spglib-users — Mailing list for the spglib users

Re: [Spglib-users] test_get_symmetry_dataset & test_refine_cell failure

[fatemeh h. <fat...@gm...>]

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
>

Re: [Spglib-users] test_get_symmetry_dataset & test_refine_cell failure

[Atsushi T. <atz...@gm...>]

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

Re: [Spglib-users] test_get_symmetry_dataset & test_refine_cell failure

[fatemeh h. <fat...@gm...>]

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
>

Re: [Spglib-users] test_get_symmetry_dataset & test_refine_cell failure

[Atsushi T. <atz...@gm...>]

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

Re: [Spglib-users] test_get_symmetry_dataset & test_refine_cell failure

[Atsushi T. <atz...@gm...>]

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

[Spglib-users] test_get_symmetry_dataset & test_refine_cell failure

[fatemeh h. <fat...@gm...>]

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] doubts in compilation of spglib - Reg

[singaravelan T R <trs...@gm...>]

Dear all,
i couldn't get the meaning of the commands in
*" make DESTDIR=/some/where install"* in the compilation of spglib.

when i compiled like this "$ *make DESTDIR=/home/local install*"  it
doesn't work it showed the error as follows:* $ make: *** No rule to make
target 'install '.  Stop.*
(note : compiler says like this. where i created an empty folder called
local within the home directory. Why it doesn't work ?)

So i organised the following what i have done and output on the screen in a
sequence. Please help me in this regard.

1) I have downloaded spglib within the home directory as follows:

*/home/sky/spglib-develop*

2) issued the command: mkdir _build && _build ,

/*home/sky/spglib-develop/_build *

_build directory also formed

3) when i given this command:  cmake -DCMAKE_INSTALL_PREFIX="" ..



* Build type: Release-- Configuring done-- Generating done-- Build files
have been written to: /home/sky/spglib-develop/_build*

