def __init__(self,
lattice=None,
basis=None,
coords=None,
cartesian=False,
wrap_coords=False):
super().__init__()
if basis is None:
basis = BasisAtoms()
else:
basis = BasisAtoms(basis)
basis.lattice = lattice
if lattice is not None and coords is not None:
for atom, pos in zip(basis, coords):
atom.lattice = lattice
if not cartesian:
atom.rs = pos
else:
atom.rs = lattice.cartesian_to_fractional(pos)
self.lattice = lattice
self.basis = basis
self.wrap_coords = wrap_coords
self.fmtstr = "{lattice!r}, {basis!r}, {coords!r}, " + \
"cartesian=False, wrap_coords={wrap_coords!r}"
def from_pymatgen_structure(cls, structure):
atoms = BasisAtoms()
for site in structure.sites:
atoms.append(BasisAtom(element=site.specie.symbol,
x=site.x, y=site.y, z=site.z))
return cls(lattice=Crystal2DLattice(
cell_matrix=structure.lattice.matrix), basis=atoms)
def __init__(self, lattice=None, basis=None, coords=None, cartesian=False,
wrap_coords=False, unit_cell=None, scaling_matrix=None):
super().__init__()
if unit_cell is None and basis is not None:
basis = BasisAtoms(basis)
basis.lattice = lattice
if lattice is not None and coords is not None:
for atom, pos in zip(basis, coords):
atom.lattice = lattice
if not cartesian:
atom.rs = pos
else:
atom.rs = lattice.cartesian_to_fractional(pos)
# if basis is None:
# basis = BasisAtoms()
# These attributes may be reset in the `@scaling_matrix.setter`
# method and so they need to be initialized *before* setting
# `self.scaling_matrix`.
self.basis = basis
self.lattice = lattice
self.unit_cell = unit_cell
self.wrap_coords = wrap_coords
self.scaling_matrix = scaling_matrix
self.fmtstr = \
"lattice={lattice!r}, basis={basis!r}, coords={coords!r}, " + \
"cartesian=False, wrap_coords={wrap_coords!r}, " + \
"unit_cell={unit_cell!r}, scaling_matrix={scaling_matrix!r}"
def test4():
lattice = Crystal3DLattice.cubic(a=5.0)
basis = BasisAtoms(atoms=['C', 'C'])
print(basis)
print(basis.lattice)
assert_true(basis.lattice is None)
basis.lattice = lattice
assert_true(isinstance(basis.lattice, Crystal3DLattice))
def generate_unit_cell(self):
"""Generate the nanotube unit cell."""
eps = 0.01
e1 = self.element1
e2 = self.element2
N = self.N
T = self.T
rt = self.rt
psi, tau, dpsi, dtau = self.unit_cell_symmetry_params
a = compute_Ch(self.n, self.m, bond=self.bond)
b = self.layer_spacing
c = compute_T(self.n, self.m, bond=self.bond, length=True)
lattice = Crystal3DLattice.orthorhombic(a, b, c)
basis = Atoms()
if self.verbose:
print('dpsi: {}'.format(dpsi))
print('dtau: {}\n'.format(dtau))
for i in range(N):
for j, element in enumerate((e1, e2), start=1):
theta = i * psi
h = i * tau
if j == 2:
theta += dpsi
h -= dtau
x = rt * theta
z = h
while z > T - eps:
z -= T
if z < 0:
z += T
xs, ys, zs = \
lattice.cartesian_to_fractional([x, 0, z])
if self.wrap_coords:
xs, ys, zs = \
lattice.wrap_fractional_coordinate([xs, ys, zs])
if self.debug:
print('i={}: x, z = ({:.6f}, {:.6f})'.format(i, x, z))
atom = Atom(element, lattice=lattice, xs=xs, ys=ys, zs=zs)
atom.rezero()
if self.verbose:
print('Basis Atom:\n{}'.format(atom))
