[Pw_forum] how to convert to unit of eV/atom in supercell?

Wong Kelvin wongkc81 at gmail.com
Thu Feb 4 14:22:00 CET 2010


On Thu, Feb 4, 2010 at 4:18 PM, <pw_forum-request at pwscf.org> wrote:

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> Today's Topics:
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>   1. Re: Kponts generation from kpoint.x (vtmtrinh at caltech.edu)
>   2. Re: Kponts generation from kpoint.x (Paolo Giannozzi)
>   3. Re: Kponts generation from kpoint.x (Gabriele Sclauzero)
>   4. Re: how to conver to unit of eV/atom in supercell?
>      (Gabriele Sclauzero)
>   5. Re: Kponts generation from kpoint.x (Vo, Trinh (388C))
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 3 Feb 2010 22:49:01 -0800 (PST)
> From: vtmtrinh at caltech.edu
> Subject: Re: [Pw_forum] Kponts generation from kpoint.x
> To: "PWSCF Forum" <pw_forum at pwscf.org>
> Message-ID:
>        <49417.66.215.89.65.1265266141.squirrel at webmail.caltech.edu>
> Content-Type: text/plain;charset=iso-8859-1
>
> Dear PWSCF Users,
>
> I also checked prevoius discussions in PWSCF forum.  pw.x also takes into
> consideration of the crystal symmetry, while kpoint.x uses lattice
> symmetry.  (My studied system is body-cntered tetragonal cell). It seems
> that I could not use the kpoints list given by kpoint.x.   If I would like
> to obtain a whole list of kpoints (consistent with those generated by
> pw.x), how could I do so?
>
> Thank you,
>
> Trinh
>
> > Dear Pwscf,
> >
> > I run a nscf calculation with k-point grid of 12x12x12 (automatic).  From
> > the output of pw.x, I saw 163 kpoints were generated and computed.  Since
> > I would like to get the whole 3D-band structure, I run kpoint.x to get
> > other kpoints.  A number of kpoints generated by pw.x (for the nscf
> > calcultion) could be found te coincide with those generated by kpoint.x.
> > However, there many kpoints generated by pw.x could not found in the
> > output of kpoint.x.  I am not sure about the reason why there is the
> > difference here: Is it due to reverse symmetry or something else?   I
> > appreciate very much if you could tell me why.
> >
> > Best,
> >
> > Trinh Vo
> >
> > JPL/CalTech
> >
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Thu, 4 Feb 2010 08:48:38 +0100
> From: Paolo Giannozzi <giannozz at democritos.it>
> Subject: Re: [Pw_forum] Kponts generation from kpoint.x
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <680AB988-245A-47ED-8517-BD239D213990 at democritos.it>
> Content-Type: text/plain; charset=US-ASCII; delsp=yes; format=flowed
>
>
> On Feb 4, 2010, at 7:49 , vtmtrinh at caltech.edu wrote:
>
> > If I would like to obtain a whole list of kpoints (consistent with
> > those
> > generated by pw.x), how could I do so?
>
> what do you mean by "a whole list of k-points"? one that covers the
> entire
> BZ ?  there is an option in kpoints.x . You can also use option "nosym"
> in pw.x.
>
> P.
> ---
> Paolo Giannozzi, Dept of Physics, University of Udine
> via delle Scienze 208, 33100 Udine, Italy
> Phone +39-0432-558216, fax +39-0432-558222
>
>
>
>
>
> ------------------------------
>
> Message: 3
> Date: Thu, 04 Feb 2010 09:02:45 +0100
> From: Gabriele Sclauzero <sclauzer at sissa.it>
> Subject: Re: [Pw_forum] Kponts generation from kpoint.x
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4B6A7F25.4010806 at sissa.it>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
>
>
> vtmtrinh at caltech.edu wrote:
> > Dear PWSCF Users,
> >
> > I also checked prevoius discussions in PWSCF forum.  pw.x also takes into
> > consideration of the crystal symmetry, while kpoint.x uses lattice
> > symmetry.  (My studied system is body-cntered tetragonal cell). It seems
> > that I could not use the kpoints list given by kpoint.x.   If I would