4) make command:
[  2%] Building C object CMakeFiles/symspg_static.dir/src/arithmetic.o
[  4%] Building C object CMakeFiles/symspg_static.dir/src/cell.o
[  6%] Building C object CMakeFiles/symspg_static.dir/src/debug.o
[  9%] Building C object CMakeFiles/symspg_static.dir/src/delaunay.o
[ 11%] Building C object CMakeFiles/symspg_static.dir/src/determination.o
[ 13%] Building C object CMakeFiles/symspg_static.dir/src/hall_symbol.o
[ 15%] Building C object CMakeFiles/symspg_static.dir/src/kgrid.o
[ 18%] Building C object CMakeFiles/symspg_static.dir/src/kpoint.o
/home/sky/spglib-develop/src/kpoint.c: In function ‘
get_dense_ir_reciprocal_mesh_normal’:
/home/sky/spglib-develop/src/kpoint.c:651:0: warning: ignoring #pragma omp
parallel [-Wunk
nown-pragmas]
#pragma omp parallel for private(j, grid_point_rot, address_double,
address_double_rot)
^
/home/sky/spglib-develop/src/kpoint.c: In function ‘
get_dense_ir_reciprocal_mesh_distortio
n’:
/home/sky/spglib-develop/src/kpoint.c:698:0: warning: ignoring #pragma omp
parallel [-Wunk
nown-pragmas]
#pragma omp parallel for private(j, k, grid_point_rot, address_double,
address_double_rot
^
/home/sky/spglib-develop/src/kpoint.c: In function ‘get_dense_num_ir’:
/home/sky/spglib-develop/src/kpoint.c:751:0: warning: ignoring #pragma omp
parallel [-Wunk
nown-pragmas]
#pragma omp parallel for reduction(+:num_ir)
^
[ 20%] Building C object CMakeFiles/symspg_static.dir/src/mathfunc.o
[ 22%] Building C object CMakeFiles/symspg_static.dir/src/niggli.o
[ 25%] Building C object CMakeFiles/symspg_static.dir/src/overlap.o
[ 27%] Building C object CMakeFiles/symspg_static.dir/src/pointgroup.o
[ 29%] Building C object CMakeFiles/symspg_static.dir/src/primitive.o
[ 31%] Building C object CMakeFiles/symspg_static.dir/src/refinement.o
[ 34%] Building C object CMakeFiles/symspg_static.dir/src/site_symmetry.o
[ 36%] Building C object CMakeFiles/symspg_static.dir/src/sitesym_database.o
[ 38%] Building C object CMakeFiles/symspg_static.dir/src/spacegroup.o
[ 40%] Building C object CMakeFiles/symspg_static.dir/src/spg_database.o
[ 43%] Building C object CMakeFiles/symspg_static.dir/src/spglib.o
[ 45%] Building C object CMakeFiles/symspg_static.dir/src/spin.o
/home/sky/spglib-develop/src/spin.c: In function ‘
spn_get_operations_with_site_tensors’:
/home/sky/spglib-develop/src/spin.c:207:8: warning: ‘is_found’ may be used
uninitialized i
n this function [-Wmaybe-uninitialized]
    if (is_found) {
       ^
/home/sky/spglib-develop/src/spin.c:158:31: note: ‘is_found’ was declared
here
  int i, j, k, sign, num_sym, is_found;
                              ^
[ 47%] Building C object CMakeFiles/symspg_static.dir/src/symmetry.o
[ 50%] Linking C static library libsymspg.a
[ 50%] Built target symspg_static
[ 52%] Building C object CMakeFiles/symspg.dir/src/arithmetic.o
[ 54%] Building C object CMakeFiles/symspg.dir/src/cell.o
[ 56%] Building C object CMakeFiles/symspg.dir/src/debug.o
[ 59%] Building C object CMakeFiles/symspg.dir/src/delaunay.o
[ 61%] Building C object CMakeFiles/symspg.dir/src/determination.o
[ 63%] Building C object CMakeFiles/symspg.dir/src/hall_symbol.o
[ 65%] Building C object CMakeFiles/symspg.dir/src/kgrid.o
[ 68%] Building C object CMakeFiles/symspg.dir/src/kpoint.o
/home/sky/spglib-develop/src/kpoint.c: In function ‘
get_dense_ir_reciprocal_mesh_normal’:
/home/sky/spglib-develop/src/kpoint.c:651:0: warning: ignoring #pragma omp
parallel [-Wunk
nown-pragmas]
#pragma omp parallel for private(j, grid_point_rot, address_double,
address_double_rot)
^
/home/sky/spglib-develop/src/kpoint.c: In function ‘
get_dense_ir_reciprocal_mesh_distortio
n’:
/home/sky/spglib-develop/src/kpoint.c:698:0: warning: ignoring #pragma omp
parallel [-Wunk
nown-pragmas]
#pragma omp parallel for private(j, k, grid_point_rot, address_double,
address_double_rot
^
/home/sky/spglib-develop/src/kpoint.c: In function ‘get_dense_num_ir’:
/home/sky/spglib-develop/src/kpoint.c:751:0: warning: ignoring #pragma omp
parallel [-Wunk
nown-pragmas]
#pragma omp parallel for reduction(+:num_ir)
^
[ 70%] Building C object CMakeFiles/symspg.dir/src/mathfunc.o
[ 72%] Building C object CMakeFiles/symspg.dir/src/niggli.o
[ 75%] Building C object CMakeFiles/symspg.dir/src/overlap.o
[ 77%] Building C object CMakeFiles/symspg.dir/src/pointgroup.o
[ 79%] Building C object CMakeFiles/symspg.dir/src/primitive.o
[ 81%] Building C object CMakeFiles/symspg.dir/src/refinement.o
[ 84%] Building C object CMakeFiles/symspg.dir/src/site_symmetry.o
[ 86%] Building C object CMakeFiles/symspg.dir/src/sitesym_database.o
[ 88%] Building C object CMakeFiles/symspg.dir/src/spacegroup.o
[ 90%] Building C object CMakeFiles/symspg.dir/src/spg_database.o
[ 93%] Building C object CMakeFiles/symspg.dir/src/spglib.o
[ 95%] Building C object CMakeFiles/symspg.dir/src/spin.o
/home/sky/spglib-develop/src/spin.c: In function ‘
spn_get_operations_with_site_tensors’:
/home/sky/spglib-develop/src/spin.c:207:8: warning: ‘is_found’ may be used
uninitialized i
n this function [-Wmaybe-uninitialized]
    if (is_found) {
       ^
/home/sky/spglib-develop/src/spin.c:158:31: note: ‘is_found’ was declared
here
  int i, j, k, sign, num_sym, is_found;
                              ^
[ 97%] Building C object CMakeFiles/symspg.dir/src/symmetry.o
[100%] Linking C shared library libsymspg.so
[100%] Built target symspg

5) make DESTDIR=/home/local install

*make: *** No rule to make target 'install '.  Stop.*

compiler says like this. where i created an empty folder called local
within the home directory. Why it doesn't work ?

*I also tried other options:*

6) make install  but it doesn't work.













*[ 50%] Built target symspg_static [100%] Built target symspg Install the
project... -- Install configuration: "Release" -- Installing:
/lib/libsymspg.so.1.15.1 CMake Error at cmake_install.cmake:48 (file):
 file INSTALL cannot copy file
 "/home/sky/spglib-develop/_build/libsymspg.so.1.15.1" to
 "/lib/libsymspg.so.1.15.1". Makefile:126: recipe for target 'install'
failed make: *** [install] Error 1*

*Question : Why i got error like above ?*

with thanks,
Singaravelan T R

Re: [Spglib-users] Inconsistency in `get_symmetry_dataset`

[Atsushi T. <atz...@gm...>]

This will be replied at github issue,
https://github.com/spglib/spglib/issues/105.

