def cubic_kpath():
special_path = special_paths['cubic']
points = special_points['cubic']
paths = parse_path_string(special_path)
special_kpts = [points[k] for k in paths[0]]
kpts, xs, xspecial = bandpath(special_kpts, cell=np.eye(3), npoints=500)
return kpts, xs, xspecial
def cubic_kpath(npoints=500, name=True):
"""
return the kpoint path for cubic
Parameters:
----------------
npoints: int
number of points.
Returns:
-----------------
kpts:
kpoints
xs:
x cordinates for plot
xspecial:
x cordinates for special k points
"""
special_path = special_paths['cubic']
points = special_points['cubic']
paths = parse_path_string(special_path)
special_kpts = [points[k] for k in paths[0]]
kpts, xs, xspecial = bandpath(special_kpts,
cell=np.eye(3),
npoints=npoints)
if not name:
return kpts, xs, xspecial
else:
return kpts, xs, xspecial, special_path
def set_spectrum(self, bandpath=None, reference=None):
bands = self.bands
if bandpath != None:
self.set_bandpath(bandpath)
bp = parse_path_string(self.bandpath.path)
jumps = []
kps = []
occs = []
kpoint_axis = []
kpoint_labels = []
label_coords = []
spectrum = []
icell_cv = 2 * np.pi * np.linalg.pinv(self.structure.cell).T
for segment in bp:
kpoint_labels.append(segment[0])
label_coords.append(
label_coords[-1] if len(label_coords) > 0 else 0.0)
for s1, s2 in zip(segment[:-1], segment[1:]):
energies = bands[(s1, s2)].eigenvalues
kpoints = np.dot(bands[(s1, s2)].kpoints, icell_cv)
occ = bands[(s1, s2)].occupations
kstep = np.linalg.norm(kpoints[-1, :] - kpoints[0, :])
kaxis = np.linspace(0, kstep,
kpoints.shape[0]) + label_coords[-1]
kstep += label_coords[-1]
spectrum.append(energies)
kps.append(kpoints)
occs.append(occ)
kpoint_axis.append(kaxis)
label_coords.append(kstep)
kpoint_labels.append(s2)
jumps.append(label_coords[-1])
jumps = jumps[:-1]
spectrum = np.concatenate(spectrum, axis=0)
kps = np.concatenate(kps, axis=0)
kpoint_axis = np.concatenate(kpoint_axis, axis=0)
occs = np.concatenate(occs, axis=0)
fermi_level = self.fermi_level.soc if self.soc else self.fermi_level.scalar
self.set_energy_reference(reference, self.soc)
reference, shift = self.energy_reference
sp = BandSpectrum(
atoms=self.structure.atoms,
kpoints=kps,
kpoint_axis=kpoint_axis,
eigenvalues=spectrum,
occupations=occs,
label_coords=label_coords,
kpoint_labels=kpoint_labels,
jumps=jumps,
fermi_level=fermi_level,
reference=reference,
shift=shift,
bandpath=bandpath,
)
self._spectrum = sp
def special_point_names(self):
"""Return all special point names as a list of strings.
>>> BCT(3, 5).special_point_names
['G', 'N', 'P', 'S', 'S1', 'X', 'Y', 'Y1', 'Z']
"""
labels = parse_path_string(self._variant.special_point_names)
assert len(labels) == 1 # list of lists
return labels[0]
def atoms2bandpath(atoms,
path='default',
k_points=False,
ibz_k_points=False,
dimension=3,
verbose=False):
cell = atoms.get_cell()
icell = atoms.get_reciprocal_cell()
try:
cs = crystal_structure_from_cell(cell)
except ValueError:
cs = None
if verbose:
if cs:
print('Crystal:', cs)
print('Special points:', special_paths[cs])
print('Lattice vectors:')
for i, v in enumerate(cell):
print('{}: ({:16.9f},{:16.9f},{:16.9f})'.format(i + 1, *v))
print('Reciprocal vectors:')
for i, v in enumerate(icell):
print('{}: ({:16.9f},{:16.9f},{:16.9f})'.format(i + 1, *v))
# band path
special_points = None
if path:
if path == 'default':
path = special_paths[cs]
paths = []
special_points = get_special_points(cell)
for names in parse_path_string(path):
points = []
for name in names:
points.append(np.dot(icell.T, special_points[name]))
paths.append((names, points))
else:
paths = None
# k points
points = None
if atoms.calc is not None and hasattr(atoms.calc, 'get_bz_k_points'):
bzk = atoms.calc.get_bz_k_points()
if path is None:
try:
size, offset = get_monkhorst_pack_size_and_offset(bzk)
except ValueError:
# This was not a MP-grid. Must be a path in the BZ:
path = ''.join(labels_from_kpts(bzk, cell)[2])
if k_points:
points = bzk
elif ibz_k_points:
points = atoms.calc.get_ibz_k_points()
return BandPath(cell, kpts=points, special_points=special_points)
def mybandpath(path, cell, npoints=50, eps=1e-3):
"""Make a list of kpoints defining the path between the given points.
