spglib-users — Mailing list for the spglib users

Re: [Spglib-users] What is "stabilized" irreducible k-point set

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

Hi,

I am sorry for being late to reply.
stabilized means stabilizer which is the k-point. This means that
symmetry operations are restribed by

Rk = k + G

where R is a rotation operation in reciprocal space and G is the
reciprocal lattice vector.
Note that functions for reciprocal space will be obsolete.

Togo

On Sat, Feb 8, 2025 at 6:19 PM Keith Refson <kr...@gm...> wrote:
>
> Hello.
>
> Exactly what does
>
> spg_get_stabilized_reciprocal_mesh
>
> compute? Could someone please point me at a formal definition of the "stabilized" mesh computed by this function.
>
> Keith Refson
>
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] What is "stabilized" irreducible k-point set

[Keith R. <kr...@gm...>]

Hello.

Exactly what does


      |spg_get_stabilized_reciprocal_mesh|

compute? Could someone please point me at a formal definition of the 
"stabilized" mesh computed by this function.

Keith Refson

Re: [Spglib-users] About the usage of the layer group

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

Hi,

Unfortunately, the layer group functionality is not supported at this time.
The layer group is a normalizer of the space group if I understand it
correctly. If you are interested in it and haven't studied it, you can
find good information in International Tables for Crystallography.

Togo

On Thu, Jan 9, 2025 at 10:09 PM zhouchao via Spglib-users
<spg...@li...> wrote:
>
> Dear spglib Developers,
>
> I hope this email finds you well. My name is chao zhou, and I am currently studying the symmetry of two-dimensional (2D) materials. I am new to using spglib and wanted to ask for your advice.
>
> Could you please guide me on how to determine the layer group of a 2D material using spglib? If there is some examples?
>
> Thank you very much for your time and assistance.
>
> Best regards,
> Chao Zhou
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] About the usage of the layer group

[<994...@qq...>]

Dear spglib Developers,

I hope this email finds you well. My name is chao zhou, and I am currently studying the symmetry of two-dimensional (2D) materials. I am new to using spglib and wanted to ask for your advice.

Could you please guide me on how to determine the layer group of a 2D material using spglib? If there is some examples?

Thank you very much for your time and assistance.

Best regards,
Chao Zhou

Re: [Spglib-users] How to get equivalent_atoms using fortran code

[VeiWANG <wa...@ic...>]


I got it. Thanks again. 

> 
> Yes, almost. A slight change may exist in spg_get_symmetry_with_collinear_spin.
> 
> Togo
> 
> On Thu, Jun 15, 2023 at 3:31 PM VeiWANG via Spglib-users
> <spg...@li...> wrote:
>> Hi Togo sensei,
>> Thank for your valuable advice. I have got the equivalent_atoms list by via spg_get_dataset function. By the way, I still use spglig.1.x. Is the spglig.2.x fully compatible with spglig.1.x for fortran interface?
>> Best,
>> Wang
>> 下面是被转发的邮件：
>> 发件人: Atsushi Togo <atz...@gm...>
>> 主题: 回复：[Spglib-users] How to get equivalent_atoms using fortran code
>> 日期: 2023年6月15日 GMT+8 09:14:30
>> 收件人: spg...@li...
>> 回复给: spg...@li...
>> Hi Wang,
>> Without spin, spg_get_dataset, and with spin, spg_get_magnetic_dataset
>> is recommended to use. However for the latter, the fortran interface
>> has not been written yet. A possible route is using
>> spg_get_symmetry_with_site_tensors. The interface is
>> function spg_get_symmetry_with_site_tensors(rotation, translation, &
>> & equivalent_atoms, primitive_lattice, spin_flips, max_size, lattice, &
>> & position, types, tensors, tensor_rank, num_atom, with_time_reversal, &
>> & is_axial, symprec) bind(c)
>> import c_int, c_double
>> integer(c_int), intent(out) :: rotation(3, 3, *)
>> real(c_double), intent(out) :: translation(3, *)
>> integer(c_int), intent(out) :: equivalent_atoms(*)
>> real(c_double), intent(out) :: primitive_lattice(3, 3)
>> integer(c_int), intent(out) :: spin_flips(*)
>> integer(c_int), intent(in), value :: max_size
>> real(c_double), intent(in) :: lattice(3, 3), position(3, *)
>> integer(c_int), intent(in) :: types(*)
>> real(c_double), intent(in) :: tensors(*)
>> integer(c_int), intent(in), value :: tensor_rank
>> integer(c_int), intent(in), value :: num_atom
>> integer(c_int), intent(in), value :: with_time_reversal
>> integer(c_int), intent(in), value :: is_axial
>> real(c_double), intent(in), value :: symprec
>> integer(c_int) :: spg_get_symmetry_with_site_tensors
>> end function spg_get_symmetry_with_site_tensors
>> Unfortunately, I haven't wrote any example of it, but I hope it can be
>> guessed from C-api doc.
>> https://spglib.readthedocs.io/en/latest/api.html#spg-get-symmetry-with-site-tensors
>> https://spglib.readthedocs.io/en/latest/development/magnetic_symmetry_flags.html#magnetic-action-flags
>> If you want to specify collinear spin, the array length is the number
>> of atoms, tensor_rank=0, is_axial=0, and with_time_reversal =1. For
>> the non-collinear case, the array length is the number-of-atoms x 3,
>> tensor_rank=1, is_axial=1, and with_time_reversal =1. These are the
>> typical choices.
>> The spin_flips array stores if the spin is flipped or not by the found
>> symmety operations. Therefore the length is the number of symmetry
>> operations. The number of symmetry operations is unknown before
>> running this function, so you have to prepare large enough symmetry
>> operations related arrays, whose length is considered to inform to
>> spglib by max_size.
>> Togo
>> On Tue, Jun 13, 2023 at 8:29 PM VeiWANG via Spglib-users
>> <spg...@li...> wrote:
>> Dear all,
>> I am currently trying to use Fortran code to obtain the equivalent_atoms using spglib, with input variables of lattice vectors and atom positions. Could anyone provide guidance on how to implement this?
>> If I understand correctly, to obtain the equivalent_atoms, I first simply call the spg_get_symmetry function, which requires input variables of max_size, lattice, position, types, num_atom, and optional parameter symprec. And then I use the spg_get_symmetry_with_collinear_spin function, which takes an additional input variable of spins and outputs equivalent_atoms directly from the function. I was wondering if anyone has experience using spin information with spglib and if so, how to incorporate it into the function. Thank you for your assistance.
>> Best,
>> Wang
>> _______________________________________________
>> 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

Re: [Spglib-users] Fwd: How to get equivalent_atoms using fortran code

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

Yes, almost. A slight change may exist in spg_get_symmetry_with_collinear_spin.

