# ================================== LICENSE ===================================
# Wulfric - Cell, Atoms, K-path, visualization.
# Copyright (C) 2023 Andrey Rybakov
#
# e-mail: anry@uv.es, web: adrybakov.com
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <https://www.gnu.org/licenses/>.
#
# ================================ END LICENSE =================================
from math import cos, sin, sqrt
import numpy as np
from wulfric.cell._basic_manipulation import get_params, get_reciprocal
from wulfric.crystal._crystal_validation import validate_atoms
from wulfric._spglib_interface import get_spglib_data, validate_spglib_data, SpglibData
from wulfric.crystal._conventional import get_conventional
from wulfric._exceptions import PotentialBugError
from wulfric.constants import TORADIANS
__all__ = ["hpkot_get_extended_bl_symbol"]
[docs]
def hpkot_get_extended_bl_symbol(cell, atoms, spglib_data=None):
r"""
Returns extended bravais lattice symbol as defined in the paper by Hinuma, Pizzi,
Kumagai, Oba, and Tanaka [1]_.
.. versionadded:: 0.6.3
Parameters
----------
cell : (3, 3) |array-like|_
Matrix of a cell, rows are interpreted as vectors.
atoms : dict
Dictionary with N atoms. Expected keys:
* "positions" : (N, 3) |array-like|_
Positions of the atoms in the basis of lattice vectors (``cell``). In other
words - relative coordinates of atoms.
* "names" : (N, ) list of str, optional
See Notes
* "species" : (N, ) list of str, optional
See Notes
* "spglib_types" : (N, ) list of int, optional
See Notes
.. hint::
Pass ``atoms = dict(positions=[[0, 0, 0]], spglib_types=[1])`` if you would
like to interpret the ``cell`` alone (effectively assuming that the ``cell``
is a primitive one).
spglib_data : :py:class:`.SpglibData`, optional
If you need more control on the parameters passed to the spglib, then
you can get ``spglib_data`` manually and pass it to this function.
Use wulfric's interface to |spglib|_ as
.. code-block:: python
spglib_data = wulfric.get_spglib_data(...)
using the same ``cell`` and ``atoms["positions"]`` that you are passing to this
function.
Returns
-------
extended_bl_type : str
Extended Bravais lattice symbol.
Notes
-----
|spglib|_ uses ``types`` to distinguish the atoms. To see how wulfric deduces the
``types`` for given atoms see :py:func:`wulfric.get_spglib_types`.
References
----------
.. [1] Hinuma, Y., Pizzi, G., Kumagai, Y., Oba, F. and Tanaka, I., 2017.
Band structure diagram paths based on crystallography.
Computational Materials Science, 128, pp.140-184.
Examples
--------
.. doctest::
>>> import wulfric
>>> wulfric.crystal.hpkot_get_extended_bl_symbol(
... cell=[[1, 0, 0], [0, 1, 0], [0, 0, 1]],
... atoms=dict(positions=[[0, 0, 0]], spglib_types=[1]),
... )
'cP2'
"""
# Validate that the atoms dictionary is what expected of it
validate_atoms(atoms=atoms, required_keys=["positions"], raise_errors=True)
# Call spglib
if spglib_data is None:
spglib_data = get_spglib_data(cell=cell, atoms=atoms)
# Or check that spglib_data were *most likely* produced via wulfric's interface
elif not isinstance(spglib_data, SpglibData):
raise TypeError(
f"Are you sure that spglib_data were produced via wulfric's interface? Expected SpglibData, got {type(spglib_data)}."
)
# Validate that user-provided spglib_data match user-provided structure
else:
validate_spglib_data(cell=cell, atoms=atoms, spglib_data=spglib_data)
cell = np.array(cell, dtype=float)
lattice_type = spglib_data.crystal_family + spglib_data.centring_type
# Lattice types that do not require computation of lattice parameters
if lattice_type in ["cI", "tP", "oP", "mP"]:
return f"{lattice_type}1"
if lattice_type == "cP":
if 195 <= spglib_data.space_group_number <= 206:
return "cP1"
elif 207 <= spglib_data.space_group_number <= 230:
return "cP2"
else:
raise PotentialBugError(
error_summary=f'(convention="HPKOT"), lattice type cP, space group {spglib_data.space_group_number}. Failed to define extended Bravais lattice symbol.'
)
if lattice_type == "cF":
if 195 <= spglib_data.space_group_number <= 206:
return "cF1"
elif 207 <= spglib_data.space_group_number <= 230:
return "cF2"
else:
raise PotentialBugError(
error_summary=f'(convention="HPKOT"), lattice type cF, space group {spglib_data.space_group_number}. Failed to define extended Bravais lattice symbol.'
)
if lattice_type == "hP":
if (
143 <= spglib_data.space_group_number <= 149
or 159 <= spglib_data.space_group_number <= 163
or spglib_data.space_group_number in [151, 153, 157]
):
return "hP1"
else:
return "hP2"
# Lattice types that require computation of lattice parameters
conventional_cell, _ = get_conventional(
cell=cell, atoms=atoms, convention="HPKOT", spglib_data=spglib_data
)
a, b, c, _, beta, _ = get_params(cell=conventional_cell)
if lattice_type == "tI":
if c <= a:
return "tI1"
else:
return "tI2"
if lattice_type == "oF":
if 1 / a**2 > 1 / b**2 + 1 / c**2:
return "oF1"
elif 1 / c**2 > 1 / a**2 + 1 / b**2:
return "oF2"
else:
return "oF3"
if lattice_type == "oI":
if c >= a and c >= b:
return "oI1"
if a >= b and a >= c:
return "oI2"
if b >= a and b >= c:
return "oI3"
if lattice_type == "oC":
if a <= b:
return "oC1"
else:
return "oC2"
if lattice_type == "oA":
if b <= c:
return "oA1"
else:
return "oA2"
if lattice_type == "hR":
if sqrt(3) * a <= sqrt(2) * c:
return "hR1"
else:
return "hR2"
if lattice_type == "mC":
if b <= a * sin(beta * TORADIANS):
return "mC1"
else:
if (
-a * cos(beta * TORADIANS) / c + ((a * sin(beta * TORADIANS)) / b) ** 2
<= 1
):
return "mC2"
else:
return "mC3"
if lattice_type == "aP":
_, _, _, r_alpha, r_beta, r_gamma = get_params(
cell=get_reciprocal(cell=conventional_cell)
)
if r_alpha >= 90 and r_beta >= 90 and r_gamma >= 90:
return "aP2"
else:
return "aP3"
# If lattice type is not one of the expected ones
raise PotentialBugError(
f'(convention="HPKOT"), lattice type {lattice_type}, space group {spglib_data.space_group_number}.. Failed to identify lattice type (not one of supported).'
)
