def test_primitive_cell_for_cubic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_cubic_lattice(-1)
pc = PrimitiveCell.for_cubic_lattice(self.a)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice, BravaisLattice.CUBIC)
assert_array_equal(pc.p1, (self.a, 0, 0))
assert_array_equal(pc.p2, (0, self.a, 0))
assert_array_equal(pc.p3, (0, 0, self.a))
def test_primitive_cell_for_tetragonal_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_tetragonal_lattice(-1, -2)
pc = PrimitiveCell.for_tetragonal_lattice(self.a, self.c)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice, BravaisLattice.TETRAGONAL)
assert_array_equal(pc.p1, (self.a, 0, 0))
assert_array_equal(pc.p2, (0, self.a, 0))
assert_array_equal(pc.p3, (0, 0, self.c))
def test_primitive_cell_for_orthorhombic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_orthorhombic_lattice(-1, -2, -3)
pc = PrimitiveCell.for_orthorhombic_lattice(self.a, self.b, self.c)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice, BravaisLattice.ORTHORHOMBIC)
assert_array_equal(pc.p1, (self.a, 0, 0))
assert_array_equal(pc.p2, (0, self.b, 0))
assert_array_equal(pc.p3, (0, 0, self.c))
def test_primitive_cell_for_cubic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_cubic_lattice(-1)
pc = PrimitiveCell.for_cubic_lattice(self.a)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice, BravaisLattice.CUBIC)
assert_array_equal(pc.p1, (self.a, 0, 0))
assert_array_equal(pc.p2, (0, self.a, 0))
assert_array_equal(pc.p3, (0, 0, self.a))
def test_primitive_cell_for_triclinic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_triclinic_lattice(-1, -2, -3, 0.5, 0.6, 0.7)
with self.assertRaises(ValueError):
PrimitiveCell.for_triclinic_lattice(1, 2, 3, 0, np.pi, np.pi)
with self.assertRaises(ValueError):
PrimitiveCell.for_triclinic_lattice(1, 2, 3, 0.1, 0.2, 0.8)
with self.assertRaises(ValueError):
# angles too big
PrimitiveCell.for_triclinic_lattice(1, 2, 3, 2.1, 2.1, 2.1)
cosa = np.cos(self.alpha)
cosb = np.cos(self.beta)
sinb = np.sin(self.beta)
cosg = np.cos(self.gamma)
sing = np.sin(self.gamma)
p1 = (self.a, 0, 0)
p2 = (self.b*cosg, self.b*sing, 0)
p3 = (self.c*cosb, self.c*(cosa-cosb*cosg) / sing,
self.c*np.sqrt(sinb**2 - ((cosa-cosb*cosg) / sing)**2))
pc = PrimitiveCell.for_triclinic_lattice(
self.a, self.b, self.c, self.alpha, self.beta, self.gamma)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice,
BravaisLattice.TRICLINIC)
assert_array_equal(pc.p1, p1)
assert_array_equal(pc.p2, p2)
assert_array_equal(pc.p3, p3)
def test_primitive_cell_for_triclinic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_triclinic_lattice(-1, -2, -3, 0.5, 0.6, 0.7)
with self.assertRaises(ValueError):
PrimitiveCell.for_triclinic_lattice(1, 2, 3, 0, np.pi, np.pi)
with self.assertRaises(ValueError):
PrimitiveCell.for_triclinic_lattice(1, 2, 3, 0.1, 0.2, 0.8)
with self.assertRaises(ValueError):
# angles too big
PrimitiveCell.for_triclinic_lattice(1, 2, 3, 2.1, 2.1, 2.1)
cosa = np.cos(self.alpha)
cosb = np.cos(self.beta)
sinb = np.sin(self.beta)
cosg = np.cos(self.gamma)
sing = np.sin(self.gamma)
p1 = (self.a, 0, 0)
p2 = (self.b * cosg, self.b * sing, 0)
p3 = (self.c * cosb, self.c * (cosa - cosb * cosg) / sing,
self.c * np.sqrt(sinb**2 - ((cosa - cosb * cosg) / sing)**2))
pc = PrimitiveCell.for_triclinic_lattice(self.a, self.b, self.c,
self.alpha, self.beta,
self.gamma)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice, BravaisLattice.TRICLINIC)
assert_array_equal(pc.p1, p1)
assert_array_equal(pc.p2, p2)
assert_array_equal(pc.p3, p3)
