Re: [Wien] XCrySDen
Dear Tone, You said; "This annoying issue will be fixed in the next release" I feel that this issue is not with XCrySDen but with "linux fedora 6.4.7" Tanks again Pablo Thank you, I updated my linux fedora; with linux fedora 6.2.15 there is no problem but with linux fedora 6.4.7 the letters are quite small - Linux fedora 6.2.15-100.fc36.x86_64 #1 SMP PREEMPT_DYNAMIC Thu May 11 16:51:53 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27 > 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux De: Wien en nombre de Tone Kokalj Enviado: jueves, 17 de agosto de 2023 04:10 a. m. Para: wien@zeus.theochem.tuwien.ac.at Asunto: Re: [Wien] XCrySDen Dear Pablo, You only upgraded the OS, or you got a new computer with a high screen resolution, such as Quad HD (2,560×1,440) or Ultra HD (3,840×2,160). For such high resolutions, xcrysden appearance is indeed awkward (too small). This annoying issue will be fixed in the next release. Best regards, Tone -- Jožef Stefan Institute, Ljubljana, Slovenia On Wed, 2023-08-09 at 18:36 +, delamora wrote: > I am having problems with XCrySDen; the figures and the letters are > very small. > I have the Fedora Linux; > --- > Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27 > 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > --- > In earlier versions I did not have this problem > > Saludos > > Pablo > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] XCrySDen
Thank you, I updated my linux fedora; with linux fedora 6.2.15 there is no problem but with linux fedora 6.4.7 the letters are quite small - Linux fedora 6.2.15-100.fc36.x86_64 #1 SMP PREEMPT_DYNAMIC Thu May 11 16:51:53 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27 > 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux De: Wien en nombre de Tone Kokalj Enviado: jueves, 17 de agosto de 2023 04:10 a. m. Para: wien@zeus.theochem.tuwien.ac.at Asunto: Re: [Wien] XCrySDen Dear Pablo, You only upgraded the OS, or you got a new computer with a high screen resolution, such as Quad HD (2,560×1,440) or Ultra HD (3,840×2,160). For such high resolutions, xcrysden appearance is indeed awkward (too small). This annoying issue will be fixed in the next release. Best regards, Tone -- Jožef Stefan Institute, Ljubljana, Slovenia On Wed, 2023-08-09 at 18:36 +, delamora wrote: > I am having problems with XCrySDen; the figures and the letters are > very small. > I have the Fedora Linux; > --- > Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27 > 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > --- > In earlier versions I did not have this problem > > Saludos > > Pablo > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] XCrySDen
Dear Pablo, You only upgraded the OS, or you got a new computer with a high screen resolution, such as Quad HD (2,560×1,440) or Ultra HD (3,840×2,160). For such high resolutions, xcrysden appearance is indeed awkward (too small). This annoying issue will be fixed in the next release. Best regards, Tone -- Jožef Stefan Institute, Ljubljana, Slovenia On Wed, 2023-08-09 at 18:36 +, delamora wrote: > I am having problems with XCrySDen; the figures and the letters are > very small. > I have the Fedora Linux; > --- > Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27 > 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux > --- > In earlier versions I did not have this problem > > Saludos > > Pablo > ___ > Wien mailing list > Wien@zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > SEARCH the MAILING-LIST at: > http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] XCrySDen
I am having problems with XCrySDen; the figures and the letters are very small. I have the Fedora Linux; --- Linux fedora 6.4.7-100.fc37.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Jul 27 19:56:37 UTC 2023 x86_64 x86_64 x86_64 GNU/Linux --- In earlier versions I did not have this problem Saludos Pablo ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] XCrySDen Version: 1.6.2
It might not work for other Linux distributions, but should it help, the following is what I did to install XCrySDen 1.6.2 for Ubuntu 22.04.2 LTS [1]. First, I checked if my system was set to Wayland or X11 [2]: username@computername:~/Desktop$ grep Wayland /etc/gdm3/custom.conf #WaylandEnable=false The above shows that Ubuntu after installation was set to Wayland. For using sudo commands, I had to be an administrator (or I had to ask my administrator to do those steps). The custom.conf file was edited [3]: username@computername:~/Desktop$ sudo gedit /etc/gdm3/custom.conf ... username@computername:~/Desktop$ grep Wayland /etc/gdm3/custom.conf WaylandEnable=false The above shows the edit to custom.conf that removed the comment (#) for setting Wayland to false for enabling X11. The computer was restarted to change Wayland to X11. XCrySDen 1.6.2 was installed using: username@computername:~/Desktop$ sudo apt install xcrysden ... Since I wanted to use XCrySDen in w2web, XCRYSDEN_TOPDIR variable was set in the .basrhc using: username@computername:~/Desktop$ gedit ~/.bashrc username@computername:~/Desktop$ grep XCRYSDEN ~/.bashrc export XCRYSDEN_TOPDIR=/usr/bin username@computername:~/Desktop$ source ~/.bashrc The w2web was started up: username@computername:~/Desktop$ w2web ... Then, I navigated to and clicked "view structure" in w2web. Then, the struct file was displayed [4]. [1] https://ubuntu.com/download/desktop [2] https://unix.stackexchange.com/questions/202891/how-to-know-whether-wayland-or-x11-is-being-used [3] https://askubuntu.com/questions/1410256/how-do-i-use-x-instead-of-wayland-on-22-04 [4] https://raw.githubusercontent.com/gsabo/xcrysden-Patches/main/Ubuntu%2022.04.2%20XCrySDen%201.6.2.png Kind Regards, Gavin WIEN2k user On 3/25/2023 1:47 AM, Peter Blaha wrote: The semishared version has most libraries included and runs on almost any Linux system. For the more recent version, the developers provide only a "shared" version, i.e. most libraries are NOT included, but must be present on your Linux system. On their website it is mentioned what libraries you need. At least you miss libfftw3.so.3 but probably also others. PS: I still use on most computers 1.5.60, as I do not want to install all the necessary libraries on all my machines. Am 25.03.2023 um 01:31 schrieb delamora: The only difference is semishared => shared *De:* Wien en nombre de delamora *Enviado:* viernes, 24 de marzo de 2023 06:28 p. m. *Para:* A Mailing list for WIEN2k users *Asunto:* [Wien] XCrySDen Version: 1.6.2 Dear WIEN2k community I am having trouble with XCrySDen, if I use; xcrysden-1.5.60-bin-semishared I have no problem, but if I use xcrysden-1.6.2-bin-shared +-+ |*| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---*| |* *| |* Anton Kokalj (tone.kok...@ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2019 by Anton Kokalj *| |* *| |*| +-+ Version: 1.6.2 Please report bugs to: tone.kok...@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=/home/Programas/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory - For the xcrysden-1.5.60-bin-shared I get the same answer, except for the line "Version: 1.6.2" Saludos Pablo ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at:http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- --- Peter Blaha, Inst. f. Materials Chemistry, TU Vienna, A-10
Re: [Wien] XCrySDen Version: 1.6.2
The semishared version has most libraries included and runs on almost any Linux system. For the more recent version, the developers provide only a "shared" version, i.e. most libraries are NOT included, but must be present on your Linux system. On their website it is mentioned what libraries you need. At least you miss libfftw3.so.3 but probably also others. PS: I still use on most computers 1.5.60, as I do not want to install all the necessary libraries on all my machines. Am 25.03.2023 um 01:31 schrieb delamora: The only difference is semishared => shared *De:* Wien en nombre de delamora *Enviado:* viernes, 24 de marzo de 2023 06:28 p. m. *Para:* A Mailing list for WIEN2k users *Asunto:* [Wien] XCrySDen Version: 1.6.2 Dear WIEN2k community I am having trouble with XCrySDen, if I use; xcrysden-1.5.60-bin-semishared I have no problem, but if I use xcrysden-1.6.2-bin-shared +-+ |*| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = === *| |*---*| |* *| |* Anton Kokalj (tone.kok...@ijs.si) *| |* Jozef Stefan Institute, Ljubljana, Slovenia *| |* *| |* Copyright (c) 1996--2019 by Anton Kokalj *| |* *| |*| +-+ Version: 1.6.2 Please report bugs to: tone.kok...@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=/home/Programas/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory - For the xcrysden-1.5.60-bin-shared I get the same answer, except for the line "Version: 1.6.2" Saludos Pablo ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at:http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- --- Peter Blaha, Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-158801165300 Email:peter.bl...@tuwien.ac.at WWW:http://www.imc.tuwien.ac.at WIEN2k:http://www.wien2k.at - ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] XCrySDen Version: 1.6.2
The only difference is semishared => shared De: Wien en nombre de delamora Enviado: viernes, 24 de marzo de 2023 06:28 p. m. Para: A Mailing list for WIEN2k users Asunto: [Wien] XCrySDen Version: 1.6.2 Dear WIEN2k community I am having trouble with XCrySDen, if I use; xcrysden-1.5.60-bin-semishared I have no problem, but if I use xcrysden-1.6.2-bin-shared +-+ |*| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = ===*| |*---*| |* *| |*Anton Kokalj (tone.kok...@ijs.si) *| |*Jozef Stefan Institute, Ljubljana, Slovenia*| |* *| |*Copyright (c) 1996--2019 by Anton Kokalj *| |* *| |*| +-+ Version: 1.6.2 Please report bugs to: tone.kok...@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=/home/Programas/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory - For the xcrysden-1.5.60-bin-shared I get the same answer, except for the line "Version: 1.6.2" Saludos Pablo ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] XCrySDen Version: 1.6.2
Dear WIEN2k community I am having trouble with XCrySDen, if I use; xcrysden-1.5.60-bin-semishared I have no problem, but if I use xcrysden-1.6.2-bin-shared +-+ |*| |* *| |* XCrySDen -- (X-Window) CRYstalline Structures and DENsities *| |* = === = ===*| |*---*| |* *| |*Anton Kokalj (tone.kok...@ijs.si) *| |*Jozef Stefan Institute, Ljubljana, Slovenia*| |* *| |*Copyright (c) 1996--2019 by Anton Kokalj *| |* *| |*| +-+ Version: 1.6.2 Please report bugs to: tone.kok...@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=/home/Programas/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/home/pablo/xcrys_tmp /home/Programas/xcrysden-1.6.2-bin-shared/bin/xcrys: error while loading shared libraries: libfftw3.so.3: cannot open shared object file: No such file or directory - For the xcrysden-1.5.60-bin-shared I get the same answer, except for the line "Version: 1.6.2" Saludos Pablo ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden issues with w2web
As was already hinted at in [1], if you need more help, you probably need describe better what you system(s) configuration is like such as are you only using w2web and xcrysden in Ubuntu locally (physical Linux box or in a virtual machine) or are you connecting to them remotely? If you have defined $DISPLAY, w2web might just pick that up. If you know Perl, I suggest you have a look at $WIENROOT/SRC_w2web/htdocs/util/viewcrys.pl. The xserver that you mentioned, is it setup for X11 forwarding? If you are not using w2web locally with an offline setup [2], but are instead using an online setup were w2web is connected to the internet (or a local network) and is unable to get xcrysden to open in w2web, are you able to get it to open instead using an ssh connection with X11 forwarding? Refer to [3,4]. [1] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg20243.html [2] https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01124.html [3] http://sites.science.oregonstate.edu/~tatej/COURSES/ph575/doku.php?id=xcrysden [4] https://users.wfu.edu/natalie/s11phy752/lecturenote/PHY752lectLAPW.pdf On 6/22/2020 2:21 PM, Johnathon Street wrote: When typing echo $DISPLAY into the terminal I am seeing :0. I still continue to see "requires X-Windows System..." when I try to view the crystal in w2web. Is there a way to set the DISPLAY variable inside the w2web process so