From U.Wedig at fkf.mpg.de Fri Jun 19 11:33:26 2020 From: U.Wedig at fkf.mpg.de (Ulrich Wedig) Date: Fri, 19 Jun 2020 11:33:26 +0200 Subject: [xcrysden] XCrySDen on Linux, X-Server on Windows Message-ID: <24c55bbe-1880-8abd-aa62-fd2e99564a56@fkf.mpg.de> Dear XCrySDen user, in times of Covid-19 and home-office you sometimes have to proceed unconventionally. I'm running XCrySDen (1.6.2) on a Linux node in the institute, using the X-Server on my Windows-PC at home (Xming). This is of course not the most efficient way to display 3D-graphics. A local Cygwin installations is surely faster. However the remote execution as described above may be reasonable, if e.g. the CRYSTAL integration is needed, e.g. with the properties menu. Using the standard distribution of XCrySDen does not work in this way. It is known, that the accumulation buffer has to be disabled, if XCrySDen is running on Windows. This is captured in the file $XCRYSDEN_TOPDIR/Tcl/toglOpt.tcl. However in the above case, XCrySDen runs on Linux with accumulation buffer enabled, only the x-server on Windows, giving the error 'Couldn't configure togl widget'. In order to cure this behaviour, I added the following lines to toglOpt.tcl: ??? # XCrysden running in Linux with X-Server (like Xming) on Windows ??? # toglOpt(accum) = false (set environment variable IF_XMING to Xming) ??? if { [info exists env(IF_XMING)] } { ??????? if { [string match -nocase *Xming* $env(IF_XMING)] } { ??????????????? # disable accumulation buffer ??????????????? set toglOpt(accum) false ??????????????? puts stderr "?? accumulation buffer disabled" ??????? } ??? } If I now define (and export) the environment variable IF_XMING=Xming, the accumulation buffer will be disabled, and XCrySDen is running properly with my local Windows X-server. Best regards, Ulrich -- ----------------------------------------------------------------- Dr. Ulrich Wedig Tel. 0711/6891535 Max-Planck-Institut fuer Festkoerperforschung FAX 0711/6891502 Heisenbergstr. 1 70569 Stuttgart U.Wedig at fkf.mpg.de ----------------------------------------------------------------- From martin at ruby.chemie.uni-freiburg.de Fri Jun 19 14:58:53 2020 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Fri, 19 Jun 2020 14:58:53 +0200 (CEST) Subject: [xcrysden] XCrySDen on Linux, X-Server on Windows In-Reply-To: <24c55bbe-1880-8abd-aa62-fd2e99564a56@fkf.mpg.de> Message-ID: <20200619125853.205ABF008FD@ruby.chemie.uni-freiburg.de> I wonder if this can be automated further by relying on the presence of the environment variable DISNO that XMing seems to use to store its display number, rather than having to define your own ? Also with 1.6.2 it should be possible to specify Togl options in your private configuration file (.xcrysden/custom-definitions) rather than having to mess with the global settings in the tcl scripts directly. Regards Martin > Dear XCrySDen user, > > in times of Covid-19 and home-office you sometimes have to proceed > unconventionally. > > I'm running XCrySDen (1.6.2) on a Linux node in the institute, using the > X-Server on my Windows-PC at home (Xming). > > This is of course not the most efficient way to display 3D-graphics. A > local Cygwin installations is surely faster. However the remote > execution as described above may be reasonable, if e.g. the CRYSTAL > integration is needed, e.g. with the properties menu. > > Using the standard distribution of XCrySDen does not work in this way. > It is known, that the accumulation buffer has to be disabled, if > XCrySDen is running on Windows. This is captured in the file > $XCRYSDEN_TOPDIR/Tcl/toglOpt.tcl. However in the above case, XCrySDen > runs on Linux with accumulation buffer enabled, only the x-server on > Windows, giving the error 'Couldn't configure togl widget'. > > In order to cure this behaviour, I added the