From emoujaes at fisica.ufmg.br Thu Mar 1 23:25:23 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Thu, 1 Mar 2012 19:25:23 -0300 Subject: [xcrysden] cannot start XCRYSDEN In-Reply-To: <1330329437.7856.8.camel@catalyst.ijs.si> References: <20120224181625.M99053@proto.fisica.ufmg.br> <1330329437.7856.8.camel@catalyst.ijs.si> Message-ID: <20120301221257.M95469@proto.fisica.ufmg.br> Dear Tone, Thanks very much for your suggestion. I have actually restarted the whole procedure again and untarred the XCRYSDEN-1.5.24-src-all version and when I typed ./xcrysden I got the error: ./xcrysden: line 165: /XCrySDen-1.5.24-src-all/scripts/xcLib.sh: file or directory not found but when I check the scripts folder the file is actually there.. XCRYSDEN is not finding it for some reason. I know I have bothered you with this a lot but i am a Linux newbee. I need to know whatcan I do to resolve the problem Thanks in advance On Mon, 27 Feb 2012 08:57:17 +0100, Tone Kokalj wrote > On Fri, 2012-02-24 at 15:25 -0300, Elie Albert Moujaes wrote: > > Dear all, > > > > I have uninstalled a previous version of XCRYSDEN and now I am re installing > > the XCRYSDEN -1.5.24-src version on my laptop. the "untarring" of the tarred > > package goes fine. When I type ./xcConfigure, the program automatically > > assigns the $XCRYSDEN_TOPDIR and $XCRYSDN_SCRATCH to: > > > > XCRYSDEN_TOPDIR=/XcrySDen-1.5.24-src > > XCRYSDEN_SCRATCH=/Elie-molecules/xcrys_tmp. > > PATH="$XCRYSDEN_TOPDIR:$PATH:$XCRYSDEN_TOPDIR/scripts:$XCRYSDEN_TOPDIR/util" > > > > The problem here is in XCRYSDEN_SCRATCH where Elie-molecules folder does not > > exist. I deleted it when I deleted the previous version. Somehow XCRYSDEN > > still retains this "path". This is giving an error once I run ./xcrysden : > > > > ./xcrysden: line 165:/Elie-molecules/XcrySDen-1.5.23-src- all/scripts/xcLib.sh: > > no such file or directory. > > Which means that you did not update the definition of XCRYSDEN_TOPDIR > variable in your profile (e.g., $HOME/.bashrc). Either correct that > manually or simply unset the XCRYSDEN_TOPDIR variable (preferred). > > 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 -- Departamento de Fisica - UFMG/ICEx From tone.kokalj at ijs.si Fri Mar 2 11:10:51 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 02 Mar 2012 11:10:51 +0100 Subject: [xcrysden] cannot start XCRYSDEN In-Reply-To: <20120301221257.M95469@proto.fisica.ufmg.br> References: <20120224181625.M99053@proto.fisica.ufmg.br> <1330329437.7856.8.camel@catalyst.ijs.si> <20120301221257.M95469@proto.fisica.ufmg.br> Message-ID: <1330683051.25610.2.camel@catalyst.ijs.si> On Thu, 2012-03-01 at 19:25 -0300, Elie Albert Moujaes wrote: > Dear Tone, > > Thanks very much for your suggestion. I have actually restarted the whole > procedure again and untarred the XCRYSDEN-1.5.24-src-all version and when I > typed ./xcrysden I got the error: > ./xcrysden: line 165: /XCrySDen-1.5.24-src-all/scripts/xcLib.sh: file or > directory not found but when I check the scripts folder the file is actually > there.. which indicates that XCRYSDEN_TOPDIR is still defined and points to the wrong place. Try the following: unset XCRYSDEN_TOPDIR ./xcrysden (note that you downloaded the source package, which should be compiled) 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 quanyundi at gmail.com Fri Mar 2 21:42:27 2012 From: quanyundi at gmail.com (Yundi Quan) Date: Fri, 2 Mar 2012 12:42:27 -0800 Subject: [xcrysden] wien2k fermi surface calculation Message-ID: Hi, When using xcrysden to calculate the Fermi surface for WIEN2k, it seems that xcrysden does not take into consideration the LDA+U. I mean, xcrysden does not have an option for x lapw1 -up -orb. Is it fine for me to run x lapw1 -up -orb separately? Yundi From emoujaes at fisica.ufmg.br Fri Mar 2 22:58:27 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Fri, 2 Mar 2012 18:58:27 -0300 Subject: [xcrysden] cannot start XCRYSDEN In-Reply-To: <1330683051.25610.2.camel@catalyst.ijs.si> References: <20120224181625.M99053@proto.fisica.ufmg.br> <1330329437.7856.8.camel@catalyst.ijs.si> <20120301221257.M95469@proto.fisica.ufmg.br> <1330683051.25610.2.camel@catalyst.ijs.si> Message-ID: <20120302215135.M857@proto.fisica.ufmg.br> Dear Tone, I have tried what you have suggested but I am still getting the same error which basically suggests that I need TOPDIR_XCRYSDEN to point to the right place. Does this mean I need to redefine the path? Can you please let me know of any other possible solution? Thanks Elie On Fri, 02 Mar 2012 11:10:51 +0100, Tone Kokalj wrote > On Thu, 2012-03-01 at 19:25 -0300, Elie Albert Moujaes wrote: > > Dear Tone, > > > > Thanks very much for your suggestion. I have actually restarted the whole > > procedure again and untarred the XCRYSDEN-1.5.24-src-all version and when I > > typed ./xcrysden I got the error: > > ./xcrysden: line 165: /XCrySDen-1.5.24-src-all/scripts/xcLib.sh: file or > > directory not found but when I check the scripts folder the file is actually > > there.. > > which indicates that XCRYSDEN_TOPDIR is still defined and points to the > wrong place. Try the following: > > unset XCRYSDEN_TOPDIR > ./xcrysden > > (note that you downloaded the source package, which should be > compiled) > > 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 -- Departamento de Fisica - UFMG/ICEx From tone.kokalj at ijs.si Sat Mar 3 10:17:05 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Sat, 03 Mar 2012 10:17:05 +0100 Subject: [xcrysden] cannot start XCRYSDEN In-Reply-To: <20120302215135.M857@proto.fisica.ufmg.br> References: <20120224181625.M99053@proto.fisica.ufmg.br> <1330329437.7856.8.camel@catalyst.ijs.si> <20120301221257.M95469@proto.fisica.ufmg.br> <1330683051.25610.2.camel@catalyst.ijs.si> <20120302215135.M857@proto.fisica.ufmg.br> Message-ID: <1330766225.3857.8.camel@catalyst.ijs.si> On Fri, 2012-03-02 at 18:58 -0300, Elie Albert Moujaes wrote: > Dear Tone, > > I have tried what you have suggested but I am still getting the same error > which basically suggests that I need TOPDIR_XCRYSDEN to point to the right > place. This cannot be. There a few possibilities: 1) you mistyped something when unsetting (i.e., unset XCRYSDEN_TOPDIR) 2) you are not using the 1.5* version new versions xcrysden prints the XCRYSDEN_TOPDIR duing startup, e.g., 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_TOPDIR=/home/tone/prog/XCrySDen-1.x XCRYSDEN_SCRATCH=/temp/tone/xcrys_tmp what is your printed XCRYSDEN_TOPDIR line? 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 Sat Mar 3 10:29:56 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Sat, 03 Mar 2012 10:29:56 +0100 Subject: [xcrysden] wien2k fermi surface calculation In-Reply-To: References: Message-ID: <1330766996.3857.14.camel@catalyst.ijs.si> On Fri, 2012-03-02 at 12:42 -0800, Yundi Quan wrote: > Hi, > When using xcrysden to calculate the Fermi surface for WIEN2k, it > seems that xcrysden does not take into consideration the LDA+U. I > mean, xcrysden does not have an option for x lapw1 -up -orb. Is it > fine for me to run x lapw1 -up -orb separately? Yes, I believe so. You can do all the required steps manually and then click the "Render Fermi Surface" button. 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 emoujaes at fisica.ufmg.br Sat Mar 3 17:09:29 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Sat, 3 Mar 2012 13:09:29 -0300 Subject: [xcrysden] cannot start XCRYSDEN In-Reply-To: <1330766225.3857.8.camel@catalyst.ijs.si> References: <20120224181625.M99053@proto.fisica.ufmg.br> <1330329437.7856.8.camel@catalyst.ijs.si> <20120301221257.M95469@proto.fisica.ufmg.br> <1330683051.25610.2.camel@catalyst.ijs.si> <20120302215135.M857@proto.fisica.ufmg.br> <1330766225.3857.8.camel@catalyst.ijs.si> Message-ID: <20120303160407.M20728@proto.fisica.ufmg.br> Dear Tone, in fact I have Cygwin so I downloaded the tarred source xc-1.5.18-cygwin- shared.tar.gz and I have untarred, entered the XCrSDen-1.5.18-bin-shared and did ./xcConfigure and the following were assigned: XCRYSDEN_TOPDIR=/XCrSDen-1.5.18-bin-shared XCRYSDEN_SCRATCH=/home/User/xcrys_tmp then I executed ./xcrysden and I got the error: ./xcrysden: line 160: /XCrySDen-1.5.24-scr/scripts/xcLib.sh :no such file or directory I have typed unset XCRYSDEN_TOPDIR and then ./xcrysden again and I got: XCRYSDEN_TOPDIR=/XCrySDen-1.5.18-bin-shared XCRYSDEN_SCRATCH=/home/User/xcrys_tmp Application initialization failed: no display name and no $DISPLAY envir ariable Error in startup script: no display name and no $DISPLAY environment var while executing "load /usr/lib/tk8.5/../../bin/libtk8.5.dll Tk" ("package ifneeded Tk 8.5.11" script) invoked from within "load $system(TOPDIR)/bin/xcrys.dll" invoked from within "if { [file exists $system(TOPDIR)/bin/xcrys.dll] } { load $system(TOPDIR)/bin/xcrys.dll}" (file "/XCrySDen-1.5.18-bin-shared/Tcl/xcInit.tcl" line 426) Please can you guide me on how to correct this...Many thanks Elie On Sat, 03 Mar 2012 10:17:05 +0100, Tone Kokalj wrote > On Fri, 2012-03-02 at 18:58 -0300, Elie Albert Moujaes wrote: > > Dear Tone, > > > > I have tried what you have suggested but I am still getting the same error > > which basically suggests that I need TOPDIR_XCRYSDEN to point to the right > > place. > > This cannot be. There a few possibilities: > > 1) you mistyped something when unsetting (i.e., unset > XCRYSDEN_TOPDIR) 2) you are not using the 1.5* version > > new versions xcrysden prints the XCRYSDEN_TOPDIR duing startup, e.g., > > 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_TOPDIR=/home/tone/prog/XCrySDen-1.x > XCRYSDEN_SCRATCH=/temp/tone/xcrys_tmp > > what is your printed XCRYSDEN_TOPDIR line? > > 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 -- Departamento de Fisica - UFMG/ICEx From tone.kokalj at ijs.si Mon Mar 5 09:10:20 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 05 Mar 2012 09:10:20 +0100 Subject: [xcrysden] cannot start XCRYSDEN In-Reply-To: <20120303160407.M20728@proto.fisica.ufmg.br> References: <20120224181625.M99053@proto.fisica.ufmg.br> <1330329437.7856.8.camel@catalyst.ijs.si> <20120301221257.M95469@proto.fisica.ufmg.br> <1330683051.25610.2.camel@catalyst.ijs.si> <20120302215135.M857@proto.fisica.ufmg.br> <1330766225.3857.8.camel@catalyst.ijs.si> <20120303160407.M20728@proto.fisica.ufmg.br> Message-ID: <1330935020.4546.6.camel@catalyst.ijs.si> On Sat, 2012-03-03 at 13:09 -0300, Elie Albert Moujaes wrote: > Dear Tone, > > in fact I have Cygwin so I downloaded the tarred source xc-1.5.18-cygwin- > shared.tar.gz and I have untarred, entered the XCrSDen-1.5.18-bin-shared and > did ./xcConfigure and the following were assigned: > > XCRYSDEN_TOPDIR=/XCrSDen-1.5.18-bin-shared > XCRYSDEN_SCRATCH=/home/User/xcrys_tmp > > then I executed ./xcrysden and I got the error: > > ./xcrysden: line 160: /XCrySDen-1.5.24-scr/scripts/xcLib.sh :no such file or > directory Why do you insist using xcConfigure (in 1.5.* its use is deprecated)? You can notice that there is a mismatch in the definition of XCRYSDEN_TOPDIR, because the actual definition points to /XCrySDen-1.5.24-scr and not to /XCrSDen-1.5.18-bin-shared. The problem is that if XCRYSDEN_TOPDIR is already defined, one needs to update its definition manually, xcConfigure wan't do it in this case! > > I have typed unset XCRYSDEN_TOPDIR > and then ./xcrysden again and I got: > > XCRYSDEN_TOPDIR=/XCrySDen-1.5.18-bin-shared > XCRYSDEN_SCRATCH=/home/User/xcrys_tmp > > Application initialization failed: no display name and no $DISPLAY envir > ariable OK, it works now (in principle)! The problem you are facing is that you tried to run xcrysden without running X-window. First, launch the X-window system in your cygwin and then from, say, xterm launch the xcrysden (but makes sure the XCRYSDEN_TOPDIR is either undefined or correctly defined)! 