that it may work there as well. Where do you recommend I set DISPLAY? Thank you *From:* Wien on behalf of Gavin Abo *Sent:* Saturday, June 13, 2020 4:55 PM *To:* wien@zeus.theochem.tuwien.ac.at *Subject:* Re: [Wien] Xcrysden issues with w2web Maybe there is still a problem with your XCRYSDEN_TOPDIR, refer to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html [mail-archive.com] <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEkzRTEgp$> http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html [democritos.it] <https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpElJMWCG9$> Regarding DISPLAY, maybe the following link to a xcrysden mailing list post can help: http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html [democritos.it] <https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEmZACKf6$> On 6/11/2020 2:51 PM, Johnathon Street wrote: Thank you for the response. That did resolve the issue. I am now seeing "Requires X-windows system..." in the view struct portion of w2web. I do have an xserver runner, as I am running on Ubuntu. Is there a place where I need to set DISPLAY? *From:* Wien <mailto:wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Gavin Abo <mailto:gs...@crimson.ua.edu> *Sent:* Saturday, June 6, 2020 11:05 AM *To:* wien@zeus.theochem.tuwien.ac.at <mailto:wien@zeus.theochem.tuwien.ac.at> <mailto:wien@zeus.theochem.tuwien.ac.at> *Subject:* Re: [Wien] Xcrysden issues with w2web Most likely you just need to kill and restart w2web. Refer to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html [mail-archive.com] <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html [mail-archive.com] <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$> On 6/6/2020 11:49 AM, Johnathon Street wrote: I unable to view crystal with Xcrysden in w2web environment. However, I am able to view directly from terminal when typing Xcrysden in command line. I have found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be set to. Any help would be appreciated. I am running WIEN2k_19.2 and Xcrysden version 1.6.2. Current Directory XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Xcrysden issues with w2web
Is the w2web program running on the same system, and under the same user ID as the terminal you used for the test ? If not, you could try setting "xhost localhost" (or if you trust your firewall, even "xhost +") to allow connections to your instance of the X server from other users/other systems on the network -- Dr. Martin Kroekermar...@ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden issues with w2web
When typing echo $DISPLAY into the terminal I am seeing :0. I still continue to see "requires X-Windows System..." when I try to view the crystal in w2web. Is there a way to set the DISPLAY variable inside the w2web process so that it may work there as well. Where do you recommend I set DISPLAY? Thank you From: Wien on behalf of Gavin Abo Sent: Saturday, June 13, 2020 4:55 PM To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Xcrysden issues with w2web Maybe there is still a problem with your XCRYSDEN_TOPDIR, refer to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html [mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEkzRTEgp$> http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html [democritos.it]<https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpElJMWCG9$> Regarding DISPLAY, maybe the following link to a xcrysden mailing list post can help: http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html [democritos.it]<https://urldefense.com/v3/__http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html__;!!LNEL6vXnN3x8o9c!wOFlUzcyu_b8T0m5p3xrOisn5mqtXqTGifQSvDBIX9DI1D0YgI-CoKIpEmZACKf6$> On 6/11/2020 2:51 PM, Johnathon Street wrote: Thank you for the response. That did resolve the issue. I am now seeing "Requires X-windows system..." in the view struct portion of w2web. I do have an xserver runner, as I am running on Ubuntu. Is there a place where I need to set DISPLAY? From: Wien <mailto:wien-boun...@zeus.theochem.tuwien.ac.at> on behalf of Gavin Abo <mailto:gs...@crimson.ua.edu> Sent: Saturday, June 6, 2020 11:05 AM To: wien@zeus.theochem.tuwien.ac.at<mailto:wien@zeus.theochem.tuwien.ac.at> <mailto:wien@zeus.theochem.tuwien.ac.at> Subject: Re: [Wien] Xcrysden issues with w2web Most likely you just need to kill and restart w2web. Refer to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html [mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html [mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$> On 6/6/2020 11:49 AM, Johnathon Street wrote: I unable to view crystal with Xcrysden in w2web environment. However, I am able to view directly from terminal when typing Xcrysden in command line. I have found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be set to. Any help would be appreciated. I am running WIEN2k_19.2 and Xcrysden version 1.6.2. Current Directory XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden issues with w2web
Maybe there is still a problem with your XCRYSDEN_TOPDIR, refer to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg18555.html http://www.democritos.it/pipermail/xcrysden/2020-January/001975.html Regarding DISPLAY, maybe the following link to a xcrysden mailing list post can help: http://www.democritos.it/pipermail/xcrysden/2020-May/001993.html On 6/11/2020 2:51 PM, Johnathon Street wrote: Thank you for the response. That did resolve the issue. I am now seeing "Requires X-windows system..." in the view struct portion of w2web. I do have an xserver runner, as I am running on Ubuntu. Is there a place where I need to set DISPLAY? *From:* Wien on behalf of Gavin Abo *Sent:* Saturday, June 6, 2020 11:05 AM *To:* wien@zeus.theochem.tuwien.ac.at *Subject:* Re: [Wien] Xcrysden issues with w2web Most likely you just need to kill and restart w2web. Refer to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html [mail-archive.com] <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html [mail-archive.com] <https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$> On 6/6/2020 11:49 AM, Johnathon Street wrote: I unable to view crystal with Xcrysden in w2web environment. However, I am able to view directly from terminal when typing Xcrysden in command line. I have found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be set to. Any help would be appreciated. I am running WIEN2k_19.2 and Xcrysden version 1.6.2. Current Directory XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden issues with w2web