path: list or str
Can be:
* a string that parse_path_string() understands: 'GXL'
* a list of BZ points: [(0, 0, 0), (0.5, 0, 0)]
* or several lists of BZ points if the the path is not continuous.
cell: 3x3
Unit cell of the atoms.
npoints: int
Length of the output kpts list.
Return list of k-points, list of x-coordinates and list of
x-coordinates of special points."""
if isinstance(path, str):
special = get_special_points(cell,eps=eps)
paths = []
for names in parse_path_string(path):
paths.append([special[name] for name in names])
elif np.array(path[0]).ndim == 1:
paths = [path]
else:
paths = path
points = np.concatenate(paths)
dists = points[1:] - points[:-1]
lengths = [np.linalg.norm(d) for d in kpoint_convert(cell, skpts_kc=dists)]
i = 0
for path in paths[:-1]:
i += len(path)
lengths[i - 1] = 0
length = sum(lengths)
kpts = []
x0 = 0
x = []
X = [0]
for P, d, L in zip(points[:-1], dists, lengths):
n = max(2, int(round(L * (npoints - len(x)) / (length - x0))))
for t in np.linspace(0, 1, n)[:-1]:
kpts.append(P + t * d)
x.append(x0 + t * L)
x0 += L
X.append(x0)
kpts.append(points[-1])
x.append(x0)
return np.array(kpts), np.array(x), np.array(X)
def read_bands(self):
outputyaml = self.outputdir.joinpath("band.yaml")
assert outputyaml.exists(), "File band.yaml not found."
with open(outputyaml, "r") as stream:
try:
data = yaml.safe_load(stream)
except yaml.YAMLError as exc:
raise Exception(exc)
labels = data["labels"]
bpstring = []
for i, pair in enumerate(labels):
if i == 0:
bpstring.append(pair[0])
elif i == len(labels) - 1:
bpstring.append(pair[0])
bpstring.append(pair[1])
else:
bpstring.append(pair[0])
bpstring = "".join(bpstring)
bpstring = bpstring.replace("|", ",")
bplist = parse_path_string(bpstring)
special_points = (self.structure.cell.get_bravais_lattice().bandpath().
special_points)
self._bandpath = BandPath(path=bpstring,
cell=self.structure.cell,
special_points=special_points)
phon = data["phonon"]
nqpoints = data["segment_nqpoint"]
qpoints = np.array([k["q-position"] for k in phon], dtype=np.float32)
pbands = np.array([[l["frequency"] for l in k["band"]] for k in phon],
dtype=np.float32)
b = namedtuple("band", ["qpoints", "frequencies"])
count = 0
bands = {}
i = 0
for segment in bplist:
for pair in zip(segment[:-1], segment[1:]):
j1, j2 = count, nqpoints[i] + count
count = j2
qp = qpoints[j1:j2, :]
pb = pbands[j1:j2, :]
bands[pair] = b(qp, pb)
rev = (pair[1], pair[0])
bands[rev] = b(qp[::-1], pb[::-1])
i += 1
return bands
def set_spectrum(self, bandpath=None, unit=r"cm$^{-1}$"):
assert unit in [r"cm$^{-1}$", "Thz"], "Unit not recognized."
