[ase-users] Creating non-common surface using ASE surface function
Protik Das
protik77 at gmail.com
Mon Dec 12 09:03:57 CET 2016
Sorry for reviving the post. Can I please get attention of developers
regarding the issue?
Thanks.
On Tue, Nov 29, 2016 at 2:23 PM Protik Das <protik77 at gmail.com> wrote:
> I tried with supercells, but that does not work either. Only the lattice
> vectors get multiplied with number of unit cells in respective direction.
>
> On Tue, Nov 29, 2016 at 2:04 PM Tristan Maxson <tgmaxson at gmail.com> wrote:
>
> This cell does appear to have caused a problem, it is possible that
> surfaces() expects a different type of cell? I see that it is expecting a
> conventional cell, not a primitive cell from the documentation.
>
>
> Tristan Maxson
>
> On Tue, Nov 29, 2016 at 4:42 PM, Protik Das via ase-users <
> ase-users at listserv.fysik.dtu.dk> wrote:
>
> Hi Dr. Larsen,
>
> In fact I am trying to figure out whether it's correct or not.
>
> For example when I create a surface (0 23 27) with 1 layer, the c lattice
> vector is only 0.16489 angstrom. Which does not make sense to me. For more
> common surfaces the c vectors are more than 2 angstroms. If I increase the
> number of layers, the c vectors become more reasonable. But the number of
> atoms in the unit cell increases substantially which makes it difficult to
> simulate.
>
> On Tue, Nov 29, 2016 at 1:28 PM Ask Hjorth Larsen <asklarsen at gmail.com>
> wrote:
>
> Hi Protik
>
> 2016-11-29 21:36 GMT+01:00 Protik Das via ase-users
> <ase-users at listserv.fysik.dtu.dk>:
> > Unfortunately this is my first work with quartz too.
> >
> > I am using the structure from here:
> > https://materialsproject.org/materials/mp-559091/
> >
> > I have tried up to 30 layers. It seems the b lattice vector remains the
> > same.
> >
> > The lattice vectors for the first 20 layers without adding any vacuum in
> the
> > z-direction are:
> >
> > (5.112298, 241.75895414589255, 0.16489741510638289)
> > (5.112298, 241.75895414589255, 0.32979483021276579)
> > (5.112298, 241.75895414589255, 0.49469224531915179)
> > (5.112298, 241.75895414589255, 0.65958966042553158)
> > (5.112298, 241.75895414589255, 0.82448707553193601)
> > (5.112298, 241.75895414589255, 0.98938449063830358)
> > (5.112298, 241.75895414589255, 1.1542819057446709)
> > (5.112298, 241.75895414589255, 1.3191793208510632)
> > (5.112298, 241.75895414589255, 1.4840767359574307)
> > (5.112298, 241.75895414589255, 1.648974151063872)
> > (5.112298, 241.75895414589255, 1.8138715661702149)
> > (5.112298, 241.75895414589255, 1.9787689812766072)
> > (5.112298, 241.75895414589255, 2.1436663963829989)
> > (5.112298, 241.75895414589255, 2.3085638114893419)
> > (5.112298, 241.75895414589255, 2.4734612265957834)
> > (5.112298, 241.75895414589255, 2.6383586417021263)
> > (5.112298, 241.75895414589255, 2.8032560568085185)
> > (5.112298, 241.75895414589255, 2.9681534719148615)
> > (5.112298, 241.75895414589255, 3.1330508870213025)
> > (5.112298, 241.75895414589255, 3.297948302127744)
> >
> > I may have to find another tool for the purpose.
>
> Is it not correct? Which result do you expect and why?
>
> Best regards
> Ask
>
> >
> > On Tue, Nov 29, 2016 at 12:03 AM Niels Bendtsen Halck <ntben at dtu.dk>
> wrote:
> >>
> >> I am afraid that I am not familiar with quartz at all.
> >>
> >> The surface cutter tool does sometimes have a preference for making odd
> >> unit cell shapes and this is a very high index surface.
> >>
> >> Are you sure about your bulk structure though? I googled a bit and could
> >> not find that particular structure.
> >>
> >> You should probably add more layers and the unit cell can sometimes
> change
> >> as a funciton of layers.
> >>
> >> Sincerely
> >> Niels Bendtsen Halck
> >> Postdoc
> >> DTU Energy
> >> Bygning 309
> >> 2800 Kgs. Lyngby
> >> ntben at dtu.dk
> >> ________________________________________
> >> Fra: Protik Das [protik77 at gmail.com]
> >> Sendt: 28. november 2016 22:09
> >> Til: Niels Bendtsen Halck
> >> Cc: ase-users at listserv.fysik.dtu.dk
> >> Emne: Re: [ase-users] Creating non-common surface using ASE surface
> >> function
> >>
> >> Thanks! I think the conversation mentioned in the file is correct.
