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From: cheng s. <sha...@gm...> - 2021-06-20 16:58:44
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Dear Prof. Togo, Thanks for your reply. I was thinking about using the rotation symmetry operator to find the irreducible k points from the k point list. For example, I want to apply the symmetry operator to find all the duplicates of the current k_point and check if any of them is in the irreducible k point list. However, I am a bit confused about how the rotation symmetry operator should be used. In the get_symmetry section, it says new_vector[3x1] = rotation[3x3] * vector[3x1] + translation[3x1] While in the definitions and conventions section, there is an equation: (𝐚̃ ,𝐛̃ ,𝐜̃ )=(𝐚,𝐛,𝐜)𝑊 Should I use the rotation * k_point, or using k_point * rotation? Do I need to apply some modifications like inversion and transpose to the rotation matrix before applying it to the k points? Sorry for bothering you again, and I am appreciated if you could help me out here. Best, Cheng On Sun, Jun 20, 2021 at 5:42 PM Atsushi Togo <atz...@gm...> wrote: > Hi, > > No. It's not possible. > But it is trivial to implement. > > Togo > > On Sun, Jun 20, 2021 at 4:13 PM cheng shao <sha...@gm...> wrote: > > > > Dear Prof. Togo, > > > > I am a new user of the spglib, and thanks for your efforts in developing > and maintain it. > > > > I have a quick question: is it possible to find the irreducible k points > from the custom-defined k mesh? > > > > Say I have a uniform k mesh points (in a different order as the > auto-generated one from spglib), > > Is it possible to identify the irreducible k points and the weight > factor from it. > > > > In the example, there is a function `grid = get_ir_reciprocal_mesh(mesh, > cell, is_shift=[0, 0, 0])`, > > can we replace the integer number mesh to a vector of k points? > > > > Best, > > Cheng > > ---- > > Dr. Cheng Shao > > Post-Doctoral Researcher > > Dept. of Mechanical Engineering > > The University of Tokyo > > > > > > > > _______________________________________________ > > Spglib-users mailing list > > Spg...@li... > > https://lists.sourceforge.net/lists/listinfo/spglib-users > > > > -- > Atsushi Togo > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > |
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From: Atsushi T. <atz...@gm...> - 2021-06-20 08:42:22
|
Hi, No. It's not possible. But it is trivial to implement. Togo On Sun, Jun 20, 2021 at 4:13 PM cheng shao <sha...@gm...> wrote: > > Dear Prof. Togo, > > I am a new user of the spglib, and thanks for your efforts in developing and maintain it. > > I have a quick question: is it possible to find the irreducible k points from the custom-defined k mesh? > > Say I have a uniform k mesh points (in a different order as the auto-generated one from spglib), > Is it possible to identify the irreducible k points and the weight factor from it. > > In the example, there is a function `grid = get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0, 0])`, > can we replace the integer number mesh to a vector of k points? > > Best, > Cheng > ---- > Dr. Cheng Shao > Post-Doctoral Researcher > Dept. of Mechanical Engineering > The University of Tokyo > > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
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From: cheng s. <sha...@gm...> - 2021-06-20 07:13:23
|
Dear Prof. Togo, I am a new user of the spglib, and thanks for your efforts in developing and maintain it. I have a quick question: is it possible to find the irreducible k points from the custom-defined k mesh? Say I have a uniform k mesh points (in a different order as the auto-generated one from spglib), Is it possible to identify the irreducible k points and the weight factor from it. In the example, there is a function `grid = get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0, 0])`, can we replace the integer number mesh to a vector of k points? Best, Cheng ---- Dr. Cheng Shao Post-Doctoral Researcher Dept. of Mechanical Engineering The University of Tokyo |
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From: Daniel R. <dan...@ma...> - 2021-03-16 09:03:53
|
Ok, Thank you for your help. Dani -----Original Message----- From: Atsushi Togo <atz...@gm...> Sent: 16 March 2021 09:01 To: spglib-users <spg...@li...> Subject: Re: [Spglib-users] get_symmetry['equivalent_atoms'] - discriminate between rotation and translation Hi, It is difficult for me where I should start to explain, which depends on your knowledge on crystallography. You can have a list of symmetry operations (coset representatives of space group operations with respect to translation group) as 'rotations' and 'translations' in https://spglib.github.io/spglib/python-spglib.html#get-symmetry-dataset The number of symmetry operations to map a site to another site may not be only one. But this kind of information is found in the textbooks and not here to explain. Togo On Tue, Mar 16, 2021 at 5:52 PM Daniel Reta <dan...@ma...> wrote: > > Dear Togo, > > Thank you for your reply. > > If I may, I'll rephrase my question to make sure that it cannot be done. > > Say one has the following mapping of symmetry-related atoms: > > get_symmetry['equivalent_atoms'] = [ 0, 0 ,0, 1, 1, 1 ] > > so this is telling me that atoms 0, 1 and 2 are related by symmetry (same for atoms 3, 4, 5). Instead, I would want to know the type of symmetry operation (pure rotation, pure translation or combination) that relates atom 0 with 1, atom 0 with 2, etc. > > Thank you. > > Dani > > -----Original Message----- > From: Atsushi Togo <atz...@gm...> > Sent: 16 March 2021 01:27 > To: spglib-users <spg...@li...> > Subject: Re: [Spglib-users] get_symmetry['equivalent_atoms'] - > discriminate between rotation and translation > > Hi, > > If I understand correctly your question, probably what you want to do is not able to do with spglib. > Spglib relies on periodicity of crystal lattice in theory. This is the reason why I think so. > > Togo > > On Tue, Mar 16, 2021 at 2:04 AM Daniel Reta <dan...@ma...> wrote: > > > > Dear all, > > > > > > > > I am writing a script that generates a supercell, extracts individual molecules and calculates charges and dipoles on them. This info is later passed to another program to build some sort of embedded cluster approach. > > > > > > > > To reduce the number of calculations, I would like to consider only the molecules within the unitcell. For that, is there a way to get `get_symmetry` to return a list where the symmetry operations are broken down into rotations and translations? In the same way the key ‘equivalent_atoms’ gives a mapping table of atoms to symmetrically independent atoms, but now differentiating rotation and translations. > > > > > > > > Thank you in advance, > > > > Dani > > > > > > > > -- > > Dr. Daniel Reta, MRSC > > Post-doctoral Research Associate > > Dept. of Chemistry, The University of Manchester Oxford Road, > > Manchester, M13 9PL, United Kingdom > > > > Email: dan...@ma... > > -- > > > > > > > > _______________________________________________ > > Spglib-users mailing list > > Spg...@li... > > https://lists.sourceforge.net/lists/listinfo/spglib-users > > > > -- > Atsushi Togo > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo _______________________________________________ Spglib-users mailing list Spg...@li... https://lists.sourceforge.net/lists/listinfo/spglib-users |
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From: Atsushi T. <atz...@gm...> - 2021-03-16 09:01:27
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Hi, It is difficult for me where I should start to explain, which depends on your knowledge on crystallography. You can have a list of symmetry operations (coset representatives of space group operations with respect to translation group) as 'rotations' and 'translations' in https://spglib.github.io/spglib/python-spglib.html#get-symmetry-dataset The number of symmetry operations to map a site to another site may not be only one. But this kind of information is found in the textbooks and not here to explain. Togo On Tue, Mar 16, 2021 at 5:52 PM Daniel Reta <dan...@ma...> wrote: > > Dear Togo, > > Thank you for your reply. > > If I may, I'll rephrase my question to make sure that it cannot be done. > > Say one has the following mapping of symmetry-related atoms: > > get_symmetry['equivalent_atoms'] = [ 0, 0 ,0, 1, 1, 1 ] > > so this is telling me that atoms 0, 1 and 2 are related by symmetry (same for atoms 3, 4, 5). Instead, I would want to know the type of symmetry operation (pure rotation, pure translation or combination) that relates atom 0 with 1, atom 0 with 2, etc. > > Thank you. > > Dani > > -----Original Message----- > From: Atsushi Togo <atz...@gm...> > Sent: 16 March 2021 01:27 > To: spglib-users <spg...@li...> > Subject: Re: [Spglib-users] get_symmetry['equivalent_atoms'] - discriminate between rotation and translation > > Hi, > > If I understand correctly your question, probably what you want to do is not able to do with spglib. > Spglib relies on periodicity of crystal lattice in theory. This is the reason why I think so. > > Togo > > On Tue, Mar 16, 2021 at 2:04 AM Daniel Reta <dan...@ma...> wrote: > > > > Dear all, > > > > > > > > I am writing a script that generates a supercell, extracts individual molecules and calculates charges and dipoles on them. This info is later passed to another program to build some sort of embedded cluster approach. > > > > > > > > To reduce the number of calculations, I would like to consider only the molecules within the unitcell. For that, is there a way to get `get_symmetry` to return a list where the symmetry operations are broken down into rotations and translations? In the same way the key ‘equivalent_atoms’ gives a mapping table of atoms to symmetrically independent atoms, but now differentiating rotation and translations. > > > > > > > > Thank you in advance, > > > > Dani > > > > > > > > -- > > Dr. Daniel Reta, MRSC > > Post-doctoral Research Associate > > Dept. of Chemistry, The University of Manchester Oxford Road, > > Manchester, M13 9PL, United Kingdom > > > > Email: dan...@ma... > > -- > > > > > > > > _______________________________________________ > > Spglib-users mailing list > > Spg...@li... > > https://lists.sourceforge.net/lists/listinfo/spglib-users > > > > -- > Atsushi Togo > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
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From: Daniel R. <dan...@ma...> - 2021-03-16 08:52:43
|
