.. _python_spglib:

Spglib for Python
==================

.. contents::
   :depth: 2
   :local:

Installation
-------------

The source code is downloaded at
https://github.com/atztogo/spglib/releases .
But minor updates are not included in this package. If you want the
latest version, you can git-clone the spglib repository::

   % git clone https://github.com/atztogo/spglib.git

It is also possible to install spglib for python via the following
package distribution services or from building using setup.py.

The following pip and conda packages are made and maintained by
`Paweł T. Jochym <https://github.com/jochym>`_, which is of great help
to keeping spglib handy and useful.

Using pip
^^^^^^^^^

Numpy is required before the python-spglib installation. The command to
install spglib is::

   % pip install --user spglib

If you see the error message like below in the installation process::

   _spglib.c:35:20: fatal error: Python.h: No such file or directory

development tools for building python module are additionally
necessary and are installed using OS's package management system,
e.g.,::

   % sudo apt-get install python-dev

If your installation by pip failed, you may need to
upgrade setuptools, e.g., by::

   % pip install --upgrade --user setuptools

Using conda
^^^^^^^^^^^

Conda is another choice::

   % conda install -c conda-forge spglib

Building using setup.py
^^^^^^^^^^^^^^^^^^^^^^^

To manually install python-spglib using ``setup.py``, python header
files (python-dev), C-compiler (e.g., gcc, clang), and numpy are
required before the build. The installation steps are shown as
follows:

1. Go to the :file:`python` directory
2. Type the command::

      % python setup.py install --user

   Document about where spglib is installed is found at the
   links below:

   - https://docs.python.org/2/install/#alternate-installation-the-user-scheme
   - https://docs.python.org/3/install/#alternate-installation-the-user-scheme

If your installation by setup.py failed, you may need to upgrade
setuptools, e.g., by::

   % pip install --upgrade --user setuptools


Test
-----

The test script :file:`test_spglib.py` is found in :file:`python/test`
directory. Got to this directory and run this script. It will be like below::

   % python test_spglib.py
   test_find_primitive (__main__.TestSpglib) ... ok
   test_get_symmetry (__main__.TestSpglib) ... ok
   test_get_symmetry_dataset (__main__.TestSpglib) ... ok
   test_refine_cell (__main__.TestSpglib) ... ok

   ----------------------------------------------------------------------
   Ran 4 tests in 13.147s

   OK

How to import spglib module
---------------------------

**Change in version 1.9.0!**

For versions 1.9.x or later::

   import spglib

For versions 1.8.x or before::

   from pyspglib import spglib

If the version is not sure::

   try:
       import spglib as spg
   except ImportError:
       from pyspglib import spglib as spg

Version number
--------------

In version 1.8.3 or later, the version number is obtained by
``spglib.__version__`` or :ref:`method_get_version`.

Example
--------

Examples are found in `examples
<https://github.com/atztogo/spglib/tree/master/python/examples>`_
directory.

.. _py_variables:

Variables
----------

.. _py_variables_crystal_structure:

Crystal structure (``cell``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

A crystal structure is given by a **tuple**. This tuple format is
supported at version 1.9.1 or later.

The tuple format is shown as follows. There are three or four elements
in the tuple: ``cell = (lattice, positions, numbers)`` or ``cell =
(lattice, positions, numbers, magmoms)`` where ``magmoms`` represents
collinear polarizations on atoms and is optional.

Lattice parameters ``lattice`` are given by a 3x3 matrix with floating
point values, where :math:`\mathbf{a}, \mathbf{b}, \mathbf{c}` are
given as rows, which results in the transpose of the definition for
C-API (:ref:`variables_lattice`). Fractional atomic positions
``positions`` are given by a Nx3 matrix with floating point values,
where N is the number of atoms. Numbers to distinguish atomic species
``numbers`` are given by a list of N integers. The collinear polarizations
``magmoms`` only work with ``get_symmetry`` and are given
as a list of N floating point values.

::

   lattice = [[a_x, a_y, a_z],
              [b_x, b_y, b_z],
              [c_x, c_y, c_z]]
   positions = [[a_1, b_1, c_1],
                [a_2, b_2, c_2],
                [a_3, b_3, c_3],
                ...]
   numbers = [n_1, n_2, n_3, ...]
   magmoms = [m_1, m_2, m_3, ...]  # Only works with get_symmetry

Version 1.9.5 or later: The methods that use the crsytal strcutre
will return ``None`` when a crystal structure is not properly given.

