From martin at ruby.chemie.uni-freiburg.de Sun Apr 1 00:07:34 2012 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Sun, 1 Apr 2012 00:07:34 +0200 (CEST) Subject: [xcrysden] xc-1.5.53 on linux with 32bit visuals Message-ID: <20120331220734.7C378801B3@ruby.chemie.uni-freiburg.de> Hi, with a self-compiled 1.5.53 on 64bit Linux (various openSuSE 11.x boxes with either NVIDIA or AMD graphics cards), we have encountered XError aborts when the right mouse button is pressed. Apparently, when the popup menu is to be created, some Tk function calls XQueryColors to enumerate the colormap. On our systems, this consistently failed with a "BadValue" error, and as XCrysDen does not install its own X error handler, the stock XErrorFunction kicks in and terminates XCrysDen after printing its error message. After adding a more benign error handler in the main() function of C/xcAppInit.C, posting the button menu worked, but most of the menu apart from the color selector was empty and my error handler recorded a stream of further BadMatch/BadValue errors. Searching the internet for similar cases led me to believe that the underlying problem is that XCrysDen picks up a 32bit visual on our machines, and the XQueryColors call fails possibly due to an Xlib bug, where the pixel range available with RGBA visuals exceeds that accepted by XQueryColors. The solution gleaned from similar cases (e.g., Nedit) was to add export XLIB_SKIP_ARGB_VISUALS=1 to the xcrysden script. (A more invasive alternative being to disable the "Composite" extension in the xorg.conf - both make xcrysden pick a regular 24bit visual with no adverse effects). As what appears to be the same problem was reported in June last year by Hongsheng Zhao and reportedly solved by using a 32bit binary, the above-mentioned misbehaviour of XQueryColors et al. seems to be limited to 64bit systems. Regards Martin -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From quanyundi at gmail.com Mon Apr 2 23:28:41 2012 From: quanyundi at gmail.com (Yundi Quan) Date: Mon, 2 Apr 2012 14:28:41 -0700 Subject: [xcrysden] 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/20120402/920f9f35/attachment.htm From aladin331 at yahoo.com Tue Apr 3 10:36:32 2012 From: aladin331 at yahoo.com (Aladin Hamid) Date: Tue, 3 Apr 2012 01:36:32 -0700 (PDT) Subject: [xcrysden] structure Builder GUI for the CRYSTAL 9 Message-ID: <1333442192.54170.YahooMailNeo@web161401.mail.bf1.yahoo.com> Dear all Thank you Anton Kokalj for your advices about Fermi surface vasualization. I would like to ask about the structure Builder GUI for the CRYSTAL-95/98/03/06 program? and to creat new CRYSTAL-95/98/03/06 input ? I used? file-->New Crystal, then I went on the processes up to View Crystal finally I found the following massage ERROR: while executing exec/xcrys_tmp/xc_9041/xc_gengeom9041. ? ? Sincerely Alaa S Hamid Associate prof. of Physics Qassim University Deanship of Educational Services P.O. Box 6644 Buraidah 51452 Saudi Arabia Tel. (Work) + 966-6-3800050 (8050) mob. +966-0552006051 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120403/b600a7d3/attachment.htm From tone.kokalj at ijs.si Tue Apr 3 11:27:12 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 03 Apr 2012 11:27:12 +0200 Subject: [xcrysden] wien2k fermi surface In-Reply-To: References: Message-ID: <1333445232.15373.25.camel@catalyst.ijs.si> On Fri, 2012-03-30 at 20:13 -0700, Yundi Quan wrote: > 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? All these button follow the idea of old "Wien in a box" GUI. Normally, one generates a very dense k-mesh for Fermi surface visualization. The denser the mesh the more reliable the shape of Fermi surface. Perhaps the best explanation for these buttons (although not direct/explicit) would be the Wien user guide or by asking this question to Wien mailing list. 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 Apr 3 11:32:13 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 03 Apr 2012 11:32:13 +0200 Subject: [xcrysden] xc-1.5.53 on linux with 32bit visuals In-Reply-To: <20120331220734.7C378801B3@ruby.chemie.uni-freiburg.de> References: <20120331220734.7C378801B3@ruby.chemie.uni-freiburg.de> Message-ID: <1333445533.15373.29.camel@catalyst.ijs.si> On Sun, 2012-04-01 at 00:07 +0200, Martin Kroeker wrote: > Hi, > with a self-compiled 1.5.53 on 64bit Linux (various openSuSE 11.x boxes > with either NVIDIA or AMD graphics cards), we have encountered XError > aborts when the right mouse button is pressed. Martin, your info is very valuable. Thanks! If you wish you may send me your implementation of X error handler and I'll add it to the code. > The solution gleaned from similar cases (e.g., Nedit) was to add > export XLIB_SKIP_ARGB_VISUALS=1 > to the xcrysden script. (A more invasive alternative being to disable > the "Composite" extension in the xorg.conf - both make xcrysden pick > a regular 24bit visual with no adverse effects). So if I understand correctly, you suggest that the best solution would be to add "export XLIB_SKIP_ARGB_VISUALS="1 to xcrysden script? 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 Apr 3 11:35:38 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 03 Apr 2012 11:35:38 +0200 Subject: [xcrysden] structure Builder GUI for the CRYSTAL 9 In-Reply-To: <1333442192.54170.YahooMailNeo@web161401.mail.bf1.yahoo.com> References: <1333442192.54170.YahooMailNeo@web161401.mail.bf1.yahoo.com> Message-ID: <1333445738.15373.32.camel@catalyst.ijs.si> On Tue, 2012-04-03 at 01:36 -0700, Aladin Hamid wrote: > Dear all > Thank you Anton Kokalj for your advices about Fermi surface > vasualization. > I would like to ask about the structure Builder GUI for the > CRYSTAL-95/98/03/06 program > and to creat new CRYSTAL-95/98/03/06 input > > I used file-->New Crystal, then I went on the processes up to View > Crystal > finally I found the following massage > ERROR: while executing > exec/xcrys_tmp/xc_9041/xc_gengeom9041. You will need to provide more info, so that one can reconstruct the sequence that leads to error. You may also send the content of the ***/xcrys_tmp/xc_**** temporary directory. 