No subject
Mon Feb 2 10:44:46 CET 2015
,<br>
and for some reason it wants to open a datagrid, but I really can't tel=
l<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=3D""><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 P=
Wscf.<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 at mohaddeseh-<wbr>Vostro1310:~/Desktop$ xcrysden --pwi in-Ti-=
OV<br>
><br>
> +-----------------------------<wbr>------------------------------<wbr>=
------+<br>
> |*****************************<wbr>******************************<wbr>=
******|<br>
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0*|<br>
> |*=C2=A0 XCrySDen -- (X-Window) CRYstalline Structures and DENsities=
=C2=A0 *|<br>
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=3D=C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0=3D=3D=3D=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=3D=C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =3D=3D=3D=C2=A0 =C2=A0 =C2=A0=
=C2=A0 *|<br>
> |*----------------------------<wbr>------------------------------<wbr>=
-----*|<br>
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0*|<br>
> |*=C2=A0 =C2=A0 Anton Kokalj (<a href=3D"mailto:tone.kokalj at ijs.si">to=
ne.kokalj at ijs.si</a><br>
</span>> <mailto:<a href=3D"mailto:tone.kokalj at ijs.si">tone.kokalj at ij=
s.si</a>>)=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0=
=C2=A0 =C2=A0 =C2=A0 =C2=A0 *|<br>
<span class=3D"">> |*=C2=A0 =C2=A0 Jozef Stefan Institute, Ljubljana, Sl=
ovenia=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 *|<br>
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0*|<br>
> |*=C2=A0 =C2=A0 Copyright (c) 1996--2012 by Anton Kokalj=C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0*|<br>
> |*=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =
=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=
=A0 =C2=A0*|<br>
> |*****************************<wbr>******************************<wbr>=
******|<br>
> +-----------------------------<wbr>------------------------------<wbr>=
------+<br>
><br>
>=C2=A0 =C2=A0Version: 1.5.53<br>
><br>
</span>>=C2=A0 =C2=A0Please report bugs to: <a href=3D"mailto:tone.kokal=
j at ijs.si">tone.kokalj at ijs.si</a> <mailto:<a href=3D"mailto:tone.kokalj at i=
js.si">tone.kokalj at ijs.si</a>><br>
<div><div class=3D"h5">><br>
><br>
>=C2=A0 =C2=A0TERMS OF USE:<br>
>=C2=A0 =C2=A0-------------<br>
>=C2=A0 =C2=A0XCRYSDEN is released under the GNU General Public License.=
<br>
><br>
>=C2=A0 =C2=A0Whenever graphics generated by XCRYSDEN are used in scient=
ific<br>
>=C2=A0 =C2=A0publications, it shall be greatly appreciated to include a=
n explicit<br>
>=C2=A0 =C2=A0reference. The preferred form is the following:<br>
><br>
>=C2=A0 =C2=A0[ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.=
<br>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0Code available from <a href=3D"http:/=
/www.xcrysden.org/" rel=3D"noreferrer" target=3D"_blank">http://www.xcrysde=
n.org/</a>.<br>
><br>
> XCRYSDEN_TOPDIR=3D/opt/exp_<wbr>softs/tools/xcrysden-1.5.53/<wbr>share=
/xcrysden-1.5.53<br>
> XCRYSDEN_SCRATCH=3D/tmp<br>
><br>
> Running on platform : unix<br>
>=C2=A0 =C2=A0 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>s=
cripts/pwi2xsf.sh<br>
> /home/mohaddeseh/Desktop/in-<wbr>Ti-OV<br>
> reading PRIMCOORD<br>
> Number of Atoms:=C2=A0 0<br>
> Number of Frames: 0<br>
> Estimated number of bonds =3D 0<br>
> sInfo(dim) =3D 3; periodic(dim) =3D 3<br>
> Executing:<br>
> /opt/exp_softs/tools/xcrysden-<wbr>1.5.53/lib/xcrysden-1.5.53/<wbr>gen=
geom 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>gen=
geom 2 1 11<br>
> 1 1 1 1 /tmp/xc_3330/xc_struc.3330 /tmp/xc_3330/pwi2xsf.xsf_out.<wbr>r=
aw<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>
>=C2=A0 =C2=A0 =C2=A0while executing<br>
> "if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) } {<br>
