Dear Gabriele Sclauzero
Thanks alot for your answer. I changed my molecule and added 4 Au atoms
instead of 2. I am getting an error after running it. could you help me
please?
input file:
&control
calculation = 'relax'
restart_mode='from_scratch',
prefix='adn',
tprnfor = .true.
pseudo_dir = '/home/khalili/espresso-5.0.2/pseudo',
outdir='./'
/
&system
ibrav= 0, celldm(1)=6.0,
nat= 23, ntyp= 5,
noncolin=.true.,
lspinorb=.true.,
starting_magnetization(1)=0.0,
ecutwfc = 35.0,
ecutrho = 350.0,
occupations='smearing',
smearing='methfessel-paxton',
degauss=0.01
/
&electrons
diagonalization='david'
electron_maxstep = 500,
mixing_mode = 'plain'
mixing_beta = 0.3
conv_thr = 1.0d-8
/
&ions
ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
C 12.0107 C.pbe-n-kjpaw.UPF
H 1.0 H.pbe-kjpaw.UPF
N 14.0067 N.pbe-kjpaw.UPF
Au 196.96655 Au.pbe-dn-kjpaw.UPF
S 32.065 S.pbe-n-kjpaw.UPF
ATOMIC_POSITIONS
N 0.170976000 0.000000000 0.000000000
C -0.170976000 0.000000000 0.000000000
N -0.382005000 0.268863000 0.000000000
C -0.210257000 0.563407000 0.000016000
C 0.142155000 0.600825000 -0.000027000
C 0.334612000 0.302284000 0.000800000
N 0.676126000 0.302006000 0.001939000
N 0.233362000 0.942208000 -0.004019000
C -0.064351000 1.105626000 -0.011570000
N -0.330002000 0.881899000 0.000315000
S -0.270976000 -0.450000000 0.000000000
H 0.798025000 0.039749000 0.001986000
H 0.805314000 0.502022000 -0.000734000
S -0.064351000 1.568242000 -0.011570000
H -0.553279000 0.914575000 0.131427000
Au -0.464351000 1.914575000 -0.011570000
Au 0.335649000 1.914575000 -0.011570000
Au -0.064351000 1.914575000 -0.411570000
Au -0.064351000 1.914575000 0.388430000
Au -0.670976000 -0.950000000 0.000000000
Au 0.129024000 -0.950000000 0.000000000
Au -0.270976000 -0.950000000 0.400000000
Au -0.270976000 -0.950000000 -0.400000000
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 1 1 1 1
mpirun -np 20 /home/khalili/espresso-5.0.2/bin/pw.x -in adn.rx.in | tee
adn.rx.out
output:
.
.
.
per-process dynamical memory: 627.4 Mb
Self-consistent Calculation
iteration # 1 ecut= 35.00 Ry beta=0.70
Davidson diagonalization with overlap
===================================================================================
= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
= EXIT CODE: 9
= CLEANING UP REMAINING PROCESSES
= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions.
Thanks and Regards
On Wed, Jan 22, 2014 at 1:46 PM, Gabriele Sclauzero <
gabriele.sclauzero at epfl.ch> wrote:
> Dear Khadije 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.
>
>
> I could not find the file for the scattering region in your attachments.
> In any case, I think it is not sufficient to include one gold atom on each
> side of the molecule, because the scattering cell has to describe a 1D
> geometry, not just an isolated molecule (scatterer). In other words, the
> scattering region must contain part of the left and the right leads at the
> sides of the scatterer.
> You need to include enough gold atoms on each side such that the Kohn-Sham
> potential at the apex of the scattering region does not "feel" the
> perturbation of the molecule in the middle. See, for instance, Fig.1 of
> http://prb.aps.org/abstract/PRB/v85/i16/e165411.
> You can check this by comparing the complex band structure of the one atom
> cell obtained by cutting out an edge of the scattering cell (using
> prefixt="benzene" and bdl=..., see the PWcond user guide) with that of the
> lead region. See Alexander Smogunov's paper
> http://www.sciencedirect.com/science/article/pii/S0039602803004539, and
> following ones citing this one.
>
> By the way, I think that in your case you could make the scattering cell
> symmetric and use ikind=1 for the transmission calculation. There is no
> need for distinct left and right leads.
> Moreover, have you actually understood the meaning of ikind? ikind=0 is
> for the complex band structure calculation, while for the transmission you
> need ikind=1 (equal leads) or ikind=2 (distinct left and right leads).
> Please see here http://iramis.cea.fr/Pisp/alexander.smogunov/ and have a
> careful look to the examples in PWcond/examples.
>
>
> 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?
>
>
> Relaxing or not the atomic structure in the scattering region is a
> delicate matter with this geometry, because you do not have massive leads
> and you cannot just fully relax all atoms in the scattering region. You
> might try to relax the molecule and a few gold atoms on each side, while
> keeping fixed those toward the edges (after you include them). You might
> also repeat this operation for different values of the cell size along the
> transport direction and take the one with the lowest energy.
> In any case, to get realistic conductance value you need to include
> massive leads (i.e., gold surfaces or tips, see our other 2012 PRB:
> http://prb.aps.org/abstract/PRB/v85/i16/e165412).
>
> HTH
>
> Gabriele Sclauzero
> Materials Theory, ETHZ
>
>
> 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
>
>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org
> http://pwscf.org/mailman/listinfo/pw_forum
>
--
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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