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 s.irrera at caspur.it Tue Apr 3 11:35:49 2012 From: s.irrera at caspur.it (Simona) Date: Tue, 3 Apr 2012 11:35:49 +0200 Subject: [xcrysden] unsubscribe Message-ID: <57C93A95-608A-489B-BF5E-1454932009AC@caspur.it> Hi I would like to unsubscribe from this list my email is irrera at caspur.it Thank you Simona ------------------------------- Dr Simona Irrera (Ph. D) Newton Alumnus Research Fellow Dipartimento di Chimica Sapienza, Universita` di Roma P.le Aldo Moro 5 00185 Roma Tel/Fax: +39 06 4991 3819 Email: s.irrera at caspur.it Honorary Research Associate Department of Chemistry University College London 20 Gordon Street London WC1H 0AJ Tel: +44 (0)20 7679 7465 Fax: +44 (0)20 7679 7463 Email: s.irrera at ucl.ac.uk Website: http://www.chem.uniroma1.it/persone/simona-irrera -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120403/6e37a528/attachment.htm From Lorenzo.Paulatto at impmc.upmc.fr Tue Apr 3 13:16:47 2012 From: Lorenzo.Paulatto at impmc.upmc.fr (Lorenzo Paulatto) Date: Tue, 03 Apr 2012 13:16:47 +0200 Subject: [xcrysden] unsubscribe In-Reply-To: <57C93A95-608A-489B-BF5E-1454932009AC@caspur.it> References: <57C93A95-608A-489B-BF5E-1454932009AC@caspur.it> Message-ID: On Tue, 03 Apr 2012 11:35:49 +0200, Simona wrote: > I would like to unsubscribe from this list You can, and have, to do it yourself from the web interface: http://www.democritos.it/mailman/listinfo/xcrysden bests -- Lorenzo Paulatto IdR @ IMPMC/CNRS & Universit? Paris 6 phone: +33 (0)1 44275 084 / skype: paulatz www: http://www-int.impmc.upmc.fr/~paulatto/ mail: 23-24/4?16 Bo?te courrier 115, 4 place Jussieu 75252 Paris C?dex 05 From rourke at gmail.com Fri Apr 6 15:39:08 2012 From: rourke at gmail.com (Patrick Rourke) Date: Fri, 6 Apr 2012 14:39:08 +0100 Subject: [xcrysden] New program for extracting quantum oscillation information from calculated Fermi surfaces Message-ID: Dear XCrysDen user community, I would like to bring to your attention a new program for extracting quantum oscillation frequencies and effective masses from calculated Fermi surfaces. It also extracts the band contribution to the electronic density of states (to facilitate comparison with specific heat experiments). This program is called the "Supercell K-space Extremal Area Finder" ("SKEAF"), and is written in Fortran 90. It reads band energies stored in the BXSF format, which can be produced using WIEN2k and XCrysDen. You can read about the algorithm in P.M.C. Rourke and S.R. Julian, Computer Physics Communications 183, 324 (2012) (or on the arXiv at http://arxiv.org/abs/0803.1895 ) -- please cite this paper if you use SKEAF in your research. The SKEAF source code and program instructions can be downloaded from the WIEN2k "Unsupported software goodies" page ( http://www.wien2k.at/reg_user/unsupported/ ). I hope you will find this code helpful in your calculations! Best regards, Dr. Patrick Rourke From quanyundi at gmail.com Sun Apr 15 08:54:54 2012 From: quanyundi at gmail.com (Yundi Quan) Date: Sat, 14 Apr 2012 23:54:54 -0700 Subject: [xcrysden] working on a cluster Message-ID: Dear Sir/Madam, I use WIEN2k to do calculations. In WIEN2k, the size of case.vector file is very big (more than 1G). It is difficult to transfer files from the cluster to my local computer. Is it possible to use xcrysden directly on the cluster using SSH? From tone.kokalj at ijs.si Mon Apr 16 18:09:50 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 16 Apr 2012 18:09:50 +0200 Subject: [xcrysden] working on a cluster In-Reply-To: References: Message-ID: <1334592590.29462.45.camel@catalyst.ijs.si> On Sat, 2012-04-14 at 23:54 -0700, Yundi Quan wrote: > Dear Sir/Madam, > I use WIEN2k to do calculations. In WIEN2k, the size of case.vector > file is very big (more than 1G). It is difficult to transfer files > from the cluster to my local computer. Is it possible to use xcrysden > directly on the cluster using SSH? If you can mount the cluster filesystem consider using this possibility. Another possibility would be a sshfs. http://en.wikipedia.org/wiki/SSHFS 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 mendesjuliana at hotmail.com Thu Apr 19 15:11:12 2012 From: mendesjuliana at hotmail.com (Juliana .) Date: Thu, 19 Apr 2012 10:11:12 -0300 Subject: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in startup script Message-ID: Dear friends, I facing some problems to install xcrysden version 1.5.18 in cygwin plataform on Windows 7.Everythings works fine, ./xcConfigure and . ~/.bashrc, but when I call for the program with the command ./xcrysden, it returns me this error:+----------------------------------------------------------------+|****************************************************************||* *||* XCrySDen - (X-Window) CRYstalline Structures and DENsities *||* = === = === *||*--------------------------------------------------------------*||* *||* Anton Kokalj (Tone.Kokalj at ijs.si) *||* Jozef Stefan Institute, Ljubljana, Slovenia *||* *||* Copyright (c) 1996--2004 by Anton Kokalj *||* *||****************************************************************|+----------------------------------------------------------------+ Version: 1.5.18 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/Juliana/XCrySDen-1.5.18-bin-sharedXCRYSDEN_SCRATCH=/home/Juliana/xcrys_tmp Application initialization failed: no display name and no $DISPLAY environment variableError in startup script: no display name and no $DISPLAY environment variable 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 "/home/Juliana/XCrySDen-1.5.18-bin-shared/Tcl/xcInit.tcl" line 426) Does anyone knows what is happening?Does anyone knows if the problem is Windows 7 or the cygwin version 2.769?This problem starter after I updated the cygwin to the 2.769 version :(Thanks in advance!Juliana. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120419/667245e8/attachment.htm From tone.kokalj at ijs.si Thu Apr 19 17:51:01 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 19 Apr 2012 17:51:01 +0200 Subject: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in startup script In-Reply-To: References: Message-ID: <1334850661.14030.14.camel@catalyst.ijs.si> On Thu, 2012-04-19 at 10:11 -0300, Juliana . wrote: > Dear friends, > > > I facing some problems to install xcrysden version 1.5.18 in cygwin > plataform on Windows 7. > Everythings works fine, ./xcConfigure and . ~/.bashrc, but when I call > for the program with the command ./xcrysden, it returns me this error: > Application initialization failed: no display name and no $DISPLAY environment variable > Error in startup script: no display name and no $DISPLAY environment variable Which means you tried to run xcrysden without/outside X-Window. First start the X-Window and only then run xcrysden. 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 Fri Apr 20 03:54:25 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Thu, 19 Apr 2012 23:54:25 -0200 Subject: [xcrysden] XCRYSDEN or other software? Message-ID: <20120420014547.M59693@proto.fisica.ufmg.br> Dear all, I need your help in something. I am trying to find a software to be used to build polymers (such as PPES) and find their positions (in angstroms, for example), the same as a nanotube modeler would do when one inserts chiralities and carbon bonds where the output would be the positions of the C atoms. I also want to attach the polymer to a SWNT; can XCRYSDEN do that or does anyone have a suggestion of a software for me? I would really be grateful. Thank you Elie Moujaes University of Notts NG7 2RD UK -- Departamento de Fisica - UFMG/ICEx From mendesjuliana at hotmail.com Sat Apr 21 00:27:18 2012 From: mendesjuliana at hotmail.com (Juliana .) Date: Fri, 20 Apr 2012 19:27:18 -0300 Subject: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in X-Window In-Reply-To: References: Message-ID: Dear Tone, Thank you very much for your reply!I made what you said. I ran the xcrysden in X-Window. For a few minutes it was possible to see the xcrysden window,but this window dissapeared seconds later and it gave me a new error.This is the new error: XCRYSDEN_TOPDIR=/home/Juliana/XCrySDen-1.5.18-bin-sharedXCRYSDEN_SCRATCH=/tmp Running on platform: cygwin 1 [main] wish 4668 child_copy: linked dll data write copy failed, 0x2EE000..0x2F27EC, done 0, windows pid 4740, Win32 error 487 27571 [main] wish8.5 5300 exception::handle: Exception: STATUS_ACCESS_VIOLATION 28082 [main] wish8.5 5300 open_stackdumpfile: Dumping stack trace to wish8.5.exe.stackdumpPackage ImageMagick's convert: /usr/bin/convertPackage ImageMagick's import: /usr/bin/import3402022 [main] wish8.5 3924 exception::handle: Exception: STATUS_ACCESS_VIOLATION3402538 [main] wish8.5 3924 open_stackdumpfile: Dumping stack trace to wish8.5.exe.stackdump3571963 [main] wish 4668 child_copy: linked dll data write copy failed, 0x2EE000..0x2F27EC, done 0, windows pid 4740, Win32 error 487Executing: /home/Juliana/XCrySDen-1.5.18-bin-shared/bin/ftnunit./xcrysden: line 206: 4668 Segmentation fault (core dumped) exec wish ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null Can you help me again? Thank you.Regards, Juliana. > From: xcrysden-request at democritos.it > Subject: XCrySDen Digest, Vol 51, Issue 7 > To: xcrysden at democritos.it > Date: Fri, 20 Apr 2012 09:48:14 +0200 > > Send XCrySDen mailing list submissions to > xcrysden at democritos.it > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body 'help' to > xcrysden-request at democritos.it > > You can reach the person managing the list at > xcrysden-owner at democritos.it > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > 1. xcrysden-1.5.18-cygwin-bin-shared error in startup script > (Juliana .) > 2. Re: xcrysden-1.5.18-cygwin-bin-shared error in startup script > (Tone Kokalj) > 3. XCRYSDEN or other software? (Elie Albert Moujaes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 19 Apr 2012 10:11:12 -0300 > From: "Juliana ." > Subject: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in startup > script > To: > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Dear friends, > I facing some problems to install xcrysden version 1.5.18 in cygwin plataform on Windows 7.Everythings works fine, ./xcConfigure and . ~/.bashrc, but when I call for the program with the command ./xcrysden, it returns me this error:+----------------------------------------------------------------+|****************************************************************||* *||* XCrySDen - (X-Window) CRYstalline Structures and DENsities *||* = === = === *||*--------------------------------------------------------------*||* *||* Anton Kokalj (Tone.Kokalj at ijs.si) *||* Jozef Stefan Institute, Ljubljana, Slovenia *||* *||* Copyright (c) 1996--2004 by Anton Kokalj *||* *||****************************************************************|+----------------------------------------------------------------+ > Version: 1.5.18 > 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/Juliana/XCrySDen-1.5.18-bin-sharedXCRYSDEN_SCRATCH=/home/Juliana/xcrys_tmp > Application initialization failed: no display name and no $DISPLAY environment variableError in startup script: no display name and no $DISPLAY environment variable 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 "/home/Juliana/XCrySDen-1.5.18-bin-shared/Tcl/xcInit.tcl" line 426) > Does anyone knows what is happening?Does anyone knows if the problem is Windows 7 or the cygwin version 2.769?This problem starter after I updated the cygwin to the 2.769 version :(Thanks in advance!Juliana. > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120419/667245e8/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Thu, 19 Apr 2012 17:51:01 +0200 > From: Tone Kokalj > Subject: Re: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in > startup script > To: xcrysden at democritos.it > Message-ID: <1334850661.14030.14.camel at catalyst.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Thu, 2012-04-19 at 10:11 -0300, Juliana . wrote: > > Dear friends, > > > > > > I facing some problems to install xcrysden version 1.5.18 in cygwin > > plataform on Windows 7. > > Everythings works fine, ./xcConfigure and . ~/.bashrc, but when I call > > for the program with the command ./xcrysden, it returns me this error: > > > Application initialization failed: no display name and no $DISPLAY environment variable > > Error in startup script: no display name and no $DISPLAY environment variable > > Which means you tried to run xcrysden without/outside X-Window. > First start the X-Window and only then run xcrysden. > > 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 > > > > ------------------------------ > > Message: 3 > Date: Thu, 19 Apr 2012 23:54:25 -0200 > From: "Elie Albert Moujaes" > Subject: [xcrysden] XCRYSDEN or other software? > To: xcrysden at democritos.it > Message-ID: <20120420014547.M59693 at proto.fisica.ufmg.br> > Content-Type: text/plain; charset=iso-8859-1 > > > Dear all, > > I need your help in something. I am trying to find a software to be used to > build polymers (such as PPES) and find their positions (in angstroms, for > example), the same as a nanotube modeler would do when one inserts chiralities > and carbon bonds where the output would be the positions of the C atoms. I also > want to attach the polymer to a SWNT; can XCRYSDEN do that or does anyone have a > suggestion of a software for me? I would really be grateful. > > Thank you > > Elie Moujaes > University of Notts > NG7 2RD > UK > -- > Departamento de Fisica - UFMG/ICEx > > > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 51, Issue 7 > *************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120420/e115f24c/attachment.htm From eyert at physik.uni-augsburg.de Mon Apr 23 11:47:07 2012 From: eyert at physik.uni-augsburg.de (Volker Eyert) Date: Mon, 23 Apr 2012 11:47:07 +0200 Subject: [xcrysden] XCRYSDEN or other software? In-Reply-To: <4F951C13.1030307@materialsdesign.com> References: <4F951C13.1030307@materialsdesign.com> Message-ID: <4F95251B.2020907@physik.uni-augsburg.de> Elie, actually, the new MedeA(R) polymer builder of Materials Design can do this. With this tool, you can sketch arbitrary repeat units and their connection points - and you can polymerize any desired polymer from these. Once you have created a polymer, you can attach it to a nano-tube, using the Molecular Editor in MedeA. Details can be found on our webpage www.materialsdesign.com or just contact our experts Clive Freeman and Dave Rigby (whom I cc). Hope this helps Volker On 4/20/12 3:54 AM, Elie Albert Moujaes wrote: > > Dear all, > > I need your help in something. I am trying to find a software to be used to > build polymers (such as PPES) and find their positions (in angstroms, for > example), the same as a nanotube modeler would do when one inserts chiralities > and carbon bonds where the output would be the positions of the C atoms. I also > want to attach the polymer to a SWNT; can XCRYSDEN do that or does anyone have a > suggestion of a software for me? I would really be grateful. > > Thank you > > Elie Moujaes > University of Notts > NG7 2RD > UK > -- > Departamento de Fisica - UFMG/ICEx > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- veyert at materialsdesign.com phone: +33 1 7061 5814, ext. 324 cell: +49 162 4146998 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120423/c2abbbec/attachment.htm From emoujaes at fisica.ufmg.br Mon Apr 23 20:00:19 2012 From: emoujaes at fisica.ufmg.br (Elie Albert Moujaes) Date: Mon, 23 Apr 2012 16:00:19 -0200 Subject: [xcrysden] XCRYSDEN or other software? In-Reply-To: <4F95251B.2020907@physik.uni-augsburg.de> References: <4F951C13.1030307@materialsdesign.com> <4F95251B.2020907@physik.uni-augsburg.de> Message-ID: <20120423175510.M37006@proto.fisica.ufmg.br> Thanks a lot for your help. I am new to this and I want to do a molecular dynamics simulation to nanotubes merged with some polymners. Will check the website or will contact Clive or Dave in case I encountered problems. Thanks again Elie On Mon, 23 Apr 2012 11:47:07 +0200, Volker Eyert wrote > Elie, > > actually, the new MedeA(R) polymer builder of Materials Design can do > this. With this tool, you can sketch arbitrary repeat units and their > connection points - and you can polymerize any desired polymer from > these. Once you have created a polymer, you can attach it to a > nano-tube, using the Molecular Editor in MedeA. Details can be found > on our webpage www.materialsdesign.com or just contact our experts Clive > Freeman and Dave Rigby (whom I cc). > > Hope this helps > > Volker > > On 4/20/12 3:54 AM, Elie Albert Moujaes wrote: > > > > Dear all, > > > > I need your help in something. I am trying to find a software