Dear Togo, Thank you for your reply. If I may, I'll rephrase my question to make sure that it cannot be done. Say one has the following mapping of symmetry-related atoms: get_symmetry['equivalent_atoms'] = [ 0, 0 ,0, 1, 1, 1 ] so this is telling me that atoms 0, 1 and 2 are related by symmetry (same for atoms 3, 4, 5). Instead, I would want to know the type of symmetry operation (pure rotation, pure translation or combination) that relates atom 0 with 1, atom 0 with 2, etc. Thank you. Dani -----Original Message----- From: Atsushi Togo <atz...@gm...> Sent: 16 March 2021 01:27 To: spglib-users <spg...@li...> Subject: Re: [Spglib-users] get_symmetry['equivalent_atoms'] - discriminate between rotation and translation Hi, If I understand correctly your question, probably what you want to do is not able to do with spglib. Spglib relies on periodicity of crystal lattice in theory. This is the reason why I think so. Togo On Tue, Mar 16, 2021 at 2:04 AM Daniel Reta <dan...@ma...> wrote: > > Dear all, > > > > I am writing a script that generates a supercell, extracts individual molecules and calculates charges and dipoles on them. This info is later passed to another program to build some sort of embedded cluster approach. > > > > To reduce the number of calculations, I would like to consider only the molecules within the unitcell. For that, is there a way to get `get_symmetry` to return a list where the symmetry operations are broken down into rotations and translations? In the same way the key ‘equivalent_atoms’ gives a mapping table of atoms to symmetrically independent atoms, but now differentiating rotation and translations. > > > > Thank you in advance, > > Dani > > > > -- > Dr. Daniel Reta, MRSC > Post-doctoral Research Associate > Dept. of Chemistry, The University of Manchester Oxford Road, > Manchester, M13 9PL, United Kingdom > > Email: dan...@ma... > -- > > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo _______________________________________________ Spglib-users mailing list Spg...@li... https://lists.sourceforge.net/lists/listinfo/spglib-users |
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From: Atsushi T. <atz...@gm...> - 2021-03-16 01:27:24
|
Hi, If I understand correctly your question, probably what you want to do is not able to do with spglib. Spglib relies on periodicity of crystal lattice in theory. This is the reason why I think so. Togo On Tue, Mar 16, 2021 at 2:04 AM Daniel Reta <dan...@ma...> wrote: > > Dear all, > > > > I am writing a script that generates a supercell, extracts individual molecules and calculates charges and dipoles on them. This info is later passed to another program to build some sort of embedded cluster approach. > > > > To reduce the number of calculations, I would like to consider only the molecules within the unitcell. For that, is there a way to get `get_symmetry` to return a list where the symmetry operations are broken down into rotations and translations? In the same way the key ‘equivalent_atoms’ gives a mapping table of atoms to symmetrically independent atoms, but now differentiating rotation and translations. > > > > Thank you in advance, > > Dani > > > > -- > Dr. Daniel Reta, MRSC > Post-doctoral Research Associate > Dept. of Chemistry, The University of Manchester > Oxford Road, Manchester, M13 9PL, United Kingdom > > Email: dan...@ma... > -- > > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
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From: Daniel R. <dan...@ma...> - 2021-03-15 17:04:09
|
Dear all, I am writing a script that generates a supercell, extracts individual molecules and calculates charges and dipoles on them. This info is later passed to another program to build some sort of embedded cluster approach. To reduce the number of calculations, I would like to consider only the molecules within the unitcell. For that, is there a way to get `get_symmetry` to return a list where the symmetry operations are broken down into rotations and translations? In the same way the key 'equivalent_atoms' gives a mapping table of atoms to symmetrically independent atoms, but now differentiating rotation and translations. Thank you in advance, Dani -- Dr. Daniel Reta, MRSC Post-doctoral Research Associate Dept. of Chemistry, The University of Manchester Oxford Road, Manchester, M13 9PL, United Kingdom Email: dan...@ma... -- |
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From: <bal...@un...> - 2021-02-04 11:38:00
|
> Yes, autotools files were removed. ok > Why do you need all header files? Actually I don't use spglib directly: I use a sotfware (critic2) which uses it. I noticed that on upgrade from rev.n. 1233 to 1235 the installed headers reduced to the single spglib.h and just wanted to be sure that wasn't any mistake on my side (also considering the autotools->cmake switch). Now everything is clear thanks you very much for your valuable work ciao -gabriele |
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From: Atsushi T. <atz...@gm...> - 2021-02-04 11:03:12
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Hi gabriele, Yes, autotools files were removed. Why do you need all header files? Togo On Thu, Feb 4, 2021 at 7:30 PM <bal...@un...> wrote: > > hello > > just installed git master (5eedbb3982e36f14fced8a2dbd2f9ca18573f39e) > and noticed that autotools have been dropped > > Building with cmake (default options) installs only a spglib.h header in > /usr/include, where previously (<=21227701516ec0ec7ce3ec8a982df6df592cbb60) > /usr/include/spglib was populated with a number of headers: > > ----8<---- > arithmetic.h > cell.h > debug.h > delaunay.h > determination.h > hall_symbol.h > kgrid.h > kpoint.h > mathfunc.h > niggli.h > overlap.h > pointgroup.h > primitive.h > refinement.h > site_symmetry.h > sitesym_database.h > spacegroup.h > spg_database.h > spglib.h > spin.h > symmetry.h > version.h > ---->8---- > > Is this correct? Or am I missing any cmake options to install all the > headers? > > thank you very much for your valuable work > > ciao > -gabriele > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
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From: <bal...@un...> - 2021-02-04 10:29:54
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hello
just installed git master (5eedbb3982e36f14fced8a2dbd2f9ca18573f39e)
and noticed that autotools have been dropped
Building with cmake (default options) installs only a spglib.h header in
/usr/include, where previously (<=21227701516ec0ec7ce3ec8a982df6df592cbb60)
/usr/include/spglib was populated with a number of headers:
----8<----
arithmetic.h
cell.h
debug.h
delaunay.h
determination.h
hall_symbol.h
kgrid.h
kpoint.h
mathfunc.h
niggli.h
overlap.h
pointgroup.h
primitive.h
refinement.h
site_symmetry.h
sitesym_database.h
spacegroup.h
spg_database.h
spglib.h
spin.h
symmetry.h
version.h
---->8----
Is this correct? Or am I missing any cmake options to install all the
headers?
thank you very much for your valuable work
ciao
-gabriele
|
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From: Atsushi T. <atz...@gm...> - 2020-12-19 03:44:29
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Hi, I think the answer is No. Togo On Fri, Dec 18, 2020 at 10:40 PM VeiWANG via Spglib-users <spg...@li...> wrote: > > Dear spglib’s developers, > > Is it possible to identify the symmetry of 2D materials in the future version of spglib? > > Best, > Vei > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
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From: VeiWANG <wa...@ic...> - 2020-12-18 13:40:01
|
Dear spglib’s developers, Is it possible to identify the symmetry of 2D materials in the future version of spglib? Best, Vei |
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From: Yongsheng Z. <ysh...@ya...> - 2020-12-14 03:53:48
|
Hi Togo,
Thanks for your quick reply. The problem is fixed following your suggestions.
Cheers,Yongsheng
On Monday, December 14, 2020, 9:07:33 AM GMT+8, Atsushi Togo <atz...@gm...> wrote:
Hi,
It's a bug. Thanks for your report. My fix is found in the develop
branch of spglib and exactly here:
https://github.com/spglib/spglib/blob/60a384b47e451de09b270fb5197c34c8531b5d02/example/spglib_f08.f90#L605-L607
The following is my test after the fix
## My test
Rutile:
Standardized crystal cell
4.0000000000000000 0.0000000000000000 0.0000000000000000
0.0000000000000000 4.0000000000000000 0.0000000000000000
0.0000000000000000 0.0000000000000000 2.5999999046325684
n_std_atoms 6
std_types 1 1 2 2 2
2
Standardized atomic positions
0.0000000000000000 0.0000000000000000 0.0000000000000000
0.50000000000000000 0.50000000000000000 0.50000000000000000
0.30000001192092896 0.30000001192092896 0.0000000000000000
0.69999998807907104 0.69999998807907104 0.0000000000000000
0.19999998807907104 0.80000001192092896 0.50000000000000000
0.80000001192092896 0.19999998807907104 0.50000000000000000
## How to compile
% mkdir build && cd build
% cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_EXPORT_COMPILE_COMMANDS=1
-DCMAKE_VERBOSE_MAKEFILE=1 ..
% make DESTDIR=. install
% cd ../example
** modify Makefile_f08 like lib = ../build/lib/libsymspg.a **
% make -f Makefile_f08
...
gfortran -g -fcheck=all -fbacktrace -c spglib_f08.f90
gfortran -g -fcheck=all -fbacktrace example_f08.f90 spglib_f08.o
../build/lib/libsymspg.a -o example
...
Togo
On Sun, Dec 13, 2020 at 11:24 PM Yongsheng Zhang via Spglib-users
<spg...@li...> wrote:
>
> Dear Spglib,
>
> In the spglib-1.16.0/example, I am trying to get the standardized information of the crystals based on the spglib_f08.f90 and libsymspg.a in the Fortran framework. Then, I added the following lines in the write_syminfo subroutine of the example_f08.f90 file,
>
> print*, 'Standardized crystal cell'
> do i=1,3
> print*, dset%std_lattice(i,:)
> end do
> print*,
> print*, 'n_std_atoms',dset%n_std_atoms
> print*, 'std_types',dset%std_types
> print*,
> print*, 'Standardized atomic positions'
> do i=1,num_atom
> print*, dset%std_positions(:,i)
> end do
>
>
> It turns our that the std_lattice looks good, but the std_positions are weird. For "Rutile":
> Standardized crystal cell
> 4.0000000000000000 0.0000000000000000 0.0000000000000000
> 0.0000000000000000 4.0000000000000000 0.0000000000000000
> 0.0000000000000000 0.0000000000000000 2.5999999046325684
>
> n_std_atoms 6
> std_types 1 1 2 2 2 2
>
> Standardized atomic positions
> 0.0000000000000000 0.0000000000000000 0.0000000000000000
> 0.0000000000000000 0.0000000000000000 0.0000000000000000
> 0.0000000000000000 1071644672.0000000 0.0000000000000000
> 1071644672.0000000 0.0000000000000000 1071644672.0000000
> 1073741824.0000000 1070805811.0000000 1073741824.0000000
> 1070805811.0000000 0.0000000000000000 0.0000000000000000
>
> Would you please let me know to get the correct std_positions? Thank you very much!
