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Hi,<br>
<br>
Thank you for your suggestion. I will try to run again the cell_opt
as you suggest. The question remains, why VASP leads to a different
structure, expended yes but not to that extend. Both a and c reach
about 9.2 and b reaches 43.<br>
<br>
Regards,<br>
Pierre<br>
<br>
<div class="moz-cite-prefix">On 25/10/2019 15:44, Travis wrote:<br>
</div>
<blockquote type="cite"
cite="mid:325eba17-1ca3-4a...@googlegroups.com">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div dir="ltr">
<div>Hi,</div>
<div><br>
</div>
<div>Your input structure is very compressed. It should expand
and your final structure looks much more reasonable. The
amount it is expanding by, I would actually suggest redoing
the CELL_OPT from the final structure as your effective cutoff
decreases when the cell volume increases. Coordinates are
unwrapped intentionally in all calculations. You can impose
PBC to wrap the coordinates using an external program. I
recommend Atomic Simulation Environment,</div>
<div><br>
</div>
<div>Grab last image from foo-pos-1.xyz:<br>
</div>
<div><a class="moz-txt-link-freetext" href="https://github.com/pollardtp/asepylot/blob/master/general/pos2xyz.py">https://github.com/pollardtp/asepylot/blob/master/general/pos2xyz.py</a></div>
<div><br>
</div>
<div>Add cell parameters from command line args:<br>
</div>
<div><a class="moz-txt-link-freetext" href="https://github.com/pollardtp/asepylot/blob/master/general/xyz2vasp.py">https://github.com/pollardtp/asepylot/blob/master/general/xyz2vasp.py</a></div>
<div><br>
</div>
<div>Generated structure is in POSCAR format, viewable with
VESTA. Adapt to your suiting.</div>
<div class="subprettyprint"><span style="color: #000;"
class="styled-by-prettify"><br>
</span></div>
<div class="subprettyprint"><span style="color: #000;"
class="styled-by-prettify">Delete this bit, it's specific to
my setup.<br>
</span>
<div style="background-color: rgb(250, 250, 250);
border-color: rgb(187, 187, 187); border-style: solid;
border-width: 1px; overflow-wrap: break-word;"
class="prettyprint"><code class="prettyprint">
<div class="subprettyprint"><span style="color: #008;"
class="styled-by-prettify">from</span><span
style="color: #000;" class="styled-by-prettify"> </span><span
style="color: #008;" class="styled-by-prettify">require</span><span
style="color: #000;" class="styled-by-prettify"> </span><span
style="color: #008;" class="styled-by-prettify">import</span><span
style="color: #000;" class="styled-by-prettify">
check_ase<br>
check_ase</span><span style="color: #660;"
class="styled-by-prettify">()</span><span
style="color: #000;" class="styled-by-prettify"><br>
</span></div>
</code></div>
<span style="color: #000;" class="styled-by-prettify"></span></div>
<div><br>
</div>
<div>-T<br>
</div>
<div><br>
</div>
<br>
On Friday, October 25, 2019 at 5:46:21 AM UTC-3, Pierre-André
Cazade wrote:
<blockquote class="gmail_quote" style="margin: 0;margin-left:
0.8ex;border-left: 1px #ccc solid;padding-left: 1ex;">
<div dir="ltr">
<div>Dear CP2K users,</div>
<div><br>
</div>
<div>I am running a CELL_OPT on a 280 atoms unit cell. It
was poorly resolved experimentally, yet I am surprised
that some atoms wander out of the unit cell and are not
wrapped back in. It is quite unexpected. According to the
following topic: <a
href="https://groups.google.com/forum/#!topic/cp2k/rqOO2W04OPc"
target="_blank" rel="nofollow"
onmousedown="this.href='https://groups.google.com/forum/#!topic/cp2k/rqOO2W04OPc';return
true;"
onclick="this.href='https://groups.google.com/forum/#!topic/cp2k/rqOO2W04OPc';return
true;" moz-do-not-send="true">https://groups.google.<wbr>com/forum/#!topic/cp2k/<wbr>rqOO2W04OPc</a> ,
CP2K does not wrap atoms, at least in MD mode. This is
very strange. Is it intentional? Is it a bug? And does it
affect in any kind of way calculations?</div>
<div><br>
</div>
<div>I am bothered by the optimized structure which shows a
considerable increase of the "a" parameter. Again, I
compared with VASP and the final structure with the latter
is much more reasonable. I do not expect identical
optimized structure but they should not drift so much away
from each other. Could this lack of wrapping explain the
divergence or it comes from inadequate SCF parameters?</div>
<div><br>
</div>
<div>I attached the input file and the final restart file.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Pierre</div>
</div>
</blockquote>
</div>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Dr Pierre Cazade, PhD
AD3-023, Bernal Institute,
University of Limerick,
Plassey Park Road,
Castletroy, co. Limerick,
Ireland</pre>
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