basis.append(atom)
self.unit_cell = UnitCell(lattice=lattice, basis=basis)
def scaling_matrix(self, value):
if value is None:
self._scaling_matrix = np.asmatrix(np.ones(3, dtype=int))
return
if not isinstance(value, (int, float, tuple, list, np.ndarray)):
return
if isinstance(value, np.ndarray) and \
((value.shape == np.ones(3).shape and
np.allclose(value, np.ones(3))) or
(value.shape == np.eye(3).shape and
np.allclose(value, np.eye(3)))):
self._scaling_matrix = np.asmatrix(value)
return
if isinstance(value, numbers.Number):
value = self.lattice.nd * [int(value)]
scaling_matrix = np.asmatrix(value, dtype=int)
# scaling_matrix = np.asmatrix(value)
if scaling_matrix.shape != self.lattice.matrix.shape:
scaling_matrix = np.diagflat(scaling_matrix)
self._scaling_matrix = scaling_matrix
self.lattice = self.lattice.__class__(cell_matrix=self.scaling_matrix *
self.lattice.matrix)
tvecs = \
np.asarray(
np.asmatrix(supercell_lattice_points(self.scaling_matrix)) *
self.lattice.matrix)
basis = self.basis[:]
self.basis = BasisAtoms()
for atom in basis:
for tvec in tvecs:
xs, ys, zs = \
self.lattice.cartesian_to_fractional(atom.r + tvec)
if self.wrap_coords:
xs, ys, zs = \
self.lattice.wrap_fractional_coordinate(
[xs, ys, zs])
self.basis.append(
BasisAtom(atom.element,
lattice=self.lattice,
xs=xs,
ys=ys,
zs=zs))
def __init__(self, a=lattparams['alpha_quartz']['a'],
c=lattparams['alpha_quartz']['c'], **kwargs):
lattice = Crystal3DLattice.hexagonal(a, c)
basis = BasisAtoms(3 * ["Si"] + 6 * ["O"])
coords = [[0.4697, 0.0000, 0.0000],
[0.0000, 0.4697, 0.6667],
[0.5305, 0.5303, 0.3333],
[0.4133, 0.2672, 0.1188],
[0.2672, 0.4133, 0.5479],
[0.7328, 0.1461, 0.7855],
[0.5867, 0.8539, 0.2145],
[0.8539, 0.5867, 0.4521],
[0.1461, 0.7328, 0.8812]]
alpha_quartz = pymatgen_structure(lattice.cell_matrix,
basis.symbols, coords)
alpha_quartz = \
Crystal3DStructure.from_pymatgen_structure(alpha_quartz)
# alpha_quartz = \
# HexagonalStructure.from_spacegroup(154, a, c, ["Si", "O"],
# [[0.4697, 0.0000, 0.0000],
# [0.4135, 0.2669, 0.1191]],
# scaling_matrix=scaling_matrix)
super().__init__(structure=alpha_quartz, **kwargs)
def from_pymatgen_structure(cls, structure):
"""Return a `Crystal3DStructure` from a \
:class:`pymatgen:pymatgen.core.Structure`.
Parameters
----------
structure : :class:`pymatgen:pymatgen.core.Structure`
Returns
-------
:class:`Crystal3DStructure`
"""
atoms = BasisAtoms()
for site in structure.sites:
atoms.append(BasisAtom(site.specie.symbol,
x=site.x, y=site.y, z=site.z))
return cls(lattice=Crystal3DLattice(
cell_matrix=structure.lattice.matrix), basis=atoms)
def __init__(self,
lattice=None,
basis=None,
coords=None,
cartesian=False,
wrap_coords=False,
unit_cell=None,
scaling_matrix=None):
super().__init__()
if unit_cell is None and basis is not None:
basis = BasisAtoms(basis)
basis.lattice = lattice
if lattice is not None and coords is not None:
for atom, pos in zip(basis, coords):
atom.lattice = lattice
if not cartesian:
atom.rs = pos
else:
atom.rs = lattice.cartesian_to_fractional(pos)