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 seipek at gyte.edu.tr Mon Mar 5 12:08:35 2012 From: seipek at gyte.edu.tr (Semran ipek) Date: Mon, 5 Mar 2012 11:08:35 +0000 Subject: [xcrysden] (no subject) Message-ID: Dear Dr. Tone; I am trying to install XCrySDen-1.5.25-bin-semishared version of Xcrysden to my PC. it gives error after running the binary and it says "error while loading shared libraries: libXss.so.1: wrong ELF class: ELFCLASS32". I have already had libXss.so.1 library in /usr/lib/libXss.so.1. I have already edit my LD_LIBRARY_PATH to include that library . it did not work. Also I made a soft link to /usr/lib64/. Here's the output of ./xcrysden -d. ****************************************************** Version: 1.5.25 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/. TCL_LIBRARY=/home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/tcl8.5 linux-vdso.so.1 => (0x00007fff9ffff000) libfftw3.so.3 => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libfftw3.so.3 (0x00007f38b11e4000) libmeschach.so.1.2 => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libmeschach.so.1.2 (0x00007f38b0f97000) libtk8.5.so => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libtk8.5.so (0x00007f38b0c4b000) libtcl8.5.so => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libtcl8.5.so (0x00007f38b092e000) libGLU.so.1 => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libGLU.so.1 (0x00007f38b06b7000) libGL.so.1 => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libGL.so.1 (0x00007f38b00a2000) libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x00000032b5c00000) libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000039ffe00000) libm.so.6 => /lib64/libm.so.6 (0x00000033f8600000) libc.so.6 => /lib64/libc.so.6 (0x00000033f7600000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00000033f7a00000) libXss.so.1 => not found libXext.so.6 => /usr/lib64/libXext.so.6 (0x0000003a00200000) libdl.so.2 => /lib64/libdl.so.2 (0x00000033f7e00000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003166e00000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000039ffa00000) libXt.so.6 => /usr/lib64/libXt.so.6 (0x00000032b6400000) libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000033fb600000) /lib64/ld-linux-x86-64.so.2 (0x00000033f7200000) libSM.so.6 => /usr/lib64/libSM.so.6 (0x00000032b5800000) libICE.so.6 => /usr/lib64/libICE.so.6 (0x0000003408200000) libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000033fba00000) libuuid.so.1 => /lib64/libuuid.so.1 (0x00000032b5400000) XCRYSDEN_TOPDIR=/home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared XCRYSDEN_SCRATCH=/home/ipek/xcrys_tmp GNU gdb (GDB) Fedora (7.2.90.20110429-36.fc15) Copyright (C) 2011 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 "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: ... Reading symbols from /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/bin/xcrys ..done. /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/bin/xcrys: error while loading shared libraries: libXss.so.1: wrong ELF class: ELFCLASS32 [Inferior 1 (process 2322) exited with code 0177] Missing separate debuginfos, use: debuginfo-install glibc-2.14.1-5.x86_64 (gdb) ***************************************************** My linux configuration is: Linux dirac 2.6.42.3-2.fc15.x86_64 #1 SMP Thu Feb 9 01:42:06 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux I hope that you could help . Best regards; ipek -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120305/d36c5eed/attachment.htm From seipek at gyte.edu.tr Mon Mar 5 12:14:17 2012 From: seipek at gyte.edu.tr (Semran ipek) Date: Mon, 5 Mar 2012 11:14:17 +0000 Subject: [xcrysden] wrong ELF class while running xcrysden Message-ID: Dear Dr. Tone; I am trying to install XCrySDen-1.5.25-bin-semishared version of Xcrysden to my PC. it gives error after running the binary and it says "error while loading shared libraries: libXss.so.1: wrong ELF class: ELFCLASS32". I have already had libXss.so.1 library in /usr/lib/libXss.so.1. I have already edit my LD_LIBRARY_PATH to include that library . it did not work. Also I made a soft link to /usr/lib64/. Here's the output of ./xcrysden -d. ****************************************************** Version: 1.5.25 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/. TCL_LIBRARY=/home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/tcl8.5 linux-vdso.so.1 => (0x00007fff9ffff000) libfftw3.so.3 => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libfftw3.so.3 (0x00007f38b11e4000) libmeschach.so.1.2 => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libmeschach.so.1.2 (0x00007f38b0f97000) libtk8.5.so => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libtk8.5.so (0x00007f38b0c4b000) libtcl8.5.so => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libtcl8.5.so (0x00007f38b092e000) libGLU.so.1 => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libGLU.so.1 (0x00007f38b06b7000) libGL.so.1 => /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/external/lib/libGL.so.1 (0x00007f38b00a2000) libXmu.so.6 => /usr/lib64/libXmu.so.6 (0x00000032b5c00000) libX11.so.6 => /usr/lib64/libX11.so.6 (0x00000039ffe00000) libm.so.6 => /lib64/libm.so.6 (0x00000033f8600000) libc.so.6 => /lib64/libc.so.6 (0x00000033f7600000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00000033f7a00000) libXss.so.1 => not found libXext.so.6 => /usr/lib64/libXext.so.6 (0x0000003a00200000) libdl.so.2 => /lib64/libdl.so.2 (0x00000033f7e00000) libstdc++.so.6 => /usr/lib64/libstdc++.so.6 (0x0000003166e00000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00000039ffa00000) libXt.so.6 => /usr/lib64/libXt.so.6 (0x00000032b6400000) libxcb.so.1 => /usr/lib64/libxcb.so.1 (0x00000033fb600000) /lib64/ld-linux-x86-64.so.2 (0x00000033f7200000) libSM.so.6 => /usr/lib64/libSM.so.6 (0x00000032b5800000) libICE.so.6 => /usr/lib64/libICE.so.6 (0x0000003408200000) libXau.so.6 => /usr/lib64/libXau.so.6 (0x00000033fba00000) libuuid.so.1 => /lib64/libuuid.so.1 (0x00000032b5400000) XCRYSDEN_TOPDIR=/home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared XCRYSDEN_SCRATCH=/home/ipek/xcrys_tmp GNU gdb (GDB) Fedora (7.2.90.20110429-36.fc15) Copyright (C) 2011 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 "x86_64-redhat-linux-gnu". For bug reporting instructions, please see: ... Reading symbols from /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/bin/xcrys ..done. /home/ipek/Desktop/XCrySDen-1.5.25-bin-semishared/bin/xcrys: error while loading shared libraries: libXss.so.1: wrong ELF class: ELFCLASS32 [Inferior 1 (process 2322) exited with code 0177] Missing separate debuginfos, use: debuginfo-install glibc-2.14.1-5.x86_64 (gdb) ***************************************************** My linux configuration is: Linux dirac 2.6.42.3-2.fc15.x86_64 #1 SMP Thu Feb 9 01:42:06 UTC 2012 x86_64 x86_64 x86_64 GNU/Linux I hope that you could help . Best regards; ipek -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120305/ca451eaf/attachment.htm From emoujaes at fisica.ufmg.br Mon Mar 5 20:12:47 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Mon, 5 Mar 2012 16:12:47 -0300 Subject: [xcrysden] cannot start XCRYSDEN In-Reply-To: <1330935020.4546.6.camel@catalyst.ijs.si> References: <20120224181625.M99053@proto.fisica.ufmg.br> <1330329437.7856.8.camel@catalyst.ijs.si> <20120301221257.M95469@proto.fisica.ufmg.br> <1330683051.25610.2.camel@catalyst.ijs.si> <20120302215135.M857@proto.fisica.ufmg.br> <1330766225.3857.8.camel@catalyst.ijs.si> <20120303160407.M20728@proto.fisica.ufmg.br> <1330935020.4546.6.camel@catalyst.ijs.si> Message-ID: <20120305191217.M60422@proto.fisica.ufmg.br> Dear Tone, Thanks very much for your help. I finally got it to actually work.. Regards Elie On Mon, 05 Mar 2012 09:10:20 +0100, Tone Kokalj wrote > On Sat, 2012-03-03 at 13:09 -0300, Elie Albert Moujaes wrote: > > Dear Tone, > > > > in fact I have Cygwin so I downloaded the tarred source xc-1.5.18-cygwin- > > shared.tar.gz and I have untarred, entered the XCrSDen-1.5.18-bin-shared and > > did ./xcConfigure and the following were assigned: > > > > XCRYSDEN_TOPDIR=/XCrSDen-1.5.18-bin-shared > > XCRYSDEN_SCRATCH=/home/User/xcrys_tmp > > > > then I executed ./xcrysden and I got the error: > > > > ./xcrysden: line 160: /XCrySDen-1.5.24-scr/scripts/xcLib.sh :no such file or > > directory > > Why do you insist using xcConfigure (in 1.5.* its use is deprecated)? > You can notice that there is a mismatch in the definition of > XCRYSDEN_TOPDIR, because the actual definition points > to /XCrySDen-1.5.24-scr and not to /XCrSDen-1.5.18-bin-shared. The > problem is that if XCRYSDEN_TOPDIR is already defined, one needs to > update its definition manually, xcConfigure wan't do it in this case! > > > > > I have typed unset XCRYSDEN_TOPDIR > > and then ./xcrysden again and I got: > > > > XCRYSDEN_TOPDIR=/XCrySDen-1.5.18-bin-shared > > XCRYSDEN_SCRATCH=/home/User/xcrys_tmp > > > > Application initialization failed: no display name and no $DISPLAY envir > > ariable > > OK, it works now (in principle)! The problem you are facing is that you > tried to run xcrysden without running X-window. First, launch the > X-window system in your cygwin and then from, say, xterm launch the > xcrysden (but makes sure the XCRYSDEN_TOPDIR is either undefined or > correctly defined)! > > 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 -- Departamento de Fisica - UFMG/ICEx From watheqzako at yahoo.com Tue Mar 6 01:38:47 2012 From: watheqzako at yahoo.com (Watheq Elias) Date: Mon, 5 Mar 2012 16:38:47 -0800 (PST) Subject: [xcrysden] Installing XCrySDen on Scientific Linux 6.1 Message-ID: <1330994327.48884.YahooMailNeo@web45803.mail.sp1.yahoo.com> Dear XCrySDen users, I have installed a precompiled version of?XCrySDen on scientific linux 6.1. When I?run it I got the following error: ? /home/Watheq/XCrySDen-1.5.25-bin-semishared/xcrysden: line 224: /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys: cannot execute binary file ? I have copied what i did in attached txt file. I will be very grateful if you could kindly help me to fix this problem. My regards, Watheq Elias -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120305/8ea21a43/attachment-0001.htm -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: installing XCrySDen.txt Url: http://www.democritos.it/pipermail/xcrysden/attachments/20120305/8ea21a43/attachment-0001.txt From tone.kokalj at ijs.si Tue Mar 6 14:39:08 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 06 Mar 2012 14:39:08 +0100 Subject: [xcrysden] Installing XCrySDen on Scientific Linux 6.1 In-Reply-To: <1330994327.48884.YahooMailNeo@web45803.mail.sp1.yahoo.com> References: <1330994327.48884.YahooMailNeo@web45803.mail.sp1.yahoo.com> Message-ID: <1331041148.3396.1.camel@catalyst.ijs.si> On Mon, 2012-03-05 at 16:38 -0800, Watheq Elias wrote: > Dear XCrySDen users, > I have installed a precompiled version of XCrySDen on scientific linux > 6.1. When I run it I got the following error: > > /home/Watheq/XCrySDen-1.5.25-bin-semishared/xcrysden: line > 224: /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys: cannot > execute binary file This looks like you are trying to run 64bit application on 32bit linux. Provide more info! Do the following: file /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys uname -a What does the two commands report? 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 Tue Mar 6 14:49:02 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 06 Mar 2012 14:49:02 +0100 Subject: [xcrysden] wrong ELF class while running xcrysden In-Reply-To: References: Message-ID: <1331041742.3396.6.camel@catalyst.ijs.si> On Mon, 2012-03-05 at 11:14 +0000, Semran ipek wrote: > > > Dear Dr. Tone; > > I am trying to install XCrySDen-1.5.25-bin-semishared version of > Xcrysden to my PC. it gives error after > running the binary and it says "error while loading shared libraries: > libXss.so.1: wrong ELF class: ELFCLASS32". Which means that the system wants the 64bit library yet you have a 32 bit library. > I have already had libXss.so.1 library in /usr/lib/libXss.so.1. Seems your OS has 32bit libraries in /usr/lib/ and 64bit libraries in /usr/lib64. > Also I made a soft link to /usr/lib64/. No, this will not work, you should install a 64bit version of libXss.so.1 library instead. What is the package that contains this library probably depends on the linux distribution, e.g., in Debian it is the libxss1 package. 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 muirs at onid.orst.edu Wed Mar 7 05:50:40 2012 From: muirs at onid.orst.edu (Sean Muir) Date: Tue, 6 Mar 2012 20:50:40 -0800 Subject: [xcrysden] Question about Fermi surface velocity shading Message-ID: Hello XCrySDen users, I am interested in learning how to generate a Fermi surface image which is shaded by electron/hole velocity at the Fermi energy. Can anyone within the XCrySDen community explain to me how this is done, as in what programs are used? I currently am using use Wien2K for calculations. It is my understanding that XCrySDen is unable to do this currently, thus I am wondering what other programs people might use, or better yet, is there actually a way to do this in XCrySDen that I have yet to encounter? Any insights or pointers to a previous thread discussing this matter would be appreciated. Cheers, Sean Muir Oregon State University > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120306/7fc83fec/attachment.htm From arshadfarhan at hotmail.com Wed Mar 7 09:31:26 2012 From: arshadfarhan at hotmail.com (=?windows-1256?B?483jzyDH0dTPIN3Rzcfk?