<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
</head>
<body bgcolor="#FFFFFF" text="#000000">
<div class="moz-cite-prefix">yes<br>
start from the perfect relaxed geometry (as obtained from
vc-relax)<br>
remove an atom and relax the internal structure.<br>
at the end also perform a vc-relaxation (from the fixed-cell
relaxed geometry)<br>
stefano <br>
<br>
On 06/08/2017 17:33, Manu Hegde wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CA+g44DssN3wwBuGO+hoTRcSfLdmC89ovmQ9KHxesvrK83eqRxg@mail.gmail.com">
<div dir="ltr">
<div class="gmail_default"
style="font-family:arial,helvetica,sans-serif">Hello Stephano,</div>
<div class="gmail_default"
style="font-family:arial,helvetica,sans-serif">Thanks for your
reply. Just to double check what you meant before starting the
calculations, you mean take the equilibrium values from the
vc-relax calculation (perfect cell, only co-ordinates) and do
the 'relax' calculation with defect?. </div>
<div class="gmail_default"
style="font-family:arial,helvetica,sans-serif">Manu</div>
<div class="gmail_default"
style="font-family:arial,helvetica,sans-serif">(University of
Waterloo).</div>
<div class="gmail_default"
style="font-family:arial,helvetica,sans-serif">
<div class="gmail_default"><br>
</div>
</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Sun, Aug 6, 2017 at 11:15 AM,
stefano de gironcoli <span dir="ltr"><<a
href="mailto:degironc@sissa.it" target="_blank"
moz-do-not-send="true">degironc@sissa.it</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
<div class="m_-8357465357166681915moz-cite-prefix">does
the energy (enthalpy) decreases as the vc-relaxation
progresses ? <br>
The local structure around the defect may be quite
different. It may just take long.<br>
<br>
I would start by performing a fixed cell relaxation with
the cell parameters fixed at the undefected equilibrium
values. And only after that I would start the vc-relax
calculation from the so relaxed configuration to
evaluate the vacancy formation volume. The local
arrangement around the defect should be already more or
less ok (if the supercell is large enough). <br>
<br>
HTH<br>
stefano
<div>
<div class="h5"><br>
<br>
<br>
On 06/08/2017 16:40, Manu Hegde wrote:<br>
</div>
</div>
</div>
<blockquote type="cite">
<div>
<div class="h5">
<div dir="ltr">
<div class="gmail_default">
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">Hello,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"><br>
</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">I am trying to
optimize anatase TiO2 supercell with 48
atoms. The supercell converges in 15 BFGS
cycles for a perfect cell. But when I
introduce defect (by removing one of the
oxygen atom), the vc-relax is not t all
converging. I am using the same parameters
in both the cases. Can anyone give some
feedback on this.?. Here is my input,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"><br>
</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"><br>
</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">&control</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
calculation = 'vc-relax' ,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
restart_mode = 'from_scratch' ,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
outdir = '/work/mhegde/tmp_tiodef/',</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
pseudo_dir = '/home/mhegde/tio_project/def_<wbr>tio/',</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
prefix = 'tioan',</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
verbosity = 'high',</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"><br>
</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"> /</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"> &system</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
ibrav = 0,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
nat = 47,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
ntyp = 2,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
ecutwfc =40,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
ecutrho=400,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
occupations='smearing',</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
degauss=0.003</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"><br>
</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"> /</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"> &electrons</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
conv_thr = 1.D-6,</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
mixing_beta=0.1</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">/</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">&ions</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
ion_dynamics='bfgs'</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"><br>
</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">/</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">&cell</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
cell_dynamics='bfgs'</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"><br>
</font></div>
<div class="gmail_default"><span
style="font-family:arial,helvetica,sans-serif">/</span><br>
</div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">ATOMIC_SPECIES</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"> Ti 47.867000
Ti.pw91-nsp-van.UPF</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"> O 15.99900
O.pw91-van_ak.UPF</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif"><br>
</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">ATOMIC_POSITIONS
