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: Evgeny B. <eb...@ti...> - 2016-04-06 16:40:50
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<div><div>Good day, colleagues,</div><div> </div><div><div><div>On JavaScript: we may see, it becomes more popular in the materials informatics. E.g. it is heavily used by Exabyte.io (materials discovery cloud), ChemDoodle (crystalline visualizations) and others. Bonus is, both client & server may employ the same language, i.e. stack homogeneity.</div><div> </div><div>Thanks for the bugreport. Actually, my app honestly warns "Reading of symmetry operations is not yet implemented", which is not an issue of spglib, but rather of the CIF <-> spglibjs interface. I will implement full support of CIFs there soon.</div></div></div></div><div>EB</div><div> </div><div>06.04.2016, 17:43, "Shyue Ping Ong" <sh...@gm...>:</div><blockquote type="cite"><div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1);margin:0px;line-height:auto;">Hi Togo,</div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1);margin:0px;line-height:auto;"> </div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1);margin:0px;line-height:auto;">Yes, Evgeny’s app is client side and mine is server side.</div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1);margin:0px;line-height:auto;">I guess I am biased, since I hate Javascript as a language. :-) I only deal with it when I have to minimally. But I can see the advantages of having a pure client-side app like spglibjs. </div><div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1);margin:0px;line-height:auto;"> </div>BTW, Evgeny, I would like to report a small bug. I tried the spglibjs web app with a disordered structure (Li10GeP2S12). It says that it has P1 symmetry, though spglib itself gives P4_2/nmc. The CIF I used to test is available at <a href="https://github.com/materialsproject/pymatgen/blob/master/test_files/Li10GeP2S12.cif">https://github.com/materialsproject/pymatgen/blob/master/test_files/Li10GeP2S12.cif</a><div><div><div style="font-family:helvetica,arial;font-size:13px;"><br />Shyue Ping</div></div><div style="color:black;"><br />From: <span style="color:black;">Atsushi Togo</span> <a href="mailto:atz...@gm..."><atz...@gm...></a><br />Reply: <span style="color:black;">Atsushi Togo</span> <a href="mailto:atz...@gm..."><atz...@gm...></a><br />Date: <span style="color:black;">April 6, 2016 at 8:10:28 AM</span><br />To: <span style="color:black;">Shyue Ping Ong</span> <a href="mailto:sh...@gm..."><sh...@gm...></a><br />CC: <span style="color:black;">spglib-users</span> <a href="mailto:spg...@li..."><spg...@li...></a>, <span style="color:black;"><a href="mailto:spg...@li...">spg...@li...</a></span> <a href="mailto:spg...@li..."><spg...@li...></a><br />Subject: <span style="color:black;"> Re: [Spglib-users] Spglib-users Digest, Vol 9, Issue 1 </span></div> <blockquote type="cite"><div><div> </div><div><span>Hi Shyue Ping,<br /><br />Thanks for your information. I have already found your web app<br />yesterday or the day before yesterday :)<br /><br />Before I didn't have a compiler and I had to write machine code for my<br />Z80 CPU to make my computer game run fast.<br /><br />Now my favourite language is C that is a little bit similar to<br />assembly language. It's interesting for me to see how numpy array is<br />designed in C. LLVM used to compile C to JS is far beyond my ability<br />to understand, however compiler is the tool that I dreamt to use in my<br />old days.<br /><br />Evgeny's web app runs on user-side and Shyue Ping's web app works on<br />server side (am I right?). So they are different. But technically the<br />former is exciting for me, but I think the later would be more<br />versatile at this moment.<br /><br />Togo<br /><br />On Wed, Apr 6, 2016 at 10:11 PM, Shyue Ping Ong <<a href="mailto:sh...@gm...">sh...@gm...