<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Usually, you would NEVER edit a cif file, unless you know very
well the corresponding rules.</p>
<p>You have two possibilities to modify a structure:</p>
<p>I 've seen that the cif file is from VESTA. VESTA allows you to
remove atoms, create larger cells, ....</p>
<p>Then export it as cif file and import it into WIEN2k. Then run
the symmetry programs nn, sgroup and symmetry.</p>
<p><br>
</p>
<p>Alternatively, convert the cif into a struct file and use the
wien2k tools (x supercell) and the structeditor to remove atoms. <br>
</p>
<p>In any case, it is your responsibility to create a "reasonable"
model. You cannot expect that I search the literature to find out
the typical vacancy concentration of HfO2. But it should be clear:
for a 3% vacancy concentration you need a supercell with about 30
oxygen atoms, .....<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">Am 20.06.2023 um 09:18 schrieb Pranjal
Nandi:<br>
</div>
<blockquote type="cite"
cite="mid:AS5PR07MB10084CA0D1E2E50F80006B4F3AB5CA@AS5PR07MB10084.eurprd07.prod.outlook.com">
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
<meta name="Generator" content="Microsoft Word 15 (filtered
medium)">
<style>@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}@font-face
{font-family:"Calibri Light";
panose-1:2 15 3 2 2 2 4 3 2 4;}@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0in;
font-size:10.0pt;
font-family:"Courier New";}p.MsoListParagraph, li.MsoListParagraph, div.MsoListParagraph
{mso-style-priority:34;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:11.0pt;
font-family:"Calibri",sans-serif;}span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:Consolas;}span.EmailStyle22
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;
mso-ligatures:none;}div.WordSection1
{page:WordSection1;}ol
{margin-bottom:0in;}ul
{margin-bottom:0in;}</style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
<div class="WordSection1">
<p class="MsoNormal"><span lang="EN-US">Dear Peter and Laurence,
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US">Thank you for your
valuable inputs. I have some followup queries.
<o:p></o:p></span></p>
<ol type="1" start="1">
<li class="MsoListParagraph"
style="margin-bottom:12.0pt;mso-list:l0 level1 lfo2">
<span lang="EN-US">In the attached CIF file, I want to do
DFT simulation on two situations. One when there is excess
oxygen and one in less oxygen. However, I am confused as
which part of the cif file I should modify/implement the
changes
<o:p></o:p></span></li>
<ol type="a" start="1">
<li class="MsoListParagraph"
style="margin-bottom:12.0pt;mso-list:l0 level2 lfo2">
<span lang="EN-US">If I add a new line and add more
oxygen, I am unsure of what I should set in other
parameters such as label, occupancy, fract_x,y,z etc.
<o:p></o:p></span></li>
<li class="MsoListParagraph"
style="margin-bottom:12.0pt;mso-list:l0 level2 lfo2">
<span lang="EN-US">I am also confused on how many
additions/removal can be considered as significant
addition/reduction.
<o:p></o:p></span></li>
</ol>
<li class="MsoListParagraph"
style="margin-bottom:12.0pt;mso-list:l0 level1 lfo2">
<span lang="EN-US">When I am adding/subtracting oxygen, for
realistic results (matching simulation with lab
experimental data), I should be doing the simulations on a
large supercell or unit cell (for oxygen vacancies, I know
that I should do a supercell as I cannot create it in the
unit cell cif file)?<o:p></o:p></span></li>
</ol>
<p class="MsoNormal"><span lang="EN-US">Once again, thank you so
much for your continuous support to the community.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal">With warm regards,<o:p></o:p></p>
<p class="MsoNormal">Pranjal<span
style="font-size:12.0pt;font-family:"Calibri
Light",sans-serif"><o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1
1.0pt;padding:3.0pt 0in 0in 0in">
<p class="MsoNormal"><b><span lang="EN-US">From:</span></b><span
lang="EN-US"> Wien
<a class="moz-txt-link-rfc2396E" href="mailto:wien-bounces@zeus.theochem.tuwien.ac.at"><wien-bounces@zeus.theochem.tuwien.ac.at></a>
<b>On Behalf Of </b>Peter Blaha<br>
<b>Sent:</b> Thursday, June 15, 2023 5:11 PM<br>
<b>To:</b> <a class="moz-txt-link-abbreviated" href="mailto:wien@zeus.theochem.tuwien.ac.at">wien@zeus.theochem.tuwien.ac.at</a><br>
<b>Subject:</b> Re: [Wien] Requesting gentle
clarification on OMP_NUM_THREADS, run_lapw, volume
optimisation and wien2k update.<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p>In addition to what L. Marks has already said:<o:p></o:p></p>
<p>A unit cell with 216 atoms should be run in mpi parallel
mode. You won't have too many k-points probably, in
particularly when doing position optimization.<o:p></o:p></p>
<p>About OMP Laurence Marks has already answered. The Intel mkl
does not scale to higher OMP numbers. But: Test it out
yourself. Set OMP_NUM_TREADS to 1 and run one iteration. Check
the dayfile how long it takes. Set it to 2,4,8,16 and check
the timing .... You should see that lapw0 will benefit when
you set it to 64 (for your 216 atom cell), but unfortunately
not much speedup in lapw1/2 anymore.<o:p></o:p></p>
<p>Update of WIEN2k: You should install wien2k into a new
directory, thus you do not destroy the old installation. In
addition, there is a "copy" function in siteconfig which would
copy the old settings to the new installation. It is briefly
described on the download page .and in the (new !) usersguide
as well as in the "update" site of wien2k.<o:p></o:p></p>
<p>Updating is strongly recommended since the new init_lapw has
some automatic precision settings and you won't run your
supercell with 1000 k-points .....<o:p></o:p></p>
<p>Volume optimization for high vacancy concentration is ok.
