Re: [Spglib-users] Spglib-users Digest, Vol 9, Issue 1
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Re: [Spglib-users] Spglib-users Digest, Vol 9, Issue 1
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From: Shyue P. O. <sh...@gm...> - 2016-04-06 13:11:30
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Actually, we have recently implemented a web app version of pymatgen at http://www.materialsvirtuallab.org/matgenie . This includes symmetry analysis via spglib. I think it’s better to build via Python web frameworks than to try to build spglib into a JS form and having to deal with multiple programming languages. Shyue Ping On April 6, 2016 at 2:02:15 AM, spg...@li... (spg...@li...) wrote: Send Spglib-users mailing list submissions to spg...@li... To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/spglib-users or, via email, send a message with subject or body 'help' to spg...@li... You can reach the person managing the list at spg...@li... When replying, please edit your Subject line so it is more specific than "Re: Contents of Spglib-users digest..." Today's Topics: 1. Spglib in JavaScript for in-browser usage (Evgeny Blokhin) 2. Re: Spglib in JavaScript for in-browser usage (Atsushi Togo) 3. Spglib 1.9.x (Atsushi Togo) 4. Symmetry identification of POSCAR with corner atoms (AP Jena) 5. Re: Symmetry identification of POSCAR with corner atoms (Atsushi Togo) 6. Determine spacegroup given symmetry operations (Keith Refson) ---------------------------------------------------------------------- Message: 1 Date: Sat, 19 Sep 2015 02:43:08 +0200 From: Evgeny Blokhin <eb...@ti...> Subject: [Spglib-users] Spglib in JavaScript for in-browser usage To: spg...@li... Message-ID: <263...@we...> Content-Type: text/plain; charset="us-ascii" An HTML attachment was scrubbed... ------------------------------ Message: 2 Date: Sun, 20 Sep 2015 10:01:01 +0900 From: Atsushi Togo <atz...@gm...> Subject: Re: [Spglib-users] Spglib in JavaScript for in-browser usage To: Evgeny Blokhin <eb...@ti...> Cc: spglib-users <spg...@li...> Message-ID: <CAA...@ma...> Content-Type: text/plain; charset=UTF-8 Hi Evgeny, This is interesting. I like the idea that it works on client side. It may be the time for me to learn JS and around. What spglib can do can be done by bilbao-crystallographic server. So if some better service is provided, it may be nicer, e.g., to provide machine friendly interface. Togo On Sat, Sep 19, 2015 at 9:43 AM, Evgeny Blokhin <eb...@ti...> wrote: > Dear Dr. Atsushi Togo-san and Spglib users, > > as you probably know any C code can be transpiled to JavaScript with the aid > of source-to-source code compiler. After a successful experience with > converting RasMol to JavaScript (https://bitbucket.org/jam31/rasmoljs), i > decided to keep on with Spglib. This is to draw your attention to the > result, SpglibJS. Now to determine crystalline symmetry you need only a > browser (without any plugins). SpglibJS is a pure experiment, and to foster > any possible ideas and usecases i created an example web-app, providing > symmetry validation functionality for CIF or POSCAR files. An explicit > symmetry information is absent in POSCARs and often omitted in CIFs, so this > web-app provides a quick way of checking the symmetry. No server is used > after loading, so it is possible to drop a file there and check it without > Internet connection (and without any concerns about privacy). > > The link is https://github.com/blokhin/spglibjs > > I would be happy if you find any further inspiration from my code. Lastly, a > big thanks to Dr. Atsushi Togo-san for Spglib. > > Regards, > Evgeny Blokhin > > > ------------------------------------------------------------------------------ > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > -- Atsushi Togo http://atztogo.github.com/ atz...@gm... ------------------------------ Message: 3 Date: Sun, 10 Jan 2016 18:47:00 +0900 From: Atsushi Togo <atz...@gm...> Subject: [Spglib-users] Spglib 1.9.x To: spglib-users <spg...@li...> Message-ID: <CAAfkA7dY-jV12vqqJBE-v9QZYo1w2a3ZO=KG5...@ma...> Content-Type: text/plain; charset=UTF-8 Dear spglib users, Some news. Spglib 1.9.0 was released. No new features were added from version 1.8.x. The module name change in python wrapper may be a big issue. Pypi and conda packages were made by Pawe? T. Jochym. Now we can install spglib via pip or conda. These packages will be updated along with github releases. Python module name was changed to spglib. http://spglib.sourceforge.net/python-spglib.html#python-spglib Best wishes, Togo -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... ------------------------------ Message: 4 Date: Thu, 14 Jan 2016 10:44:42 +0530 From: AP Jena <ap...@gm...> Subject: [Spglib-users] Symmetry identification of POSCAR with corner atoms To: spg...