From david.grifith at gmail.com Mon Jan 3 09:23:18 2011 From: david.grifith at gmail.com (David Grifith) Date: Mon, 3 Jan 2011 11:53:18 +0330 Subject: [xcrysden] line 129 of xcLib.sh file Message-ID: Dear XCrysden users when I try to run XCrysden under Cygwin in windows I get the below error : ./xcrysden: line 129 : /scripts/xcLib.sh : no such file or directory As I have checked there are only 45 lines in xcLib.sh file but the program want to read the line 129. I appreciate your help in advance. -- Sincerely Yours David G. JCU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110103/5ba71d12/attachment.htm From erwin.rossen at gmail.com Fri Jan 7 09:58:06 2011 From: erwin.rossen at gmail.com (Erwin Rossen) Date: Fri, 7 Jan 2011 09:58:06 +0100 Subject: [xcrysden] Periodic xyz-file Message-ID: I want to visualize a periodic structure which I have in xyz format. How should the format look like to be able to read in XCrySDen? For instance the xyz-file in the example below? 3 1 0 0 0 1 0 0 0 1 Ag 0.2 0.2 0.5 Ag 0.5 0.5 0.8 H 0.0 0.0 0.0 From tone.kokalj at ijs.si Fri Jan 7 10:18:20 2011 From: tone.kokalj at ijs.si (tone) Date: Fri, 07 Jan 2011 10:18:20 +0100 Subject: [xcrysden] line 129 of xcLib.sh file In-Reply-To: References: Message-ID: <1294391900.4320.2.camel@catalyst.ijs.si> On Mon, 2011-01-03 at 11:53 +0330, David Grifith wrote: > Dear XCrysden users > > when I try to run XCrysden under Cygwin in windows I get the below > error : > > ./xcrysden: line 129 : /scripts/xcLib.sh : no such file or directory > > As I have checked there are only 45 lines in xcLib.sh file but the > program want to read the line 129. I appreciate your help in advance. This means that you are likely using the old 1.4* version of xcrysden and you did not define the XCRYSDEN_TOPDIR enviromental variable. Consider using the newer 1.5* version, and the problem will vanish, because the newer version does not require the XCRYSDEN_TOPDIR variable anymore. 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 sebastijan.peljhan at ijs.si Fri Jan 7 10:26:33 2011 From: sebastijan.peljhan at ijs.si (Sebastijan Peljhan) Date: Fri, 07 Jan 2011 10:26:33 +0100 Subject: [xcrysden] Periodic xyz-file In-Reply-To: References: Message-ID: <1294392393.2649.42.camel@surf> You have to transform your xyz file into xsf file. The detailed description of xsf file is located at http://www.xcrysden.org/doc/XSF.html The xsf file for your structure should look like this: DIM-GROUP 3 1 PRIMVEC 1 0 0 0 1 0 0 0 1 PRIMCOORD 3 1 Ag 0.2 0.2 0.5 Ag 0.5 0.5 0.8 H 0.0 0.0 0.0 Also, you have to change PRIMVEC and PRIMCOORD from your units to angstroms. Cheers, Sebastijan On Fri, 2011-01-07 at 09:58 +0100, Erwin Rossen wrote: > I want to visualize a periodic structure which I have in xyz format. > How should the format look like to be able to read in XCrySDen? For > instance the xyz-file in the example below? > > 3 > > 1 0 0 > 0 1 0 > 0 0 1 > > Ag 0.2 0.2 0.5 > Ag 0.5 0.5 0.8 > H 0.0 0.0 0.0 > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Sebastijan Peljhan Department of Physical and Organic Chemistry "Jozef Stefan" Institute Jamova 39 1000 Ljubljana Slovenia tel.:+386 1 4773 523 fax.:+386 1 4773 822 email: sebastijan.peljhan at IJS.SI From david.grifith at gmail.com Sat Jan 15 00:03:05 2011 From: david.grifith at gmail.com (David Grifith) Date: Sat, 15 Jan 2011 02:33:05 +0330 Subject: [xcrysden] label of atoms Message-ID: Dear XCrysden Users Atomic symbols can be displayed by XCrysden but there is not any button in Display section for displaying the atomic labels. Is there any solution ? -- Sincerely Yours David G. JCU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110115/0f6e7acc/attachment.htm From azzizuc at libero.it Mon Jan 17 16:41:00 2011 From: azzizuc at libero.it (azzizuc at libero.it) Date: Mon, 17 Jan 2011 16:41:00 +0100 (CET) Subject: [xcrysden] istallation problems Message-ID: <9031499.2223471295278860369.JavaMail.defaultUser@defaultHost> Dear