[gpaw-users] AE electrostatic potential

Thu Jun 16 12:05:18 CEST 2016

Dear Jens,

Did you have a chance to consider this further? Would be great to avoid needing to go to Wien2k for this!

Cheers,
Toma

> On 03 Jun 2016, at 16:23, Jannik Meyer <jannik.meyer at univie.ac.at> wrote:
> 
> Hi Jens,
> 
> the potential should be on a 3D grid in all of real space (in and near the sample).
> 
> One pixel will contain the nucleus, where the potential becomes infinite numerically. However, the integrated value of the nuclear potential over any finite volume is finite. It will be important that the integrated potential over the volume corresponds to reality, but it can be handled (e.g. if the grid is fine enough, one can find and fix the singularities).
> 
> Jannik
> 
> 
> 
> On Fri, Jun 3, 2016 at 4:07 PM, Jens Jørgen Mortensen <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>> wrote:
> On 06/03/2016 04:01 PM, Toma Susi wrote:
> Hi Jens,
> 
> We don't specifically care about the projectors or their correctors – what we need is the all-electron-and-core electrostatic potential for use in detailed TEM image simulations.
> 
> The standard way is to use Wien2k, but that gets rather difficult for any larger system. If we could squeeze out something equivalent from GPAW, it would enable many new systems to be studied (not to mention make things much easier and faster).
> 
> But perhaps this just isn't possible?
> 
> It must be possible somehow, but I don't know anything about TEM. How would you like to have the potential?  On a very fine grid in real-space?  In all of space?  I mean, will the potential not be singular at the positions of the nuclei? In what format do you get the potential from Wien2k?
> 
> Jens Jørgen
> 
> -Toma
> 
> 
> On 03 Jun 2016, at 15:45, Jens Jørgen Mortensen <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>> wrote:
> 
> On 05/30/2016 06:03 PM, Ask Hjorth Larsen via gpaw-users wrote:
> (I took the liberty of changing the subject line so it's possible to
> see what the thread is about without opening it)
> 
> 2016-05-28 19:04 GMT+02:00 Toma Susi via gpaw-users
> <gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>>:
> Dear gpaw-users,
> 
> I would like to bring this discussion on the all-electron electrostatic potential back up. Has there been any additional work on this by anyone?
> 
> The potential would be highly useful for simulating TEM/STEM phase images, specifically on defects with charge transfer that require large unit cells and are thus often prohibitively expensive to tackle using pure all-electron codes such as Wien2k. If I understood the earlier discussion correctly, it is possible to get the all-electron potential with the help of the get_electrostatic_corrections() function, but the potential from the cores themselves would still be missing. Is this correct?
> Yes, get_electrostatic_corrections() will just give you the integral of the PAW correction to the potential as described here:
> 
> https://wiki.fysik.dtu.dk/gpaw/devel/electrostatic_potential.html <https://wiki.fysik.dtu.dk/gpaw/devel/electrostatic_potential.html>
> 
> Wouldn't the core potentials be well approximated by a lattice of positive point charges of Z of the atomic species placed at the atomic locations in the unit cell? I'm thinking that even if this is not implemented in GPAW, we might be able to generate it by hand...?
> No, the corrections are non-zero only inside the atomic augmentation spheres.  Maybe you don't need the corrections?
> 
> Jens Jørgen
> 
> Any thoughts would be very welcome, especially if Manana has worked on this more!
> 
> Thanks a lot,
> Toma
> 
> 
> 
> On 10 Jan 2014, at 13:19, gpaw-users-request at listserv.fysik.dtu.dk <mailto:gpaw-users-request at listserv.fysik.dtu.dk> wrote:
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> Today's Topics:
> 
>    1. Re: All-electron electrostatic potential (Jens J?rgen Mortensen)
>    2. Re: All-electron electrostatic potential (manana koberidze)
>    3. Re: Slab vs bulk energy (Jens J?rgen Mortensen)
>    4. Re: All-electron electrostatic potential (Jens J?rgen Mortensen)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 10 Jan 2014 12:20:41 +0100
> From: Jens J?rgen Mortensen <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>>
