No subject

and for some reason it wants to open a datagrid, but I really can't tell
more without the input.

Maybe try pwi2xsf.sh in the terminal by itself:

pwi2xsf.sh in-Ti-OV

and try to see if there are any errors in the xsf file it produces. Hope
this helps,

best regards,

Matic

Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia

On 08/25/2016 07:27 AM, mohaddeseh abbasnejad wrote:
> Dear users,
> 
> It is about a few days I have faced a strange problem.
> Actually, xcrysden is working for visualising all the input files of PWscf.
> Unfortunately, after I updated one of the input files ( obtained from
> the vc-relax calculations), it stops and give me such an error:
> ERROR: an error occurred while trying to update a structure; Error
> reading file /tmp/xc_3330/xc_struc.3330.
> However, the PWscf is running well with the updated structure.
> I used the following command:
> 
> mohaddeseh at mohaddeseh-Vostro1310:~/Desktop$ xcrysden --pwi in-Ti-OV
> 
> +-----------------------------------------------------------------+
> |*****************************************************************|
> |*                                                               *|
> |*  XCrySDen -- (X-Window) CRYstalline Structures and DENsities  *|
> |*               =         ===         =              ===        *|
> |*---------------------------------------------------------------*|
> |*                                                               *|
> |*    Anton Kokalj (tone.kokalj at ijs.si
> <mailto:tone.kokalj at ijs.si>)                          *|
> |*    Jozef Stefan Institute, Ljubljana, Slovenia                *|
> |*                                                               *|
> |*    Copyright (c) 1996--2012 by Anton Kokalj                   *|
> |*                                                               *|
> |*****************************************************************|
> +-----------------------------------------------------------------+
> 
>   Version: 1.5.53
> 
>   Please report bugs to: tone.kokalj at ijs.si <mailto:tone.kokalj at ijs.si>
> 
> 
>   TERMS OF USE:
>   -------------
>   XCRYSDEN is released under the GNU General Public License.
> 
>   Whenever graphics generated by XCRYSDEN are used in scientific
>   publications, it shall be greatly appreciated to include an explicit
>   reference. The preferred form is the following:
> 
>   [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003.
>         Code available from http://www.xcrysden.org/.
> 
> XCRYSDEN_TOPDIR=/opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53
> XCRYSDEN_SCRATCH=/tmp
> 
> Running on platform : unix
>    Operating system : Linux
> Package ImageMagick's convert: /usr/bin/convert
> Package ImageMagick's import: /usr/bin/import
> Package Ppmtompeg: /usr/bin/ppmtompeg
> Package Babel: /usr/bin/babel
> Package Xwd: /usr/bin/xwd
> Executing: /opt/exp_softs/tools/xcrysden-1.5.53/lib/xcrysden-1.5.53/ftnunit
> TEXT-WIDGET: .a1.f1.t
> Executing: sh
> /opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53/scripts/pwi2xsf.sh
> /home/mohaddeseh/Desktop/in-Ti-OV
> reading PRIMCOORD
> Number of Atoms:  0
> Number of Frames: 0
> Estimated number of bonds = 0
> sInfo(dim) = 3; periodic(dim) = 3
> 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
> 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
> reading PRIMCOORD
> reading CONVCOORD
> "/tmp/xc_3330/xc_struc.3330"
> Error in startup script: can't read "sInfo(ldatagrid2D)": no such variable
>     while executing
> "if { $sInfo(ldatagrid2D) || $sInfo(ldatagrid3D) } {
>     $m.menu entryconfig "Data Grid" -state normal
>     } else {
>     $m.menu entryconfig "Data Grid" -stat..."
>     (procedure "Get_sInfoArray" line 13)
>     invoked from within
> "Get_sInfoArray"
>     (procedure "xsfOpen" line 92)
>     invoked from within
> "xsfOpen $program_output .mesa"
>     (procedure "openExtStruct" line 183)
>     invoked from within
> "openExtStruct 3 crystal external  [list sh
> $system(TOPDIR)/scripts/pwi2xsf.sh]  pwi2xsf.xsf_out  {PWSCF Input File}
> ANGS  -file $filedir  -preset pwIn..."
>     invoked from within
> "if [file exists $filedir] {
>             # pop-up Viewer
>             ViewMol .
>             openExtStruct 3 crystal external  [list sh
> $system(TOPDIR)/scripts/pwi2xsf.sh]  pwi2xsf..."
>     (procedure "parseComLinArg" line 89)
>     invoked from within
> "parseComLinArg [lrange $argv 2 end]"
>     invoked from within
> "if { [llength $argv] > 2 } {
>     parseComLinArg [lrange $argv 2 end]
> } else {
>     ViewMol .
> }"
>     (file
> "/opt/exp_softs/tools/xcrysden-1.5.53/share/xcrysden-1.5.53/Tcl/xcInit.tcl"
> line 609)
> 
> Any help would be appreciated.
> Thanks in advance.
> Regards,
> Mohaddeseh
>  
> 
> -- 
> ---------------------------------------------------------
> 
> Mohaddeseh Abbasnejad,
> Room No. 323, Department of Physics,
> University of Tehran, North Karegar Ave.,
> Tehran, P.O. Box: 14395-547- IRAN
> Tel. No.: +98 21 6111 8634  & Fax No.: +98 21 8800 4781
> Cellphone: +98 917 731 7514
> E-Mail:     m.abbasnejad at gmail.com <mailto:m.abbasnejad at gmail.com>
> Website:  http://physics.ut.ac.ir
> 
> ---------------------------------------------------------
> 
> 
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