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 Z?rich, 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://pwscf.org/pipermail/pw_forum/attachments/20140128/e0f4742d/attachment.html
