From paulatto at sissa.it Wed Feb 4 15:09:11 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Wed, 04 Feb 2009 15:09:11 +0100 Subject: [xcrysden] xcd aborts maybe in conjunction with some libraries Message-ID: Dear Tone and XCD users, since some recent updated of my system (maybe from openSUSE 11.0 to 11.1, or same later stage) I cannot run XCD anymore, as I get some very cryptic "Aborted" error messages. This holds for all binary versions and for the "bare" source version, which I have compiled against Tcl/Tk 8.5.5 and freeglut 080721 / Mesa 7.2. The following is the output of "./xcrysden -d", and the consequent backtrace in gdb (xcd source was compiled with -g switch) Nothe that /usr/X11R6/lib/libGL.so.1 belogs to nvidia binary drivers, but even if I force it to the Mesa one (using LD_PRELOAD) the outcome is the same. cheers $./xcrysden -d +----------------------------------------------------------------+ |****************************************************************| |* *| |* 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/. linux-gate.so.1 => (0xffffe000) libtk8.5.so => /usr/lib/libtk8.5.so (0xb7ea1000) libtcl8.5.so => /usr/lib/libtcl8.5.so (0xb7d85000) libGLU.so.1 => /usr/lib/libGLU.so.1 (0xb7d12000) libGL.so.1 => /usr/X11R6/lib/libGL.so.1 (0xb7c58000) libXmu.so.6 => /usr/lib/libXmu.so.6 (0xb7c3e000) libX11.so.6 => /usr/lib/libX11.so.6 (0xb7b0b000) libXext.so.6 => /usr/lib/libXext.so.6 (0xb7afa000) libm.so.6 => /lib/libm.so.6 (0xb7ad1000) libc.so.6 => /lib/libc.so.6 (0xb7975000) libpthread.so.0 => /lib/libpthread.so.0 (0xb795b000) libXss.so.1 => /usr/lib/libXss.so.1 (0xb7956000) libXft.so.2 => /usr/lib/libXft.so.2 (0xb7941000) libfreetype.so.6 => /usr/lib/libfreetype.so.6 (0xb78c0000) libz.so.1 => /lib/libz.so.1 (0xb78ab000) libfontconfig.so.1 => /usr/lib/libfontconfig.so.1 (0xb787a000) libXrender.so.1 => /usr/lib/libXrender.so.1 (0xb7870000) libdl.so.2 => /lib/libdl.so.2 (0xb786a000) libstdc++.so.6 => /usr/lib/libstdc++.so.6 (0xb7776000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0xb7767000) libGLcore.so.1 => /usr/X11R6/lib/libGLcore.so.1 (0xb68fc000) libnvidia-tls.so.1 => /usr/lib/tls/libnvidia-tls.so.1 (0xb68fa000) libXt.so.6 => /usr/lib/libXt.so.6 (0xb689e000) libSM.so.6 => /usr/lib/libSM.so.6 (0xb6895000) libICE.so.6 => /usr/lib/libICE.so.6 (0xb687a000) libxcb-xlib.so.0 => /usr/lib/libxcb-xlib.so.0 (0xb6877000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0xb6859000) libXau.so.6 => /usr/lib/libXau.so.6 (0xb6855000) /lib/ld-linux.so.2 (0xb7ffb000) libexpat.so.1 => /lib/libexpat.so.1 (0xb682c000) libuuid.so.1 => /lib/libuuid.so.1 (0xb6826000) XCRYSDEN_TOPDIR=/tmp/XCrySDen-1.5.17-src XCRYSDEN_SCRATCH=/tmp/xc-paulatto GNU gdb (GDB; openSUSE 11.1) 6.8.50.20081120-cvs Copyright (C) 2008 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "i586-suse-linux". For bug reporting instructions, please see: ... [Thread debugging using libthread_db enabled] Running on platform: unix Taking settings for 1280x800 screen-resolution !!! ------------------- Small Font Size set to: -14 Normal Font Size set to: -12 Package ImageMagick's import: /usr/bin/import can't find package: gifsicle Package Whirlgif: /usr/bin/whirlgif can't find package: mencoder can't find package: ppmtompeg can't find package: babel Package Xwd: /usr/bin/xwd Executing: /tmp/XCrySDen-1.5.17-src/bin/ftnunit Program received signal SIGABRT, Aborted. 0xffffe430 in __kernel_vsyscall () (gdb) bt #0 0xffffe430 in __kernel_vsyscall () #1 0xb7984990 in raise () from /lib/libc.so.6 #2 0xb79862c8 in abort () from /lib/libc.so.6 #3 0xb79c6683 in ?? () from /lib/libc.so.6 #4 0xb79c7edb in free () from /lib/libc.so.6 #5 0xb68dfa60 in ?? () from /usr/lib/tls/libnvidia-tls.so.1 #6 0xb7d8f956 in TclInvokeStringCommand () from /usr/lib/libtcl8.5.so #7 0xb7d927cb in ?? () from /usr/lib/libtcl8.5.so #8 0xb7ddc1f6 in ?? () from /usr/lib/libtcl8.5.so #9 0xb7e27c2f in TclObjInterpProcCore () from /usr/lib/libtcl8.5.so #10 0xb7e29590 in TclObjInterpProc () from /usr/lib/libtcl8.5.so #11 0xb7d927cb in ?? () from /usr/lib/libtcl8.5.so #12 0xb7d935e9 in ?? () from /usr/lib/libtcl8.5.so #13 0xb7d9401e in Tcl_EvalEx () from /usr/lib/libtcl8.5.so #14 0xb7d9449d in TclEvalObjEx () from /usr/lib/libtcl8.5.so #15 0xb7d9bcdd in ?? () from /usr/lib/libtcl8.5.so #16 0xb7d927cb in ?? () from /usr/lib/libtcl8.5.so #17 0xb7d9398e in ?? () from /usr/lib/libtcl8.5.so #18 0xb7d9401e in Tcl_EvalEx () from /usr/lib/libtcl8.5.so #19 0xb7e0440f in Tcl_FSEvalFileEx () from /usr/lib/libtcl8.5.so #20 0xb7ebfc43 in Tk_MainEx () from /usr/lib/libtk8.5.so #21 0x08051cef in main (argc=4, argv=0xbfffe874) at xcAppInit.c:432 (gdb) q The program is running. Quit anyway (and kill it)? (y or n) y best regards! -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From tone.kokalj at ijs.si Wed Feb 4 17:39:33 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 04 Feb 2009 17:39:33 +0100 Subject: [xcrysden] xcd aborts maybe in conjunction with some libraries In-Reply-To: References: Message-ID: <1233765573.4412.38.camel@walk.ijs.si> On Wed, 2009-02-04 at 15:09 +0100, Lorenzo Paulatto wrote: > Dear Tone and XCD users, > since some recent updated of my system (maybe from openSUSE 11.0 to 11.1, > or same later stage) I cannot run XCD anymore, as I get some very cryptic > "Aborted" error messages. This holds for all binary versions Did you try the 32bit version? It is difficult to say what is goin on, but according to your debug message seems it crashes due to Tcl/Tk not due to libGL (Mesa). Does the plain tclsh8.5 (and wish8.5) work on your computer? Does the $XCRYSDEN_TOPDIR/bin/xctclsh work? Does the $XCRYSDEN_TOPDIR/bin/xcrys work? Could you make me an account on your computer, so that I may check what is going on? 