From liangxy123 at hotmail.com Fri Jul 10 18:52:58 2020 From: liangxy123 at hotmail.com (LEUNG Clarence) Date: Fri, 10 Jul 2020 16:52:58 +0000 Subject: [xcrysden] installation issue in windows with Cygwin Message-ID: Dear Developer, I am trying to install xcrysden in windows 10 using cygwin but I am getting an error: XCRYSDEN_TOPDIR=/home/Clarence/xcrysden-1.6.2-bin-shared XCRYSDEN_SCRATCH=/tmp D:/cygwin64/home/Clarence/xcrysden-1.6.2-bin-shared/bin/xcrys.exe: error while l oading shared libraries: libTogl2.0.dll: cannot open shared object file: No such file or directory I am using windows 10, I can run xcrysden-1.5.60, but I cann't run xcrysden-1.6.2. Thanks. Clarence -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200710/2414c376/attachment.htm From matic.poberznik at gmail.com Mon Jul 13 11:02:54 2020 From: matic.poberznik at gmail.com (Matic) Date: Mon, 13 Jul 2020 11:02:54 +0200 Subject: [xcrysden] installation issue in windows with Cygwin In-Reply-To: References: Message-ID: <7670bd6c-db81-ee46-99bd-dc858aef047b@gmail.com> Dear Clarence, what you are missing is to add the path to libtogl2.0.dll to your PATH variable in the terminal (this is a cygwin specific issue): make sure that? libtogl2.0.dll is in /usr/lib/ and? add the line: export PATH=$PATH:/usr/lib to your ~/.bashrc and then: source ~/.bashrc Hope this helps, Best, Matic Poberznik > Dear Developer, > > I am trying to install xcrysden in windows 10 using cygwin but I am > getting > an error: > > XCRYSDEN_TOPDIR=/home/Clarence/xcrysden-1.6.2-bin-shared > XCRYSDEN_SCRATCH=/tmp > > D:/cygwin64/home/Clarence/xcrysden-1.6.2-bin-shared/bin/xcrys.exe: > error while l > oading shared libraries: libTogl2.0.dll: cannot open shared object > file: No such > ?file or directory > > I am using windows 10, I can run xcrysden-1.5.60, but I cann't run > xcrysden-1.6.2. > > Thanks. > > Clarence > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden -- Matic Poberznik J. Stefan Institute, Jamova 39, Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200713/82af0afa/attachment.htm From liangxy123 at hotmail.com Tue Jul 14 18:18:35 2020 From: liangxy123 at hotmail.com (LEUNG Clarence) Date: Tue, 14 Jul 2020 16:18:35 +0000 Subject: [xcrysden] =?gb2312?b?Y2Fuoa90IHNlbGVjdCBhdG9t?= Message-ID: Dear Developer and Xcrysden users, When I using Xcrysden 1.6.2 by crgwin in windows 10, it is strange that I can?t select atom when I measure the bond length. Have anyone came across this problem? Many thanks. Clarence [cid:e56dd8bb-3cc9-4029-9177-e85b01fbc1f4] -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200714/29d72e79/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: Outlook-fytyoxsq.png Type: image/png Size: 146152 bytes Desc: Outlook-fytyoxsq.png Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200714/29d72e79/attachment-0001.png From emilie.gaudry at univ-lorraine.fr Wed Jul 15 09:09:42 2020 From: emilie.gaudry at univ-lorraine.fr (Emilie Gaudry) Date: Wed, 15 Jul 2020 09:09:42 +0200 (CEST) Subject: [xcrysden] PhD position - Nancy, France In-Reply-To: <05efca7e9515aa127f832240f452b9ed9316d836.camel@ijs.si> References: <1223677746.296963.1589270830266.JavaMail.zimbra@univ-lorraine.fr> <2086717906.334835.1589271613435.JavaMail.zimbra@univ-lorraine.fr> <05efca7e9515aa127f832240f452b9ed9316d836.camel@ijs.si> Message-ID: <619635574.162125.1594796982180.JavaMail.zimbra@univ-lorraine.fr> Dear Colleagues, We invite applications for a three-year junior scientist position, to be filled at a doctoral level at the Universit? de Lorraine, Nancy, France. The position is funded in a joint project by PIs Profs. Gaudry (Institut Jean Lamour, lab for fundamental and applied research in materials science) and Sur (LORIA, lab for basic and applied research in computer sciences). The project aims to reveal new efficient intermetallic catalysts, based on machine learning methods coupled with Density Functional Theory (DFT). Heterogeneous catalysis on complex intermetallic compounds is a quickly