Togo

On Thu, Jun 11, 2020 at 1:18 AM Gaël Donval via Spglib-users
<spg...@li...> wrote:
>
> Hi,
>
> I'm using spglib 1.15.1's python interface to identify the sets of
> transformations needed to go back-and-forth between original supercells
> and spglib's standard and primitive representations in non-orthorhombic
> systems.
>
> It *works* for 3 (non-ortho) systems but not on the 4th one (attached).
> Note that you need to relax the symprec tolerance to 2e-4 for it to
> work. Hall number should be 15.
>
> To make things very simple, I have reasons to believe the
> transformation matrix provided by `get_symmetry_dataset` is wrong. It
> is different from P by directly solving:
>
> (a, b, c) P = (a', b', c').
>
> Note that the origin shift is zero and that by "different" I really
> mean "different": `transformation_matrix` is diagonal (or can be made
> so by simple axis swaps) and P is not. This is not a transpose or
> numerical accuracy problem.
>
> So is it a bug or did I forget an important part of the calculation?
>
> Thanks.
>
> Best regards,
> Gaël
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] Inconsistency in `get_symmetry_dataset`

[Gaël D. <gg...@ba...>]

Hi,

I'm using spglib 1.15.1's python interface to identify the sets of
transformations needed to go back-and-forth between original supercells
and spglib's standard and primitive representations in non-orthorhombic 
systems.

It *works* for 3 (non-ortho) systems but not on the 4th one (attached).
Note that you need to relax the symprec tolerance to 2e-4 for it to
work. Hall number should be 15.

To make things very simple, I have reasons to believe the
transformation matrix provided by `get_symmetry_dataset` is wrong. It
is different from P by directly solving:

(a, b, c) P = (a', b', c').

Note that the origin shift is zero and that by "different" I really
mean "different": `transformation_matrix` is diagonal (or can be made
so by simple axis swaps) and P is not. This is not a transpose or
numerical accuracy problem.

So is it a bug or did I forget an important part of the calculation?

Thanks.

Best regards,
Gaël

Re: [Spglib-users] Bug in symmetry detection in spglib 1.15

[Atsushi T. <atz...@gm...>]

Hi Lorenzo,
(I forgot to reply to spglib-users.)

Thanks for your report. This issue will be easier to discuss on spglib
github issues, https://github.com/spglib/spglib/issues, so could you
open an issue on this? In addition, I want to ask you not to use ASE
but use the tuple format written here,
https://spglib.github.io/spglib/python-spglib.html#crystal-structure-cell.

Togo

On Sat, Jun 6, 2020 at 1:25 AM Lorenzo Monacelli
<mes...@gm...> wrote:
>
> Dear developers,
>
> I think I found a bug that is affecting the newest version of spglib
> (version 1.14 works), or at least the python interface.
>
> When I ask the symmetry group of a structure by with a python script, by
> passing a threshold, it correctly identify the group.
>
> However, when I ask the symmetry operations, it seems to ignore the
> threshold parameters.
>
> I attach an example that works properly with spglib==1.14.1 but not with
> spglib==1.15.1.
>
> The example requires ASE installed to read the ".cif" file. It is a
> slightly displaced C2/c group structure.
>
> If I ask the symmetry group without specifying a threshold, it correctly
> says it is P1 (1), while if I use a small threshold (0.05) it recognizes
> the C2/c (4) group.
>
> Then I ask the code the symmetries and the rotations, by specifying the
> same threshold that allows to recognize the C2/c group, but it returns
> just the identity matrix.
>
> As I told you, if I use an older version of spglib, the code works properly.
>
>
> Is it a bug? will it be solved in the next release?
>
> Thanks for your attention,
>
> Best regards,
>
> Lorenzo Monacelli
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] Bug in symmetry detection in spglib 1.15

[Lorenzo M. <mes...@gm...>]

Dear developers,

I think I found a bug that is affecting the newest version of spglib 
(version 1.14 works), or at least the python interface.

When I ask the symmetry group of a structure by with a python script, by 
passing a threshold, it correctly identify the group.

However, when I ask the symmetry operations, it seems to ignore the 
threshold parameters.

I attach an example that works properly with spglib==1.14.1 but not with 
spglib==1.15.1.

The example requires ASE installed to read the ".cif" file. It is a 
slightly displaced C2/c group structure.

If I ask the symmetry group without specifying a threshold, it correctly 
says it is P1 (1), while if I use a small threshold (0.05) it recognizes 
the C2/c (4) group.

Then I ask the code the symmetries and the rotations, by specifying the 
same threshold that allows to recognize the C2/c group, but it returns 
just the identity matrix.

As I told you, if I use an older version of spglib, the code works properly.


Is it a bug? will it be solved in the next release?

