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# fmt: off
from itertools import product
from math import cos, pi, sin
from typing import Any, Dict, Optional, Tuple, Union
import numpy as np
from matplotlib.patches import FancyArrowPatch
from mpl_toolkits.mplot3d import Axes3D, proj3d
from scipy.spatial.transform import Rotation
from ase.cell import Cell
def bz_vertices(icell, dim=3):
"""Return the vertices and the normal vector of the BZ.
See https://xkcd.com/1421 ..."""
from scipy.spatial import Voronoi
icell = icell.copy()
if dim < 3:
icell[2, 2] = 1e-3
if dim < 2:
icell[1, 1] = 1e-3
indices = (np.indices((3, 3, 3)) - 1).reshape((3, 27))
G = np.dot(icell.T, indices).T
vor = Voronoi(G)
bz1 = []
for vertices, points in zip(vor.ridge_vertices, vor.ridge_points):
if -1 not in vertices and 13 in points:
normal = G[points].sum(0)
normal /= (normal**2).sum()**0.5
bz1.append((vor.vertices[vertices], normal))
return bz1
class FlatPlot:
"""Helper class for 1D/2D Brillouin zone plots."""
axis_dim = 2 # Dimension of the plotting surface (2 even if it's 1D BZ).
point_options = {'zorder': 5}
def new_axes(self, fig):
return fig.gca()
def adjust_view(self, ax, minp, maxp, symmetric: bool = True):
"""Ajusting view property of the drawn BZ. (1D/2D)
Parameters
----------
ax: Axes
matplotlib Axes object.
minp: float
minimum value for the plotting region, which detemines the
bottom left corner of the figure. if symmetric is set as True,
this value is ignored.
maxp: float
maximum value for the plotting region, which detemines the
top right corner of the figure.
symmetric: bool
if True, set the (0,0) position (Gamma-bar position) at the center
of the figure.
"""
ax.autoscale_view(tight=True)
s = maxp * 1.05
if symmetric:
ax.set_xlim(-s, s)
ax.set_ylim(-s, s)
else:
ax.set_xlim(minp * 1.05, s)
ax.set_ylim(minp * 1.05, s)
ax.set_aspect('equal')
def draw_arrow(self, ax, vector, **kwargs):
ax.arrow(0, 0, vector[0], vector[1],
lw=1,
length_includes_head=True,
head_width=0.03,
head_length=0.05,
**kwargs)
def label_options(self, point):
ha_s = ['right', 'left', 'right']
va_s = ['bottom', 'bottom', 'top']
x, y = point
ha = ha_s[int(np.sign(x))]
va = va_s[int(np.sign(y))]
return {'ha': ha, 'va': va, 'zorder': 4}
def view(self):
pass
class SpacePlot:
"""Helper class for ordinary (3D) Brillouin zone plots.
Attributes
----------
azim : float
Azimuthal angle in radian for viewing 3D BZ.
default value is pi/5
elev : float
Elevation angle in radian for viewing 3D BZ.
default value is pi/6
"""
axis_dim = 3
point_options: Dict[str, Any] = {}
def __init__(self, *, azim: Optional[float] = None,
elev: Optional[float] = None):
class Arrow3D(FancyArrowPatch):
def __init__(self, ax, xs, ys, zs, *args, **kwargs):
FancyArrowPatch.__init__(self, (0, 0), (0, 0), *args, **kwargs)
self._verts3d = xs, ys, zs
self.ax = ax
def draw(self, renderer):
xs3d, ys3d, zs3d = self._verts3d
xs, ys, _zs = proj3d.proj_transform(xs3d, ys3d,
zs3d, self.ax.axes.M)
self.set_positions((xs[0], ys[0]), (xs[1], ys[1]))
FancyArrowPatch.draw(self, renderer)