Togo

On Thu, Jun 15, 2023 at 3:31 PM VeiWANG via Spglib-users
<spg...@li...> wrote:
>
> Hi Togo sensei,
>
> Thank for your valuable advice. I have got the equivalent_atoms list by via spg_get_dataset function. By the way, I still use spglig.1.x. Is the spglig.2.x fully compatible with spglig.1.x for fortran interface?
>
> Best,
> Wang
>
>
> 下面是被转发的邮件：
>
> 发件人: Atsushi Togo <atz...@gm...>
> 主题: 回复：[Spglib-users] How to get equivalent_atoms using fortran code
> 日期: 2023年6月15日 GMT+8 09:14:30
> 收件人: spg...@li...
> 回复给: spg...@li...
>
> Hi Wang,
>
> Without spin, spg_get_dataset, and with spin, spg_get_magnetic_dataset
> is recommended to use. However for the latter, the fortran interface
> has not been written yet. A possible route is using
> spg_get_symmetry_with_site_tensors. The interface is
>
> function spg_get_symmetry_with_site_tensors(rotation, translation, &
> & equivalent_atoms, primitive_lattice, spin_flips, max_size, lattice, &
> & position, types, tensors, tensor_rank, num_atom, with_time_reversal, &
> & is_axial, symprec) bind(c)
> import c_int, c_double
> integer(c_int), intent(out) :: rotation(3, 3, *)
> real(c_double), intent(out) :: translation(3, *)
> integer(c_int), intent(out) :: equivalent_atoms(*)
> real(c_double), intent(out) :: primitive_lattice(3, 3)
> integer(c_int), intent(out) :: spin_flips(*)
> integer(c_int), intent(in), value :: max_size
> real(c_double), intent(in) :: lattice(3, 3), position(3, *)
> integer(c_int), intent(in) :: types(*)
> real(c_double), intent(in) :: tensors(*)
> integer(c_int), intent(in), value :: tensor_rank
> integer(c_int), intent(in), value :: num_atom
> integer(c_int), intent(in), value :: with_time_reversal
> integer(c_int), intent(in), value :: is_axial
> real(c_double), intent(in), value :: symprec
> integer(c_int) :: spg_get_symmetry_with_site_tensors
> end function spg_get_symmetry_with_site_tensors
>
> Unfortunately, I haven't wrote any example of it, but I hope it can be
> guessed from C-api doc.
> https://spglib.readthedocs.io/en/latest/api.html#spg-get-symmetry-with-site-tensors
> https://spglib.readthedocs.io/en/latest/development/magnetic_symmetry_flags.html#magnetic-action-flags
>
> If you want to specify collinear spin, the array length is the number
> of atoms, tensor_rank=0, is_axial=0, and with_time_reversal =1. For
> the non-collinear case, the array length is the number-of-atoms x 3,
> tensor_rank=1, is_axial=1, and with_time_reversal =1. These are the
> typical choices.
> The spin_flips array stores if the spin is flipped or not by the found
> symmety operations. Therefore the length is the number of symmetry
> operations. The number of symmetry operations is unknown before
> running this function, so you have to prepare large enough symmetry
> operations related arrays, whose length is considered to inform to
> spglib by max_size.
>
> Togo
>
> On Tue, Jun 13, 2023 at 8:29 PM VeiWANG via Spglib-users
> <spg...@li...> wrote:
>
>
> Dear all,
>
> I am currently trying to use Fortran code to obtain the equivalent_atoms using spglib, with input variables of lattice vectors and atom positions. Could anyone provide guidance on how to implement this?
>
> If I understand correctly, to obtain the equivalent_atoms, I first simply call the spg_get_symmetry function, which requires input variables of max_size, lattice, position, types, num_atom, and optional parameter symprec. And then I use the spg_get_symmetry_with_collinear_spin function, which takes an additional input variable of spins and outputs equivalent_atoms directly from the function. I was wondering if anyone has experience using spin information with spglib and if so, how to incorporate it into the function. Thank you for your assistance.
>
> Best,
> Wang
> _______________________________________________
> 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] Fwd: How to get equivalent_atoms using fortran code

[VeiWANG <wa...@ic...>]

Hi Togo sensei,

Thank for your valuable advice. I have got the equivalent_atoms list by via spg_get_dataset function. By the way, I still use spglig.1.x. Is the spglig.2.x fully compatible with spglig.1.x for fortran interface?