to be used to > > build polymers (such as PPES) and find their positions (in angstroms, for > > example), the same as a nanotube modeler would do when one inserts chiralities > > and carbon bonds where the output would be the positions of the C atoms. I also > > want to attach the polymer to a SWNT; can XCRYSDEN do that or does anyone have a > > suggestion of a software for me? I would really be grateful. > > > > Thank you > > > > Elie Moujaes > > University of Notts > > NG7 2RD > > UK > > -- > > Departamento de Fisica - UFMG/ICEx > > > > _______________________________________________ > > XCrySDen mailing list > > XCrySDen at democritos.it > > http://www.democritos.it/mailman/listinfo/xcrysden > > -- > veyert at materialsdesign.com > phone: +33 1 7061 5814, ext. 324 > cell: +49 162 4146998 -- Departamento de Fisica - UFMG/ICEx From mendesjuliana at hotmail.com Tue Apr 24 19:11:33 2012 From: mendesjuliana at hotmail.com (Juliana .) Date: Tue, 24 Apr 2012 14:11:33 -0300 Subject: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in X-Window In-Reply-To: References: , Message-ID: Dear Tone, Thank you very much for your reply!I made what you said. I ran the xcrysden in X-Window. For a few minutes it was possible to see the xcrysden window,but this window dissapeared seconds later and it gave me a new error.This is the new error: XCRYSDEN_TOPDIR=/home/Juliana/XCrySDen-1.5.18-bin-sharedXCRYSDEN_SCRATCH=/tmp Running on platform: cygwin 1 [main] wish 4668 child_copy: linked dll data write copy failed, 0x2EE000..0x2F27EC, done 0, windows pid 4740, Win32 error 487 27571 [main] wish8.5 5300 exception::handle: Exception: STATUS_ACCESS_VIOLATION 28082 [main] wish8.5 5300 open_stackdumpfile: Dumping stack trace to wish8.5.exe.stackdumpPackage ImageMagick's convert: /usr/bin/convertPackage ImageMagick's import: /usr/bin/import3402022 [main] wish8.5 3924 exception::handle: Exception: STATUS_ACCESS_VIOLATION3402538 [main] wish8.5 3924 open_stackdumpfile: Dumping stack trace to wish8.5.exe.stackdump3571963 [main] wish 4668 child_copy: linked dll data write copy failed, 0x2EE000..0x2F27EC, done 0, windows pid 4740, Win32 error 487Executing: /home/Juliana/XCrySDen-1.5.18-bin-shared/bin/ftnunit./xcrysden: line 206: 4668 Segmentation fault (core dumped) exec wish ${XCRYSDEN_TOPDIR}/Tcl/xcInit.tcl $USE -- $XCRYSDEN_TOPDIR $XCRYSDEN_SCRATCH $ARGS > /dev/null Can you help me again? Thank you.Regards, Juliana. > From: xcrysden-request at democritos.it > Subject: XCrySDen Digest, Vol 51, Issue 7 > To: xcrysden at democritos.it > Date: Fri, 20 Apr 2012 09:48:14 +0200 > > Send XCrySDen mailing list submissions to > xcrysden at democritos.it > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.democritos.it/mailman/listinfo/xcrysden > or, via email, send a message with subject or body 'help' to > xcrysden-request at democritos.it > > You can reach the person managing the list at > xcrysden-owner at democritos.it > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of XCrySDen digest..." > > > Today's Topics: > > 1. xcrysden-1.5.18-cygwin-bin-shared error in startup script > (Juliana .) > 2. Re: xcrysden-1.5.18-cygwin-bin-shared error in startup script > (Tone Kokalj) > 3. XCRYSDEN or other software? (Elie Albert Moujaes) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 19 Apr 2012 10:11:12 -0300 > From: "Juliana ." > Subject: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in startup > script > To: > Message-ID: > Content-Type: text/plain; charset="iso-8859-1" > > > Dear friends, > I facing some problems to install xcrysden version 1.5.18 in cygwin plataform on Windows 7.Everythings works fine, ./xcConfigure and . ~/.bashrc, but when I call for the program with the command ./xcrysden, it returns me this error:+----------------------------------------------------------------+|****************************************************************||* *||* XCrySDen - (X-Window) CRYstalline Structures and DENsities *||* = === = === *||*--------------------------------------------------------------*||* *||* Anton Kokalj (Tone.Kokalj at ijs.si) *||* Jozef Stefan Institute, Ljubljana, Slovenia *||* *||* Copyright (c) 1996--2004 by Anton Kokalj *||* *||****************************************************************|+----------------------------------------------------------------+ > Version: 1.5.18 > 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/Juliana/XCrySDen-1.5.18-bin-sharedXCRYSDEN_SCRATCH=/home/Juliana/xcrys_tmp > Application initialization failed: no display name and no $DISPLAY environment variableError in startup script: no display name and no $DISPLAY environment variable 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 "/home/Juliana/XCrySDen-1.5.18-bin-shared/Tcl/xcInit.tcl" line 426) > Does anyone knows what is happening?Does anyone knows if the problem is Windows 7 or the cygwin version 2.769?This problem starter after I updated the cygwin to the 2.769 version :(Thanks in advance!Juliana. > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120419/667245e8/attachment-0001.htm > > ------------------------------ > > Message: 2 > Date: Thu, 19 Apr 2012 17:51:01 +0200 > From: Tone Kokalj > Subject: Re: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in > startup script > To: xcrysden at democritos.it > Message-ID: <1334850661.14030.14.camel at catalyst.ijs.si> > Content-Type: text/plain; charset="UTF-8" > > On Thu, 2012-04-19 at 10:11 -0300, Juliana . wrote: > > Dear friends, > > > > > > I facing some problems to install xcrysden version 1.5.18 in cygwin > > plataform on Windows 7. > > Everythings works fine, ./xcConfigure and . ~/.bashrc, but when I call > > for the program with the command ./xcrysden, it returns me this