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From: Atsushi T. <atz...@gm...> - 2016-10-06 15:45:37
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Hi, 1. I couldn't reproduce the segfault, but I hope this segfault has been already fixed at version 1.9.5. 2. Thanks to your hint, the infinite loop behaviour is probably fixed. This fix is released with the next version. Thanks. Togo On Thu, Oct 6, 2016 at 3:39 PM, Keith Refson <kr...@gm...> wrote: > Dear Togo, > > We are currently using 1.9.4 with CASTEP (where it went into an infinite > loop instead), but I tested the "C" testcase with the git head. > > Keith Refson > > > > On 06/10/16 14:27, Atsushi Togo wrote: >> >> Hi Keith, >> >> I confirmed the problem happening when atoms are very out of the box. >> Segfault is related but another problem I think. Which version of >> spglib do you use? >> >> Thanks, >> >> Togo >> >> On Thu, Oct 6, 2016 at 1:04 PM, Keith Refson <kr...@gm...> wrote: >>> >>> Hi, >>> >>> I have a case where "spg_get_multiplicity" segfaults if the fractional >>> co-ordinates of atoms are outside the primitive cell. >>> >>> The attached testcase segfaults and gives a valgrind traceback of: >>> >>> >>> ==7780== Invalid read of size 8 >>> ==7780== at 0x4E459FC: get_operations (symmetry.c:247) >>> ==7780== by 0x4E418AA: search_spacegroup (spacegroup.c:293) >>> ==7780== by 0x4E42494: spa_get_spacegroup (spacegroup.c:224) >>> ==7780== by 0x4E42B65: get_dataset (spglib.c:811) >>> ==7780== by 0x4E437B6: get_multiplicity (spglib.c:1016) >>> ==7780== by 0x4E437B6: spg_get_multiplicity (spglib.c:331) >>> ==7780== by 0x4012F5: test_spg_get_multiplicity_1 (in >>> /home/kr/CASTEP/BUGS/Chris_Symmetry_Cmca/out-of-cell) >>> ==7780== by 0x4009BA: main (in >>> /home/kr/CASTEP/BUGS/Chris_Symmetry_Cmca/out-of-cell) >>> ==7780== Address 0x0 is not stack'd, malloc'd or (recently) free'd >>> >>> Keith Refson >>> >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Check out the vibrant tech community on one of the world's most >>> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >>> _______________________________________________ >>> 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... |
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From: Keith R. <kr...@gm...> - 2016-10-06 13:39:33
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Dear Togo, We are currently using 1.9.4 with CASTEP (where it went into an infinite loop instead), but I tested the "C" testcase with the git head. Keith Refson On 06/10/16 14:27, Atsushi Togo wrote: > Hi Keith, > > I confirmed the problem happening when atoms are very out of the box. > Segfault is related but another problem I think. Which version of > spglib do you use? > > Thanks, > > Togo > > On Thu, Oct 6, 2016 at 1:04 PM, Keith Refson <kr...@gm...> wrote: >> Hi, >> >> I have a case where "spg_get_multiplicity" segfaults if the fractional >> co-ordinates of atoms are outside the primitive cell. >> >> The attached testcase segfaults and gives a valgrind traceback of: >> >> >> ==7780== Invalid read of size 8 >> ==7780== at 0x4E459FC: get_operations (symmetry.c:247) >> ==7780== by 0x4E418AA: search_spacegroup (spacegroup.c:293) >> ==7780== by 0x4E42494: spa_get_spacegroup (spacegroup.c:224) >> ==7780== by 0x4E42B65: get_dataset (spglib.c:811) >> ==7780== by 0x4E437B6: get_multiplicity (spglib.c:1016) >> ==7780== by 0x4E437B6: spg_get_multiplicity (spglib.c:331) >> ==7780== by 0x4012F5: test_spg_get_multiplicity_1 (in >> /home/kr/CASTEP/BUGS/Chris_Symmetry_Cmca/out-of-cell) >> ==7780== by 0x4009BA: main (in >> /home/kr/CASTEP/BUGS/Chris_Symmetry_Cmca/out-of-cell) >> ==7780== Address 0x0 is not stack'd, malloc'd or (recently) free'd >> >> Keith Refson >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, SlashDot.org! http://sdm.link/slashdot >> _______________________________________________ >> Spglib-users mailing list >> Spg...@li... >> https://lists.sourceforge.net/lists/listinfo/spglib-users >> > > |
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From: Atsushi T. <atz...@gm...> - 2016-10-06 13:27:19
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Hi Keith, I confirmed the problem happening when atoms are very out of the box. Segfault is related but another problem I think. Which version of spglib do you use? Thanks, Togo On Thu, Oct 6, 2016 at 1:04 PM, Keith Refson <kr...@gm...> wrote: > Hi, > > I have a case where "spg_get_multiplicity" segfaults if the fractional > co-ordinates of atoms are outside the primitive cell. > > The attached testcase segfaults and gives a valgrind traceback of: > > > ==7780== Invalid read of size 8 > ==7780== at 0x4E459FC: get_operations (symmetry.c:247) > ==7780== by 0x4E418AA: search_spacegroup (spacegroup.c:293) > ==7780== by 0x4E42494: spa_get_spacegroup (spacegroup.c:224) > ==7780== by 0x4E42B65: get_dataset (spglib.c:811) > ==7780== by 0x4E437B6: get_multiplicity (spglib.c:1016) > ==7780== by 0x4E437B6: spg_get_multiplicity (spglib.c:331) > ==7780== by 0x4012F5: test_spg_get_multiplicity_1 (in > /home/kr/CASTEP/BUGS/Chris_Symmetry_Cmca/out-of-cell) > ==7780== by 0x4009BA: main (in > /home/kr/CASTEP/BUGS/Chris_Symmetry_Cmca/out-of-cell) > ==7780== Address 0x0 is not stack'd, malloc'd or (recently) free'd > > Keith Refson > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, SlashDot.org! http://sdm.link/slashdot > _______________________________________________ > 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... |
