From poojavyas1251995 at gmail.com Wed Jan 8 06:35:56 2020 From: poojavyas1251995 at gmail.com (Pooja Vyas) Date: Wed, 8 Jan 2020 11:05:56 +0530 Subject: [xcrysden] atomic position Message-ID: I opened an input file which has two atomic positions(Ca 0.0 0.0 0.0, O 0.5 0.5 0.5) in X-crysden. Then it showed me a structure with 27 atoms whose co-ordinates (read by atoms info) are as follows: Ca 0.5 0.5 0.0 Ca 0.0 0.0 0.0 Ca 0.5 0.0 0.5 Ca 0.0 0.5 0.5 O 0.0 0.0 0.5 O 0.5 0.5 0.5 O 0.0 0.5 0.0 O 0.5 0.0 0.0 Ca 0.5 0.5 1.0 Ca 0.0 0.0 1.0 O 0.0 0.5 1.0 O 0.5 0.0 1.0 Ca 0.0 1.0 0.0 Ca 0.5 1.0 0.5 O 0.0 1.0 0.5 O 0.5 1.0 0.0 Ca 0.0 1.0 1.0 O 0.5 1.0 1.0 Ca 1.0 0.0 0.0 Ca 1.0 0.5 0.5 O 1.0 0.0 0.5 O 1.0 0.5 0.0 Ca 1.0 0.0 1.0 O 1.0 0.5 1.0 Ca 1.0 1.0 0.0 O 1.0 1.0 0.5 Ca 1.0 1.0 1.0 I want to calculate the energy due to vacancy in quantum-espresso. So, don't I have to include all this atomic positions and then remove one atom, while calculating energy due to vacancy? If I include all the positions and calculate energy, it shows me the following error, %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 17 from check_atoms : error # 1 atoms # 1 and # 2 differ by lattice vector (-1, 1, 0) in crystal axis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% -------------- next part -------------- An HTML attachment was scrubbed... URL: http://www.democritos.it/pipermail/xcrysden/attachments/20200108/05c47b55/attachment.htm From tone.kokalj at ijs.si Wed Jan 8 09:15:01 2020 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 08 Jan 2020 09:15:01 +0100 Subject: [xcrysden] atomic position In-Reply-To: References: Message-ID: Dear Pooja Vyas Nobody can help you, unless you provide the input file. Best regards, Tone PS: please sing your emails with your affiliation as to comply with the mailing list rules. -- Jo?ef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax: +386-1-251-9385) On Wed, 2020-01-08 at 11:05 +0530, Pooja Vyas wrote: > I opened an input file which has two atomic positions(Ca 0.0 0.0 0.0, > O 0.5 0.5 0.5) in X-crysden. Then it showed me a structure with 27 > atoms whose co-ordinates (read by atoms info) are as follows: > Ca 0.5 0.5 0.0 > Ca 0.0 0.0 0.0 > Ca 0.5 0.0 0.5 > Ca 0.0 0.5 0.5 > O 0.0 0.0 0.5 > O 0.5 0.5 0.5 > O 0.0 0.5 0.0 > O 0.5 0.0 0.0 > Ca 0.5 0.5 1.0 > Ca 0.0 0.0 1.0 > O 0.0 0.5 1.0 > O 0.5 0.0 1.0 > Ca 0.0 1.0 0.0 > Ca 0.5 1.0 0.5 > O 0.0 1.0 0.5 > O 0.5 1.0 0.0 > Ca 0.0 1.0 1.0 > O 0.5 1.0 1.0 > Ca 1.0 0.0 0.0 > Ca 1.0 0.5 0.5 > O 1.0 0.0 0.5 > O 1.0 0.5 0.0 > Ca 1.0 0.0 1.0 > O 1.0 0.5 1.0 > Ca 1.0 1.0 0.0 > O 1.0 1.0 0.5 > Ca 1.0 1.0 1.0 > I want to calculate the energy due to vacancy in quantum-espresso. > So, don't I have to include all this atomic positions and then remove > one atom, while calculating energy due to vacancy? > If I include all the positions and calculate energy, it shows me the > following error, > > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%% > task # 17 > from check_atoms : error # 1 > atoms # 1 and # 2 differ by lattice vector (-1, 1, 0) in > crystal axis > %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% > %%%%%%%%%% > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden From tone.kokalj at ijs.si Wed Jan 8 09:37:44 