error: > > > Application initialization failed: no display name and no $DISPLAY environment variable > > Error in startup script: no display name and no $DISPLAY environment variable > > Which means you tried to run xcrysden without/outside X-Window. > First start the X-Window and only then run xcrysden. > > 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 > > > > ------------------------------ > > Message: 3 > Date: Thu, 19 Apr 2012 23:54:25 -0200 > From: "Elie Albert Moujaes" > Subject: [xcrysden] XCRYSDEN or other software? > To: xcrysden at democritos.it > Message-ID: <20120420014547.M59693 at proto.fisica.ufmg.br> > Content-Type: text/plain; charset=iso-8859-1 > > > Dear all, > > I need your help in something. I am trying to find a software to be used to > build polymers (such as PPES) and find their positions (in angstroms, for > example), the same as a nanotube modeler would do when one inserts chiralities > and carbon bonds where the output would be the positions of the C atoms. I also > want to attach the polymer to a SWNT; can XCRYSDEN do that or does anyone have a > suggestion of a software for me? I would really be grateful. > > Thank you > > Elie Moujaes > University of Notts > NG7 2RD > UK > -- > Departamento de Fisica - UFMG/ICEx > > > > ------------------------------ > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > > End of XCrySDen Digest, Vol 51, Issue 7 > *************************************** -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120424/c03e0e26/attachment.htm From xhzheng at foxmail.com Wed Apr 25 09:15:12 2012 From: xhzheng at foxmail.com (Xiaohong Zheng) Date: Wed, 25 Apr 2012 15:15:12 +0800 Subject: [xcrysden] 1.5.53 installation Message-ID: <4F97A480.8070802@foxmail.com> Dear all, I was trying to install 1.5.53 on RedHat Enterprise 4.6. However, I have tried all the packages (xcrysden-1.5.53.tar.gz , xcrysden-1.5.53-linux_x86_64-shared.tar.gz and xcrysden-1.5.53-linux_x86_64-semishared.tar.gz ). None of them works. I am very much depressed. Could you kindly help me, please? Thank you very much in advance. Sincerely, Xiaohong When I tried to install from the source package xcrysden-1.5.53.tar.gz , I got: /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclInterp.o)(.text+0x491b): In function `Tcl_InterpObjCmd': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclIO.o)(.text+0x3af2): In function `Tcl_BadChannelOption': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclIO.o)(.text+0x41be): In function `Tcl_GetChannelOption': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclIO.o)(.text+0x6493): In function `WriteChars': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclMain.o)(.text+0x5bc): In function `Tcl_SourceRCFile': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclMain.o)(.text+0xf01): more undefined references to `__stack_chk_fail' follow /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x14a0): In function `TtySetOptionProc': : undefined reference to `__isoc99_sscanf' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x1a28): In function `TtySetOptionProc': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x1d79): In function `TtyInit': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x1ec1): In function `TcpAccept': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x1fb4): In function `MakeTcpClientChannelMode': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x2139): In function `Tcl_MakeFileChannel': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x2516): more undefined references to `__stack_chk_fail' follow /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0xe59): In function `TclpObjNormalizePath': : undefined reference to `__realpath_chk' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0xf4c): In function `TclpObjNormalizePath': : undefined reference to `__realpath_chk' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x101c): In function `TclpObjNormalizePath': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1571): In function `TclpObjRemoveDirectory': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1771): In function `TclpObjCopyDirectory': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1c91): In function `DoCopyFile': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1ec4): In function `DoRenameFile': : undefined reference to `__realpath_chk' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1edd): In function `DoRenameFile': : undefined reference to `__realpath_chk' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1fdf): In function `DoRenameFile': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x18c): In function `TclNativeCreateNativeRep': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x20d): In function `TclpNativeToNormalized': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x598): In function `TclpObjLink': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x67a): In function `TclpReadlink': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x768): more undefined references to `__stack_chk_fail' follow collect2: ld returned 1 exit status make[2]: *** [tclsh] Error 1 /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclInterp.o)(.text+0x491b): In function `Tcl_InterpObjCmd': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclIO.o)(.text+0x3af2): In function `Tcl_BadChannelOption': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclIO.o)(.text+0x41be): In function `Tcl_GetChannelOption': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclIO.o)(.text+0x6493): In function `WriteChars': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclMain.o)(.text+0x5bc): In function `Tcl_SourceRCFile': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclMain.o)(.text+0xf01): more