[Pw_forum] tranmission calculation

raha khalili khadije.khalili at gmail.com
Tue Jan 28 13:50:41 CET 2014 

Dear Dr. Gabriele Sclauzero

Very thanks for your reply and suggestions.

Sincerely yours


On Tue, Jan 28, 2014 at 2:48 PM, Sclauzero Gabriele <
gabriele.sclauzero at mat.ethz.ch> wrote:

>
>
>
> 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.
>
> Good!
>
> 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
>
> You can also calculate transport for a system geometry with leads made of
> "thick" nanowires or extend 2D surfaces as in the paper you cite. The
> latter case requires to sample the k_perpendicular-dependent transmission
> in the 2D Brillouin zone. Moreover, the calculation for each k_perp. is
> much more demanding than in the monatomic chain case.
> I would suggest you to start with the simple case of the monatomic chain
> and then move to the massive leads.
> The two PRB papers I have mentioned in my first reply can give you a good
> idea for the two cases. Those calculations have been performed with PWscf
> and PWCOND.
>
> GS
>
>
> Wishes
>
>
> On Tue, Jan 28, 2014 at 1:41 PM, Gabriele Sclauzero <
> gabriele.sclauzero at epfl.ch<mailto: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<
> http://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.
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org<mailto: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<mailto:kh.khalili at stu.umz.ac.ir>
>
> _______________________________________________
> Pw_forum mailing list
> Pw_forum at pwscf.org<mailto:Pw_forum at pwscf.org>
> http://pwscf.org/mailman/listinfo/pw_forum
>
>
> Dr. Gabriele Sclauzero
> Materials Theory - ETHZ
> ETH Zurich, HIT G 43.2
> Wolfgang-Pauli-Str. 27
> 8093 Zürich, Switzerland
>
> Phone +41 44 633 94 10
> Fax +41 44 633 14 59
> gabriele.sclauzero at mat.ethz.ch<mailto:gabriele.sclauzero at mat.ethz.ch>
> www.theory.mat.ethz.ch
>
>
> _______________________________________________
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.quantum-espresso.org/pipermail/users/attachments/20140128/e0f4742d/attachment.html>

More information about the users mailing list