Best,
Wang


> 下面是被转发的邮件：
> 
> 发件人: Atsushi Togo <atz...@gm...>
> 主题: 回复：[Spglib-users] How to get equivalent_atoms using fortran code
> 日期: 2023年6月15日 GMT+8 09:14:30
> 收件人: spg...@li...
> 回复给: spg...@li...
> 
> Hi Wang,
> 
> Without spin, spg_get_dataset, and with spin, spg_get_magnetic_dataset
> is recommended to use. However for the latter, the fortran interface
> has not been written yet. A possible route is using
> spg_get_symmetry_with_site_tensors. The interface is
> 
> function spg_get_symmetry_with_site_tensors(rotation, translation, &
> & equivalent_atoms, primitive_lattice, spin_flips, max_size, lattice, &
> & position, types, tensors, tensor_rank, num_atom, with_time_reversal, &
> & is_axial, symprec) bind(c)
> import c_int, c_double
> integer(c_int), intent(out) :: rotation(3, 3, *)
> real(c_double), intent(out) :: translation(3, *)
> integer(c_int), intent(out) :: equivalent_atoms(*)
> real(c_double), intent(out) :: primitive_lattice(3, 3)
> integer(c_int), intent(out) :: spin_flips(*)
> integer(c_int), intent(in), value :: max_size
> real(c_double), intent(in) :: lattice(3, 3), position(3, *)
> integer(c_int), intent(in) :: types(*)
> real(c_double), intent(in) :: tensors(*)
> integer(c_int), intent(in), value :: tensor_rank
> integer(c_int), intent(in), value :: num_atom
> integer(c_int), intent(in), value :: with_time_reversal
> integer(c_int), intent(in), value :: is_axial
> real(c_double), intent(in), value :: symprec
> integer(c_int) :: spg_get_symmetry_with_site_tensors
> end function spg_get_symmetry_with_site_tensors
> 
> Unfortunately, I haven't wrote any example of it, but I hope it can be
> guessed from C-api doc.
> https://spglib.readthedocs.io/en/latest/api.html#spg-get-symmetry-with-site-tensors
> https://spglib.readthedocs.io/en/latest/development/magnetic_symmetry_flags.html#magnetic-action-flags
> 
> If you want to specify collinear spin, the array length is the number
> of atoms, tensor_rank=0, is_axial=0, and with_time_reversal =1. For
> the non-collinear case, the array length is the number-of-atoms x 3,
> tensor_rank=1, is_axial=1, and with_time_reversal =1. These are the
> typical choices.
> The spin_flips array stores if the spin is flipped or not by the found
> symmety operations. Therefore the length is the number of symmetry
> operations. The number of symmetry operations is unknown before
> running this function, so you have to prepare large enough symmetry
> operations related arrays, whose length is considered to inform to
> spglib by max_size.
> 
> Togo
> 
> On Tue, Jun 13, 2023 at 8:29 PM VeiWANG via Spglib-users
> <spg...@li...> wrote:
>> 
>> Dear all,
>> 
>> I am currently trying to use Fortran code to obtain the equivalent_atoms using spglib, with input variables of lattice vectors and atom positions. Could anyone provide guidance on how to implement this?
>> 
>> If I understand correctly, to obtain the equivalent_atoms, I first simply call the spg_get_symmetry function, which requires input variables of max_size, lattice, position, types, num_atom, and optional parameter symprec. And then I use the spg_get_symmetry_with_collinear_spin function, which takes an additional input variable of spins and outputs equivalent_atoms directly from the function. I was wondering if anyone has experience using spin information with spglib and if so, how to incorporate it into the function. Thank you for your assistance.
>> 
>> Best,
>> Wang
>> _______________________________________________
>> 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] How to get equivalent_atoms using fortran code

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

Hi Wang,

Without spin, spg_get_dataset, and with spin, spg_get_magnetic_dataset
is recommended to use. However for the latter, the fortran interface
has not been written yet. A possible route is using
spg_get_symmetry_with_site_tensors. The interface is

function spg_get_symmetry_with_site_tensors(rotation, translation, &
& equivalent_atoms, primitive_lattice, spin_flips, max_size, lattice, &
& position, types, tensors, tensor_rank, num_atom, with_time_reversal, &
& is_axial, symprec) bind(c)
import c_int, c_double
integer(c_int), intent(out) :: rotation(3, 3, *)
real(c_double), intent(out) :: translation(3, *)
integer(c_int), intent(out) :: equivalent_atoms(*)
real(c_double), intent(out) :: primitive_lattice(3, 3)
integer(c_int), intent(out) :: spin_flips(*)
integer(c_int), intent(in), value :: max_size
real(c_double), intent(in) :: lattice(3, 3), position(3, *)
integer(c_int), intent(in) :: types(*)
real(c_double), intent(in) :: tensors(*)
integer(c_int), intent(in), value :: tensor_rank
integer(c_int), intent(in), value :: num_atom
integer(c_int), intent(in), value :: with_time_reversal
integer(c_int), intent(in), value :: is_axial
real(c_double), intent(in), value :: symprec
integer(c_int) :: spg_get_symmetry_with_site_tensors
end function spg_get_symmetry_with_site_tensors

Unfortunately, I haven't wrote any example of it, but I hope it can be
guessed from C-api doc.
https://spglib.readthedocs.io/en/latest/api.html#spg-get-symmetry-with-site-tensors
https://spglib.readthedocs.io/en/latest/development/magnetic_symmetry_flags.html#magnetic-action-flags

If you want to specify collinear spin, the array length is the number
of atoms, tensor_rank=0, is_axial=0, and with_time_reversal =1. For
the non-collinear case, the array length is the number-of-atoms x 3,
tensor_rank=1, is_axial=1, and with_time_reversal =1. These are the
typical choices.
The spin_flips array stores if the spin is flipped or not by the found
symmety operations. Therefore the length is the number of symmetry
operations. The number of symmetry operations is unknown before
running this function, so you have to prepare large enough symmetry
operations related arrays, whose length is considered to inform to
spglib by max_size.

Togo

On Tue, Jun 13, 2023 at 8:29 PM VeiWANG via Spglib-users
<spg...@li...> wrote:
>
> Dear all,
>
> I am currently trying to use Fortran code to obtain the equivalent_atoms using spglib, with input variables of lattice vectors and atom positions. Could anyone provide guidance on how to implement this?
>
> If I understand correctly, to obtain the equivalent_atoms, I first simply call the spg_get_symmetry function, which requires input variables of max_size, lattice, position, types, num_atom, and optional parameter symprec. And then I use the spg_get_symmetry_with_collinear_spin function, which takes an additional input variable of spins and outputs equivalent_atoms directly from the function. I was wondering if anyone has experience using spin information with spglib and if so, how to incorporate it into the function. Thank you for your assistance.
>
> Best,
> Wang
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] How to get equivalent_atoms using fortran code

[VeiWANG <wa...@ic...>]

Dear all,

I am currently trying to use Fortran code to obtain the equivalent_atoms using spglib, with input variables of lattice vectors and atom positions. Could anyone provide guidance on how to implement this?