following lines to toglOpt.tcl: > > ??? # XCrysden running in Linux with X-Server (like Xming) on Windows > ??? # toglOpt(accum) = false (set environment variable IF_XMING to Xming) > > ??? if { [info exists env(IF_XMING)] } { > ??????? if { [string match -nocase *Xming* $env(IF_XMING)] } { > ??????????????? # disable accumulation buffer > ??????????????? set toglOpt(accum) false > ??????????????? puts stderr "?? accumulation buffer disabled" > ??????? } > ??? } > > If I now define (and export) the environment variable IF_XMING=Xming, > the accumulation buffer will be disabled, and XCrySDen is running > properly with my local Windows X-server. > > Best regards, > > Ulrich > > -- > ----------------------------------------------------------------- > Dr. Ulrich Wedig Tel. 0711/6891535 > Max-Planck-Institut fuer Festkoerperforschung FAX 0711/6891502 > Heisenbergstr. 1 > 70569 Stuttgart U.Wedig at fkf.mpg.de > ----------------------------------------------------------------- > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > -- 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 Fri Jun 19 15:22:39 2020 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 19 Jun 2020 15:22:39 +0200 Subject: [xcrysden] XCrySDen on Linux, X-Server on Windows In-Reply-To: <20200619125853.205ABF008FD@ruby.chemie.uni-freiburg.de> References: <20200619125853.205ABF008FD@ruby.chemie.uni-freiburg.de> Message-ID: <8697cb8ac05566b79f29b1658523f6c89cc60262.camel@ijs.si> On Fri, 2020-06-19 at 14:58 +0200, Martin Kroeker wrote: > I wonder if this can be automated further by relying on the presence > of the environment variable DISNO that XMing seems to use to store > its display number, rather than having to define your own ? Dear Urlich and Martin Thanks for the useful "inputs". I agree with Martin: the check should rely on some system variable rather than the user defined variable. > Also with 1.6.2 it should be possible to specify Togl options in > your private configuration file (.xcrysden/custom-definitions) > rather than having to mess with the global settings in the tcl > scripts directly. Such manual specification is, of course, always possible, but if toglOpt(accum) = false is de-facto required for Xming, then it can be automated as suggested above. Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From mforti at cnea.gov.ar Mon Jun 22 18:45:45 2020 From: mforti at cnea.gov.ar (Mariano Forti) Date: Mon, 22 Jun 2020 13:45:45 -0300 Subject: [xcrysden] version 1.6 in open suse Message-ID: Hellow everybody ! I am tryng to install xcrysden in opensuse 15.1. the main problem is that libtogl is not in the repositories ( I could not find it). I downloaded the sourceforge files and installed to /usr/lib64 in my computer. however, when trying to run xcrysden, I get the error: /usr/local/xcrysden-1.6.2-bin-shared//bin/xcrys: error while loading shared libraries: libTogl.so.2: wrong ELF class: ELFCLASS32 I placed the libTogl.so.2 in various places: /usr/lib/libTogl.so.2 /usr/lib64/libTogl.so.2 but the bin/xcrys files can not find the library: ldd /usr/local/xcrysden-1.6.2-bin-shared/bin/xcrys ... ?libTogl.so.2 => not found ... (it is the only one that says not found!) I also tried to compile from source with no success , but I will insist on that later Thankyou all for your help! -- Mariano Forti From john.kissane at tyndall.ie Mon Jun 22 18:56:31 2020 From: john.kissane at tyndall.ie (John Kissane) Date: Mon, 22 Jun 2020 16:56:31 +0000 Subject: [xcrysden] version 1.6 in open suse In-Reply-To: References: Message-ID: <6FF414E46FCAF642936FA32D5A06493F01AFEC9060@MAILBOXSERVER.tyndall.ie> Had a problem with that library in Fedora also, this was the fix that worked for me. (I compiled my own version): On Fri, 2020-02-28 at 14:12 +0100, Matic wrote: Hi John, what you are missing is libtogl2 (at