[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
>>     >
>>     > ---------------------------------------------------------
>>     >
>>     >
>>     > _______________________________________________
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>>     > XCrySDen at democritos.it <mailto:XCrySDen at democritos.it>
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>>     <http://www.democritos.it/mailman/listinfo/xcrysden>
>>     >
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>>     <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
> 
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