From tone.kokalj at ijs.si Fri Apr 2 10:55:55 2021 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 02 Apr 2021 10:55:55 +0200 Subject: [xcrysden] MaX e-School on Advanced Materials and Molecular Modelling with Quantum ESPRESSO (17 - 28 May 2021) Message-ID: <8b9561d45db776fe233cd07fc7c0fc3d081abd6b.camel@ijs.si> The ICTP in collaboration with MaX and the Quantum ESPRESSO Foundation, together with the support of SISSA, CECAM, Shangai University, CINECA and the Jo?ef Stefan Institute hosts the first "MaX e-School on Advanced Materials and Molecular Modelling with Quantum ESPRESSO". The virtual event is scheduled between 17 and 28 May 2021 (registration deadline: 30 April 2021) The school will introduce students and young researchers to materials and molecular modelling with Quantum ESPRESSO (QE), covering basic concepts, recent advances and developments, with emphasis on density- functional-theory (DFT) based methods and high-performance computing (HPC). The school aims to train beginners in computational materials sciences to the efficient use of QE on modern massively parallel architectures, with special emphasis on the emerging architectures based on GPGPUs and on the use of advanced tools for generating, managing, storing, and sharing results. Additional detailed information as well as the link to the online form for application are available at the following link: http://indico.ictp.it/event/9616 Organizers: Stefano Baroni (SISSA) Ralph Gebauer (ICTP) Anton Kokalj (Jo?ef Stefan Institute) Wei Ren (Shanghai University) Alessandro Stroppa (CNR-Spin) Local Organizer: Ivan Girotto (ICTP) From bnrj.rudra at live.com Wed Apr 7 09:45:10 2021 From: bnrj.rudra at live.com (Rudra Banerjee) Date: Wed, 7 Apr 2021 07:45:10 +0000 Subject: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) Message-ID: Hi, I am trying to run xcrysden in fedora 34. On running xcrysden, I am getting error: CRYSDEN_TOPDIR=/opt/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp/xcrys_tmp Running on platform : unix Operating system : Linux Package ImageMagick's convert: /usr/bin/convert Package ImageMagick's import: /usr/bin/import Executing: /opt/xcrysden-1.6.2-bin-shared/bin/ftnunit Error in startup script: 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 "/opt/xcrysden-1.6.2-bin-shared/Tcl/xcInit.tcl" line 633) This is apparently identical to http://www.democritos.it/pipermail/xcrysden/2020-February/001980.html which was working until fedora 33. But on 34, in spite of having Togl in xcrysden itself as Togl2.0-8.4-Linux as /opt/xcrysden-1.6.2-bin- shared/Togl2.0-8.4-Linux/lib and libTogl.so.2 -> libTogl2.0.so I am still facing the same error. Kindly help. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210407/18527203/attachment.htm From gsabo at crimson.ua.edu Mon Apr 19 06:19:58 2021 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Sun, 18 Apr 2021 22:19:58 -0600 Subject: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) In-Reply-To: References: Message-ID: <9795fa95-ab1d-dce7-0e6d-9a615b7e3955@crimson.ua.edu> If it helps, the simplest way to get xcrysden 1.6.2 to run in Fedora 34 might be to compile it from source. The following seemed to work in a virtual machine (i.e., VirtualBox) on Windows 10.? So it will most likely work starting at step 10 on a computer when Fedora 34 is installed on the 'hardware' instead of in a 'virtual machine'. 1. Went to: https://getfedora.org/en/workstation/download/ 2. Downloaded Fedora 34: x86_64 DVD ISO: Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso 3. Went to: https://www.virtualbox.org/wiki/Downloads 4. Downloaded Windows hosts: VirtualBox-6.1.18-142142-Win.exe 5. Installed VirtualBox in Windows 10 ?? a. Ran: VirtualBox-6.1.18-142142-Win.exe ?? b. Clicked Next ?? c. Clicked Next ?? d. Clicked Next ?? e. Clicked Yes ?? f. Clicked Install ?? g. Clicked Finish 6. If needed, enable 64 bit virtualization as described at: https://superuser.com/questions/1241956/virtualbox-only-allowing-32-bit-os 7. Setup VirtualBox ?? a. On desktop, ran: Oracle VM VirtualBox ?? b. Clicked Machine -> New... ?? c. For Name typed: Fedora 34 ?? d. Selected Type: Linux ?? e. Selected Version: Fedora (64 bit) ?? f. Clicked Next ?? g. Put 3064 and click Next ?? h. Selected "Create a virtual hard disk now" and click Create ?? i. Selected "VDI (Virtual Disk Image" and click Next ?? j. Selected "Dynamically allocated" and click Next ?? k. Put 50.00 GB and click Create ?? l. Under Storage, click on [Optical Drive] Empty, click "Choose a disk file..." and open Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso ?? n. Click Settings -> System -> Processor, set Processors to 2, then click OK ?? n. Clicked Start 8. Installed Fedora 34 ?? a. Selected "Start Fedora-Workstation-Live 34_Beta" ?? b. Clicked "Install to Hard Drive" ?? c. Selected English and clicked Continue ?? d. Clicked "I want to proceed" ?? e. Clicked "Installation Destination" ?? f. Clicked Done ?? g. Clicked "Begin Installation" ?? h. Clicked "Finish Installation" ?? i. In Fedora Live click on battery icon, click Poweroff/Log Out -> Power Off... and Power Off ?? j. Under Storage in VirtualBox, click on [Optical Drive] Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso and clicked "Remove disk form virtual drive" ?? k. In VirtualBox, clicked Start 9. Setup Fedora 34 ?? a. Clicked "Start Setup" ?? b. Turn off "Location Services" and "Automatic Problem Reporting", then click Next ?? c. Click "Skip" to Online Accounts ?? d. Type a Full Name and Username and click Next ?? e. Type a password and click Next ?? f. Click "Start Using Fedora" 10. Opened a terminal in Fedora 34 and performed the following: [username at fedora ~]$ sudo yum install patch ImageMagick openbabel mesa-libGL-devel mesa-libGLU-devel tcl-devel tk-devel fftw-devel libXmu-devel gfortran ... Is this ok [y/N]: y ... [username at fedora ~]$ wget https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-src.tar.gz/download ... [username at fedora ~]$ tar xvf download ... [username at fedora ~]$ cd Togl2.0/ [username at fedora Togl2.0]$ ./configure --with-tcl=/usr/lib64 --with-tk=/usr/lib64 --enable-64bit [username at fedora Togl2.0]$ make [username at fedora Togl2.0]$ cd .. [username at fedora ~]$ wget http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz ... [username at fedora ~]$ tar xvf xcrysden-1.6.2.tar.gz ... [username at fedora ~]$ cd xcrysden-1.6.2/ [username at fedora xcrysden-1.6.2]$ cp system/Make.sys-semishared Make.sys [username at fedora xcrysden-1.6.2]$ wget https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Make-fedora34.patch ... [username at fedora xcrysden-1.6.2]$ patch -b Make.sys Make-fedora34.patch patching file Make.sys [username at fedora xcrysden-1.6.2]$ make all ... [username at fedora xcrysden-1.6.2]$ echo 'export XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2'>>~/.bashrc [username at fedora xcrysden-1.6.2]$ echo 'export PATH=$PATH:$XCRYSDEN_TOPDIR'>>~/.bashrc [username at fedora xcrysden-1.6.2]$ echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0'>>~/.bashrc [username at fedora xcrysden-1.6.2]$ source ~/.bashrc On 4/7/2021 1:45 AM, Rudra Banerjee wrote: > Hi, > > I am trying to run xcrysden? in fedora 34. > On running xcrysden, I am getting error: > > CRYSDEN_TOPDIR=/opt/xcrysden-1.6.2-bin-shared > XCRYSDEN_SCRATCH=/tmp/xcrys_tmp > > Running on platform : unix > ? ?Operating system : Linux > Package ImageMagick's convert: /usr/bin/convert > Package ImageMagick's import: /usr/bin/import > Executing: /opt/xcrysden-1.6.2-bin-shared/bin/ftnunit > Error in startup script: > 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 "/opt/xcrysden-1.6.2-bin-shared/Tcl/xcInit.tcl" line 633) > > This is apparently identical to > http://www.democritos.it/pipermail/xcrysden/2020-February/001980.html > > > which was working until fedora 33. But on 34, in spite of having Togl > in xcrysden itself as Togl2.0-8.4-Linux as /opt/xcrysden-1.6.2-bin- > shared/Togl2.0-8.4-Linux/lib and libTogl.so.2 ->libTogl2.0.so > > I am still facing the same error. > > Kindly help. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210418/6d75a4eb/attachment-0001.htm From melendez at unex.es Fri Apr 23 17:02:07 2021 From: melendez at unex.es (Juan Jose Melendez Martinez) Date: Fri, 23 Apr 2021 17:02:07 +0200 (CEST) Subject: [xcrysden] Saving the grid for an expanded system Message-ID: <1506966585.67296069.1619190127584.JavaMail.zimbra@unex.es> Dear all I have generated a supercell by expanding a single unit cell along each crystal axis; xcrysden behaves very nicely for this. I can also expand a 3D grid defined for the unit cell to the whole supercell, and then I can see the charge distribution within the latter, for instance. Once I got the grid (say the charge density) in the whole supercell, I saved it via the "Save Grid" command. And then I found a couple of issues: 1) The xsf file saved from the previous procedure contains the atoms in the supercell. However, when I load the file, I get the unit cell, not the supercell that I expected. 2) I realized that the grid was saved for the unit cell only, not for the whole supercell. I can expand the grid again, but I cannot use it to compute charge differences, for instance. Did any of you experience something like this before? Any help, please? Thanks very much in advance. Juanjo Juan J. Mel?ndez Department of Physics University of Extremadura Badajoz (Spain) From gsabo at crimson.ua.edu Sat Apr 24 18:44:03 2021 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Sat, 24 Apr 2021 10:44:03 -0600 Subject: [xcrysden] Saving the grid for an expanded system In-Reply-To: <1506966585.67296069.1619190127584.JavaMail.zimbra@unex.es> References: <1506966585.67296069.1619190127584.JavaMail.zimbra@unex.es> Message-ID: <7cec0d4e-1186-f9b0-35d5-a0af502a78d2@crimson.ua.edu> If I recall correctly, while viewing a unit cell in xcrysden, there is option that can be selected that can repeat the unit cell in different directions so that it looks like a supercell.? It only worked view only and could not edit and save the structure. What you describe is similar to that, so the behavior you describe sounds normal for xcrysden but others in the mailing list may correct me if I'm wrong about that. If you want xcryden to show the supercell instead of unit cell, you most likely have to go back to your DFT program and change it there from a unit cell to a supercell.? For example, if you were using WEIN2k, you would have to change case.struct file. As described at http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html WIEN2k has a "supercell" or "structeditor" program that can take the unit cell and duplicate it in multiple directions to have a supercell. If you feel it is not necessary for you to have the supercell in the DFT calculation, either rerun the charge density calculation on the unit cell to get the view as you described or you could look into modifying the case.xsf file by hand.? The XSF format is described at: http://www.xcrysden.org/doc/XSF.html On 4/23/2021 9:02 AM, Juan Jose Melendez Martinez wrote: > Dear all > > I have generated a supercell by expanding a single unit cell along each crystal axis; xcrysden behaves very nicely for this. I can also expand a 3D grid defined for the unit cell to the whole supercell, and then I can see the charge distribution within the latter, for instance. Once I got the grid (say the charge density) in the whole supercell, I saved it via the "Save Grid" command. And then I found a couple of issues: > > 1) The xsf file saved from the previous procedure contains the atoms in the supercell. However, when I load the file, I get the unit cell, not the supercell that I expected. > > 2) I realized that the grid was saved for the unit cell only, not for the whole supercell. I can expand the grid again, but I cannot use it to compute charge differences, for instance. > > Did any of you experience something like this before? Any help, please? > > Thanks very much in advance. > > Juanjo > > Juan J. Mel?ndez > Department of Physics > University of Extremadura > Badajoz (Spain) From melendez at unex.es Mon Apr 26 09:44:12 2021 From: melendez at unex.es (=?utf-8?Q?Juanjo_Mel=C3=A9ndez?