least that is the package name in debian): https://packages.debian.org/buster/libtogl2 I tried the old trick of linking the newer version that comes with Fedora 30 but that then produces a different error: #ln -s /usr/lib64/tcl8.6/Togl2.1/libTogl2.1.so libTogl.so. It seems very strange to that the version of Togl in Fedora is 2.1, whereas the latest listed on the Togl download page is 2.0: http://togl.sourceforge.net/download.html#getting I would suggest you try to compile this package and add the path to the $LD_LIBRARY_PATH or find a Fedora equivalent package for Togl2.0. I hope this helps, Best, Matic -----Original Message----- From: xcrysden-bounces at democritos.it On Behalf Of Mariano Forti Sent: Monday 22 June 2020 17:46 To: xcrysden at democritos.it Subject: [xcrysden] version 1.6 in open suse Hellow everybody ! I am tryng to install xcrysden in opensuse 15.1. the main problem is that libtogl is not in the repositories ( I could not find it). I downloaded the sourceforge files and installed to /usr/lib64 in my computer. however, when trying to run xcrysden, I get the error: /usr/local/xcrysden-1.6.2-bin-shared//bin/xcrys: error while loading shared libraries: libTogl.so.2: wrong ELF class: ELFCLASS32 I placed the libTogl.so.2 in various places: /usr/lib/libTogl.so.2 /usr/lib64/libTogl.so.2 but the bin/xcrys files can not find the library: ldd /usr/local/xcrysden-1.6.2-bin-shared/bin/xcrys ... libTogl.so.2 => not found ... (it is the only one that says not found!) I also tried to compile from source with no success , but I will insist on that later Thankyou all for your help! -- Mariano Forti _______________________________________________ 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/20200622/71570d90/attachment.htm From martin at ruby.chemie.uni-freiburg.de Mon Jun 22 19:15:51 2020 From: martin at ruby.chemie.uni-freiburg.de (Martin Kroeker) Date: Mon, 22 Jun 2020 19:15:51 +0200 (CEST) Subject: [xcrysden] version 1.6 in open suse In-Reply-To: Message-ID: <20200622171551.96D5AF0092C@ruby.chemie.uni-freiburg.de> The error message basically says "your libTogl is a 32bit library" while your xcrysden is 64bit. What errors did you get when compiling Togl from source ? > Hellow everybody ! I am tryng to install xcrysden in opensuse 15.1. the > main problem is that libtogl is not in the repositories ( I could not > find it). I downloaded the sourceforge files and installed to /usr/lib64 > in my computer. > > however, when trying to run xcrysden, I get the error: > > /usr/local/xcrysden-1.6.2-bin-shared//bin/xcrys: error while loading > shared libraries: libTogl.so.2: wrong ELF class: ELFCLASS32 > -- 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 gsabo at crimson.ua.edu Wed Jun 24 09:08:38 2020 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Wed, 24 Jun 2020 01:08:38 -0600 Subject: [xcrysden] version 1.6 in open suse In-Reply-To: References: Message-ID: Have you tried Togl2.0-8.4-Linux64.tar.gz at: https://sourceforge.net/projects/togl/files/Togl/2.0/ username at linux-6hha:~> cat /etc/os-release NAME="openSUSE Leap" VERSION="15.1 " ID="opensuse-leap" ID_LIKE="suse opensuse" VERSION_ID="15.1" PRETTY_NAME="openSUSE Leap 15.1" ANSI_COLOR="0;32" CPE_NAME="cpe:/o:opensuse:leap:15.1" BUG_REPORT_URL="https://bugs.opensuse.org" HOME_URL="https://www.opensuse.org/" username at linux-6hha:~> wget http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz ... username at linux-6hha:~> tar xvf xcrysden-1.6.2-linux_x86_64-shared.tar.gz ... username at linux-6hha:~> sudo zypper install libgfortran5 ... Continue? [y/n/v/...? shows all options] (y): y ... username at linux-6hha:~> sudo zypper install openbabel ... Continue? [y/n/v/...? shows all options] (y): y ... username at linux-6hha:~> sudo zypper install ImageMagick ... Continue? [y/n/v/...? shows all options] (y): y ... username at linux-6hha:~> sudo zypper install tk ... 