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From: Keith R. <kr...@gm...> - 2016-10-06 11:04:30
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Hi, I have a case where "spg_get_multiplicity" segfaults if the fractional co-ordinates of atoms are outside the primitive cell. The attached testcase segfaults and gives a valgrind traceback of: ==7780== Invalid read of size 8 ==7780== at 0x4E459FC: get_operations (symmetry.c:247) ==7780== by 0x4E418AA: search_spacegroup (spacegroup.c:293) ==7780== by 0x4E42494: spa_get_spacegroup (spacegroup.c:224) ==7780== by 0x4E42B65: get_dataset (spglib.c:811) ==7780== by 0x4E437B6: get_multiplicity (spglib.c:1016) ==7780== by 0x4E437B6: spg_get_multiplicity (spglib.c:331) ==7780== by 0x4012F5: test_spg_get_multiplicity_1 (in /home/kr/CASTEP/BUGS/Chris_Symmetry_Cmca/out-of-cell) ==7780== by 0x4009BA: main (in /home/kr/CASTEP/BUGS/Chris_Symmetry_Cmca/out-of-cell) ==7780== Address 0x0 is not stack'd, malloc'd or (recently) free'd Keith Refson |
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From: Nicholas F. <nf...@gm...> - 2016-09-27 19:57:02
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Greetings, I ran into some installation trouble but don't know whether to call it an issue with the code. Can anyone advise whether I need to adjust configuration on my machine, or report an issue to spglib, or to setuptools, etc? I run 32 bit Python 3.5 on Windows and have Numpy1.11+MKL installed from a pre-built wheel. I cloned the spglib repository from github and ran python setup.py install Watching in the log, all the .obj files compiled. However, the linker failed, and the output shows that build_ext issued a command that does not quote the paths of the library files. Since I have paths with spaces in my installation, the automatic link command fails unless I manually fix it. I have seen that within distutils and numpy, LIBPATH quoting was identified and fixed long ago: http://bugs.python.org/issue13765 https://github.com/numpy/numpy/pull/5765 Thanks for the useful library. Best regards, Nicholas Fette P.S. Excerpts from install output: setuptools is used. running install ... running build_py running build_ext No module named 'numpy.distutils._msvccompiler' in numpy.distutils; trying from distutils building 'spglib._spglib' extension C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\cl.exe ... Found executable C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe LINK : fatal error LNK1181: cannot open input file 'Files.obj' error: Command "C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\BIN\link.exe /nologo /INCREMENTAL:NO /LTCG /DLL /MANIFEST:EMBED,ID=2 /MANIFESTUAC:NO /LIBPATH:C:\Program Files (x86)\Python35-32\libs /LIBPATH:C:\Program Files (x86)\Python35-32\PCbuild\win32 ..." failed with exit status 1181 |
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From: Atsushi T. <atz...@gm...> - 2016-09-17 00:50:37
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Dear spglib users, Spglib-1.9.5 has been released. The source distribution is found at https://sourceforge.net/projects/spglib/files/spglib/spglib-1.9/ Pypi and conda packages of this version are also prepared by Paweł T. Jochym. Overlapping of atoms having the same type is checked from this version. If atoms that are overlapping are found, the symmetry search will fail. When a symmetry search failed, some message is left internally and those messages are accessed through the following APIs: For C-spglib, http://atztogo.github.io/spglib/api.html#spg-get-error-code-and-spg-get-error-message and for python-spglib http://atztogo.github.io/spglib/python-spglib.html#get-error-message Togo -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Atsushi T. <atz...@gm...> - 2016-06-18 12:24:41
