From m.abbasnejad at gmail.com Thu Aug 25 07:27:54 2016 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Thu, 25 Aug 2016 09:57:54 +0430 Subject: [xcrysden] Regrading problem in updating the structure Message-ID: 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) *| |* 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 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 Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160825/aee2f200/attachment.htm From matic.poberznik at gmail.com Thu Aug 25 10:57:50 2016 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Thu, 25 Aug 2016 10:57:50 +0200 Subject: [xcrysden] Regrading problem in updating the structure In-Reply-To: References: Message-ID: <22dd7a69-af1a-768d-72d4-cbc0c279f900@gmail.com> Dear Mohaddeseh, Could you attach the pw.in you're trying to open as well (in-Ti-OV)? From m.abbasnejad at gmail.com Thu Aug 25 22:55:26 2016 From: m.abbasnejad at gmail.com (mohaddeseh abbasnejad) Date: Fri, 26 Aug 2016 01:25:26 +0430 Subject: [xcrysden] Regrading problem in updating the structure In-Reply-To: <22dd7a69-af1a-768d-72d4-cbc0c279f900@gmail.com> References: <22dd7a69-af1a-768d-72d4-cbc0c279f900@gmail.com> Message-ID: 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 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 > > ) *| > > |* 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 > > > > > > 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 > > Website: http://physics.ut.ac.ir > > > > --------------------------------------------------------- > > > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > 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 Website: http://physics.ut.ac.ir --------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160826/daa449d3/attachment-0001.htm From gsabo at crimson.ua.edu Fri Aug 26 05:48:37 2016 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Thu, 25 Aug 2016 21:48:37 -0600 Subject: [xcrysden] Regrading problem in updating the structure In-Reply-To: References: <22dd7a69-af1a-768d-72d4-cbc0c279f900@gmail.com> Message-ID: <5a66e413-8ef0-4e3a-f390-8bade1115458@crimson.ua.edu> 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 > > 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 > > >) > *| > > |* 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 > > > > > > > > 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 > > > > Website: http://physics.ut.ac.ir > > > > --------------------------------------------------------- > > > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > 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 > Website: http://physics.ut.ac.ir -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160825/c4f81b26/attachment.htm From matic.poberznik at gmail.com Fri Aug 26 09:47:53 2016 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Fri, 26 Aug 2016 09:47:53 +0200 Subject: [xcrysden] Regrading problem in updating the structure In-Reply-To: <5a66e413-8ef0-4e3a-f390-8bade1115458@crimson.ua.edu> References: <22dd7a69-af1a-768d-72d4-cbc0c279f900@gmail.com> <5a66e413-8ef0-4e3a-f390-8bade1115458@crimson.ua.edu> Message-ID: <2932a88c-24c0-597c-faee-b99a77b38dbf@gmail.com> 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 >> > 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 >> > >) >> *| >> > |* 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 >> > > >> > >> > >> > 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 >> > > >> > Website: http://physics.ut.ac.ir >> > >> > --------------------------------------------------------- >> > >> > >> > _______________________________________________ >> > XCrySDen mailing list >> > XCrySDen at democritos.it >> > http://www.democritos.it/mailman/listinfo/xcrysden >> >> > >> _______________________________________________ >> XCrySDen mailing list >> XCrySDen at democritos.it >> 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 >> Website: http://physics.ut.ac.ir > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > From uttamphy at gmail.com Tue Aug 30 08:22:24 2016 From: uttamphy at gmail.com (Uttam Paliwal) Date: Tue, 30 Aug 2016 11:52:24 +0530 Subject: [xcrysden] problem on cygwin Message-ID: Res sir when i run ./xcrysden then following problem is encountered. kindly suggest me solution """ Application initialization failed: no display name and no $DISPLAY environment variable Error in startup script: can't read "tk_version": no such variable while executing "package provide Tk $tk_version" (file "/cygdrive/c/XcrySDen-1.4.1bin-shared/Tcl/xcInit.tcl" line 400) """ No further action is proceeded. Kindly suggest me the solution -- Uttam Paliwal *Assistant Professor* Department of Physics J.N.V. University Jodhpur (India) Phone- 7597908441 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160830/aa9036ff/attachment.htm From matic.poberznik at gmail.com Tue Aug 30 10:00:05 2016 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Tue, 30 Aug 2016 10:00:05 +0200 Subject: [xcrysden] problem on cygwin In-Reply-To: References: Message-ID: <3942f3a7-6c78-aa90-b3c9-66cc38bd3f59@gmail.com> Dear Uttam, I suggest you download the latest binary of xcrysden for cygwin (xcrysden-1.5.60-cygwin.tar.gz) from here: http://www.xcrysden.org/Download.html > "package provide Tk $tk_version" > (file "/cygdrive/c/XcrySDen-1.4.1bin-shared/Tcl/xcInit.tcl" line 400) > """ Make sure you install other required packages as well, I think the above error results from missing the tcl-tk package. > Application initialization failed: no display name and no $DISPLAY > environment variable I think this error is from missing the xorg-server package, you should install it. I suggest that you install some kind of desktop environment as well (e.g. mate desktop environment), some instructions on how to do this are here: http://www.cygwin.com/xfree/docs/ug/using.html Hope this helps. Best regards, Matic Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia