def test_changing_tolerance_lattice_type(self, lattices):
for lattice_type, primitive_cell in lattices.items():
# double precision (numpy.float64)
p1, p2, p3 = self._get_primitive_vectors(primitive_cell)
# given perturbation
p1[0] += 1.e-4
# when
tolerance = 1.e-6
# then
actual = lattice_tools.is_bravais_lattice_consistent(p1, p2, p3,
lattice_type,
tolerance)
self.assertFalse(actual)
# when
tolerance = 1.e-3
# then
actual = lattice_tools.is_bravais_lattice_consistent(p1, p2, p3,
lattice_type,
tolerance)
self.assertTrue(actual)
def test_exception_zero_length_vectors(self):
# given
p1, p2, p3 = (0., 1., 0.), (0., 0., 0.), (1., 0., 0.)
# then
for bravais_lattice in BravaisLattice:
with self.assertRaises(ValueError):
lattice_tools.is_bravais_lattice_consistent(
p1, p2, p3, bravais_lattice)
def test_exception_for_vectors_with_inf(self):
# given
p1, p2, p3 = ((numpy.inf, 0., 0.), ) * 3
# then
for bravais_lattice in BravaisLattice:
with self.assertRaises(ValueError):
lattice_tools.is_bravais_lattice_consistent(
p1, p2, p3, bravais_lattice)
def test_exception_zero_length_vectors(self):
# given
p1, p2, p3 = (0., 1., 0.), (0., 0., 0.), (1., 0., 0.)
# then
for bravais_lattice in BravaisLattice:
with self.assertRaises(ValueError):
lattice_tools.is_bravais_lattice_consistent(p1, p2, p3,
bravais_lattice)
def test_exception_for_vectors_with_inf(self):
# given
p1, p2, p3 = ((numpy.inf, 0., 0.),)*3
# then
for bravais_lattice in BravaisLattice:
with self.assertRaises(ValueError):
lattice_tools.is_bravais_lattice_consistent(p1, p2, p3,
bravais_lattice)
def test_incompatible_lattice_type(self):
''' Test if some specific lattices are incompatible with some others
e.g. a strict BravaisLattice.TRICLINIC lattice
cannot be considered as any other lattice of higher symmetry
All other lattices are triclinic in its loose definition
'''
lattices = builder(get_specific_primitive_cell_factories()).example()
for bravais_lattice, primitive_cell in lattices.items():
# given
aligned_vectors = self._get_primitive_vectors(primitive_cell)
p1, p2, p3 = rotate_permute_flip(aligned_vectors)
# when
exclusives = (set(BravaisLattice) -
set(specific_map2_general[bravais_lattice]) -
set([bravais_lattice, BravaisLattice.TRICLINIC]))
# then
# bravais_lattice cannot be compatible with lattice
# types in `exclusive`
msg = "Expected {!r} not be considered as {!r}"
for exclusive in exclusives:
self.assertFalse(
lattice_tools.is_bravais_lattice_consistent(
p1, p2, p3, exclusive),
msg.format(bravais_lattice, exclusive))
def test_incompatible_lattice_type(self):
''' Test if some specific lattices are incompatible with some others
e.g. a strict BravaisLattice.TRICLINIC lattice
cannot be considered as any other lattice of higher symmetry
All other lattices are triclinic in its loose definition
'''
lattices = builder(get_specific_primitive_cell_factories()).example()
for bravais_lattice, primitive_cell in lattices.items():
# given
aligned_vectors = self._get_primitive_vectors(primitive_cell)
p1, p2, p3 = rotate_permute_flip(aligned_vectors)
# when
exclusives = (set(BravaisLattice) -
set(specific_map2_general[bravais_lattice]) -
set([bravais_lattice, BravaisLattice.TRICLINIC]))
# then
# bravais_lattice cannot be compatible with lattice
# types in `exclusive`
msg = "Expected {!r} not be considered as {!r}"
for exclusive in exclusives:
self.assertFalse(
lattice_tools.is_bravais_lattice_consistent(p1, p2, p3,
exclusive),
msg.format(bravais_lattice, exclusive))
def test_changing_tolerance_lattice_type(self, lattices):
for lattice_type, primitive_cell in lattices.items():
# double precision (numpy.float64)
p1, p2, p3 = self._get_primitive_vectors(primitive_cell)
# given perturbation
p1[0] += 1.e-4
# when
tolerance = 1.e-6
# then
actual = lattice_tools.is_bravais_lattice_consistent(
p1, p2, p3, lattice_type, tolerance)
self.assertFalse(actual)
# when
tolerance = 1.e-3
# then
actual = lattice_tools.is_bravais_lattice_consistent(
p1, p2, p3, lattice_type, tolerance)
self.assertTrue(actual)
def test_subtype_of_general_lattices(self, lattices):
''' Test if more symmetric lattices are part of more general lattices
'''
for specific, primitive_cell in lattices.items():
# given
aligned_vectors = self._get_primitive_vectors(primitive_cell)
p1, p2, p3 = rotate_permute_flip(aligned_vectors)
# then
msg = "Expected {!r} to be a symmetric case of {!r}. False."