=) Date: Wed, 7 Mar 2012 17:31:26 +0900 Subject: [xcrysden] problem in compiling Xcrysden Message-ID: Dear Prof. Kokalj & Xcrysden users, i had been trying to compile the Xcrysden 1.5.24 with the src_all libraries package.after selecting the system, when i try execute the command "make all" , it gives the following two errors: one error with a lot of warnings is : "SyntaxError: invalid syntax make[5]: *** No rule to make target `depend', needed by `default'. Stop. make[5]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' make[4]: *** [subdirs] Error 1 make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src' make[3]: *** [default] Error 1 make[3]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1' make[2]: *** [linux] Error 2 make[2]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1' make[2]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1' make[3]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src' make[4]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/glsl' make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/glsl' make[4]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/glapi' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/glapi' make[4]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' running makedepend make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' make[4]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' gcc -c -I../../../include -I../../../src/mapi -Wall -Wmissing-prototypes -Wdeclaration-after-statement -Wpointer-arith -O3 -g -fPIC -D_POSIX_SOURCE -D_POSIX_C_SOURCE=199309L -D_SVID_SOURCE -D_BSD_SOURCE -D_GNU_SOURCE -DPTHREADS -DUSE_XSHM -DHAVE_POSIX_MEMALIGN -I/usr/X11R6/include -std=c99 -ffast-math -fno-strict-aliasing -DMAPI_ABI_HEADER=\"vgapi/vgapi_tmp.h\" ../../../src/mapi/mapi/entry.c -o entry.o gcc -c -I../../../include -I../../../src/mapi -Wall -Wmissing-prototypes -Wdeclaration-after-statement -Wpointer-arith -O3 -g -fPIC -D_POSIX_SOURCE -D_POSIX_C_SOURCE=199309L -D_SVID_SOURCE -D_BSD_SOURCE -D_GNU_SOURCE -DPTHREADS -DUSE_XSHM -DHAVE_POSIX_MEMALIGN -I/usr/X11R6/include -std=c99 -ffast-math -fno-strict-aliasing -DMAPI_ABI_HEADER=\"vgapi/vgapi_tmp.h\" ../../../src/mapi/mapi/mapi.c -o mapi.o ../../../src/mapi/mapi/mapi.c:39: error: ?MAPI_TABLE_NUM_STATIC? undeclared here (not in a function) ../../../src/mapi/mapi/mapi.c:39: error: ?MAPI_TABLE_NUM_DYNAMIC? undeclared here (not in a function) make[4]: *** [mapi.o] Error 1 make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' make[3]: *** [install] Error 1 make[3]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src' make[2]: *** [install] Error 1 make[2]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1' make[1]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src' " & the error in the end of comilation is reads : "fft3d.c:4:19: error: fftw3.h: No such file or directory In file included from fft3d.c:6: shankland.h:4:30: error: meschach/matrix2.h: No such file or directory In file included from fft3d.c:6: shankland.h:49: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:49: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:50: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:50: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:62: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:64: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:65: error: expected declaration specifiers or ?...? before ?MAT? shankland.h:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?*? token shankland.h:69: error: expected declaration specifiers or ?...? before ?MAT? fft3d.c: In function ?fft3d_interpolate?: fft3d.c:88: error: ?fftw_complex? undeclared (first use in this function) fft3d.c:88: error: (Each undeclared identifier is reported only once fft3d.c:88: error: for each function it appears in.) fft3d.c:88: error: ?aux? undeclared (first use in this function) fft3d.c:88: error: ?fftw2? undeclared (first use in this function) fft3d.c:89: error: ?fftw_plan? undeclared (first use in this function) fft3d.c:89: error: expected ?;? before ?pfor? fft3d.c:96: error: expected expression before ?)? token fft3d.c:97: error: expected expression before ?)? token fft3d.c:99: error: ?pfor? undeclared (first use in this function) fft3d.c:99: error: ?FFTW_ESTIMATE? undeclared (first use in this function) fft3d.c:100: error: ?pbak? undeclared (first use in this function) fft3d.c:110: error: too many arguments to function ?fft3d_enlarge_complex_r2c? make[2]: *** [fft3d.o] Error 1 make[2]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/C' make: *** [src-C] Error 2 " kindly guide me through the compilation as i'm new to Linux. Regards, M. Arshad Farhan -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120307/9df0df2a/attachment.htm From rlarrosa at uma.es Wed Mar 7 15:39:29 2012 From: rlarrosa at uma.es (rafael) Date: Wed, 7 Mar 2012 15:39:29 +0100 Subject: [xcrysden] problem compiling and executing xcrysden Message-ID: Hello, We have been compiling xcrysden from xc-1.5.24-src-all.tar.gz using several compilers, at the end we selected gcc 4.4.2 for compiling it on a x86-64 with SLES (SuSE Linux Enterprise Server) 10.2 We have needed to change the source to make it compile, with those changes: In C/shank_Hinv.c add: #define M_PI 3.14159265358979323846 In C/shankland.h and C/shank_util.c the compiler gives errors on those functions : extern void print_complex_vector(FILE *stream, const char *name, size_t m, fftw_complex *mat); extern void print_complex_matrix(FILE *stream, const char *name, size_t m, size_t n, fftw_complex *mat); shank_util.c: In function ?print_complex_vector?: shank_util.c:124: error: subscripted value is neither array nor pointer shank_util.c:124: error: subscripted value is neither array nor pointer shank_util.c: In function ?print_complex_matrix?: shank_util.c:164: error: subscripted value is neither array nor pointer shank_util.c:164: error: subscripted value is neither array nor pointer So I modified them putting an extra asterisk : extern void print_complex_vector(FILE *stream, const char *name, size_t m, fftw_complex **mat); ... extern void print_complex_matrix(FILE *stream, const char *name, size_t m, size_t n, fftw_complex **mat); After those changes it compiles, but when executing it gives a segmentation fault: TCL_LIBRARY=/export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all XCRYSDEN_SCRATCH=/export/home_users/home/soft/xcrysden/xcrys_tmp Running on platform : unix Operating system : Linux Package Ppmtompeg: /usr/bin/ppmtompeg Package Xwd: /usr/X11R6/bin/xwd Executing: /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/bin/ftnunit /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/xcrysden: line 227: 30136 Segmentation fault ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH "$@" >/dev/null I have debugged (-d) it and it shows: Executing: /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/bin/ftnunit Program received signal SIGSEGV, Segmentation fault. [Switching to Thread 47700007662880 (LWP 29800)] 0xffffffffffffffff in ?? () (gdb) bt #0 0xffffffffffffffff in ?? () #1 0x000000000043df17 in LoadLights () #2 0x00000000004440f6 in XC_SetGLparamCmd () #3 0x00002b620408dc8f in TclInvokeStringCommand () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #4 0x00002b620408f131 in TclEvalObjvInternal () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #5 0x00002b62040d8659 in TclExecuteByteCode () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #6 0x00002b6204117e1b in TclObjInterpProcCore () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #7 0x00002b620408f131 in TclEvalObjvInternal () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #8 0x00002b620408f879 in TclEvalEx () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #9 0x00002b620408ffc6 in Tcl_EvalEx () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #10 0x00002b62040904fd in TclEvalObjEx () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #11 0x00002b620409af21 in Tcl_EvalObjCmd () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #12 0x00002b620408f131 in TclEvalObjvInternal () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #13 0x00002b620408f879 in TclEvalEx () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #14 0x00002b620408ffc6 in Tcl_EvalEx () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #15 0x00002b62040fae91 in Tcl_FSEvalFileEx () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtcl8.5.so #16 0x00002b6203e6d67c in Tk_MainEx () from /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/external/lib/libtk8.5.so #17 0x000000000040d3ef in main () I have put a strace before the executable and the last that it shows is: stat("/export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/Tcl/menu.tcl", {st_mode=S_IFREG|0644, st_size=67758, ...}) = 0 open("/export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/Tcl/menu.tcl", O_RDONLY) = 5 fcntl(5, F_SETFD, FD_CLOEXEC) = 0 ioctl(5, SNDCTL_TMR_TIMEBASE or TCGETS, 0x7fff1255cc90) = -1 ENOTTY (Inappropriate ioctl for device) read(5, "################################"..., 4096) = 4096 read(5, "--------------------------------"..., 4096) = 4096 read(5, "tem(BINDIR)/fhi_inpini2ftn34 \\\n\t"..., 4096) = 4096 read(5, "Files} {.xyz} }\n\t\t\t } -initial"..., 4096) = 4096 read(5, "{ $file != \"\" } {\n\t\tg98Cube $fil"..., 4096) = 4096 read(5, "$mdis1 add radiobutton \\\n\t -l"..., 4096) = 4096 read(5, "nd . SetWignerSeitzInit\n\n "..., 4096) = 4096 read(5, "ultiSlab change]\n\n\n #--------"..., 4096) = 4096 read(5, "{\n\tset dir $system(PWD)\n } el"..., 4096) = 4096 read(5, "tr $file $can}] } {\n\tErrorDialog"..., 4096) = 4096 brk(0xadd000) = 0xadd000 brk(0xad3000) = 0xad3000 read(5, "== \"cell\"} { \n\tset MODE2 $geng(M"..., 4096) = 4096 read(5, " 10004\n set mody(R_OUTLINEWI"..., 4096) = 4096 read(5, "_FOG) 30\n se"..., 4096) = 4096 read(5, " \n }\n return\n}\n\n\n\f\nproc M"..., 4096) = 4096 read(5, "l(green) * 255)] ]\n set cellc"..., 4096) = 4096 read(5, "save structure\" \\\n\t\twarning 1 No"..., 4096) = 4096 read(5, " set top .perspective\n if "..., 4096) = 2222 read(5, "", 4096) = 0 close(5) = 0 brk(0xaf4000) = 0xaf4000 --- SIGSEGV (Segmentation fault) @ 0 (0) --- +++ killed by SIGSEGV +++ Executing with -T it shows: ... Package Xwd: /usr/X11R6/bin/xwd determine_movie_encoders ; level == 1 FtnName ; level == 1 xcCatchExecReturn /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/bin/ftnunit ; level == 2 destroyWelcome ; level == 3 xcDebug -stderr {{Executing: /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/bin/ftnunit}} ; level == 3 Executing: /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/bin/ftnunit GetGengM3Arg ANGS none ; level == 2 ModConst ; level == 2 /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/xcrysden: line 227: 30155 Segmentation fault ${XCRYSDEN_TOPDIR}/bin/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH "$@" >/dev/null If you need more information I can provide it. Does someone have any tips to make it work ? Thanks, Rafael From watheqzako at yahoo.com Wed Mar 7 16:05:18 2012 From: watheqzako at yahoo.com (Watheq Elias) Date: Wed, 7 Mar 2012 07:05:18 -0800 (PST) Subject: [xcrysden] Installing XCrySDen on Scientific Linux 6.1 In-Reply-To: <1331041148.3396.1.camel@catalyst.ijs.si> References: <1330994327.48884.YahooMailNeo@web45803.mail.sp1.yahoo.com> <1331041148.3396.1.camel@catalyst.ijs.si> Message-ID: <1331132718.32613.YahooMailNeo@web45808.mail.sp1.yahoo.com> Dear Mr Kokalj I did as you have advised me to do and this is what I got? [Watheq at Nasam XCrySDen-1.5.25-bin-semishared]$ file /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys: ELF 64-bit LSB executable, x86-64, version 1 (SYSV), dynamically linked (uses shared libs), for GNU/Linux 2.6.26, not stripped [Watheq at Nasam XCrySDen-1.5.25-bin-semishared]$ uname -a Linux Nasam 2.6.32-220.4.1.el6.i686 #1 SMP Mon Jan 23 17:25:22 CST 2012 i686 i686 i386 GNU/Linux [Watheq at Nasam XCrySDen-1.5.25-bin-semishared]$ Thanks a lot for your help ? With best wishes, Watheq Zako Elias ________________________________ From: Tone Kokalj To: xcrysden at democritos.it Sent: Tuesday, 6 March 2012, 13:39 Subject: Re: [xcrysden] Installing XCrySDen on Scientific Linux 6.1 On Mon, 2012-03-05 at 16:38 -0800, Watheq Elias wrote: > Dear XCrySDen users, > I have installed a precompiled version of XCrySDen on scientific linux > 6.1. When I run it I got the following error: >? > /home/Watheq/XCrySDen-1.5.25-bin-semishared/xcrysden: line > 224: /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys: cannot > execute binary file This looks like you are trying to run 64bit application on 32bit linux. Provide more info! Do the following: file /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys uname -a What does the two commands report? 