[DFTB-Plus-User] DFTB-Plus-User Digest, Vol 15, Issue 2
matias berdakin
matiasberdakin at gmail.com
Fri Nov 6 19:39:01 CET 2015
Hi Gabriele thanks for answering in such a short time. First of all, yes,
I think that I copied and pasted the input too fast. The input I have sent
is a copy where I was trying switching to scc. Sorry about that, I will be
more careful next time. (of course, the input it is not complete for scc).
The structure is actually armchair. Was generated by the repetition of the
unit cell, and no further optimization was employed.
When you zoom in, each spike have actually two features of 4 meV width.
Thank you for the information about the decimation, I will check the
manual. I agree that are small spikes and probably not harmful at all. I
wrote because I'm just learning to use the code and I though that maybe was
doing something wrong.
Thanks everybody for you help
Matias Berdakin
2015-11-06 14:56 GMT-03:00 <dftb-plus-user-request at mailman.zfn.uni-bremen.de
>:
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> Today's Topics:
>
> 1. Re: NEGF_MPI: rare DOS results (Gabriele Penazzi)
> 2. Re: NEGF_MPI: rare DOS results (NACIR M. TIT)
> 3. Re: DFTB-Plus-User Digest, Vol 15, Issue 1 (matias berdakin)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Fri, 6 Nov 2015 17:50:29 +0100
> From: Gabriele Penazzi <penazzi at uni-bremen.de>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] NEGF_MPI: rare DOS results
> Message-ID: <563CDA55.6060908 at uni-bremen.de>
> Content-Type: text/plain; charset=windows-1252
>
> Hi Matias,
>
> First a point about the input. When you run a non-scc calculation the
> code should actually complain if you specify any Eigensolver other than
> TransportOnly. The Eigensolver block takes care of the solution of the
> density, and if SCC=No is specified, the code should refuse to continue
> to perform instructions in the Analysis block if not explicitely
> instructed (hence the "dummy" Eigensolver TransportOnly).
>
> With this input file the code should exit with an error code, doesn't it?
>
> Second, I maybe you refer to the "small" spikes which look like noise,
> as the singularities are normal.
>
> I guess that your system is a zigzag. Sometimes small "numerical"
> scattering can be to small distorsion in the lattice.
>
> However, assuming that you can rule this out, there's still numerical
> issue which can prevent an "ideal" solution. I think that the decimation
> algorithm used to evaluate the self energies struggle a bit with band
> crossing in Gamma, it happened to me as well to see a small spike at
> Fermi level in a zigzag tube (never in armchair, though). Usually they
> are in the order of 1meV width therefore I didn't really bother (how
> many k-points would you need to have a resolution reliable up to 1
> meV?). You can reduce their width by decreasing Delta (see manual), but
> eventually you'll hit anyway some hardcoded parameters in the decimation
> implementation.
>
> Still, I can't magnify clearly the picture and I don't understand if
> they should be matter of concern. What's the width of the spikes? Did
> you generate the structure numerically by repetition of a unit cell or
> you relaxed it?
>
> Best,
> Gabriele
>
>
> On 11/06/2015 04:18 PM, matias berdakin wrote:
> > sorry I forgot to say bye in the last mail
> >
> > Thanks in advance
> > Matias Berdakin
> >
> > 2015-11-06 10:18 GMT-03:00 matias berdakin <matiasberdakin at gmail.com
> > <mailto:matiasberdakin at gmail.com>>:
> >
> > Hi everybody
> >
> > I'm doing my firsts trials with the DFTB+_NEGF_MPI (after the
> > Tutorial examples). I'm computing the DOS and the transmission
> > function (non scc) of a conducting carbon nanotube. At first
> > glance, the overall feature of the DOS is what is expected for this
> > system (see attached figure). Nevertheless the result present a
> > series of symmetric spikes that make no sense.
> > I can not find the error in the calculation. So an idea is welcome.
> > At the end of the message I have pasted the geometry and the
> > dftb_in.hsd files.