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Hi, What you need is probably only lattice vectors. So you can use get_dataset, http://atztogo.github.io/spglib/api.html#spg-get-dataset-and-spg-get-dataset-with-hall-number where you can find transformation_matrix. http://atztogo.github.io/spglib/api.html#origin-shift-and-lattice-transformation You have original lattice parameters and these are transformed to the new lattice parameters that are equivalent to those obtained by refine_cell but with the original coordinate system. Togo On Tue, Jun 14, 2016 at 6:39 PM, Joseph Montoya <mon...@lb...> wrote: > I am trying to develop an algorithm to standardize tensor quantities calculated for a given unit cell input into vasp, which involves finding the appropriate coordinate axes relative to the conventional cell. Is it possible, given an input unit cell, to get a refined structure that has the same coordinate axes, i. e. that does not implicitly rotate the structure relative to the input structure? As far as I can tell, the get_refined_cell method, since it constructs the cell from symmetry information, doesn’t guarantee that its output would be in the same reference frame as the input structure. > > Best, > Joey > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > _______________________________________________ > 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... |
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From: Joseph M. <mon...@lb...> - 2016-06-14 16:39:44
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I am trying to develop an algorithm to standardize tensor quantities calculated for a given unit cell input into vasp, which involves finding the appropriate coordinate axes relative to the conventional cell. Is it possible, given an input unit cell, to get a refined structure that has the same coordinate axes, i. e. that does not implicitly rotate the structure relative to the input structure? As far as I can tell, the get_refined_cell method, since it constructs the cell from symmetry information, doesn’t guarantee that its output would be in the same reference frame as the input structure. Best, Joey |
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From: Atsushi T. <atz...@gm...> - 2016-06-02 11:18:20
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Hi, Let k1 = (x, y, z), k' = (x', y', z') in reduced coordinates. You can check if the following is true: abs((x - x') mod 1) < epsilon and abs((y - y') mod 1) < epsilon and abs((z - z') mod 1) < epsilon epsilon is a positive small number. This is dependent on the implementation of mod function. I suppose mod gives the number closest to 0. Togo On Thu, Jun 2, 2016 at 7:42 PM, Hongliang Yang <hly...@gm...> wrote: > Dear users and devlopers: > > How to check if two k-points is equivalent? For example, one k-point is > outside the FBZ and the other is in FBZ. > > Best wishes. > > Yang > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning reports. https://ad.doubleclick.net/ddm/clk/305295220;132659582;e > _______________________________________________ > 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... |
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From: Hongliang Y. <hly...@gm...> - 2016-06-02 10:42:57
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Dear users and devlopers: How to check if two k-points is equivalent? For example, one k-point is outside the FBZ and the other is in FBZ. Best wishes. Yang |
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From: Atsushi T. <atz...@gm...> - 2016-04-19 01:48:22
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Dear spglib-users, I have released spglib 1.9.2. The source code can be downloaded at https://sourceforge.net/projects/spglib/files/spglib/spglib-1.9/ I think no big change is made from version 1.9.0 or 1.9.1, but some bugs are fixed. Best regards, Togo -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Atsushi T. <atz...@gm...> - 2016-04-10 23:22:40
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Hi, I think it's better for you first to ask your question in the community of ShengBTE. Togo On Mon, Apr 11, 2016 at 5:34 AM, n16031320 <n16...@ma...> wrote: > Dear users and devlopers: > > I got some trouble when I tried to install ShengBTE. > First, I install the spglib ver. 1.9.1 , I follow the step on the website, > the terminal showed that "Libraries have been installed in : > /usr/local/lib", so I think I install it completely. > Then I tried to install ShengBTE, I use gfortran and lapack from apt-get, > but I got the error: > - > mpif90 -O3 -g -o ../ShengBTE conductivity.o config.o data.o input.o > iterations.o misc.o gruneisen.o phonon_routines.o integrals.o processes.o > scaling.o symmetry.o wedgetc.o dos_routines.o ShengBTE.o -g -pthread > -llapack -lblas -L/usr/local/lib > symmetry.o: In function `__symmetry_MOD_get_operations': > /home/yh/download/ShengBTE/Src/symmetry.f90:93: undefined reference > to「spg_get_symmetry_」 > /home/yh/download/ShengBTE/Src/symmetry.f90:95: undefined reference > to「spg_get_international_」 > symmetry.o: In function `__symmetry_MOD_get_num_operations': > /home/yh/download/ShengBTE/Src/symmetry.f90:56: undefined reference > to「spg_get_multiplicity_」 > collect2: error: ld returned 