=) Date: Mon, 26 Apr 2021 09:44:12 +0200 Subject: [xcrysden] Saving the grid for an expanded system In-Reply-To: <7cec0d4e-1186-f9b0-35d5-a0af502a78d2@crimson.ua.edu> References: <1506966585.67296069.1619190127584.JavaMail.zimbra@unex.es> <7cec0d4e-1186-f9b0-35d5-a0af502a78d2@crimson.ua.edu> Message-ID: Dear Gavin Thanks for your reply. I think that it will be easier to edit the xsf file. Thanks a lot! Best Juanjo Juan J. Mel?ndez Mart?nez Departamento de F?sica Universidad de Extremadura Avda. de Elvas, s/n 06006 Badajoz Tel?fono: 924 28 96 55 Fax: 924 28 96 51 Email: melendez at unex.es Web: materiales.unex.es/miembros/personal/jj-melendez/Index.html > El 24 abr 2021, a las 18:44, Gavin Abo escribi?: > > If I recall correctly, while viewing a unit cell in xcrysden, there is > option that can be selected that can repeat the unit cell in different > directions so that it looks like a supercell. It only worked view only > and could not edit and save the structure. What you describe is similar > to that, so the behavior you describe sounds normal for xcrysden but > others in the mailing list may correct me if I'm wrong about that. > > If you want xcryden to show the supercell instead of unit cell, you most > likely have to go back to your DFT program and change it there from a > unit cell to a supercell. For example, if you were using WEIN2k, you > would have to change case.struct file. > > As described at > > http://susi.theochem.tuwien.ac.at/reg_user/faq/supercells.html > > WIEN2k has a "supercell" or "structeditor" program that can take the > unit cell and duplicate it in multiple directions to have a supercell. > > If you feel it is not necessary for you to have the supercell in the DFT > calculation, either rerun the charge density calculation on the unit > cell to get the view as you described or you could look into modifying > the case.xsf file by hand. The XSF format is described at: > > http://www.xcrysden.org/doc/XSF.html > > On 4/23/2021 9:02 AM, Juan Jose Melendez Martinez wrote: >> Dear all >> >> I have generated a supercell by expanding a single unit cell along each crystal axis; xcrysden behaves very nicely for this. I can also expand a 3D grid defined for the unit cell to the whole supercell, and then I can see the charge distribution within the latter, for instance. Once I got the grid (say the charge density) in the whole supercell, I saved it via the "Save Grid" command. And then I found a couple of issues: >> >> 1) The xsf file saved from the previous procedure contains the atoms in the supercell. However, when I load the file, I get the unit cell, not the supercell that I expected. >> >> 2) I realized that the grid was saved for the unit cell only, not for the whole supercell. I can expand the grid again, but I cannot use it to compute charge differences, for instance. >> >> Did any of you experience something like this before? Any help, please? >> >> Thanks very much in advance. >> >> Juanjo >> >> Juan J. Mel?ndez >> Department of Physics >> University of Extremadura >> Badajoz (Spain) > _______________________________________________ > 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/20210426/961ae1a1/attachment.htm From bnrj.rudra at live.com Fri Apr 30 07:56:11 2021 From: bnrj.rudra at live.com (Rudra Banerjee) Date: Fri, 30 Apr 2021 05:56:11 +0000 Subject: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) In-Reply-To: <9795fa95-ab1d-dce7-0e6d-9a615b7e3955@crimson.ua.edu> References: , <9795fa95-ab1d-dce7-0e6d-9a615b7e3955@crimson.ua.edu> Message-ID: Dear all, I confirm that the problem reported is problem due to Wayland. in xorg, it is working fine. Is there any solution please? ________________________________ From: xcrysden-bounces at democritos.it on behalf of Gavin Abo Sent: 19 April 2021 09:49 To: xcrysden at democritos.it Subject: Re: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) If it helps, the simplest way to get xcrysden 1.6.2 to run in Fedora 34 might be to compile it from source. The following seemed to work in a virtual machine (i.e., VirtualBox) on Windows 10. So it will most likely work starting at step 10 on a computer when Fedora 34 is installed on the 'hardware' instead of in a 'virtual machine'. 