From wenzhi_wu at 163.com Tue Oct 2 07:22:40 2012 From: wenzhi_wu at 163.com (=?GBK?B?zuLOxNa+?=) Date: Tue, 2 Oct 2012 13:22:40 +0800 (CST) Subject: [xcrysden] tone.kokalj@ijs.si Message-ID: <6c7d75f6.526f.13a1fed104b.Coremail.wenzhi_wu@163.com> Dear Tone,I was trying to install xcrysden-1.5.53-cygwin on Windows 7(64-bit) using the new cygwin installations. Everythings works fine, but when I call for the program with the command ./xcrysden, the graphics of xcrysden appear, but it returns me this error at the same time:ERROR:while executing exec /home/wuwz/xcrysden-1.5.53-bin-cygwin/bin/ftnuit(the error info is: couldn?t fork child process:resource temporarily unavailable). And the xcrysden does not work.I am very much depressed. Could you kindly help me,please? Thank you very much in advance. Sincerely,WenzhiWhen I tried to install from the xcrysden-1.5.53-cygwin.tar.gz, I got:$ ./xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2012 by Anton Kokalj *| |* *| |*****************************************************************| +-----------------------------------------------------------------+ Version: 1.5.53 Please report bugs to: tone.kokalj at ijs.si TERMS OF USE: ------------- XCRYSDEN is released under the GNU General Public License. Whenever graphics generated by XCRYSDEN are used in scientific publications, it shall be greatly appreciated to include an explicit reference. The preferred form is the following: [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003. Code available from http://www.xcrysden.org/. XCRYSDEN_TOPDIR=/home/wuwz/xcrysden-1.5.53-bin-cygwin XCRYSDEN_SCRATCH=/tmp Running on platform : unix Operating system : CYGWIN_NT-6.1-WOW64 0 [main] xcrys 31816 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x510000) 0 [main] xcrys 32496 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x610000) 0 [main] xcrys 29176 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x510000) 0 [main] xcrys 31492 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x620000) Package Ppmtompeg: /usr/bin/ppmtompeg Package Xwd: /usr/bin/xwd Executing: /home/wuwz/xcrysden-1.5.53-bin-cygwin/bin/ftnunit 0 [main] xcrys 30156 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x510000) TEXT-WIDGET: .a0.f1.t XCrySDen has received the following signal: Interupt (2) Deleting directory: /tmp/xc_32324 ... Quit ! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20121002/4fd895a7/attachment.htm From wenzhi_wu at 163.com Tue Oct 2 07:27:42 2012 From: wenzhi_wu at 163.com (=?GBK?B?zuLOxNa+?=) Date: Tue, 2 Oct 2012 13:27:42 +0800 (CST) Subject: [xcrysden] xcrysden-1.5.53-cygwin ERROR:while executing exec /home/wuwz/xcrysden-1.5.53-bin-cygwin/bin/ftnuit Message-ID: <193077eb.52a0.13a1ff1aa94.Coremail.wenzhi_wu@163.com> Dear Tone,I was trying to install xcrysden-1.5.53-cygwin on Windows 7(64-bit) using the new cygwin installations. Everythings works fine, but when I call for the program with the command ./xcrysden, the graphics of xcrysden appear, but it returns me this error at the same time:ERROR:while executing exec /home/wuwz/xcrysden-1.5.53-bin-cygwin/bin/ftnuit(the error info is: couldn?t fork child process:resource temporarily unavailable). And the xcrysden does not work.I am very much depressed. Could you kindly help me,please? Thank you very much in advance. Sincerely,WenzhiWhen I tried to install from the xcrysden-1.5.53-cygwin.tar.gz, I got:$ ./xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2012 by Anton Kokalj *| |* *| |*****************************************************************| +-----------------------------------------------------------------+ Version: 1.5.53 Please report bugs to: tone.kokalj at ijs.si TERMS OF USE: ------------- XCRYSDEN is released under the GNU General Public License. Whenever graphics generated by XCRYSDEN are used in scientific publications, it shall be greatly appreciated to include an explicit reference. The preferred form is the following: [ref] A. Kokalj, Comp. Mater. Sci., Vol. 28, p. 155, 2003. Code available from http://www.xcrysden.org/. XCRYSDEN_TOPDIR=/home/wuwz/xcrysden-1.5.53-bin-cygwin