[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.
>
> _______________________________________________
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> 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
>
>
> _______________________________________________
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>
--
*Dr. Siddheshwar chopra,*
*M.Sc., Ph.D (Physics)Assistant Professor (Physics),*
*Amity University, Noida, India.*
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