From khattori at ms.naist.jp Mon Feb 7 11:15:02 2011 From: khattori at ms.naist.jp (Ken Hattori) Date: Mon, 07 Feb 2011 19:15:02 +0900 Subject: [xcrysden] How to activate atom radius in script file ? Message-ID: <4D4FC626.4000405@ms.naist.jp> Dear all, I would like to ask you how to activate atom radius description in script files. When we Save Current State and Structure as a script file (.xcrysden), the information of "Atomic radii" is saved as, for instance, xc_newvalue .mesa 4 1 1.532000 xc_newvalue .mesa 10004 1 1.499000 The former should be Display radius and the latter should be covalent radius, for hydrogen. However, it does not work when I Open XCrySDen Scripting File, that is, their radii are still 0.532000 and 0.499000, respectively, in the display in my system. Other descriptions, e.g., atomic colors, work. I am not sure that this is a problem of my installing/setting, or not. My system is XCrySDen 1.4.1, binary package for *Linux-i386* (statically linked), installed on Ubuntu-8.04-Japanese.vdi, in Oracle VM VirtualBox 3.2.10 r66523, and in Windows 7. Would you please suggest me the way to activate atom radius description ? Ken Hattori -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110207/d99e1ecf/attachment.htm From germaneau at gucas.ac.cn Sat Feb 19 19:33:50 2011 From: germaneau at gucas.ac.cn (Eric Germaneau) Date: Sat, 19 Feb 2011 13:33:50 -0500 Subject: [xcrysden] xcrysden & QE Message-ID: <4D600D0E.7060707@gucas.ac.cn> Dear all, I've installed *XCrySDen 1.5.21* (src-all) and *quantum-espresso (QE) 4.2.1*. I've spent hours trying to display the output of a molecular dynamics run (output cp.x from QE package). When I do a $XCRYSDEN_TOPDIR/scripts/pwo2xsf.sh -ic ./si.out I get "(standard_in) 1: syntax error". Do you have any idea about what's going wrong here? Eric. -- /Be the change you wish to see in the world / --- Mahatma Gandhi --- Dr. ?ric Germaneau College of Physical Sciences Graduate University of ChineseAcademy of Sciences Yuquan Road 19A Beijing 100049 China /Please consider the environment before printing this email. Consid?rez svp l'environnement avant d'imprimer cet email. / -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110219/06715eda/attachment.htm From sclauzer at sissa.it Tue Feb 22 11:59:25 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Tue, 22 Feb 2011 11:59:25 +0100 Subject: [xcrysden] xcrysden & QE In-Reply-To: <4D600D0E.7060707@gucas.ac.cn> References: <4D600D0E.7060707@gucas.ac.cn> Message-ID: <820CFF7A-6DB6-43FD-9A90-189D817D6C01@sissa.it> Dear Eric, I believe it is difficult to say anything with such a small piece of information. You should provide at least the cp output file. The pwo2xsf.sh is a BASH script, if you are familiar with such scripting language you can try to put some debug printout inside it, so that you'll be able to locate better the problem. GS Il giorno 19/feb/2011, alle ore 19.33, Eric Germaneau ha scritto: > Dear all, > > I've installed XCrySDen 1.5.21 (src-all) and quantum-espresso (QE) 4.2.1. > I've spent hours trying to display the output of a molecular dynamics run (output cp.x from QE package). > When I do a $XCRYSDEN_TOPDIR/scripts/pwo2xsf.sh -ic ./si.out > I get "(standard_in) 1: syntax error". > > Do you have any idea about what's going wrong here? > > Eric. > > -- > Be the change you wish to see in the world > ? Mahatma Gandhi ? > > Dr. ?ric Germaneau > > College of Physical Sciences > Graduate University of ChineseAcademy of Sciences > Yuquan Road 19A > Beijing 100049 > China > > Please consider the environment before printing this email. > Consid?rez svp l'environnement avant d'imprimer cet email. > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden ? Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110222/b0fdd4e7/attachment.htm From tone.kokalj at ijs.si Fri Feb 25 14:42:55 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 25 Feb 2011 14:42:55 +0100 Subject: [xcrysden] How to activate atom radius in script file ? In-Reply-To: <4D4FC626.4000405@ms.naist.jp> References: <4D4FC626.4000405@ms.naist.jp> Message-ID: <1298641375.7891.10.camel@catalyst.ijs.si> On Mon, 2011-02-07 at 19:15 +0900, Ken Hattori wrote: > Dear all, > > I would like to ask you how to activate atom radius description in > script files. > When we Save Current State and Structure as a script file (.xcrysden), > the information of "Atomic radii" is saved as, for instance, > xc_newvalue .mesa 4 1 1.532000 > xc_newvalue .mesa 10004 1 1.499000 > The former should be Display radius and the latter should be covalent > radius, > for hydrogen. > > However, it does not work when I Open XCrySDen Scripting File, > that is, their radii are still 0.532000 and 0.499000, respectively, > in the display in my system. > > Other descriptions, e.g., atomic colors, work. > > I am not sure that this is a problem of my installing/setting, or not. > My system is XCrySDen 1.4.1, binary package for Linux-i386 (statically > linked), Try with 1.5.* version of code, and if it still does not work let me know. The above recipe seems ok. 32bit-linux: http://www.xcrysden.org/download/xc-1.5.17-linux_x86-semishared.tar.gz 64bit-linux: http://www.xcrysden.org/download/xc-1.5.21-linux_x86_64-semishared.tar.gz Regards, -- 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 leila at ss.buaa.edu.cn Sat Feb 26 03:54:08 2011 From: leila at ss.buaa.edu.cn (leila) Date: Sat, 26 Feb 2011 10:54:08 +0800 Subject: [xcrysden] xcrysden in WIN7 Message-ID: <498688936.10816@buaa.edu.cn> Dear all, I used to use xcrysden in winXP, and it performed well. When I change my system into WIN7, I met this error warning "Failed to copy #/Xcrysden_defaults files." I don't know if it is a common problem or if there is some solutions. I would be really grateful if you can help. Best wishes! Yours sincerely, leila -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110226/97cc6be1/attachment.htm