2020 From: tone.kokalj at ijs.si (Tone Kokalj) Date: Wed, 08 Jan 2020 09:37:44 +0100 Subject: [xcrysden] New XCRYSDEN version: 1.6.2 In-Reply-To: <0aa1654c-9801-615f-aaae-442fb0491a65@crimson.ua.edu> References: <07ab2fa8fc9bb623e4a4e9f9ad93c434d079931f.camel@ijs.si> <0aa1654c-9801-615f-aaae-442fb0491a65@crimson.ua.edu> Message-ID: <0e6fe000ae031c7d728857102c024ba09b08f874.camel@ijs.si> On Mon, 2019-12-30 at 07:49 -0700, Gavin Abo wrote: > Tone, > Thanks for the new XCrySDen version. It looks like the new 1.6.2 > version has the WIEN2k k-point improvement [1] and a gfortran 8.2.0 > fix [2]. Even though, I'm not seeing it mentioned on the News > webpage [3]. The "Bug fixes" description on the News" indeed does not mention all fixed bugs. > It looks like the popular Linux precompiled semishared version is not > available for 1.6.2. But the shared version is available. The reason is that it is very easy to install the required system libraries with a linux-distro package manager system (such as apt for Debian). Required libraries are listed on the Download page. > It took me some time to figure out what packages I needed for > Ubuntu 18.04.3 LTS to install it from the source code instead, Thanks for the feednack. Note that needed packages for compilation are stated in ./system/README file (but perhaps some are missing). > If it helps other Ubuntu > users, the packages I had to install to build it are listed below: > In a Ubuntu 18.04.3 LTS terminal, entered the commands: > cd ~ > sudo apt update > sudo apt install libquadmath0 gfortran build-essential libglu1-mesa- > dev libtogl-dev tcl-dev tk-dev libfftw3-dev libxmu-dev > wget http://www.xcrysden.org/download/xcrysden-1.6.2.tar.gz > tar xvf xcrysden-1.6.2.tar.gz > cd xcrysden-1.6.2 > cp ./system/Make.sys-shared Make.sys > make all > cd scripts > ./xcConfigure.sh Note that "./xcConfigure.sh" is obsolete (I should purge it). All that is required is to add xcrysden top directory to the PATH (or make a link from a directory that is on the PATH to the xcrysden script). Optionally one can also define XCRYSDEN_TOPDIR enviromental variable in ~/.bashrc. Best regards, Tone Kokalj -- Jo?ef Stefan Institute, Jamova 39, 1000 Ljubljana, Slovenia (tel: +386-1-477-3523 // fax: +386-1-251-9385) > source ~/.bashrc > xcrysden > > [1] https://www.mail-archive.com/wien at zeus.theochem.tuwien.ac.at/msg1 > 5219.html > [2] http://www.democritos.it/pipermail/xcrysden/2018-October/001929.h > tml > [3] http://www.xcrysden.org/News.html > Sincerely, > Gavin > On 10/28/2019 10:21 AM, Tone Kokalj wrote: > > Dear colleagues, > > > > I would like to inform you about new xcrysden version 1.6, which > > includes several new features and bug fixes, documented here: > > http://www.xcrysden.org/News.html > > Perhaps, the most useful new feature is the "reload" button, which > > reloads the structure from the file. > > > > New version is available in source form and as precompiled for > > Linux, > > MacOS, and Windows. For more details see: > > http://www.xcrysden.org/Download.html > > > > Best regards, > > Tone Kokalj > > _______________________________________________ > XCrySDen mailing list > XCrySDen at democritos.it > http://www.democritos.it/mailman/listinfo/xcrysden