[xcrysden] Regrading problem in updating the structure

Gavin Abo gsabo at crimson.ua.edu
Fri Aug 26 05:48:37 CEST 2016


The path name in your email has xcrysden-1.5.53.  Have you tried with 
the latest xcrysden-1.5.60 [ http://www.xcrysden.org/Download.html ]?

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 xcrysden-1.5.53 
doesn't have.

On 8/25/2016 2:55 PM, mohaddeseh abbasnejad wrote:
> 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 <mailto:matic.poberznik at gmail.com>> wrote:
>
>     Dear Mohaddeseh,
>
>     Could you attach the pw.in <http://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>
>     > <mailto: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> <mailto: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>
>     <mailto:m.abbasnejad at gmail.com <mailto:m.abbasnejad at gmail.com>>
>     > Website: http://physics.ut.ac.ir
>     >
>     > ---------------------------------------------------------
>     >
>     >
>     > _______________________________________________
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>     > XCrySDen at democritos.it <mailto:XCrySDen at democritos.it>
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>     >
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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 <mailto:m.abbasnejad at gmail.com>
> Website: http://physics.ut.ac.ir
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