growing field. M odeling the many diverse active sites and reaction paths on these complex surfaces is a challenging task. This project has an internatonal dimension and takes place within the Integrated European Center for the Development of New Alloys and Metallic Compounds (htps://ecmetac.eu/), the research network Open space between aperiodic order and physics & chemistry of materials (http://irn-aperiodic.grenoble.cnrs.fr/) and the Internatonal Lab between IJL and the Joseph Stefan Institute (JSI, Ljubljana, Slovenia). We are seeking candidates with a strong background in physics, chemistry, materials science, or machine learning. Please include any relevant documents (CV, letter, transcripts, and names and contact information of two referees) in your application. Best regards, ?milie Gaudry -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200715/db7c2591/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: these-IA.pdf Type: application/pdf Size: 237257 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200715/db7c2591/attachment-0001.pdf From gsabo at crimson.ua.edu Fri Jul 17 07:06:06 2020 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Thu, 16 Jul 2020 23:06:06 -0600 Subject: [xcrysden] =?utf-8?q?can=E2=80=99t_select_atom?= In-Reply-To: References: Message-ID: There is a temporary link to a screenshot at [1]. In the screenshot, you should see two Carbon atoms selected in the Distance window from clicking on the highlighted atoms (in green) with XCrySDen 1.6.2 [2] using Cygwin (setup version 2.905 download from the website [3] on July 16, 2020) on Windows 10 Home.? The graphene.in displayed in XCrySDen is from 1-4b_Day1-done_Timrov.tar at [4]. [1] https://drive.google.com/file/d/1337njrdXOtumWxRVGOewvlTUcuW9addp/view?usp=sharing [2] http://www.xcrysden.org/Download.html (XCrySDen 1.6.2 for Cygwin package: xcrysden-1.6.2-cygwin.tar.gz) [3] https://www.cygwin.com/ [4] https://www.materialscloud.org/learn/data/learn/files/Zem3D6woIu3r/ On 7/14/2020 10:18 AM, LEUNG Clarence wrote: > > Dear Developer and Xcrysden users, > > When I using Xcrysden 1.6.2 by crgwin in windows 10, it is strange > that I can?t select atom when I measure the bond length.? Have anyone > came across this problem? > > Many thanks. > > Clarence > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200716/4297beec/attachment.htm From mforti at cnea.gov.ar Thu Jul 16 23:38:33 2020 From: mforti at cnea.gov.ar (Mariano Forti) Date: Thu, 16 Jul 2020 18:38:33 -0300 Subject: [xcrysden] printed pdf with errors Message-ID: <26f01b0e-5122-ac3d-9a8b-b1955f76333e@cnea.gov.ar> Hi everyone ! thank you all for your time! I am tryng to print pdf from isosurfaces in xcrysden (i.e. fermi surfaces) and got some errors in the pdf rendering as shown in the attached screenshot. Recently I discussed a similar issue in the gl2ps library: https://gitlab.onelab.info/gl2ps/gl2ps/-/issues/34 which the author solved and implemented in another package. I see that xcrysden includes de gl2ps.c source in the C directory, but I wasnt able to compile it into an xcrysden executable to get the fix. any help will be appreciated! -- Mariano Forti Ingeniero en Materiales, Instituto Sabato. marianodforti at gmail.com www.mendeley.com/profiles/mariano-forti/ Unidad de Actividad Materiales Comisi?n de Energ?a At?mica (+5411)67727832 mforti at cnea.gov.ar Argentina -------------- next part -------------- A non-text attachment was scrubbed... Name: Screenshot_20200716_183240.png Type: image/png Size: 61985 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200716/87a710b3/attachment-0001.png From tone.kokalj at ijs.si Fri Jul 17 09:16:35 2020 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 17 Jul 2020 09:16:35 +0200 Subject: [xcrysden] printed pdf with errors In-Reply-To: <26f01b0e-5122-ac3d-9a8b-b1955f76333e@cnea.gov.ar> References: <26f01b0e-5122-ac3d-9a8b-b1955f76333e@cnea.gov.ar> Message-ID: On Thu, 2020-07-16 at 18:38 -0300, Mariano Forti wrote: > Hi everyone ! thank you all