From radu_download at yahoo.com Fri Mar 1 14:50:02 2013 From: radu_download at yahoo.com (radu i) Date: Fri, 1 Mar 2013 05:50:02 -0800 (PST) Subject: [xcrysden] minimal package list for X11 Message-ID: <1362145802.49776.YahooMailNeo@web126205.mail.ne1.yahoo.com> Dear XCrysDen users and developers, Is there a minimal list of cywgin packages to be installed in order to have a functional X-server (for Xcrysden)? (A full X11 installed is to big) Thank you for your time and support! radu -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130301/9773e571/attachment.htm From devan.umd at gmail.com Wed Mar 6 21:09:54 2013 From: devan.umd at gmail.com (dev pe) Date: Wed, 6 Mar 2013 15:09:54 -0500 Subject: [xcrysden] Combining many PWscf output files for animation Message-ID: Hello Xcrysden Users I am running a Molecular dynamics simulation in steps. For each step, I have a PWscf output file. Is there a way to combine all the output files in running a complete Xcrysden animation? Any help is appreciated. Thanks Dev PhD student UMCP -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130306/87fbe381/attachment.htm From lorenzo.paulatto at impmc.upmc.fr Wed Mar 6 22:44:59 2013 From: lorenzo.paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Wed, 6 Mar 2013 22:44:59 +0100 Subject: [xcrysden] Combining many PWscf output files for animation In-Reply-To: References: Message-ID: On 6 March 2013 21:09, dev pe wrote: > Hello Xcrysden Users > > I am running a Molecular dynamics simulation in steps. For each step, I have > a PWscf output file. Is there a way to combine all the output files in > running a complete Xcrysden animation? cat file1 file2 file3 > all_together bests -- 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 From tone.kokalj at ijs.si Thu Mar 7 17:31:40 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 07 Mar 2013 17:31:40 +0100 Subject: [xcrysden] minimal package list for X11 In-Reply-To: <1362145802.49776.YahooMailNeo@web126205.mail.ne1.yahoo.com> References: <1362145802.49776.YahooMailNeo@web126205.mail.ne1.yahoo.com> Message-ID: <1362673900.18805.4.camel@catalyst.ijs.si> On Fri, 2013-03-01 at 05:50 -0800, radu i wrote: > > Dear XCrysDen users and developers, > > Is there a minimal list of cywgin packages to be installed in order to > have a functional X-server (for Xcrysden)? (A full X11 installed is to > big) What you mean by a full X11 installation I do not know, but you will need at least a working X server + window manager + some basic utilities such as xterm (or any other terminal emulator for X). In addition, xcrysden depends on the following cygwin packages (see the README.cygwin file inside the xcrysden package): * tcl-tk * fftw3 * libGL1 * libGLU1 * xorg-server * bash * bc * coreutils * gawk * grep * gzip * ImageMagick * less * more 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 200210qb at gmail.com Fri Mar 8 02:10:39 2013 From: 200210qb at gmail.com (Bo Qiu) Date: Thu, 7 Mar 2013 20:10:39 -0500 Subject: [xcrysden] A few issues with Xcrysden In-Reply-To: References: <1361809894.47147.YahooMailNeo@web126203.mail.ne1.yahoo.com> Message-ID: Just a quick update on my previous problems with Xcrysden 1.5, I tried it on a RHEL6 system (with the help of great university staff) and now it works like a charm. Thanks, Bo On Mon, Feb 25, 2013 at 1:19 PM, Bo Qiu <200210qb at gmail.com> wrote: > 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/20130307/26b7216a/attachment.htm From ndimakis at gmail.com Sat Mar 9 03:36:16 2013 From: ndimakis at gmail.com (Nicholas Dimakis) Date: Fri, 8 Mar 2013 20:36:16 -0600 Subject: [xcrysden] Charge Difference Maps for CO/Pt vs CO/Ru Message-ID: Hello I am trying to plot Charge Difference Maps for CO/Pt vs CO/Ru using xcrysden. The calculations are via crystal09. It looks that crystal executes the first *map-1.d3 file with no problems but the *map-2.d3 gives an error as "error reading unit 25". I found out that the problem has to do by editing the second script and changing anything in section COORDINA. Also fort.25.A and fort.25.B are generated in the tmp location. I had used xcrysden in the past for CO/Pt and CO/PtRu alloys with no problem. However, the structure of the two files was the same (Ru atoms had replaced the Pt in the same positions). Thank you. -- Nikolaos Dimakis Associate Professor and Interim Chair Department of Physics and Geology University of Texas-Pan American 1201 W. University Drive Edinburg, TX 78539-2999 Phone: (956) 380-8761 Fax:(956) 381-2423 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130308/6ac3be08/attachment.htm From pango_122 at yahoo.com Thu Mar 14 11:37:37 2013 From: pango_122 at yahoo.com (PANGO) Date: Thu, 14 Mar 2013 10:37:37 +0000 (GMT) Subject: [xcrysden] problem with pressing right mouse button Message-ID: <1363257457.19219.YahooMailNeo@web171605.mail.ir2.yahoo.com> Dear xcrysden experts I'm a novice user of xcrysden and I have installed xcrysden but when I press right mouse button on the main window, it closes and I get this error : ?