def test_primitive_cell_for_orthorhombic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_orthorhombic_lattice(-1, -2, -3)
pc = PrimitiveCell.for_orthorhombic_lattice(self.a, self.b, self.c)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice,
BravaisLattice.ORTHORHOMBIC)
assert_array_equal(pc.p1, (self.a, 0, 0))
assert_array_equal(pc.p2, (0, self.b, 0))
assert_array_equal(pc.p3, (0, 0, self.c))
def test_primitive_cell_for_tetragonal_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_tetragonal_lattice(-1, -2)
pc = PrimitiveCell.for_tetragonal_lattice(self.a, self.c)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice,
BravaisLattice.TETRAGONAL)
assert_array_equal(pc.p1, (self.a, 0, 0))
assert_array_equal(pc.p2, (0, self.a, 0))
assert_array_equal(pc.p3, (0, 0, self.c))
def test_primitive_cell_for_monoclinic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_monoclinic_lattice(-1, -2, -3, np.pi / 4)
with self.assertRaises(ValueError):
PrimitiveCell.for_monoclinic_lattice(1, 2, 3, np.pi)
pc = PrimitiveCell.for_monoclinic_lattice(self.a, self.b, self.c,
self.beta)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice, BravaisLattice.MONOCLINIC)
assert_array_equal(
pc.p1, (self.a * np.sin(self.beta), 0, self.a * np.cos(self.beta)))
assert_array_equal(pc.p2, (0, self.b, 0))
assert_array_equal(pc.p3, (0, 0, self.c))
def test_primitive_cell_for_monoclinic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_monoclinic_lattice(-1, -2, -3, np.pi/4)
with self.assertRaises(ValueError):
PrimitiveCell.for_monoclinic_lattice(1, 2, 3, np.pi)
pc = PrimitiveCell.for_monoclinic_lattice(
self.a, self.b, self.c, self.beta)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice,
BravaisLattice.MONOCLINIC)
assert_array_equal(pc.p1,
(self.a*np.sin(self.beta), 0,
self.a*np.cos(self.beta)))
assert_array_equal(pc.p2, (0, self.b, 0))
assert_array_equal(pc.p3, (0, 0, self.c))
def test_primitive_cell_for_rhombohedral_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_rhombohedral_lattice(-1, np.pi / 4)
with self.assertRaises(ValueError):
PrimitiveCell.for_rhombohedral_lattice(1, np.pi)
with self.assertRaises(ValueError):
# angle too big
PrimitiveCell.for_rhombohedral_lattice(1, np.pi * 2. / 3. + 0.1)
cosa = np.cos(self.alpha)
sina = np.sin(self.alpha)
p1 = (self.a, 0, 0)
p2 = (self.a * cosa, self.a * sina, 0)
p3 = (self.a * cosa, self.a * (cosa - cosa**2) / sina,
self.a * np.sqrt(sina**2 - ((cosa - cosa**2) / sina)**2))
pc = PrimitiveCell.for_rhombohedral_lattice(self.a, self.alpha)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice, BravaisLattice.RHOMBOHEDRAL)
assert_array_equal(pc.p1, p1)
assert_array_equal(pc.p2, p2)
assert_array_equal(pc.p3, p3)
def test_primitive_cell_for_rhombohedral_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_rhombohedral_lattice(-1, np.pi/4)
with self.assertRaises(ValueError):
PrimitiveCell.for_rhombohedral_lattice(1, np.pi)
with self.assertRaises(ValueError):
# angle too big
PrimitiveCell.for_rhombohedral_lattice(1, np.pi*2./3.+0.1)
cosa = np.cos(self.alpha)
sina = np.sin(self.alpha)
p1 = (self.a, 0, 0)
p2 = (self.a*cosa, self.a*sina, 0)
p3 = (self.a*cosa, self.a*(cosa-cosa**2) / sina,
self.a*np.sqrt(sina**2 - ((cosa-cosa**2) / sina)**2))
pc = PrimitiveCell.for_rhombohedral_lattice(self.a, self.alpha)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice,
BravaisLattice.RHOMBOHEDRAL)
assert_array_equal(pc.p1, p1)
assert_array_equal(pc.p2, p2)
assert_array_equal(pc.p3, p3)
