[Pw_forum] Do we need to saturate the dangling bonds? and how to add vacuum?

siddheshwar chopra sidhusai at gmail.com
Fri Jul 4 05:50:16 CEST 2014


Dear Dr. Gabriele Sclauzero,
Thank you for the valuable inputs regarding addition of vacuum. Sir, I am
unable to understand how to add VACUUM in the input file of PWscf. While
using PWGUI, I need to enter cell parameters only when ibrav=0. Here I
understand that I could add vacuum in z-direction. But if I use ibrav=4,
then I am only supposed to add atomic positions. This is what I am unable
to understand. How do I enter vacuum in this case.
I use AVOGADRO to draw the geometry.
Any help would be welcomed.

Kind Regards,


On Thu, Jul 3, 2014 at 6:18 PM, Sclauzero Gabriele <
gabriele.sclauzero at mat.ethz.ch> wrote:

>
> Dear Siddheshwar Chopra,
>
>     Do you want to study a graphene flake or an infinite graphene layer.
> In the first case you need to saturate edges with H, and add enough vacuum
> both within the plane of the flake and out of the plane (remember that the
> code uses periodic boundary conditions in all three directions).
> In the second case, you don't need to saturate and you can just use the
> graphene unit cell with 2 atoms per cell. A vacuum layer is needed to
> separate the graphene plane by its periodic replicas along the out of plane
> direction.
>
>
> HTH
>
>
> GS
>
>
>
> Dear QE users,
> I am new to QE and need your help. I am making scf input file for
> graphene. Please see the following list of commands. I need to know that do
> we need to saturate the edge atoms with hydrogen for proper optimization or
> not? I am pre-optimizing it with Avogadro (with saturating it), but it is
> not happening. Please let me know what should be done. Also I don't know
> how to set "celldm(1)". I just know the cell parameters and atomic
> positions. In addition how should I add vacuum space below and above the
> sheet?
>
>  &CONTROL
>                        title = Graphene-128 ,
>                  calculation = 'scf' ,
>                  max_seconds = 99999999999 ,
>                 restart_mode = 'from_scratch' ,
>                   wf_collect = .true. ,
>                       outdir = '/home/sid/Desktop/QE/' ,
>                       wfcdir = '/home/sid/Desktop/QE/' ,
>                   pseudo_dir = '/home/sid/Desktop/QE/' ,
>                  lkpoint_dir = .false. ,
>                etot_conv_thr = 200 ,
>                forc_conv_thr = 1 ,
>                      tprnfor = .true. ,
>  /
>  &SYSTEM
>                        ibrav = 0,
>                    celldm(1) = 17.04,
>                          nat = 128,
>                         ntyp = 1,
>                      ecutwfc = 200 ,
>                      ecutrho = 100 ,
>                        nosym = .true. ,
>                    nosym_evc = .true. ,
>                        noinv = .true. ,
>                     smearing = 'gaussian' ,
>                        nspin = 1 ,
>                     ecutfock = 100 ,
>  /
>  &ELECTRONS
>                     conv_thr = 1.0d-10 ,
>                  mixing_beta = 0.01 ,
>  /
> CELL_PARAMETERS angstrom
>     17.040000000    0.000000000    0.000000000
>     -0.000000000   19.676100000    0.000000000
>     -0.000000000   -0.000000000   10.000000000
> ATOMIC_SPECIES
>     C   12.01070  C.pz-rrkjus.UPF
> ATOMIC_POSITIONS angstrom
>     C     15.722520000    0.834730000    5.619990000
>     C     16.356730000    2.009200000    5.615300000
>     C     15.576260000    3.299230000    5.553680000
>     C     16.261880000    4.515780000    5.517120000
>     C     15.560930000    5.719480000    5.429420000
>     C     16.324780000    7.053610000    5.405830000
>     C     15.491390000    8.240360000    4.989750000
>     C     16.087340000    9.556080000    4.662570000
>     C     15.489550000   10.503400000    4.629030000
>     C     16.131110000   11.745140000    4.583320000
>     C     15.414480000   12.947870000    4.597170000
>     C     16.072830000   14.205500000    4.084620000
>     C     15.275500000   15.229760000    3.777390000
>     C     15.797890000   16.477710000    3.206330000
>     C     15.038210000   17.575620000    3.195510000
>     C     15.585370000   18.852810000    2.627500000
>     C     13.489380000    2.052160000    5.513920000
>     C     14.180750000    3.265630000    5.518670000
>     C     13.469720000    4.464600000    5.459800000
>     C     14.165530000    5.671040000    5.406180000
>     C     13.441290000    6.845010000    5.243540000
>     C     14.168320000    8.111880000    4.912640000
>     C     13.299200000    9.207730000    4.444270000
>     C     14.092820000   10.502450000    4.631750000
>     C     13.413730000   11.706170000    4.804660000
>     C     14.033690000   12.957960000    4.818930000
>     C     13.431160000   13.927640000    4.860700000
>     C     13.794070000   15.081980000    3.962150000
>     C     13.160820000   16.419400000    4.256050000
>     C     13.715860000   17.564480000    3.843170000
>     C     12.994000000   18.835360000    4.027540000
>     C     14.225560000    0.713430000    5.561950000
>     C     11.404290000    0.840590000    5.375470000
>     C     12.094940000    2.051970000    5.435390000
>     C     11.386130000    3.254650000    5.398500000
>     C     12.073320000    4.469310000    5.408990000
>     C     11.362860000    5.672720000    5.352430000
>     C     12.048050000    6.886110000    5.256210000
>     C     11.367130000    8.111760000    5.205670000
>     C     11.933630000    9.111270000    5.087850000
>     C     11.161050000   10.374320000    4.871970000