> >>
> >> Now I am having another issue. I am trying to create a ST-cut surface of
> >> Beta Quartz. The miller index for ST-cut is (0 23 -23 27). I converted
> the
> >> 4-index to 3-index which is (0 23 27). I tried to create a surface
> using the
> >> surface function. But it seems the lattice constants of the surface is
> very
> >> unusual. They are: (5.11, 241.759, 0.16). Is this a bug or am I missing
> >> something? Any help regarding this is really appreciated.
> >>
> >> The code I used to generate the surface is:
> >>
> >> import ase.io.vasp as vp
> >> from pymatgen.io.ase import AseAtomsAdaptor as pmg
> >>
> >> b_qrtz='beta_quartz_bulk.vasp'
> >> b_bottom = vp.read_vasp(b_qrtz)
> >> b_bot_q=surface(b_bottom, indices=(0, 23, 27), layers=1)
> >> vp.write_vasp('beta_quartz_surf.vasp', b_bot_q, label='beta quartz (0 23
> >> 27) surface',direct=False,sort=True, vasp5=True)
> >> b_surf_pmg=pmg.get_structure(b_bot_q)
> >> print(b_surf_pmg.lattice.abc)
> >>
> >> The bulk POSCAR that I read named beta_quartz_bulk.vasp is:
> >>
> >> Si4 O8
> >> 1.0
> >> 5.112298 0.000000 0.000000
> >> -2.556149 4.427380 0.000000
> >> 0.000000 0.000000 8.629591
> >> Si O
> >> 4 8
> >> direct
> >> 0.666667 0.333333 0.062783 Si
> >> 0.666667 0.333333 0.437217 Si
> >> 0.333333 0.666667 0.937217 Si
> >> 0.333333 0.666667 0.562783 <0562-783> Si
> >> 0.000000 0.579353 0.000000 O
> >> 0.420647 0.000000 0.500000 O
> >> 0.579353 0.579353 0.500000 O
> >> 0.579353 0.000000 0.000000 O
> >> 0.000000 0.420647 0.500000 O
> >> 0.666667 0.333333 0.250000 O
> >> 0.333333 0.666667 0.750000 O
> >> 0.420647 0.420647 0.000000 O
> >>
> >>
> >>
> >> On Mon, Nov 28, 2016 at 12:02 AM Niels Bendtsen Halck
> >> <ntben at dtu.dk<mailto:ntben at dtu.dk>> wrote:
> >> I presume the structure is a hexagonal unit cell.
> >>
> >> You can convert between the 3 index miller notation and hte 4 index
> >> miller-bravais notation.
> >>
> >> My quick google search gave me a nice example
> >> http://www.labosoft.com.pl/download/hex.pdf
> >>
> >> However, I would encourage you to maybe find a more credible source.
> >> Postdoc
> >> DTU Energy
> >> Bygning 309
> >> 2800 Kgs. Lyngby
> >> ntben at dtu.dk<mailto:ntben at dtu.dk>
> >> ________________________________________
> >> Fra:
> >> ase-users-bounces at listserv.fysik.dtu.dk<mailto:
> ase-users-bounces at listserv.fysik.dtu.dk>
> >> [ase-users-bounces at listserv.fysik.dtu.dk<mailto:
> ase-users-bounces at listserv.fysik.dtu.dk>]
> >> på vegne af Protik Das via ase-users
> >> [ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk
> >]
> >> Sendt: 27. november 2016 21:36
> >> Til:
> >> ase-users at listserv.fysik.dtu.dk<mailto:ase-users at listserv.fysik.dtu.dk>
> >> Emne: [ase-users] Creating non-common surface using ASE surface function
> >>
> >> Hi ASE-users,
> >>
> >> I am trying to create a non-common surface using surface function of
> ASE.
> >> The surface have miller indices (0 1 -1 1). But the surface function
> does
> >> not take 4 indices as argument. Does anyone have experience of creating
> a
> >> surface with 4-index Miller index? Your help is really appreciated.
> >>
> >> Thanks.
> >>
> >>
> >> --
> >> Protik Das,
> >> ECE Graduate Student,
> >> LATTE (http://latte.ece.ucr.edu),
> >> University of California, Riverside.
> >> --
> >> Protik Das,
> >> ECE Graduate Student,
> >> LATTE (http://latte.ece.ucr.edu),
> >> University of California, Riverside.
> >
> > --
> > Protik Das,
> > ECE Graduate Student,
> > LATTE (http://latte.ece.ucr.edu),
> > University of California, Riverside.
> >
> > _______________________________________________
> > ase-users mailing list
> > ase-users at listserv.fysik.dtu.dk
> > https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
> --
> Protik Das,
> ECE Graduate Student,
> LATTE (http://latte.ece.ucr.edu),
> University of California, Riverside.
>
> _______________________________________________
> ase-users mailing list
> ase-users at listserv.fysik.dtu.dk
> https://listserv.fysik.dtu.dk/mailman/listinfo/ase-users
>
>
> --
> Protik Das,
> ECE Graduate Student,
> LATTE (http://latte.ece.ucr.edu),
> University of California, Riverside.
>
--
Protik Das,
ECE Graduate Student,
LATTE (http://latte.ece.ucr.edu),
University of California, Riverside.
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