in some cases.
I usually see the PDOS as an indicator of how much the Bloch states retain a kind of
"atomic character" in the solid (so that in this case summing PDOS of equivalent atoms is
the more meaningful thing, as Lex pointed out), but also as a way to identify the symmetry
of states.
If you place a molecule, a nanowire or maybe even a surface with slab geometry in a wise
manner in your (super-)cell you can get many information from the PDOS (summed or not).
Obviously, it does not make much sense to sum the s,p,d PDOS of all atoms in the system in
general (but in some cases it may), so that's why you cannot find it directly in the
output from projwfc.
It's your task to select over which atoms you can do a sum (or an average) of the PDOS
(and also placing the atoms in a smart way, first). I think you can write a script in
awk/perl/whatever, or even a small fortran program, which reads PDOS from individual files
associated to the selected atoms and sums the corresponding rows.
Gabriele
>
> On May 4, 2009, at 5:51 PM, Jonas Baltrusaitis wrote:
>
>>
>> I just successfully calculated DOS and PDOS of a very large system.
>> One thing that confuses me is the presence of s, p components to PDOS
>> for every atom, but not summed (or averaged) s and p contribution of
>> all system. I would be happy to find in my output total DOS, PDOS s
>> character and PDOS p character. Is there a way to get that instead of
>> contribution per every atom? Or how do I proceed to get s and p PDOS
>> for all system by manually processing all of my 76 atoms PDOS outputs?..
>>
>> thanks
>>
>> Jonas Baltrusaitis
>> University of Iowa
>>
>>
>> --- On Mon, 5/4/09, Prasenjit Ghosh <prasenjit.jnc at gmail.com
>> <mailto:prasenjit.jnc at gmail.com>> wrote:
>>
>>> From: Prasenjit Ghosh <prasenjit.jnc at gmail.com
>>> <mailto:prasenjit.jnc at gmail.com>>
>>> Subject: Re: [Pw_forum] dos
>>> To: jasius_1 at yahoo.com <mailto:jasius_1 at yahoo.com>, "PWSCF Forum"
>>> <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>>
>>> Date: Monday, May 4, 2009, 12:04 AM
>>> Hi Jonas,
>>>
>>> For DOS calculations one needs to do an integration over
>>> the kpts in the
>>> Brillouin zone. So you need a very fine k-point mesh than
>>> necessary for a
>>> scf calculation. Moreover you need a large number of bands.
>>> Doing an scf
>>> calculation with such a fine k-point mesh and so many bands
>>> is very
>>> expensive. So you should first do an scf calculation with
>>> the min. no. of
>>> k-points and bands and then do a nscf calculation with a
>>> finer k-point and
>>> larger no. of bands. In the nscf step, the code does an
>>> interpolation for
>>> the extra bands and k-points and not a self-consistent
>>> calculation. This
>>> saves computational time.
>>>
>>> Hope this helps.
>>>
>>> Prasenjit.
>>>
>>> 2009/5/3 Jonas Baltrusaitis <jasius_1 at yahoo.com
>>> <mailto:jasius_1 at yahoo.com>>
>>>
>>>>
>>>> Prasenjit,
>>>>
>>>> could you explain why both scf followed by nscf
>>> calculations are needed for
>>>> DOS calculations, as per example 8? If only scf
>>> density is needed for
>>>> further projection, why not to calculate only one?
>>>>
>>>> Jonas
>>>>
>>>>
>>>> --- On Sun, 5/3/09, Prasenjit Ghosh
>>> <prasenjit.jnc at gmail.com <mailto:prasenjit.jnc at gmail.com>> wrote:
>>>>
>>>>> From: Prasenjit Ghosh
>>> <prasenjit.jnc at gmail.com <mailto:prasenjit.jnc at gmail.com>>
>>>>> Subject: Re: [Pw_forum] dos
>>>>> To: "PWSCF Forum"
>>> <pw_forum at pwscf.org <mailto:pw_forum at pwscf.org>>
>>>>> Date: Sunday, May 3, 2009, 2:00 PM
>>>>> dear all user
>>>>>>
>>>>>
>>>>> Dear Yaldaa,
>>>>>
>>>>>
>>>>>> How can I project dos to molecular orbital?
>>>>>>
>>>>>
>>>>> There is a post-processing tool called projwfc.x
>>> which you
>>>>> can use to
>>>>> project dos to molecular orbital.
>>>>>
>>>>> what is the importance of nbnd in calculations
>>> for dos?
>>>>>>
>>>>> e
>>>>> "nbnd" tells the code the no. of
>>> Kohn-Sham
>>>>> states it has to
>>>>> compute.....While computing the dos, one wants to
>>> plot the
>>>>> dos for both the
>>>>> occupied & unoccupied manifold, the no. of
>>> energy
>>>>> levels is read in by the
>>>>> dos.x from the output of your scf/nscf run. So
>>> while doing
>>>>> an scf/ nscf
>>>>> calculations you can control the total no. of
>>> states with
>>>>> the variable
>>>>> "nbnd".
>>>>> Depending on the type of occupation scheme you
>>> choose the
>>>>> value of nbnd is
>>>>> nelec/2 (fixed occupation) or nelec/2+some extra
>>> bands
>>>>> (when you use
>>>>> smearing). If you want to plot the dos, usually
>>> you should
>>>>> add some extra
>>>>> levels using nbnd & do the scf or nscf
>>> calculations to
>>>>> get the unoccupied
>>>>> manifold.
>>>>>
>>>>> and for plottingdos or pdos, if the fermi energy
>>> is assumed
>>>>> to be zero
>>>>>> automatically by program?
>>>>>>
>>>>>
>>>>> No, you have to do the alignment yourself
>>>>>
>>>>> With regards,
>>>>>
>>>>> Prasenjit.
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> PRASENJIT GHOSH,
>>>>> POST-DOC,
>>>>> ROOM NO: 265, MAIN BUILDING,
>>>>> CM SECTION, ICTP,
>>>>> STRADA COSTERIA 11,
>>>>> TRIESTE, 34104,
>>>>> ITALY
>>>>> PHONE: +39 040 2240 369 (O)
>>>>> +39 3807528672 (M)
>>>>> _______________________________________________
>>>>> Pw_forum mailing list
>>>>> Pw_forum at pwscf.org <mailto:Pw_forum at pwscf.org>
>>>>>
>>> http://www.democritos.it/mailman/listinfo/pw_forum
>>>>
>>>>
>>>>
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>>>
>>>
>>>
>>> --
>>> PRASENJIT GHOSH,
>>> POST-DOC,
>>> ROOM NO: 265, MAIN BUILDING,
>>> CM SECTION, ICTP,
>>> STRADA COSTERIA 11,
>>> TRIESTE, 34104,
>>> ITALY
>>> PHONE: +39 040 2240 369 (O)
>>> +39 3807528672 (M)
>>
>>
>>
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>
> ---
> Stefano Baroni - SISSA & DEMOCRITOS National Simulation Center - Trieste
> [+39] 040 3787 406 (tel) -528 (fax) / stefanobaroni (skype)
>
> La morale est une logique de l'action comme la logique est une morale de
> la pensée - Jean Piaget
>
> Please, if possible, don't send me MS Word or PowerPoint attachments
> Why? See: http://www.gnu.org/philosophy/no-word-attachments.html
>
>
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--
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| Gabriele Sclauzero, PhD Student |
| c/o: SISSA & CNR-INFM Democritos, |
| via Beirut 2-4, 34014 Trieste (Italy) |
| email: sclauzer at sissa.it |
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