bands = self.bands
if bandpath != None:
self.set_bandpath(bandpath)
bp = parse_path_string(self.bandpath.path)
jumps = []
qps = []
qpoint_axis = []
qpoint_labels = []
label_coords = []
spectrum = []
icell_cv = 2 * np.pi * np.linalg.pinv(self.structure.cell).T
for segment in bp:
qpoint_labels.append(segment[0])
label_coords.append(
label_coords[-1] if len(label_coords) > 0 else 0.0)
for s1, s2 in zip(segment[:-1], segment[1:]):
freqs = bands[(s1, s2)].frequencies
qpoints = np.dot(bands[(s1, s2)].qpoints, icell_cv)
qstep = np.linalg.norm(qpoints[-1, :] - qpoints[0, :])
qaxis = np.linspace(0, qstep,
qpoints.shape[0]) + label_coords[-1]
qstep += label_coords[-1]
spectrum.append(freqs)
qps.append(qpoints)
qpoint_axis.append(qaxis)
label_coords.append(qstep)
qpoint_labels.append(s2)
jumps.append(label_coords[-1])
jumps = jumps[:-1]
spectrum = np.concatenate(spectrum, axis=0) # unit in Thz
# 1 Thz = 33.356 cm^-1
if unit == r"cm$^{-1}$":
spectrum *= 33.356
qps = np.concatenate(qps, axis=0)
qpoint_axis = np.concatenate(qpoint_axis, axis=0)
atoms = self.structure.copy()
sp = PhononSpectrum(
qpoints=qps,
qpoint_axis=qpoint_axis,
frequencies=spectrum,
atoms=atoms,
label_coords=label_coords,
qpoint_labels=qpoint_labels,
jumps=jumps,
unit=unit,
bandpath=bp,
)
self._spectrum = sp
def generate_kpath_ase(cell, symprec):
eig_val_max = np.real(np.linalg.eigvals(cell)).max()
eps = eig_val_max * symprec
lattice = crystal_structure_from_cell(cell, eps)
paths = special_paths.get(lattice, None)
if paths is None:
paths = special_paths['orthorhombic']
paths = parse_path_string(special_paths[lattice])
points = special_points.get(lattice)
if points is None:
try:
points = get_special_points(cell)
except Exception:
return []
return generate_kpath_parameters(points, paths, 100)
def get_bandpath_as_aims_strings(self, pbc=[True, True, True]):
"""This function sets up the band path according to Setyawan-Curtarolo conventions.
Returns:
list: List of strings containing the k-path sections.
"""
from ase.dft.kpoints import parse_path_string, kpoint_convert
atoms = self.structure.atoms
atoms.pbc = pbc
path = parse_path_string(
atoms.cell.get_bravais_lattice(pbc=atoms.pbc).bandpath().path)
# list Of lists of path segments
points = atoms.cell.get_bravais_lattice(
pbc=atoms.pbc).bandpath().special_points
segments = []
for seg in path:
section = [(i, j) for i, j in zip(seg[:-1], seg[1:])]
segments.append(section)
output_bands = []
index = 1
for seg in segments:
output_bands.append(
"## Brillouin Zone section Nr. {:d}\n".format(index))
for sec in seg:
dist = np.array(points[sec[1]]) - np.array(points[sec[0]])
length = np.linalg.norm(
kpoint_convert(atoms.cell, skpts_kc=dist))
npoints = np.int_(np.round(np.asarray(length) * 20))
vec1 = "{:.6f} {:.6f} {:.6f}".format(*points[sec[0]])
vec2 = "{:.6f} {:.6f} {:.6f}".format(*points[sec[1]])
output_bands.append(
"{vec1} \t {vec2} \t {npoints} \t {label1} {label2}".
format(
label1=sec[0],
label2=sec[1],
npoints=npoints,
vec1=vec1,
vec2=vec2,
))
index += 1
return output_bands
def set_bandpath(self, bandpathstring):
new_bandpath = parse_path_string(bandpathstring)
old_path = self.bandpath
special_points = old_path.special_points
pairs = [(s[0], s[1]) for s in self.bands.keys()]
for segment in new_bandpath:
assert len(segment) > 1, "A vertex needs at least two points."
p = zip(segment[:-1], segment[1:])
for s1, s2 in p:
assert any(x in pairs for x in ((s1, s2), (
s2,
s1))), "The k-path {}-{} has not been calculated.".format(
s1, s2)
else:
new_path = BandPath(
path=bandpathstring,
cell=self.structure.cell,
special_points=special_points,
)
self._bandpath = new_path
ax.view_init(azim=azim / pi * 180, elev=elev / pi * 180)
for X, cell in [('cubic', np.eye(3)), ('fcc', [[0, 1, 1], [1, 0, 1], [1, 1,
0]]),
('bcc', [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]),
('tetragonal', [[1, 0, 0], [0, 1, 0], [0, 0, 1.3]]),
('orthorhombic', [[1, 0, 0], [0, 1.2, 0], [0, 0, 1.4]]),
('hexagonal', [[1, 0, 0], [-0.5, 3**0.5 / 2, 0], [0, 0, 1]]),
('monoclinic', [[1, 0, 0], [0, 1, 0], [0, 0.2, 1]])]:
icell = np.linalg.inv(cell)
print(cell, X)
special_points = get_special_points(cell, X)
paths = []
for names in parse_path_string(special_paths[X]):
points = []
for name in names:
points.append(np.dot(icell, special_points[name]))
paths.append((names, points))
if X == 'bcc':
scale = 0.6
elev = pi / 13
else:
scale = 1
elev = None
plot(cell, paths, elev, scale)
plt.savefig(X + '.svg')
def bz3d_plot(cell, vectors=False, paths=None, points=None, ax=None,
elev=None, scale=1, repeat=None, transformations=None,
hide_ax=True, **kwargs):
"""
For now this is lifted from ase.dft.bz.bz3d_plot with some modifications. All copyright and
licensing terms for this and bz2d_plot are those of the current release of ASE
(Atomic Simulation Environment).
