[xcrysden] Regrading problem in updating the structure
Matic Poberznik
matic.poberznik at gmail.com
Fri Aug 26 09:47:53 CEST 2016
Yes, the input you sent opens fine with version 1.5.60,
Best,
Matic Poberznik
J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia
On 08/26/2016 05:48 AM, Gavin Abo wrote:
> 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>
>> >
>> _______________________________________________
>> 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>
>>
>>
>>
>>
>> --
>> ---------------------------------------------------------
>>
>> 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
>
More information about the XCrySDen
mailing list