</a>> wrote:<br />> Actually, we have recently implemented a web app version of pymatgen at<br />> <a href="http://www.materialsvirtuallab.org/matgenie">http://www.materialsvirtuallab.org/matgenie</a> . This includes symmetry<br />> analysis via spglib.<br />><br />> I think it’s better to build via Python web frameworks than to try to build<br />> spglib into a JS form and having to deal with multiple programming<br />> languages.<br />><br />><br />> Shyue Ping<br />><br />> On April 6, 2016 at 2:02:15 AM, <a href="mailto:spg...@li...">spg...@li...</a><br />> (<a href="mailto:spg...@li...">spg...@li...</a>) wrote:<br />><br />> Send Spglib-users mailing list submissions to<br />> <a href="mailto:spg...@li...">spg...@li...</a><br />><br />> To subscribe or unsubscribe via the World Wide Web, visit<br />> <a href="https://lists.sourceforge.net/lists/listinfo/spglib-users">https://lists.sourceforge.net/lists/listinfo/spglib-users</a><br />> or, via email, send a message with subject or body 'help' to<br />> <a href="mailto:spg...@li...">spg...@li...</a><br />><br />> You can reach the person managing the list at<br />> <a href="mailto:spg...@li...">spg...@li...</a><br />><br />> When replying, please edit your Subject line so it is more specific<br />> than "Re: Contents of Spglib-users digest..."<br />><br />><br />> Today's Topics:<br />><br />> 1. Spglib in JavaScript for in-browser usage (Evgeny Blokhin)<br />> 2. Re: Spglib in JavaScript for in-browser usage (Atsushi Togo)<br />> 3. Spglib 1.9.x (Atsushi Togo)<br />> 4. Symmetry identification of POSCAR with corner atoms (AP Jena)<br />> 5. Re: Symmetry identification of POSCAR with corner atoms<br />> (Atsushi Togo)<br />> 6. Determine spacegroup given symmetry operations (Keith Refson)<br />><br />><br />> ----------------------------------------------------------------------<br />><br />> Message: 1<br />> Date: Sat, 19 Sep 2015 02:43:08 +0200<br />> From: Evgeny Blokhin <<a href="mailto:eb...@ti...">eb...@ti...</a>><br />> Subject: [Spglib-users] Spglib in JavaScript for in-browser usage<br />> To: <a href="mailto:spg...@li...">spg...@li...</a><br />> Message-ID: <<a href="mailto:263...@we...">263...@we...</a>><br />> Content-Type: text/plain; charset="us-ascii"<br />><br />> An HTML attachment was scrubbed...<br />><br />> ------------------------------<br />><br />> Message: 2<br />> Date: Sun, 20 Sep 2015 10:01:01 +0900<br />> From: Atsushi Togo <<a href="mailto:atz...@gm...">atz...@gm...</a>><br />> Subject: Re: [Spglib-users] Spglib in JavaScript for in-browser usage<br />> To: Evgeny Blokhin <<a href="mailto:eb...@ti...">eb...@ti...</a>><br />> Cc: spglib-users <<a href="mailto:spg...@li...">spg...@li...</a>><br />> Message-ID:<br />> <<a href="mailto:CAA...@ma...">CAA...@ma...</a>><br />> Content-Type: text/plain; charset=UTF-8<br />><br />> Hi Evgeny,<br />><br />> This is interesting. I like the idea that it works on client side. It<br />> may be the time for me to learn JS and around.<br />><br />> What spglib can do can be done by bilbao-crystallographic server. So<br />> if some better service is provided, it may be nicer, e.g., to provide<br />> machine friendly interface.<br />><br />> Togo<br />><br />> On Sat, Sep 19, 2015 at 9:43 AM, Evgeny Blokhin <<a href="mailto:eb...@ti...">eb...@ti...</a>> wrote:<br />>> Dear Dr. Atsushi Togo-san and Spglib users,<br />>><br />>> as you probably know any C code can be transpiled to JavaScript with the<br />>> aid<br />>> of source-to-source code compiler. After a successful experience with<br />>> converting RasMol to JavaScript (<a href="https://bitbucket.org/jam31/rasmoljs">https://bitbucket.org/jam31/rasmoljs</a>), i<br />>> decided to keep on with Spglib. This is to draw your attention to the<br />>> result, SpglibJS. Now to determine crystalline symmetry you need only a<br />>> browser (without any plugins). SpglibJS is a pure experiment, and to<br />>> foster<br />>> any possible ideas and usecases i created an example web-app, providing<br />>> symmetry validation functionality for CIF or POSCAR files. An explicit<br />>> symmetry information is absent in POSCARs and often omitted in CIFs, so<br />>> this<br />>> web-app provides a quick way of checking the symmetry. No server is used<br />>> after loading, so it is possible to drop a file there and check it without<br />>> Internet connection (and without any concerns about privacy).