From yves.limoge at cea.fr Tue Feb 5 16:37:09 2013 From: yves.limoge at cea.fr (Yves Limoge) Date: Tue, 05 Feb 2013 16:37:09 +0100 Subject: [xcrysden] Wave unctions plot In-Reply-To: <1A9F0F275F0DE54BA1FBF55D068937C72D555B0E@ECS-EXG-P-MB05.win.lanl.gov> References: <1A9F0F275F0DE54BA1FBF55D068937C72D555B0E@ECS-EXG-P-MB05.win.lanl.gov> Message-ID: <51112725.9010401@cea.fr> Y. Limoge Dear All I am trying to plot 3D isosurface wave functions obtained from a PWSCF + PP calculation. When I launch XcrysDEN however I seem not to have acces to the "Tools/Datagrid" menu which should give rise to a plot, if I am right. This "Tools/Datagrid" button remains inert (grey), moreover i I try to open the wave function file from pwscf as a pwscf output ile, I get an error. What should I do to plot isosurface wave functions ? Thank youy for your help. Y. Limoge From tone.kokalj at ijs.si Tue Feb 5 16:56:34 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 05 Feb 2013 16:56:34 +0100 Subject: [xcrysden] Wave unctions plot In-Reply-To: <51112725.9010401@cea.fr> References: <1A9F0F275F0DE54BA1FBF55D068937C72D555B0E@ECS-EXG-P-MB05.win.lanl.gov> <51112725.9010401@cea.fr> Message-ID: <1360079794.23258.19.camel@catalyst.ijs.si> On Tue, 2013-02-05 at 16:37 +0100, Yves Limoge wrote: > Y. Limoge > > Dear All > > I am trying to plot 3D isosurface wave functions obtained from a PWSCF + PP calculation. With PWSCF + PP calculation you need to create an XSF format file, that contains the wavefunction (probably you mean the |psi|^2, i.e., plot_num=7 of PP). In XSF language, this means that the xsf file contains the datagrid section (i.e. BEGIN_BLOCK_DATAGRID* / END_BLOCK_DATAGRID*). Only then the Tools/Datagrid menu will be active. 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 yazdani.sarah at gmail.com Thu Feb 14 05:12:26 2013 From: yazdani.sarah at gmail.com (sara yazdani) Date: Thu, 14 Feb 2013 07:42:26 +0330 Subject: [xcrysden] Problem with installing the source code on fedora 18 Message-ID: Dear Sir, I want to install "xcrysden-1.5.53" on fedora 18 x86_64, I have followed the steps as follows: $ tar xvf xcrysden-1.5.53.tar.gz $ cd xcrysden-1.5.53/ $ cp system/Make.sys-shared Make.sys $ make all $ ./xcrysden but the final message I have received is this: * cat: /home/sara/CODES/xcrysden-1.5.53-bin-shared/version: No such file or directory +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* 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: 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: line 163: /home/sara/CODES/xcrysden-1.5.53-bin-shared/scripts/xcLib.sh: No such file or directory* *This is while I have removed all the prebuilt files related to xcrysden. Please kindly guide me where I am going wrong. Regards, * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130214/0fc6624b/attachment.htm From tone.kokalj at ijs.si Thu Feb 21 06:09:42 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 21 Feb 2013 06:09:42 +0100 Subject: [xcrysden] Problem with installing the source code on fedora 18 In-Reply-To: References: Message-ID: <20130221060942.51903kqjwojfzndi@nabiralnik.ijs.si> Quoting sara yazdani : > Dear Sir, > > I want to install "xcrysden-1.5.53" on fedora 18 x86_64, I have followed > the steps as follows: > > $ tar xvf xcrysden-1.5.53.tar.gz > $ cd xcrysden-1.5.53/ > $ cp system/Make.sys-shared Make.sys > $ make all > $ ./xcrysden > > but the final message I have received is this: > * > cat: /home/sara/CODES/xcrysden-1.5.53-bin-shared/version: No such file or > directory Did you really run as "./xcrysden" or just as "xcrysden". If it is the latter and you defined the XCRYSDEN_TOPDIR to point to an absolutely directory that do not exists anymore, than this is the reason. Check if the "/home/sara/CODES/xcrysden-1.5.53-bin-shared/" directory exists. Regards, Tone From 200210qb at gmail.com Sat Feb 23 07:53:54 2013 From: 200210qb at gmail.com (Bo Qiu) Date: Sat, 23 Feb 2013 01:53:54 -0500 Subject: [xcrysden] A few issues with Xcrysden Message-ID: Dear developers, I'm trying to use xcrysden installed on the computer cluster maintained by the university, however, I've met some issues that even the staff cannot help me with, so I'm trying to ask for help here: 1. when I use Xcrysden 1.4.1 to import charge density from quantum espresso output, after loading the XSF, I do Tools -> Data Grid, however, there is no