ASE Atoms-like input is deprecated.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

In the previous versions, ASE Atoms-like input was supported, but it
is deprecated. It is recommended to use the above tuple-style input
for the future support. ``DeprecationWarning`` is issued at version
1.10.0 or later.

The reason to make this feature deprecated is that ASE Atoms class is
too huge and users may expect spglib can understand its full
feature. However spglib actually collects only the following values
from the ASE Atoms-class instance::

   lattice = cell.get_cell()
   positions = cell.get_scaled_positions()
   numbers = cell.get_atomic_numbers()
   magmoms = None

for which the corresponding code is written out of API and it is found
at `here
<https://github.com/atztogo/spglib/blob/e0851894ccdad1abb87d519b228d056128b56806/python/spglib/spglib.py#L737-L741>`_. Nevertheless
the ASE Atoms-like input will be accepted for a while.  An alternative
Atoms class (`atoms.py
<https://github.com/atztogo/spglib/blob/master/python/examples/atoms.py>`_)
that contains minimum set of methods is prepared in the `examples
<https://github.com/atztogo/spglib/tree/master/python/examples>`_
directory. ``get_symmetry`` with collinear polarizations is not
supported when ASE Atoms-class instance.

Symmetry tolerance (``symprec``)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Distance tolerance in Cartesian coordinates to find crystal
symmetry. For more details, see :ref:`variables_symprec`

Methods
--------

.. _method_get_version:

``get_version``
^^^^^^^^^^^^^^^^

**New in version 1.8.3**

::

    version = get_version()

This returns version number of spglib by tuple with three numbers.

``get_error_message``
^^^^^^^^^^^^^^^^^^^^^^

**New in version 1.9.5**

**Be careful. This method is not thread safe, i.e., only safely usable
when calling one spglib method per process.**

This method is used to see roughly why spglib failed.

::

   error_message = get_error_message()

``get_spacegroup``
^^^^^^^^^^^^^^^^^^^

::

    spacegroup = get_spacegroup(cell, symprec=1e-5)

International space group short symbol and number are obtained as a
string. With ``symbol_type=1``, Schoenflies symbol is given instead of
international symbol.

.. _py_method_get_symmetry:

``get_symmetry``
^^^^^^^^^^^^^^^^^^

::

    symmetry = get_symmetry(cell, symprec=1e-5)

Symmetry operations are obtained as a dictionary. The key ``rotation``
contains a numpy array of integer, which is "number of symmetry
operations" x "3x3 matrices". The key ``translation`` contains a numpy
array of float, which is "number of symmetry operations" x
"vectors". The orders of the rotation matrices and the translation
vectors correspond with each other, e.g. , the second symmetry
operation is organized by the set of the second rotation matrix and second
translation vector in the respective arrays. Therefore a set of
symmetry operations may obtained by::

   [(r, t) for r, t in zip(dataset['rotations'], dataset['translations'])]

The operations are given with respect to the fractional coordinates
(not for Cartesian coordinates). The rotation matrix and translation
vector are used as follows::

    new_vector[3x1] = rotation[3x3] * vector[3x1] + translation[3x1]

The three values in the vector are given for the a, b, and c axes,
respectively. The key ``equivalent_atoms`` gives a mapping table of
atoms to symmetrically independent atoms. This is used to find
symmetrically equivalent atoms. The numbers contained are the indices
of atoms starting from 0, i.e., the first atom is numbered as 0, and
then 1, 2, 3, ... ``np.unique(equivalent_atoms)`` gives representative
symmetrically independent atoms. A list of atoms that are
symmetrically euivalent to some independent atom (here for example 1
is in ``equivalent_atom``) is found by
``np.where(equivalent_atom=1)[0]``. When the search failed, ``None``
is returned.

If ``cell`` is given as a tuple and collinear polarizations are given
as the fourth element of this tuple, symmetry operations are searched
considering this freedome. In ASE Atoms-class object, this is not supported.

