<div dir="ltr"><div><div><div><div>Dear users,<br><br></div>It is about a few days I have faced a strange problem.<br></div>Actually, xcrysden is working for visualising all the input files of PWscf.<br></div>Unfortunately, after I updated one of the input files ( obtained from the vc-relax calculations), it stops and give me such an error:<br>ERROR: an error occurred while trying to update a structure; Error reading file /tmp/xc_3330/xc_struc.3330.<br></div><div>However, the PWscf is running well with the updated structure.<br></div><div>I used the following command:<br><br><span style="color:rgb(11,83,148)">mohaddeseh@mohaddeseh-Vostro1310:~/Desktop$ xcrysden --pwi in-Ti-OV </span><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">+-----------------------------------------------------------------+</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|*****************************************************************|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* = === = === *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|*---------------------------------------------------------------*|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* Anton Kokalj (<a href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a>) *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* Jozef Stefan Institute, Ljubljana, Slovenia *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* Copyright (c) 1996--2012 by Anton Kokalj *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|* *|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">|*****************************************************************|</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">+-----------------------------------------------------------------+</span><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> Version: 1.5.53</span><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> Please report bugs to: <a href="mailto:tone.kokalj@ijs.si">tone.kokalj@ijs.si</a></span><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> TERMS OF USE:</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> -------------</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> XCRYSDEN is released under the GNU General Public License.</span><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> Whenever graphics generated by XCRYSDEN are used in scientific</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> publications, it shall be greatly appreciated to include an explicit</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> reference. The preferred form is the following:</span><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> Code available from <a href="http://www.xcrysden.org/">http://www.xcrysden.org/</a>.</span><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">XCRYSDEN_TOPDIR=/opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">XCRYSDEN_SCRATCH=/tmp</span><br style="color:rgb(11,83,148)"><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Running on platform : unix</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> Operating system : Linux</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Package ImageMagick's convert: /usr/bin/convert</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Package ImageMagick's import: /usr/bin/import</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Package Ppmtompeg: /usr/bin/ppmtompeg</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Package Babel: /usr/bin/babel</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Package Xwd: /usr/bin/xwd</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Executing: /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/ftnunit</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">TEXT-WIDGET: .a1.f1.t</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Executing: sh /opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53/scripts/pwi2xsf.sh /home/mohaddeseh/Desktop/in-Ti-OV</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">reading PRIMCOORD</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Number of Atoms: 0</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Number of Frames: 0</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Estimated number of bonds = 0</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">sInfo(dim) = 3; periodic(dim) = 3</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Executing: /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/gengeom 0 1 11 1 1 1 1 xc_gengeom.3330 /tmp/xc_3330/pwi2xsf.xsf_out.raw</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Executing: /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/gengeom 2 1 11 1 1 1 1 /tmp/xc_3330/xc_struc.3330 /tmp/xc_3330/pwi2xsf.xsf_out.raw</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">reading PRIMCOORD</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">reading CONVCOORD</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">"/tmp/xc_3330/xc_struc.3330"</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">Error in startup script: can't read "sInfo(ldatagrid2D)": no such variable</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> while executing</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">"if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) } {</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> $m.menu entryconfig "Data Grid" -state normal</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> } else {</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> $m.menu entryconfig "Data Grid" -stat..."</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> (procedure "Get_sInfoArray" line 13)</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> invoked from within</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">"Get_sInfoArray"</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> (procedure "xsfOpen" line 92)</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> invoked from within</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">"xsfOpen $program_output .mesa"</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> (procedure "openExtStruct" line 183)</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> invoked from within</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">"openExtStruct 3 crystal external [list sh $system(TOPDIR)/scripts/pwi2xsf.sh] pwi2xsf.xsf_out {PWSCF Input File} ANGS -file $filedir -preset pwIn..."</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> invoked from within</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">"if [file exists $filedir] {</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> # pop-up Viewer</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> ViewMol .</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> openExtStruct 3 crystal external [list sh $system(TOPDIR)/scripts/pwi2xsf.sh] pwi2xsf..."</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> (procedure "parseComLinArg" line 89)</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> invoked from within</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">"parseComLinArg [lrange $argv 2 end]"</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> invoked from within</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">"if { [llength $argv] > 2 } {</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> parseComLinArg [lrange $argv 2 end]</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">} else {</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> ViewMol .</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)">}"</span><br style="color:rgb(11,83,148)"><span style="color:rgb(11,83,148)"> (file "/opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53/Tcl/xcInit.tcl" line 609)</span><br><br></div><div>Any help would be appreciated.<br></div><div>Thanks in advance.<br></div><div>Regards,<br></div><div>Mohaddeseh<br></div><div> <br clear="all"></div><div><div><div><div><div><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 href="mailto:m.abbasnejad@gmail.com" target="_blank">m.abbasnejad@gmail.com</a><br>Website: <a href="http://physics.ut.ac.ir" target="_blank">http://physics.ut.ac.ir</a><br><br>---------------------------------------------------------<br></div>
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