OK button on the bottom of the popped-up DataGrid panel, so there is no way I can proceed from there to make the isosurface of charge density, so I try to switch to 1.5.53 2. when I use Xcrysden 1.5.53, After I opened xcrysden, I can see all the menu, tools panel items and the bottom tool panels. However, the problem is that the actual panel for molecule display is not working -- it feels like it's not refreshing. For instance, if I do File -> Open structure --> Open XSF --> choose file, then all these drop menus and dialogue windows will remain and overlap in the order they showed up and no molecule is displayed in the end. I thought it may be just laggy, but if I leave it there for hours and come back, it is still the same. Interestingly, for 1.4.1, at least I don't have such issue at all. I have attached a screen shot to this email. I used putty for SSH, used Xming for X11 client and the X11 setup works for all of my other programs. The host is a unix computer cluster. The client system is windows 7 and had firewall turned off. I actually tried on several different computers with win 7 and winXP, same observation. Strangely, the cluster staff actually didn't have my observed issues at all when he has exactly the same client setups as I have and he tried all he could but I still couldn't get this working ... Could you please let me know any possible solutions? Thanks a lot, Bo -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130223/b76d8f31/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: xcrysprob.png Type: image/png Size: 121847 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20130223/b76d8f31/attachment-0001.png From radu_download at yahoo.com Mon Feb 25 17:31:34 2013 From: radu_download at yahoo.com (radu i) Date: Mon, 25 Feb 2013 08:31:34 -0800 (PST) Subject: [xcrysden] A few issues with Xcrysden In-Reply-To: References: Message-ID: <1361809894.47147.YahooMailNeo@web126203.mail.ne1.yahoo.com> Dear Bo, A temporary solution for the second problem - because I experience the same thing on Cygwin with full X11 package installed - is to use your mouse scroll to zoom in/out and your structure will reaper. r ________________________________ From: Bo Qiu <200210qb at gmail.com> To: xcrysden at democritos.it Sent: Saturday, February 23, 2013 6:53 AM Subject: [xcrysden] A few issues with Xcrysden Dear developers, I'm trying to use xcrysden installed on the computer cluster maintained by the university, however, I've met some issues that even the staff cannot help me with, so I'm trying to ask for help here: 1. when I use Xcrysden 1.4.1 to import charge density from quantum espresso output, after loading the XSF, I do Tools -> Data Grid, however, there is no OK button on the bottom of the popped-up DataGrid panel, so there is no way I can proceed from there to make the isosurface of charge density, so I try to switch to 1.5.53 2. when I use Xcrysden 1.5.53, After I opened xcrysden, I can see all the menu, tools panel items and the bottom tool panels. However, the problem is that the actual panel for molecule display is not working -- it feels like it's not refreshing. For instance, if I do File -> Open structure --> Open XSF --> choose file, then all these drop menus and dialogue windows will remain and overlap in the order they showed up and no molecule is displayed in the end. I thought it may be just laggy, but if I leave it there for hours and come back, it is still the same. Interestingly, for 1.4.1, at least I don't have such issue at all. I have attached a screen shot to this email. I used putty for SSH, used Xming for X11 client and the X11 setup works for all of my other programs. The host is a unix computer cluster. The client system is windows 7 and had firewall turned off. I actually tried on several different computers with win 7 and winXP, same observation. Strangely, the cluster staff actually didn't have my observed issues at all when he has exactly the same client setups as I have and he tried all he could but I still couldn't get this working ... Could you please let me know any possible solutions? Thanks a lot, Bo _______________________________________________ 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/20130225/22ce2b31/attachment.htm From 200210qb at gmail.com Mon Feb 25 19:19:58 2013 From: 200210qb at gmail.com (Bo Qiu) Date: Mon, 25 Feb 2013 13:19:58 -0500 Subject: [xcrysden] A few issues with Xcrysden In-Reply-To: <1361809894.47147.YahooMailNeo@web126203.mail.ne1.yahoo.com> References: <1361809894.47147.YahooMailNeo@web126203.mail.ne1.yahoo.com> Message-ID: Dear Radu, Thanks a lot for the tips, but sadly it didn't seem to work for me. The technical staff maintaining the university cluster pointed out it might have something to do with RHEL5 system as things seem to work on RHEL6. I feel there is nothing I can do from my side then... Thanks again, Bo On Mon, Feb 25, 2013 at 11:31 AM, radu i wrote: > > Dear Bo, > > A temporary solution for the second problem - because I experience the > same thing on Cygwin with full X11 package installed - is to use your mouse > scroll to zoom in/out and your structure will reaper. > > r > > ------------------------------ > *From:* Bo Qiu <200210qb at gmail.com> > *To:* xcrysden at democritos.it > *Sent:* Saturday, February 23, 2013 6:53 AM > *Subject:* [xcrysden] A few issues with Xcrysden > > Dear developers, > > I'm trying to use xcrysden installed on the computer cluster maintained by > the university, however, I've met some issues that even the staff cannot > help me with, so I'm trying to ask for help here: > > 1. when I use Xcrysden 1.4.1 to import charge density from quantum > espresso output, after loading the XSF, I do Tools -> Data Grid, however, > there is no OK button on the bottom of the popped-up DataGrid panel, so > there is no way I can proceed from there to make the isosurface of charge > density, so I try to switch to 1.5.53 > > 2. when I use Xcrysden 1.5.53, After I opened xcrysden, I can see all the > menu, tools panel items and the bottom tool panels. However, the problem is > that the actual panel for molecule display is not working -- it feels like > it's not refreshing. For instance, if I do File -> Open structure --> Open > XSF --> choose file, then all these drop menus and dialogue windows will > remain and overlap in the order they showed up and no molecule is displayed > in the end. I thought it may be just laggy, but if I leave it there for > hours and come back, it is still the same. Interestingly, for 1.4.1, at > least I don't have such issue at all. I have attached a screen shot to this > email. > > I used putty for SSH, used Xming for X11 client and the X11 setup works > for all of my other programs. The host is a unix computer cluster. The > client system is windows 7 and had firewall turned off. I actually tried on > several different computers with win 7 and winXP, same observation. > Strangely, the cluster staff actually didn't have my observed issues at all > when he has exactly the same client setups as I have and he tried all he > could but I still couldn't get this working ... > > Could you please let me know any possible solutions? > > Thanks a lot, > Bo > > _______________________________________________ > 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 > > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130225/39944ebb/attachment.htm From eng_rageh at yahoo.com Tue Feb 26 11:25:45 2013 From: eng_rageh at yahoo.com (rageh attia) Date: Tue, 26 Feb 2013 02:25:45 -0800 (PST) Subject: [xcrysden] XCrySDen Digest, Vol 61, Issue 5 In-Reply-To: Message-ID: <1361874345.19915.YahooMailClassic@web140701.mail.bf1.yahoo.com> Dear sir ???????????please remove my e-mail from the mailing list , i made? unsubscribe? but? still receiving mails from the group. ?????????????????????????????????????????????????????????????????????????????????????????????????????????????? Regards -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130226/dc7a0218/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Tue Feb 26 11:43:31 2013 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 26 Feb 2013 11:43:31 +0100 Subject: [xcrysden] XCrySDen Digest, Vol 61, Issue 5 In-Reply-To: <1361874345.19915.YahooMailClassic@web140701.mail.bf1.yahoo.com> References: <1361874345.19915.YahooMailClassic@web140701.mail.bf1.yahoo.com> Message-ID: On 26 February 2013 11:25, rageh attia wrote: > Dear sir > please remove my e-mail from the mailing list , i made > unsubscribe but still receiving mails from the group. > > Regards > Dear rageh, did you reply to the unsubscribe confirmation email? best regards -- Dr. Lorenzo Paulatto IdR @ IMPMC -- CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130226/8815e7e4/attachment.htm