If I understand correctly, to obtain the equivalent_atoms, I first simply call the spg_get_symmetry function, which requires input variables of max_size, lattice, position, types, num_atom, and optional parameter symprec. And then I use the spg_get_symmetry_with_collinear_spin function, which takes an additional input variable of spins and outputs equivalent_atoms directly from the function. I was wondering if anyone has experience using spin information with spglib and if so, how to incorporate it into the function. Thank you for your assistance.

Best,
Wang

Re: [Spglib-users] Irreducible Kpoints from array of arbitrary Kpoints

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

Hi,

Spglib doesn't provide it. It is expected to be done by users. Because
a user knows what the data is, it is easy to work on the data, but
given unknown data, it is difficult to design those functions.

Togo

On Wed, Mar 1, 2023 at 3:35 PM Ryan Hall <rya...@un...> wrote:
>
> To whom it may concern,
>
>
>
> A useful function in the spglib python wrapper is the get_ir_reciprocal_mesh and associated map function. As I understand, these methods operate on a structure to determine the set of irreducible mesh points from a Monkhorst-pack style mesh given by a tuple of ints.
>
> I wondered whether spglib provides similar functionality for determining the irreducible set of kpoints from a non-structured set of kpoints.
>
> E.g. instead of a mesh, the input would be be an Nx3 numpy array or array_like where each row corresponds to a kpoint in fractional coordinates. The function would then return the subset and/or mapping from this set to the irreducible set.
>
>
>
>
>
> Cheers,
>
>
>
> Ryan Hall.
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] Irreducible Kpoints from array of arbitrary Kpoints

[Ryan H. <rya...@un...>]

To whom it may concern,

A useful function in the spglib python wrapper is the get_ir_reciprocal_mesh and associated map function. As I understand, these methods operate on a structure to determine the set of irreducible mesh points from a Monkhorst-pack style mesh given by a tuple of ints.

I wondered whether spglib provides similar functionality for determining the irreducible set of kpoints from a non-structured set of kpoints.

E.g. instead of a mesh, the input would be be an Nx3 numpy array or array_like where each row corresponds to a kpoint in fractional coordinates. The function would then return the subset and/or mapping from this set to the irreducible set.


Cheers,

Ryan Hall.

[Spglib-users] Spglib v2.0 released

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

Dear spglib users,

We have released spglib v2.0. This is a major update.
The summary of the updates is presented at
https://spglib.github.io/spglib/releases.html.

We are under preparation for its conda-forge package, but it may take some time.

-- 
Atsushi Togo

[Spglib-users] spglib v2.0 will be released soon

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

Dear spglib users,

We are going to release spglib v2.0 in a few days. This is a major
update of spglib, so there may be bugs. So please do not update spglib
to v2.0 before you test it carefully. If your code (especially in
python) depends on spglib, but not fixed to a specific version of
spglib, to avoid automatic update of spglib, it is probably better to
set-up dependency as spglib<2.0.

Atsushi Togo

Re: [Spglib-users] spglib/spglib.h not generated

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

Hi,

You can get it at https://github.com/spglib/spglib.

Togo

On Fri, May 6, 2022 at 10:44 AM Safikul Islam
<saf...@gm...> wrote:
>
> Dear Sir,
>
>               I am trying to install spglib for the software thirdorder py. For this software spglib/spglib.h header file is needed. But when I am installing spglib then no spglib.h is generated. Could you please help me regarding this?
>
> Best Regards,
> Safikul,
> PhD Research Scholar.
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] spglib/spglib.h not generated

[Safikul I. <saf...@gm...>]

Dear Sir,

              I am trying to install spglib for the software thirdorder py.
For this software spglib/spglib.h header file is needed. But when I am
installing spglib then no spglib.h is generated. Could you please help me
regarding this?

Best Regards,
Safikul,
PhD Research Scholar.

Re: [Spglib-users] Can not find atoms related by space group symmetry

[Đorđe D. <dan...@ho...>]

Hello,

Yeah it does. Thank you very much.

Kind regards,

Đorđe

From: Atsushi Togo<mailto:atz...@gm...>
Sent: Tuesday 29 March 2022 09:10
To: spglib-users<mailto:spg...@li...>
Subject: Re: [Spglib-users] Can not find atoms related by space group symmetry

Hi,

I haven't tested your script, but

> Part of the code that does that should be:
> new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot]

Following your definition, rotation has to be transposed:

new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot].T)
+ translations[irot]

Does this fix your problem?

