def atoms2bandstructure(atoms, parser, args):
cell = atoms.get_cell()
calc = atoms.calc
bzkpts = calc.get_bz_k_points()
ibzkpts = calc.get_ibz_k_points()
efermi = calc.get_fermi_level()
nibz = len(ibzkpts)
nspins = 1 + int(calc.get_spin_polarized())
eps = np.array([[calc.get_eigenvalues(kpt=k, spin=s)
for k in range(nibz)]
for s in range(nspins)])
if not args.quiet:
print('Spins, k-points, bands: {}, {}, {}'.format(*eps.shape))
if bzkpts is None:
if ibzkpts is None:
raise ValueError('Cannot find any k-point data')
else:
path_kpts = ibzkpts
else:
try:
size, offset = get_monkhorst_pack_size_and_offset(bzkpts)
except ValueError:
path_kpts = ibzkpts
else:
if not args.quiet:
print('Interpolating from Monkhorst-Pack grid (size, offset):')
print(size, offset)
if args.path is None:
err = 'Please specify a path!'
try:
cs = crystal_structure_from_cell(cell)
except ValueError:
err += ('\nASE cannot automatically '
'recognize this crystal structure')
else:
from ase.dft.kpoints import special_paths
kptpath = special_paths[cs]
err += ('\nIt looks like you have a {} crystal structure.'
'\nMaybe you want its special path:'
' {}'.format(cs, kptpath))
parser.error(err)
bz2ibz = calc.get_bz_to_ibz_map()
path_kpts = bandpath(args.path, atoms.cell, args.points).kpts
icell = atoms.get_reciprocal_cell()
eps = monkhorst_pack_interpolate(path_kpts, eps.transpose(1, 0, 2),
icell, bz2ibz, size, offset)
eps = eps.transpose(1, 0, 2)
special_points = get_special_points(cell)
path = BandPath(atoms.cell, kpts=path_kpts,
special_points=special_points)
return BandStructure(path, eps, reference=efermi)
def labels_from_kpts(kpts, cell, eps=1e-5):
"""Get an x-axis to be used when plotting a band structure.
The first of the returned lists can be used as a x-axis when plotting
the band structure. The second list can be used as xticks, and the third
as xticklabels.
Parameters:
kpts: list
List of scaled k-points.
cell: list
Unit cell of the atomic structure.
Returns:
Three arrays; the first is a list of cumulative distances between kpoints,
the second is x coordinates of the special points,
the third is the special points as strings.
"""
try:
crystal_structure = crystal_structure_from_cell(cell)
except ValueError:
warnings.warn('Can not recognize your crystal!')
special_points = {}
else:
special_points = get_special_points(crystal_structure, cell)
points = np.asarray(kpts)
diffs = points[1:] - points[:-1]
kinks = abs(diffs[1:] - diffs[:-1]).sum(1) > eps
N = len(points)
indices = [0]
indices.extend(np.arange(1, N - 1)[kinks])
indices.append(N - 1)
labels = []
for kpt in points[indices]:
for label, k in special_points.items():
if abs(kpt - k).sum() < eps:
break
else:
label = '?'
labels.append(label)
xcoords = [0]
for i1, i2 in zip(indices[:-1], indices[1:]):
if i1 + 1 == i2:
length = 0
else:
diff = points[i2] - points[i1]
length = np.linalg.norm(kpoint_convert(cell, skpts_kc=diff))
xcoords.extend(np.linspace(0, length, i2 - i1 + 1)[1:] + xcoords[-1])
xcoords = np.array(xcoords)
return xcoords, xcoords[indices], labels
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 bandpath(path, cell, npoints=50):
"""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, basestring):
xtal = crystal_structure_from_cell(cell)
special = get_special_points(xtal, cell)
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 main(args, parser):
atoms = read(args.calculation)
cell = atoms.get_cell()
calc = atoms.calc
bzkpts = calc.get_bz_k_points()
ibzkpts = calc.get_ibz_k_points()
efermi = calc.get_fermi_level()
nibz = len(ibzkpts)
nspins = 1 + int(calc.get_spin_polarized())
eps = np.array([[calc.get_eigenvalues(kpt=k, spin=s)
for k in range(nibz)]
for s in range(nspins)])
if not args.quiet:
print('Spins, k-points, bands: {}, {}, {}'.format(*eps.shape))
try:
size, offset = get_monkhorst_pack_size_and_offset(bzkpts)
except ValueError:
path = ibzkpts
else:
if not args.quiet:
print('Interpolating from Monkhorst-Pack grid (size, offset):')
print(size, offset)
if args.path is None:
err = 'Please specify a path!'
try:
cs = crystal_structure_from_cell(cell)
except ValueError:
err += ('\nGPAW cannot autimatically '
'recognize this crystal structure')
else:
from ase.dft.kpoints import special_paths
kptpath = special_paths[cs]
err += ('\nIt looks like you have a {} crystal structure.'