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 -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120307/3355de6e/attachment.htm From tone.kokalj at ijs.si Wed Mar 7 16:39:15 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 07 Mar 2012 16:39:15 +0100 Subject: [xcrysden] problem compiling and executing xcrysden In-Reply-To: References: Message-ID: <1331134755.3299.10.camel@catalyst.ijs.si> On Wed, 2012-03-07 at 15:39 +0100, rafael wrote: > In C/shank_Hinv.c add: > > #define M_PI 3.14159265358979323846 I know this, the M_PI isn't standard and it is not defined everywhere. It's been fixed. > > In C/shankland.h and C/shank_util.c the compiler gives errors on those functions : > extern void print_complex_vector(FILE *stream, const char *name, size_t m, fftw_complex *mat); > > extern void print_complex_matrix(FILE *stream, const char *name, size_t m, size_t n, fftw_complex *mat); > > shank_util.c: In function ?print_complex_vector?: > shank_util.c:124: error: subscripted value is neither array nor pointer > shank_util.c:124: error: subscripted value is neither array nor pointer > shank_util.c: In function ?print_complex_matrix?: > shank_util.c:164: error: subscripted value is neither array nor pointer > shank_util.c:164: error: subscripted value is neither array nor pointer This I see the first time. Probably the problem is that in your system the fftw_complex is not defined as "typedef double fftw_complex[2]" but as C99's complex double (no experience with it whatsoever). It's best to delete these functions and their prototypes as they were merely used for debugging. > After those changes it compiles, but when executing it gives a segmentation fault: > I have debugged (-d) it and it shows: > > Executing: /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/bin/ftnunit > > Program received signal SIGSEGV, Segmentation fault. > [Switching to Thread 47700007662880 (LWP 29800)] > 0xffffffffffffffff in ?? () > (gdb) bt > #0 0xffffffffffffffff in ?? () > #1 0x000000000043df17 in LoadLights () This is known issue that has been fixed. You may try to compile newer version, which should work: http://www.xcrysden.org/download/xc-1.5.32-src.tar.gz 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 Wed Mar 7 16:41:46 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 07 Mar 2012 16:41:46 +0100 Subject: [xcrysden] Installing XCrySDen on Scientific Linux 6.1 In-Reply-To: <1331132718.32613.YahooMailNeo@web45808.mail.sp1.yahoo.com> References: <1330994327.48884.YahooMailNeo@web45803.mail.sp1.yahoo.com> <1331041148.3396.1.camel@catalyst.ijs.si> <1331132718.32613.YahooMailNeo@web45808.mail.sp1.yahoo.com> Message-ID: <1331134906.3299.12.camel@catalyst.ijs.si> On Wed, 2012-03-07 at 07:05 -0800, Watheq Elias wrote: > Dear Mr Kokalj > I did as you have advised me to do and this is what I got > > [Watheq at Nasam XCrySDen-1.5.25-bin-semishared]$ > file /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys > /home/Watheq/XCrySDen-1.5.25-bin-semishared/bin/xcrys: ELF 64-bit LSB > executable, x86-64, version 1 (SYSV), dynamically linked (uses shared > libs), for GNU/Linux 2.6.26, not stripped Which means you are using 64bit complied package .... > [Watheq at Nasam XCrySDen-1.5.25-bin-semishared]$ uname -a > Linux Nasam 2.6.32-220.4.1.el6.i686 #1 SMP Mon Jan 23 17:25:22 CST > 2012 i686 i686 i386 GNU/Linux ... on 32bit linux. That will never work! Try this instead: http://www.xcrysden.org/download/xc-1.5.24-linux_x86-semishared.tar.gz 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 arshadfarhan at hotmail.com Thu Mar 8 02:21:14 2012 From: arshadfarhan at hotmail.com (=?windows-1256?B?483jzyDH0dTPIN3Rzcfk?=) Date: Thu, 8 Mar 2012 10:21:14 +0900 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: References: Message-ID: Dear Prof. Kokalj & Xcrysden users, i had been trying to compile the Xcrysden 1.5.24 with the src_all libraries package. after selecting the system, when i try execute the command "make all" , it gives the following two errors: one error with a lot of warnings is : "SyntaxError: invalid syntax make[5]: *** No rule to make target `depend', needed by `default'. Stop. make[5]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' make[4]: *** [subdirs] Error 1 make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src' make[3]: *** [default] Error 1 make[3]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1' make[2]: *** [linux] Error 2 make[2]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1' make[2]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1' make[3]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src' make[4]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/glsl' make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/glsl' make[4]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/glapi' make[4]: Nothing to be done for `install'. make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/glapi' make[4]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' running makedepend make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' make[4]: Entering directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' gcc -c -I../../../include -I../../../src/mapi -Wall -Wmissing-prototypes -Wdeclaration-after-statement -Wpointer-arith -O3 -g -fPIC -D_POSIX_SOURCE -D_POSIX_C_SOURCE=199309L -D_SVID_SOURCE -D_BSD_SOURCE -D_GNU_SOURCE -DPTHREADS -DUSE_XSHM -DHAVE_POSIX_MEMALIGN -I/usr/X11R6/include -std=c99 -ffast-math -fno-strict-aliasing -DMAPI_ABI_HEADER=\"vgapi/vgapi_tmp.h\" ../../../src/mapi/mapi/entry.c -o entry.o gcc -c -I../../../include -I../../../src/mapi -Wall -Wmissing-prototypes -Wdeclaration-after-statement -Wpointer-arith -O3 -g -fPIC -D_POSIX_SOURCE -D_POSIX_C_SOURCE=199309L -D_SVID_SOURCE -D_BSD_SOURCE -D_GNU_SOURCE -DPTHREADS -DUSE_XSHM -DHAVE_POSIX_MEMALIGN -I/usr/X11R6/include -std=c99 -ffast-math -fno-strict-aliasing -DMAPI_ABI_HEADER=\"vgapi/vgapi_tmp.h\" ../../../src/mapi/mapi/mapi.c -o mapi.o ../../../src/mapi/mapi/mapi.c:39: error: ?MAPI_TABLE_NUM_STATIC? undeclared here (not in a function) ../../../src/mapi/mapi/mapi.c:39: error: ?MAPI_TABLE_NUM_DYNAMIC? undeclared here (not in a function) make[4]: *** [mapi.o] Error 1 make[4]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' make[3]: *** [install] Error 1 make[3]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src' make[2]: *** [install] Error 1 make[2]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1' make[1]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src' " & the error in the end of comilation is reads : "fft3d.c:4:19: error: fftw3.h: No such file or directory In file included from fft3d.c:6: shankland.h:4:30: error: meschach/matrix2.h: No such file or directory In file included from fft3d.c:6: shankland.h:49: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:49: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:50: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:50: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:62: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:64: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:65: error: expected declaration specifiers or ?...? before ?MAT? shankland.h:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?*? token shankland.h:69: error: expected declaration specifiers or ?...? before ?MAT? fft3d.c: In function ?fft3d_interpolate?: fft3d.c:88: error: ?fftw_complex? undeclared (first use in this function) fft3d.c:88: error: (Each undeclared identifier is reported only once fft3d.c:88: error: for each function it appears in.) fft3d.c:88: error: ?aux? undeclared (first use in this function) fft3d.c:88: error: ?fftw2? undeclared (first use in this function) fft3d.c:89: error: ?fftw_plan? undeclared (first use in this function) fft3d.c:89: error: expected ?;? before ?pfor? fft3d.c:96: error: expected expression before ?)? token fft3d.c:97: error: expected expression before ?)? token fft3d.c:99: error: ?pfor? undeclared (first use in this function) fft3d.c:99: error: ?FFTW_ESTIMATE? undeclared (first use in this function) fft3d.c:100: error: ?pbak? undeclared (first use in this function) fft3d.c:110: error: too many arguments to function ?fft3d_enlarge_complex_r2c? make[2]: *** [fft3d.o] Error 1 make[2]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/C' make: *** [src-C] Error 2 " kindly guide me through the compilation as i'm new to Linux. Regards, M. Arshad Farhan _______________________________________________ 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/20120308/6ac4b8a8/attachment-0001.htm From tone.kokalj at ijs.si Thu Mar 8 10:13:20 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 08 Mar 2012 10:13:20 +0100 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: References: Message-ID: <1331198000.4667.45.camel@catalyst.ijs.si> On Thu, 2012-03-08 at 10:21 +0900, ???? ???? ????? wrote: > one error with a lot of warnings is : > > "SyntaxError: invalid syntax > make[5]: *** No rule to make target `depend', needed by `default'. > Stop. > make[5]: Leaving directory > `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' The problem appears in compiling the external Mesa library. You have two options: either use the system-wide libGL and libGLU libraries (if they are present on your computer) or go to /home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/ and try to compile it from there (read the corresponding Mesa documentation about compilation). > & the error in the end of comilation is reads : > > "fft3d.c:4:19: error: fftw3.h: No such file or directory Well, you also need a development version of fftw3 library (i.e. libfftw3.* library and fftw3.h header file. In addition, you will also need a Meschach library. These two libs are available from: http://www.fftw.org http://www.math.uiowa.edu/~dstewart/meschach Why don't you try first one of the available compiled packages? And if none turns out to be suitable, you may consider compiling the source package. 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 arshadfarhan at hotmail.com Fri Mar 9 06:40:21 2012 From: arshadfarhan at hotmail.com (=?windows-1256?B?483jzyDH0dTPIN3Rzcfk?=) Date: Fri, 9 Mar 2012 14:40:21 +0900 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: <1331198000.4667.45.camel@catalyst.ijs.si> References: , , <1331198000.4667.45.camel@catalyst.ijs.si> Message-ID: Dear Prof. Kokaljas you had guided me, i was able to install both Mesa Library and fftw library.however, i could not manage to solve the problem for meschach (atleast i think i could not) the Xcrysden compilation this time gives a relatively small error which reads: "In file included from fft3d.c:6: shankland.h:4:30: error: meschach/matrix2.h: No such file or directory In file included from fft3d.c:6: shankland.h:65: error: expected declaration specifiers or ?...? before ?MAT? shankland.h:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?*? token shankland.h:69: error: expected declaration specifiers or ?...? before ?MAT? make[2]: *** [fft3d.o] Error 1 make[2]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/C' make: *** [src-C] Error 2 " Kindly guide me more.thanking you in anticipation,Best Regards,M. Arshad Farhan > From: tone.kokalj at ijs.si > To: xcrysden at democritos.it > Date: Thu, 8 Mar 2012 10:13:20 +0100 > Subject: Re: [xcrysden] problem in compiling Xcrysden > > On Thu, 2012-03-08 at 10:21 +0900, ???? ???? ????? wrote: > > > one error with a lot of warnings is : > > > > "SyntaxError: invalid syntax > > make[5]: *** No rule to make target `depend', needed by `default'. > > Stop. > > make[5]: Leaving directory > > `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/src/mapi/vgapi' > > The problem appears in compiling the external Mesa library. You have two > options: either use the system-wide libGL and libGLU libraries (if they > are present on your computer) or go > to /home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/src/Mesa-7.10.1/ and try to compile it from there (read the corresponding Mesa documentation about compilation). > > > & the error in the end of comilation is reads : > > > > "fft3d.c:4:19: error: fftw3.h: No such file or directory > > Well, you also need a development version of fftw3 library (i.e. > libfftw3.* library and fftw3.h header file. In addition, you will also > need a Meschach library. These two libs are available from: > http://www.fftw.org > http://www.math.uiowa.edu/~dstewart/meschach > > Why don't you try first one of the available compiled packages? And if > none turns out to be suitable, you may consider compiling the source > package. > > 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 -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120309/e5865717/attachment.htm From tone.kokalj at ijs.si Fri Mar 9 08:12:06 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 09 Mar 2012 08:12:06 +0100 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: References: , , <1331198000.4667.45.camel@catalyst.ijs.si> Message-ID: <1331277126.3610.6.camel@catalyst.ijs.si> On Fri, 2012-03-09 at 14:40 +0900, ???? ???? ????? wrote: > Dear Prof. Kokalj > as you had guided me, i was able to install both Mesa Library and fftw > library. > however, i could not manage to solve the problem for meschach (atleast > i think i could not) > the Xcrysden compilation this time gives a relatively small error > which reads: > > "In file included from fft3d.c:6: > shankland.h:4:30: error: meschach/matrix2.h: No such file or directory Which means you either don't have the development version of meschach library installed or it is installed on non-standard place. If the latter applies then specify its location to one of the available *_INCDIR variables in Make.sys. Say, if you have meschach header files in /home/myself/include/meschach then specify -I/home/myself/include 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 indu.chem.mind86 at gmail.com Fri Mar 9 13:14:31 2012 From: indu.chem.mind86 at gmail.com (Indu Kaul) Date: Fri, 9 Mar 2012 17:44:31 +0530 Subject: [xcrysden] Changing color of isosurfaces In-Reply-To: <1331283655.69037.YahooMailNeo@web95705.mail.in.yahoo.com> References: <1331041921.19255.YahooMailNeo@web95705.mail.in.yahoo.com> <1331283655.69037.YahooMailNeo@web95705.mail.in.yahoo.com> Message-ID: Hello, I am using xcrysden 1.5.25-bin-semishared in a 64-bit machine with ubuntu 11.04. Everything works fine except I am unable to change the colour of the isosurfaces. When I go to 'set color parameter' in the window were you set the value for isosurface, a 'Set OpenGl parameter' window opens but contains no colour options. How do I make it work? -- With Regards Indu Kaul Department of Chemistry IISER Pune(MAHARASHTRA) INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120309/bc227081/attachment.htm From rlarrosa at uma.es Fri Mar 9 13:34:24 2012 From: rlarrosa at uma.es (rafael) Date: Fri, 9 Mar 2012 13:34:24 +0100 Subject: [xcrysden] problem compiling and executing xcrysden In-Reply-To: <1331134755.3299.10.camel@catalyst.ijs.si> References: <1331134755.3299.10.camel@catalyst.ijs.si> Message-ID: Hello, >> Executing: /export/home_users/home/soft/xcrysden/originals/XCrySDen-1.5.24-src-all/bin/ftnunit >> >> Program received signal SIGSEGV, Segmentation fault. >> [Switching to Thread 47700007662880 (LWP 29800)] >> 0xffffffffffffffff in ?? () >> (gdb) bt >> #0 0xffffffffffffffff in ?? () >> #1 0x000000000043df17 in LoadLights () > > This is known issue that has been fixed. You may try to compile newer > version, which should work: > http://www.xcrysden.org/download/xc-1.5.32-src.tar.gz Thank you very much, it works fine now. Rafael From tone.kokalj at ijs.si Fri Mar 9 13:50:38 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 09 Mar 2012 13:50:38 +0100 Subject: [xcrysden] Changing color of isosurfaces In-Reply-To: References: <1331041921.19255.YahooMailNeo@web95705.mail.in.yahoo.com> <1331283655.69037.YahooMailNeo@web95705.mail.in.yahoo.com> Message-ID: <1331297438.3610.35.camel@catalyst.ijs.si> On Fri, 2012-03-09 at 17:44 +0530, Indu Kaul wrote: > > Hello, > I am using xcrysden 1.5.25-bin-semishared in a 64-bit machine with > ubuntu 11.04. Everything works fine except I am unable to change the > colour of the isosurfaces. > When I go to 'set color parameter' in the window were you set the > value for isosurface, a 'Set OpenGl parameter' window opens but > contains no colour options. This is first time something like that is reported. Please be more specific and also dumb the screen with the "Set OpenGl parameters" 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 arshadfarhan at hotmail.com Mon Mar 12 04:35:45 2012 From: arshadfarhan at hotmail.com (=?iso-8859-6?B?5c3lzyDH0dTPIOHRzcfm?