# if basis is None:
# basis = BasisAtoms()
# These attributes may be reset in the `@scaling_matrix.setter`
# method and so they need to be initialized *before* setting
# `self.scaling_matrix`.
self.basis = basis
self.lattice = lattice
self.unit_cell = unit_cell
self.wrap_coords = wrap_coords
self.scaling_matrix = scaling_matrix
self.fmtstr = \
"lattice={lattice!r}, basis={basis!r}, coords={coords!r}, " + \
"cartesian=False, wrap_coords={wrap_coords!r}, " + \
"unit_cell={unit_cell!r}, scaling_matrix={scaling_matrix!r}"
def __init__(self, lattice=None, basis=None, coords=None, cartesian=False,
wrap_coords=False):
super().__init__()
if basis is None:
basis = BasisAtoms()
else:
basis = BasisAtoms(basis)
basis.lattice = lattice
if lattice is not None and coords is not None:
for atom, pos in zip(basis, coords):
atom.lattice = lattice
if not cartesian:
atom.rs = pos
else:
atom.rs = lattice.cartesian_to_fractional(pos)
self.lattice = lattice
self.basis = basis
self.wrap_coords = wrap_coords
self.fmtstr = "{lattice!r}, {basis!r}, {coords!r}, " + \
"cartesian=False, wrap_coords={wrap_coords!r}"
def test5():
atoms = \
BasisAtoms(atoms=generate_atoms(elements='periodic_table').symbols)
print(atoms[:5])
atoms_slice = atoms[5:10]
atoms[:5] = atoms_slice
assert_equal(atoms[:5], atoms[5:10])
print(atoms[:5])
atoms[:5] = ['C', 'H', 'N', 'Ar', 'He']
print(atoms[:8])
atoms[0] = 'Au'
print(atoms[:2])
def scaling_matrix(self, value):
if value is None:
self._scaling_matrix = np.asmatrix(np.ones(3, dtype=int))
return
if not isinstance(value, (int, float, tuple, list, np.ndarray)):
return
if isinstance(value, np.ndarray) and \
((value.shape == np.ones(3).shape and
np.allclose(value, np.ones(3))) or
(value.shape == np.eye(3).shape and
np.allclose(value, np.eye(3)))):
self._scaling_matrix = np.asmatrix(value)
return
if isinstance(value, numbers.Number):
value = self.lattice.nd * [int(value)]
scaling_matrix = np.asmatrix(value, dtype=int)
# scaling_matrix = np.asmatrix(value)
if scaling_matrix.shape != self.lattice.matrix.shape:
scaling_matrix = np.diagflat(scaling_matrix)
self._scaling_matrix = scaling_matrix
self.lattice = self.lattice.__class__(
cell_matrix=self.scaling_matrix * self.lattice.matrix)
tvecs = \
np.asarray(
np.asmatrix(supercell_lattice_points(self.scaling_matrix)) *
self.lattice.matrix)
basis = self.basis[:]
self.basis = BasisAtoms()
for atom in basis:
for tvec in tvecs:
xs, ys, zs = \
self.lattice.cartesian_to_fractional(atom.r + tvec)
if self.wrap_coords:
xs, ys, zs = \
self.lattice.wrap_fractional_coordinate(
[xs, ys, zs])
self.basis.append(BasisAtom(atom.element, lattice=self.lattice,
xs=xs, ys=ys, zs=zs))
class CrystalCell(BaseClass):
"""Class representation of crystal structure cell.
Parameters
----------
lattice : :class:`~sknano.core.crystallography.LatticeBase` sub-class
basis : {:class:`~python:list`, :class:`~sknano.core.atoms.BasisAtoms`}
coords : {:class:`~python:list`}, optional
cartesian : {:class:`~python:bool`}, optional
wrap_coords : {:class:`~python:bool`}, optional
unit_cell : :class:`~sknano.core.crystallography.UnitCell`
scaling_matrix : {:class:`~python:int`, :class:`~python:list`}
"""
def __init__(self,
lattice=None,
basis=None,
coords=None,
cartesian=False,
wrap_coords=False,
unit_cell=None,
scaling_matrix=None):
super().__init__()
if unit_cell is None and basis is not None:
basis = BasisAtoms(basis)
basis.lattice = lattice
if lattice is not None and coords is not None:
for atom, pos in zip(basis, coords):
atom.lattice = lattice
if not cartesian:
atom.rs = pos
else:
atom.rs = lattice.cartesian_to_fractional(pos)
