From bahaartv at gmail.com Tue Nov 1 08:35:00 2011 From: bahaartv at gmail.com (bahaareh tavakoli nejad) Date: Tue, 1 Nov 2011 00:35:00 -0700 Subject: [xcrysden] XCrySDen Digest, Vol 45, Issue 5 In-Reply-To: References: Message-ID: hello. I have a 64 bit windows7. I download ''xc-1.5.18-cygwin-shared.tar'' and also i download ''Cygwin/X'' and bash, gawk, grep, gzip, ImageMagic,less, more, opengle and tcltk. I Extract the ''xc-1.5.18-cygwin-shared.tar'' in the folder that contain cygiwn. in the Xcrysden I built tho empty folder "XCRYSDEN_TOPDIR" and "XCRYSDEN_SCRATCH". Then i use the ''$ ./xcConfigure'' command. but i get this error : bash: ./xcConfigure: No such file or directory. please explain me in detail what should i do. Thank you very much. -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20111101/ac641844/attachment.htm From tone.kokalj at ijs.si Mon Nov 7 02:45:08 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Mon, 07 Nov 2011 02:45:08 +0100 Subject: [xcrysden] XCrySDen Digest, Vol 45, Issue 5 In-Reply-To: References: Message-ID: <1320630308.3704.25.camel@catalyst.ijs.si> On Tue, 2011-11-01 at 00:35 -0700, bahaareh tavakoli nejad wrote: > hello. > I have a 64 bit windows7. I download ''xc-1.5.18-cygwin-shared.tar'' > and also i download ''Cygwin/X'' and bash, gawk, grep, gzip, > ImageMagic,less, more, opengle and tcltk. > I Extract the ''xc-1.5.18-cygwin-shared.tar'' in the folder that > contain cygiwn. in the Xcrysden I built tho empty folder > "XCRYSDEN_TOPDIR" and "XCRYSDEN_SCRATCH". Then i use the > ''$ ./xcConfigure'' command. but i get this error : > bash: ./xcConfigure: No such file or directory. Which means you are not in the xcrysden's root directory. Note that XCRYSDEN_TOPDIR is not an empty directory, but the root directory where the xcrysden package is installed. In particular in your case you should do: $ tar zxvf xc-1.5.18-cygwin-shared.tar.gz $ cd XCrySDen-1.5.18-bin-shared/ $ ./xcrysden That's all. Note, however, that if you have wrongly defined XCRYSDEN_TOPDIR, then either unset it, i.e., unset XCRYSDEN_TOPDIR, or correct it to point to the correct place. Regards, Tone -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From muirs at onid.orst.edu Mon Nov 7 17:52:45 2011 From: muirs at onid.orst.edu (Sean Muir) Date: Mon, 7 Nov 2011 08:52:45 -0800 Subject: [xcrysden] XCrySDen Digest, Vol 45, Issue 5 In-Reply-To: References: Message-ID: Hi Folks Just in case it helps, here are some instructions I once wrote on how to get XCrysden running on Windows for a solid state physics class I was in. I had no previous knowledge of UNIX commands at the time so hopefully they are simple enough that a person entirely new to UNIX and command line can follow. Also they are written from the perspective of wanting to generate a Fermi structure from Wien2K data or k path for use in Wien2K but have general info on running xcrysden as well. Cheers, Sean Muir Oregon State University How to get XCrySDen running on a server with Windows (via Cygwin) [SM 05-17-10] Cygwin is a UNIX emulation engine. Aside from the main engine, additional ?packages? must be downloaded and installed. Each package adds additional functionality to the emulation engine, all can be viewed and marked for download via the main Cygwin setup program. Go to http://cygwin.com/install.html and get the setup.exe file (download link in the beginning text of the webpage). Once you run the setup.exe file hit next> and then choose install from internet, next>. Select install for all users and choose a root directory for Cygwin (i.e. where you want it installed). Next choose a download location for storing temporary files related to the setup (just go with default folder if you have no other preference). Select next>. Choose Direct Connection next>. Choose a website to download more needed files (specifically outlined below) from. The ftp ones seemed to be quicker than the http. Select next> and it should connect to the site and a select packages screen will appear. All the packages which may ever be needed are listed alphabetically below. It is possible that the first package, cygwin, and the last one, xinit, are the only two needed for opening an X Windows terminal and running XCrySDen on the Jansen server, however the others are needed when running XCrySDen on your own machine. Since the file size of each package is pretty small it doesn't hurt to download them all in case they may be called upon by the program in some way. cygwin bash bc