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<p>I appreciate the help. If ESM does not require this symmetry, can
you explain what is meant by the manual's statement of:</p>
<p>:</p>
<p>"<font color="#ff0000">Requires cell with a_3 lattice vector
along z,
</font></p>
<pre style="font-size: 14px; color: rgb(0, 0, 0); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: 2; text-align: -webkit-left; text-indent: 0px; text-transform: none; widows: 2; word-spacing: 0px; -webkit-text-stroke-width: 0px; background-color: rgb(255, 255, 255); text-decoration-style: initial; text-decoration-color: initial; margin-top: 0em; margin-bottom: -1em;"><font color="#ff0000"> normal to the xy plane, with the slab centered
around z=0</font>. Also requires symmetry checking to be
disabled along z, either by setting <a href="http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nosym">nosym</a> = .TRUE.
or by very slight displacement (i.e., 5e-4 a.u.)
of the slab along z."
</pre>
<p>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.</p>
<p><br>
</p>
<p>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>
</p>
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</pre>
<br>
<div class="moz-cite-prefix">On 7/28/17 6:41 PM, 大谷実 wrote:<br>
</div>
<blockquote type="cite"
cite="mid:38DEA408-9D97-479E-B7A8-38BEAD147ABA@aist.go.jp">
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<div dir="auto" class="" style="word-wrap:break-word">Dear
Robert,
<div class=""><br class="">
</div>
<div 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. </div>
<div class=""><br class="">
</div>
<div class="">
<blockquote type="cite">
<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0px 0px
0px 0.8ex; border-left-width:1px;
border-left-style:solid;
border-left-color:rgb(204,204,204);
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<pre class="" style="font-size:14px; background-color:rgb(255,255,255); margin-top:0em">Also requires symmetry checking to be
disabled along z, either by setting <a href="http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nosym" target="_blank" class="" moz-do-not-send="true">nosym</a> = .TRUE.
or by very slight displacement (i.e., 5e-4 a.u.)
of the slab along z.</pre>
</div>
</blockquote>
</div>
</div>
</blockquote>
<div class=""><br class="">
</div>
</div>
<div class=""><br class="">
</div>
<div class="">Best regard,</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=""
moz-do-not-send="true">minoru.otani@aist.go.jp</a><br
class="">
<div class="">---------------------------------------------------------------------------------------------------------</div>
</div>
</div>
<div class=""><br class="">
</div>
<div class="">
<div class="AppleOriginalContents" style="direction:ltr">
<blockquote type="cite">
<div class="">On Jul 29, 2017, at 5:15, Lorenzo Paulatto
<a class="moz-txt-link-rfc2396E" href="mailto:lorenzo.paulatto@impmc.upmc.fr"><lorenzo.paulatto@impmc.upmc.fr></a> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div dir="auto" class="">It does not matter, it is
only need to be roughly centered <br class="">
<br class="">
<div class="">-- <br class="">
Lorenzo Paulatto<br class="">
Written on a virtual keyboard with real fingers</div>
</div>
<div class="gmail_extra"><br class="">
<div class="gmail_quote">On 28 Jul 2017 9:36 p.m.,
"Dr. Robert Molt Jr." <<a
href="mailto:r.molt.chemical.physics@gmail.com"
class="" moz-do-not-send="true">r.molt.chemical.physics@gmail.com</a>>
wrote:<br type="attribution" class="">
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex; border-left:1px #ccc solid;
padding-left:1ex">
<div bgcolor="#FFFFFF" class="">
<p class="">Good evening,</p>
<p class="">I am confused by the "centering"
requirements of ESM. It is stated that:</p>
<pre class="" style="font-size:14px; font-style:normal; font-weight:normal; letter-spacing:normal; text-indent:0px; text-transform:none; word-spacing:0px; background-color:rgb(255,255,255); margin-top:0em">Requires cell with a_3 lattice vector along z,
normal to the xy plane, with the slab centered
around z=0. Also requires symmetry checking to be
disabled along z, either by setting <a href="http://www.quantum-espresso.org/wp-content/uploads/Doc/INPUT_PW.html#nosym" target="_blank" class="" moz-do-not-send="true">nosym</a> = .TRUE.
or by very slight displacement (i.e., 5e-4 a.u.)
of the slab along z.
</pre>
<p class="">I have constructed a slab which is
symmetric about the xy plane and centered
around z=0 contour. This is fine and good.</p>
<p 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="">
</p>
<p class=""><br class="">
</p>
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