def test_primitive_cell_for_base_centered_monoclinic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_base_centered_monoclinic_lattice(-1, -2, -3, 0.5)
with self.assertRaises(ValueError):
PrimitiveCell.for_base_centered_monoclinic_lattice(1, 2, 3, np.pi)
p1 = (self.a * np.sin(self.beta), 0, self.a * np.cos(self.beta))
p2 = (self.a * np.sin(self.beta) / 2, self.b / 2,
self.a * np.cos(self.beta) / 2)
pc = PrimitiveCell.for_base_centered_monoclinic_lattice(
self.a, self.b, self.c, self.beta)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice,
BravaisLattice.BASE_CENTERED_MONOCLINIC)
assert_array_equal(pc.p1, p1)
assert_array_equal(pc.p2, p2)
assert_array_equal(pc.p3, (0, 0, self.c))
def setUp(self):
self.addTypeEqualityFunc(
DataContainer, partial(compare_data_containers, testcase=self))
self.addTypeEqualityFunc(
LatticeNode, partial(compare_lattice_nodes, testcase=self))
self.primitive_cell = PrimitiveCell.for_cubic_lattice(0.2)
self.size = (5, 10, 15)
self.origin = (-2.0, 0.0, 1.0)
self.container = self.container_factory(
'my_name', self.primitive_cell, self.size, self.origin)
def test_lattice_source_name(self):
# given
primitive_cell = PrimitiveCell.for_cubic_lattice(0.1)
lattice = VTKLattice.empty('my_lattice', primitive_cell,
(5, 10, 12), (0, 0, 0))
# when
source = self.tested_class(cuds=lattice)
# then
self.assertEqual(source.name, 'my_lattice (CUDS Lattice)')
def test_exception_guess_vectors_with_unsorted_points(self):
# given
primitive_cell = PrimitiveCell.for_rhombohedral_lattice(0.1, 0.7)
# when
p1, p2, p3 = self._get_primitive_vectors(primitive_cell)
points = create_points_from_pc(p1, p2, p3, (4, 5, 3))
numpy.random.shuffle(points)
# then
with self.assertRaises(ValueError):
lattice_tools.guess_primitive_vectors(points)
def test_exception_guess_vectors_with_unsorted_points(self):
# given
primitive_cell = PrimitiveCell.for_rhombohedral_lattice(0.1, 0.7)
# when
p1, p2, p3 = self._get_primitive_vectors(primitive_cell)
points = create_points_from_pc(p1, p2, p3, (4, 5, 3))
numpy.random.shuffle(points)
# then
with self.assertRaises(ValueError):
lattice_tools.guess_primitive_vectors(points)
def test_source_from_a_vtk_lattice(self):
# given
primitive_cell = PrimitiveCell.for_cubic_lattice(0.1)
lattice = VTKLattice.empty(
'test', primitive_cell, (5, 10, 12), (0, 0, 0))
# when
source = self.tested_class(cuds=lattice)
# then
self.assertIs(source._vtk_cuds, lattice)
self.assertIs(source.data, lattice.data_set)
def test_primitive_cell_for_base_centered_monoclinic_lattice(self):
with self.assertRaises(ValueError):
PrimitiveCell.for_base_centered_monoclinic_lattice(
-1, -2, -3, 0.5)
with self.assertRaises(ValueError):
PrimitiveCell.for_base_centered_monoclinic_lattice(
1, 2, 3, np.pi)
p1 = (self.a*np.sin(self.beta), 0, self.a*np.cos(self.beta))
p2 = (self.a*np.sin(self.beta)/2, self.b/2,
self.a*np.cos(self.beta)/2)
pc = PrimitiveCell.for_base_centered_monoclinic_lattice(
self.a, self.b, self.c, self.beta)
self.assertIsInstance(pc, PrimitiveCell)
self.assertEqual(pc.bravais_lattice,
BravaisLattice.BASE_CENTERED_MONOCLINIC)
assert_array_equal(pc.p1, p1)
assert_array_equal(pc.p2, p2)
assert_array_equal(pc.p3, (0, 0, self.c))
def make_face_centered_cubic_lattice(name, h, size, origin=(0, 0, 0)):
"""Create and return a 3D face-centered cubic lattice.
Parameters
----------
name : str
h : float
lattice spacing
size : int[3]
Number of lattice nodes in each axis direction.
origin : float[3], default value = (0, 0, 0)
lattice origin
Returns
-------
lattice : Lattice
A reference to a Lattice object.