Thanks for your attention,

Best regards,

Lorenzo Monacelli

[Spglib-users] spglib github repository has been moved to spglib github organization

[Atsushi T. <atz...@gm...>]

Dear spglib users and developers,

Spglib github repository has been moved to spglib github organization.
https://github.com/spglib/spglib

Togo

-- 
Atsushi Togo

[Spglib-users] spglib release v1.15.1 due to a critical bug

[Atsushi T. <atz...@gm...>]

Dear spglib users,

I released spglib release v1.15.1 because a critical bug was found.
This bug was in the collinear magnetic type symmetry finding. This bug
probably appeared in v1.15.0, so if you hit this bug, please update
spglib to v1.15.1.

ChangeLog is found here,
https://github.com/atztogo/spglib/blob/master/ChangeLog

Togo

-- 
Atsushi Togo

[Spglib-users] spglib v1.15 has been released.

[Atsushi T. <atz...@gm...>]

Dear spglib users,

Spglib v1.15 has been released.
ChangeLog is found at https://github.com/atztogo/spglib/blob/master/ChangeLog.

Togo

-- 
Atsushi Togo

Re: [Spglib-users] Potential bug

[Atsushi T. <atz...@gm...>]

Your crystal structure is different from the first one you gave.
Now for it, I get #227 as follows. So probably you make some mistake
in using spglib, but not the bug.

In [1]: lattice = [[5, 5, 0], [5, 0, 5], [0, 5, 5]]

In [2]: positions = [[0, 0, 0], [0.25, 0.25, 0.25]]

In [3]: numbers = [1, 1]

In [4]: import spglib

In [5]: cell = (lattice, positions, numbers)

In [6]: spglib.get_spacegroup(cell)
Out[6]: 'Fd-3m (227)'

Togo

On Wed, Mar 25, 2020 at 9:46 PM Norbert Janik <trz...@gm...> wrote:
>
> Hi,
>
> Because diamond structure (#227 space group) has primitive cell and follows:
> lattice (for example):
> 5 5 0
> 5 0 5
> 0 5 5
> (number '5' can be replaced with anything).
> And atomic positions:
> 0 0 0
> 0.25 0.25 0.25
> (one type of atoms).
>
> Link to information about this space group:
> http://lampx.tugraz.at/~hadley/ss1/crystalstructure/structures/diamond/diamond.php
>
> For provided values, I get result #71, when it should be #227.
>
> Could you please take a look at it? It'd be very thankful.
>
> Norbert
>
>
>
> śr., 25 mar 2020 o 12:51 Atsushi Togo <atz...@gm...> napisał(a):
>>
>> Hi,
>>
>> Please tell the reason why you think so.
>>
>> Togo
>>
>> On Wed, Mar 25, 2020 at 7:35 PM Norbert Janik <trz...@gm...> wrote:
>> >
>> > Hello,
>> >
>> > I am currently checking possibilities of this library, which seems to be very mighty tool.
>> > During my symmetry check tests I think I found a bug with #227 space group symmetry.
>> > When I give input like this (which should be #227):
>> > lattice:
>> > 0 5 5
>> > 5 0 5
>> > 5 5 0
>> > atom positions (all of them are the same type):
>> > 0 0 0
>> > 0.5 0.5 0.5
>> > 0.25 0.25 0.25
>> > 0.75 0.25 0.75
>> >
>> > I am getting as a result #74. I was using function "spg_get_international".
>> > If there is a mistake in my input please let me know, otherwise please inform me when the bug will be gone.
>> >
>> > Best Regards,
>> > Norbert
>> > _______________________________________________
>> > 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



-- 
Atsushi Togo

Re: [Spglib-users] Potential bug

[Atsushi T. <atz...@gm...>]

Hi,

Please tell the reason why you think so.

Togo

On Wed, Mar 25, 2020 at 7:35 PM Norbert Janik <trz...@gm...> wrote:
>
> Hello,
>
> I am currently checking possibilities of this library, which seems to be very mighty tool.
> During my symmetry check tests I think I found a bug with #227 space group symmetry.
> When I give input like this (which should be #227):
> lattice:
> 0 5 5
> 5 0 5
> 5 5 0
> atom positions (all of them are the same type):
> 0 0 0
> 0.5 0.5 0.5
> 0.25 0.25 0.25
> 0.75 0.25 0.75
>
> I am getting as a result #74. I was using function "spg_get_international".
> If there is a mistake in my input please let me know, otherwise please inform me when the bug will be gone.
>
> Best Regards,
> Norbert
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] Potential bug

[Norbert J. <trz...@gm...>]

Hello,

I am currently checking possibilities of this library, which seems to be
very mighty tool.
During my symmetry check tests I think I found a bug with #227 space group
symmetry.
When I give input like this (which should be #227):
lattice:
0 5 5
5 0 5
5 5 0
atom positions (all of them are the same type):
0 0 0
0.5 0.5 0.5
0.25 0.25 0.25
0.75 0.25 0.75

I am getting as a result #74. I was using function "spg_get_international".
If there is a mistake in my input please let me know, otherwise please
inform me when the bug will be gone.