> > Im?genes integradas 1
> > Geometry = GenFormat {
> > <<< 'coords_grande.gen'
> > }
> >
> > Transport {
> > Device {
> > AtomRange = 1 240
> > FirstLayerAtoms = 1 121
> > }
> > Contact {
> > Id = "source"
> > AtomRange = 241 480
> > FermiLevel [eV] = -4.602
> > potential [eV] = 0.0
> > }
> > Contact {
> > Id = "drain"
> > AtomRange = 481 720
> > FermiLevel [eV] = -4.602
> > potential [eV] = 0.0
> > }
> > }
> >
> > Hamiltonian = DFTB {
> > SCC = No
> > MaxAngularMomentum = {
> > C = "p"
> > }
> >
> > SlaterKosterFiles = Type2FileNames {
> > Prefix = "/mio-1-1/"
> >
> > Separator = "-"
> > Suffix = ".skf"
> > }
> >
> > Eigensolver = GreensFunction {
> > ContourPoints = 50 50
> > }
> >
> > Analysis = {
> > TunnelingAndDos {
> > Verbosity = 101
> > EnergyRange [eV] = -7.0 -3.0
> > EnergyStep [eV] = 0.005
> > Region = {
> > Atoms = 1 240
> > }
> > }
> > }
> >
> >
> >
> >
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> >
>
> --
> --
> Dr. Gabriele Penazzi
> BCCMS - University of Bremen
>
> http://www.bccms.uni-bremen.de/
> http://sites.google.com/site/gabrielepenazzi/
> phone: +49 (0) 421 218 62337
> mobile: +49 (0) 151 19650383
>
>
> ------------------------------
>
> Message: 2
> Date: Fri, 6 Nov 2015 16:45:27 +0000
> From: "NACIR M. TIT" <ntit at uaeu.ac.ae>
> To: User list for DFTB+ related questions
> <dftb-plus-user at mailman.zfn.uni-bremen.de>
> Subject: Re: [DFTB-Plus-User] NEGF_MPI: rare DOS results
> Message-ID:
> <3E95E8061211964CAC31DA991758D27F54B60200 at PEXMBOX20104.uaeu.ac.ae>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Matias,
>
> I agree with Marton. Your results look just fine. DOS is constant at Fermi
> level for a range of about 1.5 eV. This must be CNT-AC (armchair). Even
> Fermi level is about -4.6 which is about the Work Function of graphene.
> You should feel confident with what you obtain. Good Luck!
>
> Nacir
>
> **********************************
> Dr. Nacir Tit
> Professor of Computational Physics
> Physics Department
> UAE University
> Al-Ain
> United Arab Emirates
> Tel: +971 3 7136 326
> Fax: +971 3 7671 291
> Email: ntit at uaeu.ac.ae<mailto:ntit at uaeu.ac.ae>
> **********************************
> ________________________________
> From: dftb-plus-user-bounces at mailman.zfn.uni-bremen.de [
> dftb-plus-user-bounces at mailman.zfn.uni-bremen.de] on behalf of matias
> berdakin [matiasberdakin at gmail.com]
> Sent: Friday, November 06, 2015 7:18 PM
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] NEGF_MPI: rare DOS results
>
> sorry I forgot to say bye in the last mail
>
> Thanks in advance
> Matias Berdakin
>
> 2015-11-06 10:18 GMT-03:00 matias berdakin <matiasberdakin at gmail.com
> <mailto:matiasberdakin at gmail.com>>:
> Hi everybody
>
> I'm doing my firsts trials with the DFTB+_NEGF_MPI (after the Tutorial
> examples). I'm computing the DOS and the transmission function (non scc) of
> a conducting carbon nanotube. At first glance, the overall feature of the
> DOS is what is expected for this system (see attached figure).
> Nevertheless the result present a series of symmetric spikes that make no
> sense.
> I can not find the error in the calculation. So an idea is welcome.
> At the end of the message I have pasted the geometry and the dftb_in.hsd
> files.