1 exit status > make: *** [../ShengBTE] Error 1 > - > here is my arch.make file: > export FFLAGS=-O3 -g > export LDFLAGS=-g -pthread > export MPIFC=mpif90 > export LAPACK= -llapack -lblas > export LIBS= -llapack -lblas -L/usr/local/lib > which part I did wrong? > Could you please help me fix it ? I really need to use this software. > Thank you in advance! > -- > Yao-Hong Huang > Master student > Tainan, Taiwan > National Cheng Kung University > Department of Mechanical Engineering > > ------------------------------------------------------------------------------ > Find and fix application performance issues faster with Applications Manager > Applications Manager provides deep performance insights into multiple tiers > of > your business applications. It resolves application problems quickly and > reduces your MTTR. Get your free trial! http://pubads.g.doubleclick.net/ > gampad/clk?id=1444514301&iu=/ca-pub-7940484522588532 > _______________________________________________ > 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... |
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From: n16031320 <n16...@ma...> - 2016-04-10 20:50:41
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Dear users and devlopers: I got some trouble when I tried to install ShengBTE. First, I install the spglib ver. 1.9.1 , I follow the step on the website, the terminal showed that "Libraries have been installed in : /usr/local/lib", so I think I install it completely. Then I tried to install ShengBTE, I use gfortran and lapack from apt-get, but I got the error: - mpif90 -O3 -g -o ../ShengBTE conductivity.o config.o data.o input.o iterations.o misc.o gruneisen.o phonon_routines.o integrals.o processes.o scaling.o symmetry.o wedgetc.o dos_routines.o ShengBTE.o -g -pthread   -llapack -lblas -L/usr/local/lib symmetry.o: In function `__symmetry_MOD_get_operations': /home/yh/download/ShengBTE/Src/symmetry.f90:93: undefined reference to「spg_get_symmetry_」 /home/yh/download/ShengBTE/Src/symmetry.f90:95: undefined reference to「spg_get_international_」 symmetry.o: In function `__symmetry_MOD_get_num_operations': /home/yh/download/ShengBTE/Src/symmetry.f90:56: undefined reference to「spg_get_multiplicity_」 collect2: error: ld returned 1 exit status make: *** [../ShengBTE] Error 1 - here is my arch.make file: export FFLAGS=-O3 -g export LDFLAGS=-g -pthread    export MPIFC=mpif90 export LAPACK= -llapack -lblas export LIBS= -llapack -lblas -L/usr/local/lib which part I did wrong? Could you please help me fix it ? I really need to use this software. Thank you in advance! -- Yao-Hong Huang Master student Tainan, Taiwan National Cheng Kung University Department of Mechanical Engineering |
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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> |
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From: Shyue P. O. <sh...@gm...> - 2016-04-06 15:43:48
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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: > > 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 > ****************************************** > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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... |
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From: Atsushi T. <atz...@gm...> - 2016-04-06 15:10:35
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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: > > 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 > ****************************************** > > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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... |
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From: Atsushi T. <atz...@gm...> - 2016-04-06 14:27:10
|
Hi, It's a nice feature. If the symmetry operations and lattice parameters are those for the primitive cell, it will be very easy (I supposed this case before). If not, some more implementation is necessary. But in principle, as an input, lattice parameters are unnecessary. I will think. Togo On Wed, Apr 6, 2016 at 6:01 PM, Keith Refson <kr...@gm...> wrote: > 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 -- Atsushi Togo Elements Strategy Initiative for Structural Materials, Kyoto university E-mail: atz...@gm... |
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From: Shyue P. O. <sh...@gm...> - 2016-04-06 13:11:30
|
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 ****************************************** |
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From: Keith R. <kr...@gm...> - 2016-04-06 09:02:12
|
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. |
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From: Atsushi T. <atz...@gm...> - 2016-01-15 05:32:25
|
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.