Best Regards,
Norbert

[Spglib-users] Clarification of Crystallographic Choice and Rotation

[Daniel M. <dan...@gm...>]

Hi Spg Mailing LIst,

I"m a bit confused with regard to the Transformation Matrix. I"m following
the example given in the documentation:
https://atztogo.github.io/spglib/definition.html#crystallographic-choice-and-rigid-rotation

The original lattice is:

lattice = [[7.17851431, 0, 0],  # a
           [0, 3.99943947, 0],  # b
           [0, 0, 8.57154746]]  # c


The modified lattice is constructed by swapping 'a' and 'b':

lattice = [[8.57154746, 0, 0],  # a
           [0, 3.99943947, 0],  # b
           [0, 0, 7.17851431]]  # c


My confusion is with regards of the 'transformation matrix':

Transformation matrix:
   0  0  1
   0  1  0
  -1  0  0


According to Equation 6
<https://atztogo.github.io/spglib/definition.html#equation-transformation-matrix>
I
should be able to recover the original matrix via:

(a b c) = (as bs cs) P

However, in my case the Transformation Matrix above, does not restore the
original lattice, rather it generates:

matrix([[ 0. , 0. , 8.57154746],
             [ 0. , 3.99943947, 0. ],
             [-7.17851431, 0. , 0. ]])

This is similar, but not the exact same as my original lattice. I'm
guessing the two are equivalent. In my use case I want to recover the exact
original lattice, is this possible, perhaps with a final step that puts the
lattice in a 'standard' form?

Best,

Daniel

Re: [Spglib-users] Space Group is wrongly identified

[Zhiyong Z. <zhi...@gm...>]

In the context of Bravais lattice, The 3 atoms make up a “basis”, and the basis is repeated in a simple cubic lattice.


Sent from my iPhone

> On Jul 20, 2019, at 00:56, Atsushi Togo <atz...@gm...> wrote:
> 
> Why do you think so?
> 
> Togo
> 
>> On Sat, Jul 20, 2019 at 6:54 AM Zhiyong Zhu <zhi...@gm...> wrote:
>> 
>> Dear Togo,
>> 
>> As I understand, this is a simple cubic structure, and space group should be 221. Am I wrong?
>> 
>> Zhiyong
>> 
>> Sent from my iPhone
>> 
>>> On Jul 20, 2019, at 00:44, Atsushi Togo <atz...@gm...> wrote:
>>> 
>>> Hi,
>>> 
>>> What is expected space group?
>>> 
>>> Togo
>>> 
>>>> On Sat, Jul 20, 2019 at 6:39 AM Zhiyong Zhu <zhi...@gm...> wrote:
>>>> 
>>>> Dear All,
>>>> 
>>>> 
>>>> I just found that the following simple cubic cell is wrongly identified as a P1 triclinic structure. Can you please help to check if I am doing something wrong?
>>>> 
>>>> 
>>>> VASP POSCAR file:
>>>> 
>>>> =========
>>>> 
>>>> POSCAR
>>>>  4.000
>>>>    1.000    0.000    0.000
>>>>    0.000    1.000    0.000
>>>>    0.000    0.000    1.000
>>>>  Pt P
>>>>   1 2
>>>> Direct
>>>> 0.000  0.000  0.000
>>>> 0.100  0.200  0.300
>>>> 0.500  0.200  0.300
>>>> 
>>>> =========
>>>> 
>>>> 
>>>> The cell parameter of the “get_symmetry_dataset” method:
>>>> 
>>>> =========
>>>> 
>>>> (array([[4., 0., 0.],
>>>>      [0., 4., 0.],
>>>>      [0., 0., 4.]]), array([[0. , 0. , 0. ],
>>>>      [0.1, 0.2, 0.3],
>>>>      [0.5, 0.2, 0.3]]), [1, 2, 2], [0, 0, 0])
>>>> 
>>>> =========
>>>> 
>>>> 
>>>> The results I got is:
>>>> 
>>>> =========
>>>> 
>>>> {'number': 1, 'hall_number': 1, 'international': 'P1', 'hall': 'P 1', 'choice': '', 'transformation_matrix': array([[1., 0., 0.],
>>>> 
>>>>      [0., 1., 0.],
>>>> 
>>>>      [0., 0., 1.]]), 'origin_shift': array([0., 0., 0.]), 'rotations': array([[[1, 0, 0],
>>>> 
>>>>       [0, 1, 0],
>>>> 
>>>>       [0, 0, 1]]], dtype=int32), 'translations': array([[0., 0., 0.]]), 'wyckoffs': ['a', 'a', 'a'], 'site_symmetry_symbols': ['1', '1', '1'], 'equivalent_atoms': array([0, 1, 2], dtype=int32), 'mapping_to_primitive': array([0, 1, 2], dtype=int32), 'std_lattice': array([[4.0000000e+00, 0.0000000e+00, 0.0000000e+00],
>>>> 
>>>>      [2.4492936e-16, 4.0000000e+00, 0.0000000e+00],
>>>> 
>>>>      [2.4492936e-16, 2.4492936e-16, 4.0000000e+00]]), 'std_types': array([1, 2, 2], dtype=int32), 'std_positions': array([[0. , 0. , 0. ],
>>>> 
>>>>      [0.1, 0.2, 0.3],
>>>> 
>>>>      [0.5, 0.2, 0.3]]), 'std_rotation_matrix': array([[1., 0., 0.],
>>>> 
>>>>      [0., 1., 0.],
>>>> 
>>>>      [0., 0., 1.]]), 'std_mapping_to_primitive': array([0, 1, 2], dtype=int32), 'pointgroup': '1'}
>>>> 
>>>> =========
>>>> 
>>>> 
>>>> The version of spglib I am using is 1.13.0.post6.
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> Sent from my iPhone
>>>> _______________________________________________
>>>> 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...
>>> 
>>> 
>>> _______________________________________________
>>> 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...
> 
> 
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users

