From chan.modeller at gmail.com Tue Aug 18 06:51:40 2020 From: chan.modeller at gmail.com (Stephen Chan) Date: Tue, 18 Aug 2020 12:51:40 +0800 Subject: [xcrysden] Unable to open PWscf input file Xcrysden 1.6.2 Message-ID: Hi, I managed to compile the new version. The graphic looks much nicer. However, it seems there're some problems in loading QE input file, that can be visualised in 1.5.60 before. The strcuture is monoclinic with ibrav 14, spacegroup=14, and uniqueB=True. Atomic positions are in crystal_sg setting. Apparently, the new version requires pw.x from quantum espresso to convert the data in xsf format. Even after I added the path of pw.x in PATH variable, there is an error from the pwi2xsf.sh that: PRIMCOORD 1 (standard_in) 1: syntax error Could anyone give some help please? Many thanks Stephen -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200818/7422f1be/attachment.htm From c.friedrich at fz-juelich.de Tue Aug 18 17:02:02 2020 From: c.friedrich at fz-juelich.de (C.Friedrich) Date: Tue, 18 Aug 2020 17:02:02 +0200 Subject: [xcrysden] Isosurfaces Message-ID: <87086f91-1edc-1c11-79a0-e9541dfe4976@fz-juelich.de> Dear all, I am sorry if this has been asked already. I have not found a way to search the mailing-list archives. My program plots several 3D grids into a single XSF file in the following form: BEGIN_BLOCK_DATAGRID_3D Wannier orbitals BEGIN_DATAGRID_3D_orbital=1 ... (definition of 3D grid) ... ... (grid data) ... END_DATAGRID_3D BEGIN_DATAGRID_3D_orbital=2 ... (definition of 3D grid) ... ... (grid data) ... END_DATAGRID_3D ... (more grids) ... END_BLOCK_DATAGRID_3D When I open "Tools->data grid" in XCrySDen, it lets me choose any of the grids (or a linear combination) to plot. This works fine. However, when I want to look at a different data grid (from the same perspective) and "close" the isosurface, going to "Tools->data grid" just reopens the same isosurface again. It does not give me the menu from which to choose a data grid. The only possibility is to hit "File->close" and reopen the xsf file, but then I have lost the perspective (and all other parameters I might have adjusted). Thank you and best wishes Christoph ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Volker Rieke Geschaeftsfuehrung: Prof. Dr.-Ing. Wolfgang Marquardt (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ From matic.poberznik at gmail.com Tue Aug 18 21:14:42 2020 From: matic.poberznik at gmail.com (Matic) Date: Tue, 18 Aug 2020 21:14:42 +0200 Subject: [xcrysden] Isosurfaces In-Reply-To: <87086f91-1edc-1c11-79a0-e9541dfe4976@fz-juelich.de> References: <87086f91-1edc-1c11-79a0-e9541dfe4976@fz-juelich.de> Message-ID: <780ffa85-1f90-cc86-4844-87aeee55a437@gmail.com> Dear Cristoph, > My program plots several 3D grids into a single XSF file in the > following form: as far as I know plotting multiple grids from one xsf file with prespecified parameters isn't possible (I might be wrong), however there is a simple alternative to get the behavior you need, I suggest you store each grid in a separate xsf file (keeping PRIMVEC and PRIMCOORD the same in every file). You can then load one of the xsf files; set up the isovalues/perspective etc. and then use "Save current state", this will make a *xcrysden file that stores the parameters. You can then plot the other grids with the command: xcrysden --state your-state.xcrysden --xsf your.xsf you can also just loop over the xsf files as: for i in *.xsf; do xcrysden --state your-state.xcrysden --xsf $i ; done I hope this helps, Best regards, Matic Poberznik -- Matic Poberznik J. Stefan Institute, Jamova 39, Ljubljana, Slovenia From mhmtdogan at gmail.com Mon Aug 24 06:58:06 2020 From: mhmtdogan at gmail.com (=?UTF-8?Q?Mehmet_Do=C4=9Fan?=) Date: Sun, 23 Aug 2020 21:58:06 -0700 Subject: [xcrysden] Anti-aliasing not working in version 1.6.2 on MacOS 10.15 Message-ID: Dear colleagues, I am a long-time user of XCrysDen, however, after upgrading my OS, I installed XCrysDen version 1.6.2 on MacOS 10.15, and realized that anti-aliasing doesn't work properly. When I turn it on and off, there is no visual difference, except that the atoms slightly shift left and right. Playing with the anti-aliasing settings doesn't make any difference. Every other function that I've tried seems to be working as expected. I installed it using 3 different methods (precompiled, macports, fink), and they're all identical as far as I can tell. Any help would be greatly appreciated. Thank you! Mehmet Dogan Postdoc, UC Berkeley -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200823/d0094988/attachment.htm From chan.modeller at gmail.com Wed Aug 26 04:56:36 2020 From: chan.modeller at gmail.com (Stephen Chan) Date: Wed, 26 Aug 2020 10:56:36 +0800 Subject: [xcrysden] Unable to open PWscf input file Xcrysden 1.6.2 In-Reply-To: References: Message-ID: OK. I found the solution myself. The pw.x and probably the openmpi have to be installed and functioning, before the data conversion could work. On Tue, Aug 18, 2020 at 12:51 PM Stephen Chan wrote: > Hi, > > I managed to compile the new version. The graphic looks much nicer. > However, it seems there're some problems in loading QE input file, that can > be visualised in 1.5.60 before. > > The strcuture is monoclinic with ibrav 14, spacegroup=14, and > uniqueB=True. Atomic positions are in crystal_sg setting. Apparently, the > new version requires pw.x from quantum espresso to convert the data in xsf > format. Even after I added the path of pw.x in PATH variable, there is an > error from the pwi2xsf.sh that: > PRIMCOORD > 1 > (standard_in) 1: syntax error > > Could anyone give some help please? > > Many thanks > Stephen > -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200826/5c26aaea/attachment.htm