for your time! > > I am tryng to print pdf from isosurfaces in xcrysden (i.e. fermi > surfaces) and got some errors in the pdf rendering as shown in the > attached screenshot. Recently I discussed a similar issue in the > gl2ps > library: > > https://gitlab.onelab.info/gl2ps/gl2ps/-/issues/34 > > which the author solved and implemented in another package. I see > that xcrysden includes de gl2ps.c source in the C directory, but I > wasnt able to compile it into an xcrysden executable to get the fix. > any help will be appreciated! Simply copy new gl2ps.c and gl2ps.h files into C/ subdirectory and recompile. But do you really need to print isosurfaces in PDF? The corresponding files will be huge. I suggest you maximize the plot on the screen, turn on antialiasing, and print in PNG instead. Best regards, Tone -- Jo?ef Stefan Institute, Ljubljana, Slovenia From liangxy123 at hotmail.com Fri Jul 17 07:57:18 2020 From: liangxy123 at hotmail.com (LEUNG Clarence) Date: Fri, 17 Jul 2020 05:57:18 +0000 Subject: [xcrysden] =?gb2312?b?u9i4tDogIGNhbqGvdCBzZWxlY3QgYXRvbQ==?= In-Reply-To: References: , Message-ID: Dear Gavin, Thanks for your sharing. I have two laptop: one is windows 10, can't select; another is windows 7, can select like you. It is very strange and I have no idea at all. Best regards, Clarence ________________________________ ???: xcrysden-bounces at democritos.it ?? Gavin Abo ????: 2020?7?17? 13:06 ???: xcrysden at democritos.it ??: Re: [xcrysden] can?t select atom There is a temporary link to a screenshot at [1]. In the screenshot, you should see two Carbon atoms selected in the Distance window from clicking on the highlighted atoms (in green) with XCrySDen 1.6.2 [2] using Cygwin (setup version 2.905 download from the website [3] on July 16, 2020) on Windows 10 Home. The graphene.in displayed in XCrySDen is from 1-4b_Day1-done_Timrov.tar at [4]. [1] https://drive.google.com/file/d/1337njrdXOtumWxRVGOewvlTUcuW9addp/view?usp=sharing [2] http://www.xcrysden.org/Download.html (XCrySDen 1.6.2 for Cygwin package: xcrysden-1.6.2-cygwin.tar.gz) [3] https://www.cygwin.com/ [4] https://www.materialscloud.org/learn/data/learn/files/Zem3D6woIu3r/ On 7/14/2020 10:18 AM, LEUNG Clarence wrote: Dear Developer and Xcrysden users, When I using Xcrysden 1.6.2 by crgwin in windows 10, it is strange that I can?t select atom when I measure the bond length. Have anyone came across this problem? Many thanks. Clarence -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200717/19292684/attachment.htm From gsabo at crimson.ua.edu Sat Jul 18 19:36:30 2020 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Sat, 18 Jul 2020 11:36:30 -0600 Subject: [xcrysden] =?utf-8?b?5Zue5aSNOiBjYW7igJl0IHNlbGVjdCBhdG9t?= In-Reply-To: References: Message-ID: I don't know if it helps or not, but I'm using as you probably saw the following Windows 10. Edition: Windows 10 Home Version: 2004 OS build: 19041.388 I didn't see if you mentioned if you are using the exact same Windows 10 or if the "About Your PC" window [1] on your system is showing something different. I also used Cygwin with setup version "2.905 (64 bit)".? Perhaps I missed it in your previous posts where you mentioned which Cygwin setup version you used. Or more specifically, which Cygwin packages are you using? I have tcl-tk 8.6.8-1, tcl-togl 2.0-4, ImageMagick 6.9.10.11-4, xinit 1.4.1-1, mesa 19.1.6-1, libGLU1 9.0.1-1, libfftw3 3.3.8-1, and libgfortran4 7.4.0-1 [2]. [1] https://support.microsoft.com/en-us/help/4027078/windows-view-your-pc-info [2] Temporarily link: https://drive.google.com/file/d/1HVFGpFlbT68QY78r0_tIfQBZip3NLwdQ/view?usp=sharing On 7/16/2020 11:57 PM, LEUNG Clarence wrote: > Dear Gavin, > > Thanks for your sharing. > > I have two laptop: one is windows 10, can't select; another is windows > 7, can select like you. > > It is very strange and I have no idea at all. > > Best regards, > Clarence > ------------------------------------------------------------------------ > *???:* xcrysden-bounces at democritos.it > ?? Gavin Abo > *????:* 2020?7?17? 