From U.Wedig at fkf.mpg.de Thu Mar 12 11:26:08 2020 From: U.Wedig at fkf.mpg.de (Ulrich Wedig) Date: Thu, 12 Mar 2020 11:26:08 +0100 Subject: [xcrysden] XCrySDen 1.6.2 and CRYSTAL fort.9 Message-ID: <4c419e82-3cb2-eca0-ebda-4f10a9ed3dd1@fkf.mpg.de> Dear XCrySDen community, when reading the fort.9 file of CRYSTAL as input, XCrySDen starts the CRYSTAL properties program with some input containing the BASE keyword. The BASE keyword for properties was for the last time documented in the manual for CRYSTAL98. Since CRYSTAL03 it is no longer mentioned. The use of the BASE keyword is not caught by the properties program but may lead to errors. This may lead to consecutive problems with the execution of XCrySDen (independent of the version). With BASE just some information on basis set and computational parameters is printed out, not relevant for the further execution of XCysSDen. So BASE can be omitted in order to avoid the problems associated with this keyword. I have made the following modifications to *propInit.tcl* and *propC95.tcl*: wedig@~/XCrySDen/xcrysden-1.6.2/Tcl> diff propInit.tcl.orig propInit.tcl 125c125,126 #??? set input "BASE\n0\nEXTPRT\nCOORPRT\nEND" >???? set input "EXTPRT\nCOORPRT\nEND" wedig@~/XCrySDen/xcrysden-1.6.2/Tcl> diff propC95.tcl.orig propC95.tcl 37c37 #???? set input "BASE\n0\n" With these modifications I encountered no problems when processing fort.9 with XCrySDen. Best regards, Ulrich Wedig -- ----------------------------------------------------------------- Dr. Ulrich Wedig Tel. 0711/6891535 Max-Planck-Institut fuer Festkoerperforschung FAX 0711/6891502 Heisenbergstr. 1 70569 Stuttgart U.Wedig at fkf.mpg.de ----------------------------------------------------------------- -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200312/5d358b3c/attachment.htm From lange12 at llnl.gov Thu Mar 26 20:40:38 2020 From: lange12 at llnl.gov (Lange, Andrew) Date: Thu, 26 Mar 2020 19:40:38 +0000 Subject: [xcrysden] Issues running XCrySDen for the first time (error while loading shared libraries: libTog12.0.dll: cannot open shared object file: No such file or directory) Message-ID: Hi All, I am a new user and am having difficulty running XCrySDen for the first time. I'm using the pre-compiled Cygwin version 1.6.2. I believe I've install all of the required packaged through the Cygwin installer. Here is what I see after I start an Xterm and send the ./xcrysden command within the parent, unpackaged tar.gz directory (note error in bold): $ ./xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2014 by Anton Kokalj *| |* *| |*****************************************************************| +-----------------------------------------------------------------+ Version: 1.6.2 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, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999. Code available from http://www.xcrysden.org/. XCRYSDEN_TOPDIR=/cygdrive/c/Users/lange12/Desktop/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp .../xcrysden-1.6.2-bin-shared/bin/xcrys.exe: error while lo ading shared libraries: libTogl2.0.dll: cannot open shared object file: No such file or directory Seems that tcl-togl is not installed, but here's the proof: Cygwin Package Information Package Version Status tcl-togl 2.0-4 OK Thanks in advance for any ideas! Best, Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200326/5fc3fea4/attachment.htm From john.kissane at tyndall.ie Thu Mar 26 21:21:05 2020 From: john.kissane at tyndall.ie (John Kissane) Date: Thu, 26 Mar 2020 20:21:05 +0000 Subject: [xcrysden] Issues running XCrySDen for the first time (error while loading shared libraries: libTog12.0.dll: cannot open shared object file: No such file or directory) In-Reply-To: References: Message-ID: <6FF414E46FCAF642936FA32D5A06493F01AFE7E4AC@MAILBOXSERVER.tyndall.ie> I had a similar problem with that library but on Linux rather than Cygwin. See this discussion on the forum which might be of help. http://www.democritos.it/pipermail/xcrysden/2020-February/001982.html John. ________________________________ From: xcrysden-bounces at democritos.it [xcrysden-bounces at democritos.it] on behalf of Lange, Andrew [lange12 at llnl.gov] Sent: 26 March 2020 19:40 To: xcrysden at democritos.it Subject: [xcrysden] Issues running XCrySDen for the first time (error while loading shared libraries: libTog12.0.dll: cannot open shared object file: No such file or directory) Hi All, I am a new user and am having difficulty running XCrySDen for the first time. I?m using the pre-compiled Cygwin version 1.6.2. I believe I?ve install all of the required packaged through the Cygwin installer. Here is what I see after I start an Xterm and send the ./xcrysden command within the parent, unpackaged tar.gz directory (note error in bold): $ ./xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2014 by Anton Kokalj *| |* *| |*****************************************************************| +-----------------------------------------------------------------+ Version: 1.6.2 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, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999. Code available from http://www.xcrysden.org/. XCRYSDEN_TOPDIR=/cygdrive/c/Users/lange12/Desktop/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp ?/xcrysden-1.6.2-bin-shared/bin/xcrys.exe: error while lo ading shared libraries: libTogl2.0.dll: cannot open shared object file: No such file or directory Seems that tcl-togl is not installed, but here?s the proof: Cygwin Package Information Package Version Status tcl-togl 2.0-4 OK Thanks in advance for any ideas! Best, Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200326/36d3f9ee/attachment-0001.htm From john.kissane at tyndall.ie Thu Mar 26 21:23:17 2020 From: john.kissane at tyndall.ie (John Kissane) Date: Thu, 26 Mar 2020 20:23:17 +0000 Subject: [xcrysden] Issues running XCrySDen for the first time (error while loading shared libraries: libTog12.0.dll: cannot open shared object file: No such file or directory) In-Reply-To: References: Message-ID: <6FF414E46FCAF642936FA32D5A06493F01AFE7E4C5@MAILBOXSERVER.tyndall.ie> I had a similar problem but on Linux rather than Cygwin. See this discussion on the forum in case it's of help. http://www.democritos.it/pipermail/xcrysden/2020-February/001982.html John. ________________________________ From: xcrysden-bounces at democritos.it [xcrysden-bounces at democritos.it] on behalf of Lange, Andrew [lange12 at llnl.gov] Sent: 26 March 2020 19:40 To: xcrysden at democritos.it Subject: [xcrysden] Issues running XCrySDen for the first time (error while loading shared libraries: libTog12.0.dll: cannot open shared object file: No suh file or directory) Hi All, I am a new user and am having difficulty running XCrySDen for the first time. I?m using the pre-compiled Cygwin version 1.6.2. I believe I?ve install all of the required packaged through the Cygwin installer. Here is what I see after I start an Xterm and send the ./xcrysden command within the parent, unpackaged tar.gz directory (note error in bold): $ ./xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2014 by Anton Kokalj *| |* *| |*****************************************************************| +-----------------------------------------------------------------+ Version: 1.6.2 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, J. Mol. Graph. Model., Vol. 17, pp. 176-179, 1999. Code available from http://www.xcrysden.org/. XCRYSDEN_TOPDIR=/cygdrive/c/Users/lange12/Desktop/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp ?/xcrysden-1.6.2-bin-shared/bin/xcrys.exe: error while lo ading shared libraries: libTogl2.0.dll: cannot open shared object file: No such file or directory Seems that tcl-togl is not installed, but here?s the proof: Cygwin Package Information Package Version Status tcl-togl 2.0-4 OK Thanks in advance for any ideas! Best, Andrew -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200326/b27fc658/attachment.htm From matic.poberznik at gmail.com Thu Mar 26 22:31:30 2020 From: matic.poberznik at gmail.com (Matic) Date: Thu, 26 Mar 2020 22:31:30 +0100 Subject: [xcrysden] Issues running XCrySDen for the first time (error while loading shared libraries: libTog12.0.dll: cannot open shared object file: No such file or directory) In-Reply-To: <6FF414E46FCAF642936FA32D5A06493F01AFE7E4C5@MAILBOXSERVER.tyndall.ie> References: <6FF414E46FCAF642936FA32D5A06493F01AFE7E4C5@MAILBOXSERVER.tyndall.ie> Message-ID: <6eb40553-a88b-1184-5b42-5dddcc3d40d9@gmail.com> Hi Andrew, cygwin has a peculiar issue that it doesn't find libraries in /usr/lib, so for it to find the library just add /usr/lib to your path (check that libTogl2.0.dll is there, alternatively it can be in /usr/lib/Togl2.0). Add this line to your ~/.bashrc file: export PATH=$PATH:/usr/lib and then type command: source ~/.bashrc Best Regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, Ljubljana, Slovenia From lange12 at llnl.gov Thu Mar 26 22:50:43 2020 From: lange12 at llnl.gov (Lange, Andrew) Date: Thu, 26 Mar 2020 21:50:43 +0000 Subject: [xcrysden] Issues running XCrySDen for the first time (error while loading shared libraries: libTog12.0.dll: cannot open shared object file: No such file or directory) In-Reply-To: <6eb40553-a88b-1184-5b42-5dddcc3d40d9@gmail.com> References: <6FF414E46FCAF642936FA32D5A06493F01AFE7E4C5@MAILBOXSERVER.tyndall.ie> <6eb40553-a88b-1184-5b42-5dddcc3d40d9@gmail.com> Message-ID: Hi Matic, That worked, thanks! -Andrew -----Original Message----- From: xcrysden-bounces at democritos.it On Behalf Of Matic Sent: Thursday, March 26, 2020 2:32 PM To: XCrySDen mailing list Subject: Re: [xcrysden] Issues running XCrySDen for the first time (error while loading shared libraries: libTog12.0.dll: cannot open shared object file: No such file or directory) Hi Andrew, cygwin has a peculiar issue that it doesn't find libraries in /usr/lib, so for it to find the library just add /usr/lib to your path (check that libTogl2.0.dll is there, alternatively it can be in /usr/lib/Togl2.0). Add this line to your ~/.bashrc file: export PATH=$PATH:/usr/lib and then type command: source ~/.bashrc Best Regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, Ljubljana, Slovenia _______________________________________________ XCrySDen mailing list XCrySDen at democritos.it http://www.democritos.it/mailman/listinfo/xcrysden