Re: [Spglib-users] Space Group is wrongly identified

[Atsushi T. <atz...@gm...>]

Why do you think so?

Togo

On Sat, Jul 20, 2019 at 6:54 AM Zhiyong Zhu <zhi...@gm...> wrote:
>
> Dear Togo,
>
> As I understand, this is a simple cubic structure, and space group should be 221. Am I wrong?
>
> Zhiyong
>
> Sent from my iPhone
>
> > On Jul 20, 2019, at 00:44, Atsushi Togo <atz...@gm...> wrote:
> >
> > Hi,
> >
> > What is expected space group?
> >
> > Togo
> >
> >> On Sat, Jul 20, 2019 at 6:39 AM Zhiyong Zhu <zhi...@gm...> wrote:
> >>
> >> Dear All,
> >>
> >>
> >> I just found that the following simple cubic cell is wrongly identified as a P1 triclinic structure. Can you please help to check if I am doing something wrong?
> >>
> >>
> >> VASP POSCAR file:
> >>
> >> =========
> >>
> >> POSCAR
> >>   4.000
> >>     1.000    0.000    0.000
> >>     0.000    1.000    0.000
> >>     0.000    0.000    1.000
> >>   Pt P
> >>    1 2
> >> Direct
> >>  0.000  0.000  0.000
> >>  0.100  0.200  0.300
> >>  0.500  0.200  0.300
> >>
> >> =========
> >>
> >>
> >> The cell parameter of the “get_symmetry_dataset” method:
> >>
> >> =========
> >>
> >> (array([[4., 0., 0.],
> >>       [0., 4., 0.],
> >>       [0., 0., 4.]]), array([[0. , 0. , 0. ],
> >>       [0.1, 0.2, 0.3],
> >>       [0.5, 0.2, 0.3]]), [1, 2, 2], [0, 0, 0])
> >>
> >> =========
> >>
> >>
> >> The results I got is:
> >>
> >> =========
> >>
> >> {'number': 1, 'hall_number': 1, 'international': 'P1', 'hall': 'P 1', 'choice': '', 'transformation_matrix': array([[1., 0., 0.],
> >>
> >>       [0., 1., 0.],
> >>
> >>       [0., 0., 1.]]), 'origin_shift': array([0., 0., 0.]), 'rotations': array([[[1, 0, 0],
> >>
> >>        [0, 1, 0],
> >>
> >>        [0, 0, 1]]], dtype=int32), 'translations': array([[0., 0., 0.]]), 'wyckoffs': ['a', 'a', 'a'], 'site_symmetry_symbols': ['1', '1', '1'], 'equivalent_atoms': array([0, 1, 2], dtype=int32), 'mapping_to_primitive': array([0, 1, 2], dtype=int32), 'std_lattice': array([[4.0000000e+00, 0.0000000e+00, 0.0000000e+00],
> >>
> >>       [2.4492936e-16, 4.0000000e+00, 0.0000000e+00],
> >>
> >>       [2.4492936e-16, 2.4492936e-16, 4.0000000e+00]]), 'std_types': array([1, 2, 2], dtype=int32), 'std_positions': array([[0. , 0. , 0. ],
> >>
> >>       [0.1, 0.2, 0.3],
> >>
> >>       [0.5, 0.2, 0.3]]), 'std_rotation_matrix': array([[1., 0., 0.],
> >>
> >>       [0., 1., 0.],
> >>
> >>       [0., 0., 1.]]), 'std_mapping_to_primitive': array([0, 1, 2], dtype=int32), 'pointgroup': '1'}
> >>
> >> =========
> >>
> >>
> >> The version of spglib I am using is 1.13.0.post6.
> >>
> >>
> >>
> >>
> >>
> >> Sent from my iPhone
> >> _______________________________________________
> >> 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...
> >
> >
> > _______________________________________________
> > 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...

