From tone.kokalj at ijs.si Fri Feb 7 19:12:01 2020 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 07 Feb 2020 19:12:01 +0100 Subject: [xcrysden] Software development position in IOM-CNR, Trieste Message-ID: <7c57589a9dcd3f9608ad19c26c82a0fde5d4f85e.camel@ijs.si> A post-doctoral position in the field of electronic-structure software development is available at IOM-CNR, Trieste, Italy. The position, funded by the MaX - Materials at the exascale EU Horizon2020 Centre of Excellence, is for one year, renewable for another year. Requirements include a PhD in a scientific discipline and research experience in computer simulations and/or in scientific software programming. Experience with density-functional theory (DFT) calculations, especially with the plane wave-pseudopotential method, is a plus. The successful candidate will work on the Quantum ESPRESSO software distribution in one or more of the following topics, depending upon his/her skill set: - development of new methods and algorithms for advanced DFT functionals; - refactoring and modularisation of the code basis, notably for first- principle molecular dynamics, linear response, computational spectroscopy; - porting of Quantum ESPRESSO new heterogeneous accelerated architectures (e.g., GPUs); - improvement of Quantum ESPRESSO user experience, users? and developers? documentation, testing. The work requires coordination and interactions with the Quantum ESPRESSO users' and developers' community and with the MaX EU Centre of Excellence. The official announcement and forms are available at the following link: https://bandi.urp.cnr.it/doc-assegni/documentazione/9530_DOC_IT. pdf (English version at page 10 and 17-21). Interested people, including those not satisfying all requirements, may contact Paolo Giannozzi for more information. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200207/b28c004e/attachment.htm From yangjio4849 at hotmail.com Sun Feb 9 04:39:27 2020 From: yangjio4849 at hotmail.com (John Yang) Date: Sun, 9 Feb 2020 03:39:27 +0000 Subject: [xcrysden] xcrysden 1.6.2 can't startup Message-ID: Hi all, This is John. I downloaded the source code of xcrysden 1.6.2. I planned to play it on my CentOS 8 installed in VMware. Since it is the newest version, I naively assumed xcrysden 1.6.2 can work well on my 3000x2000 resolution screen. Looking at older version of xcrysden is too painful. I started with the Make.sys-semishared, and did small adjustments. During the process, I have many packages installed by yum. Finally make went through without error. But when I tried to run ./xcrysden, it gave me this: Error in startup script: bad pad value "0m": must be positive screen distance while executing "pack .title.f.l .title.f.l2 -side top -fill both -padx 0m -pady 0m" invoked from within "if { "[lindex $argv 2]" != "--quiet" } { # MACOSX has problems with wm iconify/wm deiconify requests, so # don't use them if { $tcl_plat..." So dead end for me. I also tried xcrysden-1.6.2-bin-shared, same error message. Please help me out of this. Thank you so much. I can provide any information necessary. --------------------- John -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200209/e7ecfe05/attachment.htm From tone.kokalj at ijs.si Mon Feb 10 13:24:59 2020 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 10 Feb 2020 13:24:59 +0100 Subject: [xcrysden] xcrysden 1.6.2 can't startup In-Reply-To: References: Message-ID: On Sun, 2020-02-09 at 03:39 +0000, John Yang wrote: > Hi all, > > This is John. I downloaded the source code of xcrysden 1.6.2. I > planned to play it on my CentOS 8 installed in VMware. Since it is > the newest version, I naively assumed xcrysden 1.6.2 can work well on > my 3000x2000 resolution screen. Looking at older version of xcrysden > is too painful. > I started with the Make.sys-semishared, and did small adjustments. > During the process, I have many packages installed by yum. Finally > make went through without error. > But when I tried to run ./xcrysden, it gave me this: > > Error in startup script: bad pad value "0m": must be positive screen > distance > while executing > "pack .title.f.l .title.f.l2 -side top -fill both -padx 0m -pady 0m" This appears like a system problem: it seems your X cannot convert "millimeter" units to pixels. Check with xdpyinfo, i.e.: xdpyinfo | grep dimensions I get: dimensions: 1680x1050 pixels (444x277 millimeters) but I suppose you will get something like: dimensions: 3000x2000 pixels (0x0 millimeters) You can solve this with: xrandr --dpi 96 The alternative is that you modify the xcrysden code and replace the millimeter specs with the pixel specs. For the particular error you got, edit the Tcl/xcInit.tcl file and change "0m" to "0" in the line: "pack .title.f.l .title.f.l2 -side top -fill both -padx 0m -pady 0m" Best regards, Tone -- Jo?ef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386- 1-477-3523 // fax: +386-1-251-9385) From yangjio4849 at hotmail.com Tue Feb 11 13:25:48 2020 From: yangjio4849 at hotmail.com (John Yang) Date: Tue, 11 Feb 2020 12:25:48 +0000 Subject: [xcrysden] =?utf-8?b?IOWbnuWkjTogIHhjcnlzZGVuIDEuNi4yIGNhbid0IHN0?= =?utf-8?q?artup?= In-Reply-To: References: , Message-ID: Hi Tone, After xrandr --dpi 96, I still got: dimensions: 3000x2000 pixels (0x0 millimeters) resolution: -2147483648x-2147483648 dots per inch Please look at the resolution, a very funny value. I start to suspect it is because I?m using the VMware rather than an physical monitor. Everytime I maximize, full screen the guest system CentOS 8, the monitor does changes. And I don?t even have a monitor.conf in /etc/X11/xorg.conf.d . Very strange. Anyway, thanks for your help. --------------------- John ???: Tone Kokalj ????: 2020?2?10? 