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 paulatto at sissa.it Thu Feb 5 10:59:26 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 05 Feb 2009 10:59:26 +0100 Subject: [xcrysden] xcd aborts maybe in conjunction with some libraries In-Reply-To: <1233765573.4412.38.camel@walk.ijs.si> References: <1233765573.4412.38.camel@walk.ijs.si> Message-ID: On Wed, 04 Feb 2009 17:39:33 +0100, Tone Kokalj wrote: > Did you try the 32bit version? yes, anyway, the same happens for the source version > > It is difficult to say what is goin on, but according to your debug > message seems it crashes due to Tcl/Tk not due to libGL (Mesa). > Does the plain tclsh8.5 (and wish8.5) work on your computer? > Does the $XCRYSDEN_TOPDIR/bin/xctclsh work? yes, well I get a % prompt, then I'm clueless > Does the $XCRYSDEN_TOPDIR/bin/xcrys work? yes, same as above, plus it creates a small empty window. > Could you make me an account on your computer, so that I may check what > is going on? It's my laptop :-(, yet I can arrange an ssh session if you need it. -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From paulatto at sissa.it Thu Feb 5 14:10:37 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Thu, 05 Feb 2009 14:10:37 +0100 Subject: [xcrysden] (solved) xcd aborts maybe in conjunction with some libraries In-Reply-To: References: <1233765573.4412.38.camel@walk.ijs.si> Message-ID: On Thu, 05 Feb 2009 10:59:26 +0100, Lorenzo Paulatto wrote: >> It is difficult to say what is goin on, but according to your debug >> message seems it crashes due to Tcl/Tk not due to libGL (Mesa). As anticipated to Tone, I was finally able to solve the problem. It looks like somewhere in the code there is a double free or double alloc. It should not be a fatal problem in itself, but cause the program to be aborted if the environment variable MALLOC_CHECK_ (with a trailing underscore) is set to "2" or "3". An easy workaround is to unset the variable, or to set it to "0" or "1", further info can be found in the malloc man page. Just add the following line at the beginning of $XCRYSDEN_TOPDIR/xcrysden to fix it forever: unset MALLOC_CHECK_ cheers, and thanks to Tone for the support -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From mpayami at aeoi.org.ir Wed Feb 11 09:52:50 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 11 Feb 2009 00:52:50 -0800 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) References: <1233765573.4412.38.camel@walk.ijs.si> Message-ID: Dear XC_1.6 users, I have used the semishared version of XC_1.6 and followed the instruction_for_impatients. When I type "xcrysden", it starts with a significant delay!! Any help is highly appreciated. Mahmoud Payami --- Physics Group Atomic Energy Organization of Iran Tehran-Iran E-mail(1): mpayami at aeoi.org.ir Phone: +98 (21) 82064393 --- From rabehiamel at yahoo.fr Wed Feb 11 15:48:35 2009 From: rabehiamel at yahoo.fr (RABEHI) Date: Wed, 11 Feb 2009 14:48:35 +0000 (GMT) Subject: [xcrysden] install xcrysden Message-ID: <59387.85414.qm@web24501.mail.ird.yahoo.com> Dear XCrysden's users, followed the? longer installation instructions.I have tryed to install the semishared version of XC (on suse 10.2) but When I have executed "xcConfigure, i got : more: option inconnue "-m" usage: more [-dflpcsu] [+no-de-ligne | +/patron] nom1 nom2 .. Any help is highly appreciated. __________________________________________________________________________________________________ Ne pleurez pas si votre Webmail ferme ! R?cup?rez votre historique sur Yahoo! Mail ! http://fr.docs.yahoo.com/mail/transfert_mails.html -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090211/95b3f8dc/attachment.htm From mpayami at aeoi.org.ir Thu Feb 12 16:27:00 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 12 Feb 2009 07:27:00 -0800 Subject: [xcrysden] Compilation problem in Xcrysden 1.6 References: <1233765573.4412.38.camel@walk.ijs.si> Message-ID: <930DEB41637F4AF6A24D33B2104B661B@ctpm> Dear Tone, I have tried to compile the source file using "possibility-2" using "Make.linux-static" as "Make.sys" and disabled all in "possibility-1". The compilation goes well until the end which the message appears: togl.c:40:76: error :X11/Xmu/StdCmap.h: No such file or directory. I have also tried other compiling possibilities but "static" one seemed less problematic. I