<br />>><br />>> The link is <a href="https://github.com/blokhin/spglibjs">https://github.com/blokhin/spglibjs</a><br />>><br />>> I would be happy if you find any further inspiration from my code. Lastly,<br />>> a<br />>> big thanks to Dr. Atsushi Togo-san for Spglib.<br />>><br />>> Regards,<br />>> Evgeny Blokhin<br />>><br />>><br />>><br />>> ------------------------------------------------------------------------------<br />>><br />>> _______________________________________________<br />>> Spglib-users mailing list<br />>> <a href="mailto:Spg...@li...">Spg...@li...</a><br />>> <a href="https://lists.sourceforge.net/lists/listinfo/spglib-users">https://lists.sourceforge.net/lists/listinfo/spglib-users</a><br />>><br />><br />><br />><br />> --<br />> Atsushi Togo<br />> <a href="http://atztogo.github.com/">http://atztogo.github.com/</a><br />> <a href="mailto:atz...@gm...">atz...@gm...</a><br />><br />><br />><br />> ------------------------------<br />><br />> Message: 3<br />> Date: Sun, 10 Jan 2016 18:47:00 +0900<br />> From: Atsushi Togo <<a href="mailto:atz...@gm...">atz...@gm...</a>><br />> Subject: [Spglib-users] Spglib 1.9.x<br />> To: spglib-users <<a href="mailto:spg...@li...">spg...@li...</a>><br />> Message-ID:<br />> <<a href="mailto:CAAfkA7dY-jV12vqqJBE-v9QZYo1w2a3ZO=KG5...@ma...">CAAfkA7dY-jV12vqqJBE-v9QZYo1w2a3ZO=KG5...@ma...</a>><br />> Content-Type: text/plain; charset=UTF-8<br />><br />> Dear spglib users,<br />><br />> Some news.<br />><br />> Spglib 1.9.0 was released. No new features were added from version<br />> 1.8.x. The module name change in python wrapper may be a big issue.<br />><br />> Pypi and conda packages were made by Pawe? T. Jochym. Now we can<br />> install spglib via pip or conda. These packages will be updated along<br />> with github releases.<br />><br />> Python module name was changed to spglib.<br />> <a href="http://spglib.sourceforge.net/python-spglib.html#python-spglib">http://spglib.sourceforge.net/python-spglib.html#python-spglib</a><br />><br />> Best wishes,<br />><br />> Togo<br />><br />> --<br />> Atsushi Togo<br />> Elements Strategy Initiative for Structural Materials, Kyoto university<br />> E-mail: <a href="mailto:atz...@gm...">atz...@gm...</a><br />><br />><br />><br />> ------------------------------<br />><br />> Message: 4<br />> Date: Thu, 14 Jan 2016 10:44:42 +0530<br />> From: AP Jena <<a href="mailto:ap...@gm...">ap...@gm...</a>><br />> Subject: [Spglib-users] Symmetry identification of POSCAR with corner<br />> atoms<br />> To: <a href="mailto:spg...@li...">spg...@li...</a><br />> Message-ID:<br />> <<a href="mailto:CADmxT8AD5gHWFr9pEM6j4h0WsP=Fnr...@ma...">CADmxT8AD5gHWFr9pEM6j4h0WsP=Fnr...@ma...</a>><br />> Content-Type: text/plain; charset="utf-8"<br />><br />> Dear all,<br />> For an ideal bcc conventional cell with all the corner atoms explicitly<br />> listed in POSCAR, I wanted to find the symmetry and reduce to primitive<br />> cell using spglib. I?m not able to manage spglib identify the symmetry. Any<br />> suggestion appreciated.<br />> POSCAR::<br />><br />> Fe<br />> 1.0<br />> 1.<span>0000000000000000 0</span>.<span>0000000000000000 0</span>.<span>0000000000000000</span><br />> 0.<span>0000000000000000 1</span>.<span>0000000000000000 0</span>.<span>0000000000000000</span><br />> 0.<span>0000000000000000 0</span>.<span>0000000000000000 1</span>.<span>0000000000000000</span><br />> Fe<br />> 9<br />> Direct<br />> 0.<span>500000 0</span>.<span>500000 0</span>.500000<br />> 0.<span>000000 0</span>.<span>000000 0</span>.000000<br />> 0.