coreutils gawk grep gzip ImageMagick less mesa more opengl openssh tcltk X-start-menu-icons xterm xinit Use the search box in the corner to locate these. The easiest thing is to have the select package screen in category view mode (button upper right to change view). Type in the search word for each package in the list above (e.g. cygwin). After the word All at the top of the file structure tree click on the word Default so that it changes to Install. This may download some unnecessary stuff but it is OK. For the bc package using the search bar brings up a bunch of stuff since those letters appear next to each other in a lot of the available Cygwin packages. The only thing needed is bc: The GNU numeric?. under the utils heading. Select next> and let it download and install any dependent files if needed (it will warn you if so). You should be able to grab all the packages in one go, but if not continue to rerun the Cygwin setup.exe file with all the same initial root directory and download folder options until each has been installed. After having completed the above steps, you should have two new program folders available within the program start menu, these are Cygwin and Cygwin-X. The first contains one program Cygwin Bash Shell. This is a UNIX command line interface, which is needed if you want to get XCrySDen running on your own PC (see below). The second, Cygwin-X, contains a few programs, XWin Server and xterm. These programs allow XCrySDen located on a server somewhere to run on your PC. XCrySDen on your own machine You can download XCrySDen from http://www.xcrysden.org/. Some configuration of the software will be necessary. XCrySDen on a PC running Windows [SM 05-17-10] First obtain all the necessary Cygwin packages as outlined above for getting XCrysden on the Jansen server running on a PC. Once done you are ready to get XCrySDen. Go to http://www.xcrysden.org and download the xc-1.5.18-cygwin-shared.tar.gz file. THESE INSTRUCTIONS WERE TESTED USING THE XCrySDen CYGWIN BINARY PACKAGE 1.5.18. You will need a program to unzip the .tar.gz file. Recommended is 7-zip, http://www.7-zip.org/. After unzipping the .tar.gz file and the .tar file that is inside, rename the uncompressed folder (XCrySDen-1.5.18-bin-shared) to something shorter (e.g. xcrysden) and copy. We will now place it in the Cygwin root directory that you created on initial installation of Cygwin. Specifically paste the uncompressed folder in the Cygwin?home?username folder (i.e. the path including the pasted file would be something like C:\Cygwin\home\yourusername\XCrySDen if your Cygwin root directory was placed directly on the C drive). Now we can go command-line-o. Open up Cygwin bash shell which should be under your program menu. This is the UNIX emulator and a command line interface. The user directory you are placed in when you open it is the Cygwin?home?username folder (from above). We want to go into the folder XCrySDen which we just moved. To do this we give a change directory command followed by the name of the folder we want (i.e. type cd XCrySDen). Some environmental settings need to be configured. In the XCrySDen directory, enter ./XcConfigure.sh . Enter either 'no' or the default setting should be fine for everything. The last setup procedure is to run 'source ~/.bashrc' in the terminal. To go back to the username folder (if needed) type cd with nothing after it. Now, type the command ./xcrysden . This will launch the program XCrySDen and you should see its interface open up. The configuration needs to be done only once, but GOING INTO THE XCRYSDEN DIRECTORY IS NEEDED TO LAUNCH THE PROGRAM EVERY TIME. All that is left to do is place a Wien2K structure file into the XCrySDen folder. To do this go onto your Wien2K via W2Web session and go to files? struct file(s)? and download/copy the case.struct file to XCrySDen (the folder from above). Now from inside XCrySDen go File?Open Wien2K?Open Wien2K Struct file. Choose the case.struct file you downloaded and open. You should see the real space structure model. Up at the top if you go to Tools?k-path selection the reciprocal lattice view appears and it seems you should be able to generate the k path file such as would be needed for Wien2K dispersion calculations. However when the k-path file is generated having used OpenWien2K? Open Wien2K Struct file the option to save as the appropriate .klist file is not available (only .kpath and 2 other options are present). If we were running XCrysden