Togo

On Tue, Mar 29, 2022 at 3:44 PM Đorđe Dangić <dan...@ho...> wrote:
>
> Hello again,
>
>
>
> I apologize I accidently hit send.
>
>
>
> I apologize for the confusion. I was copy/paste-ing part from a larger code and I have not checked the script.  I am attaching the script with the email. Test contains the python code.
>
>
>
> Let’s say the position of an atom in the primitive cell in crystal coordinates is x1, and it is a component of the vector of all atomic positions inside primitive cell X. If I act with the space group symmetry on x1 I would get, as you said x’:
>
>
>
> x' = (R|t) x1 = Rx1 + t
>
>
>
> Part of the code that does that should be:
>
>
>
> new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot]
>
>
>
> Now, I would expect that x’ is also a position of some atom in the primitive cell, maybe translated by the lattice vector. If I compare x’ with each component of X I should get a match for some x2. That would mean that my original x1 that I transformed transforms to some other atomic position x2 (which could be the same). Now I could say that space group symmetry (R|t) maps atom x1 to atom x2. Am I correct in saying this? Matching of transformed and original atomic positions should be done with this part of the code:
>
>
>
>         for iat in range(natom):
>
>                 found = False
>
>                 for jat in range(natom):
>
>                         pos = new_pos[iat] - scaled_positions[jat]
>
>                         pos -= np.rint(pos)
>
>                         if(check_if_R(pos)):
>
>                                 atom_image[irot, iat] = jat
>
>                                 found = True
>
>                                 break
>
>
>
> I hope now you can run the code and see that I do not match all of the transformed atoms. Can you help me fix this?
>
>
>
> Kind regards,
>
>
>
> Đorđe
>
>
>
> From: Atsushi Togo
> Sent: Tuesday 29 March 2022 03:04
> To: spglib-users
> Subject: Re: [Spglib-users] Can not find atoms related by space group symmetry
>
>
>
> Hi,
>
> Please define what you want to do more clearly. For example,
>
> Given a space group operation (R|t), and a point x in crystallographic
> coordinates
>
> x' = (R|t) x = Rx + t
>
> Then what do you want to do?
>
> In addition, your script doesn't work as it is.
>
> Togo
>
> On Mon, Mar 28, 2022 at 4:26 PM Dorde Dangic <Dan...@ho...> wrote:
> >
> > Dear all,
> >
> > I am having trouble finding atoms related by a spacegroup symmetry. I am not sure what I am doing wrong. I am sending a script that I am using to find symmetry-related atoms.
> >
> > POSCAR:
> >
> >   H
> >   1.00000000
> >   0.59175841  -0.59175841  1.52600353
> >   0.59175841  0.59175841  1.52600353
> >   -0.59175841  -0.59175841  1.52600353
> >   H
> > 2
> > Direct
> >   0.00000000  0.00000000  0.00000000
> >   0.50000000  -0.25000000  0.25000000
> >
> > test.py:
> >
> > import numpy as np
> > import spglib
> > from phonopy.interface.calculator import read_crystal_structure
> >
> > # Function to check if the vector is the translational lattice vector
> > def check_if_R(vec):
> >         rvec = False
> >         for i in range(-1,2):
> >                 if not rvec:
> >                         for j in range(-1,2):
> >                                 if not rvec:
> >                                         for k in range(-1,2):
> >                                                 vec1 = vec + np.array([float(i), float(j), float(k)])
> >                                                 if(np.linalg.norm(vec1) < 1.0e-5):
> >                                                         rvec = True
> >                                                         break
> >         return rvec
> >
> > unitcell, _ = read_crystal_structure("POSCAR", interface_mode='vasp') # read in structure
> > cell = (unitcell.cell, unitcell.scaled_positions, unitcell.numbers)
> >
> > dataset = spglib.get_symmetry_dataset(cell, symprec=1e-5, angle_tolerance=-1.0, hall_number=0) # get datasets
> > rotations = dataset['rotations'].copy()
> > translations = dataset['translations'].copy()
> >
> > print(scaled_positions)
> >
> > atom_image = np.zeros((len(rotations), len(numbers))) + len(numbers) # array to store to which atom we go with symmetry
> > for irot in range(len(rotations)):
> >         new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot] # symmetry operation on the scaled positions
> >         for iat in range(natom): # Try to match rotated atom with the original set
> >                 found = False
> >                 for jat in range(natom):
> >                         pos = new_pos[iat] - scaled_positions[jat]
> >                         pos -= np.rint(pos)
> >                         if(check_if_R(pos)):
> >                                 atom_image[irot, iat] = jat
> >                                 found = True
> >                                 break
> >                 if(not found): # Print rotated atom if could not match
> >                         print(irot, iat)
> >                         print(new_pos[iat])
> > # Print atom images
> > print(atom_image)
> >
> > Could you please tell me what am I missing?
> >
> > Thank you for your help.
> > _______________________________________________
> > 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

Re: [Spglib-users] Can not find atoms related by space group symmetry

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

Hi,

I haven't tested your script, but

> Part of the code that does that should be:
> new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot]

Following your definition, rotation has to be transposed:

new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot].T)
+ translations[irot]

Does this fix your problem?

Togo

On Tue, Mar 29, 2022 at 3:44 PM Đorđe Dangić <dan...@ho...> wrote:
>
> Hello again,
>
>
>
> I apologize I accidently hit send.
>
>
>
> I apologize for the confusion. I was copy/paste-ing part from a larger code and I have not checked the script.  I am attaching the script with the email. Test contains the python code.
>
>
>
> Let’s say the position of an atom in the primitive cell in crystal coordinates is x1, and it is a component of the vector of all atomic positions inside primitive cell X. If I act with the space group symmetry on x1 I would get, as you said x’:
>
>
>
> x' = (R|t) x1 = Rx1 + t
>
>
>
> Part of the code that does that should be:
>
>
>
> new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot]
>
>
>
> Now, I would expect that x’ is also a position of some atom in the primitive cell, maybe translated by the lattice vector. If I compare x’ with each component of X I should get a match for some x2. That would mean that my original x1 that I transformed transforms to some other atomic position x2 (which could be the same). Now I could say that space group symmetry (R|t) maps atom x1 to atom x2. Am I correct in saying this? Matching of transformed and original atomic positions should be done with this part of the code:
>
>
>
>         for iat in range(natom):
>
>                 found = False
>
>                 for jat in range(natom):
>
>                         pos = new_pos[iat] - scaled_positions[jat]
>
>                         pos -= np.rint(pos)
>
>                         if(check_if_R(pos)):
>
>                                 atom_image[irot, iat] = jat
>
>                                 found = True
>
>                                 break
>
>
>
> I hope now you can run the code and see that I do not match all of the transformed atoms. Can you help me fix this?
>
>
>
> Kind regards,
>
>
>
> Đorđe
>
>
>
> From: Atsushi Togo
> Sent: Tuesday 29 March 2022 03:04
> To: spglib-users
> Subject: Re: [Spglib-users] Can not find atoms related by space group symmetry
>
>
>
> Hi,
>
> Please define what you want to do more clearly. For example,
>
> Given a space group operation (R|t), and a point x in crystallographic
> coordinates
>
> x' = (R|t) x = Rx + t
>
> Then what do you want to do?
>
> In addition, your script doesn't work as it is.
>
> Togo
>
> On Mon, Mar 28, 2022 at 4:26 PM Dorde Dangic <Dan...@ho...> wrote:
> >
> > Dear all,
> >
> > I am having trouble finding atoms related by a spacegroup symmetry. I am not sure what I am doing wrong. I am sending a script that I am using to find symmetry-related atoms.
> >
> > POSCAR:
> >
> >   H
> >   1.00000000
> >   0.59175841  -0.59175841  1.52600353
> >   0.59175841  0.59175841  1.52600353
> >   -0.59175841  -0.59175841  1.52600353
> >   H
> > 2
> > Direct
> >   0.00000000  0.00000000  0.00000000
> >   0.50000000  -0.25000000  0.25000000
> >
> > test.py:
> >
> > import numpy as np
> > import spglib
> > from phonopy.interface.calculator import read_crystal_structure
> >
> > # Function to check if the vector is the translational lattice vector
> > def check_if_R(vec):
> >         rvec = False
> >         for i in range(-1,2):
> >                 if not rvec:
> >                         for j in range(-1,2):
> >                                 if not rvec:
> >                                         for k in range(-1,2):
> >                                                 vec1 = vec + np.array([float(i), float(j), float(k)])
> >                                                 if(np.linalg.norm(vec1) < 1.0e-5):
> >                                                         rvec = True
> >                                                         break
> >         return rvec
> >
> > unitcell, _ = read_crystal_structure("POSCAR", interface_mode='vasp') # read in structure
> > cell = (unitcell.cell, unitcell.scaled_positions, unitcell.numbers)
> >
> > dataset = spglib.get_symmetry_dataset(cell, symprec=1e-5, angle_tolerance=-1.0, hall_number=0) # get datasets
> > rotations = dataset['rotations'].copy()
> > translations = dataset['translations'].copy()
> >
> > print(scaled_positions)
> >
> > atom_image = np.zeros((len(rotations), len(numbers))) + len(numbers) # array to store to which atom we go with symmetry
> > for irot in range(len(rotations)):
> >         new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot] # symmetry operation on the scaled positions
> >         for iat in range(natom): # Try to match rotated atom with the original set
> >                 found = False
> >                 for jat in range(natom):
> >                         pos = new_pos[iat] - scaled_positions[jat]
> >                         pos -= np.rint(pos)
> >                         if(check_if_R(pos)):
> >                                 atom_image[irot, iat] = jat
> >                                 found = True
> >                                 break
> >                 if(not found): # Print rotated atom if could not match
> >                         print(irot, iat)
> >                         print(new_pos[iat])
> > # Print atom images
> > print(atom_image)
> >
> > Could you please tell me what am I missing?
> >
> > Thank you for your help.
> > _______________________________________________
> > 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