'tk' is already installed. ... username at linux-6hha:~> sudo zypper install libfftw3-3 ... 'libfftw3-3' is already installed. ... username at linux-6hha:~> sudo zypper install libXmu6 ... 'libXmu6' is already installed. ... username at linux-6hha:~> sudo zypper install libGLU1 ... 'libGLU1' is already installed. ... username at linux-6hha:~/Togl2.0> sudo zypper install tcllib ... Continue? [y/n/v/...? shows all options] (y): y ... username at linux-6hha:~> wget https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-8.4-Linux64.tar.gz/download ... tar xvf download ... username at linux-6hha:~> ln -s /home/username/Togl2.0-8.4-Linux/lib/Togl2.0/libTogl2.0.so /home/username/Togl2.0-8.4-Linux/lib/libTogl.so.2 username at linux-6hha:~> echo "export XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2-bin-shared" >> ~/.bashrc username at linux-6hha:~> echo "export PATH=$PATH:$XCRYSDEN_TOPDIR" >> ~/.bashrc username at linux-6hha:~> echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0-8.4-Linux/lib" >> ~/.bashrc username at linux-6hha:~> source ~/.bashrc username at linux-6hha:~> xcrysden On 6/22/2020 10:45 AM, Mariano Forti wrote: > Hellow everybody ! I am tryng to install xcrysden in opensuse 15.1. the > main problem is that libtogl is not in the repositories ( I could not > find it). I downloaded the sourceforge files and installed to /usr/lib64 > in my computer. > > however, when trying to run xcrysden, I get the error: > > /usr/local/xcrysden-1.6.2-bin-shared//bin/xcrys: error while loading > shared libraries: libTogl.so.2: wrong ELF class: ELFCLASS32 > > I placed the libTogl.so.2 in various places: > > /usr/lib/libTogl.so.2 > /usr/lib64/libTogl.so.2 > > but the bin/xcrys files can not find the library: > > ldd /usr/local/xcrysden-1.6.2-bin-shared/bin/xcrys > > ... > > ?libTogl.so.2 => not found > > ... > > (it is the only one that says not found!) > > > I also tried to compile from source with no success , but I will insist > on that later > > > Thankyou all for your help! > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200624/abf6b1a4/attachment.htm From mforti at cnea.gov.ar Wed Jun 24 11:22:39 2020 From: mforti at cnea.gov.ar (Mariano Forti) Date: Wed, 24 Jun 2020 06:22:39 -0300 Subject: [xcrysden] version 1.6 in open suse In-Reply-To: References: Message-ID: <369ed4da-fc1d-a1e8-9b08-807ab9432353@cnea.gov.ar> Yes , the linux64 version of the library solved the issue! thanks for the reply ! Mariano Forti Ingeniero en Materiales, Instituto Sabato. marianodforti at gmail.com www.mendeley.com/profiles/mariano-forti/ Unidad de Actividad Materiales Comisi?n de Energ?a At?mica (+5411)67727832 mforti at cnea.gov.ar Argentina On 24/6/20 04:08, Gavin Abo wrote: > > Have you tried Togl2.0-8.4-Linux64.tar.gz at: > > https://sourceforge.net/projects/togl/files/Togl/2.0/ > > username at linux-6hha:~> cat /etc/os-release > NAME="openSUSE Leap" > VERSION="15.1 " > ID="opensuse-leap" > ID_LIKE="suse opensuse" > VERSION_ID="15.1" > PRETTY_NAME="openSUSE Leap 15.1" > ANSI_COLOR="0;32" > CPE_NAME="cpe:/o:opensuse:leap:15.1" > BUG_REPORT_URL="https://bugs.opensuse.org" > HOME_URL="https://www.opensuse.org/" > username at linux-6hha:~> wget > http://www.xcrysden.org/download/xcrysden-1.6.2-linux_x86_64-shared.tar.gz > ... > username at linux-6hha:~> tar xvf xcrysden-1.6.2-linux_x86_64-shared.tar.gz > ... > username at linux-6hha:~> sudo zypper install libgfortran5 > ... > Continue? [y/n/v/...? shows all options] (y): y > ... > username at linux-6hha:~> sudo zypper install openbabel > ... > Continue? [y/n/v/...? shows all options] (y): y > ... > username at linux-6hha:~> sudo zypper install ImageMagick > ... > Continue? [y/n/v/...? shows all options] (y): y > ... > username at linux-6hha:~> sudo zypper