=) Date: Mon, 12 Mar 2012 12:35:45 +0900 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: <1331277126.3610.6.camel@catalyst.ijs.si> References: ,, ,, <1331198000.4667.45.camel@catalyst.ijs.si>, , <1331277126.3610.6.camel@catalyst.ijs.si> Message-ID: Dear Prof. Kokalj,i compiled the libraries you told me to but i'm stuck for meschach library.when i tarred the package, there were many pre-compiled files.i copied the header files & library into /XCrySDen-1.5.24-src-all/external/include/ and/XCrySDen-1.5.24-src-all/external/lib directories and tried to compile the package again.it gave me this error & i defined the value of pi as suggested by you to the questioner (from a previous thread of yours ; http://www.democritos.it/pipermail/xcrysden/2012-January/001071.html) now it gives the following error: " -o xcrys -ltk8.5 -L/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/lib -ltcl8.5 -lGLU -lGL -lXmu -lX11 -lXext -lm fft3d.o: In function `fft3d_interpolate': fft3d.c:(.text+0x4a9): undefined reference to `fftw_malloc' fft3d.c:(.text+0x4d1): undefined reference to `fftw_malloc' fft3d.c:(.text+0x4f4): undefined reference to `fftw_plan_dft_r2c_3d' fft3d.c:(.text+0x517): undefined reference to `fftw_plan_dft_c2r_3d' fft3d.c:(.text+0x524): undefined reference to `fftw_execute' fft3d.c:(.text+0x5e3): undefined reference to `fftw_execute' fft3d.c:(.text+0x5ec): undefined reference to `fftw_destroy_plan' fft3d.c:(.text+0x5f5): undefined reference to `fftw_destroy_plan' fft3d.c:(.text+0x5fe): undefined reference to `fftw_free' fft3d.c:(.text+0x607): undefined reference to `fftw_free' shank3d.o: In function `shankland3d_interpolate': shank3d.c:(.text+0x517): undefined reference to `fftw_malloc' shank3d.c:(.text+0x543): undefined reference to `fftw_plan_dft_r2c_3d' shank3d.c:(.text+0x56f): undefined reference to `fftw_plan_dft_c2r_3d' shank3d.c:(.text+0x78f): undefined reference to `fftw_execute' shank3d.c:(.text+0xaac): undefined reference to `fftw_execute' shank3d.c:(.text+0xb08): undefined reference to `fftw_destroy_plan' shank3d.c:(.text+0xb11): undefined reference to `fftw_destroy_plan' shank3d.c:(.text+0xb1a): undefined reference to `fftw_free' shank_Hinv.o: In function `shank_HinvObj': shank_Hinv.c:(.text+0x26): undefined reference to `m_get' shank_Hinv.o: In function `shank_Hinv': shank_Hinv.c:(.text+0x9f): undefined reference to `m_get' shank_Hinv.c:(.text+0x4ab): undefined reference to `m_inverse' shank_Hinv.c:(.text+0x4b4): undefined reference to `m_free' shank_Hinv.o: In function `shank1d_lambda': shank_Hinv.c:(.text+0x69a): undefined reference to `m_free' shank_Hinv.o: In function `shank2d_lambda': shank_Hinv.c:(.text+0x98b): undefined reference to `m_free' shank_Hinv.c:(.text+0x994): undefined reference to `m_free' shank_Hinv.o: In function `shank3d_lambda': shank_Hinv.c:(.text+0xdb9): undefined reference to `m_free' shank_Hinv.o:shank_Hinv.c:(.text+0xdcc): more undefined references to `m_free' follow collect2: ld returned 1 exit status make[2]: *** [xcrys] Error 1 make[2]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/mafarhan/programs/XCrySDen-1.5.24-src-all/C' make: *** [src-C] Error 2 "& one more thing , as i do not have super user rights so i installed fftw library some where else and copied it to /XCrysden..../external/ directory. also i have tried copying the math.h & malloc.h files from the /usr/local/ but no effect.kindly guide me through .Regards,M. Arshad Farhan > From: tone.kokalj at ijs.si > To: xcrysden at democritos.it > Date: Fri, 9 Mar 2012 08:12:06 +0100 > Subject: Re: [xcrysden] problem in compiling Xcrysden > > On Fri, 2012-03-09 at 14:40 +0900, ???? ???? ????? wrote: > > Dear Prof. Kokalj > > as you had guided me, i was able to install both Mesa Library and fftw > > library. > > however, i could not manage to solve the problem for meschach (atleast > > i think i could not) > > the Xcrysden compilation this time gives a relatively small error > > which reads: > > > > "In file included from fft3d.c:6: > > shankland.h:4:30: error: meschach/matrix2.h: No such file or directory > > Which means you either don't have the development version of meschach > library installed or it is installed on non-standard place. If the > latter applies then specify its location to one of the available > *_INCDIR variables in Make.sys. Say, if you have meschach header files > in /home/myself/include/meschach then specify -I/home/myself/include > > 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 -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120312/45eff175/attachment.htm From indu.chem.mind86 at gmail.com Mon Mar 12 14:27:28 2012 From: indu.chem.mind86 at gmail.com (Indu Kaul) Date: Mon, 12 Mar 2012 18:57:28 +0530 Subject: [xcrysden] Fwd: In-Reply-To: <1331558489.83201.YahooMailNeo@web95718.mail.in.yahoo.com> References: <1331558489.83201.YahooMailNeo@web95718.mail.in.yahoo.com> Message-ID: Hello, As mentioned in the earlier mail, I don't see the color options in "Set OpenGl parameter" window. So, I have attached the picture of the screen with the window. All I am doing is, opening a xsf file in xcrysden and ploting the isosurface. In order to change the color of the isosurface, I go to the "Set color parameter" after which it open the blank window. -- With Regards Indu Kaul Department of Chemistry IISER Pune(MAHARASHTRA) INDIA -------------- next part -------------- An HTML attachment was scrubbed... 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Name: Screenshot.jpg Type: image/jpeg Size: 25580 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20120312/44c8209f/attachment-0001.jpg From tone.kokalj at ijs.si Mon Mar 12 21:46:53 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 12 Mar 2012 21:46:53 +0100 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: References: ,, ,, <1331198000.4667.45.camel@catalyst.ijs.si> , , <1331277126.3610.6.camel@catalyst.ijs.si> Message-ID: <1331585213.25620.6.camel@catalyst.ijs.si> On Mon, 2012-03-12 at 12:35 +0900, ???? ???? ????? wrote: > Dear Prof. Kokalj, > i compiled the libraries you told me to but i'm stuck for meschach > library. > when i tarred the package, there were many pre-compiled files. > i copied the header files & > library into /XCrySDen-1.5.24-src-all/external/include/ > and > /XCrySDen-1.5.24-src-all/external/lib > > directories and tried to compile the package again. > it gave me this error & i defined the value of pi as suggested by you > to the questioner (from a previous thread of yours ; > http://www.democritos.it/pipermail/xcrysden/2012-January/001071.html) > > now it gives the following error: > > " -o xcrys -ltk8.5 > -L/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/lib > -ltcl8.5 -lGLU -lGL -lXmu -lX11 -lXext -lm > fft3d.o: In function `fft3d_interpolate': > fft3d.c:(.text+0x4a9): undefined reference to `fftw_malloc' Add the -lfftw3 to some ***_LIB variable in Make.sys Alternatively, consider compiling the newest version instead: http://www.xcrysden.org/download/xcrysden-1.5.53.tar.gz The compilation procedure has been improved and compilation should be smoother. Use the ./system/Make.sys-semishared as a Make.sys, i.e.: 1. cp system/Make.sys-semishared Make.sys 2. $EDITOR Make.sys ([optional]; EDITOR is an editor of your choice) 3. make all 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 Mon Mar 12 21:49:26 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 12 Mar 2012 21:49:26 +0100 Subject: [xcrysden] Fwd: In-Reply-To: References: <1331558489.83201.YahooMailNeo@web95718.mail.in.yahoo.com> Message-ID: <1331585366.25620.9.camel@catalyst.ijs.si> On Mon, 2012-03-12 at 18:57 +0530, Indu Kaul wrote: > > Hello, > As mentioned in the earlier mail, I don't see the color options in > "Set OpenGl parameter" window. So, I have attached the picture of the > screen with the window. This is awkward and it's the first time I see something like this. Try to resize that window (or to iconify and deiconify it), maybe this will invoke a correct remapping of the window's widgets. What is your OS and what xcrysden version you use? 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 arshadfarhan at hotmail.com Tue Mar 13 09:27:35 2012 From: arshadfarhan at hotmail.com (=?iso-8859-6?B?5c3lzyDH0dTPIOHRzcfm?=) Date: Tue, 13 Mar 2012 17:27:35 +0900 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: <1331585213.25620.6.camel@catalyst.ijs.si> References: ,,, ,,, <1331198000.4667.45.camel@catalyst.ijs.si>,, ,, <1331277126.3610.6.camel@catalyst.ijs.si>, , <1331585213.25620.6.camel@catalyst.ijs.si> Message-ID: Dear Prof. Kokalj,thank you very much for your help.i had successfully compiled Xcrysden-1.5.53 ; however when i executed the program for FERMI SURFACE rendering, it crashed just like the previous version (the reason why i started to compile it again).the error reads:"*** glibc detected *** /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys: free(): invalid next size (normal): 0x000000001bf55700 *** ======= Backtrace: ========= /lib64/libc.so.6[0x30c787245f] /lib64/libc.so.6(cfree+0x4b)[0x30c78728bb] /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys[0x4719ca] /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys[0x48b15d] /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys[0x49119e] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(TclInvokeStringCommand+0x6f)[0x2ac97999efbf] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799a01b9] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799e2d70] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(TclObjInterpProcCore+0x11d)[0x2ac979a229ad] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799a01b9] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799e2d70] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(TclObjInterpProcCore+0x11d)[0x2ac979a229ad] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799a01b9] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(Tcl_EvalObjv+0x43)[0x2ac9799a1393] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(TclEvalObjEx+0x390)[0x2ac9799a17f0] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac979a23321] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799a01b9] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799e2d70] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(TclObjInterpProcCore+0x11d)[0x2ac979a229ad] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799a01b9] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so[0x2ac9799a0e16] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(Tcl_EvalEx+0x16)[0x2ac9799a1196] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so(Tk_BindEvent+0x802)[0x2ac97966cda2] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so[0x2ac9796ae94d] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so[0x2ac9796af5af] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so(Tk_HandleEvent+0x544)[0x2ac979677a24] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so[0x2ac979677ce0] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(Tcl_ServiceEvent+0x5d)[0x2ac979a1451d] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so(Tcl_DoOneEvent+0x8e)[0x2ac979a1478e] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so(Tk_MainLoop+0x1b)[0x2ac97967724b] /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so(Tk_MainEx+0x357)[0x2ac979684827] /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys[0x40cb8a] /lib64/libc.so.6(__libc_start_main+0xf4)[0x30c781d994] /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys[0x40bf59] ======= Memory