'\nMaybe you want its special path:'
' {}'.format(cs, kptpath))
parser.error(err)
bz2ibz = calc.get_bz_to_ibz_map()
path = bandpath(args.path, atoms.cell, args.points)[0]
icell = atoms.get_reciprocal_cell()
eps = monkhorst_pack_interpolate(path, eps.transpose(1, 0, 2),
icell, bz2ibz, size, offset)
eps = eps.transpose(1, 0, 2)
emin, emax = (float(e) for e in args.range)
bs = BandStructure(atoms.cell, path, eps, reference=efermi)
bs.plot(emin=emin, emax=emax)
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 test_monoclinic():
"""Test band structure from different variations of hexagonal cells."""
import numpy as np
from ase import Atoms
from ase.calculators.test import FreeElectrons
from ase.geometry import (crystal_structure_from_cell, cell_to_cellpar,
cellpar_to_cell)
from ase.dft.kpoints import get_special_points
mc1 = [[1, 0, 0], [0, 1, 0], [0, 0.2, 1]]
par = cell_to_cellpar(mc1)
mc2 = cellpar_to_cell(par)
mc3 = [[1, 0, 0], [0, 1, 0], [-0.2, 0, 1]]
mc4 = [[1, 0, 0], [-0.2, 1, 0], [0, 0, 1]]
path = 'GYHCEM1AXH1'
firsttime = True
for cell in [mc1, mc2, mc3, mc4]:
a = Atoms(cell=cell, pbc=True)
a.cell *= 3
a.calc = FreeElectrons(nvalence=1, kpts={'path': path})
cs = crystal_structure_from_cell(a.cell)
assert cs == 'monoclinic'
r = a.cell.reciprocal()
k = get_special_points(a.cell)['H']
print(np.dot(k, r))
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
assert ''.join(labels) == path
e_skn = bs.energies
# bs.plot()
if firsttime:
coords1 = coords
labelcoords1 = labelcoords
e_skn1 = e_skn
firsttime = False
else:
for d in [
coords - coords1, labelcoords - labelcoords1,
e_skn - e_skn1
]:
print(abs(d).max())
assert abs(d).max() < 1e-13, d
def get_cellinfo(cell, lattice=None, eps=2e-4):
from ase.build.tools import niggli_reduce_cell
rcell, M = niggli_reduce_cell(cell)
latt = crystal_structure_from_cell(rcell, niggli_reduce=False)
if lattice:
assert latt == lattice.lower(), latt
if latt == 'monoclinic':
# Transform From Niggli to Setyawana-Curtarolo cell:
a, b, c, alpha, beta, gamma = cell_to_cellpar(rcell, radians=True)
if abs(beta - np.pi / 2) > eps:
T = np.array([[0, 1, 0], [-1, 0, 0], [0, 0, 1]])
scell = np.dot(T, rcell)
elif abs(gamma - np.pi / 2) > eps:
T = np.array([[0, 0, 1], [1, 0, 0], [0, -1, 0]])
else:
raise ValueError('You are using a badly oriented ' +
'monoclinic unit cell. Please choose one with ' +
'either beta or gamma != pi/2')
scell = np.dot(np.dot(T, rcell), T.T)
a, b, c, alpha, beta, gamma = cell_to_cellpar(scell, radians=True)
assert alpha < np.pi / 2, 'Your monoclinic angle has to be < pi / 2'
M = np.dot(M, T.T)
eta = (1 - b * cos(alpha) / c) / (2 * sin(alpha)**2)
nu = 1 / 2 - eta * c * cos(alpha) / b
points = {
'G': [0, 0, 0],
'A': [1 / 2, 1 / 2, 0],
'C': [0, 1 / 2, 1 / 2],
'D': [1 / 2, 0, 1 / 2],
'D1': [1 / 2, 0, -1 / 2],
'E': [1 / 2, 1 / 2, 1 / 2],
'H': [0, eta, 1 - nu],
'H1': [0, 1 - eta, nu],
'H2': [0, eta, -nu],
'M': [1 / 2, eta, 1 - nu],
'M1': [1 / 2, 1 - eta, nu],
'M2': [1 / 2, eta, -nu],
'X': [0, 1 / 2, 0],
'Y': [0, 0, 1 / 2],
'Y1': [0, 0, -1 / 2],
'Z': [1 / 2, 0, 0]
}
elif latt == 'rhombohedral type 1':