1. Went to: https://getfedora.org/en/workstation/download/ 2. Downloaded Fedora 34: x86_64 DVD ISO: Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso 3. Went to: https://www.virtualbox.org/wiki/Downloads 4. Downloaded Windows hosts: VirtualBox-6.1.18-142142-Win.exe 5. Installed VirtualBox in Windows 10 a. Ran: VirtualBox-6.1.18-142142-Win.exe b. Clicked Next c. Clicked Next d. Clicked Next e. Clicked Yes f. Clicked Install g. Clicked Finish 6. If needed, enable 64 bit virtualization as described at: https://superuser.com/questions/1241956/virtualbox-only-allowing-32-bit-os 7. Setup VirtualBox a. On desktop, ran: Oracle VM VirtualBox b. Clicked Machine -> New... c. For Name typed: Fedora 34 d. Selected Type: Linux e. Selected Version: Fedora (64 bit) f. Clicked Next g. Put 3064 and click Next h. Selected "Create a virtual hard disk now" and click Create i. Selected "VDI (Virtual Disk Image" and click Next j. Selected "Dynamically allocated" and click Next k. Put 50.00 GB and click Create l. Under Storage, click on [Optical Drive] Empty, click "Choose a disk file..." and open Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso n. Click Settings -> System -> Processor, set Processors to 2, then click OK n. Clicked Start 8. Installed Fedora 34 a. Selected "Start Fedora-Workstation-Live 34_Beta" b. Clicked "Install to Hard Drive" c. Selected English and clicked Continue d. Clicked "I want to proceed" e. Clicked "Installation Destination" f. Clicked Done g. Clicked "Begin Installation" h. Clicked "Finish Installation" i. In Fedora Live click on battery icon, click Poweroff/Log Out -> Power Off... and Power Off j. Under Storage in VirtualBox, click on [Optical Drive] Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso and clicked "Remove disk form virtual drive" k. In VirtualBox, clicked Start 9. Setup Fedora 34 a. Clicked "Start Setup" b. Turn off "Location Services" and "Automatic Problem Reporting", then click Next c. Click "Skip" to Online Accounts d. Type a Full Name and Username and click Next e. Type a password and click Next f. Click "Start Using Fedora" 10. Opened a terminal in Fedora 34 and performed the following: [username at fedora ~]$ sudo yum install patch ImageMagick openbabel mesa-libGL-devel mesa-libGLU-devel tcl-devel tk-devel fftw-devel libXmu-devel gfortran ... Is this ok [y/N]: y ... [username at fedora ~]$ wget https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-src.tar.gz/download ... [username at fedora ~]$ tar xvf download ... [username at fedora ~]$ cd Togl2.0/ [username at fedora Togl2.0]$ ./configure --with-tcl=/usr/lib64 --with-tk=/usr/lib64 --enable-64bit [username at fedora Togl2.0]$ make [username at fedora Togl2.0]$ cd .. [username at fedora ~]$ wget http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz ... [username at fedora ~]$ tar xvf xcrysden-1.6.2.tar.gz ... [username at fedora ~]$ cd xcrysden-1.6.2/ [username at fedora xcrysden-1.6.2]$ cp system/Make.sys-semishared Make.sys [username at fedora xcrysden-1.6.2]$ wget https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Make-fedora34.patch ... [username at fedora xcrysden-1.6.2]$ patch -b Make.sys Make-fedora34.patch patching file Make.sys [username at fedora xcrysden-1.6.2]$ make all ... [username at fedora xcrysden-1.6.2]$ echo 'export XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2'>>~/.bashrc [username at fedora xcrysden-1.6.2]$ echo 'export PATH=$PATH:$XCRYSDEN_TOPDIR'>>~/.bashrc [username at fedora xcrysden-1.6.2]$ echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0'>>~/.bashrc [username at fedora xcrysden-1.6.2]$ source ~/.bashrc On 4/7/2021 1:45 AM, Rudra Banerjee wrote: Hi, I am trying to run xcrysden in fedora 34. On running xcrysden, I am getting error: CRYSDEN_TOPDIR=/opt/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp/xcrys_tmp Running on platform : unix Operating system : Linux Package ImageMagick's convert: /usr/bin/convert Package ImageMagick's import: /usr/bin/import Executing: /opt/xcrysden-1.6.2-bin-shared/bin/ftnunit Error in startup script: 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 "/opt/xcrysden-1.6.2-bin-shared/Tcl/xcInit.tcl" line 633) This is apparently identical to http://www.democritos.it/pipermail/xcrysden/2020-February/001980.html which was working until fedora 33. But on 34, in spite of having Togl in xcrysden itself as Togl2.0-8.4-Linux as /opt/xcrysden-1.6.2-bin- shared/Togl2.0-8.4-Linux/lib and libTogl.so.2 -> libTogl2.0.so I am still facing the same error. Kindly help. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210430/f1687a4e/attachment-0001.htm From gsabo at crimson.ua.edu Fri Apr 30 11:35:30 2021 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Fri, 30 Apr 2021 03:35:30 -0600 Subject: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) In-Reply-To: References: <9795fa95-ab1d-dce7-0e6d-9a615b7e3955@crimson.ua.edu> Message-ID: <0fc0d68e-5c39-0437-c778-950bdddd54c5@crimson.ua.edu> Thanks as I wasn't aware that Fedora switched Xorg to Wayland. That might explain why I had to compile xcrysden following the steps in my previous post below for it to work with Wayland. There is a lot of interesting information on Wayland. https://wiki.archlinux.org/index.php/wayland#XWayland https://gist.github.com/probonopd/9feb7c20257af5dd915e3a9f2d1f2277 https://www.osnews.com/story/132975/think-twice-before-abandoning-xorg-wayland-breaks-everything/ I haven't tried following Fedora's documentation myself yet to switch Wayland to XOrg to see if the xcrysden 1.6.2 binary package (xcrysden-1.6.2-linux_x86_64-shared.tar.gz) will run on my computer with having to compile it with (xcrysden-1.6.2.tar.gz). https://docs.fedoraproject.org/en-US/quick-docs/configuring-xorg-as-default-gnome-session/ On 4/29/2021 11:56 PM, Rudra Banerjee wrote: > Dear all, I confirm that the problem reported is problem due to > Wayland. in xorg, it is working fine. > Is there any solution please? > ------------------------------------------------------------------------ > *From:* xcrysden-bounces at democritos.it > on behalf of Gavin > *Sent:* 19 April 2021 09:49 > *To:* xcrysden at democritos.it > *Subject:* Re: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) > > If it helps, the simplest way to get xcrysden 1.6.2 to run in Fedora > 34 might be to compile it from source. The following seemed to work in > a virtual machine (i.e., VirtualBox) on Windows 10.? So it will most > likely work starting at step 10 on a computer when Fedora 34 is > installed on the 'hardware' instead of in a 'virtual machine'. > > 1. Went to: https://getfedora.org/en/workstation/download/ > > 2. Downloaded Fedora 34: x86_64 DVD ISO: > Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso > 3. Went to: https://www.virtualbox.org/wiki/Downloads > > 4. Downloaded Windows hosts: VirtualBox-6.1.18-142142-Win.exe > 5. Installed VirtualBox in Windows 10 > ?? a. Ran: VirtualBox-6.1.18-142142-Win.exe > ?? b. Clicked Next > ?? c. Clicked Next > ?? d. Clicked Next > ?? e. Clicked Yes > ?? f. Clicked Install > ?? g. Clicked Finish > 6. If needed, enable 64 bit virtualization as described at: > https://superuser.com/questions/1241956/virtualbox-only-allowing-32-bit-os > > 7. Setup VirtualBox > ?? a. On desktop, ran: Oracle VM VirtualBox > ?? b. Clicked Machine -> New... > ?? c. For Name typed: Fedora 34 > ?? d. Selected Type: Linux > ?? e. Selected Version: Fedora (64 bit) > ?? f. Clicked Next > ?? g. Put 3064 and click Next > ?? h. Selected "Create a virtual hard disk now" and click Create > ?? i. Selected "VDI (Virtual Disk Image" and click Next > ?? j. Selected "Dynamically allocated" and click Next > ?? k. Put 50.00 GB and click Create > ?? l. Under Storage, click on [Optical Drive] Empty, click "Choose a > disk file..." and open Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso > ?? n. Click Settings -> System -> Processor, set Processors to 2, then > click OK > ?? n. Clicked Start > 8. Installed Fedora 34 > ?? a. Selected "Start Fedora-Workstation-Live 34_Beta" > ?? b. Clicked "Install to Hard Drive" > ?? c. Selected English and clicked Continue > ?? d. Clicked "I want to proceed" > ?? e. Clicked "Installation Destination" > ?? f. Clicked Done > ?? g. Clicked "Begin Installation" > ?? h. Clicked "Finish Installation" > ?? i. In Fedora Live click on battery icon, click Poweroff/Log Out -> > Power Off... and Power Off > ?? j. Under Storage in VirtualBox, click on [Optical Drive] > Fedora-Workstation-Live-x86_64-34_Beta-1.3.iso and clicked "Remove > disk form virtual drive" > ?? k. In VirtualBox, clicked Start > 9. Setup Fedora 34 > ?? a. Clicked "Start Setup" > ?? b. Turn off "Location Services" and "Automatic Problem Reporting", > then click Next > ?? c. Click "Skip" to Online Accounts > ?? d. Type a Full Name and Username and click Next > ?? e. Type a password and click Next > ?? f. Click "Start Using Fedora" > 10. Opened a terminal in Fedora 34 and performed the following: > > [username at fedora ~]$ sudo yum install patch ImageMagick openbabel > mesa-libGL-devel mesa-libGLU-devel tcl-devel tk-devel fftw-devel > libXmu-devel gfortran > ... > Is this ok [y/N]: y > ... > [username at fedora ~]$ wget > https://sourceforge.net/projects/togl/files/Togl/2.0/Togl2.0-src.tar.gz/download > > ... > [username at fedora ~]$ tar xvf download > ... > [username at fedora ~]$ cd Togl2.0/ > [username at fedora Togl2.0]$ ./configure --with-tcl=/usr/lib64 > --with-tk=/usr/lib64 --enable-64bit > [username at fedora Togl2.0]$ make > [username at fedora Togl2.0]$ cd .. > [username at fedora ~]$ wget > http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz > > ... > [username at fedora ~]$ tar xvf xcrysden-1.6.2.tar.gz > ... > [username at fedora ~]$ cd xcrysden-1.6.2/ > [username at fedora xcrysden-1.6.2]$ cp system/Make.sys-semishared Make.sys > [username at fedora xcrysden-1.6.2]$ wget > https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Make-fedora34.patch > > ... > [username at fedora xcrysden-1.6.2]$ patch -b Make.sys Make-fedora34.patch > patching file Make.sys > [username at fedora xcrysden-1.6.2]$ make all > ... > [username at fedora xcrysden-1.6.2]$ echo 'export > XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2'>>~/.bashrc > [username at fedora xcrysden-1.6.2]$ echo 'export > PATH=$PATH:$XCRYSDEN_TOPDIR'>>~/.bashrc > [username at fedora xcrysden-1.6.2]$ echo 'export > LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/username/Togl2.0'>>~/.bashrc > [username at fedora xcrysden-1.6.2]$ source ~/.bashrc > > > On 4/7/2021 1:45 AM, Rudra Banerjee wrote: >> Hi, >> >> I am trying to run xcrysden? in fedora 34. >> On running xcrysden, I am getting error: >> >> CRYSDEN_TOPDIR=/opt/xcrysden-1.6.2-bin-shared >> XCRYSDEN_SCRATCH=/tmp/xcrys_tmp >> >> Running on platform : unix >> ? ?Operating system : Linux >> Package ImageMagick's convert: /usr/bin/convert >> Package ImageMagick's import: /usr/bin/import >> Executing: /opt/xcrysden-1.6.2-bin-shared/bin/ftnunit >> Error in startup script: >> 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 "/opt/xcrysden-1.6.2-bin-shared/Tcl/xcInit.tcl" line 633) >> >> This is apparently identical to >> http://www.democritos.it/pipermail/xcrysden/2020-February/001980.html >> >> >> which was working until fedora 33. But on 34, in spite of having Togl >> in xcrysden itself as Togl2.0-8.4-Linux as /opt/xcrysden-1.6.2-bin- >> shared/Togl2.0-8.4-Linux/lib and libTogl.so.2 ->libTogl2.0.so >> >> I am still facing the same error. >> >> Kindly help. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210430/0be335fa/attachment-0001.htm From gsabo at crimson.ua.edu Fri Apr 30 12:30:50 2021 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Fri, 30 Apr 2021 04:30:50 -0600 Subject: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) In-Reply-To: <0fc0d68e-5c39-0437-c778-950bdddd54c5@crimson.ua.edu> References: <9795fa95-ab1d-dce7-0e6d-9a615b7e3955@crimson.ua.edu> <0fc0d68e-5c39-0437-c778-950bdddd54c5@crimson.ua.edu> Message-ID: <1b7c55cb-6104-0130-bae5-6ee1e105d4b4@crimson.ua.edu> I can now confirm it also worked for me when I clicked the gear icon on the login screen on Fedora 34 and selected "GNOME on Xorg" following the Fedora documentation at: https://docs.fedoraproject.org/en-US/quick-docs/configuring-xorg-as-default-gnome-session/ I got the xcrysden-1.6.2-linux_x86_64-shared.tar.gz at http://www.xcrysden.org/Download.html and decompressed it (tar xvf xcrysden-1.6.2-linux_x86_64-shared.tar.gz). I got the Togl2.0-8.4-Linux64.tar.gz at https://sourceforge.net/projects/togl/files/Togl/2.0/ and decompressed it (tar xvf Togl2.0-8.4-Linux64.tar.gz). In the extracted Togl2.0-8.4-Linux\lib\Togl2.0 directory, I created a symbolic link (ln -s libTogl2.0.so libTogl.0.2) following the post at: http://www.democritos.it/pipermail/xcrysden/2020-February/001980.html I set XCRYSDEN_TOPDIR in my .bashrc: export XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2-bin-shared export PATH=$PATH:$XCRYSDEN_TOPDIR I set the LD_LIBRARY_PATH to the Togl2.0-8.4-Linux\lib\Togl2.0 directory following the post at: http://www.democritos.it/pipermail/xcrysden/2020-February/001982.html I closed and opened a new terminal to load the new .bashrc settings. Finally, it opened without error when I ran in a terminal the command: xcrysden On 4/30/2021 3:35 AM, Gavin Abo wrote: > > Thanks as I wasn't aware that Fedora