map: ======== 00400000-004d9000 r-xp 00000000 08:11 3758224213 /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys 006d9000-006de000 rw-p 000d9000 08:11 3758224213 /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys 006de000-00747000 rw-p 006de000 00:00 0 1b580000-1d4de000 rw-p 1b580000 00:00 0 [heap] 30c7000000-30c701c000 r-xp 00000000 08:01 12747083 /lib64/ld-2.5.so 30c721c000-30c721d000 r--p 0001c000 08:01 12747083 /lib64/ld-2.5.so 30c721d000-30c721e000 rw-p 0001d000 08:01 12747083 /lib64/ld-2.5.so 30c7800000-30c794e000 r-xp 00000000 08:01 12747084 /lib64/libc-2.5.so 30c794e000-30c7b4e000 ---p 0014e000 08:01 12747084 /lib64/libc-2.5.so 30c7b4e000-30c7b52000 r--p 0014e000 08:01 12747084 /lib64/libc-2.5.so 30c7b52000-30c7b53000 rw-p 00152000 08:0/home/mafarhan/programs/xcrysden-1.5.53/xcrysden: line 233: 13879 Aborted ${XCRYSDEN_XCRYS_DIR}/xcrys ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH "$@" > /dev/null" please help me in this regard.thanking you in anticipation.Regards,M. Arshad Farhan > From: tone.kokalj at ijs.si > To: xcrysden at democritos.it > Date: Mon, 12 Mar 2012 21:46:53 +0100 > Subject: Re: [xcrysden] problem in compiling Xcrysden > > On Mon, 2012-03-12 at 12:35 +0900, ???? ???? ????? wrote: > > Dear Prof. Kokalj, > > i compiled the libraries you told me to but i'm stuck for meschach > > library. > > when i tarred the package, there were many pre-compiled files. > > i copied the header files & > > library into /XCrySDen-1.5.24-src-all/external/include/ > > and > > /XCrySDen-1.5.24-src-all/external/lib > > > > directories and tried to compile the package again. > > it gave me this error & i defined the value of pi as suggested by you > > to the questioner (from a previous thread of yours ; > > http://www.democritos.it/pipermail/xcrysden/2012-January/001071.html) > > > > now it gives the following error: > > > > " -o xcrys -ltk8.5 > > -L/home/mafarhan/programs/XCrySDen-1.5.24-src-all/external/lib > > -ltcl8.5 -lGLU -lGL -lXmu -lX11 -lXext -lm > > fft3d.o: In function `fft3d_interpolate': > > fft3d.c:(.text+0x4a9): undefined reference to `fftw_malloc' > > Add the -lfftw3 to some ***_LIB variable in Make.sys > > Alternatively, consider compiling the newest version instead: > http://www.xcrysden.org/download/xcrysden-1.5.53.tar.gz > > The compilation procedure has been improved and compilation should be > smoother. Use the ./system/Make.sys-semishared as a Make.sys, i.e.: > > 1. cp system/Make.sys-semishared Make.sys > 2. $EDITOR Make.sys ([optional]; EDITOR is an editor of your choice) > 3. make all > > 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 -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120313/ba1e4667/attachment-0001.htm From tone.kokalj at ijs.si Tue Mar 13 09:45:44 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 13 Mar 2012 09:45:44 +0100 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: References: ,,, ,,, <1331198000.4667.45.camel@catalyst.ijs.si> ,, ,, <1331277126.3610.6.camel@catalyst.ijs.si> , , <1331585213.25620.6.camel@catalyst.ijs.si> Message-ID: <1331628344.32270.10.camel@catalyst.ijs.si> On Tue, 2012-03-13 at 17:27 +0900, ???? ???? ????? wrote: > Dear Prof. Kokalj, > thank you very much for your help. > i had successfully compiled Xcrysden-1.5.53 ; however when i executed > the program for FERMI SURFACE rendering, it crashed just like the > previous version (the reason why i started to compile it again). > the error reads: > "*** glibc detected > *** /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys: free(): invalid > next size (normal): 0x000000001bf55700 *** Check if you have gdb debugger and if so, then compile xcrysden with enabled debugging (i.e. set CFLAGS = -g in Make.sys). Do: 1. make clean 2. make xcrysden 3. ./xcrysden -d and after crash say "where" in the gdb prompt. Perhaps the message will be informative. Send me the info. 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 arshadfarhan at hotmail.com Tue Mar 13 13:18:06 2012 From: arshadfarhan at hotmail.com (=?iso-8859-6?B?5c3lzyDH0dTPIOHRzcfm?=) Date: Tue, 13 Mar 2012 21:18:06 +0900 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: <1331628344.32270.10.camel@catalyst.ijs.si> References: ,,,, ,,,, <1331198000.4667.45.camel@catalyst.ijs.si>,,, ,,, <1331277126.3610.6.camel@catalyst.ijs.si>,, ,, <1331585213.25620.6.camel@catalyst.ijs.si>, , <1331628344.32270.10.camel@catalyst.ijs.si> Message-ID: dear prof. Kokalj,yes our system has gdb installed. i recompiled the package and it crashed again.this time command "WHERE" resulted in : "Program received signal SIGSEGV, Segmentation fault. 0x00000030c7873155 in _int_malloc () from /lib64/libc.so.6 (gdb) Quit (gdb) where #0 0x00000030c7873155 in _int_malloc () from /lib64/libc.so.6 #1 0x00000030c7874e2e in malloc () from /lib64/libc.so.6 #2 0x00000030c78754e8 in realloc () from /lib64/libc.so.6 #3 0x0000000000462b7a in xcRealloc (ptr=0x0, size=1336) at memory.c:47 #4 0x0000000000481480 in cryIsosurfClip (in=0x1184820, n=..., p0=...) at cryClip.c:236 #5 0x000000000047a969 in CropBz_New (wc=0x108b2c0, iso=0x108acb0) at fs.c:257 #6 0x0000000000480a33 in CRY_SurfCmd (clientData=0x778010, interp=0x737340, argc=26, argv=0x739aa0) at crySurf.c:540 #7 0x00002aaaab123fbf in TclInvokeStringCommand () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #8 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #9 0x00002aaaab167d70 in TclExecuteByteCode () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #10 0x00002aaaab1a79ad in TclObjInterpProcCore () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #11 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #12 0x00002aaaab167d70 in TclExecuteByteCode () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #13 0x00002aaaab1a79ad in TclObjInterpProcCore () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #14 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #15 0x00002aaaab126393 in Tcl_EvalObjv () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #16 0x00002aaaab1267f0 in TclEvalObjEx () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #17 0x00002aaaab1a8321 in Tcl_UplevelObjCmd () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #18 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #19 0x00002aaaab167d70 in TclExecuteByteCode () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #20 0x00002aaaab1a79ad in TclObjInterpProcCore () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #21 0x00002aaaab1251b9 in TclEvalObjvInternal () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #22 0x00002aaaab125e16 in TclEvalEx () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #23 0x00002aaaab126196 in Tcl_EvalEx () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #24 0x00002aaaaadf1da2 in Tk_BindEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so #25 0x00002aaaaae3394d in CanvasDoEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so #26 0x00002aaaaae345af in CanvasBindProc () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so #27 0x00002aaaaadfca24 in Tk_HandleEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so #28 0x00002aaaaadfcce0 in WindowEventProc () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so #29 0x00002aaaab19951d in Tcl_ServiceEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #30 0x00002aaaab19978e in Tcl_DoOneEvent () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtcl8.5.so #31 0x00002aaaaadfc24b in Tk_MainLoop () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so #32 0x00002aaaaae09827 in Tk_MainEx () from /home/mafarhan/programs/xcrysden-1.5.53/external/lib/libtk8.5.so #33 0x0000000000405a60 in main (argc=4, argv=0x7fffffffd368) at xcAppInit.c:412 "i don't know if this info points any where or not !Regards,M. Arshad Farhan > From: tone.kokalj at ijs.si > To: xcrysden at democritos.it > Date: Tue, 13 Mar 2012 09:45:44 +0100 > Subject: Re: [xcrysden] problem in compiling Xcrysden > > On Tue, 2012-03-13 at 17:27 +0900, ???? ???? ????? wrote: > > Dear Prof. Kokalj, > > thank you very much for your help. > > i had successfully compiled Xcrysden-1.5.53 ; however when i executed > > the program for FERMI SURFACE rendering, it crashed just like the > > previous version (the reason why i started to compile it again). > > the error reads: > > "*** glibc detected > > *** /home/mafarhan/programs/xcrysden-1.5.53/bin/xcrys: free(): invalid > > next size (normal): 0x000000001bf55700 *** > > Check if you have gdb debugger and if so, then compile xcrysden > with enabled debugging (i.e. set CFLAGS = -g in Make.sys). Do: > > 1. make clean > 2. make xcrysden > 3. ./xcrysden -d > > and after crash say "where" in the gdb prompt. Perhaps the message will > be informative. Send me the info. > > 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 -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120313/a8e55c25/attachment.htm From indu.chem.mind86 at gmail.com Tue Mar 13 13:41:21 2012 From: indu.chem.mind86 at gmail.com (Indu Kaul) Date: Tue, 13 Mar 2012 08:41:21 -0400 Subject: [xcrysden] Changing isosurface colour Message-ID: Hello Kokalj Sir, I tried resizing as u had mentioned in your reply. But it didn't work. I'm using ubuntu, version 11.04. -- With Regards Indu Kaul Department of Chemistry IISER Pune(MAHARASHTRA) INDIA From tone.kokalj at ijs.si Tue Mar 13 14:12:00 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 13 Mar 2012 14:12:00 +0100 Subject: [xcrysden] Changing isosurface colour In-Reply-To: References: Message-ID: <1331644320.32270.31.camel@catalyst.ijs.si> On Tue, 2012-03-13 at 08:41 -0400, Indu Kaul wrote: > Hello Kokalj Sir, > I tried resizing as u had mentioned in your reply. But it didn't work. > I'm using ubuntu, version 11.04. 32bit or 64bit? Which version of xcrysden you are using? 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 Tue Mar 13 14:15:50 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 13 Mar 2012 14:15:50 +0100 Subject: [xcrysden] problem in compiling Xcrysden In-Reply-To: References: ,,,, ,,,, <1331198000.4667.45.camel@catalyst.ijs.si> ,,, ,,, <1331277126.3610.6.camel@catalyst.ijs.si> ,, ,, <1331585213.25620.6.camel@catalyst.ijs.si> , ,<1331628344.32270.10.camel@catalyst.ijs.si> Message-ID: <1331644550.32270.32.camel@catalyst.ijs.si> On Tue, 2012-03-13 at 21:18 +0900, ???? ???? ????? wrote: > dear prof. Kokalj, > yes our system has gdb installed. i recompiled the package and it > crashed again. this time command "WHERE" resulted in : Yes, but this time we know where it crashed, yet code inspection reveals that there is nothing suspicious. This implies that memory corruption happened before the actual crash, hence finding the actual problem will be rather difficult. Would you tell me a bit more what precisely you were doing to get the crash, i.e., did you try the xcrysden's examples or you tried your own examples? If the latter applies, would you send me the Fermi surface (i.e. BXSF) file to my person email along with description of all the steps taken before the crash appeared. 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 emoujaes at fisica.ufmg.br Tue Mar 13 20:07:51 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Tue, 13 Mar 2012 16:07:51 -0300 Subject: [xcrysden] problems with installing XCRYSDEN-1.5.24-src-all again Message-ID: <20120313182723.M46680@proto.fisica.ufmg.br> Dear all, I want to apologize as I have bothered you a lot with my problems on installing XCrysden; i really want to thank you for all the help you are providing me with. I am trying to install XCrysden-1.5.24-src-all on a Debian LINUX machine. I came across a script (Make.sys where I have enabled possibility 2) that I have added to the folder where Xcrysden was extracted; this made use of make all followed by xcConfigure. make all is producing the following error: " gcc -ansi -funroll-loops -fPIC -DUSE_FONTS -DUSE_FONTS - I/home_cluster/fis718/eliemouj/XCrySDen-1.5.24-src- all/external/src/tcl8.5.9/generic -I/home_cluster/fis718/eliemouj/XCrySDen- 1.5.24-src-all/external/src/tk8.5.9/generic - I/home_cluster/fis718/eliemouj/XCrySDen-1.5.24-src-all/external/include - I/usr/X11R6/include -c fft3d.c fft3d.c:4:19: error: fftw3.h: No such file or directory In file included from fft3d.c:6: shankland.h:4:30: error: meschach/matrix2.h: No such file or directory In file included from fft3d.c:6: shankland.h:49: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:49: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:50: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:50: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:62: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:64: error: expected declaration specifiers or ?...? before ?fftw_complex? shankland.h:65: error: expected declaration specifiers or ?...? before ?MAT? shankland.h:68: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?