:param cell:
:param vectors:
:param paths:
:param points:
:param elev:
:param scale:
:return:
"""
try:
from ase.dft.bz import bz_vertices # dynamic because we do not require ase
except ImportError:
warnings.warn('You will need to install ASE (Atomic Simulation Environment) to use this feature.')
raise ImportError('You will need to install ASE before using Brillouin Zone plotting')
class Arrow3D(FancyArrowPatch):
def __init__(self, xs, ys, zs, *args, **kwargs):
FancyArrowPatch.__init__(self, (0, 0), (0, 0), *args, **kwargs)
self._verts3d = xs, ys, zs
def draw(self, renderer):
xs3d, ys3d, zs3d = self._verts3d
xs, ys, zs = proj3d.proj_transform(xs3d, ys3d, zs3d, renderer.M)
self.set_positions((xs[0], ys[0]), (xs[1], ys[1]))
FancyArrowPatch.draw(self, renderer)
icell = np.linalg.inv(cell).T
kpoints = points
if isinstance(paths, str):
from ase.dft.kpoints import (get_special_points, special_paths, parse_path_string,
crystal_structure_from_cell)
special_points = get_special_points(cell)
structure = crystal_structure_from_cell(cell)
path_string = special_paths[structure] if paths == 'all' else paths
paths = []
for names in parse_path_string(path_string):
points = []
for name in names:
points.append(np.dot(icell.T, special_points[name]))
paths.append((names, points))
if ax is None:
fig = plt.figure(figsize=(5, 5))
ax = fig.gca(projection='3d')
azim = np.pi / 5
elev = elev or np.pi / 6
x = np.sin(azim)
y = np.cos(azim)
view = [x * np.cos(elev), y * np.cos(elev), np.sin(elev)]
bz1 = bz_vertices(icell)
maxp = 0.0
if repeat is None:
repeat = (1, 1, 1,)
dx, dy, dz = icell[0], icell[1], icell[2]
rep_x, rep_y, rep_z = repeat
if isinstance(rep_x, int):
rep_x = (0, rep_x)
if isinstance(rep_y, int):
rep_y = (0, rep_y)
if isinstance(rep_z, int):
rep_z = (0, rep_z)
c = kwargs.pop('c', 'k')
c = kwargs.pop('color', c)
for ix, iy, iz in itertools.product(range(*rep_x), range(*rep_y), range(*rep_z)):
delta = dx * ix + dy * iy + dz * iz
for points, normal in bz1:
color = c
if np.dot(normal, view) < 0:
ls = ':'
else:
ls = '-'
cosines = np.dot(icell, normal)/ np.linalg.norm(normal) / np.linalg.norm(icell, axis=1)
for idx, cosine in enumerate(cosines):
if np.abs(np.abs(cosine) - 1) < 1e-6 and False: # debugging this
tup = [rep_x, rep_y, rep_z][idx]
current = [ix, iy, iz][idx]
if cosine < 0:
current = current - 1
if tup[0] < current + 1 < tup[1]:
color = (1, 1, 1, 0)
if current + 1 != tup[1] and current != tup[0]:
ls = ':'
color='blue'
x, y, z = np.concatenate([points, points[:1]]).T
x, y, z = x + delta[0], y + delta[1], z + delta[2]
ax.plot(x, y, z, c=color, ls=ls, **kwargs)
maxp = max(maxp, points.max())
if vectors:
ax.add_artist(Arrow3D([0, icell[0, 0]],
[0, icell[0, 1]],
[0, icell[0, 2]],
mutation_scale=20, lw=1,
arrowstyle='-|>', color='k'))
ax.add_artist(Arrow3D([0, icell[1, 0]],
[0, icell[1, 1]],
[0, icell[1, 2]],
mutation_scale=20, lw=1,
arrowstyle='-|>', color='k'))
ax.add_artist(Arrow3D([0, icell[2, 0]],
[0, icell[2, 1]],
[0, icell[2, 2]],
mutation_scale=20, lw=1,
arrowstyle='-|>', color='k'))
maxp = max(maxp, 0.6 * icell.max())
if paths is not None:
for names, points in paths:
x, y, z = np.array(points).T
ax.plot(x, y, z, c='r', ls='-')
for name, point in zip(names, points):
x, y, z = point
if name == 'G':
name = '\\Gamma'
elif len(name) > 1:
name = name[0] + '_' + name[1]
ax.text(x, y, z, '$' + name + '$',
ha='center', va='bottom', color='r')
if kpoints is not None:
for p in kpoints:
ax.scatter(p[0], p[1], p[2], c='b')
if hide_ax:
ax.set_axis_off()
ax.autoscale_view(tight=True)
s = maxp / 0.5 * 0.45 * scale
ax.set_xlim(-s, s)
ax.set_ylim(-s, s)
ax.set_zlim(-s, s)
ax.set_aspect('equal')
ax.view_init(azim=azim / np.pi * 180, elev=elev / np.pi * 180)
def special_point_names(self):
labels = parse_path_string(self._variant.special_point_names)
assert len(labels) == 1 # list of lists
return labels[0]
ax.view_init(azim=azim / pi * 180, elev=elev / pi * 180)
for X, cell in [
('cubic', np.eye(3)),
('fcc', [[0, 1, 1], [1, 0, 1], [1, 1, 0]]),
('bcc', [[-1, 1, 1], [1, -1, 1], [1, 1, -1]]),
('tetragonal', [[1, 0, 0], [0, 1, 0], [0, 0, 1.3]]),
('orthorhombic', [[1, 0, 0], [0, 1.2, 0], [0, 0, 1.4]]),
('hexagonal', [[1, 0, 0], [-0.5, 3**0.5 / 2, 0], [0, 0, 1]]),
('monoclinic', [[1, 0, 0], [0, 1, 0], [0, 0.2, 1]])]:
icell = np.linalg.inv(cell)
special_points = get_special_points(X, cell)
paths = []
for names in parse_path_string(special_paths[X]):
points = []
for name in names:
points.append(np.dot(icell, special_points[name]))
paths.append((names, points))
if X == 'bcc':
scale = 0.6
elev = pi / 13
else:
scale = 1
elev = None
plot(cell, paths, elev, scale)
plt.savefig(X + '.svg')
def bz2d_plot(cell, vectors=False, paths=None, points=None, repeat=None, ax=None,
transformations=None, offset=None, hide_ax=True, set_equal_aspect=True,
**kwargs):
"""
This piece of code modified from ase.ase.dft.bz.py:bz2d_plot and follows copyright and license for ASE.
Plots a Brillouin zone corresponding to a given unit cell
:param cell:
:param vectors:
:param paths:
:param points:
:return:
"""
kpoints = points
bz1, icell, cell = twocell_to_bz1(cell)
if ax is None:
ax = plt.axes()
if isinstance(paths, str):
from ase.dft.kpoints import (get_special_points, special_paths, parse_path_string,
crystal_structure_from_cell)
special_points = get_special_points(cell)
structure = crystal_structure_from_cell(cell)
path_string = special_paths[structure] if paths == 'all' else paths
paths = []
for names in parse_path_string(path_string):
points = []
for name in names:
points.append(np.dot(icell.T, special_points[name]))
paths.append((names, points))
maxp = 0.0
c = kwargs.pop('c', 'k')
c = kwargs.pop('color', c)
ls = kwargs.pop('ls', kwargs.pop('linestyle', '-'))
for points, normal in bz1:
points = apply_transformations(points, transformations)
x, y, z = np.concatenate([points, points[:1]]).T
ax.plot(x, y, c=c, ls=ls, **kwargs)
maxp = max(maxp, points.max())
if repeat is not None:
dx, dy = icell[0], icell[1]
rep_x, rep_y = repeat
if isinstance(rep_x, int):
rep_x = (0, rep_x)
if isinstance(rep_y, int):
rep_y = (0, rep_y)
for ix, iy in itertools.product(range(*rep_x), range(*rep_y)):
delta = dx * ix + dy * iy
for points, normal in bz1:
x, y, z = np.concatenate([points, points[:1]]).T
x, y = x + delta[0], y + delta[1]
x, y, z = apply_transformations(np.asarray([x, y, z]).T, transformations).T
c = kwargs.pop('c', 'k')
c = kwargs.pop('color', c)
ax.plot(x, y, c=c, ls=ls, **kwargs)
maxp = max(maxp, points.max())
if vectors:
ax.arrow(0, 0, icell[0, 0], icell[0, 1],
lw=1, color='k',
length_includes_head=True,
head_width=0.03, head_length=0.05)
ax.arrow(0, 0, icell[1, 0], icell[1, 1],
lw=1, color='k',
length_includes_head=True,
head_width=0.03, head_length=0.05)
if paths is not None:
annotate_special_paths(ax, paths, offset=offset, transformations=transformations)