-------------------------------------------------------------------------------------------------------- ?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:? 5227 ?? Current serial number in output stream:? 5227 ?---------------------------------------------------------------------------------------------------------- ?Regards ?Erfan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130314/6cc1471d/attachment.htm From tone.kokalj at ijs.si Fri Mar 15 17:00:48 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 15 Mar 2013 17:00:48 +0100 Subject: [xcrysden] Charge Difference Maps for CO/Pt vs CO/Ru In-Reply-To: References: Message-ID: <1363363248.25127.10.camel@catalyst.ijs.si> On Fri, 2013-03-08 at 20:36 -0600, Nicholas Dimakis wrote: > Hello > > > I am trying to plot Charge Difference Maps for CO/Pt vs CO/Ru using > xcrysden. The calculations are via crystal09. It looks that crystal > executes the first *map-1.d3 file with no problems but the *map-2.d3 > gives an error as "error reading unit 25". I found out that the > problem has to do by editing the second script and changing anything > in section COORDINA. Also fort.25.A and fort.25.B are generated in the > tmp location. It is difficult to say what is the problem. If your system is not too big and the fort.9 is not too large, try to send the fort.9 file to my email, with the sufficient description that I may reproduce the error. 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 tone.kokalj at ijs.si Fri Mar 15 17:03:09 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 15 Mar 2013 17:03:09 +0100 Subject: [xcrysden] problem with pressing right mouse button In-Reply-To: <1363257457.19219.YahooMailNeo@web171605.mail.ir2.yahoo.com> References: <1363257457.19219.YahooMailNeo@web171605.mail.ir2.yahoo.com> Message-ID: <1363363389.25127.13.camel@catalyst.ijs.si> On Thu, 2013-03-14 at 10:37 +0000, PANGO wrote: > Dear xcrysden experts > > > I'm a novice user of xcrysden and I have installed xcrysden but when I > press right mouse button on the main window, it closes and I get this > error : > -------------------------------------------------------------------------------------------------------- > > 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: 5227 > Current serial number in output stream: 5227 This is the nasty X failed request; it's difficult to determine the cause. Did you really mean right-mouse button? Then try not to press it; but if you meant the left-button instead, well then ... 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 sarayzdn at gmail.com Sun Mar 24 13:57:28 2013 From: sarayzdn at gmail.com (sara yzdn) Date: Sun, 24 Mar 2013 17:27:28 +0430 Subject: [xcrysden] fatal error on X11/Xlib.h Message-ID: Hello I am trying to install xcrysden source package on on fedora 18, I have followed below steps: 1. $ tar xvf xcrysden-1.5.53.tar.gz 2. $ cd xcrysden-1.5.53/ 3. $ XCRYSDEN_TOPDIR=/usr/local/xcrysden 4. $ XCRYSDEN_SCRATCH=/usr/local/xcrysden_scratch 5. $ mkdir /usr/local/xcrysden_scratch 6. $ cp ./system/Make.sys-shared Make.sys 7. $ make all and I am receiving the following error: /home/Packages/xcrysden-1.5.53/external/src/tk8.5.11/unix/../generic/tk.h:76:23: fatal error: X11/Xlib.h: No such file or directory compilation terminated. make[2]: *** [tk3d.o] Error 1 make[2]: Leaving directory `/home/sara/Packages/xcrysden-1.5.53/external/src/tk8.5.11/unix' make[1]: *** [tk] Error 2 make[1]: Leaving directory `/home/sara/Packages/xcrysden-1.5.53/external/src' make: *** [tk] Error 2 * * *Please kindly let me know how to solve this problem. * -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20130324/50309539/attachment.htm From tone.kokalj at ijs.si Tue Mar 26 19:35:51 2013 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 26 Mar 2013 19:35:51 +0100 Subject: [xcrysden] fatal error on X11/Xlib.h In-Reply-To: References: Message-ID: <1364322951.30393.49.camel@catalyst.ijs.si> On Sun, 2013-03-24 at 17:27 +0430, sara yzdn wrote: > > /home/Packages/xcrysden-1.5.53/external/src/tk8.5.11/unix/../generic/tk.h:76:23: fatal error: X11/Xlib.h: No such file or directory This means that you don't have the development version of X11 library installed on your system. Search which package on fedora contains the X11/Xlib.h file and install it. On Debian its name is libx11-dev ; it should be similar (but probably not identical) on fedora. 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