Thank you for the response. That did resolve the issue. I am now seeing "Requires X-windows system..." in the view struct portion of w2web. I do have an xserver runner, as I am running on Ubuntu. Is there a place where I need to set DISPLAY? From: Wien on behalf of Gavin Abo Sent: Saturday, June 6, 2020 11:05 AM To: wien@zeus.theochem.tuwien.ac.at Subject: Re: [Wien] Xcrysden issues with w2web Most likely you just need to kill and restart w2web. Refer to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html [mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Iqc3q-u$> https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html [mail-archive.com]<https://urldefense.com/v3/__https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html__;!!LNEL6vXnN3x8o9c!y3eR68_jwMy-ieFTucnQK_nzeOCOUwzEtSNG-uwkPO_yATLz4wAk2gM46Lm0FwxV$> On 6/6/2020 11:49 AM, Johnathon Street wrote: I unable to view crystal with Xcrysden in w2web environment. However, I am able to view directly from terminal when typing Xcrysden in command line. I have found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be set to. Any help would be appreciated. I am running WIEN2k_19.2 and Xcrysden version 1.6.2. Current Directory XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden issues with w2web
Most likely you just need to kill and restart w2web. Refer to: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html On 6/6/2020 11:49 AM, Johnathon Street wrote: I unable to view crystal with Xcrysden in w2web environment. However, I am able to view directly from terminal when typing Xcrysden in command line. I have found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be set to. Any help would be appreciated. I am running WIEN2k_19.2 and Xcrysden version 1.6.2. Current Directory XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Xcrysden issues with w2web
I unable to view crystal with Xcrysden in w2web environment. However, I am able to view directly from terminal when typing Xcrysden in command line. I have found through the mailing list that XCRYSDEN_TOPDIR needs to be set, but I am unsure what it should be set to. Any help would be appreciated. I am running WIEN2k_19.2 and Xcrysden version 1.6.2. Current Directory XCRYSDEN_TOPDIR=/usr/local/share/xcrysden-1.6.2 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] xcrysden installed but not able to integrate with wien2k interface
Sure, you can manually add/edit XCRYSDEN_TOPDIR according to the XCrySDen website: http://www.xcrysden.org/doc/install.html However, I installed XCrySDen on Fedora 28 starting with step 8 at http://www.democritos.it/pipermail/xcrysden/2015-March/001697.html and it installed just fine for me. The ./xcConfigure.sh step was still able to automatically setup the XCrySDen environmental variables like XCRYSDEN_TOPDIR. The w2web was running before I installed XCrySDen such that "view structure" was not working in w2web. However, it started working fine after following previous advise in the mailing list to kill and restart w2web: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg11246.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01987.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg04236.html To use w2web offline, the system's hostname can be set to [ https://en.wikipedia.org/wiki/Localhost ]: localhost https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg01124.html https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15629.html On 10/27/2018 12:43 PM, Ashwani Kumar wrote: Hi, i have installed xcrysden and know there some changes required in "TOP DIRECTORY" to integrate it into wien2k user interface. I tried changing it but remain unsuccessful. Browsed threads for the same problem, found plenty in wien2k mailing list but still could not understand how to do it. I am using xcrysden offline. Please help with this. thanks, Ashwani Kumar ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] xcrysden installed but not able to integrate with wien2k interface
Hi, i have installed xcrysden and know there some changes required in "TOP DIRECTORY" to integrate it into wien2k user interface. I tried changing it but remain unsuccessful. Browsed threads for the same problem, found plenty in wien2k mailing list but still could not understand how to do it. I am using xcrysden offline. Please help with this. thanks, Ashwani Kumar ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] XCrysDen
I just tried and the xcrysden semishared binary package successfully ran on openSUSE 15.0 installed on a USB stick. So I would expect a full openSUSE install to be no different. The installation process was very similar to CentOS, Fedora, and Ubuntu [ http://www.democritos.it/pipermail/xcrysden/2017-December/001902.html ]. 1. Went to: http://download.opensuse.org/distribution/leap/15.0/live/ 2. Downloaded: openSUSE-Leap-15.0-GNOME-Live-x86_64-Snapshot20.21-Media.iso 3. Went to: https://rufus.akeo.ie/ 4. Downloaded Rufus 3.1 Portable: rufus-3.1p.exe 5. Used Rufus to burn the above iso to a USB stick 6. Booted from the USB stick a. Selected openSUSE Leap 15.0 GNOME Live b. Connected to the Internet 7. Opened a terminal and performed the following: linux@localhost:~> wget http://www.xcrysden.org/download/xcrysden-1.5.60-linux_x86_64-semishared.tar.gz ... linux@localhost:~> tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz ... linux@localhost:~> cd xcrysden-1.5.60-bin-semishared/scripts/ linux@localhost:~/xcrysden-1.5.60-bin-semishared/scripts> ./xcConfigure.sh more: unknown option -more Try 'more --help' for more information. Please specify XCRYSDEN_SCRATCH directory (default: /home/linux/xcrys_tmp): Do you have a CRYSTAL package ([y]es/[n]o): n Is this correct ([y]es/[n]o): y ... Would you like to add xcrysden icon to the desktop ([y]es/[n]o): y ... Then type: xcrysden linux@localhost:~/xcrysden-1.5.60-bin-semishared/scripts> source ~/.bashrc linux@localhost:~/xcrysden-1.5.60-bin-semishared/scripts> xcrysden Your problem sounds very similar to this old post: http://www.democritos.it/pipermail/xcrysden/2010-March/000778.html However, I don't know how they solved it. Though, I did encounter the same error of can't read "xcrys(platform)": no such variable seen at that old post, but that was using KDE (openSUSE-Leap-15.0-KDE-Live-x86_64-Snapshot20.21-Media.iso) instead of GNOME. Though, it seemed to work fine after following the advice in bug report [ https://bugzilla.redhat.com/show_bug.cgi?id=1043686 ], i.e.: ~]$ xrdb -load /dev/null ~]$ xrdb -query ~]$ xcrysden However, in your post, it is not clear to me how you are running xcrysden on the cluster node. VNC connection to a GUI desktop on the cluster? Or are you X11 forwarding the display from the cluster to have it display on another system [ https://lists.freedesktop.org/archives/xorg/2011-April/052647.html , https://users.wfu.edu/natalie/s11phy752/lecturenote/PHY752lectLAPW.pdf ]? Sometime X11 forwarding works fine, but it many cases I found xcrysden to be very slow or hang doing X11 forwarding. Thus, I usually preferred either the VNC connection or using xcrysden on my local box (where I would just transfer necessary WIEN2k files from the cluster to the local computer, then display it using xcrysden). For latter local using files from the cluster, it can take some work to figure out files are needed, but it is doable. I gave somewhat of an example when I mentioned that case.struct, case.klist, case.clmdn, case.outputkgen, and case.output1up (are needed) in one case for displaying a fermi surface in xcrysden: https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg17847.html Hope that helps and good luck. On 8/28/2018 5:29 PM, FonsPaul wrote: I have installed the latest stable version of OpenSuse, version 15 on a node in a cluster and have found that the semi-shared binary I was using of XCrystDen no longer works. When I attempt to run XCrysDen, I see the splash window, but then an error window pops up without any indications of what the error is. I then downloaded the sourcecode to version 1.5 only to find that the make script is broken (it attempts to download dependent libraries and the links seem to be broken). Has anyone run into this problem before and is there a simple solution? ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] XCrysDen
I have installed the latest stable version of OpenSuse, version 15 on a node in a cluster and have found that the semi-shared binary I was using of XCrystDen no longer works. When I attempt to run XCrysDen, I see the splash window, but then an error window pops up without any indications of what the error is. I then downloaded the sourcecode to version 1.5 only to find that the make script is broken (it attempts to download dependent libraries and the links seem to be broken). Has anyone run into this problem before and is there a simple solution? ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden works for structure view, not for electron density display
After you click the "Calculate density with XCrysden" button, 1) the "Requires X-Windows system ... Calc" message appears immediately or 2) does the XCrySDen program open, the "Choose 2D/3D Density Plot" window appears (like that shown at http://www.xcrysden.org/doc/wien.html#__toc__6 ), then the "Requires X-Windows system ... Calc" message only shows up after you close XCrySDen. If 2 above occurs, then that is normal and nothing is wrong. If 1 above occurs, then there is a problem. However, I'm not able to reproduce the error with the information you have provided. I'm using the latest WIEN2k (17.1) and XCrySDen (xcrysden-1.5.60-linux_x86_64-semishared [ http://www.xcrysden.org/Download.html ]) as well and the "Calculate density with XCrysden" run locally in w2web seems to work fine for me. Without any additional hints you might have, the problem may go unresolved like what happened to a user before [ https://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/msg15585.html ]. If you try the same thing in the terminal, does it work or provide any additional information (like an error message). For example, first navigate to the directory containing your case.struct file: username@computername:~/Desktop$ cd ~/wiendata/test username@computername:~/wiendata/test$ ls test.struct test.struct Back out of the directory so that you are in the directory containing your case folder and run the density calculation with XCrySDen [ http://www.xcrysden.org/doc/wien.html#__toc__1 ]: username@computername:~/wiendata/test$ cd .. username@computername:~/wiendata$ xcrysden --wien_density test On 6/28/2018 8:17 AM, Luc Fruchter wrote: Dear all, Xcrysden works fine from the w2web interface (run locally), when viewing a structure. So, I think it is correctly installed and configured. However, it displays "requires X-Windows system ... Calc" when trying to use the "Calculate density with Xcrysden" button, or "requires X-Windows system ... Render" when I use the "Preview density button". When I use the "Rhoplot" button, the density is correctly displayed (so the density file must be ok). ( I use latest versions for Wien2k and Xcrysden). Thanks for any help. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Xcrysden works for structure view, not for electron density display
Dear all, Xcrysden works fine from the w2web interface (run locally), when viewing a structure. So, I think it is correctly installed and configured. However, it displays "requires X-Windows system ... Calc" when trying to use the "Calculate density with Xcrysden" button, or "requires X-Windows system ... Render" when I use the "Preview density button". When I use the "Rhoplot" button, the density is correctly displayed (so the density file must be ok). ( I use latest versions for Wien2k and Xcrysden). Thanks for any help. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] XCrysDen problem in Wien2k16