> Cheers,
> Yongsheng
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users
--
Atsushi Togo
_______________________________________________
Spglib-users mailing list
Spg...@li...
https://lists.sourceforge.net/lists/listinfo/spglib-users
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From: Atsushi T. <atz...@gm...> - 2020-12-14 01:07:30
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Hi, It's a bug. Thanks for your report. My fix is found in the develop branch of spglib and exactly here: https://github.com/spglib/spglib/blob/60a384b47e451de09b270fb5197c34c8531b5d02/example/spglib_f08.f90#L605-L607 The following is my test after the fix ## My test Rutile: Standardized crystal cell 4.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 4.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 2.5999999046325684 n_std_atoms 6 std_types 1 1 2 2 2 2 Standardized atomic positions 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.50000000000000000 0.50000000000000000 0.50000000000000000 0.30000001192092896 0.30000001192092896 0.0000000000000000 0.69999998807907104 0.69999998807907104 0.0000000000000000 0.19999998807907104 0.80000001192092896 0.50000000000000000 0.80000001192092896 0.19999998807907104 0.50000000000000000 ## How to compile % mkdir build && cd build % cmake -DCMAKE_INSTALL_PREFIX="" -DCMAKE_EXPORT_COMPILE_COMMANDS=1 -DCMAKE_VERBOSE_MAKEFILE=1 .. % make DESTDIR=. install % cd ../example ** modify Makefile_f08 like lib = ../build/lib/libsymspg.a ** % make -f Makefile_f08 ... gfortran -g -fcheck=all -fbacktrace -c spglib_f08.f90 gfortran -g -fcheck=all -fbacktrace example_f08.f90 spglib_f08.o ../build/lib/libsymspg.a -o example ... Togo On Sun, Dec 13, 2020 at 11:24 PM Yongsheng Zhang via Spglib-users <spg...@li...> wrote: > > Dear Spglib, > > In the spglib-1.16.0/example, I am trying to get the standardized information of the crystals based on the spglib_f08.f90 and libsymspg.a in the Fortran framework. Then, I added the following lines in the write_syminfo subroutine of the example_f08.f90 file, > > print*, 'Standardized crystal cell' > do i=1,3 > print*, dset%std_lattice(i,:) > end do > print*, > print*, 'n_std_atoms',dset%n_std_atoms > print*, 'std_types',dset%std_types > print*, > print*, 'Standardized atomic positions' > do i=1,num_atom > print*, dset%std_positions(:,i) > end do > > > It turns our that the std_lattice looks good, but the std_positions are weird. For "Rutile": > Standardized crystal cell > 4.0000000000000000 0.0000000000000000 0.0000000000000000 > 0.0000000000000000 4.0000000000000000 0.0000000000000000 > 0.0000000000000000 0.0000000000000000 2.5999999046325684 > > n_std_atoms 6 > std_types 1 1 2 2 2 2 > > Standardized atomic positions > 0.0000000000000000 0.0000000000000000 0.0000000000000000 > 0.0000000000000000 0.0000000000000000 0.0000000000000000 > 0.0000000000000000 1071644672.0000000 0.0000000000000000 > 1071644672.0000000 0.0000000000000000 1071644672.0000000 > 1073741824.0000000 1070805811.0000000 1073741824.0000000 > 1070805811.0000000 0.0000000000000000 0.0000000000000000 > > Would you please let me know to get the correct std_positions? Thank you very much! > Cheers, > Yongsheng > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
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From: Yongsheng Z. <ysh...@ya...> - 2020-12-13 14:24:19
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Dear Spglib, In the spglib-1.16.0/example, I am trying to get the standardized information of the crystals based on the spglib_f08.f90 and libsymspg.a in the Fortran framework. Then, I added the following lines in the write_syminfo subroutine of the example_f08.f90 file, print*, 'Standardized crystal cell' do i=1,3 print*, dset%std_lattice(i,:) end do print*, print*, 'n_std_atoms',dset%n_std_atoms print*, 'std_types',dset%std_types print*, print*, 'Standardized atomic positions' do i=1,num_atom print*, dset%std_positions(:,i) end do It turns our that the std_lattice looks good, but the std_positions are weird. For "Rutile": Standardized crystal cell 4.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 4.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 2.5999999046325684 n_std_atoms 6 std_types 1 1 2 2 2 2 Standardized atomic positions 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 0.0000000000000000 1071644672.0000000 0.0000000000000000 1071644672.0000000 0.0000000000000000 1071644672.0000000 1073741824.0000000 1070805811.0000000 1073741824.0000000 1070805811.0000000 0.0000000000000000 0.0000000000000000 Would you please let me know to get the correct std_positions? Thank you very much!Cheers,Yongsheng |
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From: Atsushi T. <atz...@gm...> - 2020-12-10 12:32:32
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Hi, There are many options depending on what you want to do. So please read the documentation to find your answer. Togo On Thu, Dec 10, 2020 at 8:13 PM Arijit Sinha <ari...@gm...> wrote: > > Dear Atsushi, > After going through some materials online, I think I understand the reason for the discrepancy. Actually, there is a standard-setting implemented by spglib according to which it is modifying my input structures and changing lattice parameter orders. Is there any way to turn off the standard-setting and continuing with the input structure only? > -- > Thanking you, > > Arijit Sinha > Junior Research Fellow > JNCASR (Theoretical Sciences Unit), > Jakkur, Bangalore(India). > > > > > On Wed, Dec 9, 2020 at 7:46 PM Arijit Sinha <ari...@gm...> wrote: >> >> Sir, >> As you said I have constructed the structure by hand and try to get the space group but the problem(lattice parameters getting jumbled up) is appearing again I'm sending you the script and the relevant change in the input and the corresponding output. >> ********************************************************************************************************************************************************************************************************************************** >> Input structure: >> TNS = ([(3.416000127800, 0.000000000000, 0.00000000000), >> (0.000000000000, 12.123309135400, 0.00000007500), >> (0.000000000000, -0.000000093700, 15.1484184265)], >> [(0.000000000, 0.221787274, 0.108938992), >> (0.000000000, 0.778212726, 0.891061008), >> (0.000000000, 0.778212667, 0.608938992), >> (0.000000000, 0.221787304, 0.391061008), >> (0.500000000, 0.721793473, 0.108937271), >> (0.500000000, 0.278206497, 0.891062737), >> (0.500000000, 0.278206557, 0.608937263), >> (0.500000000, 0.721793473, 0.391062707), >> (0.000000000, 0.699588060, 0.250000000), >> (0.000000000, 0.300411940, 0.750000000), >> (0.500000000, 0.199598417, 0.250000000), >> (0.500000000, 0.800401568, 0.750000000), >> (0.500000000, 0.082921132, 0.136132896), >> (0.500000000, 0.917078853, 0.863867104), >> (0.500000000, 0.917078853, 0.636132836), >> (0.500000000, 0.082921162, 0.363867134), >> (0.000000000, 0.582922995, 0.136127144), >> (0.000000000, 0.417077035, 0.863872886), >> (0.000000000, 0.417077065, 0.636127174), >> (0.000000000, 0.582922935, 0.363872826), >> (0.000000000, 0.147209421, 0.950776219), >> (0.000000000, 0.852790594, 0.049223803), >> (0.000000000, 0.852790534, 0.450776190), >> (0.000000000, 0.147209466, 0.549223840), >> (0.500000000, 0.647215426, 0.950776398), >> (0.500000000, 0.352784544, 0.049223613), >> (0.500000000, 0.352784604, 0.450776398), >> (0.500000000, 0.647215426, 0.549223602), >> (0.000000000, 0.322443128, 0.250000000), >> (0.000000000, 0.677556872, 0.750000000), >> (0.500000000, 0.822440684, 0.250000000), >> (0.500000000, 0.177559301, 0.750000000)], >> [73, 73, 73, 73, 73, 73, 73, 73, 28, 28, 28, 28, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16]) >> >> ************************************************************************************************************************************************************* >> Relevant output: >> Input structure >> Basis vectors: >> a 15.14842 0.00000 0.00000 >> b 0.00000 3.41600 0.00000 >> c 0.00000 0.00000 12.12331 >> Atomic points: >> 73 0.10894 0.00000 0.22179 >> 73 0.89106 0.00000 0.77821 >> 73 0.60894 0.00000 0.77821 >> 73 0.39106 0.00000 0.22179 >> 73 0.10894 0.50000 0.72179 >> 73 0.89106 0.50000 0.27821 >> 73 0.60894 0.50000 0.27821 >> 73 0.39106 0.50000 0.72179 >> 28 0.25000 0.00000 0.69959 >> 28 0.75000 0.00000 0.30041 >> 28 0.25000 0.50000 0.19960 >> 28 0.75000 0.50000 0.80040 >> 16 0.13613 0.50000 0.08292 >> 16 0.86387 0.50000 0.91708 >> 16 0.63613 0.50000 0.91708 >> 16 0.36387 0.50000 0.08292 >> 16 0.13613 0.00000 0.58292 >> 16 0.86387 0.00000 0.41708 >> 16 0.63613 0.00000 0.41708 >> 16 0.36387 0.00000 0.58292 >> 16 0.95078 0.00000 0.14721 >> 16 0.04922 0.00000 0.85279 >> 16 0.45078 0.00000 0.85279 >> 16 0.54922 0.00000 0.14721 >> 16 0.95078 0.50000 0.64722 >> 16 0.04922 0.50000 0.35278 >> 16 0.45078 0.50000 0.35278 >> 16 0.54922 0.50000 0.64722 >> 16 0.25000 0.00000 0.32244 >> 16 0.75000 0.00000 0.67756 >> 16 0.25000 0.50000 0.82244 >> 16 0.75000 0.50000 0.17756 >> ********************************************************************************************************************************************************************* >> Unable to get >> -- >> Thanking you, >> >> Arijit Sinha >> Junior Research Fellow >> JNCASR (Theoretical Sciences Unit), >> Jakkur, Bangalore(India). >> >> >> >> >> On Wed, Dec 9, 2020 at 6:16 PM Atsushi Togo <atz...