would be grateful if you please help me to resolve it. Bests, Mahmoud Payami From tone.kokalj at ijs.si Thu Feb 12 16:36:50 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 12 Feb 2009 16:36:50 +0100 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) In-Reply-To: References: <1233765573.4412.38.camel@walk.ijs.si> Message-ID: <1234453010.26486.3.camel@walk.ijs.si> On Wed, 2009-02-11 at 00:52 -0800, Mahmoud Payami wrote: > Dear XC_1.6 users, > > I have used the semishared version of XC_1.6 and followed the > instruction_for_impatients. > When I type "xcrysden", it starts with a significant delay!! > Any help is highly appreciated. It is not possible to help: the info you provided is not sufficient. how large is your significant delay: 10s, 10min, 1h? You may wish to run xcrysden as: xcrysden -T You will see where it pauses. 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 Thu Feb 12 16:44:15 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 12 Feb 2009 16:44:15 +0100 Subject: [xcrysden] install xcrysden In-Reply-To: <59387.85414.qm@web24501.mail.ird.yahoo.com> References: <59387.85414.qm@web24501.mail.ird.yahoo.com> Message-ID: <1234453455.26486.11.camel@walk.ijs.si> On Wed, 2009-02-11 at 14:48 +0000, RABEHI wrote: > Dear XCrysden's users, > followed the longer installation instructions. Don't! As a first trial simply say: ./xcrysden (it should work out of the box without any xcConfigure.sh mumbo jumbo) 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 Thu Feb 12 16:54:22 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 12 Feb 2009 16:54:22 +0100 Subject: [xcrysden] Compilation problem in Xcrysden 1.6 In-Reply-To: <930DEB41637F4AF6A24D33B2104B661B@ctpm> References: <1233765573.4412.38.camel@walk.ijs.si> <930DEB41637F4AF6A24D33B2104B661B@ctpm> Message-ID: <1234454062.26486.22.camel@walk.ijs.si> On Thu, 2009-02-12 at 07:27 -0800, Mahmoud Payami wrote: > Dear Tone, > > I have tried to compile the source file using "possibility-2" using > "Make.linux-static" as "Make.sys" and disabled all in "possibility-1". The > compilation goes well until the end which the message appears: > togl.c:40:76: error :X11/Xmu/StdCmap.h: No such file or directory. > I have also tried other compiling possibilities but "static" one seemed less > problematic. > I would be grateful if you please help me to resolve it. This means you don't have libXmu header files. Note that compiling xcrysden sources requires development versions of some X11 libraries (which include the header files). Now, I will describe how you do it for example for Debian GNU Linux. Debian automatic installer is called apt-get. 1. go to the Debian Package page: http://packages.debian.org/ and select the "search the contents of packages" 2. in the entry type StdCmap.h and you will get the list of packages that contains this file. (the results is: libxmu-headers) 3. as sudo or root execute: apt-get install libxmu-headers That's all! Now the StdCmap.h is on your system. For other Linux distributions the recipe would be analogous. For example, for RedHat the installer (as far as I know) is called "yum", so one needs first to find the package name for the corresponding RedHat package and then install it as "yum install packageName". 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 mpayami at aeoi.org.ir Tue Feb 17 07:48:32 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Mon, 16 Feb 2009 22:48:32 -0800 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si> Message-ID: <0B272198DBEE4B2A9F48CB51217F7852@ctpm> Dear Tone, Sorry for the delay, I was involved in some other setups. The delay in startup od semishared XC1.6 is 100 seconds. In fact it sleeps after the line: XCRYSDEN_SCRATCH=/home/mahmoud_payami/xcrys_tmp and after 100 seconds, other things work on fly. Best regards, Mahmoud >> Dear XC_1.6 users, >> >> I have used the semishared version of XC_1.6 and followed the >> instruction_for_impatients. >> When I type "xcrysden", it starts with a significant delay!! >> Any help is highly appreciated. > > It is not possible to help: the info you provided is not sufficient. > how large is your significant delay: 10s, 10min, 1h? > > You may wish to run xcrysden as: > > xcrysden -T > > You will see where it pauses. > > 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 > > From tone.kokalj at ijs.si Tue Feb 17 11:44:46 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 17 Feb 2009 11:44:46 +0100 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) In-Reply-To: <0B272198DBEE4B2A9F48CB51217F7852@ctpm> References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si> <0B272198DBEE4B2A9F48CB51217F7852@ctpm> Message-ID: <1234867486.23760.11.camel@walk.ijs.si> On Mon, 2009-02-16 at 22:48 -0800, Mahmoud Payami wrote: > Dear Tone, > > Sorry for the delay, I was involved in some other setups. > The delay in startup od semishared XC1.6 is 100 seconds. > In fact it sleeps after the line: > XCRYSDEN_SCRATCH=/home/mahmoud_payami/xcrys_tmp > and after 100 seconds, other things work on fly. ??? I believe this is the line from your ~/.bashrc file ... 