> [Im?genes integradas 1]
> Geometry = GenFormat {
> <<< 'coords_grande.gen'
> }
>
> Transport {
> Device {
> AtomRange = 1 240
> FirstLayerAtoms = 1 121
> }
> Contact {
> Id = "source"
> AtomRange = 241 480
> FermiLevel [eV] = -4.602
> potential [eV] = 0.0
> }
> Contact {
> Id = "drain"
> AtomRange = 481 720
> FermiLevel [eV] = -4.602
> potential [eV] = 0.0
> }
> }
>
> Hamiltonian = DFTB {
> SCC = No
> MaxAngularMomentum = {
> C = "p"
> }
>
> SlaterKosterFiles = Type2FileNames {
> Prefix = "/mio-1-1/"
>
> Separator = "-"
> Suffix = ".skf"
> }
>
> Eigensolver = GreensFunction {
> ContourPoints = 50 50
> }
>
> Analysis = {
> TunnelingAndDos {
> Verbosity = 101
> EnergyRange [eV] = -7.0 -3.0
> EnergyStep [eV] = 0.005
> Region = {
> Atoms = 1 240
> }
> }
> }
>
>
>
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>
> ------------------------------
>
> Message: 3
> Date: Fri, 6 Nov 2015 14:56:16 -0300
> From: matias berdakin <matiasberdakin at gmail.com>
> To: dftb-plus-user at mailman.zfn.uni-bremen.de
> Subject: Re: [DFTB-Plus-User] DFTB-Plus-User Digest, Vol 15, Issue 1
> Message-ID:
> <
> CACbPrm5qYK6K-TJB-uZbg+D0D_mT-KfuYUZMoHA0FG6J23FTAQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi Marton thanks for answering in such a short time. Yes, as you say, the
> intense peaks at ~-3.8 eV, -5.4 eV, -6 eV etc, are Ok. The spikes that I'm
> worried about are those small features at -4.6, -4.5, and not so small, at
> -6.2, -6.1, -3 ? etc
>
> cheers
> Matias
>
> 2015-11-06 12:58 GMT-03:00 <
> dftb-plus-user-request at mailman.zfn.uni-bremen.de
> >:
>
> > Send DFTB-Plus-User mailing list submissions to
> > dftb-plus-user at mailman.zfn.uni-bremen.de
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> >
> > or, via email, send a message with subject or body 'help' to
> > dftb-plus-user-request at mailman.zfn.uni-bremen.de
> >
> > You can reach the person managing the list at
> > dftb-plus-user-owner at mailman.zfn.uni-bremen.de
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of DFTB-Plus-User digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: NEGF_MPI: rare DOS results (matias berdakin)
> > 2. Re: NEGF_MPI: rare DOS results (Marton)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 6 Nov 2015 12:18:00 -0300
> > From: matias berdakin <matiasberdakin at gmail.com>
> > To: dftb-plus-user at mailman.zfn.uni-bremen.de
> > Subject: Re: [DFTB-Plus-User] NEGF_MPI: rare DOS results
> > Message-ID:
> > <
> > CACbPrm44reK3HshVbVGOxyaDxbKmzTPMgKTkON2zyAD9ZvXebg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > sorry I forgot to say bye in the last mail
> >
> > Thanks in advance
> > Matias Berdakin
> >
> > 2015-11-06 10:18 GMT-03:00 matias berdakin <matiasberdakin at gmail.com>:
> >
> > > Hi everybody
> > >
> > > I'm doing my firsts trials with the DFTB+_NEGF_MPI (after the Tutorial
> > > examples). I'm computing the DOS and the transmission function (non
> scc)
> > of
> > > a conducting carbon nanotube. At first glance, the overall feature of
> > the
> > > DOS is what is expected for this system (see attached figure).
> > Nevertheless
> > > the result present a series of symmetric spikes that make no sense.
> > > I can not find the error in the calculation. So an idea is welcome.
> > > At the end of the message I have pasted the geometry and the
> dftb_in.hsd
> > > files.
> > > [image: Im?genes integradas 1]
> > > Geometry = GenFormat {
> > > <<< 'coords_grande.gen'
> > > }
> > >
> > > Transport {
> > > Device {
> > > AtomRange = 1 240
> > > FirstLayerAtoms = 1 121
> > > }
> > > Contact {
> > > Id = "source"
> > > AtomRange = 241 480
> > > FermiLevel [eV] = -4.602
> > > potential [eV] = 0.0
> > > }
> > > Contact {
> > > Id = "drain"
> > > AtomRange = 481 720
> > > FermiLevel [eV] = -4.602
> > > potential [eV] = 0.0
> > > }
> > > }
> > >
> > > Hamiltonian = DFTB {
> > > SCC = No
> > > MaxAngularMomentum = {
> > > C = "p"
> > > }
> > >
> > > SlaterKosterFiles = Type2FileNames {
> > > Prefix = "/mio-1-1/"
> > >
> > > Separator = "-"
> > > Suffix = ".skf"
> > > }
> > >
> > > Eigensolver = GreensFunction {
> > > ContourPoints = 50 50
> > > }
> > >
> > > Analysis = {
> > > TunnelingAndDos {
> > > Verbosity = 101
> > > EnergyRange [eV] = -7.0 -3.0
> > > EnergyStep [eV] = 0.005
> > > Region = {
> > > Atoms = 1 240
> > > }
> > > }
> > > }
> > >
> > >
> > >
> > -------------- next part --------------
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> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 6 Nov 2015 09:57:19 -0600
> > From: Marton <vormar at gmail.com>
> > To: "User list for DFTB+ related questions"
> > <dftb-plus-user at mailman.zfn.uni-bremen.de>
> > Subject: Re: [DFTB-Plus-User] NEGF_MPI: rare DOS results
> > Message-ID:
> > <CAEFsdKUe-vhzUXfPTkgf6fbU3F53TfV=
> > BrgWNG_XK-Vn_Rrujg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi Matias,
> >
> > Do you mean the high intensity spikes at energies ~-3.8 eV, -5.4 eV, -6
> eV,
> > etc?
