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<p>Hi Minoru,</p>
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<p> Thank you for clarifying! I will proceed to calculate, is it worth making a QE example for this? It would be quite nice to have your result in there!</p>
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<p>Kindest regards,</p>
<p>Louis<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> pw_forum-bounces@pwscf.org <pw_forum-bounces@pwscf.org> on behalf of Minoru Otani <minoru.otani@aist.go.jp><br>
<b>Sent:</b> 24 February 2017 14:24:31<br>
<b>To:</b> PWSCF Forum<br>
<b>Subject:</b> Re: [Pw_forum] ESM Example (Al slab with bc2) and Otani/Sugino example</font>
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Dear Louis,</div>
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Thank you for using the ESM. The figure 1 in the paper shows how does the unit cell place in the z-direction. As you see, we need to put enough vacuum region on both sides of a slab. Accordingly, the 3rd cell parameter (Lz) becomes large. The z0 is not equal
to Lz but equal to Lz/2.</div>
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There are some example calculations in ESM_examle directory. I recommend you to have a look at the Aluminum (001) slab calculations with various boundary conditions. </div>
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Best regards,</div>
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Minoru</div>
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<div class="">--------------------------------------------------------------------------------------------------------</div>
<div class="">Minoru Otani</div>
<div class="">National Institute of Advanced Industrial Science and Technology</div>
<div class="">Research Centre for Computational Design of Advanced Functional Materials</div>
<div class="">email : <a href="mailto:minoru.otani@aist.go.jp" class="">minoru.otani@aist.go.jp</a><br class="">
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<div class="">On Feb 23, 2017, at 21:42, Louis Fry-Bouriaux <<a href="mailto:ellf@leeds.ac.uk" class="">ellf@leeds.ac.uk</a>> wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi there,</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""> I am trying to understand the ESM example with bc2 (metal-slab-metal) distributed with QE 6.0 which consists of an Al(001) slab between two electrodes, and at the same time I am trying to replicate
the results of Otani and Sugino in their paper (Phys. Rev. B, 73, 115407, 2006) which consists of an Al/Si(111)/Al slab between two screening boundaries.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I have a few questions:<br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">** 1. ** In the QE example the following cell params and atomic positions are specified:</div>
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<div class="">CELL_PARAMETERS bohr<br class="">
10.82227686 0.00000000 0.00000000<br class="">
0.00000000 10.82227686 0.00000000<br class="">
0.00000000 0.00000000 22.67672253<br class="">
ATOMIC_POSITIONS bohr<br class="">
Al 0.00000000 0.00000000 0.00000000<br class="">
Al 5.41113843 0.00000000 0.00000000<span class="Apple-converted-space"> </span><br class="">
Al 0.00000000 5.41113843 0.00000000<span class="Apple-converted-space"> </span><br class="">
Al 5.41113843 5.41113843 0.00000000 </div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">My understanding is that the cell will repeat without overlapping atoms along X and Y. What I'm not clear on is why the 3rd lattice vector is so large?</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">The parameter 'esm_w' defaults to zero and is not specified in the example, so does this large value mean that there is a region of vacuum? Or does it just repeat the atoms such that in the Z-direction
there are 5 Al layers? I'm guessing that this 3rd cell parameter Z-value corresponds to L_z, which in the paper corresponds to z_0?</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">** 2. ** I have reproduced the 'surface unit cell' from Otani/Sugino's paper using VESTA.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">My concern here is with the correct repetition of atoms in X and Y, and what exactly happens with the Z direction. I realize I must first rotate the unit cell such that the repeated Al atoms lie perpendicular
to the Z Cartesian axis which I have not done yet.</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I have tested the repetition of this cell within VESTA along vectors perpendicular to the Al plane. So my most important question is: if the height of the cell along Z is ~14.4281 Angstrom (measured
from Al center plane), then the third 'CELL_PARAMETERS' entry (after rotation) should be this value exactly + the 'decay length' of the wavefunction in Z? Then the parameter 'esm_w' is used to set z_1 from the paper I suppose?<br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">I will generate an xyz file of the surface cell, but if I repeat by 3.816 A along a surface lattice vector, it is a matter of just deleting the entries that cause an overlap of the atoms I suppose?</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Thank you for your time and sorry for the very long email,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Kindest regards,</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">Louis<br class="">
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