From leila at ss.buaa.edu.cn Mon Dec 6 09:21:22 2010 From: leila at ss.buaa.edu.cn (leila) Date: Mon, 6 Dec 2010 16:21:22 +0800 Subject: [xcrysden] problems on start-up Message-ID: <491623678.13716@buaa.edu.cn> Dear all, Xcrysden used to be stable on my computer under LINUX (with virtual machine). However, it comes to the following problems when I install it under cygwin. The xcrysden is successfully installed. When I launch the program by $xcrysden, some unfavorable things happen. Sometimes, the program can successfully start, but most of the times, it flashes for 2 seconds and disappear without any error and warnings. Any advice is welcome. Best wishes! Yours, Leila -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20101206/ee3491e4/attachment.htm From binshao1118 at gmail.com Wed Dec 8 03:53:08 2010 From: binshao1118 at gmail.com (Bin Shao) Date: Wed, 8 Dec 2010 10:53:08 +0800 Subject: [xcrysden] error info. in wm_readbakgen.f Message-ID: Dear all, I intend to plot the fermi surface using wien2k, I encountered an error after "Render Fermi Surface", here is the error info.: At line 125 of file wn_readbakgen.f (unit = 8, file = 'case.outputkgen') Fortran runtime error: Bad integer for item 1 in list input So, what's the problem? I am not familiar with fortran language, please give some suggestion, thank you in advanced! BTW, I finished the first three steps (generate k-mesh; x lapw1; x lapw2 -fermi) successfully. Best regards, -- Bin Shao, Ph.D. Candidate College of Information Technical Science, Nankai University 94 Weijin Rd. Nankai Dist. Tianjin 300071, China Email: binshao1118 at gmail.com -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20101208/fc877848/attachment.htm From s.sheikholeslami10 at gmail.com Wed Dec 8 18:39:13 2010 From: s.sheikholeslami10 at gmail.com (somayyeh sheikholeslami) Date: Wed, 8 Dec 2010 09:39:13 -0800 Subject: [xcrysden] error executing Message-ID: Dear users could anybody help me to solve this error, please? somy at somy-laptop:~$ xcrysden +----------------------------------------------------------------+ |****************************************************************| |* *| |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*--------------------------------------------------------------*| |* *| |* Anton Kokalj (Tone.Kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2004 by Anton Kokalj *| |* *| |****************************************************************| +----------------------------------------------------------------+ Version: 1.5.17 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=/home/somy/SOURCE/XCrySDen-1.5.17-bin-shared XCRYSDEN_SCRATCH=bashrc Running on platform: unix Error in startup script: wrong # args: should be "set varName ?newValue?" while executing "set system(c95_crystal) -p: not found" (file "/home/somy/.xcrysden/custom-definitions" line 14) invoked from within "source $env(HOME)/.xcrysden/custom-definitions" invoked from within "if { [file exists $env(HOME)/.xcrysden/custom-definitions] } { source $env(HOME)/.xcrysden/custom-definitions } else { source $system(TOPDIR)/Tc..." ("eval" body line 20) invoked from within "eval [info body xcInit]" (file "/home/somy/SOURCE/XCrySDen-1.5.17-bin-shared/Tcl/xcInit.tcl" line 530) From tone.kokalj at ijs.si Fri Dec 10 15:33:44 2010 From: tone.kokalj at ijs.si (tone) Date: Fri, 10 Dec 2010 15:33:44 +0100 Subject: [xcrysden] problems on start-up In-Reply-To: <000701cb951e$914fe180$b3efa480$@buaa.edu.cn> References: <000701cb951e$914fe180$b3efa480$@buaa.edu.cn> Message-ID: <1291991624.3443.1.camel@catalyst.ijs.si> On Mon, 2010-12-06 at 16:21 +0800, leila wrote: > Dear all, > > Xcrysden used to be stable on my computer under LINUX (with virtual > machine). However, it comes to the following problems when I install > it under cygwin. > > The xcrysden is successfully installed. When I launch the program by > $xcrysden, some unfavorable things happen. > > > > Sometimes, the program can successfully start, but most of the times, > it flashes for 2 seconds and disappear without any error and warnings. Dear Leila, With so little provided info, I believe nobody will be able to help you. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Fri Dec 10 15:36:17 2010 From: tone.kokalj at ijs.si (tone) Date: Fri, 10 Dec 2010 15:36:17 +0100 Subject: [xcrysden] error info. in wm_readbakgen.f In-Reply-To: References: Message-ID: <1291991777.3443.3.camel@catalyst.ijs.si> On Wed, 2010-12-08 at 10:53 +0800, Bin Shao wrote: > Dear all, > > I intend to plot the fermi surface using wien2k, I encountered an > error after "Render Fermi Surface", here is the error info.: > > At line 125 of file wn_readbakgen.f (unit = 8, file = > 'case.outputkgen') > Fortran runtime error: Bad integer for item 1 in list input > > So, what's the problem? I am not familiar with fortran language, > please give some suggestion, thank you in advanced! Difficult to say. Send me your case.outputkgen file (to private email), and I can try to inspect it. Regards, tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From tone.kokalj at ijs.si Fri Dec 10 15:39:36 2010 From: tone.kokalj at ijs.si (tone) Date: Fri, 10 Dec 2010 15:39:36 +0100 Subject: [xcrysden] error executing In-Reply-To: References: Message-ID: <1291991976.3443.6.camel@catalyst.ijs.si> On Wed, 2010-12-08 at 09:39 -0800, somayyeh sheikholeslami wrote: > Dear users > could anybody help me to solve this error, please? > somy at somy-laptop:~$ xcrysden > > +----------------------------------------------------------------+ > |****************************************************************| > |* *| > |* XCrySDen - (X-Window) CRYstalline Structures and DENsities *| > |* = === = === *| > |*--------------------------------------------------------------*| > |* *| > |* Anton Kokalj (Tone.Kokalj at ijs.si) *| > |* Jozef Stefan Institute, Ljubljana, Slovenia *| > |* *| > |* Copyright (c) 1996--2004 by Anton Kokalj *| > |* *| > |****************************************************************| > +----------------------------------------------------------------+ > > Version: 1.5.17 > > 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=/home/somy/SOURCE/XCrySDen-1.5.17-bin-shared > XCRYSDEN_SCRATCH=bashrc > > Running on platform: unix > Error in startup script: wrong # args: should be "set > varName ?newValue?" > while executing > "set system(c95_crystal) -p: not found" > (file "/home/somy/.xcrysden/custom-definitions" line 14) The problem is wprecisely what the error-text says: you have a syntax error in your /home/somy/.xcrysden/custom-definitions file at line 14. Edit /home/somy/.xcrysden/custom-definitions and correct it. If you don't know how, then consult: http://www.xcrysden.org/doc/custom.html Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From d_shiri at yahoo.com Mon Dec 20 20:07:50 2010 From: d_shiri at yahoo.com (Daryoush Shiri) Date: Mon, 20 Dec 2010 11:07:50 -0800 (PST) Subject: [xcrysden] .XSF shows always atoms not density/potential Message-ID: <718135.84517.qm@web121808.mail.ne1.yahoo.com> Hello, I have used rho2xsf program and generated .XSF file including data blocks of RHO, LDOS of SIESTA. But when I open it using Xcrysden I always see the atoms only and Data Grid section in tools does not show me the density or potential plots. Your helps are appreciated. I have version 1.4.1 of Xcrysden. Regards Darius -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20101220/c3f70942/attachment.htm From tone.kokalj at ijs.si Fri Dec 24 15:09:54 2010 From: tone.kokalj at ijs.si (tone) Date: Fri, 24 Dec 2010 15:09:54 +0100 Subject: [xcrysden] .XSF shows always atoms not density/potential In-Reply-To: <718135.84517.qm@web121808.mail.ne1.yahoo.com> References: <718135.84517.qm@web121808.mail.ne1.yahoo.com> Message-ID: <1293199794.3325.6.camel@catalyst.ijs.si> On Mon, 2010-12-20 at 11:07 -0800, Daryoush Shiri wrote: > Hello, > > > I have used rho2xsf program and generated .XSF file including data > blocks of RHO, LDOS of SIESTA. But when I open it using Xcrysden I > always see the atoms only and Data Grid section in tools does not show > me the density or potential plots. This is from the FAQ: Q: I am trying to display the isosurface/contours, but I cannot see them? A: Most likely the reason is that Lighting-Off display-mode is switched on, which cannot render the isosurface/contour. The Lighting-Off display-mode can render only molecules or crystals and nothing more. If you want to display isosurfaces, forces, Wigner-Seitz cells, etc., then switch to Lighting-On mode. Read here the description about Lighting-Off and Lighting-On display-modes. If this does not solve the problem, please, check these documents: http://www.xcrysden.org/doc/density.html http://www.xcrysden.org/doc/isocontrol.html http://www.xcrysden.org/doc/plane1control.html and if you still cannot see anything, send another email describing the sequence of steps you followed in trying to see the density. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From d_shiri at yahoo.com Fri Dec 24 18:52:08 2010 From: d_shiri at yahoo.com (Daryoush Shiri) Date: Fri, 24 Dec 2010 09:52:08 -0800 (PST) Subject: [xcrysden] .XSF shows always atoms not density/potential In-Reply-To: <1293199794.3325.6.camel@catalyst.ijs.si> References: <718135.84517.qm@web121808.mail.ne1.yahoo.com> <1293199794.3325.6.camel@catalyst.ijs.si> Message-ID: <587394.60731.qm@web121805.mail.ne1.yahoo.com> Hello, I think the problem was due to my Xcrysden version 1.4.1. I installed newer version (pre 1.6) and the problem is solved now. Thank you Daryoush University of Waterloo, Nanotechnology Program Waterloo, ON, Canada ________________________________ From: tone To: XCrySDen mailing list Sent: Fri, December 24, 2010 9:09:54 AM Subject: Re: [xcrysden] .XSF shows always atoms not density/potential On Mon, 2010-12-20 at 11:07 -0800, Daryoush Shiri wrote: > Hello, > > > I have used rho2xsf program and generated .XSF file including data > blocks of RHO, LDOS of SIESTA. But when I open it using Xcrysden I > always see the atoms only and Data Grid section in tools does not show > me the density or potential plots. This is from the FAQ: Q: I am trying to display the isosurface/contours, but I cannot see them? A: Most likely the reason is that Lighting-Off display-mode is switched on, which cannot render the isosurface/contour. The Lighting-Off display-mode can render only molecules or crystals and nothing more. If you want to display isosurfaces, forces, Wigner-Seitz cells, etc., then switch to Lighting-On mode. Read here the description about Lighting-Off and Lighting-On display-modes. If this does not solve the problem, please, check these documents: http://www.xcrysden.org/doc/density.html http://www.xcrysden.org/doc/isocontrol.html http://www.xcrysden.org/doc/plane1control.html and if you still cannot see anything, send another email describing the sequence of steps you followed in trying to see the density. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20101224/abac0473/attachment.htm