Dear Wien2k group, I have one well known problem in working with XCrysDen in Wien2k. I recently updated to Wien2k16. Now while trying to plot Electron Density and selecting k-path for band structure using XCrySDen, I get "Requires X-Windows system ... Calc" and "Requires X-Windows system ..." messages respectively. I run Wine2k16 in openSUSE Linux installed in Windows10 system using Oracle Virtual Box. I am using 10 GB RAM for Linux with 2 cores from quad core processors. I tested with TiC case only; but getting the XCrySDen issues. I have properly installed X11 from X.org via openSUSE download site. Please let me get some input to solve this issue. Thanks. With regards K. Balamurugan NIT Trichy, India. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden problem
I solved this problem for RED HAT; In a terminal I tried to run xcrysden and there was a program missing, so I installed it, then another one, again I installed it. With these two programs and their dependences XCrySDen worked. Pablo De: wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at en nombre de Peter Blaha pbl...@theochem.tuwien.ac.at Enviado: viernes, 10 de octubre de 2014 01:10 a.m. Para: A Mailing list for WIEN2k users Asunto: Re: [Wien] Xcrysden problem After installation of xcrysden you must kill w2web (ps -ef |grep w2web and kill the corresponding processes). Then make sure your environment is ok (eventually logout/login) and restart w2web. PS: before starting w2web, the environment variable XCRYSDEN_TOPDIR must be set. Am 10.10.2014 04:51, schrieb bayarr temuujin: Dear Wien2k users, I am new to Wien2k and i am running Wien2k version 13.1 on Ubuntu 14.04. LTS. I have problem with Xcrysden not showing up when i run electron density calculation. The button Calculate density with XCrysden doesnt show up. I have re-installed Xcrysden and XCrysden is working fine. Please help me out. Best regards, Temuujin ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pbl...@theochem.tuwien.ac.at - ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden problem
After installation of xcrysden you must kill w2web (ps -ef |grep w2web and kill the corresponding processes). Then make sure your environment is ok (eventually logout/login) and restart w2web. PS: before starting w2web, the environment variable XCRYSDEN_TOPDIR must be set. Am 10.10.2014 04:51, schrieb bayarr temuujin: Dear Wien2k users, I am new to Wien2k and i am running Wien2k version 13.1 on Ubuntu 14.04. LTS. I have problem with Xcrysden not showing up when i run electron density calculation. The button Calculate density with XCrysden doesnt show up. I have re-installed Xcrysden and XCrysden is working fine. Please help me out. Best regards, Temuujin ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pbl...@theochem.tuwien.ac.at - ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Xcrysden problem
Dear Wien2k users, I am new to Wien2k and i am running Wien2k version 13.1 on Ubuntu 14.04. LTS. I have problem with Xcrysden not showing up when i run electron density calculation. The button Calculate density with XCrysden doesnt show up. I have re-installed Xcrysden and XCrysden is working fine. Please help me out. Best regards,Temuujin ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrysden problem
Temuujin and WIEN2k users, I want to add that this also happens with Fedora 19 and up. XCrySDen works fine for Fedora 18 and down. Pablo de la Mora De: wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at en nombre de bayarr temuujin fox_temuu...@yahoo.com Enviado: jueves, 09 de octubre de 2014 09:51 p.m. Para: wien@zeus.theochem.tuwien.ac.at Asunto: [Wien] Xcrysden problem Dear Wien2k users, I am new to Wien2k and i am running Wien2k version 13.1 on Ubuntu 14.04. LTS. I have problem with Xcrysden not showing up when i run electron density calculation. The button Calculate density with XCrysden doesnt show up. I have re-installed Xcrysden and XCrysden is working fine. Please help me out. Best regards, Temuujin ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] XCrySDen error
Dear members, After installing XCrysden, and when I run, I see this message?? /home/ali13btf/Bureau/XCrySDen-1.5.17-bin-semishared/xcrysden: 160: .: Can't open /complete_path_to/XCrySDen-1.5.17-src-all/scripts/xcLib.sh Where is the problem?!Cordially ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] XCrySDen error
Hello, I think you forgot to replace complete_path_to in your XCRYSDEN_TOP_DIR variable. It should be your local install path. Kind regards, Michael Sluydts ali betaouaf schreef op 1/18/2014 1:15 PM: Dear members, After installing XCrysden, and when I run, I see this message?? /home/ali13btf/Bureau/XCrySDen-1.5.17-bin-semishared/xcrysden: 160: .: Can't open /complete_path_to/XCrySDen-1.5.17-src-all/scripts/xcLib.sh Where is the problem?! Cordially ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Xcrysden
Dear Anton Kokalj sir, Is there any demo version of XCrysden available? Is it possible to install in windows 7 or windows 8 system? If yes, then how to do, please guide me. Warm regards Dr Swati Chaudhury Visiting Scientist ICRISAT, India___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] xcrysden large multipler k-points
actually, i used only 300 k-points and this specific problem arose when i tried to select k-path for band structure calculations. my system has monoclinic symmetry so there are a couple of special points in k-path i wanted to adopt with coordinates like (0.64xxx, 0.32xxx, 0.5). i selected the total number of divisions (k-points) of this path again 300. the code insists on having an integer coordinate with a multiplier. for 300 k-points, the multiplier was quite large and the integer coordinates printed in case.klist_band file were **. Prof. Tone asked for my structure file and he too got into same error. Let me copy - paste his reply: On Mon, 2012-07-16 at 17:37 +0900, ? wrote: here are the .struct file and complete .klist_band file. i tried to solve this problem by making separate kpath klist files for every two points. the idea was to join them manually use different multipliers for different path. Yes, you are right. I could reproduce your problems. I believe that the problem is due to Wien2K. Your case is a nasty case for Wien2K. Why? Because it insist on representing the real number (rational number) as the fraction p/q of two integers with a fixed format. As your case is not a high symmetry case, the p q numbers are simple too large and the stars () are displayed. As a work-around: you could use the coordinates of special k-points as given by xcrysden, and then you need to construct out of that semi-manually a klist file suitable for Wien2K (this would involve some manual editing + some small scripting to interpolate points between pairs of special k-points). Regards. Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) so, therefore i thought may be it is due to same problem you guys are discussing, just pushed my mail . . . . ;D any way, thnx. for ur reply. M. Arshad Farhan On Mon, Jul 30, 2012 at 3:32 PM, Gavin Abo gsabo at crimson.ua.edu wrote: What large values did you use in xcrysden for the multiplier and k-points? Someone else might be able to comment on whether you can use smaller values and still get accurate results. I see your posts on the xcrysden mailing list: http://www.democritos.it/pipermail/xcrysden/2012-July/001215.html http://www.democritos.it/pipermail/xcrysden/2012-July/001223.html From the posts, it looks like the number of k-points you used is possibly greater than 99672. You currently cannot use multipiler*k-points 5-digits (i.e., 99,999) If the larger outputted values are really needed, it could probably be done by changing all the 4I5 to say 4I8 in F/kPath.f that is in the xcrysden source package (xcrysden-1.5.53.tar.gz). However, you have to compile the xcrysden code. There are some useful instructions on the web for compiling the xcrysden source in Debian or Ubuntu ( https://sites.google.com/site/jamesanalytis/xcrysden-in-ubuntu-10-04), but have not seen for other Linux distributions if one wants to attempt it. Since your not quite a linux guy, you will probably want to send your struct file (while providing also the multiplier and k-points value used) to Tone as requested on the xcrysden mailing list so that a linux binary package with changes can be provided if needed. On 7/29/2012 7:54 PM, ? wrote: Dear Prof. Lawrance Gavin-Abo, i've not tested the latest version of Wien2k but, let me mention one more place where real*4 are used that is in the creation of case.klist_band. for any complicated coordinate in the k-path (mainly in monoclinic systems) by using Xcrysden, the multiplier goes shooting high and coordinate value exceeds real*4 consequently printing ** in places of k-point coordinates in case.klist_band file. the XcrySden developers claim it to be on part of Wien2k where it insists on real value but restricts it to 4 digits. if possible, please also look into it and of-course suggest me a solution as i'm quite not a linux guy. regards, ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- * ?* Dept of Chemistry, Pohang Univ of Sci Tech Pohang, Republic of Korea -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120801/cba6c98d/attachment.htm
[Wien] xcrysden large multipler k-points
What large values did you use in xcrysden for the multiplier and k-points? Someone else might be able to comment on whether you can use smaller values and still get accurate results. I see your posts on the xcrysden mailing list: http://www.democritos.it/pipermail/xcrysden/2012-July/001215.html http://www.democritos.it/pipermail/xcrysden/2012-July/001223.html From the posts, it looks like the number of k-points you used is possibly greater than 99672. You currently cannot use multipiler*k-points 5-digits (i.e., 99,999) If the larger outputted values are really needed, it could probably be done by changing all the 4I5 to say 4I8 in F/kPath.f that is in the xcrysden source package (xcrysden-1.5.53.tar.gz). However, you have to compile the xcrysden code. There are some useful instructions on the web for compiling the xcrysden source in Debian or Ubuntu (https://sites.google.com/site/jamesanalytis/xcrysden-in-ubuntu-10-04), but have not seen for other Linux distributions if one wants to attempt it. Since your not quite a linux guy, you will probably want to send your struct file (while providing also the multiplier and k-points value used) to Tone as requested on the xcrysden mailing list so that a linux binary package with changes can be provided if needed. On 7/29/2012 7:54 PM, ? wrote: Dear Prof. Lawrance Gavin-Abo, i've not tested the latest version of Wien2k but, let me mention one more place where real*4 are used that is in the creation of case.klist_band. for any complicated coordinate in the k-path (mainly in monoclinic systems) by using Xcrysden, the multiplier goes shooting high and coordinate value exceeds real*4 consequently printing ** in places of k-point coordinates in case.klist_band file. the XcrySden developers claim it to be on part of Wien2k where it insists on real value but restricts it to 4 digits. if possible, please also look into it and of-course suggest me a solution as i'm quite not a linux guy. regards, -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120730/c4abd12a/attachment.htm
[Wien] xcrysden to plot Fermi surface
You are using an old version of xcrysden. The new version does not suggest these changes anymore. You do not need to follow the steps listed in xcrysden, but can do all this (except the real plotting, i.e. the last step) by hand. You need: A very dense UNSHIFTED k-mesh.(x kgen) run x lapw1with this mesh x lapw2 -fermi Now call xcrysden and just visualize the FS. Am 13.04.2012 23:21, schrieb Yundi Quan: Dear Sir/Madam, My question may not be directly related to WIEN2k. When plotting Fermi surface using XCrysden, it says that case.in1 should be changed into unit 5. But if I change case.in1 to unit 5, I would always get an error message saying that kpoints in case.in1 is inconsistent with the kpoints in case.kgen. Should case.in1 be changed into unit 5? ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pblaha at theochem.tuwien.ac.at -
[Wien] xcrysden to plot Fermi surface
Dear Sir/Madam, My question may not be directly related to WIEN2k. When plotting Fermi surface using XCrysden, it says that case.in1 should be changed into unit 5. But if I change case.in1 to unit 5, I would always get an error message saying that kpoints in case.in1 is inconsistent with the kpoints in case.kgen. Should case.in1 be changed into unit 5?