> like
>
> You got the point!
>
> > to obtain a whole list of kpoints (consistent with those generated by
> > pw.x), how could I do so?
>
> I'm not sure that your request is totally clear to me. If you want the full
> list of
> k-points, without any symmetry reduction, you can use kpoints.x: it has an
> option which
> prints on output the full list, together with an index which tells you if
> there is in the
> list another k-point which is equivalent by symmetry.
> I think you could even generate the mesh "by hand" in crystal coordinates:
> it is a
> regularly spaced grid in a three dimensional cube, possibly shifted from
> the origin.
> Give a look inside PW/kpoint_grid.f90:
>
>   do i=1,nk1
>      do j=1,nk2
>         do k=1,nk3
>            !  this is nothing but consecutive ordering
>            n = (k-1) + (j-1)*nk3 + (i-1)*nk2*nk3 + 1
>            !  xkg are the components of the complete grid in crystal axis
>            xkg(1,n) = DBLE(i-1)/nk1 + DBLE(k1)/2/nk1
>            xkg(2,n) = DBLE(j-1)/nk2 + DBLE(k2)/2/nk2
>            xkg(3,n) = DBLE(k-1)/nk3 + DBLE(k3)/2/nk3
>         end do
>      end do
>   end do
>
> However maybe there is no need to do this if you simply want to run a nscf
> calculation on
> a full 3D grid of k-point; try with
>
> nosym=.TRUE.
> noinv=.TRUE.
>
> It should disable any symmetry reduction in the generation of the k-point
> list (but also
> symmetrization of charge).
>
>
>
> HTH
>
> GS
>
>
>
> >
> > Thank you,
> >
> > Trinh
> >
> >> Dear Pwscf,
> >>
> >> I run a nscf calculation with k-point grid of 12x12x12 (automatic).
>  From
> >> the output of pw.x, I saw 163 kpoints were generated and computed.
>  Since
> >> I would like to get the whole 3D-band structure, I run kpoint.x to get
> >> other kpoints.  A number of kpoints generated by pw.x (for the nscf
> >> calcultion) could be found te coincide with those generated by kpoint.x.
> >> However, there many kpoints generated by pw.x could not found in the
> >> output of kpoint.x.  I am not sure about the reason why there is the
> >> difference here: Is it due to reverse symmetry or something else?   I
> >> appreciate very much if you could tell me why.
> >>
> >> Best,
> >>
> >> Trinh Vo
> >>
> >> JPL/CalTech
> >>
> >>
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >>
> >
> >
> > _______________________________________________
> > Pw_forum mailing list
> > Pw_forum at pwscf.org
> > http://www.democritos.it/mailman/listinfo/pw_forum
> >
>
> --
>
>
> 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                             |
> o ------------------------------------------------ o
>
>
> ------------------------------
>
> Message: 4
> Date: Thu, 04 Feb 2010 09:08:41 +0100
> From: Gabriele Sclauzero <sclauzer at sissa.it>
> Subject: Re: [Pw_forum] how to conver to unit of eV/atom in supercell?
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <4B6A8089.9080009 at sissa.it>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Wong Kelvin wrote:
> > Dear all
> >
> > when i calculate a single atomc Cu primitive cell, the energy is ~ -87
>
> What are you trying to compute? An isolated atom or a bulk phase? In any
> case, if you are
> using pseudopotentials the total energy has not any physical meaning by
> itself. What is
> physically relevant are energy differences.
>
> > Ry. How to convert it to the eV/atom which normally is around -3.7 eV?
>
> Where did you get this value of -3.7 and what does it actually refer to? I
> mean, to which
> physical quantity?
>
>
> GS
> > Thanks
> > Wong
> >
> >
> 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                             |
> o ------------------------------------------------ o
>
> Dear Gabriele
Thanks for reply!