@gm...> wrote: >>> >>> Hi, >>> >>> I tested your POSCAR using phonopy (phonopy uses spglib.) I doubt your script. >>> You use ASE. Please write your script without using ASE. See >>> https://spglib.github.io/spglib/python-spglib.html#crystal-structure-cell. >>> >>> Togo >>> >>> On Wed, Dec 9, 2020 at 9:40 PM Arijit Sinha <ari...@gm...> wrote: >>> > >>> > Dear Atsushi, >>> > Thank you for your fast reply I have done that also but nothing changed. I think this is not related to symmetry tolerance because the code is reading the lattice parameters wrong all together it is printing a as c, c as b nd so on. the atomic position order is also jumbled up. I am writing down the input and output for your convenience below >>> > ********************************************************************************************************************************************************************************************************************************* >>> > Input: >>> > XCrySDen XSF file >>> > 1.0 >>> > 3.416000127800 0.000000000000 0.000000000000 >>> > 0.000000000000 12.123309135400 0.000000075000 >>> > 0.000000000000 -0.000000093700 15.148418426500 >>> > Ta Ni S >>> > 8 4 20 >>> > Direct >>> > 0.000000000 0.221787274 0.108938992 >>> > 0.000000000 0.778212726 0.891061008 >>> > 0.000000000 0.778212667 0.608938992 >>> > 0.000000000 0.221787304 0.391061008 >>> > 0.500000000 0.721793473 0.108937271 >>> > 0.500000000 0.278206497 0.891062737 >>> > 0.500000000 0.278206557 0.608937263 >>> > 0.500000000 0.721793473 0.391062707 >>> > 0.000000000 0.699588060 0.250000000 >>> > 0.000000000 0.300411940 0.750000000 >>> > 0.500000000 0.199598417 0.250000000 >>> > 0.500000000 0.800401568 0.750000000 >>> > 0.500000000 0.082921132 0.136132896 >>> > 0.500000000 0.917078853 0.863867104 >>> > 0.500000000 0.917078853 0.636132836 >>> > 0.500000000 0.082921162 0.363867134 >>> > 0.000000000 0.582922995 0.136127144 >>> > 0.000000000 0.417077035 0.863872886 >>> > 0.000000000 0.417077065 0.636127174 >>> > 0.000000000 0.582922935 0.363872826 >>> > 0.000000000 0.147209421 0.950776219 >>> > 0.000000000 0.852790594 0.049223803 >>> > 0.000000000 0.852790534 0.450776190 >>> > 0.000000000 0.147209466 0.549223840 >>> > 0.500000000 0.647215426 0.950776398 >>> > 0.500000000 0.352784544 0.049223613 >>> > 0.500000000 0.352784604 0.450776398 >>> > 0.500000000 0.647215426 0.549223602 >>> > 0.000000000 0.322443128 0.250000000 >>> > 0.000000000 0.677556872 0.750000000 >>> > 0.500000000 0.822440684 0.250000000 >>> > 0.500000000 0.177559301 0.750000000 >>> > **************************************************************************************************************************************************************************** >>> > Output Standardize_cell using , tprimitive=0, no_idealize=0): >>> > Basis vectors: >>> > a 15.14842 0.00000 0.00000 >>> > b 0.00000 3.41600 0.00000 >>> > c 0.00000 0.00000 12.12331 >>> > Atomic points: >>> > 73 0.10894 0.00000 0.22179 >>> > 73 0.89106 0.00000 0.77821 >>> > 73 0.60894 0.00000 0.77821 >>> > 73 0.39106 0.00000 0.22179 >>> > 73 0.10894 0.50000 0.72179 >>> > 73 0.89106 0.50000 0.27821 >>> > 73 0.60894 0.50000 0.27821 >>> > 73 0.39106 0.50000 0.72179 >>> > 28 0.25000 0.00000 0.69959 >>> > 28 0.75000 0.00000 0.30041 >>> > 28 0.25000 0.50000 0.19960 >>> > 28 0.75000 0.50000 0.80040 >>> > 16 0.13613 0.50000 0.08292 >>> > 16 0.86387 0.50000 0.91708 >>> > 16 0.63613 0.50000 0.91708 >>> > 16 0.36387 0.50000 0.08292 >>> > 16 0.13613 0.00000 0.58292 >>> > 16 0.86387 0.00000 0.41708 >>> > 16 0.63613 0.00000 0.41708 >>> > 16 0.36387 0.00000 0.58292 >>> > 16 0.95078 0.00000 0.14721 >>> > 16 0.04922 0.00000 0.85279 >>> > 16 0.45078 0.00000 0.85279 >>> > 16 0.54922 0.00000 0.14721 >>> > 16 0.95078 0.50000 0.64722 >>> > 16 0.04922 0.50000 0.35278 >>> > 16 0.45078 0.50000 0.35278 >>> > 16 0.54922 0.50000 0.64722 >>> > 16 0.25000 0.00000 0.32244 >>> > 16 0.75000 0.00000 0.67756 >>> > 16 0.25000 0.50000 0.82244 >>> > 16 0.75000 0.50000 0.17756 >>> > ************************************************************************************************************************************************************************************** >>> > >>> > Thanking you, >>> > >>> > Arijit Sinha >>> > Junior Research Fellow >>> > JNCASR (Theoretical Sciences Unit), >>> > Jakkur, Bangalore(India). >>> > >>> > >>> > >>> > >>> > On Wed, Dec 9, 2020 at 5:56 PM Atsushi Togo <atz...@gm...> wrote: >>> >> >>> >> Hi, >>> >> >>> >> You can loosen the symmetry search tolerance (e.g. symprec=1e-3). >>> >> >>> >> Togo >>> >> >>> >> On Wed, Dec 9, 2020 at 8:31 PM Arijit Sinha <ari...@gm...> wrote: >>> >> > >>> >> > Dear Users and Experts, >>> >> > I am new in spglib but my material which has a symmetry of Cmcm is not getting captured correctly by spglib in python it is jumbling up the lattice vectors order given in poscar (but FINDSYM showing the correct symmetry) below I am attaching the code as well as the files please tell me if it is my mistake or something else. >>> >> > -- >>> >> > Thanking you, >>> >> > >>> >> > Arijit Sinha >>> >> > Junior Research Fellow >>> >> > JNCASR (Theoretical Sciences Unit), >>> >> > Jakkur, Bangalore(India). >>> >> > >>> >> > >>> >> > _______________________________________________ >>> >> > Spglib-users mailing list >>> >> > Spg...@li... >>> >> > https://lists.sourceforge.net/lists/listinfo/spglib-users >>> >> >>> >> >>> >> >>> >> -- >>> >> Atsushi Togo >>> >> >>> >> >>> >> _______________________________________________ >>> >> Spglib-users mailing list >>> >> Spg...@li... >>> >> https://lists.sourceforge.net/lists/listinfo/spglib-users >>> > >>> > _______________________________________________ >>> > Spglib-users mailing list >>> > Spg...@li... >>> > https://lists.sourceforge.net/lists/listinfo/spglib-users >>> >>> >>> >>> -- >>> Atsushi Togo >>> >>> >>> _______________________________________________ >>> Spglib-users mailing list >>> Spg...@li... >>> https://lists.sourceforge.net/lists/listinfo/spglib-users > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
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From: Arijit S. <ari...@gm...> - 2020-12-10 11:12:56
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Dear Atsushi, After going through some materials online, I think I understand the reason for the discrepancy. Actually, there is a standard-setting implemented by spglib according to which it is modifying my input structures and changing lattice parameter orders. Is there any way to turn off the standard-setting and continuing with the input structure only? -- Thanking you, *Arijit SinhaJunior Research FellowJNCASR (Theoretical Sciences Unit),Jakkur, Bangalore(India).* On Wed, Dec 9, 2020 at 7:46 PM Arijit Sinha <ari...@gm...> wrote: > Sir, > As you said I have constructed the structure by hand and try to get the > space group but the problem(lattice parameters getting jumbled up) is > appearing again I'm sending you the script and the relevant change in the > input and the corresponding output. > > ********************************************************************************************************************************************************************************************************************************** > Input structure: > TNS = ([(3.416000127800, 0.000000000000, 0.00000000000), > (0.000000000000, 12.123309135400, 0.00000007500), > (0.000000000000, -0.000000093700, 15.1484184265)], > [(0.000000000, 0.221787274, 0.108938992), > (0.000000000, 0.778212726, 0.891061008), > (0.000000000, 0.778212667, 0.608938992), > (0.000000000, 0.221787304, 0.391061008), > (0.500000000, 0.721793473, 0.108937271), > (0.500000000, 0.278206497, 0.891062737), > (0.500000000, 0.278206557, 0.608937263), > (0.500000000, 0.721793473, 0.391062707), > (0.000000000, 0.699588060, 0.250000000), > (0.000000000, 0.300411940, 0.750000000), > (0.500000000, 0.199598417, 0.250000000), > (0.500000000, 0.800401568, 0.750000000), > (0.500000000, 0.082921132, 0.136132896), > (0.500000000, 0.917078853, 0.863867104), > (0.500000000, 0.917078853, 0.636132836), > (0.500000000, 0.082921162, 0.363867134), > (0.000000000, 0.582922995, 0.136127144), > (0.000000000, 0.417077035, 0.863872886), > (0.000000000, 0.417077065, 0.636127174), > (0.000000000, 0.582922935, 0.363872826), > (0.000000000, 0.147209421, 0.950776219), > (0.000000000, 0.852790594, 0.049223803), > (0.000000000, 0.852790534, 0.450776190), > (0.000000000, 0.147209466, 0.549223840), > (0.500000000, 0.647215426, 0.950776398), > (0.500000000, 0.352784544, 0.049223613), > (0.500000000, 0.352784604, 0.450776398), > (0.500000000, 0.647215426, 0.549223602), > (0.000000000, 0.322443128, 0.250000000), > (0.000000000, 0.677556872, 0.750000000), > (0.500000000, 0.822440684, 0.250000000), > (0.500000000, 0.177559301, 0.750000000)], > [73, 73, 73, 73, 73, 73, 73, 73, 28, 28, 28, 28, 16, 16, 16, 16, > 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16, 