>=C2=A0 =C2=A0 =C2=A0$m.menu entryconfig "Data Grid" -state no=
rmal<br>
>=C2=A0 =C2=A0 =C2=A0} else {<br>
>=C2=A0 =C2=A0 =C2=A0$m.menu entryconfig "Data Grid" -stat...&=
quot;<br>
>=C2=A0 =C2=A0 =C2=A0(procedure "Get_sInfoArray" line 13)<br>
>=C2=A0 =C2=A0 =C2=A0invoked from within<br>
> "Get_sInfoArray"<br>
>=C2=A0 =C2=A0 =C2=A0(procedure "xsfOpen" line 92)<br>
>=C2=A0 =C2=A0 =C2=A0invoked from within<br>
> "xsfOpen $program_output .mesa"<br>
>=C2=A0 =C2=A0 =C2=A0(procedure "openExtStruct" line 183)<br>
>=C2=A0 =C2=A0 =C2=A0invoked from within<br>
> "openExtStruct 3 crystal external=C2=A0 [list sh<br>
> $system(TOPDIR)/scripts/<wbr>pwi2xsf.sh]=C2=A0 pwi2xsf.xsf_out=C2=A0 {=
PWSCF Input File}<br>
> ANGS=C2=A0 -file $filedir=C2=A0 -preset pwIn..."<br>
>=C2=A0 =C2=A0 =C2=A0invoked from within<br>
> "if [file exists $filedir] {<br>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0# pop-up Viewer<br>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0ViewMol .<br>
>=C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0 =C2=A0openExtStruct 3 crystal=
external=C2=A0 [list sh<br>
> $system(TOPDIR)/scripts/<wbr>pwi2xsf.sh]=C2=A0 pwi2xsf..."<br>
>=C2=A0 =C2=A0 =C2=A0(procedure "parseComLinArg" line 89)<br>
>=C2=A0 =C2=A0 =C2=A0invoked from within<br>
> "parseComLinArg [lrange $argv 2 end]"<br>
>=C2=A0 =C2=A0 =C2=A0invoked from within<br>
> "if { [llength $argv] > 2 } {<br>
>=C2=A0 =C2=A0 =C2=A0parseComLinArg [lrange $argv 2 end]<br>
> } else {<br>
>=C2=A0 =C2=A0 =C2=A0ViewMol .<br>
> }"<br>
>=C2=A0 =C2=A0 =C2=A0(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=C2=A0 & Fax No.: +98 21 8800 4781<br>
> Cellphone: +98 917 731 7514<br>
</div></div>> E-Mail:=C2=A0 =C2=A0 =C2=A0<a href=3D"mailto:m.abbasnejad@=
gmail.com">m.abbasnejad at gmail.com</a> <mailto:<a href=3D"mailto:m.abbasn=
ejad at gmail.com">m.abbasnejad at gmail.com</a><wbr>><br>
> Website:=C2=A0 <a href=3D"http://physics.ut.ac.ir" rel=3D"noreferrer" =
target=3D"_blank">http://physics.ut.ac.ir</a><br>
><br>
> ------------------------------<wbr>---------------------------<br>
><br>
><br>
> ______________________________<wbr>_________________<br>
> XCrySDen mailing list<br>
> <a href=3D"mailto:XCrySDen at democritos.it">XCrySDen at democritos.it</a><b=
r>
> <a href=3D"http://www.democritos.it/mailman/listinfo/xcrysden" rel=3D"=
noreferrer" target=3D"_blank">http://www.democritos.it/<wbr>mailman/listinf=
o/xcrysden</a><br>
><br>
______________________________<wbr>_________________<br>
XCrySDen mailing list<br>
<a href=3D"mailto:XCrySDen at democritos.it">XCrySDen at democritos.it</a><br>
<a href=3D"http://www.democritos.it/mailman/listinfo/xcrysden" rel=3D"noref=
errer" target=3D"_blank">http://www.democritos.it/<wbr>mailman/listinfo/xcr=
ysden</a><br>
</blockquote></div><br><br clear=3D"all"><br>-- <br><div class=3D"gmail_sig=
nature" data-smartmail=3D"gmail_signature">--------------------------------=
-------------------------<br><br>Mohaddeseh Abbasnejad, <br>Room No. 323, D=
epartment of Physics, <br>University of Tehran, North Karegar Ave.,<br>Tehr=
an, P.O. Box: 14395-547- IRAN <br>Tel. No.: +98 21 6111 8634=C2=A0 & Fa=
x No.: +98 21 8800 4781<br>Cellphone: +98 917 731 7514<br>E-Mail:=C2=A0 =C2=
=A0=C2=A0 <a href=3D"mailto:m.abbasnejad at gmail.com" target=3D"_blank">m.abb=
asnejad at gmail.com</a><br>Website:=C2=A0 <a href=3D"http://physics.ut.ac.ir"=
target=3D"_blank">http://physics.ut.ac.ir</a><br><br>---------------------=
------------------------------------<br></div>
</div>
--001a113f905843446a053aeb9f4e--
--001a113f9058434470053aeb9f50
Content-Type: application/octet-stream; name=in-Ti-OV
Content-Disposition: attachment; filename=in-Ti-OV
Content-Transfer-Encoding: base64
X-Attachment-Id: f_isat4r1t0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--001a113f9058434470053aeb9f50--
More information about the XCrySDen
mailing list