From prasantabandyopadhyay.rs at visva-bharati.ac.in Thu Sep 15 12:40:35 2016 From: prasantabandyopadhyay.rs at visva-bharati.ac.in (Prasanta Bandyopadhyay) Date: Thu, 15 Sep 2016 16:10:35 +0530 Subject: [xcrysden] Installation Guidance Message-ID: Respected members, I am all new to the Xcrysden. Want to use it in windows PC with cygwin, but I can install it. I have seen the installation guides but still nowhere ( probably because I am not well aware about linux command systems) . Can anyone provide some simplified or video tutorials? Thanks in advance Sent with Mailtrack -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160915/efdb97cd/attachment.htm From marsusi at aut.ac.ir Thu Sep 15 14:46:57 2016 From: marsusi at aut.ac.ir (FARAH MARSUSI) Date: Thu, 15 Sep 2016 17:16:57 +0430 Subject: [xcrysden] visualization of vectors Message-ID: <1473943617591389491@aut.ac.ir> Dear Users, In order to visualise phonon modes by xcrysden, I added the atomic displacement vector to the structure specification section of the xsf file, as described in specification of forces in xcrysden doc. But nothing has happened and the "Force setting" icon is not active in "Modify' menu. Any help would be so appreciated. Best regards, F. Marsusi, Assistant Professor, Department of Physics, Amirkabir University of Technology.? Best regards, F. Marsusi, Assistant Professor, Department of Physics, Amirkabir University of Technology.? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160915/d6ce6431/attachment.htm From tone.kokalj at ijs.si Sat Sep 17 12:33:12 2016 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Sat, 17 Sep 2016 12:33:12 +0200 Subject: [xcrysden] Installation Guidance In-Reply-To: References: Message-ID: <1474108392.3105.10.camel@ijs.si> On Thu, 2016-09-15 at 16:10 +0530, Prasanta Bandyopadhyay wrote: > Respected members, > I am all new to the Xcrysden. Want to use it in windows PC with > cygwin, but I can install it. Do you instead mean that you "cannot" install it? Best regards, Tone -- J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia? (tel: +386-1-477-3523 // fax: +386-1-251-9385) From tone.kokalj at ijs.si Sat Sep 17 12:30:34 2016 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Sat, 17 Sep 2016 12:30:34 +0200 Subject: [xcrysden] visualization of vectors In-Reply-To: <1473943617591389491@aut.ac.ir> References: <1473943617591389491@aut.ac.ir> Message-ID: <1474108234.3105.8.camel@ijs.si> On Thu, 2016-09-15 at 17:16 +0430, FARAH MARSUSI wrote: > Dear Users, > > In order to visualise phonon modes by xcrysden, I added the atomic > displacement vector to the structure specification section of the xsf > file, as described in specification of forces in xcrysden doc. But > nothing has happened and the "Force setting" icon is not active in > "Modify' menu.? > Any help would be so appreciated.? To check what is going on, please provide your xsf file. Best regards, Tone Kokalj -- J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia? (tel: +386-1-477-3523 // fax: +386-1-251-9385) From matic.poberznik at gmail.com Mon Sep 19 16:33:16 2016 From: matic.poberznik at gmail.com (=?UTF-8?Q?Matic_Pober=C5=BEnik?=) Date: Mon, 19 Sep 2016 16:33:16 +0200 Subject: [xcrysden] Installation Guidance In-Reply-To: <1474108392.3105.10.camel@ijs.si> References: <1474108392.3105.10.camel@ijs.si> Message-ID: Dear Prasanta, Unfortunately there are no simple video tutorials, but the installation should be straightforward nonetheless. Make sure that you download the latest xcrysden package for cygwin (i.e. http://www.xcrysden.org/Download.html/ xcrysden-1.5.60-cygwin.tar.gz ) ### Copy it to your cygwin directory (cygdrive), and unpack it in a directory of your choice. To unpack it in the current working directory ($PWD) use the command: tar -xvf xcrysden-1.5.60-cygwin.tar.gz This should create a new directory in your $PWD named xcrysden-1.5.60-bin-shared (i.e. $PWD/xcrysden-1.5.60-bin-shared). In this directory you will find the file README.cygwin and in it a list of packages xcrysden depends upon. You need to install these packages as well, the best way to do so is by using the apt-cyg package. How to install it with cygwin is described here: https://www.fir3net.com/UNIX/Linux/cygwin-package-installation.html With this package manager you can install the other packages easily with the command: apt-cyg install package-name package-name2 ... The packages listed should be enough for xcrysden to work, be careful though, you need to start the xserver before