for general in specific_map2_general[specific]:
self.assertTrue(
lattice_tools.is_bravais_lattice_consistent(
p1, p2, p3, general), msg.format(specific, general))
def test_subtype_of_general_lattices(self, lattices):
''' Test if more symmetric lattices are part of more general lattices
'''
for specific, primitive_cell in lattices.items():
# given
aligned_vectors = self._get_primitive_vectors(primitive_cell)
p1, p2, p3 = rotate_permute_flip(aligned_vectors)
# then
msg = "Expected {!r} to be a symmetric case of {!r}. False."
for general in specific_map2_general[specific]:
self.assertTrue(
lattice_tools.is_bravais_lattice_consistent(p1, p2, p3,
general),
msg.format(specific, general))
def from_lattice(cls, lattice, node_keys=None):
""" Create a new Lattice from the provided one.
Parameters
----------
lattice : simphony.cuds.lattice.Lattice
node_keys : list
A list of point CUBA keys that we want to copy, and only those.
If None, all available and compatible keys will be copied.
Returns
-------
lattice : VTKLattice
Raises
------
ValueError
- if bravais_lattice attribute of the primitive cell indicates
a cubic/tetragonal/orthorhombic lattice but the primitive vectors
are inconsistent with this attribute
- if bravais_lattice is not a member of BravaisLattice
"""
origin = lattice.origin
primitive_cell = lattice.primitive_cell
lattice_type = primitive_cell.bravais_lattice
size = lattice.size
name = lattice.name
node_data = CUBADataAccumulator(node_keys)
data = lattice.data
if lattice_type in (
BravaisLattice.CUBIC, BravaisLattice.TETRAGONAL,
BravaisLattice.ORTHORHOMBIC):
# Cubic/Tetragonal/Orthorhombic lattice can be represented
# by tvtk.ImageData, which is more efficient than PolyData
# But we should make sure the primitive vectors do describe
# such a regular lattice type as PrimitiveCell does not
# perform this check
consistent = is_bravais_lattice_consistent(primitive_cell.p1,
primitive_cell.p2,
primitive_cell.p3,
lattice_type)
if not consistent:
message = ("primitive vectors are not consistent with the "
"bravais_lattice: {}")
raise ValueError(message.format(str(lattice_type)))
# Compute the spacing from the primitive cell
spacing = tuple(map(vector_len, (primitive_cell.p1,
primitive_cell.p2,
primitive_cell.p3)))
origin = origin
data_set = tvtk.ImageData(spacing=spacing, origin=origin)
data_set.extent = 0, size[0] - 1, 0, size[1] - 1, 0, size[2] - 1
# vtk ravels the point positions in a very weird way
# this setup has been supported by tests.
y, z, x = numpy.meshgrid(
range(size[1]), range(size[2]), range(size[0]))
indices = izip(x.ravel(), y.ravel(), z.ravel())
elif lattice_type in BravaisLattice:
# This includes any other BravaisLattice type that cannot be
# represented by ImageData. PolyData is required.
y, z, x = numpy.meshgrid(
range(size[1]), range(size[2]), range(size[0]))
points = numpy.zeros(shape=(x.size, 3), dtype='double')
# construct points using primitive cells
for idim in range(3):
points[:, idim] += primitive_cell.p1[idim]*x.ravel() +\
primitive_cell.p2[idim]*y.ravel() +\
primitive_cell.p3[idim]*z.ravel()
points[:, idim] += origin[idim]
data_set = tvtk.PolyData(points=points)
indices = izip(x.ravel(), y.ravel(), z.ravel())
else:
message = 'Unknown lattice type: {}'.format(lattice_type)
raise ValueError(message)
for node in lattice.iter(indices):
node_data.append(node.data)
node_data.load_onto_vtk(data_set.point_data)
return cls(name=name, primitive_cell=primitive_cell, data=data,
data_set=data_set)