undefined references to `__stack_chk_fail' follow /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x14a0): In function `TtySetOptionProc': : undefined reference to `__isoc99_sscanf' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x1a28): In function `TtySetOptionProc': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x1d79): In function `TtyInit': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x1ec1): In function `TcpAccept': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x1fb4): In function `MakeTcpClientChannelMode': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x2139): In function `Tcl_MakeFileChannel': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixChan.o)(.text+0x2516): more undefined references to `__stack_chk_fail' follow /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0xe59): In function `TclpObjNormalizePath': : undefined reference to `__realpath_chk' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0xf4c): In function `TclpObjNormalizePath': : undefined reference to `__realpath_chk' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x101c): In function `TclpObjNormalizePath': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1571): In function `TclpObjRemoveDirectory': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1771): In function `TclpObjCopyDirectory': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1c91): In function `DoCopyFile': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1ec4): In function `DoRenameFile': : undefined reference to `__realpath_chk' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1edd): In function `DoRenameFile': : undefined reference to `__realpath_chk' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFCmd.o)(.text+0x1fdf): In function `DoRenameFile': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x18c): In function `TclNativeCreateNativeRep': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x20d): In function `TclpNativeToNormalized': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x598): In function `TclpObjLink': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x67a): In function `TclpReadlink': : undefined reference to `__stack_chk_fail' /home/xhzheng/xcrysden-1.5.53/external/src/tcl8.5.11/unix/libtcl8.5.a(tclUnixFile.o)(.text+0x768): more undefined references to `__stack_chk_fail' follow collect2: ld returned 1 exit status make[2]: *** [tclsh] Error 1 make[1]: *** [tcl] Error 2 make: *** [tcl] Error 2 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120425/9b4444b7/attachment-0001.htm From martin at ruby.chemie.uni-freiburg.de Wed Apr 25 09:34:36 2012 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Wed, 25 Apr 2012 09:34:36 +0200 (CEST) Subject: [xcrysden] 1.5.53 installation In-Reply-To: <4F97A480.8070802@foxmail.com> Message-ID: <20120425073436.6A9BC801B3@ruby.chemie.uni-freiburg.de> The missing functions seem to be from the standard c library - older versions of the linker used to add that automatically when you compiled something. Try editing the line "MATH = -lm" near the top of your Make.sys so that it reads "MATH = -lc -lm" and then run "make" again. (You may need to run "make clean" before the "make" so that everything gets rebuilt). Hope this helps Martin -- Dr. Martin Kroeker martin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg From tone.kokalj at ijs.si Wed Apr 25 09:41:38 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 25 Apr 2012 09:41:38 +0200 Subject: [xcrysden] xcrysden-1.5.18-cygwin-bin-shared error in X-Window In-Reply-To: References: , Message-ID: <1335339698.4741.4.camel@catalyst.ijs.si> On Tue, 2012-04-24 at 14:11 -0300, Juliana . wrote: > Dear Tone, > > > Thank you very much for your reply! > I made what you said. I ran the xcrysden in X-Window. For a few > minutes it was possible to see the xcrysden window, > but this window dissapeared seconds later and it gave me a new error. Please try the new cygwin version of xcrysden that has been recently made available on the download page: http://www.xcrysden.org/download/xcrysden-1.5.53-cygwin.tar.gz I've been informed that recently some problems occurred with the old xcrysden version (1.5.18) and new cygwin installations. It has been reported that new version work. 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 xhzheng at foxmail.com Thu Apr 26 02:08:53 2012 From: xhzheng at foxmail.com (Xiaohong Zheng) Date: Thu, 26 Apr 2012 08:08:53 +0800 Subject: [xcrysden] 1.5.53 installation In-Reply-To: <20120425073436.6A9BC801B3@ruby.chemie.uni-freiburg.de> References: <20120425073436.6A9BC801B3@ruby.chemie.uni-freiburg.de> Message-ID: <4F989215.3020808@foxmail.com> Dear Martin, Thank you very much. I have tried the option "MATH = -lc -lm", but the problem is the same. Any other ideas, please? Xiaohong On 2012?04?25? 15:34, Martin Kroeker wrote: > The missing functions seem to be from the standard c library - older > versions of the linker used to add that automatically when you compiled > something. > Try editing the line "MATH = -lm" near the top of your Make.sys so that > it reads "MATH = -lc -lm" and then run "make" again. (You may need to > run "make clean" before the "make" so that everything gets rebuilt). > > Hope this helps > Martin From tone.kokalj at ijs.si Thu Apr 26 07:47:46 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 26 Apr 2012 07:47:46 +0200 Subject: [xcrysden] 1.5.53 installation In-Reply-To: <4F989215.3020808@foxmail.com> References: <20120425073436.6A9BC801B3@ruby.chemie.uni-freiburg.de> <4F989215.3020808@foxmail.com> Message-ID: <1335419266.5059.4.camel@catalyst.ijs.si> On Thu, 2012-04-26 at 08:08 +0800, Xiaohong Zheng wrote: > Dear Martin, > > Thank you very