Dear Khadije,
On top of the possible memory problem pointed out by Paolo, I see several
issues in your input.
1. Unless things have changed recently, you must use fully-relativistic
pseudopotentials in combination with lspinorb=.true. (I wonder why the code
does not stop earlier with an error message). Anyway, I suggest you to start
with scalar-relativistic collinear calculations. They are much faster and the
relaxed structure should not change much. Once you got familiar with collinear
calculations in PWscf and PWCOND you might consider investigating spin-orbit
effects.
2. You are using PAW datasets, which is a relatively recent feature. I don't
think that it has been extended to the transmission calculations with PWCOND
yet (please check).
3. The new atomic geometry is still far from what you need for the scattering
region. You are still simulating an isolated (0D) object, not a 1D object. I
would suggest you to use XCrysDen (http://www.xcrysden.org/) to visualize your
input geometry. If you repeat your unit cell along z (using shift-n key), you
will probably realize it immediately. If your left/right leads are monatomic Au
chains, then you have to put a short linear chain on each side of the molecule
(not a square as you do now) and then appropriately choose the length of the
unit cell along z.
4. Beware: in the transmission calculations the transport direction is always
along z, not along y as you instead seem to assume now. Also, the scatterer has
to be at the center of the unit cell, and the continuations of the leads
(atomic chains) at the edges. Please have a VERY CAREFUL look at the examples
in PWCOND/examples/, also with the aid of xcrysden.
5. You will need to select the k-points in a more suitable way: one k point in
the xy plane should be sufficient, while you need to check convergence along z.
But before doing this, you need to solve issue #3.
HTH
GS
ETHZ, Materials Theory
> 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.
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