> To: manana koberidze <manana.koberidze at aalto.fi <mailto:manana.koberidze at aalto.fi>>, gpaw-users
>        <gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>>
> Subject: Re: [gpaw-users] All-electron electrostatic potential
> Message-ID: <52CFD789.7080407 at fysik.dtu.dk <mailto:52CFD789.7080407 at fysik.dtu.dk>>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> 
> Den 10-01-2014 09:28, manana koberidze skrev:
> Dear all,
> 
> How is possible to get all-electron electrostatic potential in GPAW? I
> found out in the manual about get_electrostatic_corrections() method
> but how can I apply to the pseudo-electrostatic potential? My first
> guess was it would be the same size array and I could just add them
> up, but I'm obviously wrong.
> The get_electrostatic_corrections() method will return the integral of
> the PAW correction to the pseudo potential for each atom:
> 
> https://wiki.fysik.dtu.dk/gpaw/devel/electrostatic_potential.html <https://wiki.fysik.dtu.dk/gpaw/devel/electrostatic_potential.html>
> 
> Jens J?rgen
> 
> Thanks for any help.
> --
> Manana
> 
> 
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> ------------------------------
> 
> Message: 2
> Date: Fri, 10 Jan 2014 13:34:56 +0200
> From: manana koberidze <manana.koberidze at aalto.fi <mailto:manana.koberidze at aalto.fi>>
> To: Jens J?rgen Mortensen <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>>
> Cc: gpaw-users <gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>>
> Subject: Re: [gpaw-users] All-electron electrostatic potential
> Message-ID:
>        <CAFYrEYNPr+s_w29JXaOadxnpBP9ojY2g+=CkDoWA=HJUQ-Z-dw at mail.gmail.com <mailto:HJUQ-Z-dw at mail.gmail.com>>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Thanks for the comment. I had missed that this is for 'each atom'. Then by
> adding to the pseudopotential value at corresponding atoms I would get
> all-electron-potential at those atoms. Is that right? But how about full
> potential? Manual also says it's non-zero only inside the atomic
> augmentation spheres. So, is it possible to get all-electron potential
> inside the whole simulation box?
> 
> 
> Thanks again,
> 
> 
> On Fri, Jan 10, 2014 at 1:20 PM, Jens J?rgen Mortensen
> <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>>wrote:
> 
> Den 10-01-2014 09:28, manana koberidze skrev:
> 
> Dear all,
> 
> How is possible to get all-electron electrostatic potential in GPAW? I
> found out in the manual about get_electrostatic_corrections() method but
> how can I apply to the pseudo-electrostatic potential? My first guess was
> it would be the same size array and I could just add them up, but I'm
> obviously wrong.
> 
> 
> The get_electrostatic_corrections() method will return the integral of the
> PAW correction to the pseudo potential for each atom:
> 
>     https://wiki.fysik.dtu.dk/gpaw/devel/electrostatic_potential.html <https://wiki.fysik.dtu.dk/gpaw/devel/electrostatic_potential.html>
> 
> Jens J?rgen
> 
> 
> Thanks for any help.
> --
> Manana
> 
> 
> _______________________________________________
> gpaw-users mailing listgpaw-users at listserv.fysik.dtu.dkhttps://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users <http://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users>
> 
> 
> 
> --
> Manana Koberidze
> 
> Graduate Student
> Department of Applied Physics
> Aalto University School of Science
> P.O.Box 11100
> FI-00076 AALTO
> Finland
> E-mail: manana.koberidze (at) aalto.fi <http://aalto.fi/>
> Office: Y427 main building (4th floor)
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> ------------------------------
> 
> Message: 3
> Date: Fri, 10 Jan 2014 13:12:23 +0100
> From: Jens J?rgen Mortensen <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>>
> To: manana koberidze <manana.koberidze at aalto.fi <mailto:manana.koberidze at aalto.fi>>,
>        "gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>" <gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>>
> Subject: Re: [gpaw-users] Slab vs bulk energy
> Message-ID: <52CFE3A7.4010808 at fysik.dtu.dk <mailto:52CFE3A7.4010808 at fysik.dtu.dk>>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> 
> Den 10-01-2014 09:21, manana koberidze skrev:
> Dear all,
> 
> I'm trying to compare slab and bulk eigenvalues somehow. For example,
