[xcrysden] Regrading problem in updating the structure

mohaddeseh abbasnejad m.abbasnejad at gmail.com
Thu Aug 25 22:55:26 CEST 2016 

Dear Matic,

Thank you for your reply.
I have attached the input file.
The result of pwi2xsf is also OK, without any problem.
Again thank you.

Bests,
Mohaddeseh

On Thu, Aug 25, 2016 at 1:27 PM, Matic Poberznik <matic.poberznik at gmail.com>
wrote:

> Dear Mohaddeseh,
>
> Could you attach the pw.in you're trying to open as well (in-Ti-OV)?
>
> From what I can see it seems that xcrysden doesn't find any coordinates,
> 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
> >
> > ---------------------------------------------------------
> >
> >
> > _______________________________________________
> > XCrySDen mailing list
> > XCrySDen at democritos.it
> > http://www.democritos.it/mailman/listinfo/xcrysden
> >
> _______________________________________________
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>



-- 
---------------------------------------------------------

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
Website:  http://physics.ut.ac.ir

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