13:06 > *???:* xcrysden at democritos.it > *??:* Re: [xcrysden] can?t select atom > > There is a temporary link to a screenshot at [1]. > > > In the screenshot, you should see two Carbon atoms selected in the > Distance window from clicking on the highlighted atoms (in green) with > XCrySDen 1.6.2 [2] using Cygwin (setup version 2.905 download from the > website [3] on July 16, 2020) on Windows 10 Home.? The graphene.in > displayed in XCrySDen is from 1-4b_Day1-done_Timrov.tar at [4]. > > > [1] > https://drive.google.com/file/d/1337njrdXOtumWxRVGOewvlTUcuW9addp/view?usp=sharing > > [2] http://www.xcrysden.org/Download.html > (XCrySDen 1.6.2 for Cygwin > package: xcrysden-1.6.2-cygwin.tar.gz) > > [3] https://www.cygwin.com/ > > [4] https://www.materialscloud.org/learn/data/learn/files/Zem3D6woIu3r/ > > > On 7/14/2020 10:18 AM, LEUNG Clarence wrote: >> >> Dear Developer and Xcrysden users, >> >> When I using Xcrysden 1.6.2 by crgwin in windows 10, it is strange >> that I can?t select atom when I measure the bond length.? Have anyone >> came across this problem? >> >> Many thanks. >> >> Clarence >> > > _______________________________________________ > 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/20200718/9aa48b5c/attachment.htm From matic.poberznik at gmail.com Sun Jul 19 01:19:17 2020 From: matic.poberznik at gmail.com (Matic) Date: Sun, 19 Jul 2020 01:19:17 +0200 Subject: [xcrysden] =?utf-8?b?5Zue5aSNOiBjYW7igJl0IHNlbGVjdCBhdG9t?= In-Reply-To: References: Message-ID: Hi Clarence, if the cygwin version isn't working for you on Win10 perhaps try the WSL version, the installation should be straightforward, but if you have issues please share. Basically you have to install windows subsystem for Linux: https://docs.microsoft.com/en-us/windows/wsl/install-win10 and follow the instructions on the xcrysden download page for wsl: http://www.xcrysden.org/Download.html I think that version is closer to the Linux version and should work better, one problem I can think of is that maybe the X-window system you are using on windows has some issues with Xcrysden, are you using Xming or something else? Best, Matic Poberznik > Dear Gavin, > > Thanks for your sharing. > > I have two laptop: one is windows 10, can't select; another is windows > 7, can select like you. > > It is very strange and I have no idea at all. > > Best regards, > Clarence > ------------------------------------------------------------------------ -- Matic Poberznik J. Stefan Institute, Jamova 39, Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200719/315a0266/attachment.htm From shadab at phas.ubc.ca Sat Jul 18 11:59:44 2020 From: shadab at phas.ubc.ca (shadab) Date: Sat, 18 Jul 2020 02:59:44 -0700 Subject: [xcrysden] Queries about orbital plotting in xcrysden Message-ID: <88917774754824cb9f8ff172cb64338d@phas.ubc.ca> Hi, I did a Wannier90 calculation from Wien2k DFT calculations for Bi2Se3. I was trying to plot the px, py, pz orbitals for Bi and Se atoms in the unit cell using the xsf files generated from the Wannier90 calculations. Xcrysden is plotting my orbitals outside the unit cell for some of the atoms (see the attached figure showing px orbital of Bi atom plotted outside the primitive unit cell). How can I plot it inside the unit cell lying on one of the Bi atom? Thanks Regards, -- Shadab Ahamed PHAS Graduate Student Stewart Blusson Quantum Matter Institute University of British Columbia | Vancouver 280-2355 East Mall | Vancouver BC | V6T 1Z4 Canada e: shadab at phas.ubc.ca v: +1-778-325-9814 -------------- next part -------------- A non-text attachment was scrubbed... Name: Bi_px.png Type: image/png Size: 65609 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200718/82beafd7/attachment-0001.png From gsabo at crimson.ua.edu Sun Jul 19 20:21:05 2020 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Sun, 19 Jul 2020 12:21:05 -0600 Subject: [xcrysden] Queries about orbital plotting in xcrysden In-Reply-To: <88917774754824cb9f8ff172cb64338d@phas.ubc.ca> References: <88917774754824cb9f8ff172cb64338d@phas.ubc.ca> Message-ID: <683a747e-f17d-5e60-65a1-e6593740d35f@crimson.ua.edu> I don't have much experience with Wannier calculations. So I don't have an answer for that.? Perhaps, one of the others in the list will be able to provide an answer for that. However, if you think the problem comes from a dangling atom, you may want to read the discussion to see if it helps or not on the webpage at: https://github.com/quanshengwu/wannier_tools/issues/31 On 7/18/2020 3:59 AM, shadab wrote: > Hi, > > I did a Wannier90 calculation from Wien2k DFT calculations for Bi2Se3. > I was trying to plot the px, py, pz orbitals for Bi and Se atoms in > the unit cell using the xsf files generated from the Wannier90 > calculations. Xcrysden is plotting my orbitals outside the unit cell > for some of the atoms (see the attached figure showing px orbital of > Bi atom plotted outside the primitive unit cell). How can I plot it > inside the unit cell lying on one of the Bi atom? > > Thanks > > Regards, From liangxy123 at hotmail.com Mon Jul 20 14:57:06 2020 From: liangxy123 at hotmail.com (LEUNG Clarence) Date: Mon, 20 Jul 2020 12:57:06 +0000 Subject: [xcrysden] =?gb2312?b?u9i4tDogY2Fuoa90IHNlbGVjdCBhdG9t?= In-Reply-To: References: , Message-ID: Dear Gavin, Thanks for your reply. It is noted that there is some problem on X11 for Xcrysden. Now I am using Xming for Xcrysden, and it works. Clarence From: Gavin Abo Sent: 2020?7?19? 1:36 To: xcrysden at democritos.it Subject: Re: [xcrysden] ??: can?t select atom I don't know if it helps or not, but I'm using as you probably saw the following Windows 10. Edition: Windows 10 Home Version: 2004 OS build: 19041.388 I didn't see if you mentioned if you are using the exact same Windows 10 or if the "About Your PC" window [1] on your system is showing something different. I also used Cygwin with setup version "2.905 (64 bit)". Perhaps I missed it in your previous posts where you mentioned which Cygwin setup version you used. Or more specifically, which Cygwin packages are you using? I have tcl-tk 8.6.8-1, tcl-togl 2.0-4, ImageMagick 6.9.10.11-4, xinit 1.4.1-1, mesa 19.1.6-1, libGLU1 9.0.1-1, libfftw3 3.3.8-1, and libgfortran4 7.4.0-1 [2]. [1] https://support.microsoft.com/en-us/help/4027078/windows-view-your-pc-info [2] Temporarily link: https://drive.google.com/file/d/1HVFGpFlbT68QY78r0_tIfQBZip3NLwdQ/view?usp=sharing On 7/16/2020 11:57 PM, LEUNG Clarence wrote: Dear Gavin, Thanks for your sharing. I have two laptop: one is windows 10, can't select; another is windows 7, can select like you. It is very strange and I have no idea at all. Best regards, Clarence ???: xcrysden-bounces at democritos.it ?? Gavin Abo ????: 2020?7?17? 13:06 ???: xcrysden at democritos.it ??: Re: [xcrysden] can?t select atom There is a temporary link to a screenshot at [1]. In the screenshot, you should see two Carbon atoms selected in the Distance window from clicking on the highlighted atoms (in green) with XCrySDen 1.6.2 [2] using Cygwin (setup version 2.905 download from the website [3] on July 16, 2020) on Windows 10 Home. The graphene.in displayed in XCrySDen is from 1-4b_Day1-done_Timrov.tar at [4]. [1] https://drive.google.com/file/d/1337njrdXOtumWxRVGOewvlTUcuW9addp/view?usp=sharing [2] http://www.xcrysden.org/Download.html (XCrySDen 1.6.2 for Cygwin package: xcrysden-1.6.2-cygwin.tar.gz) [3] https://www.cygwin.com/ [4] https://www.materialscloud.org/learn/data/learn/files/Zem3D6woIu3r/ On 7/14/2020 10:18 AM, LEUNG Clarence wrote: Dear Developer and Xcrysden users, When I using Xcrysden 1.6.2 by crgwin in windows 10, it is strange that I can?t select atom when I measure the bond length. Have anyone came across this problem? Many thanks. Clarence _______________________________________________ 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/20200720/46b44fa3/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: 39770D9847E944F0A2C8319A8A4213A1.png Type: image/png Size: 143 bytes Desc: 39770D9847E944F0A2C8319A8A4213A1.png Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200720/46b44fa3/attachment.png From matic.poberznik at gmail.com Mon Jul 20 00:36:59 2020 From: matic.poberznik at gmail.com (Matic) Date: Mon, 20 Jul 2020 00:36:59 +0200 Subject: [xcrysden] =?utf-8?b?5Zue5aSNOiBjYW7igJl0IHNlbGVjdCBhdG9t?