> simple test on Al gives Fermi levels:
> 
> bulk Al with pbc: ~ 6 eV
> Al slab with pbc(1,1,0): ~  - 4 eV
> 
> I know that in GPAW, for slab, vacuum potential is set to zero, thus,
> energies can be regarded as absolute.  And for the bulk, average of
> electrostatic potential is zero.
> 
> Then I suppose if I shift the energies of slab with respect to
> /mean(Hartree)/, then energies must be aligned. Is that true?
> I think so - if you add the PAW correction from
> get_electrostatic_correction().
> 
> Or do I need to compare, for example, average effective or
> electrostatic potential on a single atom inside slab to that of the
> bulk, and use the difference between them to shift the energies?
> That should also work.
> 
> Related to that, gpaw output gives 'reference energy', what is it exactly?
> It's the energy of isolated atoms in a spherically symmetric spin-paired
> state.
> 
> Does this mean that the total energies are really calculated with
> respect to this energy? That is, if I shift the energies of two
> different systems with respect to their own reference energies, would
> this allow comparison of energies?
> If you compare energies for systems containing the same kind of atoms,
> then you don't have to worry about the reference energies.
> 
> Jens J?rgen
> 
> Thank you very much,
> 
> Best wishes,
> Manana
> 
> 
> 
> 
> 
> 
> _______________________________________________
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> ------------------------------
> 
> Message: 4
> Date: Fri, 10 Jan 2014 13:17:57 +0100
> From: Jens J?rgen Mortensen <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>>
> To: manana koberidze <manana.koberidze at aalto.fi <mailto:manana.koberidze at aalto.fi>>
> Cc: gpaw-users <gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>>
> Subject: Re: [gpaw-users] All-electron electrostatic potential
> Message-ID: <52CFE4F5.6070107 at fysik.dtu.dk <mailto:52CFE4F5.6070107 at fysik.dtu.dk>>
> Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
> 
> Den 10-01-2014 12:34, manana koberidze skrev:
> Thanks for the comment. I had missed that this is for 'each atom'.
> Then by adding to the pseudopotential value at corresponding atoms I
> would get all-electron-potential at those atoms. Is that right? But
> how about full potential? Manual also says it's non-zero only inside
> the atomic augmentation spheres. So, is it possible to get
> all-electron potential inside the whole simulation box?
> No, that has not been implemented.  The ae potential is not so nice - it
> diverges at the position of each atom.
> 
> Jens J?rgen
> 
> Thanks again,
> 
> 
> On Fri, Jan 10, 2014 at 1:20 PM, Jens J?rgen Mortensen
> <jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk> <mailto:jensj at fysik.dtu.dk <mailto:jensj at fysik.dtu.dk>>> wrote:
> 
>     Den 10-01-2014 09:28, manana koberidze skrev:
>     Dear all,
> 
>     How is possible to get all-electron electrostatic potential in
>     GPAW? I found out in the manual about
>     get_electrostatic_corrections() method but how can I apply to the
>     pseudo-electrostatic potential? My first guess was it would be
>     the same size array and I could just add them up, but I'm
>     obviously wrong.
>     The get_electrostatic_corrections() method will return the
>     integral of the PAW correction to the pseudo potential for each atom:
> 
>     https://wiki.fysik.dtu.dk/gpaw/devel/electrostatic_potential.html <https://wiki.fysik.dtu.dk/gpaw/devel/electrostatic_potential.html>
> 
>     Jens J?rgen
> 
>     Thanks for any help.
>     --
>     Manana
> 
> 
>     _______________________________________________
>     gpaw-users mailing list
>     gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>  <mailto:gpaw-users at listserv.fysik.dtu.dk <mailto:gpaw-users at listserv.fysik.dtu.dk>>
>     https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users <https://listserv.fysik.dtu.dk/mailman/listinfo/gpaw-users>
> 
> 
> --
> Manana Koberidze
> 
> Graduate Student
> Department of Applied Physics
> Aalto University School of Science
> P.O.Box 11100
> FI-00076 AALTO
> Finland
> E-mail: manana.koberidze (at) aalto.fi <http://aalto.fi/> <http://aalto.fi/ <http://aalto.fi/>>
> Office: Y427 main building (4th floor)
> 
> 
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