``refine_cell``
^^^^^^^^^^^^^^^^

**Behaviour changed in version 1.8.x**

::

    lattice, scaled_positions, numbers = refine_cell(cell, symprec=1e-5)

Standardized crystal structure is obtained as a tuple of lattice (a 3x3
numpy array), atomic scaled positions (a numpy array of
[number_of_atoms,3]), and atomic numbers (a 1D numpy array) that are
symmetrized following space group type. When the search
failed, ``None`` is returned.

The detailed control of standardization of unit cell is achieved using
``standardize_cell``.

``find_primitive``
^^^^^^^^^^^^^^^^^^^

**Behaviour changed in version 1.8.x**

::

   lattice, scaled_positions, numbers = find_primitive(cell, symprec=1e-5)

When a primitive cell is found, lattice parameters (a 3x3 numpy array),
scaled positions (a numpy array of [number_of_atoms,3]), and atomic
numbers (a 1D numpy array) is returned. When the search failed,
``None`` is returned.

The detailed control of standardization of unit cell can be done using
``standardize_cell``.

``standardize_cell``
^^^^^^^^^^^^^^^^^^^^^

**New in version 1.8.x**

::

   lattice, scaled_positions, numbers = standardize_cell(bulk, to_primitive=False, no_idealize=False, symprec=1e-5)

``to_primitive=True`` is used to create the standardized primitive
cell, and ``no_idealize=True`` disables to idealize lengths and angles
of basis vectors and positions of atoms according to crystal
symmetry. Now ``refine_cell`` and ``find_primitive`` are shorthands of
this method with combinations of these options. When the search
failed, ``None`` is returned.  is returned. More detailed explanation
is shown in the spglib (C-API) document.

.. _py_method_get_symmetry_dataset:

``get_symmetry_dataset``
^^^^^^^^^^^^^^^^^^^^^^^^^^

**At version 1.9.4, the member 'choice' is added.**

::

    dataset = get_symmetry_dataset(cell, symprec=1e-5, angle_tolerance=-1.0, hall_number=0)

The arguments are:

* ``cell`` and ``symprec``: See :ref:`py_variables`.
* ``angle_tolerance``: An experimental argument that controls angle
  tolerance between basis vectors. Normally it is not recommended to use
  this argument. See a bit more detail at
  :ref:`variables_angle_tolerance`.
* ``hall_number`` (see the definition of this number at
  :ref:`dataset_spg_get_dataset_spacegroup_type`): The argument to
  constrain the space-group-type search only for the Hall symbol
  corresponding to it. The mapping from Hall symbols to a
  space-group-type is the many-to-one mapping. Without specifying this
  option (i.e., in the case of ``hall_number=0``), always the first one
  (the smallest serial number corresponding to the space-group-type in
  `list of space groups (Seto's web site)
  <http://pmsl.planet.sci.kobe-u.ac.jp/~seto/?page_id=37&lang=en>`_)
  among possible choices and settings is chosen as default. This
  argument is useful when the other choice (or settting) is expected to
  be hooked. This affects to the obtained values of ``international``,
  ``hall``, ``hall_number``, ``choice``, ``transformation_matrix``,
  ``origin shift``, ``wyckoffs``, ``std_lattice``, ``std_positions``,
  ``std_types`` and ``std_rotation_matrix``, but not to ``rotations``
  and ``translations`` since the later set is defined with respect to
  the basis vectors of user's input (the ``cell`` argument).

``dataset`` is a dictionary. Short explanations of the values of the
keys are shown below. More the detail may be found at
:ref:`spglib_dataset`.

* ``number``: International space group number
* ``international``: International short symbol
* ``hall``: Hall symbol
* ``hall_number``: Hall number. This number is used in
  :ref:`py_method_get_symmetry_from_database` and
  :ref:`py_method_get_spacegroup_type`.
* ``choice``: Centring, origin, basis vector setting
* ``transformation_matrix``: See the detail at
  :ref:`dataset_origin_shift_and_transformation`.
* ``origin shift``: See the detail at
  :ref:`dataset_origin_shift_and_transformation`.
* ``wyckoffs``: Wyckoff letters
* ``site_symmetry_symbols``: Site-symmetry symbols (**experimental**)
* ``equivalent_atoms``: Mapping table to equivalent atoms
* ``mapping_to_primitive``: Mapping table to atoms in the primitive cell
* ``rotations`` and ``translations``: Rotation matrices and
  translation vectors. See :ref:`py_method_get_symmetry` for more
  details.
* ``pointgroup``: Symbol of the crystallographic point group in
  the Hermann–Mauguin notation.
* ``std_lattice``, ``std_positions``, ``std_types``: Standardized
  crystal structure corresponding to a Hall symbol found. These are
  equivalently given in the array formats of ``lattice``,
  ``positions``, and ``numbers`` presented at
  :ref:`py_variables_crystal_structure`,
  respectively.
* ``std_rotation_matrix``: See the detail at :ref:`dataset_idealized_cell`.
* ``std_mapping_to_primitive``: Mapping table from atoms in the
  standardized crystal structure to the atoms in the primitive cell.