Re: [Spglib-users] Can not find atoms related by space group symmetry

[Đorđe D. <dan...@ho...>]

Hello again,

I apologize I accidently hit send.

I apologize for the confusion. I was copy/paste-ing part from a larger code and I have not checked the script.  I am attaching the script with the email. Test contains the python code.

Let’s say the position of an atom in the primitive cell in crystal coordinates is x1, and it is a component of the vector of all atomic positions inside primitive cell X. If I act with the space group symmetry on x1 I would get, as you said x’:

x' = (R|t) x1 = Rx1 + t

Part of the code that does that should be:

new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot]

Now, I would expect that x’ is also a position of some atom in the primitive cell, maybe translated by the lattice vector. If I compare x’ with each component of X I should get a match for some x2. That would mean that my original x1 that I transformed transforms to some other atomic position x2 (which could be the same). Now I could say that space group symmetry (R|t) maps atom x1 to atom x2. Am I correct in saying this? Matching of transformed and original atomic positions should be done with this part of the code:

        for iat in range(natom):
                found = False
                for jat in range(natom):
                        pos = new_pos[iat] - scaled_positions[jat]
                        pos -= np.rint(pos)
                        if(check_if_R(pos)):
                                atom_image[irot, iat] = jat
                                found = True
                                break

I hope now you can run the code and see that I do not match all of the transformed atoms. Can you help me fix this?

Kind regards,

Đorđe

From: Atsushi Togo<mailto:atz...@gm...>
Sent: Tuesday 29 March 2022 03:04
To: spglib-users<mailto:spg...@li...>
Subject: Re: [Spglib-users] Can not find atoms related by space group symmetry

Hi,

Please define what you want to do more clearly. For example,

Given a space group operation (R|t), and a point x in crystallographic
coordinates

x' = (R|t) x = Rx + t

Then what do you want to do?

In addition, your script doesn't work as it is.

Togo

On Mon, Mar 28, 2022 at 4:26 PM Dorde Dangic <Dan...@ho...> wrote:
>
> Dear all,
>
> I am having trouble finding atoms related by a spacegroup symmetry. I am not sure what I am doing wrong. I am sending a script that I am using to find symmetry-related atoms.
>
> POSCAR:
>
>   H
>   1.00000000
>   0.59175841  -0.59175841  1.52600353
>   0.59175841  0.59175841  1.52600353
>   -0.59175841  -0.59175841  1.52600353
>   H
> 2
> Direct
>   0.00000000  0.00000000  0.00000000
>   0.50000000  -0.25000000  0.25000000
>
> test.py:
>
> import numpy as np
> import spglib
> from phonopy.interface.calculator import read_crystal_structure
>
> # Function to check if the vector is the translational lattice vector
> def check_if_R(vec):
>         rvec = False
>         for i in range(-1,2):
>                 if not rvec:
>                         for j in range(-1,2):
>                                 if not rvec:
>                                         for k in range(-1,2):
>                                                 vec1 = vec + np.array([float(i), float(j), float(k)])
>                                                 if(np.linalg.norm(vec1) < 1.0e-5):
>                                                         rvec = True
>                                                         break
>         return rvec
>
> unitcell, _ = read_crystal_structure("POSCAR", interface_mode='vasp') # read in structure
> cell = (unitcell.cell, unitcell.scaled_positions, unitcell.numbers)
>
> dataset = spglib.get_symmetry_dataset(cell, symprec=1e-5, angle_tolerance=-1.0, hall_number=0) # get datasets
> rotations = dataset['rotations'].copy()
> translations = dataset['translations'].copy()
>
> print(scaled_positions)
>
> atom_image = np.zeros((len(rotations), len(numbers))) + len(numbers) # array to store to which atom we go with symmetry
> for irot in range(len(rotations)):
>         new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot] # symmetry operation on the scaled positions
>         for iat in range(natom): # Try to match rotated atom with the original set
>                 found = False
>                 for jat in range(natom):
>                         pos = new_pos[iat] - scaled_positions[jat]
>                         pos -= np.rint(pos)
>                         if(check_if_R(pos)):
>                                 atom_image[irot, iat] = jat
>                                 found = True
>                                 break
>                 if(not found): # Print rotated atom if could not match
>                         print(irot, iat)
>                         print(new_pos[iat])
> # Print atom images
> print(atom_image)
>
> Could you please tell me what am I missing?
>
> Thank you for your help.
> _______________________________________________
> 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] Can not find atoms related by space group symmetry

[Đorđe D. <dan...@ho...>]

Hello,

I apologize for the confusion. I was copy/paste-ing part from a larger code and I have not checked the script.  I am attaching the script with the email.

