[Pw_forum] Do we need to saturate the dangling bonds? and how to add vacuum?
siddheshwar chopra
sidhusai at gmail.com
Fri Jun 27 05:48:20 CEST 2014
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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