a, b, c, alpha, beta, gamma = cell_to_cellpar(cell=cell, radians=True)
eta = (1 + 4 * np.cos(alpha)) / (2 + 4 * np.cos(alpha))
nu = 3 / 4 - eta / 2
points = {
'G': [0, 0, 0],
'B': [eta, 1 / 2, 1 - eta],
'B1': [1 / 2, 1 - eta, eta - 1],
'F': [1 / 2, 1 / 2, 0],
'L': [1 / 2, 0, 0],
'L1': [0, 0, -1 / 2],
'P': [eta, nu, nu],
'P1': [1 - nu, 1 - nu, 1 - eta],
'P2': [nu, nu, eta - 1],
'Q': [1 - nu, nu, 0],
'X': [nu, 0, -nu],
'Z': [0.5, 0.5, 0.5]
}
else:
points = ibz_points[latt]
myspecial_points = {label: np.dot(M, kpt) for label, kpt in points.items()}
return CellInfo(rcell=rcell, lattice=latt, special_points=myspecial_points)
assert np.allclose(correct_pos, positions)
# Test center away from values 0, 0.5
result_positions = wrap_positions(positions, cell,
pbc=[True, True, False],
center=0.2)
correct_pos = [[4.7425, 1.2575, 8.7425],
[2.0275, 3.9725, 8.7425],
[3.385, 2.615, 10.1],
[-0.6875, 1.2575, 8.7425],
[6.1, -0.1, 10.1],
[3.385, -2.815, 10.1],
[2.0275, -1.4575, 8.7425],
[0.67, -0.1, 10.1]]
assert np.allclose(correct_pos, result_positions)
# Get the correct crystal structure from a range of different cells
assert crystal_structure_from_cell(bulk('Al').get_cell()) == 'fcc'
assert crystal_structure_from_cell(bulk('Fe').get_cell()) == 'bcc'
assert crystal_structure_from_cell(bulk('Zn').get_cell()) == 'hexagonal'
cell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
assert crystal_structure_from_cell(cell) == 'cubic'
cell = [[1, 0, 0], [0, 1, 0], [0, 0, 2]]
assert crystal_structure_from_cell(cell) == 'tetragonal'
cell = [[1, 0, 0], [0, 2, 0], [0, 0, 3]]
assert crystal_structure_from_cell(cell) == 'orthorhombic'
cell = [[1, 0, 0], [0, 2, 0], [0.5, 0, 3]]
assert crystal_structure_from_cell(cell) == 'monoclinic'
cell = [[1, 0, 0], [0.5, 3**0.5 / 2, 0], [0, 0, 3]]
assert crystal_structure_from_cell(cell) == 'hexagonal'
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()
assert np.allclose(correct_pos, positions)
# Test center away from values 0, 0.5
result_positions = wrap_positions(positions, cell,
pbc=[True, True, False],
center=0.2)
correct_pos = [[4.7425, 1.2575, 8.7425],
[2.0275, 3.9725, 8.7425],
[3.385, 2.615, 10.1],
[-0.6875, 1.2575, 8.7425],
[6.1, -0.1, 10.1],
[3.385, -2.815, 10.1],
[2.0275, -1.4575, 8.7425],
[0.67, -0.1, 10.1]]
assert np.allclose(correct_pos, result_positions)
# Get the correct crystal structure from a range of different cells
assert crystal_structure_from_cell(bulk('Al').get_cell()) == 'fcc'
assert crystal_structure_from_cell(bulk('Fe').get_cell()) == 'bcc'
assert crystal_structure_from_cell(bulk('Zn').get_cell()) == 'hexagonal'
cell = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
assert crystal_structure_from_cell(cell) == 'cubic'
cell = [[1, 0, 0], [0, 1, 0], [0, 0, 2]]
assert crystal_structure_from_cell(cell) == 'tetragonal'
cell = [[1, 0, 0], [0, 2, 0], [0, 0, 3]]
assert crystal_structure_from_cell(cell) == 'orthorhombic'
cell = [[1, 0, 0], [0, 2, 0], [0, 1, 3]]
assert crystal_structure_from_cell(cell) == 'monoclinic'
"""Test band structure from different variations of hexagonal cells."""