it works, this is done with the command: startx This by default starts the xterm app, from which you can then run xcrysden, go to your $PWD/xcrysden-1.5.60-bin-shared/ using cd and start xcrysden from there with the command: ./xcrysden ### This is the minimum required for xcrysden to run; however I suggest the following: Add the unpack directory to the $PATH variable, which enables you to run xcrysden from any directory using just the command xcrysden This is done by adding a line to your .bashrc file (found in your home directory). Open it with your favorite text editor (i.e. pluma .bashrc), and add a line: export PATH=$PWD/xcrysden-1.5.60-bin-shared/:$PATH and save the file. (Note: instead of $PWD use the full path name) Source the changes with: source .bashrc and you should be able to run xcrysden from any directory (within cygwin). To get a more linux-like usage you can install a desktop environment as well, for example the mate desktop environment: https://cygwin.com/ml/cygwin-xfree-announce/2014-10/msg00003.html https://darrengoossens.wordpress.com/2015/02/04/using-mate-desktop-by-default-in-cygwin/ The startx command then starts the desktop environment, and by opening a terminal of your choice you can then start xcrysden in the same way as before, only it will now open in a virtual desktop that is your cygwin window. I hope this helps, if anything is unclear or doesn't work please let me know. Best Regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia 2016-09-17 12:33 GMT+02:00 Tone Kokalj : > On Thu, 2016-09-15 at 16:10 +0530, Prasanta Bandyopadhyay wrote: > > Respected members, > > I am all new to the Xcrysden. Want to use it in windows PC with > > cygwin, but I can install it. > > > Do you instead mean that you "cannot" install it? > > Best regards, Tone > -- > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > (tel: +386-1-477-3523 // fax: +386-1-251-9385) > > _______________________________________________ > 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/20160919/db3b19aa/attachment.htm From uttamphy at gmail.com Fri Sep 23 10:33:14 2016 From: uttamphy at gmail.com (Uttam Paliwal) Date: Fri, 23 Sep 2016 14:03:14 +0530 Subject: [xcrysden] problem on cygwin In-Reply-To: <3942f3a7-6c78-aa90-b3c9-66cc38bd3f59@gmail.com> References: <3942f3a7-6c78-aa90-b3c9-66cc38bd3f59@gmail.com> Message-ID: respected prof Poberznik thanks for your kind suppoort. I am compiling xcrsyden-1.5.53-cygwin on cygwin with X server. When i run ./xcrysden then found following error Error in startup script: *conflicting versions provided for package* "Tk": 8.5.18, then 8.5 while executing "package provide Tk $tk_version" (file "/cygdrive/c/XcrySDen-1.4.1bin-shared/Tcl/xcInit.tcl" line 400) kindly provide solution thanks and regards On Tue, Aug 30, 2016 at 1:30 PM, Matic Poberznik wrote: > Dear Uttam, > > I suggest you download the latest binary of xcrysden for cygwin > (xcrysden-1.5.60-cygwin.tar.gz) from here: > > http://www.xcrysden.org/Download.html > > > "package provide Tk $tk_version" > > (file "/cygdrive/c/XcrySDen-1.4.1bin-shared/Tcl/xcInit.tcl" line > 400) > > """ > > Make sure you install other required packages as well, I think the above > error results from missing the tcl-tk package. > > > Application initialization failed: no display name and no $DISPLAY > > environment variable > > I think this error is from missing the xorg-server package, you should > install it. I suggest that you install some kind of desktop environment > as well (e.g. mate desktop environment), some instructions on how to do > this are here: > > http://www.cygwin.com/xfree/docs/ug/using.html > > Hope this helps. > > Best regards, > > Matic > > > Matic Poberznik > J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- Uttam Paliwal *Assistant Professor* Department of Physics J.N.V. University Jodhpur (India) Phone- 7597908441 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160923/a29d1ded/attachment.htm From matic.poberznik at gmail.com Fri Sep 23 11:20:06 2016 From: matic.poberznik at gmail.com (Matic Poberznik) Date: Fri, 23 Sep 2016 11:20:06 +0200 Subject: [xcrysden] problem on cygwin In-Reply-To: References: <3942f3a7-6c78-aa90-b3c9-66cc38bd3f59@gmail.com> Message-ID: <0c416f4c-2d64-265f-5a68-b0621635c208@gmail.com> Dear Uttam, > thanks for your kind suppoort. I am compiling xcrsyden-1.5.53-cygwin on > cygwin with X server. When i run ./xcrysden then found following error I suggest you try the most recent package that has been pre-compiled