> >
> > If yes -- I am not familiar with the NEGF code but I think it is
> actually a
> > good sign if you get those spikes (=Van Hove singularities) in the DOS of
> > nanotubes:
> >
> >
> >
> https://www.google.com/search?q=nanotube+dos&biw=1215&bih=915&source=lnms&tbm=isch&sa=X&ved=0CAYQ_AUoAWoVChMIxaXTmpL8yAIVCjs-Ch2nLAXL
> >
> > Cheers,
> > Marton Voros
> >
> > --
> > Materials Science Division
> > Argonne National Laboratory
> >
> > On Fri, Nov 6, 2015 at 9:18 AM, matias berdakin <
> matiasberdakin at gmail.com>
> > wrote:
> >
> > > sorry I forgot to say bye in the last mail
> > >
> > > Thanks in advance
> > > Matias Berdakin
> > >
> > > 2015-11-06 10:18 GMT-03:00 matias berdakin <matiasberdakin at gmail.com>:
> > >
> > >> Hi everybody
> > >>
> > >> I'm doing my firsts trials with the DFTB+_NEGF_MPI (after the Tutorial
> > >> examples). I'm computing the DOS and the transmission function (non
> > scc) of
> > >> a conducting carbon nanotube. At first glance, the overall feature of
> > the
> > >> DOS is what is expected for this system (see attached figure).
> > Nevertheless
> > >> the result present a series of symmetric spikes that make no sense.
> > >> I can not find the error in the calculation. So an idea is welcome.
> > >> At the end of the message I have pasted the geometry and the
> dftb_in.hsd
> > >> files.
> > >> [image: Im?genes integradas 1]
> > >> Geometry = GenFormat {
> > >> <<< 'coords_grande.gen'
> > >> }
> > >>
> > >> Transport {
> > >> Device {
> > >> AtomRange = 1 240
> > >> FirstLayerAtoms = 1 121
> > >> }
> > >> Contact {
> > >> Id = "source"
> > >> AtomRange = 241 480
> > >> FermiLevel [eV] = -4.602
> > >> potential [eV] = 0.0
> > >> }
> > >> Contact {
> > >> Id = "drain"
> > >> AtomRange = 481 720
> > >> FermiLevel [eV] = -4.602
> > >> potential [eV] = 0.0
> > >> }
> > >> }
> > >>
> > >> Hamiltonian = DFTB {
> > >> SCC = No
> > >> MaxAngularMomentum = {
> > >> C = "p"
> > >> }
> > >>
> > >> SlaterKosterFiles = Type2FileNames {
> > >> Prefix = "/mio-1-1/"
> > >>
> > >> Separator = "-"
> > >> Suffix = ".skf"
> > >> }
> > >>
> > >> Eigensolver = GreensFunction {
> > >> ContourPoints = 50 50
> > >> }
> > >>
> > >> Analysis = {
> > >> TunnelingAndDos {
> > >> Verbosity = 101
> > >> EnergyRange [eV] = -7.0 -3.0
> > >> EnergyStep [eV] = 0.005
> > >> Region = {
> > >> Atoms = 1 240
> > >> }
> > >> }
> > >> }
> > >>
> > >>
> > >>
> > >
> > > _______________________________________________
> > > DFTB-Plus-User mailing list
> > > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> > >
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> > >
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> >
> > ------------------------------
> >
> > _______________________________________________
> > DFTB-Plus-User mailing list
> > DFTB-Plus-User at mailman.zfn.uni-bremen.de
> >
> https://mailman.zfn.uni-bremen.de/cgi-bin/mailman/listinfo/dftb-plus-user
> >
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