if kpoints is not None:
for p in kpoints:
ax.scatter(p[0], p[1], c='b')
if hide_ax:
ax.set_axis_off()
ax.autoscale_view(tight=True)
if set_equal_aspect:
ax.set_aspect('equal')
def __init__(self,astruct,mesh,evals,fermi_energy):
import spglib,numpy
cell=astruct_to_cell(astruct)
self.lattice=cell[0]
#celltmp=[ a if a!=float('inf') else 1.0 for a in astruct['cell']]
#self.lattice=numpy.diag(celltmp)
#print 'lattice',self.lattice
#pos=[ [ a/b if b!=float('inf') else 0.0 for a,b in zip(at.values()[0], celltmp)]for at in astruct['positions']]
#atoms=[ at.keys()[0] for at in astruct['positions']]
#ianames,iatype=numpy.unique(atoms,return_inverse=True) #[1,]*4+[2,]*4 #we should write a function for the iatype
#print 'iatype', iatype
#cell=(self.lattice,pos,iatype)
safe_print('spacegroup',spglib.get_spacegroup(cell, symprec=1e-5))
#then define the pathes and special points
import ase.dft.kpoints as ase
#we should adapt the 'cubic'
cell_tmp=astruct['cell']
#print 'cell',cell_tmp,numpy.allclose(cell_tmp,[cell_tmp[0],]*len(cell_tmp))
if numpy.allclose(cell_tmp,[cell_tmp[0],]*len(cell_tmp)):
lattice_string='cubic'
else:
lattice_string='orthorhombic'
safe_print('Lattice found:',lattice_string)
self.special_points=ase.get_special_points(lattice_string, self.lattice, eps=0.0001)
self.special_paths=ase.parse_path_string(ase.special_paths[lattice_string])
self.fermi_energy=fermi_energy
#dataset = spglib.get_symmetry_dataset(cell, symprec=1e-3)
#print dataset
#the shift has also to be put if present
mapping, grid = spglib.get_ir_reciprocal_mesh(mesh, cell, is_shift=[0, 0, 0])
lookup=[]
for ikpt in numpy.unique(mapping):
ltmp=[]
for ind, (m, g) in enumerate(zip(mapping, grid)):
if m==ikpt:
ltmp.append((g,ind))
lookup.append(ltmp)
safe_print('irreductible k-points',len(lookup))
#print 'mapping',mapping
#print 'grid',len(grid),numpy.max(grid)
coords=numpy.array(grid, dtype = numpy.float)/mesh
#print 'coords',coords
#print 'shape',coords.shape
#print grid #[ x+mesh[0]*y+mesh[0]*mesh[1]*z for x,y,z in grid]
#brillouin zone
kp=numpy.array([ k.kpt for k in evals])
ourkpt=numpy.rint(kp*(numpy.array(mesh))).astype(int)
#print ourkpt
bz=numpy.ndarray((coords.shape[0],evals[0].size),dtype=float)
#print bz
shift=(numpy.array(mesh)-1)/2
#print 'shift',shift
for ik in lookup:
irrk=None
for orbs,bzk in zip(evals,ourkpt):
for (kt,ind) in ik:
if (bzk==kt).all():
irrk=orbs
#print 'hello',orbs.kpt,kt
break
if irrk is not None: break
if irrk is None:
safe_print( 'error in ik',ik)
safe_print( 'our',ourkpt)
safe_print( 'spglib',grid)
safe_print( 'mapping',mapping)
for (kt,ind) in ik:
#r=kt+shift
#ind=numpy.argwhere([(g==kt).all() for g in grid])
#print 'ik',kt,r,ind
#print irrk.shape, bz.shape
#bz[r[0],r[1],r[2],:]=irrk.reshape(irrk.size)
bz[ind,:]=irrk.reshape(irrk.size)
#duplicate coordinates for the interpolation
bztmp=bz#.reshape((mesh[0]*mesh[1]*mesh[2], -1))
#print bztmp
ndup=7
duplicates=[[-1,0,0],[1,0,0],[0,-1,0],[0,1,0],[0,0,-1],[0,0,1]]
bztot=numpy.ndarray((ndup,bztmp.shape[0],bztmp.shape[1]))
bztot[0,:,:]=bztmp
ctot=numpy.ndarray((ndup,coords.shape[0],coords.shape[1]))
ctot[0,:,:]=coords
for i,sh in enumerate(duplicates):
bztot[i+1,:,:]=bztmp
ctot[i+1,:,:]=coords+sh
#print 'coors',coords,coords+[1.0,0,0]
bztot=bztot.reshape((ndup*bztmp.shape[0], -1))
ctot=ctot.reshape((ndup*coords.shape[0], -1))
import scipy.interpolate.interpnd as interpnd
self.interpolator=interpnd.LinearNDInterpolator(ctot,bztot)
