<div dir="ltr"><div><div>Dear <span class=""><span class="">Gabriele Sclauzero<br><br></span></span></div><span class=""><span class="">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)? <br>
</span></span></div><div><span class=""><span class="">Reference article for leads: </span></span><span class=""><span class=""><i><span class="">Physica B: Condensed Matter</span></i>, <i>Volume 406, Issue 20</i>, <i>15 October 2011</i>, <i>Pages <span class="">3969</span>-3974</i> </span></span></div>
<div><span class=""><span class=""><br></span></span></div><span class=""><span class="">Wishes<br></span></span></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Tue, Jan 28, 2014 at 1:41 PM, Gabriele Sclauzero <span dir="ltr"><<a href="mailto:gabriele.sclauzero@epfl.ch" target="_blank">gabriele.sclauzero@epfl.ch</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="word-wrap:break-word">Dear Khadije,<div><br></div><div> On top of the possible memory problem pointed out by Paolo, I see several issues in your input. </div>
<div><br></div><div>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.<br>
<div><br></div><div>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).</div><div><br></div><div>
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 (<a href="http://www.xcrysden.org/" target="_blank">http://www.xcrysden.org/</a>) 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. </div>
<div><br></div><div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div><br></div><div>HTH</div><div><br></div><div>GS</div><div>ETHZ, Materials Theory</div><div><div class="h5"><div><div><div><br></div><blockquote type="cite"><div dir="ltr"><div><div><div><div><span style><span style="background-color:rgb(238,238,238)"><span>Dear Gabriele Sclauzero <br>
<br></span></span></span></div><span style><span style="background-color:rgb(238,238,238)"><span>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?<br>
<br></span></span></span></div><span style><span style="background-color:rgb(238,238,238)"><span>input file:<br> &control<br> calculation = 'relax'<br> restart_mode='from_scratch',<br>
prefix='adn',<br> tprnfor = .true.<br> pseudo_dir = '/home/khalili/espresso-5.0.2/pseudo',<br> outdir='./'<br> /<br> &system<br> ibrav= 0, celldm(1)=6.0,<br> nat= 23, ntyp= 5,<br>
noncolin=.true.,<br> lspinorb=.true.,<br> starting_magnetization(1)=0.0,<br> ecutwfc = 35.0,<br> ecutrho = 350.0,<br> occupations='smearing',<br> smearing='methfessel-paxton',<br> degauss=0.01<br>
/<br> &electrons<br> diagonalization='david'<br> electron_maxstep = 500,<br> mixing_mode = 'plain'<br> mixing_beta = 0.3<br> conv_thr = 1.0d-8<br> /<br>&ions<br> ion_dynamics = 'bfgs'<br>
/<br>ATOMIC_SPECIES<br> C 12.0107 C.pbe-n-kjpaw.UPF<br> H 1.0 H.pbe-kjpaw.UPF<br> N 14.0067 N.pbe-kjpaw.UPF<br> Au 196.96655 Au.pbe-dn-kjpaw.UPF <br> S 32.065 S.pbe-n-kjpaw.UPF<br>ATOMIC_POSITIONS<br>
N 0.170976000 0.000000000 0.000000000<br> C -0.170976000 0.000000000 0.000000000<br> N -0.382005000 0.268863000 0.000000000<br> C -0.210257000 0.563407000 0.000016000<br> C 0.142155000 0.600825000 -0.000027000<br>
C 0.334612000 0.302284000 0.000800000<br> N 0.676126000 0.302006000 0.001939000<br> N 0.233362000 0.942208000 -0.004019000<br> C -0.064351000 1.105626000 -0.011570000<br> N -0.330002000 0.881899000 0.000315000<br>
S -0.270976000 -0.450000000 0.000000000<br> H 0.798025000 0.039749000 0.001986000<br> H 0.805314000 0.502022000 -0.000734000<br> S -0.064351000 1.568242000 -0.011570000<br> H -0.553279000 0.914575000 0.131427000<br>
Au -0.464351000 1.914575000 -0.011570000<br> Au 0.335649000 1.914575000 -0.011570000<br> Au -0.064351000 1.914575000 -0.411570000<br> Au -0.064351000 1.914575000 0.388430000<br> Au -0.670976000 -0.950000000 0.000000000<br>
Au 0.129024000 -0.950000000 0.000000000<br> Au -0.270976000 -0.950000000 0.400000000<br> Au -0.270976000 -0.950000000 -0.400000000<br>CELL_PARAMETERS cubic<br> 6.0 0.0 0.0<br> 0.0 6.0 0.0<br> 0.0 0.0 6.0<br>
K_POINTS {Automatic}<br> 2 2 1 1 1 1<br><br>mpirun -np 20 /home/khalili/espresso-5.0.2/bin/pw.x -in <a href="http://adn.rx.in/" target="_blank">adn.rx.in</a> | tee adn.rx.out<br><br><br></span></span></span></div><span style><span style="background-color:rgb(238,238,238)"><span>output: <br>
. <br> . <br> .<br> per-process dynamical memory: 627.4 Mb<br><br> Self-consistent Calculation<br><br> iteration # 1 ecut= 35.00 Ry beta=0.70<br> Davidson diagonalization with overlap<br>
<br>===================================================================================<br>= BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES<br>= EXIT CODE: 9<br>= CLEANING UP REMAINING PROCESSES<br>= YOU CAN IGNORE THE BELOW CLEANUP MESSAGES<br>
===================================================================================<br>YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Killed (signal 9)<br>This typically refers to a problem with your application.<br>Please see the FAQ page for debugging suggestions.</span></span></span></div>
</div></blockquote></div></div></div></div></div></div><br>_______________________________________________<br>
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<a href="http://pwscf.org/mailman/listinfo/pw_forum" target="_blank">http://pwscf.org/mailman/listinfo/pw_forum</a><br></blockquote></div><br><br clear="all"><br>-- <br><div dir="ltr"><div>Khadije Khalili</div><div>Ph.D Student of Solid-State Physics</div>
<div>Department of Physics</div><div>University of Mazandaran</div><div>Babolsar, Iran</div><div><a href="mailto:kh.khalili@stu.umz.ac.ir" target="_blank">kh.khalili@stu.umz.ac.ir</a></div><div> </div></div>
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