[Pw_forum] Orienting Nickel 111-P(3x3) slab surface

[Ari P Seitsonen]

Dear Elliot,

   Now I _think_ that I know what your problem is. For similar systems I 
use 'ibrav = 4', hexagonal cell that is (one needs to specify "a" and 
"c", the angle is automatically the 120 degrees), and I either use "alat" 
or "crystal" as the unit for the atomic coordinates: The former has the 
advantage that the coordinates along the z axis (along the surface normal) 
are independent of the length of your cell in that direction (value of 
"c"), the latter that laterally the coordinates are simpler to insert.

   As an example, attached please find my input for an eight-layer slab of 
Au(111) (non-reconstructed, ie no Herringbone reconstruction but 1x1 
laterally). You naturally would have to adapt the values for "a" and "c", 
create the 3x3 cell laterally (division by three and translations by 1/3 
of the new "a"), in principle the coordinates along z should not be 
changed. And of course the number of k points along the lateral dimensions 
of the Brillouin zone, amount of vacuum between the two sides of the slab 
etc are up to you.

   Hopefully this helps; please let us know if you need further 
clarifications, or this is not what you wanted.

     Greetings,

        apsi

PS No warranty about correctness though. :)

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   Physikalisch-Chemisches Institut der Universitaet Zuerich
   Tel: +41 44 63 54 497  /  Mobile: +41 79 71 90 935


On Mon, 30 Dec 2013, Elliot Menkah wrote:

> Dear Apsi,
>
> I might be getting the description wrong but what I want to do is to place an 
> adsorbate(Carbon monoxide) on the surface and run a calculation to get the 
> energy involved.
>
> And the literature I have seen, which is guiding me, has the crystal cell 
> looking perfectly like a well-oriented-vertical-standing cell (I do hope you 
> understand).
>
> I have attached a png file of the surface i have.
>
> But do I need to do something about the way a cell looks before I place 
> adsorbates on a surface to run calculations on them please.
>
> Literature: Density functional theory study of the effect of alloying 
> additions on sulfur adsorption on nickel surfaces.
> Authors : Oleksaandr I. Malyi, Ping Wu
> Applied Science 264(2013) 320-328
>
> Thank you,
>
> Happy Holidays,
>
> Regards,
>
> Elliot
>
> -- 
> Elliot S. Menkah
> Research Student - Computational Chemistry/ Computational Material Science
> Theoretical and Computational Chemistry
> Dept. of Chemistry
> Kwame Nkrumah UNiversity of Sci. and Tech.
> Kumasi
> Ghana
>
> Tel: +233 243-055-717
>
> Alt Email: elliotsmenkah at gmail.com
>           elliotsmenkah at hotmail.com
>
-------------- next part --------------
 &control
    calculation     = 'relax'
    restart_mode    = 'from_scratch'
    prefix          = '1x1-clean-lrs_08'
    pseudo_dir      = './PP_LIBRARY/'
    outdir          = './scratch/'
    tstress         = .true.
    tprnfor         = .true.
    verbosity       = 'high'
    etot_conv_thr   = 1e-6
    forc_conv_thr   = 1e-5
 /

 &system
    ibrav           = 4
    a               =  2.94616040381375026041
    c               = 50 

    ntyp            =   1
    nat             =  08
    nbnd            =  60

    occupations     = 'smearing'
    smearing        = 'fermi-dirac'
    degauss         = 0.0036749326

    ecutwfc         =  35
    ecutrho         = 500

    nspin           = 1
 /

 &electrons
    conv_thr        = 1e-9
    mixing_beta     = 0.7
 /

 &ions
 /

ATOMIC_SPECIES
Au  1.00  Au.pbe-dn-kjpaw_psl.0.3.0.UPF

ATOMIC_POSITIONS alat
Au       0.500000000   0.288675135  -2.85773803324704111452
Au       0.000000000   0.577350269  -2.04124145231931508180
Au       0.000000000  -0.000000000  -1.22474487139158904908
Au       0.500000000   0.288675135  -0.40824829046386301636
Au       0.000000000   0.577350269   0.40824829046386301636
Au       0.000000000   0.000000000   1.22474487139158904908
Au       0.500000000   0.288675135   2.04124145231931508180
Au       0.000000000   0.577350269   2.85773803324704111452

K_POINTS AUTOMATIC
 2*12 1  0 0 0