#sanity check of the interpolation
sanity=0.0
for kpt in evals:
diff=numpy.ravel(numpy.ravel(kpt)-numpy.ravel(self.interpolator([ kpt.kpt])))
sanity=max(sanity,numpy.dot(diff,diff))
print('Interpolation bias',sanity)
def plot_reciprocal_cell(atoms,
path='default',
k_points=False,
ibz_k_points=False,
plot_vectors=True,
dimension=3,
output=None,
verbose=False):
import matplotlib.pyplot as plt
cell = atoms.get_cell()
icell = atoms.get_reciprocal_cell()
try:
cs = crystal_structure_from_cell(cell)
except ValueError:
cs = None
if verbose:
if cs:
print('Crystal:', cs)
print('Special points:', special_paths[cs])
print('Lattice vectors:')
for i, v in enumerate(cell):
print('{}: ({:16.9f},{:16.9f},{:16.9f})'.format(i + 1, *v))
print('Reciprocal vectors:')
for i, v in enumerate(icell):
print('{}: ({:16.9f},{:16.9f},{:16.9f})'.format(i + 1, *v))
# band path
if path:
if path == 'default':
path = special_paths[cs]
paths = []
special_points = get_special_points(cell)
for names in parse_path_string(path):
points = []
for name in names:
points.append(np.dot(icell.T, special_points[name]))
paths.append((names, points))
else:
paths = None
# k points
points = None
if atoms.calc is not None and hasattr(atoms.calc, 'get_bz_k_points'):
bzk = atoms.calc.get_bz_k_points()
if path is None:
try:
size, offset = get_monkhorst_pack_size_and_offset(bzk)
except ValueError:
# This was not a MP-grid. Must be a path in the BZ:
path = ''.join(labels_from_kpts(bzk, cell)[2])
if k_points:
points = bzk
elif ibz_k_points:
points = atoms.calc.get_ibz_k_points()
if points is not None:
for i in range(len(points)):
points[i] = np.dot(icell.T, points[i])
kwargs = {
'cell': cell,
'vectors': plot_vectors,
'paths': paths,
'points': points
}
if dimension == 1:
bz1d_plot(**kwargs)
elif dimension == 2:
bz2d_plot(**kwargs)
else:
bz3d_plot(interactive=True, **kwargs)
if output:
plt.savefig(output)
else:
plt.show()
def set_spectrum(self, bandpath=None, reference=None):
""" Sets :class:`~aimstools.bandstructures.mulliken_bandstructure.MullikenSpectrum` for a given bandpath.
Bandpath should be ASE-formatted string, e.g., "GMKG,A", where the "," denotes jumps.
"""
bands = self.bands
atoms = self.structure.copy()
start = time.time()
if bandpath != None:
self.set_bandpath(bandpath)
bp = parse_path_string(self.bandpath.path)
jumps = []
kps = []
occs = []
kpoint_axis = []
kpoint_labels = []
label_coords = []
spectrum = []
icell_cv = 2 * np.pi * np.linalg.pinv(self.structure.cell).T
contributions = []
for segment in bp:
kpoint_labels.append(segment[0])
label_coords.append(
label_coords[-1] if len(label_coords) > 0 else 0.0)
for s1, s2 in zip(segment[:-1], segment[1:]):
if (s1, s2) in bands.keys():
data = bands[(s1, s2)].data
kpoints = np.dot(bands[(s1, s2)].kpoints, icell_cv)
energies = data[0, :, :, :,
0] # (nkpoints, nspins, nstates)
occ = data[0, :, :, :, 1] # (nkpoints, nspins, nstates)
con = data[:, :, :, :,
2:] # (natoms, nkpoints, nspins, nstates, [tot, s, p, d, f])
elif (s1, s2) in [(k, j) for j, k in bands.keys()]:
data = bands[(s2, s1)].data
kpoints = np.dot(bands[(s2, s1)].kpoints, icell_cv)[::-1]
energies = data[0, :, :, :,
0] # (nkpoints, nspins, nstates)
energies = energies[::-1, :, :]
occ = data[0, :, :, :, 1] # (nkpoints, nspins, nstates)
occ = occ[::-1, :, :]
con = data[:, :, :, :,
2:] # (natoms, nkpoints, nspins, nstates, [tot, s, p, d, f])
con = con[:, ::-1, ...]