"""
pc = PrimitiveCell.for_face_centered_cubic_lattice(h)
return Lattice(name, pc, size, origin)
def test_version(self):
filename = os.path.join(self.temp_dir, "test_file.cuds")
group_name = "dummy_component_name"
with tables.open_file(filename, "w") as handle:
group = handle.create_group(handle.root, group_name)
# given/when
H5Lattice.create_new(group, PrimitiveCell.for_cubic_lattice(0.2), size=(5, 10, 15), origin=(-2, 0, 1))
# then
self.assertTrue(isinstance(group._v_attrs.cuds_version, int))
# when
with tables.open_file(filename, "a") as handle:
handle.get_node("/{}".format(group_name))._v_attrs.cuds_version = -1
# then
with tables.open_file(filename, "a") as handle:
with self.assertRaises(ValueError):
H5Lattice(handle.get_node("/" + group_name))
def make_orthorhombic_lattice(name, hs, size, origin=(0, 0, 0)):
"""Create and return a 3D orthorhombic lattice.
Parameters
----------
name : str
hs : float[3]
lattice spacings in each axis direction
size : int[3]
Number of lattice nodes in each axis direction.
origin : float[3], default value = (0, 0, 0)
lattice origin
Returns
-------
lattice : Lattice
A reference to a Lattice object.
"""
pc = PrimitiveCell.for_orthorhombic_lattice(hs[0], hs[1], hs[2])
return Lattice(name, pc, size, origin)
def make_monoclinic_lattice(name, hs, beta, size, origin=(0, 0, 0)):
"""Create and return a 3D monoclinic lattice.
Parameters
----------
name : str
hs : float[3]
lattice spacings in each axis direction
beta: float
angle between the (conventional) unit cell edges (in radians),
size : int[3]
Number of lattice nodes in each axis direction.
origin : float[3], default value = (0, 0, 0)
lattice origin
Returns
-------
lattice : Lattice
A reference to a Lattice object.
"""
pc = PrimitiveCell.for_monoclinic_lattice(hs[0], hs[1], hs[2], beta)
return Lattice(name, pc, size, origin)
def make_hexagonal_lattice(name, hxy, hz, size, origin=(0, 0, 0)):
"""Create and return a 3D hexagonal lattice.
Parameters
----------
name : str
hxy : float
lattice spacing in the xy-plane
hz : float
lattice spacing in the z-direction
size : int[3]
Number of lattice nodes in each axis direction.
origin : float[3], default value = (0, 0, 0)
lattice origin
Returns
-------
lattice : Lattice
A reference to a Lattice object.
"""
pc = PrimitiveCell.for_hexagonal_lattice(hxy, hz)
return Lattice(name, pc, size, origin)
def make_rhombohedral_lattice(name, h, angle, size, origin=(0, 0, 0)):
"""Create and return a 3D rhombohedral lattice.
Parameters
----------
name : str
h : float
lattice spacing
angle : float
angle between the (conventional) unit cell edges (in radians)
size : int[3]
Number of lattice nodes in each axis direction.
origin : float[3], default value = (0, 0, 0)
lattice origin
Returns
-------
lattice : Lattice
A reference to a Lattice object.
"""
pc = PrimitiveCell.for_rhombohedral_lattice(h, angle)
return Lattice(name, pc, size, origin)
def test_version(self):
filename = os.path.join(self.temp_dir, 'test_file.cuds')
group_name = "dummy_component_name"
with tables.open_file(filename, 'w') as handle:
group = handle.create_group(handle.root, group_name)
# given/when
H5Lattice.create_new(group,
PrimitiveCell.for_cubic_lattice(0.2),
size=(5, 10, 15),
origin=(-2, 0, 1))
# then
self.assertTrue(isinstance(group._v_attrs.cuds_version, int))
# when
with tables.open_file(filename, 'a') as handle:
handle.get_node(
"/{}".format(group_name))._v_attrs.cuds_version = -1
# then
with tables.open_file(filename, 'a') as handle:
with self.assertRaises(ValueError):
H5Lattice(handle.get_node("/" + group_name))
def from_dataset(cls, name, data_set, data=None):
""" Create a new Lattice and try to guess the ``primitive_cell``
Parameters
----------
name : str
data_set : tvtk.ImageData or tvtk.PolyData
The dataset to wrap in the CUDS api. If it is a PolyData,
the points are assumed to be arranged in C-contiguous order
data : DataContainer
The data attribute to attach to the container. Default is None.
