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<div class="moz-cite-prefix">The path name in your email has
xcrysden-1.5.53. Have you tried with the latest xcrysden-1.5.60 [
<a class="moz-txt-link-freetext" href="http://www.xcrysden.org/Download.html">http://www.xcrysden.org/Download.html</a> ]?<br>
<br>
The file named ChangeLog in
xcrysden-1.5.60-linux_x86_64-semishared.tar.gz shows that
xcrysden-1.5.60 contains several fixes to pwi2xsf that <span
class="">xcrysden-1.5.53 doesn't have.</span><br>
<br>
On 8/25/2016 2:55 PM, mohaddeseh abbasnejad wrote:<br>
</div>
<blockquote
cite="mid:CAF3mdWML+teod=M5NLxq5wP81j=+Y-QFqrcpf_F+6Y5eaAwOVA@mail.gmail.com"
type="cite">
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<div>
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<div>Dear Matic,<br>
<br>
</div>
Thank you for your reply.<br>
</div>
I have attached the input file.<br>
</div>
The result of pwi2xsf is also OK, without any problem.<br>
</div>
Again thank you.<br>
<br>
</div>
Bests,<br>
</div>
Mohaddeseh<br>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Thu, Aug 25, 2016 at 1:27 PM, Matic
Poberznik <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:matic.poberznik@gmail.com" target="_blank">matic.poberznik@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">Dear
Mohaddeseh,<br>
<br>
Could you attach the <a moz-do-not-send="true"
href="http://pw.in" rel="noreferrer" target="_blank">pw.in</a>
you're trying to open as well (in-Ti-OV)?<br>
<br>
>From what I can see it seems that xcrysden doesn't find
any coordinates,<br>
and for some reason it wants to open a datagrid, but I
really can't tell<br>
more without the input.<br>
<br>
Maybe try pwi2xsf.sh in the terminal by itself:<br>
<br>
pwi2xsf.sh in-Ti-OV<br>
<br>
and try to see if there are any errors in the xsf file it
produces. Hope<br>
this helps,<br>
<br>
best regards,<br>
<br>
Matic<br>
<br>
Matic Poberznik<br>
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia<br>
<span class=""><br>
On 08/25/2016 07:27 AM, mohaddeseh abbasnejad wrote:<br>
> Dear users,<br>
><br>
> It is about a few days I have faced a strange
problem.<br>
> Actually, xcrysden is working for visualising all the
input files of PWscf.<br>
> Unfortunately, after I updated one of the input files
( obtained from<br>
> the vc-relax calculations), it stops and give me such
an error:<br>
> ERROR: an error occurred while trying to update a
structure; Error<br>
> reading file /tmp/xc_3330/xc_struc.3330.<br>
> However, the PWscf is running well with the updated
structure.<br>
> I used the following command:<br>
><br>
> mohaddeseh@mohaddeseh-<wbr>Vostro1310:~/Desktop$
xcrysden --pwi in-Ti-OV<br>
><br>
> +-----------------------------<wbr>------------------------------<wbr>------+<br>
> |*****************************<wbr>******************************<wbr>******|<br>
> |*
*|<br>
> |* XCrySDen -- (X-Window) CRYstalline Structures and
DENsities *|<br>
> |* = === =
=== *|<br>
> |*----------------------------<wbr>------------------------------<wbr>-----*|<br>
> |*
*|<br>
> |* Anton Kokalj (<a moz-do-not-send="true"
href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a><br>
</span>> <mailto:<a moz-do-not-send="true"
href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>>)
*|<br>
<span class="">> |* Jozef Stefan Institute, Ljubljana,
Slovenia *|<br>
> |*
*|<br>
> |* Copyright (c) 1996--2012 by Anton Kokalj
*|<br>
> |*
*|<br>
> |*****************************<wbr>******************************<wbr>******|<br>
> +-----------------------------<wbr>------------------------------<wbr>------+<br>
><br>
> Version: 1.5.53<br>
><br>
</span>> Please report bugs to: <a
moz-do-not-send="true" href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>
<mailto:<a moz-do-not-send="true"
href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>><br>
<div>
<div class="h5">><br>
><br>
> TERMS OF USE:<br>
> -------------<br>
> XCRYSDEN is released under the GNU General Public
License.<br>
><br>
> Whenever graphics generated by XCRYSDEN are used
in scientific<br>
> publications, it shall be greatly appreciated to
include an explicit<br>
> reference. The preferred form is the following:<br>
><br>
> [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p.