import numpy as np
from ase import Atoms
from ase.calculators.test import FreeElectrons
from ase.geometry import crystal_structure_from_cell
from ase.dft.kpoints import get_special_points
firsttime = True
for cell in [[[1, 0, 0], [0.5, 3**0.5 / 2, 0], [0, 0, 1]],
[[1, 0, 0], [-0.5, 3**0.5 / 2, 0], [0, 0, 1]],
[[0.5, -3**0.5 / 2, 0], [0.5, 3**0.5 / 2, 0], [0, 0, 1]]]:
a = Atoms(cell=cell, pbc=True)
a.cell *= 3
a.calc = FreeElectrons(nvalence=1, kpts={'path': 'GMKG'})
print(crystal_structure_from_cell(a.cell))
r = a.get_reciprocal_cell()
k = get_special_points(a.cell)['K']
print(np.dot(k, r))
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
assert ''.join(labels) == 'GMKG'
e_skn = bs.energies
if firsttime:
coords1 = coords
labelcoords1 = labelcoords
e_skn1 = e_skn
firsttime = False
else:
for d in [coords - coords1,
labelcoords - labelcoords1,
def get_special_points(cell, lattice=None, eps=2e-4):
"""Return dict of special points.
The definitions are from a paper by Wahyu Setyawana and Stefano
Curtarolo::
http://dx.doi.org/10.1016/j.commatsci.2010.05.010
cell: 3x3 ndarray
Unit cell.
lattice: str
Optionally check that the cell is one of the following: cubic, fcc,
bcc, orthorhombic, tetragonal, hexagonal or monoclinic.
eps: float
Tolerance for cell-check.
"""
if isinstance(cell, str):
warnings.warn('Please call this function with cell as the first '
'argument')
lattice, cell = cell, lattice
from ase.build.tools import niggli_reduce_cell
rcell, M = niggli_reduce_cell(cell)
latt = crystal_structure_from_cell(rcell, niggli_reduce=False)
if lattice:
assert latt == lattice.lower(), latt
if latt == 'monoclinic':
# Transform From Niggli to Setyawana-Curtarolo cell:
a, b, c, alpha, beta, gamma = cell_to_cellpar(rcell, radians=True)
if abs(beta - np.pi / 2) > eps:
T = np.array([[0, 1, 0], [-1, 0, 0], [0, 0, 1]])
scell = np.dot(T, rcell)
elif abs(gamma - np.pi / 2) > eps:
T = np.array([[0, 0, 1], [1, 0, 0], [0, -1, 0]])
else:
raise ValueError('You are using a badly oriented ' +
'monoclinic unit cell. Please choose one with ' +
'either beta or gamma != pi/2')
scell = np.dot(np.dot(T, rcell), T.T)
a, b, c, alpha, beta, gamma = cell_to_cellpar(scell, radians=True)
assert alpha < np.pi / 2, 'Your monoclinic angle has to be < pi / 2'
M = np.dot(M, T.T)
eta = (1 - b * cos(alpha) / c) / (2 * sin(alpha)**2)
nu = 1 / 2 - eta * c * cos(alpha) / b
points = {
'G': [0, 0, 0],
'A': [1 / 2, 1 / 2, 0],
'C': [0, 1 / 2, 1 / 2],
'D': [1 / 2, 0, 1 / 2],
'D1': [1 / 2, 0, -1 / 2],
'E': [1 / 2, 1 / 2, 1 / 2],
'H': [0, eta, 1 - nu],
'H1': [0, 1 - eta, nu],
'H2': [0, eta, -nu],
'M': [1 / 2, eta, 1 - nu],
'M1': [1 / 2, 1 - eta, nu],
'M2': [1 / 2, eta, -nu],
'X': [0, 1 / 2, 0],
'Y': [0, 0, 1 / 2],
'Y1': [0, 0, -1 / 2],
'Z': [1 / 2, 0, 0]
}
elif latt == 'rhombohedral type 1':
a, b, c, alpha, beta, gamma = cell_to_cellpar(cell=cell, radians=True)
eta = (1 + 4 * np.cos(alpha)) / (2 + 4 * np.cos(alpha))
nu = 3 / 4 - eta / 2
points = {
'G': [0, 0, 0],
'B': [eta, 1 / 2, 1 - eta],
'B1': [1 / 2, 1 - eta, eta - 1],
'F': [1 / 2, 1 / 2, 0],
'L': [1 / 2, 0, 0],