# FIXME: Compatibility fix for matplotlib 3.5.0: Handling of 3D
# artists have changed and all 3D artists now need
# "do_3d_projection". Since this class is a hack that manually
# projects onto the 3D axes we don't need to do anything in this
# method. Ideally we shouldn't resort to a hack like this.
def do_3d_projection(self, *_, **__):
return 0
self.arrow3d = Arrow3D
self.azim: float = pi / 5 if azim is None else azim
self.elev: float = pi / 6 if elev is None else elev
self.view = [
sin(self.azim) * cos(self.elev),
cos(self.azim) * cos(self.elev),
sin(self.elev),
]
def new_axes(self, fig):
return fig.add_subplot(projection='3d')
def draw_arrow(self, ax: Axes3D, vector, **kwargs):
ax.add_artist(self.arrow3d(
ax,
[0, vector[0]],
[0, vector[1]],
[0, vector[2]],
mutation_scale=20,
arrowstyle='-|>',
**kwargs))
def adjust_view(self, ax, minp, maxp, symmetric=True):
"""Ajusting view property of the drawn BZ. (3D)
Parameters
----------
ax: Axes
matplotlib Axes object.
minp: float
minimum value for the plotting region, which detemines the
bottom left corner of the figure. if symmetric is set as True,
this value is ignored.
maxp: float
maximum value for the plotting region, which detemines the
top right corner of the figure.
symmetric: bool
Currently, this is not used, just for keeping consistency with 2D
version.
"""
import matplotlib.pyplot as plt
# ax.set_aspect('equal') <-- won't work anymore in 3.1.0
ax.view_init(azim=np.rad2deg(self.azim), elev=np.rad2deg(self.elev))
# We want aspect 'equal', but apparently there was a bug in
# matplotlib causing wrong behaviour. Matplotlib raises
# NotImplementedError as of v3.1.0. This is a bit unfortunate
# because the workarounds known to StackOverflow and elsewhere
# all involve using set_aspect('equal') and then doing
# something more.
#
# We try to get square axes here by setting a square figure,
# but this is probably rather inexact.
fig = ax.get_figure()
xx = plt.figaspect(1.0)
fig.set_figheight(xx[1])
fig.set_figwidth(xx[0])
ax.set_proj_type('ortho')
minp0 = 0.9 * minp # Here we cheat a bit to trim spacings
maxp0 = 0.9 * maxp
ax.set_xlim3d(minp0, maxp0)
ax.set_ylim3d(minp0, maxp0)
ax.set_zlim3d(minp0, maxp0)
ax.set_box_aspect([1, 1, 1])
def label_options(self, point):
return dict(ha='center', va='bottom')
def normalize_name(name):
if name == 'G':
return '\\Gamma'
if len(name) > 1:
import re
m = re.match(r'^(\D+?)(\d*)$', name)
if m is None:
raise ValueError(f'Bad label: {name}')
name, num = m.group(1, 2)
if num:
name = f'{name}_{{{num}}}'
return name
def bz_plot(cell: Cell, vectors: bool = False, paths=None, points=None,
azim: Optional[float] = None, elev: Optional[float] = None,
scale=1, interactive: bool = False,
transforms: Optional[list] = None,
repeat: Union[Tuple[int, int], Tuple[int, int, int]] = (1, 1, 1),
pointstyle: Optional[dict] = None,
ax=None, show=False, **kwargs):
"""Plot the Brillouin zone of the Cell
Parameters
----------
cell: Cell
Cell object for BZ drawing.
vectors : bool
if True, show the vector.
paths : list[tuple[str, np.ndarray]] | None
Special point name and its coordinate position
points : np.ndarray
Coordinate points along the paths.
azim : float | None
Azimuthal angle in radian for viewing 3D BZ.
elev : float | None
Elevation angle in radian for viewing 3D BZ.
scale : float
Not used. To be removed?
interactive : bool
Not effectively works. To be removed?
transforms: List
List of linear transformation (scipy.spatial.transform.Rotation)
repeat: Tuple[int, int] | Tuple[int, int, int]
Set the repeating draw of BZ. default is (1, 1, 1), no repeat.
pointstyle : Dict
Style of the special point
ax : Axes | Axes3D
matplolib Axes (Axes3D in 3D) object
show : bool
If true, show the figure.
**kwargs
Additional keyword arguments to pass to ax.plot
Returns
-------
ax
A matplotlib axis object.