= In-Reply-To: References: Message-ID: Hi, it seems to me that you are using cygwin-s xwindow system (I could be wrong), perhaps try to install Xming: https://sourceforge.net/projects/xming/ make sure that it's running and before doing anything in cygwin type in the terminal: export DISPLAY=:0 ?(you can also add this to your ~/.bashrc to avoid typing it everytime) I hope this helps/works, if not please let me know, Best, Matic > Dear Matic, > > Thanks for your reply. > > I am using X11 (I am not sure). The icon is as follows: > > Thanks! > > Best regards, > > Clarence > > Postdoctoral Fellow > > City University of Hong Kong > > *From: *Matic > *Sent: *2020?7?19?7:19 > *To: *XCrySDen mailing list ; LEUNG > Clarence > *Subject: *Re: [xcrysden] ??: can?t select atom > > Hi Clarence, > > if the cygwin version isn't working for you on Win10 perhaps try the > WSL version, the installation should be straightforward, but if you > have issues please share. > > Basically you have to install windows subsystem for Linux: > > https://docs.microsoft.com/en-us/windows/wsl/install-win10 > > and follow the instructions on the xcrysden download page for wsl: > > http://www.xcrysden.org/Download.html > > I think that version is closer to the Linux version and should work > better, one problem I can think of is that maybe the X-window system > you are using on windows has some issues with Xcrysden, are you using > Xming or something else? > > Best, > > Matic Poberznik > > Dear Gavin, > > Thanks for your sharing. > > I have two laptop: one is windows 10, can't select; another is > windows 7, can select like you. > > It is very strange and I have no idea at all. > > Best regards, > > Clarence > > -- > Matic Poberznik > J. Stefan Institute, Jamova 39, Ljubljana, Slovenia > -- Matic Poberznik J. Stefan Institute, Jamova 39, Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: 4A35A62E2CFE46148EFBF673A73145D9.png Type: image/png Size: 52593 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0004.png -------------- next part -------------- A non-text attachment was scrubbed... Name: AC24C22ABF6843379F22E2506EB692E1.png Type: image/png Size: 6226 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0005.png -------------- next part -------------- A non-text attachment was scrubbed... Name: 07DFAB292E4A4A4F834B55E39AB29EDE.png Type: image/png Size: 10137 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0006.png -------------- next part -------------- A non-text attachment was scrubbed... Name: CEA277E5E1964E6F8EE52A9FB554F4FA.png Type: image/png Size: 161 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0007.png From gsabo at crimson.ua.edu Wed Jul 22 03:37:38 2020 From: gsabo at crimson.ua.edu (Gavin Abo) Date: Tue, 21 Jul 2020 19:37:38 -0600 Subject: [xcrysden] =?utf-8?b?5Zue5aSNOiBjYW7igJl0IHNlbGVjdCBhdG9t?= In-Reply-To: References: Message-ID: Clarence, Good to read at [1] that you got it to work with Xming. In my case, I did not have to use Xming.? You probably saw in the screenshot [2] that I used a XTerm window for what is described at [3]. As shown in image [4], I used Cygwin's X.org Server [5] and clicked on XWin Server under the Windows start menu (as shown in your image [6]).? Then, I right-clicked on the Cygwin-X icon in the taskbar (as shown in your image [7]) and under System Tools opened the XTerm window.? For the Cygwin Setup version 2.905 64 bit used [8], the xorg-server 1.20.5-3 was the version installed. [1] http://www.democritos.it/pipermail/xcrysden/2020-July/002020.html [2] Temporary link: https://drive.google.com/file/d/1337njrdXOtumWxRVGOewvlTUcuW9addp/view [3] http://www.democritos.it/pipermail/xcrysden/2020-July/002012.html [4] Temporary link: https://drive.google.com/file/d/1R6YqL3j1CCjSRrODjMAMFH_9xsdKQgbf/view?usp=sharing [5] https://en.wikipedia.org/wiki/X.Org_Server [6] http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0004.png [7] http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0006.png [8] http://www.democritos.it/pipermail/xcrysden/2020-July/002016.html Best Regards, Gavin On 7/19/2020 4:36 PM, Matic wrote: > Hi, > > it seems to me that you are using cygwin-s xwindow system (I could be > wrong), perhaps try to install Xming: > > https://sourceforge.net/projects/xming/ > > make sure that it's running and before doing anything in cygwin type > in the terminal: > > export DISPLAY=:0 > > ?(you can also add this to your ~/.bashrc to avoid typing it everytime) > > I hope this helps/works, if not please let me know, > > Best, > > Matic > > >> Dear Matic, >> >> Thanks for your reply. >> >> I am using X11 (I am not sure). The icon is as follows: >> >> Thanks! >> >> Best regards, >> >> Clarence >> >> Postdoctoral Fellow >> >> City University of Hong Kong >> >> *From: *Matic >> *Sent: *2020?7?19?7:19 >> *To: *XCrySDen mailing list ; LEUNG >> Clarence >> *Subject: *Re: [xcrysden] ??: can?t select atom >> >> Hi Clarence, >> >> if the cygwin version isn't working for you on Win10 perhaps try the >> WSL version, the installation should be straightforward, but if you >> have issues please share. >> >> Basically you have to install windows subsystem for Linux: >> >> https://docs.microsoft.com/en-us/windows/wsl/install-win10 >> >> and follow the instructions on the xcrysden download page for wsl: >> >> http://www.xcrysden.org/Download.html >> >> I think that version is closer to the Linux version and should work >> better, one problem I can think of is that maybe the X-window system >> you are using on windows has some issues with Xcrysden, are you using >> Xming or something else? >> >> Best, >> >> Matic Poberznik >> >> Dear Gavin, >> >> Thanks for your sharing. >> >> I have two laptop: one is windows 10, can't select; another is >> windows 7, can select like you. >> >> It is very strange and I have no idea at all. >> >> Best regards, >> >> Clarence >> >> -- >> Matic Poberznik >> J. Stefan Institute, Jamova 39, Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200721/2f2acf47/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: CEA277E5E1964E6F8EE52A9FB554F4FA.png Type: image/png Size: 161 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200721/2f2acf47/attachment.png From liangxy123 at hotmail.com Wed Jul 22 04:21:45 2020 From: liangxy123 at hotmail.com (LEUNG Clarence) Date: Wed, 22 Jul 2020 02:21:45 +0000 Subject: [xcrysden] =?big5?b?pl7OYDogY2FuoaZ0IHNlbGVjdCBhdG9t?= In-Reply-To: References: , Message-ID: Dear Gavin, Thanks for your reply. The system of my laptop (Lenovo) is: Edition: Windows 10 Home Version: 1909 OS build: 18363.959 For Cygwin, version 2.905 64 bit For the package is as follows: [cid:image001.png at 01D66011.69CA6270] [cid:image003.png at 01D66011.C41BE000] It is found that when using X11, I click the red circle, the green atom will be selected. Clarence From: Gavin Abo Sent: 2020?7?22? 9:37 To: xcrysden at democritos.it Subject: Re: [xcrysden] ??: can?t select atom Clarence, Good to read at [1] that you got it to work with Xming. In my case, I did not have to use Xming. You probably saw in the screenshot [2] that I used a XTerm window for what is described at [3]. As shown in image [4], I used Cygwin's X.org Server [5] and clicked on XWin Server under the Windows start menu (as shown in your image [6]). Then, I right-clicked on the Cygwin-X icon in the taskbar (as shown in your image [7]) and under System Tools opened the XTerm window. For the Cygwin Setup version 2.905 64 bit used [8], the xorg-server 1.20.5-3 was the version installed. [1] http://www.democritos.it/pipermail/xcrysden/2020-July/002020.html [2] Temporary link: https://drive.google.com/file/d/1337njrdXOtumWxRVGOewvlTUcuW9addp/view [3] http://www.democritos.it/pipermail/xcrysden/2020-July/002012.html [4] Temporary link: https://drive.google.com/file/d/1R6YqL3j1CCjSRrODjMAMFH_9xsdKQgbf/view?usp=sharing [5] https://en.wikipedia.org/wiki/X.Org_Server [6] http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0004.png [7] http://www.democritos.it/pipermail/xcrysden/attachments/20200720/439929d5/attachment-0006.png [8] http://www.democritos.it/pipermail/xcrysden/2020-July/002016.html Best Regards, Gavin On 7/19/2020 4:36 PM, Matic wrote: Hi, it seems to me that you are using cygwin-s xwindow system (I could be wrong), perhaps try to install Xming: https://sourceforge.net/projects/xming/ make sure that it's running and before doing anything in cygwin type in the terminal: export DISPLAY=:0 (you can also add this to your ~/.bashrc to avoid typing it everytime) I hope this helps/works, if not please let me know, Best, Matic Dear Matic, Thanks for your reply. I am using X11 (I am not sure). The icon is as follows: Thanks! Best regards, Clarence Postdoctoral Fellow City University of Hong Kong From: Matic Sent: 2020?7?19? 7:19 To: XCrySDen mailing list; LEUNG Clarence Subject: Re: [xcrysden] ??: can?t select atom Hi Clarence, if the cygwin version isn't working for you on Win10 perhaps try the WSL version, the installation should be straightforward, but if you have issues please share. Basically you have to install windows subsystem for Linux: https://docs.microsoft.com/en-us/windows/wsl/install-win10 and follow the instructions on the xcrysden download page for wsl: http://www.xcrysden.org/Download.html I think that version is closer to the Linux version and should work better, one problem I can think of is that maybe the X-window system you are using on windows has some issues with Xcrysden, are you using Xming or something else? Best, Matic Poberznik Dear Gavin, Thanks for your sharing. I have two laptop: one is windows 10, can't select; another is windows 7, can select like you. It is very strange and I have no idea at all. Best regards, Clarence -- Matic Poberznik J. Stefan Institute, Jamova 39, Ljubljana, Slovenia -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200722/ae93d717/attachment-0001.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: 56FDE99755294D38A9C6A80B6EA32A62.png Type: image/png Size: 5427 bytes Desc: 56FDE99755294D38A9C6A80B6EA32A62.png Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200722/ae93d717/attachment-0003.png -------------- next part -------------- A non-text attachment was scrubbed... Name: DDFC608EAE9A44FBADF3C845E9C3C841.png Type: image/png Size: 30444 bytes Desc: DDFC608EAE9A44FBADF3C845E9C3C841.png Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200722/ae93d717/attachment-0004.png -------------- next part -------------- A non-text attachment was scrubbed... Name: 1DBC3F3E8B5D4B878346F7084D751E05.png Type: image/png Size: 155 bytes Desc: 1DBC3F3E8B5D4B878346F7084D751E05.png Url : http://www.democritos.it/pipermail/xcrysden/attachments/20200722/ae93d717/attachment-0005.png From shadab at phas.ubc.ca Thu Jul 30 09:18:01 2020 From: shadab at phas.ubc.ca (shadab) Date: Thu, 30 Jul 2020 00:18:01 -0700 Subject: [xcrysden] Extraction of radial function from .xsf file Message-ID: Hi all, I have produced .xsf file (containing basis states) from a Wannier90 run for Bi2Se3 which can be opened in xcrysden and the isosurface of the basis. My basis contains Bi and Se px, py and pz orbitals for all the Bi and Se atoms in the crystal unit cell. I wanted to extract the radial functions corresponding to each orbital from these .xsf files. I read the .xsf file documentation, but I am still not use sure how to go about doing this. Please let me know. Thanks Regards, -- Shadab Ahamed PHAS Graduate Student Stewart Blusson Quantum Matter Institute University of British Columbia | Vancouver 280-2355 East Mall | Vancouver BC | V6T 1Z4 Canada e: shadab at phas.ubc.ca v: +1-778-325-9814