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

Sclauzero Gabriele gabriele.sclauzero at mat.ethz.ch
Thu Jul 3 14:48:24 CEST 2014


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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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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