angstrom</font></div>
<div class="gmail_default"><font face="arial,
helvetica, sans-serif">
<div class="gmail_default">Ti
0.00000000 2.84182500
1.20970000</div>
<div class="gmail_default">Ti
1.89455000 2.84182500
3.62910000</div>
<div class="gmail_default">O
0.00000000 0.94727500
1.99939216</div>
<div class="gmail_default">O
0.00000000 2.84182500
4.41879216</div>
<div class="gmail_default">O
1.89455000 0.94727500
2.83940784</div>
<div class="gmail_default">Ti
-1.89455000 0.94727500
-3.62910000</div>
<div class="gmail_default">Ti
0.00000000 0.94727500
-1.20970000</div>
<div class="gmail_default">O
-1.89455000 -0.94727500
-2.83940784</div>
<div class="gmail_default">O
-1.89455000 0.94727500
-0.42000784</div>
<div class="gmail_default">O
0.00000000 -0.94727500
-1.99939216</div>
<div class="gmail_default">O
0.00000000 0.94727500
-4.41879216</div>
<div class="gmail_default">Ti
0.00000000 -0.94727500
1.20970000</div>
<div class="gmail_default">Ti
1.89455000 -0.94727500
3.62910000</div>
<div class="gmail_default">O
0.00000000 -2.84182500
1.99939216</div>
<div class="gmail_default">O
0.00000000 -0.94727500
4.41879216</div>
<div class="gmail_default">O
1.89455000 -2.84182500
2.83940784</div>
<div class="gmail_default">O
1.89455000 -0.94727500
0.42000784</div>
<div class="gmail_default">Ti
-1.89455000 -2.84182500
-3.62910000</div>
<div class="gmail_default">Ti
0.00000000 -2.84182500
-1.20970000</div>
<div class="gmail_default">O
-1.89455000 2.84182500
-2.83940784</div>
<div class="gmail_default">O
-1.89455000 -2.84182500
-0.42000784</div>
<div class="gmail_default">O
0.00000000 2.84182500
-1.99939216</div>
<div class="gmail_default">O
0.00000000 -2.84182500
-4.41879216</div>
<div class="gmail_default">Ti
-3.78910000 2.84182500
1.20970000</div>
<div class="gmail_default">Ti
-1.89455000 2.84182500
3.62910000</div>
<div class="gmail_default">O
-3.78910000 0.94727500
1.99939216</div>
<div class="gmail_default">O
-3.78910000 2.84182500
4.41879216</div>
<div class="gmail_default">O
-1.89455000 0.94727500
2.83940784</div>
<div class="gmail_default">O
-1.89455000 2.84182500
0.42000784</div>
<div class="gmail_default">Ti
1.89455000 0.94727500
-3.62910000</div>
<div class="gmail_default">Ti
-3.78910000 0.94727500
-1.20970000</div>
<div class="gmail_default">O
1.89455000 -0.94727500
-2.83940784</div>
<div class="gmail_default">O
1.89455000 0.94727500
-0.42000784</div>
<div class="gmail_default">O
-3.78910000 -0.94727500
-1.99939216</div>
<div class="gmail_default">O
-3.78910000 0.94727500
-4.41879216</div>
<div class="gmail_default">Ti
-3.78910000 -0.94727500
1.20970000</div>
<div class="gmail_default">Ti
-1.89455000 -0.94727500
3.62910000</div>
<div class="gmail_default">O
-3.78910000 -2.84182500
1.99939216</div>
<div class="gmail_default">O
-3.78910000 -0.94727500
4.41879216</div>
<div class="gmail_default">O
-1.89455000 -2.84182500
2.83940784</div>
<div class="gmail_default">O
-1.89455000 -0.94727500
0.42000784</div>
<div class="gmail_default">Ti
1.89455000 -2.84182500
-3.62910000</div>
<div class="gmail_default">Ti
-3.78910000 -2.84182500
-1.20970000</div>
<div class="gmail_default">O
1.89455000 2.84182500
-2.83940784</div>
<div class="gmail_default">O
1.89455000 -2.84182500
-0.42000784</div>
<div class="gmail_default">O
-3.78910000 2.84182500
-1.99939216</div>
<div class="gmail_default">O
-3.78910000 -2.84182500
-4.41879216</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">
<div class="gmail_default">K_POINTS
{automatic}</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default"> 2 2 2 0 0 0</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">CELL_PARAMETERS
angstrom</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default"> 7.57820000
0.00000000 0.00000000</div>
<div class="gmail_default"> 0.00000000
7.57820000 0.00000000</div>
<div class="gmail_default"> 0.00000000
0.00000000 9.67760000</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default">Thanks,</div>
<div class="gmail_default">Manu</div>
<div class="gmail_default">(University of
Waterloo)</div>
<div class="gmail_default"><br>
</div>
<div class="gmail_default"><br>
</div>
</div>
<div><br>
</div>
</font></div>
<div
style="font-family:arial,helvetica,sans-serif"><br>
</div>
</div>
</div>
<br>
<fieldset
class="m_-8357465357166681915mimeAttachmentHeader"></fieldset>
<br>
</div>
</div>
<pre>______________________________<wbr>_________________
Pw_forum mailing list
<a class="m_-8357465357166681915moz-txt-link-abbreviated" href="mailto:Pw_forum@pwscf.org" target="_blank" moz-do-not-send="true">Pw_forum@pwscf.org</a>
<a class="m_-8357465357166681915moz-txt-link-freetext" href="http://pwscf.org/mailman/listinfo/pw_forum" target="_blank" moz-do-not-send="true">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a></pre>
</blockquote>
<p><br>
</p>
</div>
<br>
______________________________<wbr>_________________<br>
Pw_forum mailing list<br>
<a href="mailto:Pw_forum@pwscf.org" moz-do-not-send="true">Pw_forum@pwscf.org</a><br>
<a href="http://pwscf.org/mailman/listinfo/pw_forum"
rel="noreferrer" target="_blank" moz-do-not-send="true">http://pwscf.org/mailman/<wbr>listinfo/pw_forum</a><br>
</blockquote>
</div>
<br>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Pw_forum mailing list
<a class="moz-txt-link-abbreviated" href="mailto:Pw_forum@pwscf.org">Pw_forum@pwscf.org</a>
<a class="moz-txt-link-freetext" href="http://pwscf.org/mailman/listinfo/pw_forum">http://pwscf.org/mailman/listinfo/pw_forum</a></pre>
</blockquote>
<p><br>
</p>
</body>
</html>