def test_cell_tools():
# test known values: simple cubic
cell_a = 5.0
cell = np.identity(3) * cell_a
volume = cell_a**3.0
cryst_const = np.array([cell_a] * 3 + [90.0] * 3)
np.testing.assert_array_almost_equal(crys.cell2cc(cell), cryst_const)
np.testing.assert_array_almost_equal(crys.cc2cell(cryst_const), cell)
np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const))
np.testing.assert_almost_equal(volume, crys.volume_cell(cell))
np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)),
cell)
np.testing.assert_array_almost_equal(
crys.cell2cc(crys.cc2cell(cryst_const)), cryst_const)
# random
#
# volume : volume_cc() always returns positive values, whereas det() and
# volume_cell() may return the volume with negative sign but correct
# magnitude.
# cell : A random cell does also have a random orientation in space. It
# does NOT conform the usual convention: a along x, b in x-y plane.
# However, the cryst_const and volume must be invariant.
cell = np.random.rand(3, 3)
cryst_const = crys.cell2cc(cell)
volume = abs(np.linalg.det(cell))
np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const))
np.testing.assert_almost_equal(volume, abs(crys.volume_cell(cell)))
# this must always fail for random cells
try:
np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)),
cell)
except AssertionError:
pass
# Here, we convert cryst_const to a *different* cell which conforms to the
# orientation convention, and back to cryst_const.
np.testing.assert_array_almost_equal(
crys.cell2cc(crys.cc2cell(cryst_const)), cryst_const)
# 3d
cell = rand(100, 3, 3)
cc = crys.cell2cc3d(cell, axis=0)
vol_cell = np.abs(crys.volume_cell3d(cell, axis=0))
vol_cc = crys.volume_cc3d(cc, axis=0)
assert crys.cell2cc3d(cell, axis=0).shape == (100, 6)
assert crys.cc2cell3d(cc, axis=0).shape == (100, 3, 3)
assert vol_cc.shape == (100, )
assert vol_cell.shape == (100, )
aaae(vol_cell, vol_cc)
aaae(crys.cell2cc3d(crys.cc2cell3d(cc)), cc)
def test_cell_tools():
# test known values: simple cubic
cell_a = 5.0
cell = np.identity(3)*cell_a
volume = cell_a**3.0
cryst_const = np.array([cell_a]*3 + [90.0]*3)
np.testing.assert_array_almost_equal(crys.cell2cc(cell), cryst_const)
np.testing.assert_array_almost_equal(crys.cc2cell(cryst_const), cell)
np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const))
np.testing.assert_almost_equal(volume, crys.volume_cell(cell))
np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)), cell)
np.testing.assert_array_almost_equal(crys.cell2cc(crys.cc2cell(cryst_const)),
cryst_const)
# random
#
# volume : volume_cc() always returns positive values, whereas det() and
# volume_cell() may return the volume with negative sign but correct
# magnitude.
# cell : A random cell does also have a random orientation in space. It
# does NOT conform the usual convention: a along x, b in x-y plane.
# However, the cryst_const and volume must be invariant.
cell = np.random.rand(3,3)
cryst_const = crys.cell2cc(cell)
volume = abs(np.linalg.det(cell))
np.testing.assert_almost_equal(volume, crys.volume_cc(cryst_const))
np.testing.assert_almost_equal(volume, abs(crys.volume_cell(cell)))
# this must always fail for random cells
try:
np.testing.assert_array_almost_equal(crys.cc2cell(crys.cell2cc(cell)), cell)
except AssertionError:
pass
# Here, we convert cryst_const to a *different* cell which conforms to the
# orientation convention, and back to cryst_const.
np.testing.assert_array_almost_equal(crys.cell2cc(crys.cc2cell(cryst_const)),
cryst_const)
# 3d
cell = rand(100,3,3)
cc = crys.cell2cc3d(cell, axis=0)
vol_cell = np.abs(crys.volume_cell3d(cell, axis=0))
vol_cc = crys.volume_cc3d(cc, axis=0)
assert crys.cell2cc3d(cell, axis=0).shape == (100,6)
assert crys.cc2cell3d(cc, axis=0).shape == (100,3,3)
assert vol_cc.shape == (100,)
assert vol_cell.shape == (100,)
aaae(vol_cell, vol_cc)
aaae(crys.cell2cc3d(crys.cc2cell3d(cc)), cc)
def get_random_cryst_const(self):
"""Create random cryst_const.
Returns
-------
cryst_const : 1d array (6,)
Raises
------
RandomStructureFail
"""
def _get():
return np.concatenate(
(uniform(self.length_range[0], self.length_range[1], 3),
uniform(self.angle_range[0], self.angle_range[1], 3)))
cnt = 1
while cnt <= self.cell_maxtry:
cc = _get()
vol = volume_cc(cc)
if not self.vol_range[0] <= vol <= self.vol_range[1]:
cc = _get()
cnt += 1
else:
self.counters['cryst_const'] = cnt
return cc
raise RandomStructureFail("failed creating random cryst_const")
def get_random_cryst_const(self):
"""Create random cryst_const.
Returns
-------
cryst_const : 1d array (6,)
Raises
------
RandomStructureFail
"""
def _get():
return np.concatenate((uniform(self.length_range[0],
self.length_range[1], 3),
uniform(self.angle_range[0],
self.angle_range[1], 3)))
cnt = 1
while cnt <= self.cell_maxtry:
cc = _get()
vol = volume_cc(cc)
if not self.vol_range[0] <= vol <= self.vol_range[1]:
cc = _get()
cnt += 1
else:
self.counters['cryst_const'] = cnt
return cc
raise RandomStructureFail("failed creating random cryst_const")