<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Robert,<br class=""><br class=""><div class="">Let me start from the definition of the lattice vector.As defined in the manual:</div><div class=""><a href="http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm140629871958288" class="">http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#idm140629871958288</a></div><div class="">The crystal lattice vector is defined by the following expression:</div><div class=""> v1(1) <span class="Apple-tab-span" style="white-space:pre"> </span> v1(2) <span class="Apple-tab-span" style="white-space:pre"> </span> v1(3) <span class="Apple-tab-span" style="white-space:pre"> </span><span style="font-size: 14px;" class="">... 1st lattice vector<br class=""></span> v2(1) <span class="Apple-tab-span" style="white-space:pre"> </span> v2(2) <span class="Apple-tab-span" style="white-space:pre"> </span> v2(3) <span class="Apple-tab-span" style="white-space:pre"> </span><span style="font-size: 14px;" class="">...</span><span style="font-size: 14px;" class=""> 2nd lattice vector<br class=""></span> v3(1) <span class="Apple-tab-span" style="white-space:pre"> </span> v3(2) <span class="Apple-tab-span" style="white-space:pre"> </span> v3(3). <span style="font-size: 14px;" class="">... 3rd lattice vector</span></div><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">Requires cell with a_3 lattice vector along z, normal to the xy plane, with the slab centered around z=0<br class=""></blockquote></div><div class=""><br class=""></div>This sentence means that the inner product both v1 dot v3 and v2 dot v3 must be zero. Current implementation of the ESM does not allow to have finite values in v1(3), v2(3), v3(1), and v3(2).<div class=""><br class=""></div><div class=""><div class=""><blockquote type="cite" class=""> Also requires symmetry checking to be disabled along z, either by setting nosym = .TRUE.</blockquote><blockquote type="cite" class=""></blockquote></div><div class=""><blockquote type="cite" class=""></blockquote></div><blockquote type="cite" class=""><div class=""> or by very slight displacement (i.e., 5e-4 a.u.) of the slab along z.</div></blockquote><div class=""><br class=""></div>This requirement is necessary for bc2 and bc3. When we apply a bias potential to the slab, we break the symmetry along z-direction. However, if we put a symmetric (along z) slab at z=0, the pw.x find a symmetry operation in z-direction and try to symmetrize wave functions and potentials along z. You can not get a converged result with this symmetrize process. Thus I proposed two ways to avoid the symmetrize process along z:</div><div class="">The first one is to set “nosym = .TRUE.”. Note that this kills the symmetrize process not only the z-direction but also xy-direction.</div><div class="">The second one is to give a very slight displacement to the slab along z-direction. By doing this pw.x can not find any symmetry operation along z-direction but can find a symmetry operation along xy-direction.</div><div class=""><br class=""></div><div class="">If you want to calculate non-symmetric (along z) slab or you put a slab at z!=0, you can ignore this.</div><div class=""><br class=""></div><div class="">Best regards,</div><div class="">Minoru</div><div 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><div class=""><br class=""></div><div class=""><blockquote type="cite" class="">On Jul 29, 2017, at 21:13, Robert Molt <<a href="mailto:r.molt.chemical.physics@gmail.com" class="">r.molt.chemical.physics@gmail.com</a>> wrote:<br class=""><br class="">I appreciate the help. If ESM does not require this symmetry, can you explain what is meant by the manual's statement of:<br class="">:<br class="">"Requires cell with a_3 lattice vector along z,<br class=""><div class=""> normal to the xy plane, with the slab centered</div><div class=""> around z=0</div><div class="">. Also requires symmetry checking to be</div><div class=""> disabled along z, either by setting </div>nosym<div class=""> = .TRUE.</div><div class=""> or by very slight displacement (i.e., 5e-4 a.u.)</div><div class=""> of the slab along z."</div><div class=""><br class=""></div><div class=""><br class=""></div><br class="Apple-interchange-newline">I want to make sure I am in compliance with the manual's specifications, and I clearly must not understand what that means if I misinterpreted it to mean it requires symmetry along the z axis.<br class=""><br class="">Separately, given that we have no symmetry in xy, is it logically necessary to "cap" boundary atoms with hydrogens (or the like) to avoid artifacts at the boundary?<br class=""><br class="">On 7/28/17 6:41 PM, 大谷実 wrote:<br class=""><blockquote type="cite" cite="mid:38DEA408-9D97-479E-B7A8-38BEAD147ABA@aist.go.jp" 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; background-color: rgb(255, 255, 255);" class="">Dear Robert,<br class=""><br class="">Besides Lorenzo’s message, I can add one more thing. ESM does not require symmetry along z-axis, so you do not need to put an additional adsorbate molecule on the bottom. <br class=""><br class=""><blockquote type="cite" class=""><div class="">Also requires symmetry checking to be</div><div class=""> disabled along z, either by setting </div>nosym<div class=""> = .TRUE.</div><div class=""> or by very slight displacement (i.e., 5e-4 a.u.)</div><div class=""> of the slab along z.</div><br class=""></blockquote><br class=""><br class="">Best regard,<br class="">Minoru<br class="">--------------------------------------------------------------------------------------------------------<br class="">Minoru Otani<br class="">National Institute of Advanced Industrial Science and Technology<br class="">Research Centre for Computational Design of Advanced Functional Materials<br class="">email : <a href="mailto:minoru.otani@aist.go.jp" class="">minoru.otani@aist.go.jp</a><br class="">---------------------------------------------------------------------------------------------------------<br class=""><br class=""><blockquote type="cite" class="">On Jul 29, 2017, at 5:15, Lorenzo Paulatto <lorenzo.paulatto@impmc.upmc.fr> wrote:<br class=""><br class="">It does not matter, it is only need to be roughly centered <br class=""><br class="">-- <br class="">Lorenzo Paulatto<br class="">Written on a virtual keyboard with real fingers<br class=""><br class="">On 28 Jul 2017 9:36 p.m., "Dr. Robert Molt Jr." <r.molt.chemical.physics@gmail.com> wrote:<br class="">Good evening,<br class="">I am confused by the "centering" requirements of ESM. It is stated that:<br class=""><div class="">Requires cell with a_3 lattice vector along z,</div><div class=""> normal to the xy plane, with the slab centered</div><div class=""> around z=0. Also requires symmetry checking to be</div><div class=""> disabled along z, either by setting </div>nosym<div class=""> = .TRUE.</div><div class=""> or by very slight displacement (i.e., 5e-4 a.u.)</div><div class=""> of the slab along z.</div><br class="Apple-interchange-newline">I have constructed a slab which is symmetric about the xy plane and centered around z=0 contour. This is fine and good.<br class="">However, once I add the adsorbate molecule, I cannot have symmetry...unless it is intended that I add the same adsorbate molecule on the "bottom" of the simulation, too? I am unclear what is meant by the slab being "centered." Center of mass? Center of symmetry?<br class=""><br class=""><br class="">_______________________________________________<br class="">Pw_forum mailing list<br class="">Pw_forum@pwscf.org<br class="">http://pwscf.org/mailman/listinfo/pw_forum<br class="">_______________________________________________<br class="">Pw_forum mailing list<br class="">Pw_forum@pwscf.org<br class="">http://pwscf.org/mailman/listinfo/pw_forum<br class=""></blockquote><br class=""><br class=""><br class=""><div class="">_______________________________________________</div><div class="">Pw_forum mailing list</div><br class="Apple-interchange-newline">Pw_forum@pwscf.org<br class="">http://pwscf.org/mailman/listinfo/pw_forum<br class=""></blockquote><br class=""><br class=""></blockquote><br class=""></div></body></html>