16]) > > > ************************************************************************************************************************************************************* > Relevant output: > Input structure > Basis vectors: > a 15.14842 0.00000 0.00000 > b 0.00000 3.41600 0.00000 > c 0.00000 0.00000 12.12331 > Atomic points: > 73 0.10894 0.00000 0.22179 > 73 0.89106 0.00000 0.77821 > 73 0.60894 0.00000 0.77821 > 73 0.39106 0.00000 0.22179 > 73 0.10894 0.50000 0.72179 > 73 0.89106 0.50000 0.27821 > 73 0.60894 0.50000 0.27821 > 73 0.39106 0.50000 0.72179 > 28 0.25000 0.00000 0.69959 > 28 0.75000 0.00000 0.30041 > 28 0.25000 0.50000 0.19960 > 28 0.75000 0.50000 0.80040 > 16 0.13613 0.50000 0.08292 > 16 0.86387 0.50000 0.91708 > 16 0.63613 0.50000 0.91708 > 16 0.36387 0.50000 0.08292 > 16 0.13613 0.00000 0.58292 > 16 0.86387 0.00000 0.41708 > 16 0.63613 0.00000 0.41708 > 16 0.36387 0.00000 0.58292 > 16 0.95078 0.00000 0.14721 > 16 0.04922 0.00000 0.85279 > 16 0.45078 0.00000 0.85279 > 16 0.54922 0.00000 0.14721 > 16 0.95078 0.50000 0.64722 > 16 0.04922 0.50000 0.35278 > 16 0.45078 0.50000 0.35278 > 16 0.54922 0.50000 0.64722 > 16 0.25000 0.00000 0.32244 > 16 0.75000 0.00000 0.67756 > 16 0.25000 0.50000 0.82244 > 16 0.75000 0.50000 0.17756 > > ********************************************************************************************************************************************************************* > Unable to get > -- > Thanking you, > > > > > *Arijit SinhaJunior Research FellowJNCASR (Theoretical Sciences > Unit),Jakkur, Bangalore(India).* > > > > > On Wed, Dec 9, 2020 at 6:16 PM Atsushi Togo <atz...@gm...> wrote: > >> Hi, >> >> I tested your POSCAR using phonopy (phonopy uses spglib.) I doubt your >> script. >> You use ASE. Please write your script without using ASE. See >> https://spglib.github.io/spglib/python-spglib.html#crystal-structure-cell >> . >> >> Togo >> >> On Wed, Dec 9, 2020 at 9:40 PM Arijit Sinha <ari...@gm...> >> wrote: >> > >> > Dear Atsushi, >> > Thank you for your fast reply I have done that also but nothing >> changed. I think this is not related to symmetry tolerance because the code >> is reading the lattice parameters wrong all together it is printing a as c, >> c as b nd so on. the atomic position order is also jumbled up. I am writing >> down the input and output for your convenience below >> > >> ********************************************************************************************************************************************************************************************************************************* >> > Input: >> > XCrySDen XSF file >> > 1.0 >> > 3.416000127800 0.000000000000 0.000000000000 >> > 0.000000000000 12.123309135400 0.000000075000 >> > 0.000000000000 -0.000000093700 15.148418426500 >> > Ta Ni S >> > 8 4 20 >> > Direct >> > 0.000000000 0.221787274 0.108938992 >> > 0.000000000 0.778212726 0.891061008 >> > 0.000000000 0.778212667 0.608938992 >> > 0.000000000 0.221787304 0.391061008 >> > 0.500000000 0.721793473 0.108937271 >> > 0.500000000 0.278206497 0.891062737 >> > 0.500000000 0.278206557 0.608937263 >> > 0.500000000 0.721793473 0.391062707 >> > 0.000000000 0.699588060 0.250000000 >> > 0.000000000 0.300411940 0.750000000 >> > 0.500000000 0.199598417 0.250000000 >> > 0.500000000 0.800401568 0.750000000 >> > 0.500000000 0.082921132 0.136132896 >> > 0.500000000 0.917078853 0.863867104 >> > 0.500000000 0.917078853 0.636132836 >> > 0.500000000 0.082921162 0.363867134 >> > 0.000000000 0.582922995 0.136127144 >> > 0.000000000 0.417077035 0.863872886 >> > 0.000000000 0.417077065 0.636127174 >> > 0.000000000 0.582922935 0.363872826 >> > 0.000000000 0.147209421 0.950776219 >> > 0.000000000 0.852790594 0.049223803 >> > 0.000000000 0.852790534 0.450776190 >> > 0.000000000 0.147209466 0.549223840 >> > 0.500000000 0.647215426 0.950776398 >> > 0.500000000 0.352784544 0.049223613 >> > 0.500000000 0.352784604 0.450776398 >> > 0.500000000 0.647215426 0.549223602 >> > 0.000000000 0.322443128 0.250000000 >> > 0.000000000 0.677556872 0.750000000 >> > 0.500000000 0.822440684 0.250000000 >> > 0.500000000 0.177559301 0.750000000 >> > >> **************************************************************************************************************************************************************************** >> > Output Standardize_cell using , tprimitive=0, no_idealize=0): >> > Basis vectors: >> > a 15.14842 0.00000 0.00000 >> > b 0.00000 3.41600 0.00000 >> > c 0.00000 0.00000 12.12331 >> > Atomic points: >> > 73 0.10894 0.00000 0.22179 >> > 73 0.89106 0.00000 0.77821 >> > 73 0.60894 0.00000 0.77821 >> > 73 0.39106 0.00000 0.22179 >> > 73 0.10894 0.50000 0.72179 >> > 73 0.89106 0.50000 0.27821 >> > 73 0.60894 0.50000 0.27821 >> > 73 0.39106 0.50000 0.72179 >> > 28 0.25000 0.00000 0.69959 >> > 28 0.75000 0.00000 0.30041 >> > 28 0.25000 0.50000 0.19960 >> > 28 0.75000 0.50000 0.80040 >> > 16 0.13613 0.50000 0.08292 >> > 16 0.86387 0.50000 0.91708 >> > 16 0.63613 0.50000 0.91708 >> > 16 0.36387 0.50000 0.08292 >> > 16 0.13613 0.00000 0.58292 >> > 16 0.86387 0.00000 0.41708 >> > 16 0.63613 0.00000 0.41708 >> > 16 0.36387 0.00000 0.58292 >> > 16 0.95078 0.00000 0.14721 >> > 16 0.04922 0.00000 0.85279 >> > 16 0.45078 0.00000 0.85279 >> > 16 0.54922 0.00000 0.14721 >> > 16 0.95078 0.50000 0.64722 >> > 16 0.04922 0.50000 0.35278 >> > 16 0.45078 0.50000 0.35278 >> > 16 0.54922 0.50000 0.64722 >> > 16 0.25000 0.00000 0.32244 >> > 16 0.75000 0.00000 0.67756 >> > 16 0.25000 0.50000 0.82244 >> > 16 0.75000 0.50000 0.17756 >> > >> ************************************************************************************************************************************************************************************** >> > >> > Thanking you, >> > >> > Arijit Sinha >> > Junior Research Fellow >> > JNCASR (Theoretical Sciences Unit), >> > Jakkur, Bangalore(India). >> > >> > >> > >> > >> > On Wed, Dec 9, 2020 at 5:56 PM Atsushi Togo <atz...@gm...> wrote: >> >> >> >> Hi, >> >> >> >> You can loosen the symmetry search tolerance (e.g. symprec=1e-3). >> >> >> >> Togo >> >> >> >> On Wed, Dec 9, 2020 at 8:31 PM Arijit Sinha <ari...@gm...> >> wrote: >> >> > >> >> > Dear Users and Experts, >> >> > I am new in spglib but my material which has a symmetry of Cmcm is >> not getting captured correctly by spglib in python it is jumbling up the >> lattice vectors order given in poscar (but FINDSYM showing the correct >> symmetry) below I am attaching the code as well as the files please tell me >> if it is my mistake or something else. >> >> > -- >> >> > Thanking you, >> >> > >> >> > Arijit Sinha >> >> > Junior Research Fellow >> >> > JNCASR (Theoretical Sciences Unit), >> >> > Jakkur, Bangalore(India). >> >> > >> >> > >> >> > _______________________________________________ >> >> > Spglib-users mailing list >> >> > Spg...@li... >> >> > https://lists.sourceforge.net/lists/listinfo/spglib-users >> >> >> >> >> >> >> >> -- >> >> Atsushi Togo >> >> >> >> >> >> _______________________________________________ >> >> Spglib-users mailing list >> >> Spg...@li... >> >> https://lists.sourceforge.net/lists/listinfo/spglib-users >> > >> > _______________________________________________ >> > Spglib-users mailing list >> > Spg...@li... >> > https://lists.sourceforge.net/lists/listinfo/spglib-users >> >> >> >> -- >> Atsushi Togo >> >> >> _______________________________________________ >> Spglib-users mailing list >> Spg...@li... >> https://lists.sourceforge.net/lists/listinfo/spglib-users >> > |
|
From: Atsushi T. <atz...@gm...> - 2020-12-09 12:46:02
|
Hi, I tested your POSCAR using phonopy (phonopy uses spglib.) I doubt your script. You use ASE. Please write your script without using ASE. See https://spglib.github.io/spglib/python-spglib.html#crystal-structure-cell. Togo On Wed, Dec 9, 2020 at 9:40 PM Arijit Sinha <ari...@gm...> wrote: > > Dear Atsushi, > Thank you for your fast reply I have done that also but nothing changed. I think this is not related to symmetry tolerance because the code is reading the lattice parameters wrong all together it is printing a as c, c as b nd so on. the atomic position order is also jumbled up. I am writing down the input and output for your convenience below > ********************************************************************************************************************************************************************************************************************************* > Input: > XCrySDen XSF file > 1.0 > 3.416000127800 0.000000000000 0.000000000000 > 0.000000000000 12.123309135400 0.000000075000 > 0.000000000000 -0.000000093700 15.148418426500 > Ta Ni S > 8 4 20 > Direct > 0.000000000 0.221787274 0.108938992 > 0.000000000 0.778212726 0.891061008 > 0.000000000 0.778212667 0.608938992 > 0.000000000 0.221787304 0.391061008 > 0.500000000 0.721793473 0.108937271 > 0.500000000 0.278206497 0.891062737 > 0.500000000 0.278206557 0.608937263 > 0.500000000 0.721793473 0.391062707 > 0.000000000 0.699588060 0.250000000 > 0.000000000 0.300411940 0.750000000 > 0.500000000 0.199598417 0.250000000 > 0.500000000 0.800401568 0.750000000 > 0.500000000 0.082921132 0.136132896 > 0.500000000 0.917078853 0.863867104 > 0.500000000 0.917078853 0.636132836 > 0.500000000 0.082921162 0.363867134 > 0.000000000 0.582922995 0.136127144 > 0.000000000 0.417077035 0.863872886 > 0.000000000 0.417077065 0.636127174 > 0.000000000 0.582922935 0.363872826 > 0.000000000 0.147209421 0.950776219 > 0.000000000 0.852790594 0.049223803 > 0.000000000 0.852790534 0.450776190 > 0.000000000 0.147209466 0.549223840 > 0.500000000 0.647215426 0.950776398 > 0.500000000 0.352784544 0.049223613 > 0.500000000 0.352784604 0.450776398 > 0.500000000 0.647215426 0.549223602 > 0.000000000 0.322443128 0.250000000 > 0.000000000 0.677556872 0.750000000 > 0.500000000 0.822440684 0.250000000 > 0.500000000 0.177559301 0.750000000 > **************************************************************************************************************************************************************************** > Output Standardize_cell using , tprimitive=0, no_idealize=0): > Basis vectors: > a 15.14842 0.00000 0.00000 > b 0.00000 3.41600 0.00000 > c 0.00000 0.00000 12.12331 > Atomic points: > 73 0.10894 0.00000 0.22179 > 73 0.89106 0.00000 0.77821 > 73 0.60894 0.00000 0.77821 > 73 0.39106 0.00000 0.22179 > 73 0.10894 0.50000 0.72179 > 73 0.89106 0.50000 0.27821 > 73 0.60894 0.50000 0.27821 > 73 0.39106 0.50000 0.72179 > 28 0.25000 0.00000 0.69959 > 28 0.75000 0.00000 0.30041 > 28 0.25000 0.50000 0.19960 > 28 0.75000 0.50000 0.80040 > 16 0.13613 0.50000 0.08292 > 16 0.86387 0.50000 0.91708 > 16 0.63613 0.50000 0.91708 > 16 0.36387 0.50000 0.08292 > 16 0.13613 0.00000 0.58292 > 16 0.86387 0.00000 0.41708 > 16 0.63613 0.00000 0.41708 > 16 0.36387 0.00000 0.58292 > 16 0.95078 0.00000 0.14721 > 16 0.04922 0.00000 0.85279 > 16 0.45078 0.00000 0.85279 > 16 0.54922 0.00000 0.14721 > 16 0.95078 0.50000 0.64722 > 16 0.04922 0.50000 0.35278 > 16 0.45078 0.50000 0.35278 > 16 0.54922 0.50000 0.64722 > 16 0.25000 0.00000 0.32244 > 16 0.75000 0.00000 0.67756 > 16 0.25000 0.50000 0.82244 > 16 0.75000 0.50000 0.17756 > ************************************************************************************************************************************************************************************** > > Thanking you, > > Arijit Sinha > Junior Research Fellow > JNCASR (Theoretical Sciences Unit), > Jakkur, Bangalore(India). > > > > > On Wed, Dec 9, 2020 at 5:56 PM Atsushi Togo <atz...@gm...> wrote: >> >> Hi, >> >> You can loosen the symmetry search tolerance (e.g. symprec=1e-3). >> >> Togo >> >> On Wed, Dec 9, 2020 at 8:31 PM Arijit Sinha <ari...@gm...> wrote: >> > >> > Dear Users and Experts, >> > I am new in spglib but my material which has a symmetry of Cmcm is not getting captured correctly by spglib in python it is jumbling up the lattice vectors order given in poscar (but FINDSYM showing the correct symmetry) below I am attaching the code as well as the files please tell me if it is my mistake or something else. >> > -- >> > Thanking you, >> > >> > Arijit Sinha >> > Junior Research Fellow >> > JNCASR (Theoretical Sciences Unit), >> > Jakkur, Bangalore(India). >> > >> > >> > _______________________________________________ >> > Spglib-users mailing list >> > Spg...@li... >> > https://lists.sourceforge.net/lists/listinfo/spglib-users >> >> >> >> -- >> Atsushi Togo >> >> >> _______________________________________________ >> Spglib-users mailing list >> Spg...@li... >> https://lists.sourceforge.net/lists/listinfo/spglib-users > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
|
From: Arijit S. <ari...@gm...> - 2020-12-09 12:40:29
|
Dear Atsushi, Thank you for your fast reply I have done that also but nothing changed. I think this is not related to symmetry tolerance because the code is reading the lattice parameters wrong all together it is printing a as c, c as b nd so on. the atomic position order is also jumbled up. I am writing down the input and output for your convenience below ********************************************************************************************************************************************************************************************************************************* Input: XCrySDen XSF file 1.0 3.416000127800 0.000000000000 0.000000000000 0.000000000000 12.123309135400 0.000000075000 0.000000000000 -0.000000093700 15.148418426500 Ta Ni S 8 4 20 Direct 0.000000000 0.221787274 0.108938992 0.000000000 0.778212726 0.891061008 0.000000000 0.778212667 0.608938992 0.000000000 0.221787304 0.391061008 0.500000000 0.721793473 0.108937271 0.500000000 0.278206497 0.891062737 0.500000000 0.278206557 0.608937263 0.500000000 0.721793473 0.391062707 0.000000000 0.699588060 0.250000000 0.000000000 0.300411940 0.750000000 0.500000000 0.199598417 0.250000000 0.500000000 0.800401568 0.750000000 0.500000000 0.082921132 0.136132896 0.500000000 0.917078853 0.863867104 0.500000000 0.917078853 0.636132836 0.500000000 0.082921162 0.363867134 0.000000000 0.582922995 0.136127144 0.000000000 0.417077035 0.863872886 0.000000000 0.417077065 0.636127174 0.000000000 0.582922935 0.363872826 0.000000000 0.147209421 0.950776219 0.000000000 0.852790594 0.049223803 0.000000000 0.852790534 0.450776190 0.000000000 0.147209466 0.549223840 0.500000000 0.647215426 0.950776398 0.500000000 0.352784544 0.049223613 0.500000000 0.352784604 0.450776398 0.500000000 0.647215426 0.549223602 0.000000000 0.322443128 0.250000000 0.000000000 0.677556872 0.750000000 0.500000000 0.822440684 0.250000000 0.500000000 0.177559301 0.750000000 **************************************************************************************************************************************************************************** Output Standardize_cell using , tprimitive=0, no_idealize=0): Basis vectors: a 15.14842 0.00000 0.00000 b 0.00000 3.41600 0.00000 c 0.00000 0.00000 12.12331 Atomic points: 73 0.10894 0.00000 0.22179 73 0.89106 0.00000 0.77821 73 0.60894 0.00000 0.77821 73 0.39106 0.00000 0.22179 73 0.10894 0.50000 0.72179 73 0.89106 0.50000 0.27821 73 0.60894 0.50000 0.27821 73 0.39106 0.50000 0.72179 28 0.25000 0.00000 0.69959 28 0.75000 0.00000 0.30041 28 0.25000 0.50000 0.19960 28 0.75000 0.50000 0.80040 16 0.13613 0.50000 0.08292 16 0.86387 0.50000 0.91708 16 0.63613 0.50000 0.91708 16 0.36387 0.50000 0.08292 16 0.13613 0.00000 0.58292 16 0.86387 0.00000 0.41708 16 0.63613 0.00000 0.41708 16 0.36387 0.00000 0.58292 16 0.95078 0.00000 0.14721 16 0.04922 0.00000 0.85279 16 0.45078 0.00000 0.85279 16 0.54922 0.00000 0.14721 16 0.95078 0.50000 0.64722 16 0.04922 0.50000 0.35278 16 0.45078 0.50000 0.35278 16 0.54922 0.50000 0.64722 16 0.25000 0.00000 0.32244 16 0.75000 0.00000 0.67756 16 0.25000 0.50000 0.82244 16 0.75000 0.50000 0.17756 ************************************************************************************************************************************************************************************** Thanking you, *Arijit SinhaJunior Research FellowJNCASR (Theoretical Sciences Unit),Jakkur, Bangalore(India).* On Wed, Dec 9, 2020 at 5:56 PM Atsushi Togo <atz...@gm...> wrote: > Hi, > > You can loosen the symmetry search tolerance (e.g. symprec=1e-3). > > Togo > > On Wed, Dec 9, 2020 at 8:31 PM Arijit Sinha <ari...@gm...> > wrote: > > > > Dear Users and Experts, > > I am new in spglib but my material which has a symmetry of Cmcm is not > getting captured correctly by spglib in python it is jumbling up the > lattice vectors order given in poscar (but FINDSYM showing the correct > symmetry) below I am attaching the code as well as the files please tell me > if it is my mistake or something else. > > -- > > Thanking you, > > > > Arijit Sinha > > Junior Research Fellow > > JNCASR (Theoretical Sciences Unit), > > Jakkur, Bangalore(India). > > > > > > _______________________________________________ > > Spglib-users mailing list > > Spg...@li... > > https://lists.sourceforge.net/lists/listinfo/spglib-users > > > > -- > Atsushi Togo > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users > |
|
From: Atsushi T. <atz...@gm...> - 2020-12-09 12:26:33
|
Hi, You can loosen the symmetry search tolerance (e.g. symprec=1e-3). Togo On Wed, Dec 9, 2020 at 8:31 PM Arijit Sinha <ari...@gm...> wrote: > > Dear Users and Experts, > I am new in spglib but my material which has a symmetry of Cmcm is not getting captured correctly by spglib in python it is jumbling up the lattice vectors order given in poscar (but FINDSYM showing the correct symmetry) below I am attaching the code as well as the files please tell me if it is my mistake or something else. > -- > Thanking you, > > Arijit Sinha > Junior Research Fellow > JNCASR (Theoretical Sciences Unit), > Jakkur, Bangalore(India). > > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
|
From: Arijit S. <ari...@gm...> - 2020-12-09 11:31:06
|
Dear Users and Experts, I am new in spglib but my material which has a symmetry of Cmcm is not getting captured correctly by spglib in python it is jumbling up the lattice vectors order given in poscar (but FINDSYM showing the correct symmetry) below I am attaching the code as well as the files please tell me if it is my mistake or something else. -- Thanking you, *Arijit SinhaJunior Research FellowJNCASR (Theoretical Sciences Unit),Jakkur, Bangalore(India).* |
|
From: Atsushi T. <atz...@gm...> - 2020-08-07 00:28:41
|
Hi,
I tested and it was OK.