else:
raise Exception(
"Neither {}-{} nor {}-{} were found.".format(
s1, s2, s2, s1))
kstep = np.linalg.norm(kpoints[-1, :] - kpoints[0, :])
kaxis = np.linspace(0, kstep,
kpoints.shape[0]) + label_coords[-1]
kstep += label_coords[-1]
spectrum.append(energies)
kps.append(kpoints)
occs.append(occ)
contributions.append(con)
kpoint_axis.append(kaxis)
label_coords.append(kstep)
kpoint_labels.append(s2)
jumps.append(label_coords[-1])
jumps = jumps[:-1]
spectrum = np.concatenate(spectrum, axis=0)
kps = np.concatenate(kps, axis=0)
kpoint_axis = np.concatenate(kpoint_axis, axis=0)
occs = np.concatenate(occs, axis=0)
cons = np.concatenate(contributions, axis=1)
fermi_level = self.fermi_level.soc if self.soc else self.fermi_level.scalar
self.set_energy_reference(reference, self.soc)
reference, shift = self.energy_reference
spec = MullikenSpectrum(
atoms=atoms,
kpoints=kps,
kpoint_axis=kpoint_axis,
eigenvalues=spectrum,
occupations=occs,
contributions=cons,
label_coords=label_coords,
kpoint_labels=kpoint_labels,
jumps=jumps,
fermi_level=fermi_level,
reference=reference,
shift=shift,
bandpath=bp,
)
end = time.time()
logger.info(
"Creating spectrum from bands took {:.2f} seconds.".format(end -
start))
self._spectrum = spec
def plot_magnon_band(ham,
kvectors=np.array([[0, 0, 0], [0.5, 0, 0], [0.5, 0.5, 0],
[0, 0, 0], [.5, .5, .5]]),
knames=['$\Gamma$', 'X', 'M', '$\Gamma$', 'R'],
supercell_matrix=None,
npoints=100,
color='red',
ax=None,
eps=1e-3,
kpath_fname=None):
if ax is None:
fig, ax = plt.subplots()
if knames is None or kvectors is None:
from ase.build.tools import niggli_reduce_cell
rcell, M = niggli_reduce_cell(ham.cell)
fcell = fix_cell(ham.cell, eps=eps)
lattice_type = crystal_structure_from_cell(rcell,
eps=eps,
niggli_reduce=False)
labels = parse_path_string(special_paths[lattice_type])
knames = [item for sublist in labels for item in sublist]
kpts, x, X = bandpath(special_paths[lattice_type],
rcell,
npoints=npoints,
eps=1e-8)
spk = get_special_points(ham.cell, eps=1e-8)
else:
kpts, x, X = bandpath(kvectors, fix_cell(ham.cell), npoints)
spk = dict(zip(knames, kvectors))
if supercell_matrix is not None:
kvectors = [np.dot(k, supercell_matrix) for k in kvectors]
qsolver = QSolver(hamiltonian=ham)
evals, evecs = qsolver.solve_all(kpts, eigen_vectors=True)
nbands = evals.shape[1]
#evecs
imin = np.argmin(evals[:, 0])
emin = np.min(evals[:, 0])
nspin = evals.shape[1] // 3
evec_min = evecs[imin, :, 0].reshape(nspin, 3)
# write information to file
if kpath_fname is not None:
with open(kpath_fname, 'w') as myfile:
myfile.write("K-points:\n")
for name, k in spk.items():
myfile.write("%s: %s\n" % (name, k))
myfile.write("\nThe energy minimum is at:")
myfile.write("%s\n" % kpts[np.argmin(evals[:, 0])])
for i, ev in enumerate(evec_min):
myfile.write("spin %s: %s \n" % (i, ev / np.linalg.norm(ev)))
print("\nThe energy minimum is at:")
print("%s\n" % kpts[np.argmin(evals[:, 0])])
print("\n The ground state is:")
for i, ev in enumerate(evec_min):
print("spin %s: %s" % (i, ev / np.linalg.norm(ev)))
for i in range(nbands):
ax.plot(x, (evals[:, i] - emin) / 1.6e-22)
ax.set_xlabel('Q-point')
ax.set_ylabel('Energy (meV)')
ax.set_xlim(x[0], x[-1])
ax.set_ylim(0)
ax.set_xticks(X)
ax.set_xticklabels(knames)
for x in X:
ax.axvline(x, linewidth=0.6, color='gray')
return ax
