<div dir="ltr">Dear Fabian,<div><br></div><div>Thanks for your suggestions. I will try it out your suggestions and get back to you on this. Thanks again.</div><div><br></div><div>Best wishes,</div><div>Manzoor</div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Mon, May 3, 2021 at 9:35 PM Fabian Ducry <<a href="mailto:fabia...@gmail.com">fabia...@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Dear Manzoor,</p>
<p>a very simple way is to use ASE (a python package). If you have
it installed (e.g. "pip install ase" or if you use conda "conda
install -c conda-forge ase") just run the following two lines in
python:</p>
<p>from ase import io</p>
<p>io.read('CONTCAR').write('C2NTa2.xyz')</p>
<p>This will convert the CONTCAR to C2NTa2.xyz. The second line of
<a href="http://c2n.xyz" target="_blank">c2n.xyz</a> contains Lattice="xx xy xz yx yy yz zx zy zz" which are
the 9 numbers that define the lattice. You can use these to set A
xx xy xz B yx yy yz and C zx zy zz in the &CELL section of the
input file. If you explicitly set A, B,and C then ANGLE is not
needed anymore.<br>
</p>
<p>Cheers,</p>
<p>Fabian<br>
</p>
<div>On 03.05.2021 17:49, Rizwan Nabi wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div class="gmail_default" style="font-size:small">Dear Manzoor,</div>
<div class="gmail_default" style="font-size:small">Please send
me your CONTCAR, I will Send you XYZ format.</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small">Regards</div>
<div class="gmail_default" style="font-size:small">Rizwan</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div style="font-size:12.8px">
<div style="margin:0px;padding:0px;border:0px;font-stretch:inherit;font-size:12pt;line-height:inherit;font-family:Calibri,Arial,Helvetica,sans-serif;vertical-align:baseline;color:rgb(0,0,0)">
<div style="margin:0px;padding:0px;border:0px;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline"><span>-------</span></div>
<div style="margin:0px;padding:0px;border:0px;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline"><span></span><span><b>Dr
Rizwan Nabi</b></span><br style="color:rgb(32,31,30);font-size:15px">
<span>Research
Associate "European Research Council Fellow"</span><br style="color:rgb(32,31,30);font-size:15px">
<span>Department
of Chemistry, The University of Manchester</span><br style="color:rgb(32,31,30);font-size:15px">
<span>Oxford
Road, Manchester, M13 9PL, United Kingdom</span><br style="color:rgb(32,31,30);font-size:15px">
<span>t:
+44 (0)742 447 4940</span><br style="color:rgb(32,31,30);font-size:15px">
<span>e:
<a href="mailto:rizwa...@manchester.ac.uk" target="_blank">rizwa...@manchester.ac.uk</a></span></div>
<div><font face="Times New Roman, Times, serif"><span style="margin:0px;padding:0px;border:0px;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline">w: </span><a href="http://nfchilton.com/people.html" style="margin:0px;padding:0px;border:0px;font:inherit;vertical-align:baseline" target="_blank"><span style="margin:0px;padding:0px;border:0px;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline;color:rgb(0,0,0)">http://nfchilton.com/people.html</span></a><br style="color:rgb(32,31,30);font-size:15px">
</font></div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, May 3, 2021 at 4:21 PM
DAR MANZOOR <<a href="mailto:mann...@gmail.com" target="_blank">mann...@gmail.com</a>> wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Dear Dr. Rizwan,
<div><br>
</div>
<div>I don't think there is a problem with the structure of
C2N monolayer. Its structure is well documented in
literature. However, I feel I may be making some mistake
in terms of the format of the xyz file and cell parameters
in the input file. If you know how generate the xyz
coordinates for VASP CONTCAR in the CP2K format, that
might help me troubleshoot this problem.</div>
<div><br>
</div>
<div>Manzoor</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, May 3, 2021 at
7:19 PM Rizwan Nabi <<a href="mailto:rizwan...@gmail.com" target="_blank">rizwan...@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div class="gmail_default" style="font-size:small">Dear
Manzoor,</div>
<div class="gmail_default" style="font-size:small">Can