@li... Message-ID: <CADmxT8AD5gHWFr9pEM6j4h0WsP=Fnr...@ma...> Content-Type: text/plain; charset="utf-8" Dear all, For an ideal bcc conventional cell with all the corner atoms explicitly listed in POSCAR, I wanted to find the symmetry and reduce to primitive cell using spglib. I?m not able to manage spglib identify the symmetry. Any suggestion appreciated. POSCAR:: Fe 1.0 1.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 1.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 1.0000000000000000 Fe 9 Direct 0.500000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 1.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 1.000000 1.000000 0.000000 1.000000 1.000000 1.000000 A P Jena, Kolkata, India. ? -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ Message: 5 Date: Fri, 15 Jan 2016 14:32:18 +0900 From: Atsushi Togo <atz...@gm...> Subject: Re: [Spglib-users] Symmetry identification of POSCAR with corner atoms To: spglib-users <spg...@li...> Message-ID: <CAA...@ma...> Content-Type: text/plain; charset=UTF-8 Hi, Your POSCAR is wrong. It should be like this. Fe 1.0 1.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 1.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 1.0000000000000000 Fe 2 Direct 0.500000 0.500000 0.500000 0.000000 0.000000 0.000000 Togo On Thu, Jan 14, 2016 at 2:14 PM, AP Jena <ap...@gm...> wrote: > Dear all, > For an ideal bcc conventional cell with all the corner atoms explicitly > listed in POSCAR, I wanted to find the symmetry and reduce to primitive cell > using spglib. I?m not able to manage spglib identify the symmetry. Any > suggestion appreciated. > POSCAR:: > > Fe > 1.0 > 1.0000000000000000 0.0000000000000000 0.0000000000000000 > 0.0000000000000000 1.0000000000000000 0.0000000000000000 > 0.0000000000000000 0.0000000000000000 1.0000000000000000 > Fe > 9 > Direct > 0.500000 0.500000 0.500000 > 0.000000 0.000000 0.000000 > 0.000000 0.000000 1.000000 > 0.000000 1.000000 0.000000 > 0.000000 1.000000 1.000000 > 1.000000 0.000000 0.000000 > 1.000000 0.000000 1.000000 > 1.000000 1.000000 0.000000 > 1.000000 1.000000 1.000000 > > A P Jena, > Kolkata, > India. > > > ------------------------------------------------------------------------------ > Site24x7 APM Insight: Get Deep Visibility into Application Performance > APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month > Monitor end-to-end web transactions and take corrective actions now > Troubleshoot faster and improve end-user experience. Signup Now! > http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140 > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... ------------------------------ Message: 6 Date: Wed, 6 Apr 2016 10:01:59 +0100 From: Keith Refson <kr...@gm...> Subject: [Spglib-users] Determine spacegroup given symmetry operations Cc: spg...@li... Message-ID: <570...@gm...> Content-Type: text/plain; charset=windows-1252 Hi, I'd like to pick up on a question I raised a couple of years ago, as an enhancement to the spglib API. The functionality I need is to pass a lattice and set of symmetry operations as input parameters and obtain the space group - for example as an SpglibDataset. Specifically the atomic co-ordinates are NOT to be used to determine the symmetries. The reason for this is for use in electronic structure codes in the presence of symmetry-breaking. It is commonly necessary to work in a subgroup, where the symmetry is broken by, for example, a magnetic structure, an anisotropic external stress or an electric field or atomic displacement perturbation, or a supercell where the supercell lattice vectors do not transform invariantly under the full point group. The idea is that the caller works out the remaining symmetries belonging to the subgroup and passes these as input. Following your hint and looking at the code, this does not look difficult in principle. But there are API design issues which I don't feel qualified to make. And for maintenance reasons it would be best if any change was incorporated into future spglib releases. Is it realistic to request an enhancement to spglib to do this? sincerely Keith Refson On 27/03/14 04:44, Atsushi Togo wrote: > Hello, > > I'm a developer of spglib. > > 1) I think it's not a very hard work. lattice parameters are necessary > to be supplied for hal_get_hall_symbol, but for this purpose, just > dummy lattice parameters should be OK. ------------------------------ ------------------------------------------------------------------------------ ------------------------------ _______________________________________________ Spglib-users mailing list Spg...@li... https://lists.sourceforge.net/lists/listinfo/spglib-users End of Spglib-users Digest, Vol 9, Issue 1 ****************************************** |
