[Pw_forum] tranmission calculation
raha khalili
khadije.khalili at gmail.com
Tue Jan 28 11:40:36 CET 2014
Dear Gabriele Sclauzero
Thank you very much for your reply, it is really appreciated. I will
changed all parameters of my input file. I have a planer molecule in X-Y
plane and I want to use a planar lead in Y-Z. I realized I have to change
the transmission direction to Z. Could I have a lead in X-Y plane and
calculate transmission for all structure (as an extended molecule or
scattering region)?
Reference article for leads: *Physica B: Condensed Matter*, *Volume 406,
Issue 20*, *15 October 2011*, *Pages 3969-3974*
Wishes
On Tue, Jan 28, 2014 at 1:41 PM, Gabriele Sclauzero <
gabriele.sclauzero at epfl.ch> wrote:
> 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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>
--
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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