XCrysDen users, I am trying to install XCrysDen software on my 64 bit Linux machine by using the "Linux_x86_64 binary packages". Everything seems to work until I will try to tape "xcrysden" in order to lunch the program. At this point the first icon will appear just for 1 second and after that the program will abort the initialization. I don't really know why...have someone had the same problem? Do you know how can I do in order to use the software? Thanks a lot Regards Azzurra Zucchini From masoudnahali at gmail.com Tue Jan 18 10:08:49 2011 From: masoudnahali at gmail.com (Masoud Nahali) Date: Tue, 18 Jan 2011 12:38:49 +0330 Subject: [xcrysden] installation problems Message-ID: Dear Azzurra Have you ever updated your Linux kernel ? some times ago I had the same problem on a 64 bit Opensuse and it was solved by updating the Linux kernel. I do not exactly know the cause of the problem in your system, but for a primary step please update your kernel if possible. Best Wishes Masoud -------------- Masoud Nahali, Sharif University of Technology -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110118/42c479be/attachment.htm From azzizuc at libero.it Tue Jan 18 10:20:23 2011 From: azzizuc at libero.it (azzizuc at libero.it) Date: Tue, 18 Jan 2011 10:20:23 +0100 (CET) Subject: [xcrysden] installation problems Message-ID: <16940546.1202921295342423904.JavaMail.defaultUser@defaultHost> Dear XCrysDen users, at last I was able to install the program. The problem was just a not well uploaded file library! Now everything is fine!!! Thanks a lot Azzurra ----Messaggio originale---- Da: masoudnahali at gmail.com Data: 18/01/2011 10.08 A: "XCrysden" Ogg: Re: [xcrysden] installation problems Dear Azzurra Have you ever updated your Linux kernel ? some times ago I had the same problem on a 64 bit Opensuse and it was solved by updating the Linux kernel. I do not exactly know the cause of the problem in your system, but for a primary step please update your kernel if possible. Best Wishes Masoud -------------- Masoud Nahali, Sharif University of Technology From masoudnahali at gmail.com Thu Jan 20 10:02:33 2011 From: masoudnahali at gmail.com (Masoud Nahali) Date: Thu, 20 Jan 2011 12:32:33 +0330 Subject: [xcrysden] label of atoms Message-ID: Dear David You should simply follow the below instruction to display your desired labels : Modify - > Atomic Symbols/Fonts - > Edit Custom Atom-Labels and Fonts ; I hope it helps. Best Wishes Masoud -------------- Masoud Nahali, Sharif University of Technology David Wrote : Dear XCrysden Users Atomic symbols can be displayed by XCrysden but there is not any button in Display section for displaying the atomic labels. Is there any solution ? -- Sincerely Yours David G. JCU -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20110120/cff3e278/attachment.htm From sclauzer at sissa.it Thu Jan 27 14:23:11 2011 From: sclauzer at sissa.it (Gabriele Sclauzero) Date: Thu, 27 Jan 2011 14:23:11 +0100 Subject: [xcrysden] xcrysden crashes while displaying thermometer Message-ID: <4D4171BF.4030402@sissa.it> Dear Tone and users, I met a problem when trying to display a 3D charge density plot. I can visualize the density, but when I select the option to display the color thermometer (and then click "submit"), the program crashes with the following error message reading PRIMCOORD reading CONVCOORD Number of Atoms: 398 Number of Frames: 12 natoms: 398 , ndel: 0 Filtered number of atoms: 398 Estimated number of bonds = 1174 sInfo(dim) = 3; periodic(dim) = 3 coordinate system orientation is right X Error of failed request: BadValue (integer parameter out of range for operation) Major opcode of failed request: 91 (X_QueryColors) Value in failed request: 0xff000000 Serial number of failed request: 49383 Current serial number in output stream: 49383 Any idea of how to locate the problem? Regards, GS -- Gabriele Sclauzero, EPFL SB ITP CSEA PH H2 462, Station 3, CH-1015 Lausanne