..
   * ``pointgrouop_number``: Serial number of the crystallographic point
     group, which refers list of space groups (Seto’s web site)

When the search failed, ``None`` is returned.

.. _py_method_get_symmetry_from_database:

``get_symmetry_from_database``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

::

   symmetry = get_symmetry_from_database(hall_number)

A set of crystallographic symmetry operations corresponding to
``hall_number`` is returned by a dictionary where rotation parts and
translation parts are accessed by the keys ``rotations`` and
``translations``, respectively. The definition of ``hall_number`` is
found at :ref:`dataset_spg_get_dataset_spacegroup_type`.

When something wrong happened, ``None`` is returned.

.. _py_method_get_spacegroup_type:

``get_spacegroup_type``
^^^^^^^^^^^^^^^^^^^^^^^^

**New at version 1.9.4**

::

   spacegroup_type = get_spacegroup_type(hall_number)

This function allows to directly access to the space-group-type
database in spglib (spg_database.c). A dictionary is returned. To
specify the space group type with a specific choice, ``hall_number``
is used. The definition of ``hall_number`` is found at
:ref:`dataset_spg_get_dataset_spacegroup_type`. The keys of the returned
dictionary is as follows:

::

   number
   international_short
   international_full
   international
   schoenflies
   hall_symbol
   choice
   pointgroup_schoenflies
   pointgroup_international
   arithmetic_crystal_class_number
   arithmetic_crystal_class_symbol

Here ``spacegroup_type['international_short']`` is equivalent to
``dataset['international']`` of ``get_symmetry_dataset``,
``spacegroup_type['hall_symbol']`` is equivalent to
``dataset['hall']`` of ``get_symmetry_dataset``, and
``spacegroup_type['pointgroup_international']`` is equivalent to
``dataset['pointgroup_symbol']`` of ``get_symmetry_dataset``.

When something wrong happened, ``None`` is returned.

``get_hall_number_from_symmetry``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

**experimental**

``hall_number`` is obtained from the set of symmetry operations.  The
definition of ``hall_number`` is found at
:ref:`dataset_spg_get_dataset_spacegroup_type` and the corresponding
space-group-type information is obtained through
:ref:`py_method_get_spacegroup_type`.

This is expected to work well for the set of symmetry operations whose
distortion is small. The aim of making this feature is to find
space-group-type for the set of symmetry operations given by the other
source than spglib.

Note that the definition of ``symprec`` is
different from usual one, but is given in the fractional
coordinates and so it should be small like ``1e-5``.


::

   get_hall_number_from_symmetry(rotations, translations, symprec=1e-5)

``niggli_reduce``
^^^^^^^^^^^^^^^^^^

**New at version 1.9.4**

::

   niggli_lattice = niggli_reduce(lattice, eps=1e-5)

Niggli reduction is achieved using this method. The algorithm detail
is found at https://atztogo.github.io/niggli/ and the references are
there in. Original basis vectors are stored in ``lattice`` and the
Niggli reduced basis vectors are given in ``niggli_lattice``. The
format of basis vectors are found at
:ref:`py_variables_crystal_structure`. ``esp`` is the tolerance
parameter, but unlike ``symprec`` the unit is not a length. This is
used to check if difference of norms of two basis vectors is close to
zero or not and if two basis vectors are orthogonal by the value of
dot product being close to zero or not.  The detail is shown at
https://atztogo.github.io/niggli/.

When the search failed, ``None`` is returned.

