[Pw_forum] tranmission calculation

[raha khalili]

Dear QE users
I am doing transmission calculation for a molecular wire, for example, a
Benzene molecule sandwiched between two gold electrode. I did relax and scf
calculation for a benzene molecule that 2 H atoms were substituted with 2
Au atoms. Then, I did scf calculation for a single Au atom with the
coordination just like as later calculation. Could you say me if my
calculation is true? Or I have to do relax and scf calculation for a single
benzene?

aur.scf.in:
&control
   calculation='scf'
   restart_mode='from_scratch',
   pseudo_dir = '/home/client3/espresso-5.0.2/pseudo',
   outdir='./'
   prefix='aur'
/
&system
   ibrav = 0,
   celldm(1) =6.0,
   nat= 1,ntyp= 1,nspin = 1,
   ecutwfc = 35.0,
   ecutrho = 350.0
   occupations='smearing',
   smearing='methfessel-paxton',
   degauss=0.01
/
&electrons
   conv_thr = 1.0e-8
   mixing_beta = 0.7
/
ATOMIC_SPECIES
 Au  196.96655 Au.pbe-dn-kjpaw.UPF
ATOMIC_POSITIONS
Au      -0.444314932  -0.706149130   0.008586376
CELL_PARAMETERS cubic
 6.0   0.0   0.0
 0.0   6.0   0.0
 0.0   0.0   6.0
K_POINTS (automatic)
2 2 2 1 1 1

 aul.scf.in
&control
   calculation='scf'
   restart_mode='from_scratch',
   pseudo_dir = '/home/client3/espresso-5.0.2/pseudo',
   outdir='./'
   prefix='au'
/
&system
   ibrav = 0,
   celldm(1) =6.0,
   nat= 1,ntyp= 1,nspin = 1,
   ecutwfc = 35.0,
   ecutrho = 350.0
   occupations='smearing',
   smearing='methfessel-paxton',
   degauss=0.01
/
&electrons
   conv_thr = 1.0e-8
   mixing_beta = 0.7
/
ATOMIC_SPECIES
 Au  196.96655 Au.pbe-dn-kjpaw.UPF
ATOMIC_POSITIONS
Au      -0.174740372   1.847908104   0.017126043
CELL_PARAMETERS cubic
 6.0   0.0   0.0
 0.0   6.0   0.0
 0.0   0.0   6.0
K_POINTS (automatic)
2 2 2 1 1 1

benzene.cond.in
&inputcond
    outdir='./'
    prefixl='aul'
    prefixr='aur'
    prefixs='benzene'
    band_file ='bands.dat'
    ikind=0
    energy0=1.d0
    denergy=-0.1d0
    ewind=3.d0
    epsproj=1.d-4
    nz1=1
/
    1
    0.0 0.0 1.0
    40


Waiting for your reply.
Thanks and Regards
-- 
Khadije Khalili
Ph.D Student of Solid-State Physics
Department of Physics
University of Mazandaran
Babolsar, Iran
kh.khalili at stu.umz.ac.ir
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