*? token shankland.h:69: error: expected declaration specifiers or ?...? before ?MAT? fft3d.c: In function ?fft3d_interpolate?: fft3d.c:88: error: ?fftw_complex? undeclared (first use in this function) fft3d.c:88: error: (Each undeclared identifier is reported only once fft3d.c:88: error: for each function it appears in.) fft3d.c:88: error: ?aux? undeclared (first use in this function) fft3d.c:88: error: ?fftw2? undeclared (first use in this function) fft3d.c:89: error: ?fftw_plan? undeclared (first use in this function) fft3d.c:89: error: expected ?;? before ?pfor? fft3d.c:96: error: expected expression before ?)? token fft3d.c:97: error: expected expression before ?)? token fft3d.c:99: error: ?pfor? undeclared (first use in this function) fft3d.c:99: error: ?FFTW_ESTIMATE? undeclared (first use in this function) fft3d.c:100: error: ?pbak? undeclared (first use in this function) fft3d.c:110: error: too many arguments to function ?fft3d_enlarge_complex_r2c? make[2]: *** [fft3d.o] Error 1 make[2]: Leaving directory `/home_cluster/fis718/eliemouj/XCrySDen-1.5.24-src- all/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home_cluster/fis718/eliemouj/XCrySDen-1.5.24-src- all/C' make: *** [src-C] Error 2 " then when executing xcrysden I get another error: "TCL_LIBRARY=/home_cluster/fis718/eliemouj/XCrySDen-1.5.24-src- all/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home_cluster/fis718/eliemouj/XCrySDen-1.5.24-src-all XCRYSDEN_SCRATCH=/home_cluster/fis718/eliemouj/xcrys_tmp /home_cluster/fis718/eliemouj/XCrySDen-1.5.24-src-all/xcrysden: line 224: /home_cluster/fis718/eliemouj/XCrySDen-1.5.24-src-all/bin/xcrys: No such file or directory " Well the make all error could be due to missing headers due to the missing libxmu. Is there a way to install these without using sudo as I dont have access to this..I tried adding MESCHACH_LIB= -L/opt/local/lib -lmeschach FFTW3_LIB = -L/opt/local/lib -lfftw3 but this also did not work. As to the second erro, the "xcrys" file is not in bin..Please any help on this..I spent almost 3 days just trying to install it..I appreciate it a lot Regards Elie -- Departamento de Fisica - UFMG/ICEx -------------- next part -------------- A non-text attachment was scrubbed... Name: Make.sys Type: application/octet-stream Size: 3152 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20120313/a599549e/attachment-0001.obj From tone.kokalj at ijs.si Tue Mar 13 21:49:49 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 13 Mar 2012 21:49:49 +0100 Subject: [xcrysden] problems with installing XCRYSDEN-1.5.24-src-all again In-Reply-To: <20120313182723.M46680@proto.fisica.ufmg.br> References: <20120313182723.M46680@proto.fisica.ufmg.br> Message-ID: <1331671789.24374.7.camel@catalyst.ijs.si> On Tue, 2012-03-13 at 16:07 -0300, Elie Albert Moujaes wrote: > Dear all, > > I want to apologize as I have bothered you a lot with my problems on > installing XCrysden; i really want to thank you for all the help you are > providing me with. I am trying to install XCrysden-1.5.24-src-all on a Debian > LINUX machine. Since yesterday, xcrysden is in Debian Sid (unstable), see: http://packages.debian.org/unstable/main/xcrysden http://packages.debian.org/sid/xcrysden-data If you use Debian Sid (aka unstable), you may install simply as: apt-get install xcrysden Alternatively, consider compiling this package: http://www.xcrysden.org/download/xcrysden-1.5.53.tar.gz it should compile smoothly on Debian. It needs the following packages: libfftw3-dev, tk8.5-dev, tcl8.5-dev, libgl1-mesa-dev, libglu1-mesa-dev, libxmu-headers, libxmu-dev, libx11-dev, libgcc1, gfortran. Most of these are probably already install, check with dpkg -l. 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 indu.chem.mind86 at gmail.com Wed Mar 14 12:44:42 2012 From: indu.chem.mind86 at gmail.com (Indu Kaul) Date: Wed, 14 Mar 2012 07:44:42 -0400 Subject: [xcrysden] Changing colour of isosurface Message-ID: Hello Kokalj Sir, Sorry I forgot to add xcrysden version in my last mail. I am using a 64-bit machine with ubuntu(11.04) . The xcrysden version is 1.5.25-linux_x86_64-semishared. -- With Regards Indu Kaul Department of Chemistry IISER Pune(MAHARASHTRA) INDIA From emoujaes at fisica.ufmg.br Wed Mar 14 18:25:46 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Wed, 14 Mar 2012 14:25:46 -0300 Subject: [xcrysden] problems with installing XCRYSDEN-1.5.24-src-all again In-Reply-To: <1331671789.24374.7.camel@catalyst.ijs.si> References: <20120313182723.M46680@proto.fisica.ufmg.br> <1331671789.24374.7.camel@catalyst.ijs.si> Message-ID: <20120314172415.M55961@proto.fisica.ufmg.br> Thanks a lot for your help. I guess there is still something missing; when I run xcrysden I get: " /home_cluster/fis718/eliemouj/xcrysden-1.5.53-bin-semishared/bin/xcrys: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home_cluster/fis718/eliemouj/xcrysden-1.5.53-bin-semishared/bin/xcrys) /home_cluster/fis718/eliemouj/xcrysden-1.5.53-bin-semishared/bin/xcrys: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home_cluster/fis718/eliemouj/xcrysden-1.5.53-bin- semishared/external/lib/libtk8.5.so) /home_cluster/fis718/eliemouj/xcrysden-1.5.53-bin-semishared/bin/xcrys: /lib64/libc.so.6: version `GLIBC_2.7' not found (required by /home_cluster/fis718/eliemouj/xcrysden-1.5.53-bin- semishared/external/lib/libtcl8.5.so)" where can I get the GLIB_2.7 or call for it? Thanks a lot again Elie On Tue, 13 Mar 2012 21:49:49 +0100, Tone Kokalj wrote > On Tue, 2012-03-13 at 16:07 -0300, Elie Albert Moujaes wrote: > > Dear all, > > > > I want to apologize as I have bothered you a lot with my problems on > > installing XCrysden; i really want to thank you for all the help you are > > providing me with. I am trying to install XCrysden-1.5.24-src-all on a Debian > > LINUX machine. > > Since yesterday, xcrysden is in Debian Sid (unstable), see: > http://packages.debian.org/unstable/main/xcrysden > http://packages.debian.org/sid/xcrysden-data > > If you use Debian Sid (aka unstable), you may install simply as: > > apt-get install xcrysden > > Alternatively, consider compiling this package: > http://www.xcrysden.org/download/xcrysden-1.5.53.tar.gz > > it should compile smoothly on Debian. It needs the following > packages: libfftw3-dev, tk8.5-dev, tcl8.5-dev, libgl1-mesa-dev, > libglu1-mesa-dev, libxmu-headers, libxmu-dev, libx11-dev, libgcc1, > gfortran. Most of these are probably already install, check with > dpkg -l. > > 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 -- Departamento de Fisica - UFMG/ICEx From emoujaes at fisica.ufmg.br Wed Mar 14 20:58:19 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Wed, 14 Mar 2012 16:58:19 -0300 Subject: [xcrysden] problems with installing XCRYSDEN-1.5.24-src-all again In-Reply-To: <1331671789.24374.7.camel@catalyst.ijs.si> References: <20120313182723.M46680@proto.fisica.ufmg.br> <1331671789.24374.7.camel@catalyst.ijs.si> Message-ID: <20120314195126.M44031@proto.fisica.ufmg.br> Dear Tone, I have looked the error up and knew that I need to install an older version of XCrysden (I have actually installed XCrySDen-1.5.21-bin-semishared). When I run xcrysden I get the DISPLAY problem again mainly: "TCL_LIBRARY=/home_cluster/fis718/eliemouj/XCrySDen-1.5.21-bin- semishared/external/lib/tcl8.5 XCRYSDEN_TOPDIR=/home_cluster/fis718/eliemouj/XCrySDen-1.5.21-bin-semishared XCRYSDEN_SCRATCH=/home_cluster/fis718/eliemouj/xcrys_tmp Application initialization failed: no display name and no $DISPLAY environment variable Error in startup script: can't read "xcrys(platform)": no such variable while executing "if { $xcrys(platform) == "windows" } { # testing ... rename exec _tcl_exec proc exec {args} { global env # first try a normal exec..." (file "/home_cluster/fis718/eliemouj/XCrySDen-1.5.21-bin- semishared/Tcl/cygwin.tcl" line 19) invoked from within......." which is a problem of setting the DISPLAY parameter which when I write echo $DISPLAY, it displays nothing. To what should this parameter be set or how can I solve this problem. The system is LINUX and not windows. Sorry to bother you with this but it seems with all version, I am getting problems (though this last one is a an X platform one.. Regards Elie On Tue, 13 Mar 2012 21:49:49 +0100, Tone Kokalj wrote > On Tue, 2012-03-13 at 16:07 -0300, Elie Albert Moujaes wrote: > > Dear all, > > > > I want to apologize as I have bothered you a lot with my problems on > > installing XCrysden; i really want to thank you for all the help you are > > providing me with. I am trying to install XCrysden-1.5.24-src-all on a Debian > > LINUX machine. > > Since yesterday, xcrysden is in Debian Sid (unstable), see: > http://packages.debian.org/unstable/main/xcrysden > http://packages.debian.org/sid/xcrysden-data > > If you use Debian Sid (aka unstable), you may install simply as: > > apt-get install xcrysden > > Alternatively, consider compiling this package: > http://www.xcrysden.org/download/xcrysden-1.5.53.tar.gz > > it should compile smoothly on Debian. It needs the following > packages: libfftw3-dev, tk8.5-dev, tcl8.5-dev, libgl1-mesa-dev, > libglu1-mesa-dev, libxmu-headers, libxmu-dev, libx11-dev, libgcc1, > gfortran. Most of these are probably already install, check with > dpkg -l. > > 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 -- Departamento de Fisica - UFMG/ICEx From tone.kokalj at ijs.si Thu Mar 15 10:32:37 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 15 Mar 2012 10:32:37 +0100 Subject: [xcrysden] Changing colour of isosurface In-Reply-To: References: Message-ID: <1331803957.3561.30.camel@catalyst.ijs.si> On Wed, 2012-03-14 at 07:44 -0400, Indu Kaul wrote: > Hello Kokalj Sir, > Sorry I forgot to add xcrysden version in my last mail. > I am using a 64-bit machine with ubuntu(11.04) . The xcrysden version > is 1.5.25-linux_x86_64-semishared. OK, you are using relatively recent version of both. I don't know what is the cause (perhaps bad interaction between window manager and xcrysden). What is the window manager (or desktop environment) you are using (gnome, xfce, kde)? Since you are using ubuntu, perhaps you may try to install the corresponding Debian packages (see the mailing-list email from a few days ago), i.e., wget http://ftp.debian.org/debian/pool/main/x/xcrysden/xcrysden_1.5.52-1_amd64.deb wget http://ftp.us.debian.org/debian/pool/main/x/xcrysden/xcrysden-data_1.5.52-1_all.deb sudo dpkg -i xcrysden-data_1.5.52-1_all.deb xcrysden_1.5.52-1_amd64.deb I' don't know, but perhaps they may behave differently. 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 Thu Mar 15 10:34:21 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 15 Mar 2012 10:34:21 +0100 Subject: [xcrysden] problems with installing XCRYSDEN-1.5.24-src-all again In-Reply-To: <20120314172415.M55961@proto.fisica.ufmg.br> References: <20120313182723.M46680@proto.fisica.ufmg.br> <1331671789.24374.7.camel@catalyst.ijs.si> <20120314172415.M55961@proto.fisica.ufmg.br> Message-ID: <1331804061.3561.32.camel@catalyst.ijs.si> On Wed, 2012-03-14 at 14:25 -0300, Elie Albert Moujaes wrote: > Thanks a lot for your help. I guess there is still something missing; when I > run xcrysden I get: > > " > /home_cluster/fis718/eliemouj/xcrysden-1.5.53-bin-semishared/bin/xcrys: > /lib64/libc.so.6: version `GLIBC_2.7' not found (required by > /home_cluster/fis718/eliemouj/xcrysden-1.5.53-bin-semishared/b Nothing is missing, but seems like you are using too old version of debian, which has too old libc to be compatible with the xcrysden-1.5.53-bin-semishared. You may consider to compile the source version instead. 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 Mar 15 10:39:06 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 15 Mar 2012 10:39:06 +0100 Subject: [xcrysden] problems with installing XCRYSDEN-1.5.24-src-all again In-Reply-To: <20120314195126.M44031@proto.fisica.ufmg.br> References: <20120313182723.M46680@proto.fisica.ufmg.br> <1331671789.24374.7.camel@catalyst.ijs.si> <20120314195126.M44031@proto.fisica.ufmg.br> Message-ID: <1331804346.3561.36.camel@catalyst.ijs.si> On Wed, 2012-03-14 at 16:58 -0300, Elie Albert Moujaes wrote: > Dear Tone, > > I have looked the error up and knew that I need to install an older version of > XCrysden (I have actually installed XCrySDen-1.5.21-bin-semishared). When I > run xcrysden I get the DISPLAY problem again mainly: > > "TCL_LIBRARY=/home_cluster/fis718/eliemouj/XCrySDen-1.5.21-bin- > semishared/external/lib/tcl8.5 > XCRYSDEN_TOPDIR=/home_cluster/fis718/eliemouj/XCrySDen-1.5.21-bin-semishared > XCRYSDEN_SCRATCH=/home_cluster/fis718/eliemouj/xcrys_tmp > > Application initialization failed: no display name and no $DISPLAY environment > variable OK, now you get it working. The problem you are facing can be caused by, say, two possibilities: 1. you are not running X-window 2. you tried to run xcrysden remotely (this is not recommended, because a remote running is very slow). But if you insist then you need to enable X11 forwarding, e.g., use ssh -X option. 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 Lorenzo.Paulatto at impmc.upmc.fr Thu Mar 15 10:54:03 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Thu, 15 Mar 2012 10:54:03 +0100 Subject: [xcrysden] problems with installing XCRYSDEN-1.5.24-src-all again In-Reply-To: <1331804346.3561.36.camel@catalyst.ijs.si> References: <20120313182723.M46680@proto.fisica.ufmg.br> <1331671789.24374.7.camel@catalyst.ijs.si> <20120314195126.M44031@proto.fisica.ufmg.br> <1331804346.3561.36.camel@catalyst.ijs.si> Message-ID: On Thu, 15 Mar 2012 10:39:06 +0100, Tone Kokalj wrote: > 1. you are not running X-window > > 2. you tried to run xcrysden remotely (this is not recommended, because > a remote running is very slow). But if you insist then you need to > enable X11 forwarding, e.g., use ssh -X option. 