switched Xorg to Wayland. That > might explain why I had to compile xcrysden following the steps in my > previous post below for it to work with Wayland. > > > There is a lot of interesting information on Wayland. > > > https://wiki.archlinux.org/index.php/wayland#XWayland > > https://gist.github.com/probonopd/9feb7c20257af5dd915e3a9f2d1f2277 > > https://www.osnews.com/story/132975/think-twice-before-abandoning-xorg-wayland-breaks-everything/ > > > I haven't tried following Fedora's documentation myself yet to switch > Wayland to XOrg to see if the xcrysden 1.6.2 binary package > (xcrysden-1.6.2-linux_x86_64-shared.tar.gz) will run on my computer > with having to compile it with (xcrysden-1.6.2.tar.gz). > > > https://docs.fedoraproject.org/en-US/quick-docs/configuring-xorg-as-default-gnome-session/ > > > On 4/29/2021 11:56 PM, Rudra Banerjee wrote: >> Dear all, I confirm that the problem reported is problem due to >> Wayland. in xorg, it is working fine. >> Is there any solution please? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210430/dc406f65/attachment.htm From bnrj.rudra at live.com Fri Apr 30 17:09:31 2021 From: bnrj.rudra at live.com (Rudra Banerjee) Date: Fri, 30 Apr 2021 15:09:31 +0000 Subject: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) In-Reply-To: <1b7c55cb-6104-0130-bae5-6ee1e105d4b4@crimson.ua.edu> References: <9795fa95-ab1d-dce7-0e6d-9a615b7e3955@crimson.ua.edu> <0fc0d68e-5c39-0437-c778-950bdddd54c5@crimson.ua.edu>, <1b7c55cb-6104-0130-bae5-6ee1e105d4b4@crimson.ua.edu> Message-ID: Dear Gavin, May I request you to confirm your virtualbox installation is in wayland? I have tried exact same process, and got the same error as notified. ________________________________ From: xcrysden-bounces at democritos.it on behalf of Gavin Abo Sent: 30 April 2021 16:00 To: xcrysden at democritos.it Subject: Re: [xcrysden] xcrysden not starting with fedora 34 (gnome 40) I can now confirm it also worked for me when I clicked the gear icon on the login screen on Fedora 34 and selected "GNOME on Xorg" following the Fedora documentation at: https://docs.fedoraproject.org/en-US/quick-docs/configuring-xorg-as-default-gnome-session/ I got the xcrysden-1.6.2-linux_x86_64-shared.tar.gz at http://www.xcrysden.org/Download.html and decompressed it (tar xvf xcrysden-1.6.2-linux_x86_64-shared.tar.gz). I got the Togl2.0-8.4-Linux64.tar.gz at https://sourceforge.net/projects/togl/files/Togl/2.0/ and decompressed it (tar xvf Togl2.0-8.4-Linux64.tar.gz). In the extracted Togl2.0-8.4-Linux\lib\Togl2.0 directory, I created a symbolic link (ln -s libTogl2.0.so libTogl.0.2) following the post at: http://www.democritos.it/pipermail/xcrysden/2020-February/001980.html I set XCRYSDEN_TOPDIR in my .bashrc: export XCRYSDEN_TOPDIR=/home/username/xcrysden-1.6.2-bin-shared export PATH=$PATH:$XCRYSDEN_TOPDIR I set the LD_LIBRARY_PATH to the Togl2.0-8.4-Linux\lib\Togl2.0 directory following the post at: http://www.democritos.it/pipermail/xcrysden/2020-February/001982.html I closed and opened a new terminal to load the new .bashrc settings. Finally, it opened without error when I ran in a terminal the command: xcrysden On 4/30/2021 3:35 AM, Gavin Abo wrote: Thanks as I wasn't aware that Fedora switched Xorg to Wayland. That might explain why I had to compile xcrysden following the steps in my previous post below for it to work with Wayland. There is a lot of interesting information on Wayland. https://wiki.archlinux.org/index.php/wayland#XWayland https://gist.github.com/probonopd/9feb7c20257af5dd915e3a9f2d1f2277 https://www.osnews.com/story/132975/think-twice-before-abandoning-xorg-wayland-breaks-everything/ I haven't tried following Fedora's documentation myself yet to switch Wayland to XOrg to see if the xcrysden 1.6.2 binary package (xcrysden-1.6.2-linux_x86_64-shared.tar.gz) will run on my computer with having to compile it with (xcrysden-1.6.2.tar.gz). https://docs.fedoraproject.org/en-US/quick-docs/configuring-xorg-as-default-gnome-session/ On 4/29/2021 11:56 PM, Rudra Banerjee wrote: Dear all, I confirm that the problem reported is problem due to Wayland. in xorg, it is working fine. Is there any solution please? -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20210430/3cad5d1e/attachment-0001.htm