<span>000000 0</span>.<span>000000 1</span>.000000<br />> 0.<span>000000 1</span>.<span>000000 0</span>.000000<br />> 0.<span>000000 1</span>.<span>000000 1</span>.000000<br />> 1.<span>000000 0</span>.<span>000000 0</span>.000000<br />> 1.<span>000000 0</span>.<span>000000 1</span>.000000<br />> 1.<span>000000 1</span>.<span>000000 0</span>.000000<br />> 1.<span>000000 1</span>.<span>000000 1</span>.000000<br />><br />> A P Jena,<br />> Kolkata,<br />> India.<br />> ?<br />> -------------- next part --------------<br />> An HTML attachment was scrubbed...<br />><br />> ------------------------------<br />><br />> Message: 5<br />> Date: Fri, 15 Jan 2016 14:32:18 +0900<br />> From: Atsushi Togo <<a href="mailto:atz...@gm...">atz...@gm...</a>><br />> Subject: Re: [Spglib-users] Symmetry identification of POSCAR with<br />> corner atoms<br />> To: spglib-users <<a href="mailto:spg...@li...">spg...@li...</a>><br />> Message-ID:<br />> <<a href="mailto:CAA...@ma...">CAA...@ma...</a>><br />> Content-Type: text/plain; charset=UTF-8<br />><br />> Hi,<br />><br />> Your POSCAR is wrong. It should be like this.<br />><br />> Fe<br />> 1.0<br />> 1.<span>0000000000000000 0</span>.<span>0000000000000000 0</span>.<span>0000000000000000</span><br />> 0.<span>0000000000000000 1</span>.<span>0000000000000000 0</span>.<span>0000000000000000</span><br />> 0.<span>0000000000000000 0</span>.<span>0000000000000000 1</span>.<span>0000000000000000</span><br />> Fe<br />> 2<br />> Direct<br />> 0.<span>500000 0</span>.<span>500000 0</span>.500000<br />> 0.<span>000000 0</span>.<span>000000 0</span>.000000<br />><br />> Togo<br />><br />> On Thu, Jan 14, 2016 at 2:14 PM, AP Jena <<a href="mailto:ap...@gm...">ap...@gm...</a>> wrote:<br />>> Dear all,<br />>> For an ideal bcc conventional cell with all the corner atoms explicitly<br />>> listed in POSCAR, I wanted to find the symmetry and reduce to primitive<br />>> cell<br />>> using spglib. I?m not able to manage spglib identify the symmetry. Any<br />>> suggestion appreciated.<br />>> POSCAR::<br />>><br />>> Fe<br />>> 1.0<br />>> 1.<span>0000000000000000 0</span>.<span>0000000000000000 0</span>.<span>0000000000000000</span><br />>> 0.<span>0000000000000000 1</span>.<span>0000000000000000 0</span>.<span>0000000000000000</span><br />>> 0.<span>0000000000000000 0</span>.<span>0000000000000000 1</span>.<span>0000000000000000</span><br />>> Fe<br />>> 9<br />>> Direct<br />>> 0.<span>500000 0</span>.<span>500000 0</span>.500000<br />>> 0.<span>000000 0</span>.<span>000000 0</span>.000000<br />>> 0.<span>000000 0</span>.<span>000000 1</span>.000000<br />>> 0.<span>000000 1</span>.<span>000000 0</span>.000000<br />>> 0.<span>000000 1</span>.<span>000000 1</span>.000000<br />>> 1.<span>000000 0</span>.<span>000000 0</span>.000000<br />>> 1.<span>000000 0</span>.<span>000000 1</span>.000000<br />>> 1.<span>000000 1</span>.<span>000000 0</span>.000000<br />>> 1.<span>000000 1</span>.<span>000000 1</span>.000000<br />>><br />>> A P Jena,<br />>> Kolkata,<br />>> India.<br />>><br />>><br />>><br />>> ------------------------------------------------------------------------------<br />>> Site24x7 APM Insight: Get Deep Visibility into Application Performance<br />>> APM + Mobile APM + RUM: Monitor 3 App instances at just $35/Month<br />>> Monitor end-to-end web transactions and take corrective actions now<br />>> Troubleshoot faster and improve end-user experience. Signup Now!<br />>> <a href="http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140">http://pubads.g.doubleclick.net/gampad/clk?id=267308311&iu=/4140</a><br />>> _______________________________________________<br />>> Spglib-users mailing list<br />>> <a href="mailto:Spg...@li...">Spg...@li...</a><br />>> <a href="https://lists.sourceforge.net/lists/listinfo/spglib-users">https://lists.sourceforge.net/lists/listinfo/spglib-users</a><br />>><br />><br />><br />><br />> --<br />> Atsushi Togo<br />> Elements Strategy Initiative for Structural Materials, Kyoto university<br />> E-mail: <a href="mailto:atz...