Re: [Spglib-users] Space Group is wrongly identified

[Zhiyong Z. <zhi...@gm...>]

Dear Togo,

As I understand, this is a simple cubic structure, and space group should be 221. Am I wrong?

Zhiyong

Sent from my iPhone

> On Jul 20, 2019, at 00:44, Atsushi Togo <atz...@gm...> wrote:
> 
> Hi,
> 
> What is expected space group?
> 
> Togo
> 
>> On Sat, Jul 20, 2019 at 6:39 AM Zhiyong Zhu <zhi...@gm...> wrote:
>> 
>> Dear All,
>> 
>> 
>> I just found that the following simple cubic cell is wrongly identified as a P1 triclinic structure. Can you please help to check if I am doing something wrong?
>> 
>> 
>> VASP POSCAR file:
>> 
>> =========
>> 
>> POSCAR
>>   4.000
>>     1.000    0.000    0.000
>>     0.000    1.000    0.000
>>     0.000    0.000    1.000
>>   Pt P
>>    1 2
>> Direct
>>  0.000  0.000  0.000
>>  0.100  0.200  0.300
>>  0.500  0.200  0.300
>> 
>> =========
>> 
>> 
>> The cell parameter of the “get_symmetry_dataset” method:
>> 
>> =========
>> 
>> (array([[4., 0., 0.],
>>       [0., 4., 0.],
>>       [0., 0., 4.]]), array([[0. , 0. , 0. ],
>>       [0.1, 0.2, 0.3],
>>       [0.5, 0.2, 0.3]]), [1, 2, 2], [0, 0, 0])
>> 
>> =========
>> 
>> 
>> The results I got is:
>> 
>> =========
>> 
>> {'number': 1, 'hall_number': 1, 'international': 'P1', 'hall': 'P 1', 'choice': '', 'transformation_matrix': array([[1., 0., 0.],
>> 
>>       [0., 1., 0.],
>> 
>>       [0., 0., 1.]]), 'origin_shift': array([0., 0., 0.]), 'rotations': array([[[1, 0, 0],
>> 
>>        [0, 1, 0],
>> 
>>        [0, 0, 1]]], dtype=int32), 'translations': array([[0., 0., 0.]]), 'wyckoffs': ['a', 'a', 'a'], 'site_symmetry_symbols': ['1', '1', '1'], 'equivalent_atoms': array([0, 1, 2], dtype=int32), 'mapping_to_primitive': array([0, 1, 2], dtype=int32), 'std_lattice': array([[4.0000000e+00, 0.0000000e+00, 0.0000000e+00],
>> 
>>       [2.4492936e-16, 4.0000000e+00, 0.0000000e+00],
>> 
>>       [2.4492936e-16, 2.4492936e-16, 4.0000000e+00]]), 'std_types': array([1, 2, 2], dtype=int32), 'std_positions': array([[0. , 0. , 0. ],
>> 
>>       [0.1, 0.2, 0.3],
>> 
>>       [0.5, 0.2, 0.3]]), 'std_rotation_matrix': array([[1., 0., 0.],
>> 
>>       [0., 1., 0.],
>> 
>>       [0., 0., 1.]]), 'std_mapping_to_primitive': array([0, 1, 2], dtype=int32), 'pointgroup': '1'}
>> 
>> =========
>> 
>> 
>> The version of spglib I am using is 1.13.0.post6.
>> 
>> 
>> 
>> 
>> 
>> Sent from my iPhone
>> _______________________________________________
>> 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...
> 
> 
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users

Re: [Spglib-users] Space Group is wrongly identified

[Atsushi T. <atz...@gm...>]

Hi,

What is expected space group?

