[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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