>     C     11.940840000   11.632890000    5.063660000
>     C     11.362750000   12.761890000    5.442900000
>     C     12.089590000   14.041030000    5.567450000
>     C     11.146900000   15.138170000    5.101270000
>     C     11.862200000   16.443450000    5.014540000
>     C     10.999210000   17.575660000    4.577440000
>     C     11.694980000   18.850490000    4.338450000
>     C      9.305820000    2.032000000    5.227730000
>     C      9.992220000    3.243630000    5.317940000
>     C      9.281890000    4.444980000    5.315870000
>     C      9.967060000    5.658340000    5.349840000
>     C      9.255250000    6.856500000    5.409120000
>     C      9.975300000    8.052830000    5.411670000
>     C      9.238530000    9.190290000    5.726540000
>     C      9.918370000   10.394910000    5.718080000
>     C      9.250510000   11.590760000    5.948460000
>     C      9.900120000   12.796940000    5.732720000
>     C      9.258380000   14.023560000    5.622120000
>     C     10.001000000   15.157210000    5.262770000
>     C      9.254590000   16.330310000    5.058180000
>     C      9.906830000   17.533290000    4.747070000
>     C      9.183750000   18.715690000    4.588590000
>     C     10.014360000    0.829930000    5.252760000
>     C      7.240440000    0.826280000    4.875410000
>     C      7.919380000    2.030180000    5.066370000
>     C      7.212770000    3.234560000    5.065830000
>     C      7.889200000    4.442970000    5.232900000
>     C      7.178110000    5.643420000    5.297300000
>     C      7.852570000    6.852490000    5.463290000
>     C      7.111460000    8.026180000    5.659000000
>     C      7.856600000    9.179120000    5.898820000
>     C      7.199560000   10.372960000    6.169130000
>     C      7.883340000   11.588850000    6.161270000
>     C      7.221280000   12.796410000    5.970120000
>     C      7.862590000   14.002130000    5.675890000
>     C      7.117040000   15.136260000    5.334670000
>     C      7.850550000   16.321560000    5.153730000
>     C      7.152110000   17.532650000    5.076420000
>     C      7.805620000   18.725950000    4.776310000
>     C      5.168580000    2.041050000    4.589270000
>     C      5.835190000    3.241370000    4.845280000
>     C      5.135800000    4.449910000    4.845810000
>     C      5.792090000    5.650890000    5.141460000
>     C      5.083570000    6.855040000    5.227800000
>     C      5.706050000    8.070780000    5.572560000
>     C      5.114400000    9.072290000    5.674480000
>     C      5.698350000   10.308500000    6.311580000
>     C      5.090820000   11.568320000    5.753780000
>     C      5.776010000   12.694540000    5.603060000
>     C      5.180880000   13.866280000    4.923890000
>     C      5.968820000   15.119800000    5.254150000
>     C      5.289750000   16.356370000    4.750380000
>     C      6.062310000   17.547500000    5.208420000
>     C      5.375850000   18.706720000    5.792170000
>     C      5.868200000    0.834060000    4.625110000
>     C      3.122590000    0.706180000    3.972890000
>     C      3.810230000    2.038940000    4.268530000
>     C      3.120800000    3.250680000    4.199320000
>     C      3.781220000    4.440720000    4.508220000
>     C      3.086100000    5.646210000    4.461480000
>     C      3.732190000    6.802470000    4.884810000
>     C      2.932560000    8.059960000    5.014840000
>     C      3.606460000    9.150340000    5.741550000
>     C      2.944290000   10.445580000    5.272740000
>     C      3.661170000   11.641090000    5.295640000
>     C      3.083100000   12.884600000    5.003540000
>     C      3.674620000   13.865320000    5.089600000
>     C      3.030340000   15.177600000    4.705970000
>     C      3.825140000   16.397540000    5.093560000
>     C      3.253690000   17.486040000    5.625480000
>     C      4.054690000   18.671020000    5.970040000
>     C      1.054790000    2.008520000    3.477320000
>     C      1.776860000    3.287390000    3.824080000
>     C      1.101080000    4.505410000    3.731870000
>     C      1.751180000    5.697370000    4.053650000
>     C      1.012290000    7.029190000    3.874520000
>     C      1.693440000    8.191510000    4.545890000
>     C      1.032580000    9.502600000    4.698030000
>     C      1.611430000   10.443110000    4.855210000
>     C      0.986210000   11.677480000    4.677890000
>     C      1.694580000   12.873880000    4.816020000
>     C      0.909360000   14.117840000    5.147140000
>     C      1.600690000   15.254060000    5.143710000
>     C      1.016000000   16.512880000    5.616060000
>     C      1.802090000   17.562760000    5.857990000
>     C      1.193020000   18.839560000    6.360310000
>     C      1.686490000    0.835000000    3.549300000
> K_POINTS automatic
>   4 4 1   1 1 1
>
> Any help would be appreciated.
>
> Kind Regards,
>
> --
> Dr. Siddheshwar chopra,
> M.Sc., Ph.D (Physics)
> Assistant Professor (Physics),
> Amity University, Noida, India.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> Dr. Gabriele Sclauzero
> Materials Theory - ETHZ
> ETH Zurich, HIT G 43.2
> Wolfgang-Pauli-Str. 27
> 8093 Zürich, Switzerland
>
> Phone +41 44 633 94 10
> Fax +41 44 633 14 59
> gabriele.sclauzero at mat.ethz.ch<mailto:gabriele.sclauzero at mat.ethz.ch>
> www.theory.mat.ethz.ch
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>



-- 
*Dr. Siddheshwar chopra,*


*M.Sc., Ph.D (Physics)Assistant Professor (Physics),*
*Amity University, Noida, India.*
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