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 mpayami at aeoi.org.ir Tue Feb 17 12:15:50 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Tue, 17 Feb 2009 03:15:50 -0800 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si><0B272198DBEE4B2A9F48CB51217F7852@ctpm> <1234867486.23760.11.camel@walk.ijs.si> Message-ID: <21ED3A04B72644E299F59AAEDA6321DD@ctpm> . >> In fact it sleeps after the line: >> XCRYSDEN_SCRATCH=/home/mahmoud_payami/xcrys_tmp >> and after 100 seconds, other things work on fly. > > ??? > > I believe this is the line from your ~/.bashrc file ... > Dear Tone, I know that the line is from my .bashrc. Could it be because my tcl/tk are 8.4? I have checked with fedora 9 (which has tcl/tk 8.5) and runs normally. Bests, Mahmoud > 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 > > From tone.kokalj at ijs.si Tue Feb 17 12:23:57 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 17 Feb 2009 12:23:57 +0100 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) In-Reply-To: <21ED3A04B72644E299F59AAEDA6321DD@ctpm> References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si> <0B272198DBEE4B2A9F48CB51217F7852@ctpm> <1234867486.23760.11.camel@walk.ijs.si> <21ED3A04B72644E299F59AAEDA6321DD@ctpm> Message-ID: <1234869837.23760.20.camel@walk.ijs.si> On Tue, 2009-02-17 at 03:15 -0800, Mahmoud Payami wrote: > . > >> In fact it sleeps after the line: > >> XCRYSDEN_SCRATCH=/home/mahmoud_payami/xcrys_tmp > >> and after 100 seconds, other things work on fly. > > > > ??? > > > > I believe this is the line from your ~/.bashrc file ... > > > Dear Tone, > I know that the line is from my .bashrc. Could it be because my tcl/tk are > 8.4? No! I am curious: how did you estabish that it pauses after line XCRYSDEN_SCRATCH=/home/mahmoud_payami/xcrys_tmp ??? Now, I got it. I probably know what you mean. It pauses after xcrysden prints the "XCRYSDEN_SCRATCH=/home/mahmoud_payami/xcrys_tmp" to the terminal, right? (hence you we referring to printout, I was thinking in terms of source code). Please follow my previous suggestion and run xcrysden as: xcrysden -T >& log and send me the log file. Here is another suggestion; execute: $XCRYSDEN_TOPDIR/bin/xcrys [a small window should appear + a "%" prompt on the terminal (to exit type "exit")] Does it pause? 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 mpayami at aeoi.org.ir Tue Feb 17 12:42:35 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Tue, 17 Feb 2009 03:42:35 -0800 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si><0B272198DBEE4B2A9F48CB51217F7852@ctpm><1234867486.23760.11.camel@walk.ijs.si><21ED3A04B72644E299F59AAEDA6321DD@ctpm> <1234869837.23760.20.camel@walk.ijs.si> Message-ID: <6C0FE20BF0BF4B02AEFC525EEE79FA96@ctpm> Dear Tone, > xcrysden -T >& log I attached the lof file. > > > Here is another suggestion; execute: > > $XCRYSDEN_TOPDIR/bin/xcrys > > [a small window should appear + a "%" prompt on the terminal (to exit > type "exit")] Does it pause? > I executed and got: /opt/XCrySDen-1.5.17-bin-semishared/bin/xcrys: errorwhile loading shared libraries: libtk8.5.so: cannot open shared object file: No such file or directory Bests, Mahmoud > 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 -------------- A non-text attachment was scrubbed... Name: log Type: application/octet-stream Size: 21182 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20090217/7337e9dd/attachment-0001.obj From tone.kokalj at ijs.si Tue Feb 17 12:54:58 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 17 Feb 2009 12:54:58 +0100 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) In-Reply-To: <6C0FE20BF0BF4B02AEFC525EEE79FA96@ctpm> References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si> <0B272198DBEE4B2A9F48CB51217F7852@ctpm> <1234867486.23760.11.camel@walk.ijs.si> <21ED3A04B72644E299F59AAEDA6321DD@ctpm> <1234869837.23760.20.camel@walk.ijs.si> <6C0FE20BF0BF4B02AEFC525EEE79FA96@ctpm> Message-ID: <1234871698.23760.26.camel@walk.ijs.si> On Tue, 2009-02-17 at 03:42 -0800, Mahmoud Payami wrote: > Dear Tone, > > > xcrysden -T >& log > I attached the lof file. I forgot to specify in the last meail, that you should terminate it where it pauses. > I executed and got: > /opt/XCrySDen-1.5.17-bin-semishared/bin/xcrys: errorwhile loading shared > libraries: libtk8.5.so: cannot open shared object file: No such file or > directory Here is the correction, do instead: if test -z "${LD_LIBRARY_PATH}"; then LD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib" else LD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib:$LD_LIBRARY_PATH" fi $XCRYSDEN_TOPDIR/bin/xcrys Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From mpayami at aeoi.org.ir Tue Feb 17 12:59:58 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Tue, 17 Feb 2009 03:59:58 -0800 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si><0B272198DBEE4B2A9F48CB51217F7852@ctpm><1234867486.23760.11.camel@walk.ijs.si><21ED3A04B72644E299F59AAEDA6321DD@ctpm> <1234869837.23760.20.camel@walk.ijs.si> Message-ID: <4AEDC84A23794C60A46AF3AE6A326E89@ctpm> Dear Tone, I also added the lib folder from your source.all version in the top_dir of semishared_bin, and added that folder to LD_LIBRARY_PATH, then the command: "$XCRYSDEN_TOPDIR/bin/xcrys" worked without error and the small box appeared AFTER_THE_SAME_DELAY as before. mahmoud From mpayami at aeoi.org.ir Wed Feb 18 18:10:08 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 18 Feb 2009 09:10:08 -0800 Subject: [xcrysden] delay-Xcrysden 1.6 (semishared) References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si><0B272198DBEE4B2A9F48CB51217F7852@ctpm><1234867486.23760.11.camel@walk.ijs.si><21ED3A04B72644E299F59AAEDA6321DD@ctpm><1234869837.23760.20.camel@walk.ijs.si><6C0FE20BF0BF4B02AEFC525EEE79FA96@ctpm> <1234871698.23760.26.camel@walk.ijs.si> Message-ID: <5323AB890EA3451CAA55AD156C1D1DB1@ctpm> Dear Tone, I succeeded to solve my problem (of course in a dirty way): I downloaded the source files of tcl8.5 and tk8.5 and configured with --enable-shared and --prefix=my_tcl/tk. Then I added to the PATH the lib and bin of both of them, and then I modified your "xcrysden" script in the lines "if -z test ..." and added my_tcl. Of course, copied the lib of tk in the lib of tcl and the resulting in the folder where I have installed my_tcl. Now xcrysden starts on fly. But..., I think it can be done in a neat way. Would you please help me. Best regards, Mahmoud > I forgot to specify in the last meail, that you should terminate it > where it pauses. > >> I executed and got: >> /opt/XCrySDen-1.5.17-bin-semishared/bin/xcrys: errorwhile loading shared >> libraries: libtk8.5.so: cannot open shared object file: No such file or >> directory > > Here is the correction, do instead: > > if test -z "${LD_LIBRARY_PATH}"; then > LD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib" > else > LD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib:$LD_LIBRARY_PATH" > fi > $XCRYSDEN_TOPDIR/bin/xcrys > > 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 > > From mpayami at aeoi.org.ir Thu Feb 19 06:17:28 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Wed, 18 Feb 2009 21:17:28 -0800 Subject: [xcrysden] Resolved in a simple way: delay-Xcrysden 1.6 (semishared) References: <1233765573.4412.38.camel@walk.ijs.si><1234453010.26486.3.camel@walk.ijs.si><0B272198DBEE4B2A9F48CB51217F7852@ctpm><1234867486.23760.11.camel@walk.ijs.si><21ED3A04B72644E299F59AAEDA6321DD@ctpm><1234869837.23760.20.camel@walk.ijs.si><6C0FE20BF0BF4B02AEFC525EEE79FA96@ctpm><1234871698.23760.26.camel@walk.ijs.si> <5323AB890EA3451CAA55AD156C1D1DB1@ctpm> Message-ID: <5FECAC8A2B524B78884DD4A82084FA64@ctpm> I resolved the problem in a neat way: Just replaced the tcl and tk directories and libs in the /external/lib by my own compiled tcl/tk. It is now ok. The tcl/tk in the external/lib was not the right one for my box. Thank you Tone for your concern. Best regards, Mahmoud > Dear Tone, > > I succeeded to solve my problem (of course in a dirty way): > I downloaded the source files of tcl8.5 and tk8.5 and configured > with --enable-shared and --prefix=my_tcl/tk. > Then I added to the PATH the lib and bin of both of them, and then I > modified your "xcrysden" script in the lines "if -z test ..." and added > my_tcl. Of course, copied the lib of tk in the lib of tcl and the > resulting > in the folder where I have installed my_tcl. Now xcrysden starts on fly. > But..., I think it can be done in a neat way. Would you please help me. > > Best regards, > Mahmoud > > > >> I forgot to specify in the last meail, that you should terminate it >> where it pauses. >> >>> I executed and got: >>> /opt/XCrySDen-1.5.17-bin-semishared/bin/xcrys: errorwhile loading shared >>> libraries: libtk8.5.so: cannot open shared object file: No such file or >>> directory >> >> Here is the correction, do instead: >> >> if test -z "${LD_LIBRARY_PATH}"; then >> LD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib" >> else >> LD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib:$LD_LIBRARY_PATH" >> fi >> $XCRYSDEN_TOPDIR/bin/xcrys >> >> 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 >> >> > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > From tone.kokalj at ijs.si Thu Feb 19 09:13:20 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 19 Feb 2009 09:13:20 +0100 Subject: [xcrysden] Resolved in a simple way: delay-Xcrysden 1.6 (semishared) In-Reply-To: <5FECAC8A2B524B78884DD4A82084FA64@ctpm> References: <1233765573.4412.38.camel@walk.ijs.si> <1234453010.26486.3.camel@walk.ijs.si> <0B272198DBEE4B2A9F48CB51217F7852@ctpm> <1234867486.23760.11.camel@walk.ijs.si> <21ED3A04B72644E299F59AAEDA6321DD@ctpm> <1234869837.23760.20.camel@walk.ijs.si> <6C0FE20BF0BF4B02AEFC525EEE79FA96@ctpm> <1234871698.23760.26.camel@walk.ijs.si> <5323AB890EA3451CAA55AD156C1D1DB1@ctpm> <5FECAC8A2B524B78884DD4A82084FA64@ctpm> Message-ID: <1235031200.15428.2.camel@walk.ijs.si> On Wed, 2009-02-18 at 21:17 -0800, Mahmoud Payami wrote: > I resolved the problem in a neat way: > Just replaced the tcl and tk directories and libs in the /external/lib by my > own compiled tcl/tk. It is now ok. > The tcl/tk in the external/lib was not the right one for my box. I am curious why this is so! Would you provide some info about your plaform: CPU type, Linux distribution, ... 