The transformation from original basis vectors :math:`( \mathbf{a}
\; \mathbf{b} \; \mathbf{c} )` to final baiss vectors :math:`(
\mathbf{a}' \; \mathbf{b}' \; \mathbf{c}' )` is achieved by linear
combination of basis vectors with integer coefficients without
rotating coordinates. Therefore the transformation matrix is obtained
by :math:`\boldsymbol{P} = ( \mathbf{a} \; \mathbf{b} \; \mathbf{c} )
( \mathbf{a}' \; \mathbf{b}' \; \mathbf{c}' )^{-1}` and the matrix
elements have to be almost integers.

``delaunay_reduce``
^^^^^^^^^^^^^^^^^^^^

**New at version 1.9.4**

::

   delaunay_lattice = delaunay_reduce(lattice, eps=1e-5)

Delaunay reduction is achieved using this method. The algorithm is
found in the international tables for crystallography
volume A. Original basis vectors are stored in ``lattice`` and the
Delaunay reduced basis vectors are given in ``delaunay_lattice``,
where the format of basis vectors are shown in
:ref:`py_variables_crystal_structure`. ``esp`` is the tolerance
parameter, but unlike ``symprec`` the unit is not a length. This is
used as the criterion if volume is close to zero or not and if two
basis vectors are orthogonal by the value of dot product being close
to zero or not.

When the search failed, ``None`` is returned.

The transformation from original basis vectors :math:`( \mathbf{a}
\; \mathbf{b} \; \mathbf{c} )` to final basis vectors :math:`(
\mathbf{a}' \; \mathbf{b}' \; \mathbf{c}' )` is achieved by linear
combination of basis vectors with integer coefficients without
rotating coordinates. Therefore the transformation matrix is obtained
by :math:`\boldsymbol{P} = ( \mathbf{a} \; \mathbf{b} \; \mathbf{c} )
( \mathbf{a}' \; \mathbf{b}' \; \mathbf{c}' )^{-1}` and the matrix
elements have to be almost integers.

``get_ir_reciprocal_mesh``
^^^^^^^^^^^^^^^^^^^^^^^^^^^^

::

   mapping, grid = get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0, 0])

Irreducible k-points are obtained from a sampling mesh of k-points.
``mesh`` is given by three integers by array and specifies mesh
numbers along reciprocal primitive axis. ``is_shift`` is given by the
three integers by array. When ``is_shift`` is set for each reciprocal
primitive axis, the mesh is shifted along the axis in half of adjacent
mesh points irrespective of the mesh numbers. When the value is not 0,
``is_shift`` is set.

``mapping`` and ``grid`` are returned. ``grid`` gives the mesh points in
fractional coordinates in reciprocal space. ``mapping`` gives mapping to
the irreducible k-point indices that are obtained by ::

   np.unique(mapping)

Here ``np`` means the numpy module. The grid point is accessed by
``grid[index]``.

When the sesarch failed, ``None`` is returned.

An example is shown below::

   import numpy as np
   import spglib

   lattice = np.array([[0.0, 0.5, 0.5],
                       [0.5, 0.0, 0.5],
                       [0.5, 0.5, 0.0]]) * 5.4
   positions = [[0.875, 0.875, 0.875],
                [0.125, 0.125, 0.125]]
   numbers= [1,] * 2
   cell = (lattice, positions, numbers)
   print(spglib.get_spacegroup(cell, symprec=1e-5))
   mesh = [8, 8, 8]

   #
   # Gamma centre mesh
   #
   mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0, 0])

   # All k-points and mapping to ir-grid points
   for i, (ir_gp_id, gp) in enumerate(zip(mapping, grid)):
       print("%3d ->%3d %s" % (i, ir_gp_id, gp.astype(float) / mesh))

   # Irreducible k-points
   print("Number of ir-kpoints: %d" % len(np.unique(mapping)))
   print(grid[np.unique(mapping)] / np.array(mesh, dtype=float))

   #
   # With shift
   #
   mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[1, 1, 1])

   # All k-points and mapping to ir-grid points
   for i, (ir_gp_id, gp) in enumerate(zip(mapping, grid)):
       print("%3d ->%3d %s" % (i, ir_gp_id, (gp + [0.5, 0.5, 0.5]) / mesh))

   # Irreducible k-points
   print("Number of ir-kpoints: %d" % len(np.unique(mapping)))
   print((grid[np.unique(mapping)] + [0.5, 0.5, 0.5]) / mesh)
