[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
> >
> > ---------------------------------------------------------
> >
> >
> > _______________________________________________
> > XCrySDen mailing list
> > XCrySDen at democritos.it <mailto:XCrySDen at democritos.it>
> > http://www.democritos.it/mailman/listinfo/xcrysden
> <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 <mailto:m.abbasnejad at gmail.com>
> Website: http://physics.ut.ac.ir
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