for cygwin (i.e version 1.5.60 instead of 1.5.53). You can find it here: http://www.xcrysden.org/Download.html choose the package: xcrysden-1.5.60-cygwin.tar.gz When unpacked, the directory should have the name: xcrysden-1.5.60-bin-shared and not XcrySDen-1.4.1bin-shared > Error in startup script: *conflicting versions provided for package* > "Tk": 8.5.18, then 8.5 > while executing > "package provide Tk $tk_version" > (file "/cygdrive/c/XcrySDen-1.4.1bin-shared/Tcl/xcInit.tcl" line 400) The error itself seems to come from conflicting tcl-tk package versions. If the problem persists with the new version try to uninstall and reinstall that package with apt-cyg. Best Regards, Matic -- Matic Poberznik J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia From uttamphy at gmail.com Sat Sep 24 10:41:51 2016 From: uttamphy at gmail.com (Uttam Paliwal) Date: Sat, 24 Sep 2016 14:11:51 +0530 Subject: [xcrysden] error while running ./xcrysden Message-ID: i am compiling xcrysden-1.5.53-bin-cygwin version on window 7 using cygwin. when i run ./xcrysden then founf following error ./xcrysden: line 163: /cygdrive/c/XcrySDen-1.4.1bin-shared/scripts/xcLib.sh: No such file or directory kindly suggest answer -- Uttam Paliwal *Assistant Professor* Department of Physics J.N.V. University Jodhpur (India) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160924/db92cb7c/attachment.htm From gsabo at crimson.ua.edu Sun Sep 25 17:06:02 2016 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Sun, 25 Sep 2016 09:06:02 -0600 Subject: [xcrysden] error while running ./xcrysden In-Reply-To: References: Message-ID: <07befbe9-d877-bf1b-5a12-9717ddab1f31@crimson.ua.edu> I do not understand, because a) I see no mention of whether you used the 32 bit (setup-x86.exe) or 64 bit (setup-x86_64.exe) cygwin installation file. b) I don't know why you are compiling xcrysden-1.5.53-bin-cygwin. Assuming that you are using the 64 bit version of cygwin, you should try the xcrysden-1.5.60-cygwin.tar.gz binary package. If you are using the 32 bit cygwin, you should try the xcrysden-1.5.53-cygwin.tar.gz binary package. The xcrysden-1.5.60-cygwin.tar.gz and xcrysden-1.5.53-cygwin.tar.gz are already compiled. So you don't compile them. c) You say that you used xcrysden-1.5.53-cygwin.tar.gz, but the path in your email seems to indicate that your tried to run an older XcrySDen-1.4.1bin-shared. Maybe the set directory for XCRYSDEN_TOPDIR in .bashrc is pointing to the wrong location [ http://www.xcrysden.org/doc/install.html#__toc__4 ]. d) If you need to compile the xcrysden version 1.5.60 for 32 bit cygwin, you need the xcrysden-1.5.60.tar.gz source package. The steps for compiling under 64 bit cygwin on Windows 7 Professional could be used as a guide, but you would have to modify those steps yourself for compiling under 32 bit cygwin: http://www.democritos.it/pipermail/xcrysden/2014-July/001635.html On 9/24/2016 2:41 AM, Uttam Paliwal wrote: > > i am compiling xcrysden-1.5.53-bin-cygwin version on window 7 using > cygwin. when i run ./xcrysden then founf following error > > > ./xcrysden: line 163: > /cygdrive/c/XcrySDen-1.4.1bin-shared/scripts/xcLib.sh: No such file or > directory > > kindly suggest answer > > -- > Uttam Paliwal > *Assistant Professor*** > Department of Physics > J.N.V. University > Jodhpur (India) -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20160925/49c332d3/attachment.htm From tone.kokalj at ijs.si Tue Sep 27 10:03:18 2016 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Tue, 27 Sep 2016 10:03:18 +0200 Subject: [xcrysden] error while running ./xcrysden In-Reply-To: References: Message-ID: <1474963398.29885.14.camel@ijs.si> On Sat, 2016-09-24 at 14:11 +0530, Uttam Paliwal wrote: > > i am compiling xcrysden-1.5.53-bin-cygwin version on window 7 using > cygwin. when i run ./xcrysden then? founf following error? > > > ./xcrysden: line 163: /cygdrive/c/XcrySDen-1.4.1bin- > shared/scripts/xcLib.sh: No such file or directory > > kindly suggest answer Most likely you have the XCRYSDEN_TOPDIR variable defined in your ~/.bashrc file that points to an old 1.4.1 installation. As a quick check, cd into new xcrysden directory and do the following: unset XCRYSDEN_TOPDIR ./xcrysden If it works then the reason is the above one. Edit the ~/.bashrc file and remove the XCRYSDEN_TOPDIR definition (for new versions it is not required anymore). Best regards, Tone --? J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia? (tel: +386-1-477-3523 // fax: +386-1-251-9385)