on a server with Wien2Kthe other option to go File?OpenWien2K?select k-path would work but this does not appear to function when running natively on a PC. The solution and way to generate a .klist file involves going command-line-o again. From the Cygwin bash shell type cd XCrySDen (if not already there) next type ./xcrysden ?wien_kpath case.struct Where case.struct is of course the specific name of the wien structure file you downloaded. The ./xcrysden command simply launches the program just like before however the additional ?wien_kpath command tells it to launch directly into the reciprocal lattice view of your file. The difference is that by doing it this way the option to save as a .klist file will now be present . This file?s extension can then be modified to .klist_band and it can then be uploaded back to your session folder on the Jansen Wien2K server for use in the dispersion calculations. So if all you want is to see is the reciprocal lattice and to generate a .klist file you can skip the step where we launched entire program (real space view) and jump right to this part. The Fermi surface functionality does not work when running XCrySDen locally, as it requires that the program communicate with Wien2K subprograms on the Wien2K server. There may exist a way to tell it the server's address and your W2Web password but thus far I have yet to figure it out. On Tue, Nov 1, 2011 at 12:35 AM, bahaareh tavakoli nejad wrote: > hello. > I have a 64 bit windows7. I download ''xc-1.5.18-cygwin-shared.tar'' and > also i download ''Cygwin/X'' and?? bash, gawk, grep, gzip, ImageMagic,less, > more, opengle and tcltk. > I Extract? the ''xc-1.5.18-cygwin-shared.tar'' in the folder that contain > cygiwn. in the Xcrysden I built tho empty folder "XCRYSDEN_TOPDIR" and > "XCRYSDEN_SCRATCH". Then i use the? ''$ ./xcConfigure'' command. but i get > this error : bash: ./xcConfigure: No such file or directory. > please explain me in detail what should i do. > > Thank you very much. > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden > > From aplahemant at gmail.com Thu Nov 10 12:19:27 2011 From: aplahemant at gmail.com (Hemant Dixit) Date: Thu, 10 Nov 2011 12:19:27 +0100 Subject: [xcrysden] brillouin zone of CuFeO2 R-3m # 166 Message-ID: Dear Xcrysden users, I am trying to perform band structure calculation of CuFeO2 (space group: R-3m # 166) with WIEN2K. I have generated the CuFeO2-r3m.struct file from the experimental data using CuFeO2-r3m.cif file (both attached herewith). Now I try to use Xcrysden to generate the k-path for band structure, however I see that the reciprocal space lattice is much different from conventional reciprocal lattice for rhombohedral structure. Also the high symmetry points are not labelled with Xcrysden. Can anyone explain the high symmetry points for this structure? I guess it is due to the HCP basis used by WIEN code but do not understand clearly. Your help is greatly appreciated. thanks and regards, -- Hemant Dixit. PhD Student, U 313, Department of Physics University of Antwerp. Groenenborgerlaan 171, Antwerp.Belgium-2020 Telephone: +32 3 265 34 31 Mobile: 0032 486368660 -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20111110/d020d06c/attachment.htm -------------- next part -------------- A non-text attachment was scrubbed... Name: CuFeO2-r3m.cif Type: application/octet-stream Size: 979 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20111110/d020d06c/attachment.obj -------------- next part -------------- A non-text attachment was scrubbed... Name: CuFeO2-r3m.struct Type: application/octet-stream Size: 1199 bytes Desc: not available Url : http://www.democritos.it/pipermail/xcrysden/attachments/20111110/d020d06c/attachment-0001.obj From ajitkvallabhaneni at gmail.com Thu Nov 10 16:25:52 2011 From: ajitkvallabhaneni at gmail.com (Ajit Vallabhaneni) Date: Thu, 10 Nov 2011 10:25:52 -0500 Subject: [xcrysden] Query on version 1.4 Message-ID: I am a new user of Quantumespresso. Due to some issues with the linux OS i use, i can only install the older version of xcrysden (V1.4). I was wondering if this version is compatible with the QE V4.3.1 because when i tried to run some tutorials on PWSCF calculations, i can view only the input files but not the output. In some cases i cannot see the input as well. The following is the error message i get. ERROR: while executing exec sh ERROR INFO: Child process exited abnormally Thanks Ajit -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20111110/85d8763f/attachment.htm