you just add H atoms on all the C atoms and Re-run the
calculations. I guess the problem is with the Carbon
valency. Please let me know if this works?</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small"><br>
</div>
<div class="gmail_default" style="font-size:small">Regards</div>
<div class="gmail_default" style="font-size:small">Rizwan</div>
<div>
<div dir="ltr">
<div dir="ltr">
<div style="font-size:12.8px">
<div style="margin:0px;padding:0px;border:0px;font-stretch:inherit;font-size:12pt;line-height:inherit;font-family:Calibri,Arial,Helvetica,sans-serif;vertical-align:baseline;color:rgb(0,0,0)">
<div style="margin:0px;padding:0px;border:0px;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline"><span>-------</span></div>
<div style="margin:0px;padding:0px;border:0px;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline"><span></span><span><b>Dr
Rizwan Nabi</b></span><br style="color:rgb(32,31,30);font-size:15px">
<span>Research
Associate "European Research Council
Fellow"</span><br style="color:rgb(32,31,30);font-size:15px">
<span>Department
of Chemistry, The University of Manchester</span><br style="color:rgb(32,31,30);font-size:15px">
<span>Oxford
Road, Manchester, M13 9PL, United Kingdom</span><br style="color:rgb(32,31,30);font-size:15px">
<span>t:
+44 (0)742 447 4940</span><br style="color:rgb(32,31,30);font-size:15px">
<span>e:
<a href="mailto:rizwa...@manchester.ac.uk" target="_blank">rizwa...@manchester.ac.uk</a></span></div>
<div style="margin:0px;padding:0px;border:0px;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline"><font face="Times New Roman, Times, serif"><span style="margin:0px;padding:0px;border:0px;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline">w: </span><a href="http://nfchilton.com/people.html" style="margin:0px;padding:0px;border:0px;font:inherit;vertical-align:baseline" target="_blank"><span style="margin:0px;padding:0px;border:0px;font-style:inherit;font-variant:inherit;font-weight:inherit;font-stretch:inherit;font-size:12pt;line-height:inherit;vertical-align:baseline;color:rgb(0,0,0)">http://nfchilton.com/people.html</span></a><br style="color:rgb(32,31,30);font-size:15px">
</font></div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon, May 3, 2021 at
2:15 PM DAR MANZOOR <<a href="mailto:mann...@gmail.com" target="_blank">mann...@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="auto">Dear Rizwan,
<div dir="auto"><br>
</div>
<div dir="auto">Thanks for your reply. I am using an
overall charge of zero. I have run the same system
in VASP and it relaxes smoothly. However here I
faced the same problem even when I tried to relax
the structure. The structure just breaks away
whether I run the geometry optimization or MD.</div>
<div dir="auto"><br>
</div>
<div dir="auto">Best wishes,</div>
<div dir="auto">Manzoor</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Mon 3 May,
2021, 6:36 PM Rizwan Nabi, <<a href="mailto:rizwan...@gmail.com" target="_blank">rizwan...@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>Dear Manzoor, </div>
<div>Please check If the charges are correct. From
Your Coordinate file, the valency seems
unsatisfied.</div>
<div>I can not see any double bonds in the
structure. </div>
<div><br>
</div>
<div>Regards</div>
<div>Rizwan</div>
<br>
<div class="gmail_quote">
<div dir="auto" class="gmail_attr">On Monday,
May 3, 2021 at 1:34:58 PM UTC+1 <a href="mailto:ma...@gmail.com" rel="noreferrer" target="_blank">ma...@gmail.com</a>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="auto">Dear Users,
<div dir="auto"><br>
</div>
<div dir="auto">I will be extremely grateful
if anyone can take some time to look into
the above problem.</div>
<div dir="auto"><br>
</div>
<div dir="auto">Best wishes,</div>
<div dir="auto">Manzoor</div>
</div>
<br>
<div class="gmail_quote">
<div dir="ltr" class="gmail_attr">On Sat 1
May, 2021, 11:06 PM DAR MANZOOR, <<a rel="nofollow noreferrer">ma...@gmail.com</a>>
wrote:<br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">Dear CP2K developers,
<div><br>
</div>
<div>I am new to CP2K and am trying to
run abinitio MD simulation on a Ta2
dimer supported on C2N monolayer.