# if basis is None:
# basis = BasisAtoms()
# These attributes may be reset in the `@scaling_matrix.setter`
# method and so they need to be initialized *before* setting
# `self.scaling_matrix`.
self.basis = basis
self.lattice = lattice
self.unit_cell = unit_cell
self.wrap_coords = wrap_coords
self.scaling_matrix = scaling_matrix
self.fmtstr = \
"lattice={lattice!r}, basis={basis!r}, coords={coords!r}, " + \
"cartesian=False, wrap_coords={wrap_coords!r}, " + \
"unit_cell={unit_cell!r}, scaling_matrix={scaling_matrix!r}"
def __dir__(self):
return ['lattice', 'basis', 'unit_cell', 'scaling_matrix']
def __eq__(self, other):
if all([attr is not None for attr in
(self.scaling_matrix, self.unit_cell,
other.scaling_matrix, other.unit_cell)]) and \
self.scaling_matrix.shape == other.scaling_matrix.shape:
return self is other or \
(self.unit_cell == other.unit_cell and
np.allclose(self.scaling_matrix, other.scaling_matrix))
elif all(
[cell is not None for cell in (self.unit_cell, other.unit_cell)]):
return self is other or \
(self.unit_cell == other.unit_cell and
all([mat is None for mat in
(self.scaling_matrix, other.scaling_matrix)]))
def __lt__(self, other):
return (self.unit_cell < other.unit_cell and
self.scaling_matrix <= other.scaling_matrix) \
or (self.unit_cell <= other.unit_cell and
self.scaling_matrix < other.scaling_matrix)
def __iter__(self):
return iter(self.basis)
def __getattr__(self, name):
if name != 'lattice' and self.lattice is not None:
try:
return getattr(self.lattice, name)
except AttributeError:
pass
if name != 'basis' and self.basis.Natoms != 0:
try:
return getattr(self.basis, name)
except AttributeError:
pass
try:
return getattr(self.unit_cell, name)
except AttributeError:
return super().__getattr__(name)
@property
def basis(self):
return self._basis
@basis.setter
def basis(self, value):
self._basis = value
# if self.unit_cell is not None:
# self.unit_cell.basis[:] = \
# self.basis[:self.unit_cell.basis.Natoms]
@property
def lattice(self):
return self._lattice
@lattice.setter
def lattice(self, value):
self._lattice = value
if self.basis is not None:
self.basis.lattice = self.lattice
@property
def unit_cell(self):
return self._unit_cell
@unit_cell.setter
def unit_cell(self, value):
if value is not None and not isinstance(value, UnitCell):
raise ValueError('Expected a `UnitCell` object')
self._unit_cell = value
if value is not None:
if self.lattice is None:
self._lattice = self.unit_cell.lattice
if self.basis is None or self.basis.Natoms == 0:
self._basis = self.unit_cell.basis
@property
def scaling_matrix(self):
"""Scaling matrix."""
return self._scaling_matrix
@scaling_matrix.setter
def scaling_matrix(self, value):
if value is None:
self._scaling_matrix = np.asmatrix(np.ones(3, dtype=int))
return
if not isinstance(value, (int, float, tuple, list, np.ndarray)):
return
if isinstance(value, np.ndarray) and \
((value.shape == np.ones(3).shape and
np.allclose(value, np.ones(3))) or
(value.shape == np.eye(3).shape and
np.allclose(value, np.eye(3)))):
self._scaling_matrix = np.asmatrix(value)
return
if isinstance(value, numbers.Number):
value = self.lattice.nd * [int(value)]
scaling_matrix = np.asmatrix(value, dtype=int)
# scaling_matrix = np.asmatrix(value)
if scaling_matrix.shape != self.lattice.matrix.shape:
scaling_matrix = np.diagflat(scaling_matrix)
self._scaling_matrix = scaling_matrix
self.lattice = self.lattice.__class__(cell_matrix=self.scaling_matrix *
self.lattice.matrix)
tvecs = \
np.asarray(
np.asmatrix(supercell_lattice_points(self.scaling_matrix)) *
self.lattice.matrix)
basis = self.basis[:]
self.basis = BasisAtoms()
for atom in basis:
for tvec in tvecs:
xs, ys, zs = \
self.lattice.cartesian_to_fractional(atom.r + tvec)
if self.wrap_coords:
xs, ys, zs = \
self.lattice.wrap_fractional_coordinate(
[xs, ys, zs])
self.basis.append(
BasisAtom(atom.element,
lattice=self.lattice,
xs=xs,
ys=ys,
zs=zs))
def rotate(self, **kwargs):
"""Rotate crystal cell lattice, basis, and unit cell."""
if self.lattice is not None:
self.lattice.rotate(**kwargs)
if self.basis is not None:
self.basis.rotate(**kwargs)
self.unit_cell.rotate(**kwargs)
def translate(self, t, fix_anchor_points=True):
"""Translate crystal cell basis."""
if not fix_anchor_points and self.lattice is not None:
self.lattice.translate(t)
if self.basis is not None:
self.basis.translate(t, fix_anchor_points=fix_anchor_points)
self.unit_cell.translate(t, fix_anchor_points=fix_anchor_points)
def update_basis(self, element, index=None, step=None):
"""Update a crystal cell basis element."""