What I did is on Ubuntu 18.04.4 LTS (GNU/Linux 4.15.0-106-generic x86_64),
% conda create -n spglib-test -c conda-forge python=2.7
% pip install spglib
Togo
On Fri, Aug 7, 2020 at 4:54 AM xxliu <xx...@ph...> wrote:
>
> Dear all,
>
> I try to use the newest version 1.16 now.
> When I run python setup.py install --user
> With python3.6 it can run successfully.
> But with python2.7 there is an error:
>
>
> 7
> -I/home/fkp/xxliu/anaconda2/lib/python2.7/site-packages/numpy/core/include
> -c ../src/spin.c -o build/temp.linux-x86_64-2.7/../src/spin.o
> ../src/spin.c: In function ‘spn_get_operations_with_site_tensors’:
> ../src/spin.c:207:8: warning: ‘is_found’ may be used uninitialized in
> this function [-Wmaybe-uninitialized]
> if (is_found) {
> ^
> ../src/spin.c:158:31: note: ‘is_found’ was declared here
> int i, j, k, sign, num_sym, is_found;
> ^~~~~~~~
> gcc -pthread -B /home/fkp/xxliu/anaconda2/compiler_compat
> -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
> -Wall -Wstrict-prototypes -fPIC -I../src
> -I/home/fkp/xxliu/anaconda2/include/python2.7
> -I/home/fkp/xxliu/anaconda2/lib/python2.7/site-packages/numpy/core/include
> -c ../src/spg_database.c -o
> build/temp.linux-x86_64-2.7/../src/spg_database.o
> gcc -pthread -B /home/fkp/xxliu/anaconda2/compiler_compat
> -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
> -Wall -Wstrict-prototypes -fPIC -I../src
> -I/home/fkp/xxliu/anaconda2/include/python2.7
> -I/home/fkp/xxliu/anaconda2/lib/python2.7/site-packages/numpy/core/include
> -c ../src/spglib.c -o build/temp.linux-x86_64-2.7/../src/spglib.o
> gcc -pthread -B /home/fkp/xxliu/anaconda2/compiler_compat
> -Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
> -Wall -Wstrict-prototypes -fPIC -I../src
> -I/home/fkp/xxliu/anaconda2/include/python2.7
> -I/home/fkp/xxliu/anaconda2/lib/python2.7/site-packages/numpy/core/include
> -c ../src/symmetry.c -o build/temp.linux-x86_64-2.7/../src/symmetry.o
> gcc -pthread -shared -B /home/fkp/xxliu/anaconda2/compiler_compat
> -L/home/fkp/xxliu/anaconda2/lib -Wl,-rpath=/home/fkp/xxliu/anaconda2/lib
> -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/_spglib.o
> build/temp.linux-x86_64-2.7/../src/arithmetic.o
> build/temp.linux-x86_64-2.7/../src/cell.o
> build/temp.linux-x86_64-2.7/../src/delaunay.o
> build/temp.linux-x86_64-2.7/../src/debug.o
> build/temp.linux-x86_64-2.7/../src/determination.o
> build/temp.linux-x86_64-2.7/../src/hall_symbol.o
> build/temp.linux-x86_64-2.7/../src/kgrid.o
> build/temp.linux-x86_64-2.7/../src/kpoint.o
> build/temp.linux-x86_64-2.7/../src/mathfunc.o
> build/temp.linux-x86_64-2.7/../src/niggli.o
> build/temp.linux-x86_64-2.7/../src/overlap.o
> build/temp.linux-x86_64-2.7/../src/pointgroup.o
> build/temp.linux-x86_64-2.7/../src/primitive.o
> build/temp.linux-x86_64-2.7/../src/refinement.o
> build/temp.linux-x86_64-2.7/../src/sitesym_database.o
> build/temp.linux-x86_64-2.7/../src/site_symmetry.o
> build/temp.linux-x86_64-2.7/../src/spacegroup.o
> build/temp.linux-x86_64-2.7/../src/spin.o
> build/temp.linux-x86_64-2.7/../src/spg_database.o
> build/temp.linux-x86_64-2.7/../src/spglib.o
> build/temp.linux-x86_64-2.7/../src/symmetry.o
> -L/home/fkp/xxliu/anaconda2/lib -lpython2.7 -o
> build/lib.linux-x86_64-2.7/spglib/_spglib.so
> /home/fkp/xxliu/anaconda2/compiler_compat/ld:
> build/temp.linux-x86_64-2.7/_spglib.o: unable to initialize decompress
> status for section .debug_info
> /home/fkp/xxliu/anaconda2/compiler_compat/ld:
> build/temp.linux-x86_64-2.7/_spglib.o: unable to initialize decompress
> status for section .debug_info
> /home/fkp/xxliu/anaconda2/compiler_compat/ld:
> build/temp.linux-x86_64-2.7/_spglib.o: unable to initialize decompress
> status for section .debug_info
> /home/fkp/xxliu/anaconda2/compiler_compat/ld:
> build/temp.linux-x86_64-2.7/_spglib.o: unable to initialize decompress
> status for section .debug_info
> build/temp.linux-x86_64-2.7/_spglib.o: file not recognized: file format
> not recognized
> collect2: error: ld returned 1 exit status
> error: command 'gcc' failed with exit status 1
>
> Can it run under python2.7?
>
> Best,
> Xiaoxiong
>
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users
--
Atsushi Togo
|
|
From: xxliu <xx...@ph...> - 2020-08-06 19:54:10
|
Dear all,
I try to use the newest version 1.16 now.
When I run python setup.py install --user
With python3.6 it can run successfully.