install tk > ... > 'tk' is already installed. > ... > username at linux-6hha:~> sudo zypper install libfftw3-3 > ... > 'libfftw3-3' is already installed. > ... > username at linux-6hha:~> sudo zypper install libXmu6 > ... > 'libXmu6' is already installed. > ... > username at linux-6hha:~> sudo zypper install libGLU1 > ... > 'libGLU1' is already installed. > ... > username at linux-6hha:~/Togl2.0> sudo zypper install tcllib > ... > Continue? [y/n/v/...? shows all options] (y): y > ... > username at linux-6hha:~> wget > https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-8.4-Linux64.tar.gz/download > ... > tar xvf download > ... > username at linux-6hha:~> ln -s > /home/username/Togl2.0-8.4-Linux/lib/Togl2.0/libTogl2.0.so > /home/username/Togl2.0-8.4-Linux/lib/libTogl.so.2 > username at linux-6hha:~> echo "export > XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2-bin-shared" >> ~/.bashrc > username at linux-6hha:~> echo "export PATH=$PATH:$XCRYSDEN_TOPDIR" >> > ~/.bashrc > username at linux-6hha:~> echo "export > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0-8.4-Linux/lib" > >> ~/.bashrc > username at linux-6hha:~> source ~/.bashrc > username at linux-6hha:~> xcrysden > > On 6/22/2020 10:45 AM, Mariano Forti wrote: >> Hellow everybody ! I am tryng to install xcrysden in opensuse 15.1. the >> main problem is that libtogl is not in the repositories ( I could not >> find it). I downloaded the sourceforge files and installed to /usr/lib64 >> in my computer. >> >> however, when trying to run xcrysden, I get the error: >> >> /usr/local/xcrysden-1.6.2-bin-shared//bin/xcrys: error while loading >> shared libraries: libTogl.so.2: wrong ELF class: ELFCLASS32 >> >> I placed the libTogl.so.2 in various places: >> >> /usr/lib/libTogl.so.2 >> /usr/lib64/libTogl.so.2 >> >> but the bin/xcrys files can not find the library: >> >> ldd /usr/local/xcrysden-1.6.2-bin-shared/bin/xcrys >> >> ... >> >> ?libTogl.so.2 => not found >> >> ... >> >> (it is the only one that says not found!) >> >> >> I also tried to compile from source with no success , but I will insist >> on that later >> >> >> Thankyou all for your help! >> > > _______________________________________________ > 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/20200624/c159921a/attachment.htm From hongyi.zhao at gmail.com Thu Jun 25 13:34:41 2020 From: hongyi.zhao at gmail.com (Hongyi Zhao) Date: Thu, 25 Jun 2020 19:34:41 +0800 Subject: [xcrysden] Isovolume option on xcrysden's isosurface/property-plane controls panel. Message-ID: Hi, I'm reading the wannier90's solution booklet from here: https://github.com/wannier-developers/wannier90/blob/2f4aed6a35ab7e8b38dbe196aa4925ab3e9deb1b/doc/solution_booklet/Example1.tex#L60 It told the following options for using xcrysden to plot the wannier functions: Degree of triCubic Spline = 3; Isovolume = 0.95; Render +/- isovalue = yes But I really cannot find the `Isovolume' option, instead, only the `Isovalue' option existed on the xcrysden's isosurface/property-plane controls panel. Any hints for this problem? -- Hongyi Zhao From hongyi.zhao at gmail.com Thu Jun 25 14:03:08 2020 From: hongyi.zhao at gmail.com (Hongyi Zhao) Date: Thu, 25 Jun 2020 20:03:08 +0800 Subject: [xcrysden] Convert xsf to povray for plotting the isosurface. Message-ID: Hi, The following image: https://github.com/hongyi-zhao/test/blob/master/AsGa_MLWF/gaas_00001.png is created by xcrysden with the following file: https://github.com/hongyi-zhao/test/blob/master/AsGa_MLWF/gaas_00001.xsf The method and parameter used here are as follows: in the Tools --> Data Grid section: Xcrysden: Tools --> Data Grid Degree of triCubic Spline = 3; Isovalue = 0.95; Render +/- isovalue = yes But I want to render the output with povray for further image quality enhancement. Any hints for this job? -- Hongyi Zhao