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 mpayami at aeoi.org.ir Thu Feb 19 10:40:11 2009 From: mpayami at aeoi.org.ir (Mahmoud Payami) Date: Thu, 19 Feb 2009 01:40:11 -0800 Subject: [xcrysden] Resolved in a simple way: delay-Xcrysden1.6 (semishared) References: <1233765573.4412.38.camel@walk.ijs.si><1234453010.26486.3.camel@walk.ijs.si><0B272198DBEE4B2A9F48CB51217F7852@ctpm><1234867486.23760.11.camel@walk.ijs.si><21ED3A04B72644E299F59AAEDA6321DD@ctpm><1234869837.23760.20.camel@walk.ijs.si><6C0FE20BF0BF4B02AEFC525EEE79FA96@ctpm><1234871698.23760.26.camel@walk.ijs.si><5323AB890EA3451CAA55AD156C1D1DB1@ctpm><5FECAC8A2B524B78884DD4A82084FA64@ctpm> <1235031200.15428.2.camel@walk.ijs.si> Message-ID: Dear Tone, cpu= Pentium 4 3.2GHz, Linux = Redhat Enterprise 5 I also checked using CentOS 5.2 which has the same tcl/tk 8.4, but in this case, your comilation works quite normal !! (So, I am surprised too.) Bests, Mahmoud > > I am curious why this is so! Would you provide some info about your > plaform: > CPU type, Linux distribution, ... > > 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 > > From yunpwang at aphy.iphy.ac.cn Fri Feb 20 09:17:56 2009 From: yunpwang at aphy.iphy.ac.cn (=?gb2312?B?zfXUxsX0?=) Date: Fri, 20 Feb 2009 16:17:56 +0800 Subject: [xcrysden] Can several .xcf files be displayed at one picture? References: Message-ID: <200902201617559585736@aphy.iphy.ac.cn> Dear all: I have 4 .xsf files, and I want to display them all in one picture, any advise? thanks, Y.P.Wang -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090220/44f178cb/attachment.htm From paulatto at sissa.it Fri Feb 20 09:26:01 2009 From: paulatto at sissa.it (Lorenzo Paulatto) Date: Fri, 20 Feb 2009 09:26:01 +0100 Subject: [xcrysden] Can several .xcf files be displayed at one picture? In-Reply-To: <200902201617559585736@aphy.iphy.ac.cn> References: <200902201617559585736@aphy.iphy.ac.cn> Message-ID: On Fri, 20 Feb 2009 09:17:56 +0100, ????????? wrote: > Dear all: > I have 4 .xsf files, and I want to display them all in one picture, any > advise? If use the same basis vectors, you can easily combine them by hand. See the file format description: http://www.xcrysden.org/doc/XSF.html. If they don't use the same basis set, you should explain better what you want to do. cheers -- Lorenzo Paulatto SISSA & DEMOCRITOS (Trieste) phone: +39 040 3787 511 skype: paulatz www: http://people.sissa.it/~paulatto/ *** save italian brains *** http://saveitalianbrains.wordpress.com/ From sebastijan.peljhan at ijs.si Fri Feb 20 11:48:34 2009 From: sebastijan.peljhan at ijs.si (Sebastijan Peljhan) Date: Fri, 20 Feb 2009 11:48:34 +0100 Subject: [xcrysden] Can several .xcf files be displayed at one picture? In-Reply-To: References: <200902201617559585736@aphy.iphy.ac.cn> Message-ID: <1235126914.4921.53.camel@yunnan.ijs.si> You may also merge the atomic coordinates that are listed under the flag ATOMS in .xsf file and create new .xsf file: ATOMS typei xi yi zi from file i typej xj yj zj from file j ... On Fri, 2009-02-20 at 09:26 +0100, Lorenzo Paulatto wrote: > On Fri, 20 Feb 2009 09:17:56 +0100, ????????? wrote: > > > Dear all: > > I have 4 .xsf files, and I want to display them all in one picture, any > > advise? > > If use the same basis vectors, you can easily combine them by hand. See the file format description: http://www.xcrysden.org/doc/XSF.html. > > If they don't use the same basis set, you should explain better what you want to do. > > cheers > > -- Sebastijan Peljhan J. Stefan Institute Jamova 39, 1000 Ljubljana, Slovenia 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 Feb 20 12:03:32 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 20 Feb 2009 12:03:32 +0100 Subject: [xcrysden] Can several .xcf files be displayed at one picture? In-Reply-To: <1235126914.4921.53.camel@yunnan.ijs.si> References: <200902201617559585736@aphy.iphy.ac.cn> <1235126914.4921.53.camel@yunnan.ijs.si> Message-ID: <1235127812.6067.5.camel@walk.ijs.si> On Fri, 2009-02-20 at 11:48 +0100, Sebastijan Peljhan wrote: > You may also merge the atomic coordinates that are listed under the flag > ATOMS in .xsf file and create new .xsf file: > > ATOMS > typei xi yi zi from file i > typej xj yj zj from file j > ... In this case the xsf file describes a non-periodic structure, and the only structure section in the file should be "ATOMS" (no PRIMVEC/PRIMCOORD sections, see: http://www.xcrysden.org/doc/XSF.html#__toc__3 ) I use this trick often when I want two structures side by side with the same display size. In this case I merge the two structures as: ATOMS type1i x1i y1i z1i type2i x2i y2i z2i (from file i) ... type1j x1j+dx y1j+dy z1j+dz type2j x2j+dx y2j+dy z2j+dz (from file j) ... where (dx,dy,dz) is a suitable displacement vector for the 2nd structure. 