[Wien] XCRYSDEN
Dear all, I try to use XCRYSDEN to choose the plane for plotting electron density, thus, HPC installed XCRYSDEN (1.4.1) in my account so that I open XCrysDen using Xmanager on my PC. Here I have two questions concerning about it: 1. XCrysDen is extremely slow on the Xmanager window; 2. I do know how to choose and save a plane for plotting the electron density map using XCrysDen. Any suggestions, comments and instructions are highly appreciated! Thank you in advance! Bing -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20120313/2049eac0/attachment.htm
[Wien] XCrysDen in w2web?
Dear Prof. Blaha, The suggested procedure works fine. Thank you very much, Jianxin On Jan 9, 2010, at 7:05 AM, Peter Blaha wrote: At localhost issue: ssh -X hostname_where_w2web_runs(the -X option directs the X- windows system to open screens on loc.host) ps -ef |grep w2web kill (kill all pids with w2web) w2web now you can reconnect with your browser to w2web and xcrysden should open on localhost. Alternatively xcrysden can always be called from a terminal: ssh -X w2web_host (again -X is necessary!!!) cd case-directory xcrysden --wien_struct . (Try also xcrysden --help to see all options) I have a problem using XCrysDen in w2web remotely. From local host, I use the web-browser to connect to w2web in the remote machine, by safari http://hostname_where_w2web_runs:7890 and open a session successfully. However, when I click view structure on the left panel, the Xcrysden utility is started on the screen of the remote host instead of on my local machine. One way I can think of: ssh to the remote host and start up xcrysden separately and open the structure file. However, is there any other way (I mean within w2web) to have xcrysden display the picture on the local machine? Both of my machines (local and remote) are the Mac OSX systems. Any help/suggestion would be appreciated. Jianxin ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pblaha at theochem.tuwien.ac.at - ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] XCrysDen in w2web?
At localhost issue: ssh -X hostname_where_w2web_runs(the -X option directs the X-windows system to open screens on loc.host) ps -ef |grep w2web kill (kill all pids with w2web) w2web now you can reconnect with your browser to w2web and xcrysden should open on localhost. Alternatively xcrysden can always be called from a terminal: ssh -X w2web_host (again -X is necessary!!!) cd case-directory xcrysden --wien_struct . (Try also xcrysden --help to see all options) I have a problem using XCrysDen in w2web remotely. From local host, I use the web-browser to connect to w2web in the remote machine, by safari http://hostname_where_w2web_runs:7890 and open a session successfully. However, when I click view structure on the left panel, the Xcrysden utility is started on the screen of the remote host instead of on my local machine. One way I can think of: ssh to the remote host and start up xcrysden separately and open the structure file. However, is there any other way (I mean within w2web) to have xcrysden display the picture on the local machine? Both of my machines (local and remote) are the Mac OSX systems. Any help/suggestion would be appreciated. Jianxin ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pblaha at theochem.tuwien.ac.at -
[Wien] XCrysDen in w2web?
Dear Prof. Blaha and Wien2k users, I have a problem using XCrysDen in w2web remotely. From local host, I use the web-browser to connect to w2web in the remote machine, by safari http://hostname_where_w2web_runs:7890 and open a session successfully. However, when I click view structure on the left panel, the Xcrysden utility is started on the screen of the remote host instead of on my local machine. One way I can think of: ssh to the remote host and start up xcrysden separately and open the structure file. However, is there any other way (I mean within w2web) to have xcrysden display the picture on the local machine? Both of my machines (local and remote) are the Mac OSX systems. Any help/suggestion would be appreciated. Jianxin
[Wien] XCrysDen via w2web
If it works for you, it is fine.
It was in when using some years ago UNIX systems (or an early Linux),
but on the more recent platforms it was not necessary or even harms
sometimes). May depend on your X-server.
Tomohiko Tasaka schrieb:
Dear w2web users,
I tried to access xcrysden from w2web, but it's not started.
Only the following messages were displayed on w2web.
Requires X-Windows system ...
*Additionally, I had executed the command $xhost +address of X client on
ahead.
I think it's because the below line is comment out.
# $ENV{'DISPLAY'}=$ENV{'REMOTE_HOST'}:0.0;
included in bandxrys.pl, rhoxcrys.pl and viewxcrys.pl at
SRC_w2web/htdocs/util/.
If I remove a comment character(i.e. #), xcrysden starts normally.
Is this a reasonable solution? Could you please let me know what you think?
---
WIEN2k_08
X Server: Mac OS X 10.5.1
X Client: SUSE Linux Enterprise Desktop 10 SP1
Thanks in advance.
With best regards,
Tomo Tasaka
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--
P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-15671 FAX: +43-1-58801-15698
Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/
--