>
>
> ------------------------------------------------------------------------------
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>
--
Atsushi Togo
Elements Strategy Initiative for Structural Materials, Kyoto university
E-mail: atz...@gm...
|
|
From: AP J. <ap...@gm...> - 2016-01-14 05:15:27
|
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.
|
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From: Atsushi T. <atz...@gm...> - 2016-01-10 09:47:06
|
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 Paweł 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... |
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From: Atsushi T. <atz...@gm...> - 2015-09-20 01:01:09
|
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... |
|
From: Evgeny B. <eb...@ti...> - 2015-09-19 01:06:47
|
<p>Dear Dr. Atsushi Togo-san and Spglib users,</p><p>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).</p><p>The link is https://github.com/blokhin/spglibjs</p><p>I would be happy if you find any further inspiration from my code. Lastly, a big thanks to Dr. Atsushi Togo-san for Spglib.</p><p>Regards,<br />Evgeny Blokhin</p> |
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From: Atsushi T. <atz...@gm...> - 2015-07-06 07:24:07
|
What is the difficult point of the document below? http://spglib.sourceforge.net/pyspglibForASE/ Togo On Mon, Jul 6, 2015 at 4:11 PM, Éric Germaneau <ger...@sj...> wrote: > Hey, > > I think it's from atoms module. > Something has changed in the way to use it but I don't know what. > I also forgot why I needed this module actually. > I'm really wondering how do people do this thing now, it's maybe not require > anymore. > Thanks, > > Éric. > > > On 07/06/2015 03:02 PM, Atsushi Togo wrote: > > Hi, > > Where is your Atoms class installed? > > Togo > > On Mon, Jul 6, 2015 at 8:34 AM, Éric Germaneau <ger...@sj...> > wrote: > > Dear all, > > I use to use pyspglib two years ago but recently got an issue. > The following simple script doesn't work anymore: > > #!/usr/bin/python > > from numpy import * > from pyspglib import spglib > from atoms import * > > lattice = array([[4.,0.,0.], [0.,4.,0.], [0.,0.,3.]]) > position = array([ > [0.0, 0.0, 0.0], > [0.5, 0.5, 0.5], > [0.3, 0.3, 0.0], > [0.7, 0.7, 0.0], > [0.2, 0.8, 0.5], > [0.8, 0.2, 0.5] > ]) > atom_type = array([1,1,2,2,2,2]) > atom_symbols = ['H', 'H', 'He', 'He', 'He', 'He'] > atoms = Atoms( cell=lattice, scaled_positions=position, symbols=atom_symbols > ) > print atoms.symbols > print atoms.numbers > print spglib.get_spacegroup(atoms, 1e-5) > > Here is the error I get: > > Traceback (most recent call last): > File "./example2.py", line 18, in <module> > atoms = Atoms( cell=lattice, scaled_positions=position, > symbols=atom_symbols ) > NameError: name 'Atoms' is not defined > > I've installed atoms 0.1 and pyspglib 1.6.0.13 via pip. > > Can someone tell what changed and how to run this script now? > > Thanks. > > -- > Éric Germaneau (艾海克), Specialist > Center for High Performance Computing > Shanghai Jiao Tong University > Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China > Email:ger...@sj... Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn > > Chinese (Simplified) - detected > English > Chinese (Simplified) > > English > Chinese (Simplified) > > > ------------------------------------------------------------------------------ > Don't Limit Your Business. Reach for the Cloud. > GigeNET's Cloud Solutions provide you with the tools and support that > you need to offload your IT needs and focus on growing your business. > Configured For All Businesses. Start Your Cloud Today. > https://www.gigenetcloud.com/ > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > > > > > -- > Éric Germaneau (艾海克), Specialist > Center for High Performance Computing > Shanghai Jiao Tong University > Room 205 Network Center, 800 Dongchuan Road, Shanghai 200240 China > Email:ger...@sj... Mobi:+86-136-4161-6480 http://hpc.sjtu.edu.cn > > ------------------------------------------------------------------------------ > Don't Limit Your Business. Reach for the Cloud. > GigeNET's Cloud Solutions provide you with the tools and support that > you need to offload your IT needs and focus on growing your business. > Configured For All Businesses. Start Your Cloud Today. > https://www.gigenetcloud.com/ > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > -- Atsushi Togo http://atztogo.github.com/ atz...@gm... |
