[Pw_forum] dos
Jonas Baltrusaitis
jasius_1 at yahoo.com
Tue May 5 15:02:09 CEST 2009
Gabriele,
you mean physically sum up all, say, C2s PDOS? There is no averaging or similar task involved?
--- On Tue, 5/5/09, Gabriele Sclauzero <sclauzer at sissa.it> wrote:
> From: Gabriele Sclauzero <sclauzer at sissa.it>
> Subject: Re: [Pw_forum] dos
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Date: Tuesday, May 5, 2009, 12:26 AM
> 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)
> >>>>>
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> >>>>
> >>>>
> >>>>
> >>>>
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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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>
> --
>
>
> o ------------------------------------------------ o
> | Gabriele Sclauzero, PhD Student |
> | c/o: SISSA & CNR-INFM Democritos, |
> | via Beirut 2-4, 34014 Trieste (Italy) |
> | email: sclauzer at sissa.it |
> | phone: +39 040 3787 511 |
> | skype: gurlonotturno |
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