"""
import matplotlib.pyplot as plt
if pointstyle is None:
pointstyle = {}
if transforms is None:
transforms = [Rotation.from_rotvec((0, 0, 0))]
cell = cell.copy()
dimensions = cell.rank
if dimensions == 3:
plotter: Union[SpacePlot, FlatPlot] = SpacePlot(azim=azim, elev=elev)
else:
plotter = FlatPlot()
assert dimensions > 0, 'No BZ for 0D!'
if ax is None:
ax = plotter.new_axes(plt.gcf())
assert not np.array(cell)[dimensions:, :].any()
assert not np.array(cell)[:, dimensions:].any()
icell = cell.reciprocal()
kpoints = points
bz1 = bz_vertices(icell, dim=dimensions)
if len(repeat) == 2:
repeat = (repeat[0], repeat[1], 1)
maxp = 0.0
minp = 0.0
for bz_i in bz_index(repeat):
for points, normal in bz1:
shift = np.dot(np.array(icell).T, np.array(bz_i))
for transform in transforms:
shift = transform.apply(shift)
ls = '-'
xyz = np.concatenate([points, points[:1]])
for transform in transforms:
xyz = transform.apply(xyz)
x, y, z = xyz.T
x, y, z = x + shift[0], y + shift[1], z + shift[2]
if dimensions == 3:
if normal @ plotter.view < 0 and not interactive:
ls = ':'
if plotter.axis_dim == 2:
ax.plot(x, y, c='k', ls=ls, **kwargs)
else:
ax.plot(x, y, z, c='k', ls=ls, **kwargs)
maxp = max(maxp, x.max(), y.max(), z.max())
minp = min(minp, x.min(), y.min(), z.min())
if vectors:
for transform in transforms:
icell = transform.apply(icell)
assert isinstance(icell, np.ndarray)
for i in range(dimensions):
plotter.draw_arrow(ax, icell[i], color='k')
# XXX Can this be removed?
if dimensions == 3:
maxp = max(maxp, 0.6 * icell.max())
else:
maxp = max(maxp, icell.max())
if paths is not None:
for names, points in paths:
for transform in transforms:
points = transform.apply(points)
coords = np.array(points).T[:plotter.axis_dim, :]
ax.plot(*coords, c='r', ls='-')
for name, point in zip(names, points):
name = normalize_name(name)
point = point[:plotter.axis_dim]
ax.text(*point, rf'$\mathrm{{{name}}}$',
color='g', **plotter.label_options(point))
if kpoints is not None:
kw = {'c': 'b', **plotter.point_options, **pointstyle}
for transform in transforms:
kpoints = transform.apply(kpoints)
ax.scatter(*kpoints[:, :plotter.axis_dim].T, **kw)
ax.set_axis_off()
if repeat == (1, 1, 1):
plotter.adjust_view(ax, minp, maxp)
else:
plotter.adjust_view(ax, minp, maxp, symmetric=False)
if show:
plt.show()
return ax
def bz_index(repeat):
"""BZ index from the repeat
A helper function to iterating drawing BZ.
Parameters
----------
repeat: Tuple[int, int] | Tuple[int, int, int]
repeating for drawing BZ
Returns
-------
Iterator[Tuple[int, int, int]]
>>> list(_bz_index((1, 2, -2)))
[(0, 0, 0), (0, 0, -1), (0, 1, 0), (0, 1, -1)]
"""
if len(repeat) == 2:
repeat = (repeat[0], repeat[1], 1)
assert len(repeat) == 3
assert repeat[0] != 0
assert repeat[1] != 0
assert repeat[2] != 0
repeat_along_a = (
range(0, repeat[0]) if repeat[0] > 0 else range(0, repeat[0], -1)
)
repeat_along_b = (
range(0, repeat[1]) if repeat[1] > 0 else range(0, repeat[1], -1)
)
repeat_along_c = (
range(0, repeat[2]) if repeat[2] > 0 else range(0, repeat[2], -1)
)
return product(repeat_along_a, repeat_along_b, repeat_along_c)
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