3. you are trying to run xcrysden as root on some system (i.e. suse linux) Anyway, if you are in case 2, i would suggest you to use sshfs instead. bests -- Lorenzo Paulatto IdR @ IMPMC/UPMC CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www.impmc.upmc.fr/~paulatto/ mail: 23-24/4?14 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From emoujaes at fisica.ufmg.br Thu Mar 15 18:00:59 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Thu, 15 Mar 2012 14:00:59 -0300 Subject: [xcrysden] problems with installing XCRYSDEN-1.5.24-src-all again In-Reply-To: <1331804346.3561.36.camel@catalyst.ijs.si> References: <20120313182723.M46680@proto.fisica.ufmg.br> <1331671789.24374.7.camel@catalyst.ijs.si> <20120314195126.M44031@proto.fisica.ufmg.br> <1331804346.3561.36.camel@catalyst.ijs.si> Message-ID: <20120315165934.M98416@proto.fisica.ufmg.br> Thanks very much for your help. I was able to solve everything by connecting PuTTy to Xming and filling in the correct X display parameters. Now XCrySDen works perfectly well. Regards Elie On Thu, 15 Mar 2012 10:39:06 +0100, Tone Kokalj wrote > On Wed, 2012-03-14 at 16:58 -0300, Elie Albert Moujaes wrote: > > Dear Tone, > > > > I have looked the error up and knew that I need to install an older version of > > XCrysden (I have actually installed XCrySDen-1.5.21-bin-semishared). When I > > run xcrysden I get the DISPLAY problem again mainly: > > > > "TCL_LIBRARY=/home_cluster/fis718/eliemouj/XCrySDen-1.5.21-bin- > > semishared/external/lib/tcl8.5 > > XCRYSDEN_TOPDIR=/home_cluster/fis718/eliemouj/XCrySDen-1.5.21-bin- semishared > > XCRYSDEN_SCRATCH=/home_cluster/fis718/eliemouj/xcrys_tmp > > > > Application initialization failed: no display name and no $DISPLAY environment > > variable > > OK, now you get it working. The problem you are facing can be caused > by, say, two possibilities: > > 1. you are not running X-window > > 2. you tried to run xcrysden remotely (this is not recommended, because > a remote running is very slow). But if you insist then you need to > enable X11 forwarding, e.g., use ssh -X option. > > 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 > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Departamento de Fisica - UFMG/ICEx From emoujaes at fisica.ufmg.br Fri Mar 16 21:51:35 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Fri, 16 Mar 2012 17:51:35 -0300 Subject: [xcrysden] simple question about building supercells Message-ID: <20120316204519.M14952@proto.fisica.ufmg.br> Dear XCrySDen users, I was wondering if XCrySDen can build supercells ,if the atoms per unit cell of the system and lattice vectors are given. If not , any program you know of that can create supercells and display the atomic positions in the supercell.. (I want to build a supercell for monolayer and bilayer graphene). Regards Elie M University of Nott NG7 2RD UK -- Departamento de Fisica - UFMG/ICEx From aladin331 at yahoo.com Sat Mar 17 07:29:27 2012 From: aladin331 at yahoo.com (Aladin Hamid) Date: Fri, 16 Mar 2012 23:29:27 -0700 (PDT) Subject: [xcrysden] Fermi surface visualization Message-ID: <1331965767.84908.YahooMailNeo@web161406.mail.bf1.yahoo.com> Dear All I'm working with the electronic structure and Femri surface of CoSi2 using the WIEN2K code. I have finished the SCF run and get both DOS and Band structure calculation. Now I want to visualize the Fermi surface. Therefore, I installed xcrysden (1.4 static) under REDHAT linux 5.1. My qustions are; Which file of the WIEN2K should I use to get the (3D-bandgrid)?Fermi surface using the xcrysden? How can I use it? please let me know Sincerely Alaa S Hamid Associate prof. of Physics Hewan University, Cairo, Egypt P.O. Box 12912 Tel. (Work) + 202-3800050 (8050) mob. +202-0552006051 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120316/a65faa00/attachment.htm From masoudnahali at gmail.com Wed Mar 21 11:01:44 2012 From: masoudnahali at gmail.com (m) Date: Wed, 21 Mar 2012 14:31:44 +0430 Subject: [xcrysden] Atoms Info Message-ID: Hi XCrysden shows the atomic information correct in "Bohr" unit but it seems that there is something wrong with "Alat" unit. In the following input file I have used "alat" coordinates and XCrysden converts it correctly to "Bohr" even so it doesn't show the coordinates in "alat" units correctly. input: ibrav=0 celldm(1)=2.75899995 ATOMIC_POSITIONS {alat} C 0.50000000 4.33012711 0.00000000 CELL_PARAMETERS hexagonal 9.00000000 0.00000000 0.00000000 -9.13695958 15.82567816 0.00000000 0.00000000 0.00000000 10.27391917 XCrysden's Atoms Info: Display Coordinates in Units Bohr : 1.3794999974 11.946820480 0.00000000 (0.5*2.75899995) (4.33012711*2.75899995) (0.0*0.0) Alat : 0.055555556 0.481125234 0.00000000 I appreciate your reply in advance. Best Wishes, m ---------------------------------------- Masoud Nahali, Ph. D Student International School for Advanced Studies (SISSA) Sharif University of Technology masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120321/bfa8f469/attachment.htm From tone.kokalj at ijs.si Wed Mar 21 11:18:26 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 21 Mar 2012 11:18:26 +0100 Subject: [xcrysden] Fermi surface visualization In-Reply-To: <1331965767.84908.YahooMailNeo@web161406.mail.bf1.yahoo.com> References: <1331965767.84908.YahooMailNeo@web161406.mail.bf1.yahoo.com> Message-ID: <1332325106.15551.2.camel@catalyst.ijs.si> On Fri, 2012-03-16 at 23:29 -0700, Aladin Hamid wrote: > Dear All > I'm working with the electronic structure and Femri surface of CoSi2 > using the WIEN2K code. I have finished the SCF run and get both DOS > and Band structure calculation. Now I want to visualize the Fermi > surface. Therefore, I installed xcrysden (1.4 static) under REDHAT > linux 5.1. 1.4.1 is rather out of date. You should install something newer from: http://www.xcrysden.org/Download.html > My qustions are; > Which file of the WIEN2K should I use to get the (3D-bandgrid) Fermi > surface using the xcrysden? > How can I use it? > please let me know Here you may find some info: http://www.xcrysden.org/doc/wien.html in particular: http://www.xcrysden.org/doc/wien.html#__toc__11 Further useful info may also be obtained by searching the [Wien] mailing list about this issue. 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 Wed Mar 21 11:24:27 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 21 Mar 2012 11:24:27 +0100 Subject: [xcrysden] simple question about building supercells In-Reply-To: <20120316204519.M14952@proto.fisica.ufmg.br> References: <20120316204519.M14952@proto.fisica.ufmg.br> Message-ID: <1332325467.15551.8.camel@catalyst.ijs.si> On Fri, 2012-03-16 at 17:51 -0300, Elie Albert Moujaes wrote: > Dear XCrySDen users, > > I was wondering if XCrySDen can build supercells ,if the atoms per unit cell of > the system and lattice vectors are given. If not , any program you know of that > can create supercells and display the atomic positions in the supercell.. (I > want to build a supercell for monolayer and bilayer graphene). XCrySDen can build simple {N}x{M}x{K} type of supercells. To correctly extract the atoms within the supercell do the following: 1. generate the supercell via menu: Modify-->Number of units drawn 2. change unit of repetition to translational asymmetric unit via menu Display-->Unit of repetition ...-->Translation asymmetric unit 3, save the XSF file via: File-->Save XSF structure Then in the so generated file the atoms within the supercell are printed in the "ATOMS" section. 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 Wed Mar 21 11:31:12 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 21 Mar 2012 11:31:12 +0100 Subject: [xcrysden] Atoms Info In-Reply-To: References: Message-ID: <1332325872.15551.14.camel@catalyst.ijs.si> On Wed, 2012-03-21 at 14:31 +0430, m wrote: > > > Hi > > > XCrysden shows the atomic information correct in "Bohr" unit but it > seems that there is something wrong with "Alat" unit. No, it is not. Note that "alat" units means: units of A-LATtice-parameter (i.e. length of A lattice vector) and you may check that this is what you get in xcrysden. Note that in Quantum-Espresso the meaning of "alat" is extended/misused in case of custom-lattice specification (ibrav=0), because in this case alat refers to units of celldm(1) and not to units of "length of a lattice vector". > ibrav=0 > celldm(1)=2.75899995 > CELL_PARAMETERS hexagonal > 9.00000000 0.00000000 0.00000000 > -9.13695958 15.82567816 0.00000000 > 0.00000000 0.00000000 10.27391917 Note that in your case the alat (in strict sense) is 9 times larger than the celldm(1). 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 masoudnahali at gmail.com Wed Mar 21 12:10:38 2012 From: masoudnahali at gmail.com (m) Date: Wed, 21 Mar 2012 15:40:38 +0430 Subject: [xcrysden] Atoms Info Message-ID: > > Note that in Quantum-Espresso the meaning of "alat" is extended/misused > in case of custom-lattice specification (ibrav=0), because in this case > alat refers to units of celldm(1) and not to units of "length of a > lattice vector". Yes, there is a difference between the "alat" in Quantum Espresso and XCrysden when "ibrav=0" is used. And I meant may be it should be considered by XCrysden when reads such cases. Best Wishes, m ---------------------------------------- Masoud Nahali, Ph. D Student International School for Advanced Studies (SISSA) Sharif University of Technology masoud.nahali at gmail.com alum.sharif.edu/~m_nahali -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120321/bd646831/attachment.htm From tone.kokalj at ijs.si Wed Mar 21 12:17:54 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 21 Mar 2012 12:17:54 +0100 Subject: [xcrysden] Atoms Info In-Reply-To: References: Message-ID: <1332328674.15551.32.camel@catalyst.ijs.si> On Wed, 2012-03-21 at 15:40 +0430, m wrote: > > Yes, there is a difference between the "alat" in Quantum Espresso > and XCrysden when "ibrav=0" is used. > And I meant may be it should be considered by XCrysden when reads > such cases. That would be rather tricky. Note that the pipeline is: pw.x input --> XSF --> xcrysden and in XSF there are only lattice vectors + atoms (hence the information about the precise pw.x spec is lost in conversion to XSF). 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 indu.chem.mind86 at gmail.com Thu Mar 22 06:31:27 2012 From: indu.chem.mind86 at gmail.com (Indu Kaul) Date: Thu, 22 Mar 2012 11:01:27 +0530 Subject: [xcrysden] Installation of XCrysden in Ubuntu 10.04 Message-ID: Hi, Iam trying to install xcrysden1.5. source package in my PC with OS ubuntu-10.04(64bit). On confuguring ./xcConfigure.sh , it is not generating the bin directory. Same is the case with Xcrysden1.4. Can someone help me out to install xcrysden ? Is there some compatibility problem of xcysden with ubuntu? Thanks in advance for tips and suggestions -- With Regards Indu Kaul Department of Chemistry IISER Pune(MAHARASHTRA) INDIA -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120322/0ad441f9/attachment.htm From tone.kokalj at ijs.si Thu Mar 22 09:15:15 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 22 Mar 2012 09:15:15 +0100 Subject: [xcrysden] Installation of XCrysden in Ubuntu 10.04 In-Reply-To: References: Message-ID: <1332404115.23497.3.camel@catalyst.ijs.si> On Thu, 2012-03-22 at 11:01 +0530, Indu Kaul wrote: > Hi, > > Iam trying to install xcrysden1.5. source package in my PC with OS > ubuntu-10.04(64bit). On confuguring ./xcConfigure.sh , it is not > generating the bin directory. The source package should be compiled first (xcConfigure.sh does not compile and moreover its use is deprecated in newest version(s)). You may consider to compile the newest version, which should compile easier: http://www.xcrysden.org/download/xcrysden-1.5.53.tar.gz Read the "compilation" instructions in the README file therein. 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 quanyundi at gmail.com Sat Mar 31 05:13:17 2012 From: quanyundi at gmail.com (Yundi Quan) Date: Fri, 30 Mar 2012 20:13:17 -0700 Subject: [xcrysden] wien2k fermi surface Message-ID: Dear Sir/Madam, Support for WIEN2k Fermi surface calculation in Xcrysden is a good feature. But the documentation for Fermi surface calculation is somewhat limited. What are the purposes of "Generate k-mesh", "change to unit 5 in case.in1". "Edit TiO2.in1 file(optional". In the wien2k calculation, I already have a kmesh. Does "Generate k mesh" mean that the kmesh used in Fermi surface calculation can be different from the kmesh used in WIEN2k scf calculation? If I use "generate k-mesh" and "change to unit 5 in case.in1", I will always get an error message saying that " 'FERMI' - number of k-points inconsistent when reading kgen 'FERMI' - check IN1 and KGEN files! If I do not use "generate k-mesh" or "change to unit 5 in case.in1", then I do not get any error messages. Any help is much appreciated. Yundi -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120330/63a19203/attachment.htm