if index is None:
[
self.unit_cell.basis.__setitem__(i, element)
for i in range(len(self.unit_cell.basis))
]
[
self.basis.__setitem__(i, element)
for i in range(len(self.basis))
]
elif isinstance(index, int):
if step is None:
step = self.unit_cell.basis.Natoms
[
self.unit_cell.basis.__setitem__(i, element)
for i in range(index, len(self.unit_cell.basis), step)
]
[
self.basis.__setitem__(i, element)
for i in range(index, len(self.basis), step)
]
elif isinstance(index, (list, np.ndarray)):
[self.unit_cell.basis.__setitem__(i, element) for i in index]
[self.basis.__setitem__(i, element) for i in index]
def todict(self):
try:
return dict(lattice=self.lattice,
basis=self.basis.symbols.tolist(),
coords=self.basis.rs.tolist(),
wrap_coords=self.wrap_coords,
unit_cell=self.unit_cell,
scaling_matrix=self.scaling_matrix.tolist())
except AttributeError:
return dict(lattice=self.lattice,
basis=None,
coords=None,
wrap_coords=self.wrap_coords,
unit_cell=self.unit_cell,
scaling_matrix=self.scaling_matrix.tolist())
class CrystalCell(BaseClass):
"""Class representation of crystal structure cell.
Parameters
----------
lattice : :class:`~sknano.core.crystallography.LatticeBase` sub-class
basis : {:class:`~python:list`, :class:`~sknano.core.atoms.BasisAtoms`}
coords : {:class:`~python:list`}, optional
cartesian : {:class:`~python:bool`}, optional
wrap_coords : {:class:`~python:bool`}, optional
unit_cell : :class:`~sknano.core.crystallography.UnitCell`
scaling_matrix : {:class:`~python:int`, :class:`~python:list`}
"""
def __init__(self, lattice=None, basis=None, coords=None, cartesian=False,
wrap_coords=False, unit_cell=None, scaling_matrix=None):
super().__init__()
if unit_cell is None and basis is not None:
basis = BasisAtoms(basis)
basis.lattice = lattice
if lattice is not None and coords is not None:
for atom, pos in zip(basis, coords):
atom.lattice = lattice
if not cartesian:
atom.rs = pos
else:
atom.rs = lattice.cartesian_to_fractional(pos)
# if basis is None:
# basis = BasisAtoms()
# These attributes may be reset in the `@scaling_matrix.setter`
# method and so they need to be initialized *before* setting
# `self.scaling_matrix`.
self.basis = basis
self.lattice = lattice
self.unit_cell = unit_cell
self.wrap_coords = wrap_coords
self.scaling_matrix = scaling_matrix
self.fmtstr = \
"lattice={lattice!r}, basis={basis!r}, coords={coords!r}, " + \
"cartesian=False, wrap_coords={wrap_coords!r}, " + \
"unit_cell={unit_cell!r}, scaling_matrix={scaling_matrix!r}"
def __dir__(self):
return ['lattice', 'basis', 'unit_cell', 'scaling_matrix']
def __eq__(self, other):
if all([attr is not None for attr in
(self.scaling_matrix, self.unit_cell,
other.scaling_matrix, other.unit_cell)]) and \
self.scaling_matrix.shape == other.scaling_matrix.shape:
return self is other or \
(self.unit_cell == other.unit_cell and
np.allclose(self.scaling_matrix, other.scaling_matrix))
elif all([cell is not None for cell in
(self.unit_cell, other.unit_cell)]):
return self is other or \
(self.unit_cell == other.unit_cell and
all([mat is None for mat in
(self.scaling_matrix, other.scaling_matrix)]))
def __lt__(self, other):
return (self.unit_cell < other.unit_cell and
self.scaling_matrix <= other.scaling_matrix) \
or (self.unit_cell <= other.unit_cell and
self.scaling_matrix < other.scaling_matrix)
def __iter__(self):
return iter(self.basis)
def __getattr__(self, name):
if name != 'lattice' and self.lattice is not None:
try:
return getattr(self.lattice, name)
except AttributeError:
pass
if name != 'basis' and self.basis.Natoms != 0:
try:
return getattr(self.basis, name)
except AttributeError:
pass
try:
return getattr(self.unit_cell, name)
except AttributeError:
return super().__getattr__(name)
@property
def basis(self):
return self._basis
@basis.setter
def basis(self, value):
self._basis = value
# if self.unit_cell is not None:
# self.unit_cell.basis[:] = \
# self.basis[:self.unit_cell.basis.Natoms]
@property
def lattice(self):
return self._lattice
@lattice.setter
def lattice(self, value):
self._lattice = value
if self.basis is not None:
self.basis.lattice = self.lattice
@property
def unit_cell(self):
return self._unit_cell
@unit_cell.setter
def unit_cell(self, value):
if value is not None and not isinstance(value, UnitCell):
raise ValueError('Expected a `UnitCell` object')
self._unit_cell = value
if value is not None:
if self.lattice is None:
self._lattice = self.unit_cell.lattice
if self.basis is None or self.basis.Natoms == 0:
self._basis = self.unit_cell.basis
@property
def scaling_matrix(self):
"""Scaling matrix."""