However, as i run the calculation the
structure completely breaks and looks
too weird. I am attaching the input
and output files here. I will be
grateful if someone can look into the
files and help me troubleshoot the
issue. Thanks in advance.<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">Regards &
best wishes<br>
Dr. Manzoor A. Dar,</div>
<div>Assistant Professor,</div>
<div>Dept. of Chemistry,</div>
<div>IUST Awantipora.<br>
</div>
</div>
</div>
</div>
</div>
</div>
</blockquote>
</div>
</blockquote>
</div>
-- <br>
You received this message because you are
subscribed to the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving
emails from it, send an email to <a href="mailto:cp...@googlegroups.com" rel="noreferrer" target="_blank">cp...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/2ae6eb9e-43b0-4c6f-8b5a-417f7e343749n%40googlegroups.com?utm_medium=email&utm_source=footer" rel="noreferrer" target="_blank">https://groups.google.com/d/msgid/cp2k/2ae6eb9e-43b0-4c6f-8b5a-417f7e343749n%40googlegroups.com</a>.<br>
</blockquote>
</div>
-- <br>
You received this message because you are subscribed
to the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving
emails from it, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/CAKNVsq43v%2BuBTPumOkLO%3D23cpVwkfNU08-vrvPTTvhhoz2KMQg%40mail.gmail.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/CAKNVsq43v%2BuBTPumOkLO%3D23cpVwkfNU08-vrvPTTvhhoz2KMQg%40mail.gmail.com</a>.<br>
</blockquote>
</div>
-- <br>
You received this message because you are subscribed to
the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails
from it, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/CAFme2NQPnoweyGbbCzwgQ9KuQS%2BtdxW3oJdmZh8%3DGDu1dJf6WQ%40mail.gmail.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/CAFme2NQPnoweyGbbCzwgQ9KuQS%2BtdxW3oJdmZh8%3DGDu1dJf6WQ%40mail.gmail.com</a>.<br>
</blockquote>
</div>
<br clear="all">
<div><br>
</div>
-- <br>
<div dir="ltr">
<div dir="ltr">
<div>
<div dir="ltr">Regards & best wishes<br>
Dr. Manzoor A. Dar,</div>
<div>Assistant Professor,</div>
<div>Dept. of Chemistry,</div>
<div>IUST Awantipora.<br>
</div>
</div>
</div>
</div>
-- <br>
You received this message because you are subscribed to the
Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails from
it, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/CAKNVsq6wTECgsUoViVLCDumvUw9qw5a_c%2BreHBtCweZna7uMZg%40mail.gmail.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/CAKNVsq6wTECgsUoViVLCDumvUw9qw5a_c%2BreHBtCweZna7uMZg%40mail.gmail.com</a>.<br>
</blockquote>
</div>
-- <br>
You received this message because you are subscribed to the Google
Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails from it,
send an email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/CAFme2NT_Sx5DwfJfH_OopyQgN1njCvTDupgpgSbMJ9XVmoPktg%40mail.gmail.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/CAFme2NT_Sx5DwfJfH_OopyQgN1njCvTDupgpgSbMJ9XVmoPktg%40mail.gmail.com</a>.<br>
</blockquote>
</div>
<p></p>
-- <br>
You received this message because you are subscribed to the Google Groups "cp2k" group.<br>
To unsubscribe from this group and stop receiving emails from it, send an email to <a href="mailto:cp...@googlegroups.com" target="_blank">cp...@googlegroups.com</a>.<br>
To view this discussion on the web visit <a href="https://groups.google.com/d/msgid/cp2k/3145f5ad-35f6-e185-6512-6dc1cca83377%40gmail.com?utm_medium=email&utm_source=footer" target="_blank">https://groups.google.com/d/msgid/cp2k/3145f5ad-35f6-e185-6512-6dc1cca83377%40gmail.com</a>.<br>
</blockquote></div><br clear="all"><div><br></div>-- <br><div dir="ltr" class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Regards & best wishes<br>Dr. Manzoor A. Dar,</div><div>Assistant Professor,</div><div>Dept. of Chemistry,</div><div>IUST Awantipora.<br></div></div></div></div>