What you read in the UG concerns the stress tensor, which is
only NREL.<o:p></o:p></p>
<p>Hf-4f: No, these are core/semicore states. You don't need
onsite-hybrid or LDA+U. However, depending on your RMTs you
may be able to put them into the core by specifying a charge
criterium instead of an energy (like init -ecut 0.999)<o:p></o:p></p>
<p><o:p> </o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I
have some general queries and it would be great if you can
kindly provide me your feedback.
<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><br>
<br>
<br>
<o:p></o:p></p>
<ol type="1" start="1">
<li class="MsoListParagraph" style="mso-list:l1 level1
lfo1">I have 64 CPU (32 x 2) and more than 9 TB space
and the system is dedicated entirely to do simulations
on DFT. I was thinking to set the OMP_NUM_THREADS at 40
or 50 (even higher) to use the maximum potential of the
computer. But in the guidebook, it is recommended that I
do not set it higher than 8. May I please the reason for
this recommendation?<br>
<br>
<br>
<o:p></o:p></li>
<li class="MsoListParagraph" style="mso-list:l1 level1
lfo1">Is there a code to run_lapw continuously till it
reaches the convergence and not start it again after 40
cycles?<br>
<br>
<br>
<o:p></o:p></li>
<li class="MsoListParagraph" style="mso-list:l1 level1
lfo1">If I do a volume optimization for a single unit
cell and then I create a supercell of the optimized
structure. Does the supercell remains in optimized
volume condition? Or it is recommended that I do a
volume optimization for the supercell as well. Further
is WIEN2k a reliable platform for volume optimization of
HfO as in the guidebook on page 87 it mentions “The
accuracy is thus limited to first and second row
elements (maybe early 3d elements) and in particular for
the 5d series and above, large errors may occur due to
the neglect of (scalar-) relativistic corrections.”<br>
<br>
<br>
<o:p></o:p></li>
<li class="MsoListParagraph" style="mso-list:l1 level1
lfo1">Lastly, as it says on the website that it is
highly recommended to update the WIEN2K version, I am
unable to find the manual where I can follow the
instructions to update the version. As I have not done
any installation of WIEN2K (my past colleague installed
the present version), I am worried that while upgrading
I may commit some mistake. A guideline on updating would
have been very helpful.<o:p></o:p></li>
</ol>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Looking
forward to your kind feedback.
<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thank
you in advance.