XCRYSDEN_SCRATCH=/tmp Running on platform : unix Operating system : CYGWIN_NT-6.1-WOW64 0 [main] xcrys 31816 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x510000) 0 [main] xcrys 32496 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x610000) 0 [main] xcrys 29176 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x510000) 0 [main] xcrys 31492 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x620000) Package Ppmtompeg: /usr/bin/ppmtompeg Package Xwd: /usr/bin/xwd Executing: /home/wuwz/xcrysden-1.5.53-bin-cygwin/bin/ftnunit 0 [main] xcrys 30156 child_info_fork::abort: C:\cygwin\bin\libtcl8.5.dll: Loaded to different address: parent(0x630000) != child(0x510000) TEXT-WIDGET: .a0.f1.t XCrySDen has received the following signal: Interupt (2) Deleting directory: /tmp/xc_32324 ... Quit ! -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20121002/337f21b9/attachment.htm From tone.kokalj at ijs.si Thu Oct 4 18:42:12 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 04 Oct 2012 18:42:12 +0200 Subject: [xcrysden] Reg: Polyhedrons in xcrysden In-Reply-To: References: Message-ID: <1349368932.4405.15.camel@catalyst.ijs.si> On Fri, 2012-09-28 at 23:49 -0700, vijaykumar gudelli wrote: > Dear xcrysden users, > > I'm using XCrSDen-1.4.1bin-static version, This is very outdated version, why don't you try the newer 1.5.53 version. > I just want to ask one question regarding crystal structure option. > Can we plot polyhedron for the crystal structures using xcrysden? No; this feature is not implemented. 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 Oct 4 18:47:38 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 04 Oct 2012 18:47:38 +0200 Subject: [xcrysden] xcrysden-1.5.53-cygwin ERROR:while executing exec /home/wuwz/xcrysden-1.5.53-bin-cygwin/bin/ftnuit In-Reply-To: <193077eb.52a0.13a1ff1aa94.Coremail.wenzhi_wu@163.com> References: <193077eb.52a0.13a1ff1aa94.Coremail.wenzhi_wu@163.com> Message-ID: <1349369258.4405.17.camel@catalyst.ijs.si> On Tue, 2012-10-02 at 13:27 +0800, ??? wrote: > Dear Tone, > I was trying to install xcrysden-1.5.53-cygwin on Windows 7(64-bit) using the new cygwin installations. Everythings works fine, > but when I call for the program with the command ./xcrysden, the graphics of xcrysden appear, but it returns me this error at the > same time:ERROR:while executing exec /home/wuwz/xcrysden-1.5.53-bin-cygwin/bin/ftnuit(the error info is: couldn?t fork child process:resource temporarily unavailable). And the xcrysden does not work. > I am very much depressed. Could you kindly help me,please? I believe that this error is of similar typo to this: http://www.democritos.it/pipermail/xcrysden/2012-May/001179.html 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 vkgudelli at gmail.com Thu Oct 11 18:25:25 2012 From: vkgudelli at gmail.com (vijaykumar gudelli) Date: Thu, 11 Oct 2012 21:55:25 +0530 Subject: [xcrysden] Reg: Fermi surface plot Message-ID: Dear users, I am using the Xcrysden to plot the Fermi surface. But I am getting some error. I can able to plot the Fermi surface for 44*44*44 k-mesh. But I just want to do the same for higher mesh. When I'm using 58*58*58 k-mesh I am getting error like *error while executing exec...... wn_readbakgen bakgen.def * Can anyone help to resolve this problem. Thanks in advance. -- *Regards* VIJAY KUMAR GUDELLI -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20121011/b71fb7d1/attachment.htm From pblaha at theochem.tuwien.ac.at Fri Oct 12 08:50:54 2012 From: pblaha at theochem.tuwien.ac.at (Peter Blaha) Date: Fri, 12 Oct 2012 08:50:54 +0200 Subject: [xcrysden] Reg: Fermi surface plot In-Reply-To: References: Message-ID: <5077BDCE.4020101@theochem.tuwien.ac.at> I did not check it myself, but probably in wn_readbakgen.f there are some fixed dimensions of some arrays limiting the size of the k-mesh. Check the source code and eventually recompile with larger dimensions. Am 11.10.2012 18:25, schrieb vijaykumar gudelli: > Dear users, > I am using the Xcrysden to plot the Fermi surface. > But I am getting some error. > I can able to plot the Fermi surface for 