Returns
-------
lattice : VTKLattice
Raises
------
TypeError :
If data_set is not either tvtk.ImageData or tvtk.PolyData
IndexError:
If the lattice nodes are not arranged in C-contiguous order
"""
if isinstance(data_set, tvtk.ImageData):
spacing = data_set.spacing
unique_spacing = numpy.unique(spacing)
if len(unique_spacing) == 1:
primitive_cell = PrimitiveCell.for_cubic_lattice(spacing[0])
elif len(unique_spacing) == 2:
a, c = unique_spacing
if sum(spacing == a) == 2:
primitive_cell = PrimitiveCell.for_tetragonal_lattice(a, c)
else:
primitive_cell = PrimitiveCell.for_tetragonal_lattice(c, a)
else:
factory = PrimitiveCell.for_orthorhombic_lattice
primitive_cell = factory(*spacing)
return cls(name=name, primitive_cell=primitive_cell,
data=data, data_set=data_set)
if not isinstance(data_set, tvtk.PolyData):
# Not ImageData nor PolyData
message = 'Cannot convert {} to a cuds Lattice'
raise TypeError(message.format(type(data_set)))
# data_set is an instance of tvtk.PolyData
points = data_set.points.to_array()
# Assumed C-contiguous order of points
p1, p2, p3 = guess_primitive_vectors(points)
# This will raise a TypeError if no bravais lattice type matches
bravais_lattice = find_lattice_type(p1, p2, p3)
primitive_cell = PrimitiveCell(p1, p2, p3, bravais_lattice)
return cls(name=name, primitive_cell=primitive_cell,
data=data, data_set=data_set)
import numpy
from simphony.core.cuba import CUBA
from simphony.cuds.primitive_cell import PrimitiveCell
from simphony.visualisation import mayavi_tools
cubic = mayavi_tools.VTKLattice.empty(
"test", PrimitiveCell.for_cubic_lattice(0.1),
(5, 10, 12), (0, 0, 0))
lattice = cubic
new_nodes = []
for node in lattice.iter(item_type=CUBA.NODE):
index = numpy.array(node.index) + 1.0
node.data[CUBA.TEMPERATURE] = numpy.prod(index)
new_nodes.append(node)
lattice.update(new_nodes)
if __name__ == '__main__':
# Visualise the Lattice object
mayavi_tools.show(lattice)
def test_cell_volume(self):
pc = PrimitiveCell.for_triclinic_lattice(1, 1, 1, np.pi/2,
np.pi/2, np.pi/2)
self.assertAlmostEqual(pc.volume, 1)
def test_cell_volume(self):
pc = PrimitiveCell.for_triclinic_lattice(1, 1, 1, np.pi / 2, np.pi / 2,
np.pi / 2)
self.assertAlmostEqual(pc.volume, 1)
'''
# rotate x-y for angle1 about z
xy_rot = numpy.array([[numpy.cos(angle1), numpy.sin(angle1), 0],
[numpy.sin(-angle1), numpy.cos(angle1), 0],
[0, 0, 1]])
# rotate y-z for angle2 about x
yz_rot = numpy.array([[1, 0, 0],
[0, numpy.cos(angle2), numpy.sin(angle2)],
[0, numpy.sin(-angle2), numpy.cos(angle2)]])
# rotate x-y, then y-z
xyz_rot = numpy.inner(xy_rot, yz_rot)
return tuple(numpy.inner(xyz_rot, p) for p in (pc.p1, pc.p2, pc.p3))
# a cubic lattice on a rotated coordinates represented using PolyData
pcs = rotate_primitive_cell(PrimitiveCell.for_cubic_lattice(1.))
datasets.append(create_polydata_from_pc(*pcs))
# BCC lattice in a rotated coor. sys.
pcs = rotate_primitive_cell(PrimitiveCell.for_body_centered_cubic_lattice(1.))
datasets.append(create_polydata_from_pc(*pcs))
# FCC lattice in a rotated coor. sys.
pcs = rotate_primitive_cell(PrimitiveCell.for_face_centered_cubic_lattice(1.))
datasets.append(create_polydata_from_pc(*pcs))
# rhombohedral lattice in a rotated coor. sys.
pcs = rotate_primitive_cell(PrimitiveCell.for_rhombohedral_lattice(1., 1.))
datasets.append(create_polydata_from_pc(*pcs))
# tetragonal lattice in a rotated coor. sys.
def test_no_parallel_edges(self):
with self.assertRaises(ValueError):
PrimitiveCell((1, 0, 0), (1, 0, 0), (0, 0, 1),
BravaisLattice.CUBIC)
def test_edge_lengths_positive(self):
with self.assertRaises(ValueError):
PrimitiveCell((0, 0, 0), (0, 0, 0), (0, 0, 0),
BravaisLattice.CUBIC)