@gm...">atz...@gm...</a><br />><br />><br />><br />> ------------------------------<br />><br />> Message: 6<br />> Date: Wed, 6 Apr 2016 10:01:59 +0100<br />> From: Keith Refson <<a href="mailto:kr...@gm...">kr...@gm...</a>><br />> Subject: [Spglib-users] Determine spacegroup given symmetry operations<br />> Cc: <a href="mailto:spg...@li...">spg...@li...</a><br />> Message-ID: <<a href="mailto:570...@gm...">570...@gm...</a>><br />> Content-Type: text/plain; charset=windows-1252<br />><br />> Hi,<br />><br />> I'd like to pick up on a question I raised a couple of years ago, as an<br />> enhancement<br />> to the spglib API.<br />><br />> The functionality I need is to pass a lattice and set of symmetry operations<br />> as input parameters and obtain the space group - for example as an<br />> SpglibDataset.<br />> Specifically the atomic co-ordinates are NOT to be used to determine the<br />> symmetries.<br />><br />> The reason for this is for use in electronic structure codes in the<br />> presence of symmetry-breaking.<br />> It is commonly necessary to work in a subgroup, where the symmetry is<br />> broken by, for example,<br />> a magnetic structure, an anisotropic external stress or an electric<br />> field or atomic displacement<br />> perturbation, or a supercell where the supercell lattice vectors do not<br />> transform invariantly under<br />> the full point group. The idea is that the caller works out the<br />> remaining symmetries belonging to the<br />> subgroup and passes these as input.<br />><br />> Following your hint and looking at the code, this does not look<br />> difficult in principle. But there are<br />> API design issues which I don't feel qualified to make. And for<br />> maintenance reasons it would be<br />> best if any change was incorporated into future spglib releases.<br />><br />> Is it realistic to request an enhancement to spglib to do this?<br />><br />> sincerely<br />><br />> Keith Refson<br />><br />><br />> On 27/03/14 04:44, Atsushi Togo wrote:<br />>> Hello,<br />>><br />>> I'm a developer of spglib.<br />>><br />>> 1) I think it's not a very hard work. lattice parameters are necessary<br />>> to be supplied for hal_get_hall_symbol, but for this purpose, just<br />>> dummy lattice parameters should be OK.<br />><br />><br />><br />><br />> ------------------------------<br />><br />> ------------------------------------------------------------------------------<br />><br />><br />> ------------------------------<br />><br />> _______________________________________________<br />> Spglib-users mailing list<br />> <a href="mailto:Spg...@li...">Spg...@li...</a><br />> <a href="https://lists.sourceforge.net/lists/listinfo/spglib-users">https://lists.sourceforge.net/lists/listinfo/spglib-users</a><br />><br />><br />> End of Spglib-users Digest, Vol 9, Issue 1<br />> ******************************************<br />><br />><br />> ------------------------------------------------------------------------------<br />><br />> _______________________________________________<br />> Spglib-users mailing list<br />> <a href="mailto:Spg...@li...">Spg...@li...</a><br />> <a href="https://lists.sourceforge.net/lists/listinfo/spglib-users">https://lists.sourceforge.net/lists/listinfo/spglib-users</a><br />><br /><br /><br /><br />--<br />Atsushi Togo<br />Elements Strategy Initiative for Structural Materials, Kyoto university<br />E-mail: <a href="mailto:atz...@gm...">atz...@gm...</a> </span></div></div></blockquote></div></div>,<p>------------------------------------------------------------------------------</p>,<p>_______________________________________________<br />Spglib-users mailing list<br /><a href="mailto:Spg...@li...">Spg...@li...</a><br /><a href="https://lists.sourceforge.net/lists/listinfo/spglib-users">https://lists.sourceforge.net/lists/listinfo/spglib-users</a></p></blockquote> |