Let’s say the position of an atom in the primitive cell in crystal coordinates is x1, and it is a component of the vector of all atomic positions inside primitive cell X. If I act with the space group symmetry on x1 I would get, as you said x’:

x' = (R|t) x1 = Rx1 + t

Part of the code that does that should be:

new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot]

Now, I would expect that x’ is also a position of some atom in the primitive cell, maybe translated by the lattice vector. If I compare x’ with each component of X I should get a match for some x2. That would mean that my original x1 that I transformed transforms to some other atomic position x2 (which could be the same). Now I could say that space group symmetry (R|t) maps atom x1 to atom x2. Am I correct in saying this. Matching of transformed and original atomic positions should be done with this part of the code:



Kind regards,

Đorđe

From: Atsushi Togo<mailto:atz...@gm...>
Sent: Tuesday 29 March 2022 03:04
To: spglib-users<mailto:spg...@li...>
Subject: Re: [Spglib-users] Can not find atoms related by space group symmetry

Hi,

Please define what you want to do more clearly. For example,

Given a space group operation (R|t), and a point x in crystallographic
coordinates

x' = (R|t) x = Rx + t

Then what do you want to do?

In addition, your script doesn't work as it is.

Togo

On Mon, Mar 28, 2022 at 4:26 PM Dorde Dangic <Dan...@ho...> wrote:
>
> Dear all,
>
> I am having trouble finding atoms related by a spacegroup symmetry. I am not sure what I am doing wrong. I am sending a script that I am using to find symmetry-related atoms.
>
> POSCAR:
>
>   H
>   1.00000000
>   0.59175841  -0.59175841  1.52600353
>   0.59175841  0.59175841  1.52600353
>   -0.59175841  -0.59175841  1.52600353
>   H
> 2
> Direct
>   0.00000000  0.00000000  0.00000000
>   0.50000000  -0.25000000  0.25000000
>
> test.py:
>
> import numpy as np
> import spglib
> from phonopy.interface.calculator import read_crystal_structure
>
> # Function to check if the vector is the translational lattice vector
> def check_if_R(vec):
>         rvec = False
>         for i in range(-1,2):
>                 if not rvec:
>                         for j in range(-1,2):
>                                 if not rvec:
>                                         for k in range(-1,2):
>                                                 vec1 = vec + np.array([float(i), float(j), float(k)])
>                                                 if(np.linalg.norm(vec1) < 1.0e-5):
>                                                         rvec = True
>                                                         break
>         return rvec
>
> unitcell, _ = read_crystal_structure("POSCAR", interface_mode='vasp') # read in structure
> cell = (unitcell.cell, unitcell.scaled_positions, unitcell.numbers)
>
> dataset = spglib.get_symmetry_dataset(cell, symprec=1e-5, angle_tolerance=-1.0, hall_number=0) # get datasets
> rotations = dataset['rotations'].copy()
> translations = dataset['translations'].copy()
>
> print(scaled_positions)
>
> atom_image = np.zeros((len(rotations), len(numbers))) + len(numbers) # array to store to which atom we go with symmetry
> for irot in range(len(rotations)):
>         new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot] # symmetry operation on the scaled positions
>         for iat in range(natom): # Try to match rotated atom with the original set
>                 found = False
>                 for jat in range(natom):
>                         pos = new_pos[iat] - scaled_positions[jat]
>                         pos -= np.rint(pos)
>                         if(check_if_R(pos)):
>                                 atom_image[irot, iat] = jat
>                                 found = True
>                                 break
>                 if(not found): # Print rotated atom if could not match
>                         print(irot, iat)
>                         print(new_pos[iat])
> # Print atom images
> print(atom_image)
>
> Could you please tell me what am I missing?
>
> Thank you for your help.
> _______________________________________________
> 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] Can not find atoms related by space group symmetry

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

Hi,

Please define what you want to do more clearly. For example,

Given a space group operation (R|t), and a point x in crystallographic
coordinates

x' = (R|t) x = Rx + t

Then what do you want to do?

In addition, your script doesn't work as it is.

Togo

On Mon, Mar 28, 2022 at 4:26 PM Dorde Dangic <Dan...@ho...> wrote:
>
> Dear all,
>
> I am having trouble finding atoms related by a spacegroup symmetry. I am not sure what I am doing wrong. I am sending a script that I am using to find symmetry-related atoms.
>
> POSCAR:
>
>   H
>   1.00000000
>   0.59175841  -0.59175841  1.52600353
>   0.59175841  0.59175841  1.52600353
>   -0.59175841  -0.59175841  1.52600353
>   H
> 2
> Direct
>   0.00000000  0.00000000  0.00000000
>   0.50000000  -0.25000000  0.25000000
>
> test.py:
>
> import numpy as np
> import spglib
> from phonopy.interface.calculator import read_crystal_structure
>
> # Function to check if the vector is the translational lattice vector
> def check_if_R(vec):
>         rvec = False
>         for i in range(-1,2):
>                 if not rvec:
>                         for j in range(-1,2):
>                                 if not rvec:
>                                         for k in range(-1,2):
>                                                 vec1 = vec + np.array([float(i), float(j), float(k)])
>                                                 if(np.linalg.norm(vec1) < 1.0e-5):
>                                                         rvec = True
>                                                         break
>         return rvec
>
> unitcell, _ = read_crystal_structure("POSCAR", interface_mode='vasp') # read in structure
> cell = (unitcell.cell, unitcell.scaled_positions, unitcell.numbers)
>
> dataset = spglib.get_symmetry_dataset(cell, symprec=1e-5, angle_tolerance=-1.0, hall_number=0) # get datasets
> rotations = dataset['rotations'].copy()
> translations = dataset['translations'].copy()
>
> print(scaled_positions)
>
> atom_image = np.zeros((len(rotations), len(numbers))) + len(numbers) # array to store to which atom we go with symmetry
> for irot in range(len(rotations)):
>         new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot] # symmetry operation on the scaled positions
>         for iat in range(natom): # Try to match rotated atom with the original set
>                 found = False
>                 for jat in range(natom):
>                         pos = new_pos[iat] - scaled_positions[jat]
>                         pos -= np.rint(pos)
>                         if(check_if_R(pos)):
>                                 atom_image[irot, iat] = jat
>                                 found = True
>                                 break
>                 if(not found): # Print rotated atom if could not match
>                         print(irot, iat)
>                         print(new_pos[iat])
> # Print atom images
> print(atom_image)
>
> Could you please tell me what am I missing?
>
> Thank you for your help.
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] Can not find atoms related by space group symmetry