'L1': [0, 0, -1 / 2],
'P': [eta, nu, nu],
'P1': [1 - nu, 1 - nu, 1 - eta],
'P2': [nu, nu, eta - 1],
'Q': [1 - nu, nu, 0],
'X': [nu, 0, -nu],
'Z': [0.5, 0.5, 0.5]
}
else:
points = special_points[latt]
return {label: np.dot(M, kpt) for label, kpt in points.items()}
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
from ase.geometry import crystal_structure_from_cell, cell_to_cellpar, cellpar_to_cell
from ase.dft.kpoints import get_special_points
mc1 = [[1, 0, 0], [0, 1, 0], [0, 0.2, 1]]
par = cell_to_cellpar(mc1)
mc2 = cellpar_to_cell(par)
mc3 = [[1, 0, 0], [0, 1, 0], [-0.2, 0, 1]]
mc4 = [[1, 0, 0], [-0.2, 1, 0], [0, 0, 1]]
path = 'GYHCEM1AXH1'
firsttime = True
for cell in [mc1, mc2, mc3, mc4]:
a = Atoms(cell=cell, pbc=True)
a.cell *= 3
a.calc = FreeElectrons(nvalence=1, kpts={'path': path})
cs = crystal_structure_from_cell(a.cell)
assert cs == 'monoclinic'
r = a.get_reciprocal_cell()
k = get_special_points(a.cell)['H']
print(np.dot(k, r))
a.get_potential_energy()
bs = a.calc.band_structure()
coords, labelcoords, labels = bs.get_labels()
assert ''.join(labels) == path
e_skn = bs.energies
# bs.plot()
if firsttime:
coords1 = coords
labelcoords1 = labelcoords
e_skn1 = e_skn
firsttime = False
def startMeasurement(filepath, file_type, covalent_radii_cut_off, c, n1, n2,
calculate):
if n1 > n2:
print("Final m cannot be smaller than initial m")
return
print("Starting script...")
slab = read(filepath)
total_particles = len(slab)
print("Slab %s read with success. Total particles %d" %
(filepath, total_particles))
print("Creating graph...")
if file_type == 'V':
G = generateGraphFromSlabVinkFile(slab, covalent_radii_cut_off)
else:
G = generateGraphFromSlab(slab, covalent_radii_cut_off)
total_nodes = G.get_total_nodes()
if total_nodes == 0 or G.get_total_edges() == 0:
print("No edges found in graph. Check covalent_radii_cut_off")
return
print("Graph created with success. Nodes found: %d" % total_nodes)
cell = slab.get_cell()
crystal_structure = crystal_structure_from_cell(cell)
if crystal_structure != "ortorhombic" and crystal_structure != "cubic":
print("Unit cell is not orthorhombic nor cubic")
return
measurement = Measurement()
measurement.fromFile(filepath, covalent_radii_cut_off, c, n1, n2)
measurement.createFile()
(pbcX, pbcY, pbcZ) = slab.get_pbc()
(dmin, dmax) = getMaxMinSlabArray(slab)
maxM = getNumberRandomPositions(n2 - 1, total_particles)
configurationalEntropy = bg.ConfigurationalEntropy(G, 3, len(slab), pbcX,
pbcY, pbcZ, maxM)
configurationalEntropy.add_positions(slab.get_positions(wrap=True))
print("Generating random positions...")
configurationalEntropy.init_search(0, cell[0][0], 0, cell[1][1], 0,
cell[2][2], n2 - 1, maxM, dmin, dmax)
print("Random positions generated.")
H_n_values = []
for n in range(n1, n2):
measurement.start()
m = getNumberRandomPositions(n, total_particles)
H_n, H1n = run(configurationalEntropy, m, n, c)
measurement.writeResult(n, m, H_n, H1n)
measurement.end()
H_n_values.append((n, H_n, H1n, "Y"))
calculateConfigurationalEntropy(n1, n2, H_n_values, c, calculate)
print("Program ended correctly")
