Re: [Spglib-users] Spglib-users Digest, Vol 9, Issue 1

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Hi Togo,

Yes, Evgeny’s app is client side and mine is server side.
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. 

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 https://github.com/materialsproject/pymatgen/blob/master/test_files/Li10GeP2S12.cif

Shyue Ping

From: Atsushi Togo <atz...@gm...>
Reply: Atsushi Togo <atz...@gm...>
Date: April 6, 2016 at 8:10:28 AM
To: Shyue Ping Ong <sh...@gm...>
CC: spglib-users <spg...@li...>, spg...@li... <spg...@li...>
Subject:  Re: [Spglib-users] Spglib-users Digest, Vol 9, Issue 1  

Hi Shyue Ping,  

Thanks for your information. I have already found your web app  
yesterday or the day before yesterday :)  

Before I didn't have a compiler and I had to write machine code for my  
Z80 CPU to make my computer game run fast.  

Now my favourite language is C that is a little bit similar to  
assembly language. It's interesting for me to see how numpy array is  
designed in C. LLVM used to compile C to JS is far beyond my ability  
to understand, however compiler is the tool that I dreamt to use in my  
old days.  

Evgeny's web app runs on user-side and Shyue Ping's web app works on  
server side (am I right?). So they are different. But technically the  
former is exciting for me, but I think the later would be more  
versatile at this moment.  

Togo  

On Wed, Apr 6, 2016 at 10:11 PM, Shyue Ping Ong <sh...@gm...> wrote:  
> 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:  
>  
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>  
> 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  
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>> _______________________________________________  
>> 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...  
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>  
> End of Spglib-users Digest, Vol 9, Issue 1  
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>  

--  
Atsushi Togo  
Elements Strategy Initiative for Structural Materials, Kyoto university  
E-mail: atz...@gm...  