From tone.kokalj at ijs.si Wed Nov 16 09:47:19 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 16 Nov 2011 09:47:19 +0100 Subject: [xcrysden] Query on version 1.4 In-Reply-To: References: Message-ID: <1321433239.3327.8.camel@catalyst.ijs.si> On Thu, 2011-11-10 at 10:25 -0500, Ajit Vallabhaneni wrote: > I am a new user of Quantumespresso. Due to some issues with the linux > OS i use, i can only install the older version of xcrysden (V1.4). Why? Please, give more info of what is the problem. > I was wondering if this version is compatible with the QE V4.3.1 > because when i tried to run some tutorials on PWSCF calculations, i > can view only the input files but not the output. Well, v1.4 is rather outdated and much older than QE-4.3, which is why you faced problems. You should install the compiled 1.5 version. Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From ilukacevic at fizika.unios.hr Wed Nov 16 14:08:44 2011 From: ilukacevic at fizika.unios.hr (Igor Lukacevic) Date: Wed, 16 Nov 2011 14:08:44 +0100 Subject: [xcrysden] Visualizing the Fermi surface Message-ID: <4EC3B5DC.1030505@fizika.unios.hr> Dear all, I'm trying to visualize the Fermi surface using the bxsf file created by abinit. The file itself looks ok, but when I open it in xcrysden, there is no surface for any selected band, only an empty BZ. Has anyone had any similar problems? I'd appreciate any comment or suggestion. Thank you all in advance! Yours, Igor Lukacevic -- Igor Lukacevic, PhD Department of Physics University J. J. Strossmayer Trg Ljudevita Gaja 6 31000 Osijek Croatia tel. +385 31232713 fax. +385 31232701 e-mail: ilukacevic at fizika.unios.hr web: www.fizika.unios.hr/~ilukacevic -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20111116/d8a58c7f/attachment.htm From tone.kokalj at ijs.si Fri Nov 18 15:11:25 2011 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Fri, 18 Nov 2011 15:11:25 +0100 Subject: [xcrysden] Visualizing the Fermi surface In-Reply-To: <4EC3B5DC.1030505@fizika.unios.hr> References: <4EC3B5DC.1030505@fizika.unios.hr> Message-ID: <1321625485.5338.17.camel@catalyst.ijs.si> On Wed, 2011-11-16 at 14:08 +0100, Igor Lukacevic wrote: > Dear all, > > I'm trying to visualize the Fermi surface using the bxsf file created > by abinit. The file itself looks ok, but when I open it in xcrysden, > there is no surface for any selected band, only an empty BZ. Did you specify the correct Fermi energy? What does the band-widths plot show, which is displayed prior to Fermi-Surface viewer appears? Do the bands cross the Fermi energy? Regards, -- Anton Kokalj J. Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax:+386-1-477-3822) Please, if possible, avoid sending me Word or PowerPoint attachments. See: http://www.gnu.org/philosophy/no-word-attachments.html From ilukacevic at fizika.unios.hr Mon Nov 21 08:11:10 2011 From: ilukacevic at fizika.unios.hr (Igor Lukacevic) Date: Mon, 21 Nov 2011 08:11:10 +0100 Subject: [xcrysden] Visualizing the Fermi surface In-Reply-To: <1321625485.5338.17.camel@catalyst.ijs.si> References: <4EC3B5DC.1030505@fizika.unios.hr> <1321625485.5338.17.camel@catalyst.ijs.si> Message-ID: <4EC9F98E.4030808@fizika.unios.hr> Dear Anton, thank you for the reply. I've given the energy outputted by the bxsf file. Xcrysden, actually, recognized it itself. It is very close to the energy given in ABINIT output. Aaaah, now I see it! Fermi level is just at the top of the 16th band, and not crossing any other band. That's why there is no Fermi surface. Thank You for helping me. And sorry for taking Your time with this issue. Best regards, Igor L. Tone Kokalj wrote: > On Wed, 2011-11-16 at 14:08 +0100, Igor Lukacevic wrote: > >> Dear all, >> >> I'm trying to visualize the Fermi surface using the bxsf file created >> by abinit. The file itself looks ok, but when I open it in xcrysden, >> there is no surface for any selected band, only an empty BZ. >> > > Did you specify the correct Fermi energy? > > What does the band-widths plot show, which is displayed prior to > Fermi-Surface viewer appears? Do the bands cross the Fermi energy? > > Regards, > -- Igor Lukacevic, PhD Department of Physics University J. J. Strossmayer Trg Ljudevita Gaja 6 31000 Osijek Croatia tel. +385 31232713 fax. +385 31232701 e-mail: ilukacevic at fizika.unios.hr web: www.fizika.unios.hr/~ilukacevic -------------- next part -------------- An HTML attachment was scrubbed... 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