<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Louis,</div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">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><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Best regards,</div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Minoru</div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><br class=""></div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><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=""><div class="">---------------------------------------------------------------------------------------------------------</div></div><div class=""><br class=""></div></div></div><div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div><blockquote type="cite" class=""><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><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p><div class=""><div dir="ltr" class=""><div id="x_divtagdefaultwrapper" dir="ltr" style="font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols, 'Apple Color Emoji', 'Segoe UI Emoji', NotoColorEmoji, 'Segoe UI Symbol', 'Android Emoji', EmojiSymbols;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hi there,</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I have a few questions:<br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">** 1. ** In the QE example the following cell params and atomic positions are specified:</div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><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=""></div></div></div></div><span class="PersonaPaneLauncher"><div tabindex="-1" class="_pe_d _pe_12"></div></span><br class=""><p style="margin-top: 0px; margin-bottom: 0px;" class=""></p></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Pw_forum mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="mailto:Pw_forum@pwscf.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">Pw_forum@pwscf.org</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><a href="http://pwscf.org/mailman/listinfo/pw_forum" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://pwscf.org/mailman/listinfo/pw_forum</a></div></blockquote></div><br class=""></div></body></html>