# ================================== 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 typing import Iterable
import numpy as np
from wulfric.cell._basic_manipulation import get_reciprocal
from wulfric.constants._hpkot_convention import HPKOT_DEFAULT_K_PATHS
from wulfric.constants._sc_convention import SC_DEFAULT_K_PATHS
from wulfric.constants._space_groups import INVERSION_SYMMETRY
from wulfric.crystal._crystal_validation import validate_atoms
from wulfric.crystal._conventional import get_conventional
from wulfric.crystal._primitive import get_primitive
from wulfric.crystal._sc_variation import sc_get_variation
from wulfric.crystal._hpkot_extended_bl_symbol import hpkot_get_extended_bl_symbol
from wulfric._exceptions import ConventionNotSupported
from wulfric.kpoints._hpkot_points import _hpkot_get_points
from wulfric.kpoints._sc_points import _sc_get_points
from wulfric._spglib_interface import get_spglib_data, validate_spglib_data, SpglibData
__all__ = ["get_path_as_list", "get_path_as_string", "get_path_and_points"]
[docs]
def get_path_as_list(path_as_string) -> list:
r"""
Converts k=path from string to list representation.
.. code-block:: python
path_as_list = [["G", "X", "Y", "S"], ["G", "Z"]]
path_as_string = "G-X-Y-S|G-Z"
Parameters
----------
path_as_string : str
K-path as a single string.
Returns
-------
path_as_list : list of list of str
K-path as list of subpaths, where each subpath is a list of k-points.
Raises
------
ValueError
If ``path_as_string`` is not ``str``
Valueerror
If any subpath contains less than two points.
See Also
--------
:ref:`user-guide_usage_key-concepts_k-path`
"""
if not isinstance(path_as_string, str):
raise ValueError(f"path_as_string is not a string: {path_as_string}")
subpaths_as_str = path_as_string.split("|")
path_as_list = []
for s_i, subpath_as_str in enumerate(subpaths_as_str):
subpath_as_list = subpath_as_str.split("-")
# Each subpath has to contain at least two points.
# If subpath is empty, then no action required
if len(subpath_as_list) == 1:
raise ValueError(
f"Subpath {s_i + 1} has less than two points: {subpath_as_str}"
)
if len(subpath_as_list) >= 2:
path_as_list.append(subpath_as_list)
return path_as_list
[docs]
def get_path_as_string(path_as_list) -> str:
r"""
Converts k=path from list to string representation.
.. code-block:: python
path_as_string = "G-X-Y-S|G-Z"
path_as_list = [["G", "X", "Y", "S"], ["G", "Z"]]
Parameters
----------
path_as_list : list of list of str
K-path as list of subpaths, where each subpath is a list of k-points.
Returns
-------
path_as_string : str
K-path as a single string.
Raises
------
ValueError
If ``path_as_list`` is not a ``list`` of ``list``.
See Also
--------
:ref:`user-guide_usage_key-concepts_k-path`
"""
if not isinstance(path_as_list, Iterable):
raise ValueError(
f"path_as_list is not Iterable, can not convert to string:\n{path_as_list}"
)
subpaths_as_str = []
for s_i, subpath_as_list in enumerate(path_as_list):
if not isinstance(subpath_as_list, Iterable):
raise ValueError(
f"Subpath {s_i + 1} is not Iterable, can not convert to string:\n{subpath_as_list}"
)
subpaths_as_str.append("-".join(subpath_as_list))
return "|".join(subpaths_as_str)
[docs]
def get_path_and_points(
cell,
atoms,
spglib_data=None,
convention="HPKOT",
with_time_reversal=True,
relative=True,
):
r"""
Returns recommended k-path and set of high-symmetry points.
Note that high-symmetry points are the ones of the primitive cell, that is associated
with the given set of ``cell`` and ``atoms``. In other words it respects the symmetry
of the crystal.
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.
convention : str, default "HPKOT"
Convention for the definition of the conventional cell. Case-insensitive.
Supported:
* "HPKOT" for [1]_
* "SC" for [2]_
with_time_reversal : bool, default True
Whether to assume that the system has time reversal symmetry. By default
assumes that the system has it. The strategy for extending the path when
``with_time_reversal=False`` for the crystals without inversion symmetry is
described in [1]_. For the systems with inversion symmetry this parameter does
nothing.
.. versionadded:: 0.6.3
relative : bool, default True
Whether to return coordinates as relative to the reciprocal cell or in absolute
coordinates in the reciprocal Cartesian space.
Returns
-------
recommended_path : str
Recommended path in reciprocal space between the high-symmetry k points.
hs_points : dict
High symmetry points.
.. code-block:: python
hs_points = {name1: coordinate1, name2 : coordinate2, ...}
Coordinates of the points are
* (default) Relative to ``get_reciprocal(cell)`` if ``relative=True``.
* Absolute in reciprocal space if ``relative=False``.
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.
.. [2] Setyawan, W. and Curtarolo, S., 2010.
High-throughput electronic band structure calculations: Challenges and tools.
Computational materials science, 49(2), pp. 299-312.
See Also
--------
wulfric.Kpoints : Class with a convenient interface for the same information.
"""
cell = np.array(cell, dtype=float)
# 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)
conventional_cell, _ = get_conventional(
cell=cell, atoms=atoms, convention=convention, spglib_data=spglib_data
)
primitive_cell, _ = get_primitive(
cell=cell, atoms=atoms, convention=convention, spglib_data=spglib_data
)
lattice_type = spglib_data.crystal_family + spglib_data.centring_type
convention = convention.lower()
if convention == "sc":
lattice_variation = sc_get_variation(
cell=cell, atoms=atoms, spglib_data=spglib_data
)
hs_points = _sc_get_points(
conventional_cell=conventional_cell,
lattice_type=lattice_type,
lattice_variation=lattice_variation,
)
kpath = SC_DEFAULT_K_PATHS[lattice_variation]
elif convention == "hpkot":
extended_bl_symbol = hpkot_get_extended_bl_symbol(
cell=cell, atoms=atoms, spglib_data=spglib_data
)
hs_points = _hpkot_get_points(
conventional_cell=conventional_cell,
lattice_type=lattice_type,
extended_bl_symbol=extended_bl_symbol,
)
kpath = HPKOT_DEFAULT_K_PATHS[extended_bl_symbol]
else:
raise ConventionNotSupported(convention, supported_conventions=["HPKOT", "SC"])
primitive_rcell = get_reciprocal(cell=primitive_cell)
for point in hs_points:
# Here coordinates are absolute
hs_points[point] = hs_points[point] @ primitive_rcell
if relative:
# absolute -> relative
hs_points[point] = hs_points[point] @ np.linalg.inv(
get_reciprocal(cell=cell)
)
if (
not INVERSION_SYMMETRY[spglib_data.space_group_number]
and not with_time_reversal
):
# Extend k-path
extra_path = get_path_as_list(path_as_string=kpath)
for i in range(len(extra_path)):
for j in range(len(extra_path[i])):
if extra_path[i][j] != "GAMMA":
extra_path[i][j] = f"{extra_path[i][j]}_P"
kpath = f"{kpath}|{get_path_as_string(path_as_list=extra_path)}"
# Extend high-symmetry points
points = list(hs_points)
for point in points:
if point != "GAMMA":
hs_points[f"{point}_P"] = -hs_points[point]
return kpath, hs_points