I am trying to calculate the grain and twin boundary energies in metals. I
partially understand that absolute energy in pseudopotential calculation
does not provide meaningful interpretation.
The reported energies in literature for copper with PP calculations use to
be around -3.7 eV/atom. Is there anything significant abt this figure? and i
do not understand how to get it. simple by diving the total energy
calculated by number of atom in supercell? if it is so, the value (~3.7) is
way too small as compare to the 87 Ry for one copper atom primitive cell.

regards
Kelvin




> ------------------------------
>
> Message: 5
> Date: Thu, 4 Feb 2010 00:11:43 -0800
> From: "Vo, Trinh (388C)" <Trinh.Vo at jpl.nasa.gov>
> Subject: Re: [Pw_forum] Kponts generation from kpoint.x
> To: PWSCF Forum <pw_forum at pwscf.org>
> Message-ID: <C78FC13F.128B%Trinh.Vo at jpl.nasa.gov<C78FC13F.128B%25Trinh.Vo at jpl.nasa.gov>
> >
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Paol and Gabriele,
>
> Thank you very much for reply.
>
> Yes, I need kpoints for entire BZ.  Yes, I used that option (kpoint.x) to
> print out all kpoints. I then found that a number of kpoints from pw.x did
> not in the list of kpoints generated by kpoint.x, so I was confused.  I
> have
> just made further checks, I saw that they are actually equivalent within a
> reciprocal vector.  Thus it is fine now.  :-).
>
> Thank you
>
>
> On 2/4/10 12:02 AM, "Gabriele Sclauzero" <sclauzer at sissa.it> wrote:
>
> >
> >
> > vtmtrinh at caltech.edu wrote:
> >> Dear PWSCF Users,
> >>
> >> I also checked prevoius discussions in PWSCF forum.  pw.x also takes
> into
> >> consideration of the crystal symmetry, while kpoint.x uses lattice
> >> symmetry.  (My studied system is body-cntered tetragonal cell). It seems
> >> that I could not use the kpoints list given by kpoint.x.   If I would
> like
> >
> > You got the point!
> >
> >> to obtain a whole list of kpoints (consistent with those generated by
> >> pw.x), how could I do so?
> >
> > I'm not sure that your request is totally clear to me. If you want the
> full
> > list of
> > k-points, without any symmetry reduction, you can use kpoints.x: it has
> an
> > option which
> > prints on output the full list, together with an index which tells you if
> > there is in the
> > list another k-point which is equivalent by symmetry.
> > I think you could even generate the mesh "by hand" in crystal
> coordinates: it
> > is a
> > regularly spaced grid in a three dimensional cube, possibly shifted from
> the
> > origin.
> > Give a look inside PW/kpoint_grid.f90:
> >
> >    do i=1,nk1
> >       do j=1,nk2
> >          do k=1,nk3
> >             !  this is nothing but consecutive ordering
> >             n = (k-1) + (j-1)*nk3 + (i-1)*nk2*nk3 + 1
> >             !  xkg are the components of the complete grid in crystal
> axis
> >             xkg(1,n) = DBLE(i-1)/nk1 + DBLE(k1)/2/nk1
> >             xkg(2,n) = DBLE(j-1)/nk2 + DBLE(k2)/2/nk2
> >             xkg(3,n) = DBLE(k-1)/nk3 + DBLE(k3)/2/nk3
> >          end do
> >       end do
> >    end do
> >
> > However maybe there is no need to do this if you simply want to run a
> nscf
> > calculation on
> > a full 3D grid of k-point; try with
> >
> > nosym=.TRUE.
> > noinv=.TRUE.
> >
> > It should disable any symmetry reduction in the generation of the k-point
> list
> > (but also
> > symmetrization of charge).
> >
> >
> >
> > HTH
> >
> > GS
> >
> >
> >
> >>
> >> Thank you,
> >>
> >> Trinh
> >>
> >>> Dear Pwscf,
> >>>
> >>> I run a nscf calculation with k-point grid of 12x12x12 (automatic).
>  From
> >>> the output of pw.x, I saw 163 kpoints were generated and computed.
>  Since
> >>> I would like to get the whole 3D-band structure, I run kpoint.x to get
> >>> other kpoints.  A number of kpoints generated by pw.x (for the nscf
> >>> calcultion) could be found te coincide with those generated by
> kpoint.x.
> >>> However, there many kpoints generated by pw.x could not found in the
> >>> output of kpoint.x.  I am not sure about the reason why there is the
> >>> difference here: Is it due to reverse symmetry or something else?   I
> >>> appreciate very much if you could tell me why.
> >>>
> >>> Best,
> >>>
> >>> Trinh Vo
> >>>
> >>> JPL/CalTech
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> Pw_forum mailing list
> >>> Pw_forum at pwscf.org
> >>> http://www.democritos.it/mailman/listinfo/pw_forum
> >>>
> >>
> >>
> >> _______________________________________________
> >> Pw_forum mailing list
> >> Pw_forum at pwscf.org
> >> http://www.democritos.it/mailman/listinfo/pw_forum
> >>
>
>
>
> ------------------------------
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://www.democritos.it/mailman/listinfo/pw_forum
>
>
> End of Pw_forum Digest, Vol 32, Issue 7
> ***************************************
>
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