44*44*44 k-mesh. > But I just want to do the same for higher mesh. When I'm using 58*58*58 > k-mesh I am getting error like > > *error while executing exec...... wn_readbakgen bakgen.def > > * Can anyone help to resolve this problem. > Thanks in advance. > > > -- _Regards_ > > > VIJAY KUMAR GUDELLI > > > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Peter Blaha Inst.Materials Chemistry TU Vienna Getreidemarkt 9 A-1060 Vienna Austria +43-1-5880115671 From dstrubbe at civet.berkeley.edu Tue Oct 16 19:05:45 2012 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Tue, 16 Oct 2012 13:05:45 -0400 Subject: [xcrysden] xcrysden script for MacOS Message-ID: Dear Dr. Kokalj, I would like to suggest removal of these lines from the "xcrysden" script in the package. If you are trying to use libraries other than in external/lib, then these lines cause the system to look in the wrong places and the executable cannot run, and I could only make it work by commenting them out. These lines are within a check whether "external/lib" exists, which I presume is an attempt to see whether the external libraries are being used. However, the make target "xcrysden" downloads bwidget and creates that directory, so it seems to me that it is not possible to build the code without "external/lib" being created, and so these lines about DYLD_LIBRARY_PATH will always be invoked, even when that directory is not being used for TCL, TK, GL, etc. I suggest that, in general, it is the responsibility of the user to ensure that the correct search paths are set in the environment, and that a silent attempt by the program to guess and set the paths causes confusion. # if test -z "${DYLD_LIBRARY_PATH}"; then # DYLD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib" # else # DYLD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib:$DYLD_LIBRARY_PATH" # fi # export DYLD_LIBRARY_PATH Regards, David Strubbe -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20121016/9d0d1bdb/attachment.htm From tone.kokalj at ijs.si Thu Oct 18 13:43:43 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 18 Oct 2012 13:43:43 +0200 Subject: [xcrysden] xcrysden script for MacOS In-Reply-To: References: Message-ID: <1350560623.4765.10.camel@catalyst.ijs.si> On Tue, 2012-10-16 at 13:05 -0400, David Strubbe wrote: > Dear Dr. Kokalj, > > > I would like to suggest removal of these lines from the "xcrysden" > script in the package. If you are trying to use libraries other than > in external/lib, then these lines cause the system to look in the > wrong places and the executable cannot run, and I could only make it > work by commenting them out. These lines are within a check whether > "external/lib" exists, which I presume is an attempt to see whether > the external libraries are being used. No, it is just the opposite. These lines add the $XCRYSDEN_TOPDIR/external/lib to the DYLD_LIBRARY_PATH (it is implicitly assumed that external/lib is always there). I assume that what is going on is that you have compiled also some external libraries during xcrysden compilation, which now reside in external/lib, and probably they are not functioning well. To see which libraries are loaded run (with original xcrysden script without the pertinent lines removed) xcrysden as : xcrysden -d (you will probably need to edit xcrysden script and replace the "ldd" with "otool -L") Let me know what happens. 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 dstrubbe at civet.berkeley.edu Thu Oct 18 18:53:03 2012 From: dstrubbe at civet.berkeley.edu (David Strubbe) Date: Thu, 18 Oct 2012 12:53:03 -0400 Subject: [xcrysden] xcrysden script for MacOS In-Reply-To: <1350560623.4765.10.camel@catalyst.ijs.si> References: <1350560623.4765.10.camel@catalyst.ijs.si> Message-ID: I am not sure what you mean. Isn't this checking whether external/lib exists, as below: if test -d $XCRYSDEN_TOPDIR/external/lib ; then if test -z "${LD_LIBRARY_PATH}"; then LD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib" else LD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib:$LD_LIBRARY_PATH" fi export LD_LIBRARY_PATH if test -z "${DYLD_LIBRARY_PATH}"; then DYLD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib" else DYLD_LIBRARY_PATH="$XCRYSDEN_TOPDIR/external/lib:$DYLD_LIBRARY_PATH" fi export DYLD_LIBRARY_PATH fi Since external/lib will always exist after building xcrysden, DYLD_LIBRARY_PATH will always be set. No, I am not using anything from external/lib, as you can see: $ otool -L bin/xcrys bin/xcrys: /opt/local/lib/libfftw3.3.dylib (compatibility version 7.0.0, current version 7.2.0) /opt/local/lib/libmeschach.1.dylib (compatibility version 1.2.0, current version 1.2.0) /opt/local/lib/libtk8.5.dylib (compatibility version 8.5.0, current version 8.5.12) /opt/local/lib/libtcl8.5.dylib (compatibility version 8.5.0, current version 8.5.12) /usr/X11/lib/libGLU.1.dylib (compatibility version 1.3.0, current version 1.3.0) /usr/X11/lib/libGL.1.dylib (compatibility version 1.2.0, current version 1.2.0) /opt/X11/lib/libXmu.6.dylib (compatibility version 9.0.0, current version 9.0.0) /opt/X11/lib/libX11.6.dylib (compatibility version 10.0.0, current version 10.0.0) /opt/X11/lib/libXext.6.dylib (compatibility version 11.0.0, current version 11.0.0) /usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 169.3.0) /usr/lib/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1669.0.0) /opt/local/lib/gcc45/libgcc_s.1.dylib (compatibility version 1.0.0, current version 1. On Thu, Oct 18, 2012 at 7:43 AM, Tone Kokalj wrote: > On Tue, 2012-10-16 at 13:05 -0400, David Strubbe wrote: > > Dear Dr. Kokalj, > > > > > > I would like to suggest removal of these lines from the "xcrysden" > > script in the package. If you are trying to use libraries other than > > in external/lib, then these lines cause the system to look in the > > wrong places and the executable cannot run, and I could only make it > > work by commenting them out. These lines are within a check whether > > "external/lib" exists, which I presume is an attempt to see whether > > the external libraries are being used. > > No, it is just the opposite. These lines add the > $XCRYSDEN_TOPDIR/external/lib to the DYLD_LIBRARY_PATH (it is implicitly > assumed that external/lib is always there). > > I assume that what is going on is that you have compiled also some > external libraries during xcrysden compilation, which now reside in > external/lib, and probably they are not functioning well. To see which > libraries are loaded run (with original xcrysden script without the > pertinent lines removed) xcrysden as : > > xcrysden -d > > (you will probably need to edit xcrysden script and replace the "ldd" > with "otool -L") > > Let me know what happens. > > 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 > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20121018/95b464e7/attachment.htm From tone.kokalj at ijs.si Thu Oct 18 19:10:58 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 18 Oct 2012 19:10:58 +0200 Subject: [xcrysden] xcrysden script for MacOS In-Reply-To: References: <1350560623.4765.10.camel@catalyst.ijs.si> Message-ID: <1350580258.4765.21.camel@catalyst.ijs.si> On Thu, 2012-10-18 at 12:53 -0400, David Strubbe wrote: > I am not sure what you mean. Isn't this checking whether external/lib > exists, as below: > if test -d $XCRYSDEN_TOPDIR/external/lib ; then Yes, this indeed checks the existence of the external/lib (but not those lines of your former email). > Since external/lib will always exist after building xcrysden, > DYLD_LIBRARY_PATH will always be set. No, I am not using anything from > external/lib, as you can see: > > > $ otool -L bin/xcrys > bin/xcrys: No, don't run "otool" directly, run it within xcrysden script via "xcrysden -d" command (but replace "ldd" with "otool -L" in the script, line 207). The difference between "xcrysden -d" and direct "otool -L" is that within the xcrysden script several environmental variables are set, hence the bin/xcrys launched from the xcrysden script can load different libraries than the direct bin/xcrys. Regards, Tone P.S.: what is in your external/lib/, only bwidget library or also something else? -- 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