<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">With
warm regards,<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Pranjal<o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:1.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<p class="MsoNormal"><br>
<br>
<span
style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#999999">Aquest
missatge, i els fitxers adjunts que hi pugui haver, pot
contenir informació confidencial o protegida legalment i
s’adreça exclusivament a la persona o entitat
destinatària. Si no consteu com a destinatari final o no
teniu l’encàrrec de rebre’l, no esteu autoritzat a
llegir-lo, retenir-lo, modificar-lo, distribuir-lo,
copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per
error, informeu-ne el remitent i elimineu del sistema tant
el missatge com els fitxers adjunts que hi pugui haver.<br>
<br>
Este mensaje, y los ficheros adjuntos que pueda incluir,
puede contener información confidencial o legalmente
protegida y está exclusivamente dirigido a la persona o
entidad destinataria. Si usted no consta como destinatario
final ni es la persona encargada de recibirlo, no está
autorizado a leerlo, retenerlo, modificarlo, distribuirlo
o copiarlo, ni a revelar su contenido. Si lo ha recibido
por error, informe de ello al remitente y elimine del
sistema tanto el mensaje como los ficheros adjuntos que
pueda contener.<br>
<br>
This email message and any attachments it carries may
contain confidential or legally protected material and are
intended solely for the individual or organization to whom
they are addressed. If you are not the intended recipient
of this message or the person responsible for processing
it, then you are not authorized to read, save, modify,
send, copy or disclose any part of it. If you have
received the message by mistake, please inform the sender
of this and eliminate the message and any attachments it
carries from your account.</span> <br>
<br>
<o:p></o:p></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>Wien mailing list<o:p></o:p></pre>
<pre><a href="mailto:Wien@zeus.theochem.tuwien.ac.at" moz-do-not-send="true" class="moz-txt-link-freetext">Wien@zeus.theochem.tuwien.ac.at</a><o:p></o:p></pre>
<pre><a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien" moz-do-not-send="true" class="moz-txt-link-freetext">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><o:p></o:p></pre>
<pre>SEARCH the MAILING-LIST at: <a href="http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html" moz-do-not-send="true" class="moz-txt-link-freetext">http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html</a><o:p></o:p></pre>
</blockquote>
<pre>-- <o:p></o:p></pre>
<pre>-----------------------------------------------------------------------<o:p></o:p></pre>
<pre>Peter Blaha, Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna<o:p></o:p></pre>
<pre>Phone: +43-158801165300<o:p></o:p></pre>
<pre>Email: <a href="mailto:peter.blaha@tuwien.ac.at" moz-do-not-send="true" class="moz-txt-link-freetext">peter.blaha@tuwien.ac.at</a> <o:p></o:p></pre>
<pre>WWW: <a href="http://www.imc.tuwien.ac.at" moz-do-not-send="true" class="moz-txt-link-freetext">http://www.imc.tuwien.ac.at</a> WIEN2k: <a href="http://www.wien2k.at" moz-do-not-send="true" class="moz-txt-link-freetext">http://www.wien2k.at</a><o:p></o:p></pre>
<pre>-------------------------------------------------------------------------<o:p></o:p></pre>
</div>
<br>
<br>
<font size="1" face="Arial" color="#999999">Aquest missatge, i els
fitxers adjunts que hi pugui haver, pot contenir informació
confidencial o protegida legalment i s’adreça exclusivament a la
persona o entitat destinatària. Si no consteu com a destinatari
final o no teniu l’encàrrec de rebre’l, no esteu autoritzat a
llegir-lo, retenir-lo, modificar-lo, distribuir-lo, copiar-lo ni
a revelar-ne el contingut. Si l’heu rebut per error, informeu-ne
el remitent i elimineu del sistema tant el missatge com els
fitxers adjunts que hi pugui haver.<br>
<br>
Este mensaje, y los ficheros adjuntos que pueda incluir, puede
contener información confidencial o legalmente protegida y está
exclusivamente dirigido a la persona o entidad destinataria. Si
usted no consta como destinatario final ni es la persona
encargada de recibirlo, no está autorizado a leerlo, retenerlo,
modificarlo, distribuirlo o copiarlo, ni a revelar su contenido.
Si lo ha recibido por error, informe de ello al remitente y
elimine del sistema tanto el mensaje como los ficheros adjuntos
que pueda contener.<br>
<br>
This email message and any attachments it carries may contain
confidential or legally protected material and are intended
solely for the individual or organization to whom they are
addressed. If you are not the intended recipient of this message
or the person responsible for processing it, then you are not
authorized to read, save, modify, send, copy or disclose any
part of it. If you have received the message by mistake, please
inform the sender of this and eliminate the message and any
attachments it carries from your account.</font>
<br>
<fieldset class="moz-mime-attachment-header"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Wien mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Wien@zeus.theochem.tuwien.ac.at">Wien@zeus.theochem.tuwien.ac.at</a>
<a class="moz-txt-link-freetext" href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a>
SEARCH the MAILING-LIST at: <a class="moz-txt-link-freetext" href="http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html">http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html</a>
</pre>
</blockquote>
<pre class="moz-signature" cols="72">--
-----------------------------------------------------------------------
Peter Blaha, Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email: <a class="moz-txt-link-abbreviated" href="mailto:peter.blaha@tuwien.ac.at">peter.blaha@tuwien.ac.at</a>
WWW: <a class="moz-txt-link-freetext" href="http://www.imc.tuwien.ac.at">http://www.imc.tuwien.ac.at</a> WIEN2k: <a class="moz-txt-link-freetext" href="http://www.wien2k.at">http://www.wien2k.at</a>
-------------------------------------------------------------------------</pre>
</body>
</html>