[Dorde D. <Dan...@ho...>]

Dear all,

I am having trouble finding atoms related by a spacegroup symmetry. I am not sure what I am doing wrong. I am sending a script that I am using to find symmetry-related atoms.

POSCAR:

  H
  1.00000000
  0.59175841  -0.59175841  1.52600353
  0.59175841  0.59175841  1.52600353
  -0.59175841  -0.59175841  1.52600353
  H
2
Direct
  0.00000000  0.00000000  0.00000000
  0.50000000  -0.25000000  0.25000000

test.py:

import numpy as np
import spglib
from phonopy.interface.calculator import read_crystal_structure

# Function to check if the vector is the translational lattice vector
def check_if_R(vec):
        rvec = False
        for i in range(-1,2):
                if not rvec:
                        for j in range(-1,2):
                                if not rvec:
                                        for k in range(-1,2):
                                                vec1 = vec + np.array([float(i), float(j), float(k)])
                                                if(np.linalg.norm(vec1) < 1.0e-5):
                                                        rvec = True
                                                        break
        return rvec

unitcell, _ = read_crystal_structure("POSCAR", interface_mode='vasp') # read in structure
cell = (unitcell.cell, unitcell.scaled_positions, unitcell.numbers)

dataset = spglib.get_symmetry_dataset(cell, symprec=1e-5, angle_tolerance=-1.0, hall_number=0) # get datasets
rotations = dataset['rotations'].copy()
translations = dataset['translations'].copy()

print(scaled_positions)

atom_image = np.zeros((len(rotations), len(numbers))) + len(numbers) # array to store to which atom we go with symmetry
for irot in range(len(rotations)):
        new_pos = np.einsum('ij,jk->ik', scaled_positions, rotations[irot]) + translations[irot] # symmetry operation on the scaled positions
        for iat in range(natom): # Try to match rotated atom with the original set
                found = False
                for jat in range(natom):
                        pos = new_pos[iat] - scaled_positions[jat]
                        pos -= np.rint(pos)
                        if(check_if_R(pos)):
                                atom_image[irot, iat] = jat
                                found = True
                                break
                if(not found): # Print rotated atom if could not match
                        print(irot, iat)
                        print(new_pos[iat])
# Print atom images
print(atom_image)

Could you please tell me what am I missing?

Thank you for your help.

Re: [Spglib-users] Find a primitive cell

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

Hi,

Yes, I think so. But spglib is a library, so you need some other software to
1) parse cif file
2) give the crystal structure data to spglib
Spglib is imported from other codes like pymatgen, etc. You may be
able to use web app such as
https://www.materialscloud.org/work/tools/seekpath.

Togo

On Thu, Jul 22, 2021 at 7:39 PM Saeed Pourasad <sae...@gm...> wrote:
>
> Dear spglib users,
>
> Hi.
> I have a crystal structure (cif file) and I want to find its primitive cell, I was wondering If I can use "spglib" for this purpose?
> I am trying to get familiar with this package and I would be grateful if you can give me some tutorials or examples!
>
> Thanks for your attention in advance.
> Best,
> Saeed.
>
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo

[Spglib-users] Find a primitive cell

[Saeed P. <sae...@gm...>]

Dear spglib users,

Hi.
I have a crystal structure (cif file) and I want to find its primitive
cell, I was wondering If I can use "spglib" for this purpose?
I am trying to get familiar with this package and I would be grateful if
you can give me some tutorials or examples!

Thanks for your attention in advance.
Best,
Saeed.

Re: [Spglib-users] Irreducible k points from custom k mesh

[cheng s. <sha...@gm...>]

Dear Prof. Togo,

Got it! Thanks for sharing the book.

Best,
Cheng

On Mon, Jun 21, 2021 at 10:23 AM Atsushi Togo <atz...@gm...> wrote:

> Hi,
>
> Your questions are not about spglib. I can probably answer them, but
> I'm afraid that my answers will invite more questions. Then coding it
> by myself for you will be much easier for me than answering. I want to
> save my time.
> You can also find the information not from me, but from your
> supervisors or colleagues. In case that you can unfortunately not find
> people around you, I can recommend reading this book,
>
> https://www.cambridge.org/core/books/symmetry-and-condensed-matter-physics/218B3D7B149076E63A618D4584E3379B
> .
>
> Togo
>
> On Mon, Jun 21, 2021 at 1:59 AM cheng shao <sha...@gm...> wrote:
> >
> > 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
> >
> > _______________________________________________
> > 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] Irreducible k points from custom k mesh

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

Hi,

Your questions are not about spglib. I can probably answer them, but
I'm afraid that my answers will invite more questions. Then coding it
by myself for you will be much easier for me than answering. I want to
save my time.
You can also find the information not from me, but from your
supervisors or colleagues. In case that you can unfortunately not find
people around you, I can recommend reading this book,
https://www.cambridge.org/core/books/symmetry-and-condensed-matter-physics/218B3D7B149076E63A618D4584E3379B.

Togo

On Mon, Jun 21, 2021 at 1:59 AM cheng shao <sha...@gm...> wrote:
>
> 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
>
> _______________________________________________
> Spglib-users mailing list
> Spg...@li...
> https://lists.sourceforge.net/lists/listinfo/spglib-users



-- 
Atsushi Togo