much. I have tried the option "MATH = -lc -lm", but the > problem is the same. Any other ideas, please? From xhzheng at foxmail.com Thu Apr 26 08:27:30 2012 From: xhzheng at foxmail.com (Xiaohong Zheng) Date: Thu, 26 Apr 2012 14:27:30 +0800 Subject: [xcrysden] 1.5.53 installation In-Reply-To: <1335419266.5059.4.camel@catalyst.ijs.si> References: <20120425073436.6A9BC801B3@ruby.chemie.uni-freiburg.de> <4F989215.3020808@foxmail.com> <1335419266.5059.4.camel@catalyst.ijs.si> Message-ID: <4F98EAD2.4040904@foxmail.com> Dear Tone, Thank you very much for your reply. I have tried both "COMPILE_ALL = no" and "COMPILE_TCLTK = no". I still failed. The following is what I got: #------------------------------# # # # Compiling XCRYSDEN C-code # # # #------------------------------# cd C; make "TOPDIR=/home/xhzheng/Downloads/xcrysden-1.5.53" compile make[1]: Entering directory `/home/xhzheng/Downloads/xcrysden-1.5.53/C' make TOPDIR=/home/xhzheng/Downloads/xcrysden-1.5.53 make[2]: Entering directory `/home/xhzheng/Downloads/xcrysden-1.5.53/C' gcc -g -static -ansi -ffast-math -funroll-loops -DUSE_FONTS -pedantic -Wall -DUSE_FONTS -I/home/xhzheng/Downloads/xcrysden-1.5.53/external/src/tcl8.5.11/generic -I/home/xhzheng/Downloads/xcrysden-1.5.53/external/src/tk8.5.11/generic -I/home/xhzheng/Downloads/xcrysden-1.5.53/external/include -c detnsplit.c In file included from detnsplit.c:22: struct.h:47:19: error: GL/gl.h: No such file or directory In file included from detnsplit.c:22: struct.h:317: error: expected specifier-qualifier-list before ?GLboolean? struct.h:643: error: expected specifier-qualifier-list before ?GLfloat? struct.h:681: error: expected specifier-qualifier-list before ?GLuint? struct.h:712: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?DefAtCol? struct.h:715: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?DefFrameCol? struct.h:717: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?DefBg? struct.h:718: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?bg? struct.h:725: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?dimType? struct.h:730: error: expected specifier-qualifier-list before ?GLboolean? struct.h:740: warning: struct has no members struct.h:759: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?atomlabelOffset? struct.h:760: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?xyzlabelOffset? struct.h:901: error: expected specifier-qualifier-list before ?GLenum? struct.h:986: error: expected specifier-qualifier-list before ?GLsizei? struct.h:992: warning: struct has no members struct.h:1077: error: expected specifier-qualifier-list before ?GLdouble? struct.h:1082: warning: struct has no members struct.h:1093: error: expected specifier-qualifier-list before ?GLfloat? make[2]: *** [detnsplit.o] Error 1 make[2]: Leaving directory `/home/xhzheng/Downloads/xcrysden-1.5.53/C' make[1]: *** [compile] Error 2 make[1]: Leaving directory `/home/xhzheng/Downloads/xcrysden-1.5.53/C' make: *** [src-C] Error 2 So, could you tell me what to do next, please? Xiaohong On 2012?04?26? 13:47, Tone Kokalj wrote: > On Thu, 2012-04-26 at 08:08 +0800, Xiaohong Zheng wrote: >> Dear Martin, >> >> Thank you very much. I have tried the option "MATH = -lc -lm", but the >> problem is the same. Any other ideas, please? > From your previous email, it is evident that you requested to compile > tcl/tk (i.e. COMPILE_TCLTK = yes) and it is seems to be the source of > problem. Try the system libraries instead, i.e., specify COMPILE_TCLTK = > no in Make.sys or even COMPILE_ALL = no (which will prevent the > compilation of tcl/tk, mesa& fftw3). > > Regards, Tone From tone.kokalj at ijs.si Thu Apr 26 08:30:43 2012 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Thu, 26 Apr 2012 08:30:43 +0200 Subject: [xcrysden] 1.5.53 installation In-Reply-To: <4F98EAD2.4040904@foxmail.com> References: <20120425073436.6A9BC801B3@ruby.chemie.uni-freiburg.de> <4F989215.3020808@foxmail.com> <1335419266.5059.4.camel@catalyst.ijs.si> <4F98EAD2.4040904@foxmail.com> Message-ID: <1335421843.5059.9.camel@catalyst.ijs.si> On Thu, 2012-04-26 at 14:27 +0800, Xiaohong Zheng wrote: > Dear Tone, > > Thank you very much for your reply. I have tried both "COMPILE_ALL = no" > and "COMPILE_TCLTK = no". I still failed. The following is what I got: > > #------------------------------# > # # > # Compiling XCRYSDEN C-code # > # # > #------------------------------# > > cd C; make "TOPDIR=/home/xhzheng/Downloads/xcrysden-1.5.53" compile > make[1]: Entering directory `/home/xhzheng/Downloads/xcrysden-1.5.53/C' > make TOPDIR=/home/xhzheng/Downloads/xcrysden-1.5.53 > make[2]: Entering directory `/home/xhzheng/Downloads/xcrysden-1.5.53/C' > gcc -g -static -ansi -ffast-math -funroll-loops -DUSE_FONTS -pedantic > -Wall -DUSE_FONTS > -I/home/xhzheng/Downloads/xcrysden-1.5.53/external/src/tcl8.5.11/generic > -I/home/xhzheng/Downloads/xcrysden-1.5.53/external/src/tk8.5.11/generic > -I/home/xhzheng/Downloads/xcrysden-1.5.53/external/include -c detnsplit.c > In file included from detnsplit.c:22: > struct.h:47:19: error: GL/gl.h: No such file or directory Which means you don't have the development version of OpenGL libraries (i.e. Mesa on linux), hence GL/gl.h header file is missing. Install the corresponding redhat package that contain these. 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 mendesjuliana at hotmail.com Thu Apr 26 14:16:21 2012 From: mendesjuliana at hotmail.com (Juliana .) Date: Thu, 26 Apr 2012 09:16:21 -0300 Subject: [xcrysden] just to say Thank you Message-ID: Dear Tone, Thank you very much for your help! The xcrysden-1.5.53-cygwin is working fine. Best regards, Juliana. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20120426/0adfa37f/attachment.htm