return self._scaling_matrix
@scaling_matrix.setter
def scaling_matrix(self, value):
if value is None:
self._scaling_matrix = np.asmatrix(np.ones(3, dtype=int))
return
if not isinstance(value, (int, float, tuple, list, np.ndarray)):
return
if isinstance(value, np.ndarray) and \
((value.shape == np.ones(3).shape and
np.allclose(value, np.ones(3))) or
(value.shape == np.eye(3).shape and
np.allclose(value, np.eye(3)))):
self._scaling_matrix = np.asmatrix(value)
return
if isinstance(value, numbers.Number):
value = self.lattice.nd * [int(value)]
scaling_matrix = np.asmatrix(value, dtype=int)
# scaling_matrix = np.asmatrix(value)
if scaling_matrix.shape != self.lattice.matrix.shape:
scaling_matrix = np.diagflat(scaling_matrix)
self._scaling_matrix = scaling_matrix
self.lattice = self.lattice.__class__(
cell_matrix=self.scaling_matrix * self.lattice.matrix)
tvecs = \
np.asarray(
np.asmatrix(supercell_lattice_points(self.scaling_matrix)) *
self.lattice.matrix)
basis = self.basis[:]
self.basis = BasisAtoms()
for atom in basis:
for tvec in tvecs:
xs, ys, zs = \
self.lattice.cartesian_to_fractional(atom.r + tvec)
if self.wrap_coords:
xs, ys, zs = \
self.lattice.wrap_fractional_coordinate(
[xs, ys, zs])
self.basis.append(BasisAtom(atom.element, lattice=self.lattice,
xs=xs, ys=ys, zs=zs))
def rotate(self, **kwargs):
"""Rotate crystal cell lattice, basis, and unit cell."""
if self.lattice is not None:
self.lattice.rotate(**kwargs)
if self.basis is not None:
self.basis.rotate(**kwargs)
self.unit_cell.rotate(**kwargs)
def translate(self, t, fix_anchor_points=True):
"""Translate crystal cell basis."""
if not fix_anchor_points and self.lattice is not None:
self.lattice.translate(t)
if self.basis is not None:
self.basis.translate(t, fix_anchor_points=fix_anchor_points)
self.unit_cell.translate(t, fix_anchor_points=fix_anchor_points)
def update_basis(self, element, index=None, step=None):
"""Update a crystal cell basis element."""
if index is None:
[self.unit_cell.basis.__setitem__(i, element)
for i in range(len(self.unit_cell.basis))]
[self.basis.__setitem__(i, element)
for i in range(len(self.basis))]
elif isinstance(index, int):
if step is None:
step = self.unit_cell.basis.Natoms
[self.unit_cell.basis.__setitem__(i, element)
for i in range(index, len(self.unit_cell.basis), step)]
[self.basis.__setitem__(i, element)
for i in range(index, len(self.basis), step)]
elif isinstance(index, (list, np.ndarray)):
[self.unit_cell.basis.__setitem__(i, element) for i in index]
[self.basis.__setitem__(i, element) for i in index]
def todict(self):
try:
return dict(lattice=self.lattice,
basis=self.basis.symbols.tolist(),
coords=self.basis.rs.tolist(),
wrap_coords=self.wrap_coords,
unit_cell=self.unit_cell,
scaling_matrix=self.scaling_matrix.tolist())
except AttributeError:
return dict(lattice=self.lattice, basis=None, coords=None,
wrap_coords=self.wrap_coords,
unit_cell=self.unit_cell,
scaling_matrix=self.scaling_matrix.tolist())