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 lanhaiping at gmail.com Tue Feb 24 23:07:59 2009 From: lanhaiping at gmail.com (lan haiping) Date: Wed, 25 Feb 2009 06:07:59 +0800 Subject: [xcrysden] about 2D data Message-ID: Dear All, I am wondering about 2d data displaying in xcryden. I want to examine a 3D field contour along Z direction comparing with a 2D quantity integrated along Z direction. Then, can i display this 2D data with Xcrysden ? and how ? i was used to manipulate 2D data by matlab, but the color scheme isnot very consistent with xcrysden. Regards, -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090225/da84ba0d/attachment.htm From tone.kokalj at ijs.si Wed Feb 25 16:59:03 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 25 Feb 2009 16:59:03 +0100 Subject: [xcrysden] about 2D data In-Reply-To: References: Message-ID: <1235577543.21143.1.camel@walk.ijs.si> On Wed, 2009-02-25 at 06:07 +0800, lan haiping wrote: > Dear All, > > I am wondering about 2d data displaying in xcryden. > I want to examine a 3D field contour along Z direction comparing with > a 2D quantity integrated along Z direction. Then, can i display this > 2D > data with Xcrysden ? and how ? You whould like to achieve what? I don't understand your description, please elaborate! 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 Giovanni.Cantele at na.infn.it Wed Feb 25 17:05:00 2009 From: Giovanni.Cantele at na.infn.it (Giovanni Cantele) Date: Wed, 25 Feb 2009 17:05:00 +0100 Subject: [xcrysden] about 2D data In-Reply-To: <1235577543.21143.1.camel@walk.ijs.si> References: <1235577543.21143.1.camel@walk.ijs.si> Message-ID: <49A56C2C.5080906@na.infn.it> > On Wed, 2009-02-25 at 06:07 +0800, lan haiping wrote: > >> Dear All, >> >> I am wondering about 2d data displaying in xcryden. >> I want to examine a 3D field contour along Z direction comparing with >> a 2D quantity integrated along Z direction. Then, can i display this >> 2D >> data with Xcrysden ? and how ? >> As you may read here http://www.xcrysden.org/doc/XSF.html#__toc__11 both 3D and 2D scalar fields can be visualised using XCrysDen. In addition, 2D cuts of 3D scalar fields may be obtained. I guess that for displaying both 2D and 3D, you must generate the two XSF files and then properly append let's say the 2D scalar field (from BEGIN_BLOCK_DATAGRID_2D to END_BLOCK_DATAGRID_2D ) at the end the other file. Hope this helps, Giovnni -- Dr. Giovanni Cantele Coherentia CNR-INFM and Dipartimento di Scienze Fisiche Universita' di Napoli "Federico II" Complesso Universitario di Monte S. Angelo - Ed. 6 Via Cintia, I-80126, Napoli, Italy Phone: +39 081 676910 Fax: +39 081 676346 E-mail: giovanni.cantele at cnr.it giovanni.cantele at na.infn.it Web: http://people.na.infn.it/~cantele Research Group: http://www.nanomat.unina.it From tone.kokalj at ijs.si Wed Feb 25 17:19:53 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 25 Feb 2009 17:19:53 +0100 Subject: [xcrysden] about 2D data In-Reply-To: <49A56C2C.5080906@na.infn.it> References: <1235577543.21143.1.camel@walk.ijs.si> <49A56C2C.5080906@na.infn.it> Message-ID: <1235578793.21143.11.camel@walk.ijs.si> On Wed, 2009-02-25 at 17:05 +0100, Giovanni Cantele wrote: > > On Wed, 2009-02-25 at 06:07 +0800, lan haiping wrote: > > > >> Dear All, > >> > >> I am wondering about 2d data displaying in xcryden. > >> I want to examine a 3D field contour along Z direction comparing with > >> a 2D quantity integrated along Z direction. Then, can i display this > >> 2D > >> data with Xcrysden ? and how ? > >> > > As you may read here > http://www.xcrysden.org/doc/XSF.html#__toc__11 > both 3D and 2D scalar fields can be visualised using XCrysDen. In > addition, 2D cuts of 3D scalar fields may be obtained. > > I guess that for displaying both 2D and 3D, you must generate the two > XSF files and then properly append let's say the 2D scalar field (from > BEGIN_BLOCK_DATAGRID_2D to END_BLOCK_DATAGRID_2D ) at the end the other > file. This is true, but it is also true that then you cannot display both of them simultaneously, unfortunately. Xcrysden only allows for the display of a single field at the time (i.e. the one selected in the "Datagrid" popup window). 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 lanhaiping at gmail.com Wed Feb 25 18:28:47 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 26 Feb 2009 01:28:47 +0800 Subject: [xcrysden] about 2D data In-Reply-To: <1235577543.21143.1.camel@walk.ijs.si> References: <1235577543.21143.1.camel@walk.ijs.si> Message-ID: Thanks, I checked the xsf doc , and got the desired format for 2D datagrids. Regards On Wed, Feb 25, 2009 at 11:59 PM, Tone Kokalj wrote: > On Wed, 2009-02-25 at 06:07 +0800, lan haiping wrote: > > Dear All, > > > > I am wondering about 2d data displaying in xcryden. > > I want to examine a 3D field contour along Z direction comparing with > > a 2D quantity integrated along Z direction. Then, can i display this > > 2D > > data with Xcrysden ? and how ? > > You whould like to achieve what? > I don't understand