But with python2.7 there is an error:
7
-I/home/fkp/xxliu/anaconda2/lib/python2.7/site-packages/numpy/core/include
-c ../src/spin.c -o build/temp.linux-x86_64-2.7/../src/spin.o
../src/spin.c: In function ‘spn_get_operations_with_site_tensors’:
../src/spin.c:207:8: warning: ‘is_found’ may be used uninitialized in
this function [-Wmaybe-uninitialized]
if (is_found) {
^
../src/spin.c:158:31: note: ‘is_found’ was declared here
int i, j, k, sign, num_sym, is_found;
^~~~~~~~
gcc -pthread -B /home/fkp/xxliu/anaconda2/compiler_compat
-Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
-Wall -Wstrict-prototypes -fPIC -I../src
-I/home/fkp/xxliu/anaconda2/include/python2.7
-I/home/fkp/xxliu/anaconda2/lib/python2.7/site-packages/numpy/core/include
-c ../src/spg_database.c -o
build/temp.linux-x86_64-2.7/../src/spg_database.o
gcc -pthread -B /home/fkp/xxliu/anaconda2/compiler_compat
-Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
-Wall -Wstrict-prototypes -fPIC -I../src
-I/home/fkp/xxliu/anaconda2/include/python2.7
-I/home/fkp/xxliu/anaconda2/lib/python2.7/site-packages/numpy/core/include
-c ../src/spglib.c -o build/temp.linux-x86_64-2.7/../src/spglib.o
gcc -pthread -B /home/fkp/xxliu/anaconda2/compiler_compat
-Wl,--sysroot=/ -fno-strict-aliasing -g -O2 -DNDEBUG -g -fwrapv -O3
-Wall -Wstrict-prototypes -fPIC -I../src
-I/home/fkp/xxliu/anaconda2/include/python2.7
-I/home/fkp/xxliu/anaconda2/lib/python2.7/site-packages/numpy/core/include
-c ../src/symmetry.c -o build/temp.linux-x86_64-2.7/../src/symmetry.o
gcc -pthread -shared -B /home/fkp/xxliu/anaconda2/compiler_compat
-L/home/fkp/xxliu/anaconda2/lib -Wl,-rpath=/home/fkp/xxliu/anaconda2/lib
-Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-2.7/_spglib.o
build/temp.linux-x86_64-2.7/../src/arithmetic.o
build/temp.linux-x86_64-2.7/../src/cell.o
build/temp.linux-x86_64-2.7/../src/delaunay.o
build/temp.linux-x86_64-2.7/../src/debug.o
build/temp.linux-x86_64-2.7/../src/determination.o
build/temp.linux-x86_64-2.7/../src/hall_symbol.o
build/temp.linux-x86_64-2.7/../src/kgrid.o
build/temp.linux-x86_64-2.7/../src/kpoint.o
build/temp.linux-x86_64-2.7/../src/mathfunc.o
build/temp.linux-x86_64-2.7/../src/niggli.o
build/temp.linux-x86_64-2.7/../src/overlap.o
build/temp.linux-x86_64-2.7/../src/pointgroup.o
build/temp.linux-x86_64-2.7/../src/primitive.o
build/temp.linux-x86_64-2.7/../src/refinement.o
build/temp.linux-x86_64-2.7/../src/sitesym_database.o
build/temp.linux-x86_64-2.7/../src/site_symmetry.o
build/temp.linux-x86_64-2.7/../src/spacegroup.o
build/temp.linux-x86_64-2.7/../src/spin.o
build/temp.linux-x86_64-2.7/../src/spg_database.o
build/temp.linux-x86_64-2.7/../src/spglib.o
build/temp.linux-x86_64-2.7/../src/symmetry.o
-L/home/fkp/xxliu/anaconda2/lib -lpython2.7 -o
build/lib.linux-x86_64-2.7/spglib/_spglib.so
/home/fkp/xxliu/anaconda2/compiler_compat/ld:
build/temp.linux-x86_64-2.7/_spglib.o: unable to initialize decompress
status for section .debug_info
/home/fkp/xxliu/anaconda2/compiler_compat/ld:
build/temp.linux-x86_64-2.7/_spglib.o: unable to initialize decompress
status for section .debug_info
/home/fkp/xxliu/anaconda2/compiler_compat/ld:
build/temp.linux-x86_64-2.7/_spglib.o: unable to initialize decompress
status for section .debug_info
/home/fkp/xxliu/anaconda2/compiler_compat/ld:
build/temp.linux-x86_64-2.7/_spglib.o: unable to initialize decompress
status for section .debug_info
build/temp.linux-x86_64-2.7/_spglib.o: file not recognized: file format
not recognized
collect2: error: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
Can it run under python2.7?
Best,
Xiaoxiong
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From: Atsushi T. <atz...@gm...> - 2020-07-30 12:46:50
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I guess you didn't install your git version of spglib. You probably use other spglib version in your system to run the test. Togo On Thu, Jul 30, 2020 at 9:38 PM fatemeh haddadi <fat...@gm...> wrote: > > I ran the test using: > Python test_spglib.py > > So from "git log" I get: > > commit 612b0475d5a745eeb9b238655e03e72d9c5710b7 (HEAD -> develop, origin/develop, origin/HEAD) > Merge: a493d02 a7a2cce > Author: Atsushi Togo <atz...@gm...> > Date: Sun Jul 19 20:57:48 2020 +0900 > > Merge branch 'symopts-dataset' into develop > > commit a7a2ccedcdb382c6634d276a27a04e6b69c7cc74 > Author: Atsushi Togo <atz...@gm...> > Date: Sun Jul 19 20:55:02 2020 +0900 > > Updated symmetry_operations in spg_database.c > > Sets of symmetry operations in Hall numbers 212, 213, 214 started with (E|t) of non-zero t. Now they start with (E|0). This was made by subtracting t from all symmetry operations. > > commit a493d0298cbc52ee388dd82861bb0a3d00972a4b > Merge: 6751d37 49b50f5 > Author: Atsushi Togo <atz...@gm...> > Date: Sat Jul 18 21:48:50 2020 +0900 > > Merge branch 'develop' of github.com:spglib/spglib into develop > > Merge branch 'symopts-dataset' into develop > > > Fatemeh > > On Thu, Jul 30, 2020 at 2:03 PM Atsushi Togo <atz...@gm...> wrote: >> >> The test runs for the python spglib. It's independent from spglib C-API. >> How did you run the test? >> If you git clone, can you tell me the following information? >> >> % git log >> >> to see the commit hash something below. >> >> commit eec99c1296f9799f7ab62d4e4520d05b04663d3a >> Merge: 38ee5b6 2e050b3 >> Author: Atsushi Togo <atz...@gm...> >> Date: Wed Apr 29 00:22:57 2020 +0900 >> >> Merge branch 'develop' into rc >> >> Togo >> >> On Thu, Jul 30, 2020 at 6:54 PM fatemeh haddadi >> <fat...@gm...> wrote: >> > >> > Sure. >> > I have ubuntu 18.04. >> > I used the procedure below: >> > https://spglib.github.io/spglib/install.html >> > >> > Downloaded it using git clone and compiled it using cmake. >> > In the last line I used: >> > make DESTDIR=. install >> > >> > Maybe that is the problem because I don't see any lib directory. >> > >> > Fatemeh >> > >> > On Thu, Jul 30, 2020 at 11:36 AM Atsushi Togo <atz...@gm...> wrote: >> >> >> >> I can't reproduce. Can you give more details? >> >> Such as your computer system, how you installed it, ... >> >> >> >> Togo >> >> >> >> On Thu, Jul 30, 2020 at 4:32 PM fatemeh haddadi >> >> <fat...@gm...> wrote: >> >> > >> >> > Hi, >> >> > >> >> > It's 1.15.1. >> >> > >> >> > Fatemeh >> >> > >> >> > On Thu, Jul 30, 2020 at 2:49 AM Atsushi Togo <atz...@gm...> wrote: >> >> >> >> >> >> Hi, >> >> >> >> >> >> Thanks for your report. >> >> >> Could you tell which version do you use? >> >> >> >> >> >> Togo >> >> >> >> >> >> On Thu, Jul 30, 2020 at 1:06 AM fatemeh haddadi >> >> >> <fat...@gm...> wrote: >> >> >> > >> >> >> > Dear all, >> >> >> > >> >> >> > I am new to python and spglib. I'm facing a problem and wonder if anyone can help. >> >> >> > I just installed spglib and tested test_spglib.py at python/test/. Here is the output: >> >> >> > >> >> >> > test_find_primitive (__main__.TestSpglib) ... ok >> >> >> > test_get_symmetry_dataset (__main__.TestSpglib) ... FAIL >> >> >> > test_refine_cell (__main__.TestSpglib) ... FAIL >> >> >> > test_standardize_cell_and_pointgroup (__main__.TestSpglib) ... ok >> >> >> > test_standardize_cell_from_primitive (__main__.TestSpglib) ... ok >> >> >> > test_standardize_cell_to_primitive (__main__.TestSpglib) ... ok >> >> >> > >> >> >> > ====================================================================== >> >> >> > FAIL: test_get_symmetry_dataset (__main__.TestSpglib) >> >> >> > ---------------------------------------------------------------------- >> >> >> > Traceback (most recent call last): >> >> >> > File "test_spglib.py", line 105, in test_get_symmetry_dataset >> >> >> > self.assertEqual(w, w_ref, msg=("%s" % fname)) >> >> >> > AssertionError: /home/fhaddadi/spglib/python/test/data/distorted/POSCAR-11 >> >> >> > >> >> >> > ====================================================================== >> >> >> > FAIL: test_refine_cell (__main__.TestSpglib) >> >> >> > ---------------------------------------------------------------------- >> >> >> > Traceback (most recent call last): >> >> >> > File "test_spglib.py", line 184, in test_refine_cell >> >> >> > self.assertEqual(dataset_1['number'], spgnum, msg=("%s" % fname)) >> >> >> > AssertionError: /home/fhaddadi/spglib/python/test/data/distorted/POSCAR-11 >> >> >> > >> >> >> > ---------------------------------------------------------------------- >> >> >> > Ran 6 tests in 16.439s >> >> >> > >> >> >> > FAILED (failures=2) >> >> >> > >> >> >> > There are two failures as you see. >> >> >> > Can anyone tell me what the problem is? >> >> >> > Thank you in advance. >> >> >> > >> >> >> > >> >> >> > >> >> >> > Fatemeh Haddadi >> >> >> > Doctoral assistant >> >> >> > Theory and Simulation of Materials >> >> >> > École Polytechnique Fédérale de Lausanne >> >> >> > >> >> >> > >> >> >> > _______________________________________________ >> >> >> > Spglib-users mailing list >> >> >> > Spg...@li... >> >> >> > https://lists.sourceforge.net/lists/listinfo/spglib-users >> >> >> >> >> >> >> >> >> >> >> >> -- >> >> >> Atsushi Togo >> >> >> >> >> >> >> >> -- >> >> Atsushi Togo >> >> >> >> >> >> _______________________________________________ >> >> Spglib-users mailing list >> >> Spg...@li... >> >> https://lists.sourceforge.net/lists/listinfo/spglib-users >> > >> > _______________________________________________ >> > Spglib-users mailing list >> > Spg...@li... >> > https://lists.sourceforge.net/lists/listinfo/spglib-users >> >> >> >> -- >> Atsushi Togo >> >> >> _______________________________________________ >> Spglib-users mailing list >> Spg...@li... >> https://lists.sourceforge.net/lists/listinfo/spglib-users > > _______________________________________________ > Spglib-users mailing list > Spg...@li... > https://lists.sourceforge.net/lists/listinfo/spglib-users -- Atsushi Togo |