20:25 ???: xcrysden at democritos.it ??: Re: [xcrysden] xcrysden 1.6.2 can't startup On Sun, 2020-02-09 at 03:39 +0000, John Yang wrote: > Hi all, > > This is John. I downloaded the source code of xcrysden 1.6.2. I > planned to play it on my CentOS 8 installed in VMware. Since it is > the newest version, I naively assumed xcrysden 1.6.2 can work well on > my 3000x2000 resolution screen. Looking at older version of xcrysden > is too painful. > I started with the Make.sys-semishared, and did small adjustments. > During the process, I have many packages installed by yum. Finally > make went through without error. > But when I tried to run ./xcrysden, it gave me this: > > Error in startup script: bad pad value "0m": must be positive screen > distance > while executing > "pack .title.f.l .title.f.l2 -side top -fill both -padx 0m -pady 0m" This appears like a system problem: it seems your X cannot convert "millimeter" units to pixels. Check with xdpyinfo, i.e.: xdpyinfo | grep dimensions I get: dimensions: 1680x1050 pixels (444x277 millimeters) but I suppose you will get something like: dimensions: 3000x2000 pixels (0x0 millimeters) You can solve this with: xrandr --dpi 96 The alternative is that you modify the xcrysden code and replace the millimeter specs with the pixel specs. For the particular error you got, edit the Tcl/xcInit.tcl file and change "0m" to "0" in the line: "pack .title.f.l .title.f.l2 -side top -fill both -padx 0m -pady 0m" Best regards, Tone -- Jo?ef 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/20200211/12b0261e/attachment.htm From john.kissane at tyndall.ie Fri Feb 28 13:12:48 2020 From: john.kissane at tyndall.ie (John Kissane) Date: Fri, 28 Feb 2020 12:12:48 +0000 Subject: [xcrysden] XCrySDen on Fedora 30 Message-ID: <3e4bdb75a133224439a0bf201f903f6808e0a364.camel@tyndall.ie> Hello, one of our researchers asked me to install this software on Fedora 30 but the current version (1.6.2) doesn't work due to a missing library: /local/XCrySDen/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libTogl.so.2: cannot open shared object file: No such file or directory 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. xcrysden-1.6.2-bin-shared]$ ./xcrysden +-----------------------------------------------------------------+ |*****************************************************************| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---------------------------------------------------------------*| |* *| |* Anton Kokalj (tone.kokalj at ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2019 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=/local/XCrySDen/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp Running on platform : unix Operating system : Linux Package ImageMagick's convert: /usr/bin/convert Package ImageMagick's import: /usr/bin/import Package Ppmtompeg: /usr/bin/ppmtompeg Package Babel: /usr/bin/babel Package Xwd: /usr/bin/xwd Executing: /local/XCrySDen/xcrysden-1.6.2-bin-shared/bin/ftnunit Error in startup script: Can not set ident to a window path name Couldn't configure togl widget while executing "togl .mesa -width 400 -height 400 -ident .mesa -rgba $toglOpt(rgba) -redsize $toglOpt(redsize..." (procedure "PlaceGlobWin" line 107) invoked from within "PlaceGlobWin 0 [expr round(670 * $fac1)] [expr round(670 * $fac1)]" (procedure "ViewMol" line 25) invoked from within "ViewMol ." invoked from within "if { [llength $argv] > 2 } { parseComLinArg [lrange $argv 2 end] } else { ViewMol . }" (file "/local/XCrySDen/xcrysden-1.6.2-bin-shared/Tcl/xcInit.tcl" line 633) The previous version 1.5.60 is working ok but would be nice to have the latest. Just wondering if anybody has come across a workaround for this? Thanks! -- University College Cork Lee Maltings Dyke Parade Cork, Ireland -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200228/17621d67/attachment.htm From matic.poberznik at gmail.com Fri Feb 28 14:12:14 2020 From: matic.poberznik at gmail.com (Matic) Date: Fri, 28 Feb 2020 14:12:14 +0100 Subject: [xcrysden] XCrySDen on Fedora 30 In-Reply-To: <3e4bdb75a133224439a0bf201f903f6808e0a364.camel@tyndall.ie> References: <3e4bdb75a133224439a0bf201f903f6808e0a364.camel@tyndall.ie> Message-ID: <98517b57-e397-73ed-f215-c3f3a330f241@gmail.com> 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 -- Matic Poberznik J. Stefan Institute, Jamova 39, Ljubljana, Slovenia From john.kissane at tyndall.ie Fri Feb 28 15:48:50 2020 From: john.kissane at tyndall.ie (John Kissane) Date: Fri, 28 Feb 2020 14:48:50 +0000 Subject: [xcrysden] XCrySDen on Fedora 30 In-Reply-To: <98517b57-e397-73ed-f215-c3f3a330f241@gmail.com> References: <3e4bdb75a133224439a0bf201f903f6808e0a364.camel@tyndall.ie> <98517b57-e397-73ed-f215-c3f3a330f241@gmail.com> Message-ID: Thanks very much for the pointer Matic. I downloaded the 64 bit version of that file, created a softlink in its lib folder : libTogl.so.2 -> libTogl2.0.so And then added a line to the script that starts XCrySDen: export LD_LIBRARY_PATH=/opt/XCrySDen/Togl2.0-8.4-Linux/lib/Togl2.0 Thanks & regards, John -- University College Cork Lee Maltings Dyke Parade Cork, Ireland 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 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200228/fbcc6db7/attachment-0001.htm