your description, please elaborate! > > 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 > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090226/af6efa34/attachment.htm From lanhaiping at gmail.com Wed Feb 25 18:33:48 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 26 Feb 2009 01:33:48 +0800 Subject: [xcrysden] about 2D data In-Reply-To: <49A56C2C.5080906@na.infn.it> References: <1235577543.21143.1.camel@walk.ijs.si> <49A56C2C.5080906@na.infn.it> Message-ID: Thanks, Giovanni! On Thu, Feb 26, 2009 at 12:05 AM, Giovanni Cantele < Giovanni.Cantele at na.infn.it> wrote: > > > On Wed, 2009-02-25 at 06:07 +0800, lan haiping wrote: > > > >> Dear All, > >> > >> I am wondering about 2d data displaying in xcryden. > >> I want to examine a 3D field contour along Z direction comparing with > >> a 2D quantity integrated along Z direction. Then, can i display this > >> 2D > >> data with Xcrysden ? and how ? > >> > > As you may read here > http://www.xcrysden.org/doc/XSF.html#__toc__11 > both 3D and 2D scalar fields can be visualised using XCrysDen. In > addition, 2D cuts of 3D scalar fields may be obtained. > > I guess that for displaying both 2D and 3D, you must generate the two > XSF files and then properly append let's say the 2D scalar field (from > BEGIN_BLOCK_DATAGRID_2D to END_BLOCK_DATAGRID_2D ) at the end the other > file. > > Hope this helps, > > Giovnni > > -- > > > > Dr. Giovanni Cantele > Coherentia CNR-INFM and Dipartimento di Scienze Fisiche > Universita' di Napoli "Federico II" > Complesso Universitario di Monte S. Angelo - Ed. 6 > Via Cintia, I-80126, Napoli, Italy > Phone: +39 081 676910 > Fax: +39 081 676346 > E-mail: giovanni.cantele at cnr.it > giovanni.cantele at na.infn.it > Web: http://people.na.infn.it/~cantele > Research Group: http://www.nanomat.unina.it > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090226/ae38089d/attachment.htm From lanhaiping at gmail.com Wed Feb 25 19:59:32 2009 From: lanhaiping at gmail.com (lan haiping) Date: Thu, 26 Feb 2009 02:59:32 +0800 Subject: [xcrysden] about 2D data In-Reply-To: <1235578793.21143.11.camel@walk.ijs.si> References: <1235577543.21143.1.camel@walk.ijs.si> <49A56C2C.5080906@na.infn.it> <1235578793.21143.11.camel@walk.ijs.si> Message-ID: Hi, Tone, I have another question about 3D FFT data and 3D data of XSF file. I have checked the transformation routine for 3D FFT data to XSF file in QE package. In that routine, final XSF grids dimension seems not the same as 3D FFT data. In fact, most situations i found the XSF grids dimensions are (nx+1)x(ny+1)x(nz+1) where nx,ny,nz are 3D fft data's dimension. I wonder about this scheme, would you please give me some hints ? Regards On Thu, Feb 26, 2009 at 12:19 AM, Tone Kokalj wrote: > On Wed, 2009-02-25 at 17:05 +0100, Giovanni Cantele wrote: > > > On Wed, 2009-02-25 at 06:07 +0800, lan haiping wrote: > > > > > >> Dear All, > > >> > > >> I am wondering about 2d data displaying in xcryden. > > >> I want to examine a 3D field contour along Z direction comparing with > > >> a 2D quantity integrated along Z direction. Then, can i display this > > >> 2D > > >> data with Xcrysden ? and how ? > > >> > > > > As you may read here > > http://www.xcrysden.org/doc/XSF.html#__toc__11 > > both 3D and 2D scalar fields can be visualised using XCrysDen. In > > addition, 2D cuts of 3D scalar fields may be obtained. > > > > I guess that for displaying both 2D and 3D, you must generate the two > > XSF files and then properly append let's say the 2D scalar field (from > > BEGIN_BLOCK_DATAGRID_2D to END_BLOCK_DATAGRID_2D ) at the end the other > > file. > > This is true, but it is also true that then you cannot display both of > them simultaneously, unfortunately. Xcrysden only allows for the display > of a single field at the time (i.e. the one selected in the "Datagrid" > popup window). > > 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 > -- Hai-Ping Lan Department of Electronics , Peking University , Bejing, 100871 lanhaiping at gmail.com, hplan at pku.edu.cn -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20090226/cc5158a0/attachment.htm From tone.kokalj at ijs.si Wed Feb 25 20:24:26 2009 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 25 Feb 2009 20:24:26 +0100 Subject: [xcrysden] about 2D data In-Reply-To: References: <1235577543.21143.1.camel@walk.ijs.si> <49A56C2C.5080906@na.infn.it> <1235578793.21143.11.camel@walk.ijs.si> Message-ID: <1235589866.13980.1.camel@walk.ijs.si> On Thu, 2009-02-26 at 02:59 +0800, lan haiping wrote: > Hi, Tone, > I have another question about 3D FFT data and 3D data of XSF file. > I have checked the transformation routine for > 3D FFT data to XSF file in QE package. In that routine, final XSF > grids dimension seems not the same as 3D FFT data. > In fact, most situations i found the XSF grids > dimensions are (nx+1)x(ny+1)x(nz+1) where nx,ny,nz are 3D fft data's > dimension. This is absolutely correct! Why? See: http://www.xcrysden.org/doc/XSF.html#__toc__12 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