155, 2003.<br>
> Code available from <a
moz-do-not-send="true" href="http://www.xcrysden.org/"
rel="noreferrer" target="_blank">http://www.xcrysden.org/</a>.<br>
><br>
> XCRYSDEN_TOPDIR=/opt/exp_<wbr>softs/tools/xcrysden-1.5.53/<wbr>share/xcrysden-1.5.53<br>
> XCRYSDEN_SCRATCH=/tmp<br>
><br>
> Running on platform : unix<br>
> Operating system : Linux<br>
> Package ImageMagick's convert: /usr/bin/convert<br>
> Package ImageMagick's import: /usr/bin/import<br>
> Package Ppmtompeg: /usr/bin/ppmtompeg<br>
> Package Babel: /usr/bin/babel<br>
> Package Xwd: /usr/bin/xwd<br>
> Executing: /opt/exp_softs/tools/xcrysden-<wbr>1.5.53/lib/xcrysden-1.5.53/<wbr>ftnunit<br>
> TEXT-WIDGET: .a1.f1.t<br>
> Executing: sh<br>
> /opt/exp_softs/tools/xcrysden-<wbr>1.5.53/share/xcrysden-1.5.53/<wbr>scripts/pwi2xsf.sh<br>
> /home/mohaddeseh/Desktop/in-<wbr>Ti-OV<br>
> reading PRIMCOORD<br>
> Number of Atoms: 0<br>
> Number of Frames: 0<br>
> Estimated number of bonds = 0<br>
> sInfo(dim) = 3; periodic(dim) = 3<br>
> Executing:<br>
> /opt/exp_softs/tools/xcrysden-<wbr>1.5.53/lib/xcrysden-1.5.53/<wbr>gengeom
0 1 11<br>
> 1 1 1 1 xc_gengeom.3330
/tmp/xc_3330/pwi2xsf.xsf_out.<wbr>raw<br>
> Executing:<br>
> /opt/exp_softs/tools/xcrysden-<wbr>1.5.53/lib/xcrysden-1.5.53/<wbr>gengeom
2 1 11<br>
> 1 1 1 1 /tmp/xc_3330/xc_struc.3330
/tmp/xc_3330/pwi2xsf.xsf_out.<wbr>raw<br>
> reading PRIMCOORD<br>
> reading CONVCOORD<br>
> "/tmp/xc_3330/xc_struc.3330"<br>
> Error in startup script: can't read
"sInfo(ldatagrid2D)": no such variable<br>
> while executing<br>
> "if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) }
{<br>
> $m.menu entryconfig "Data Grid" -state normal<br>
> } else {<br>
> $m.menu entryconfig "Data Grid" -stat..."<br>
> (procedure "Get_sInfoArray" line 13)<br>
> invoked from within<br>
> "Get_sInfoArray"<br>
> (procedure "xsfOpen" line 92)<br>
> invoked from within<br>
> "xsfOpen $program_output .mesa"<br>
> (procedure "openExtStruct" line 183)<br>
> invoked from within<br>
> "openExtStruct 3 crystal external [list sh<br>
> $system(TOPDIR)/scripts/<wbr>pwi2xsf.sh]
pwi2xsf.xsf_out {PWSCF Input File}<br>
> ANGS -file $filedir -preset pwIn..."<br>
> invoked from within<br>
> "if [file exists $filedir] {<br>
> # pop-up Viewer<br>
> ViewMol .<br>
> openExtStruct 3 crystal external [list
sh<br>
> $system(TOPDIR)/scripts/<wbr>pwi2xsf.sh]
pwi2xsf..."<br>
> (procedure "parseComLinArg" line 89)<br>
> invoked from within<br>
> "parseComLinArg [lrange $argv 2 end]"<br>
> invoked from within<br>
> "if { [llength $argv] > 2 } {<br>
> parseComLinArg [lrange $argv 2 end]<br>
> } else {<br>
> ViewMol .<br>
> }"<br>
> (file<br>
> "/opt/exp_softs/tools/<wbr>xcrysden-1.5.53/share/<wbr>xcrysden-1.5.53/Tcl/xcInit.<wbr>tcl"<br>
> line 609)<br>
><br>
> Any help would be appreciated.<br>
> Thanks in advance.<br>
> Regards,<br>
> Mohaddeseh<br>
><br>
><br>
> --<br>
> ------------------------------<wbr>---------------------------<br>
><br>
> Mohaddeseh Abbasnejad,<br>
> Room No. 323, Department of Physics,<br>
> University of Tehran, North Karegar Ave.,<br>
> Tehran, P.O. Box: 14395-547- IRAN<br>
> Tel. No.: +98 21 6111 8634 & Fax No.: +98 21
8800 4781<br>
> Cellphone: +98 917 731 7514<br>
</div>
</div>
> E-Mail: <a moz-do-not-send="true"
href="mailto:m.abbasnejad@gmail.com">m.abbasnejad@gmail.com</a>
<mailto:<a moz-do-not-send="true"
href="mailto:m.abbasnejad@gmail.com">m.abbasnejad@gmail.com</a><wbr>><br>
> Website: <a moz-do-not-send="true"
href="http://physics.ut.ac.ir" rel="noreferrer"
target="_blank">http://physics.ut.ac.ir</a><br>
><br>
> ------------------------------<wbr>---------------------------<br>
><br>
><br>
> ______________________________<wbr>_________________<br>
> XCrySDen mailing list<br>
> <a moz-do-not-send="true"
href="mailto:XCrySDen@democritos.it">XCrySDen@democritos.it</a><br>
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rel="noreferrer" target="_blank">http://www.democritos.it/<wbr>mailman/listinfo/xcrysden</a><br>
><br>
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</blockquote>
</div>
<br>
<br clear="all">
<br>
-- <br>
<div class="gmail_signature" data-smartmail="gmail_signature">---------------------------------------------------------<br>
<br>
Mohaddeseh Abbasnejad, <br>
Room No. 323, Department of Physics, <br>
University of Tehran, North Karegar Ave.,<br>
Tehran, P.O. Box: 14395-547- IRAN <br>
Tel. No.: +98 21 6111 8634 & Fax No.: +98 21 8800 4781<br>
Cellphone: +98 917 731 7514<br>
E-Mail: <a moz-do-not-send="true"
href="mailto:m.abbasnejad@gmail.com" target="_blank">m.abbasnejad@gmail.com</a><br>
Website: <a moz-do-not-send="true"
href="http://physics.ut.ac.ir" target="_blank">http://physics.ut.ac.ir</a><br>
</div>
</div>
</blockquote>
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