Togo

On Sat, Jul 20, 2019 at 6:39 AM Zhiyong Zhu <zhi...@gm...> wrote:
>
> Dear All,
>
>
> I just found that the following simple cubic cell is wrongly identified as a P1 triclinic structure. Can you please help to check if I am doing something wrong?
>
>
> VASP POSCAR file:
>
> =========
>
> POSCAR
>    4.000
>      1.000    0.000    0.000
>      0.000    1.000    0.000
>      0.000    0.000    1.000
>    Pt P
>     1 2
> Direct
>   0.000  0.000  0.000
>   0.100  0.200  0.300
>   0.500  0.200  0.300
>
> =========
>
>
> The cell parameter of the “get_symmetry_dataset” method:
>
> =========
>
> (array([[4., 0., 0.],
>        [0., 4., 0.],
>        [0., 0., 4.]]), array([[0. , 0. , 0. ],
>        [0.1, 0.2, 0.3],
>        [0.5, 0.2, 0.3]]), [1, 2, 2], [0, 0, 0])
>
> =========
>
>
> The results I got is:
>
> =========
>
> {'number': 1, 'hall_number': 1, 'international': 'P1', 'hall': 'P 1', 'choice': '', 'transformation_matrix': array([[1., 0., 0.],
>
>        [0., 1., 0.],
>
>        [0., 0., 1.]]), 'origin_shift': array([0., 0., 0.]), 'rotations': array([[[1, 0, 0],
>
>         [0, 1, 0],
>
>         [0, 0, 1]]], dtype=int32), 'translations': array([[0., 0., 0.]]), 'wyckoffs': ['a', 'a', 'a'], 'site_symmetry_symbols': ['1', '1', '1'], 'equivalent_atoms': array([0, 1, 2], dtype=int32), 'mapping_to_primitive': array([0, 1, 2], dtype=int32), 'std_lattice': array([[4.0000000e+00, 0.0000000e+00, 0.0000000e+00],
>
>        [2.4492936e-16, 4.0000000e+00, 0.0000000e+00],
>
>        [2.4492936e-16, 2.4492936e-16, 4.0000000e+00]]), 'std_types': array([1, 2, 2], dtype=int32), 'std_positions': array([[0. , 0. , 0. ],
>
>        [0.1, 0.2, 0.3],
>
>        [0.5, 0.2, 0.3]]), 'std_rotation_matrix': array([[1., 0., 0.],
>
>        [0., 1., 0.],
>
>        [0., 0., 1.]]), 'std_mapping_to_primitive': array([0, 1, 2], dtype=int32), 'pointgroup': '1'}
>
> =========
>
>
> The version of spglib I am using is 1.13.0.post6.
>
>
>
>
>
> Sent from my iPhone
> _______________________________________________
> 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...

[Spglib-users] Space Group is wrongly identified

[Zhiyong Z. <zhi...@gm...>]

Dear All,

I just found that the following simple cubic cell is wrongly identified as a P1 triclinic structure. Can you please help to check if I am doing something wrong?

VASP POSCAR file:
=========
POSCAR
   4.000
     1.000    0.000    0.000
     0.000    1.000    0.000
     0.000    0.000    1.000
   Pt P
    1 2
Direct
  0.000  0.000  0.000
  0.100  0.200  0.300
  0.500  0.200  0.300
=========

The cell parameter of the “get_symmetry_dataset” method:
=========
(array([[4., 0., 0.],
       [0., 4., 0.],
       [0., 0., 4.]]), array([[0. , 0. , 0. ],
       [0.1, 0.2, 0.3],
       [0.5, 0.2, 0.3]]), [1, 2, 2], [0, 0, 0])
=========

The results I got is:
=========
{'number': 1, 'hall_number': 1, 'international': 'P1', 'hall': 'P 1', 'choice': '', 'transformation_matrix': array([[1., 0., 0.],
       [0., 1., 0.],
       [0., 0., 1.]]), 'origin_shift': array([0., 0., 0.]), 'rotations': array([[[1, 0, 0],
        [0, 1, 0],
        [0, 0, 1]]], dtype=int32), 'translations': array([[0., 0., 0.]]), 'wyckoffs': ['a', 'a', 'a'], 'site_symmetry_symbols': ['1', '1', '1'], 'equivalent_atoms': array([0, 1, 2], dtype=int32), 'mapping_to_primitive': array([0, 1, 2], dtype=int32), 'std_lattice': array([[4.0000000e+00, 0.0000000e+00, 0.0000000e+00],
       [2.4492936e-16, 4.0000000e+00, 0.0000000e+00],
       [2.4492936e-16, 2.4492936e-16, 4.0000000e+00]]), 'std_types': array([1, 2, 2], dtype=int32), 'std_positions': array([[0. , 0. , 0. ],
       [0.1, 0.2, 0.3],
       [0.5, 0.2, 0.3]]), 'std_rotation_matrix': array([[1., 0., 0.],
       [0., 1., 0.],
       [0., 0., 1.]]), 'std_mapping_to_primitive': array([0, 1, 2], dtype=int32), 'pointgroup': '1'}
=========

The version of spglib I am using is 1.13.0.post6.




Sent from my iPhone

[Spglib-users] Spglib version 1.13.0 released

[Atsushi T. <atz...@gm...>]

Dear spglib users,

Spglib version 1.13.0 was released. There are two fixes: the
standardization of orthorhombic system and irreducible k-point search
for special cases. See
https://github.com/atztogo/spglib/blob/master/ChangeLog.

Togo

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

[Spglib-users] Spacegroup of Gallium Oxide

[Ankit S. <ank...@gm...>]

Hi,
I downloaded the Gallium Oxide cif file from materials project for the
primitive unit cell. The conventional cell has the space group of C2/m
which matches with that given in *materials project*. But for the primitive
cell, when I use spglib to find the spacegroup the output is *Cm*, but the
cif file shows the space group to be *P1.*

It would be of great help if someone can help me with this. Attached is the
cif file for both the conventional and the primitive unit cell of Gallium
Oxide.

Thank You,
Ankit Sharma
University at Buffalo

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