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_struct(self):
"""Generate random cryst_const and atom coords.
Returns
-------
Structure
Raises
------
RandomStructureFail
"""
self.cell = cc2cell(self.get_random_cryst_const())
self.coords_frac = np.empty((self.natoms, 3))
self.counters['coords'] = []
for iatom in range(self.natoms):
if iatom == 0:
cnt = 1
self._add_random_atom(iatom)
else:
cnt = 1
while cnt <= self.atom_maxtry:
self._add_random_atom(iatom)
if self._atoms_too_close(iatom):
self._add_random_atom(iatom)
cnt += 1
else:
break
self.counters['coords'].append(cnt)
if cnt > self.atom_maxtry:
raise RandomStructureFail("failed to create random coords for "
"iatom=%i of %i" %
(iatom, self.natoms - 1))
st = Structure(symbols=self.symbols,
coords_frac=self.coords_frac,
cell=self.cell)
return st
def _get_random_struct(self):
"""Generate random cryst_const and atom coords.
Returns
-------
Structure
Raises
------
RandomStructureFail
"""
self.cell = cc2cell(self.get_random_cryst_const())
self.coords_frac = np.empty((self.natoms, 3))
self.counters['coords'] = []
for iatom in range(self.natoms):
if iatom == 0:
cnt = 1
self._add_random_atom(iatom)
else:
cnt = 1
while cnt <= self.atom_maxtry:
self._add_random_atom(iatom)
if self._atoms_too_close(iatom):
self._add_random_atom(iatom)
cnt += 1
else:
break
self.counters['coords'].append(cnt)
if cnt > self.atom_maxtry:
raise RandomStructureFail("failed to create random coords for "
"iatom=%i of %i" %(iatom,
self.natoms-1))
st = Structure(symbols=self.symbols,
coords_frac=self.coords_frac,
cell=self.cell)
return st
def test_ibrav():
# bogus
aa = 3.0
bb = 4.0
cc = 5.0
alpha = 66*pi/180
beta = 77*pi/180
gamma = 88*pi/180
ibrav = 1
celldm = [aa] + [None]*5
ibrav2cell(ibrav, celldm)
ibrav = 2
celldm = [aa] + [None]*5
ibrav2cell(ibrav, celldm)
ibrav = 3
celldm = [aa] + [None]*5
ibrav2cell(ibrav, celldm)
ibrav = 4
celldm = [aa, None, cc/aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 5
celldm = [aa, None, None, cos(alpha), None, None]
ibrav2cell(ibrav, celldm)
ibrav = 6
celldm = [aa, None, cc/aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 7
celldm = [aa, None, cc/aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 8
celldm = [aa, bb/aa, cc/aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 9
celldm = [aa, bb/aa, cc/aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 10
celldm = [aa, bb/aa, cc/aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 11
celldm = [aa, bb/aa, cc/aa, None, None, None]
ibrav2cell(ibrav, celldm)
# celldm(4)=cos(ab) in doc!?
ibrav = 12
## celldm = [aa, bb/aa, cc/aa, cos(alpha), None, None]
celldm = [aa, bb/aa, cc/aa, None, None, cos(gamma)]
ibrav2cell(ibrav, celldm)
# celldm(4)=cos(ab) in doc!?
ibrav = 13
## celldm = [aa, bb/aa, cc/aa, cos(alpha), None, None]
celldm = [aa, bb/aa, cc/aa, None, None, cos(gamma)]
ibrav2cell(ibrav, celldm)
# WOHOO!
ibrav = 14
celldm = [aa, bb/aa, cc/aa, cos(alpha), cos(beta), cos(gamma)]
cell=ibrav2cell(ibrav, celldm)
np.testing.assert_array_almost_equal(cell,
crys.cc2cell(crys.celldm2cc(celldm)))
def test_ibrav():
# bogus
aa = 3.0
bb = 4.0
cc = 5.0
alpha = 66 * pi / 180
beta = 77 * pi / 180
gamma = 88 * pi / 180
ibrav = 1
celldm = [aa] + [None] * 5
ibrav2cell(ibrav, celldm)
ibrav = 2
celldm = [aa] + [None] * 5
ibrav2cell(ibrav, celldm)
ibrav = 3
celldm = [aa] + [None] * 5
ibrav2cell(ibrav, celldm)
ibrav = 4
celldm = [aa, None, cc / aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 5
celldm = [aa, None, None, cos(alpha), None, None]
ibrav2cell(ibrav, celldm)
ibrav = 6
celldm = [aa, None, cc / aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 7
celldm = [aa, None, cc / aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 8
celldm = [aa, bb / aa, cc / aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 9
celldm = [aa, bb / aa, cc / aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 10
celldm = [aa, bb / aa, cc / aa, None, None, None]
ibrav2cell(ibrav, celldm)
ibrav = 11
celldm = [aa, bb / aa, cc / aa, None, None, None]
ibrav2cell(ibrav, celldm)
# celldm(4)=cos(ab) in doc!?
ibrav = 12
## celldm = [aa, bb/aa, cc/aa, cos(alpha), None, None]
celldm = [aa, bb / aa, cc / aa, None, None, cos(gamma)]
ibrav2cell(ibrav, celldm)
# celldm(4)=cos(ab) in doc!?
ibrav = 13
## celldm = [aa, bb/aa, cc/aa, cos(alpha), None, None]
celldm = [aa, bb / aa, cc / aa, None, None, cos(gamma)]
ibrav2cell(ibrav, celldm)
# WOHOO!
ibrav = 14
celldm = [aa, bb / aa, cc / aa, cos(alpha), cos(beta), cos(gamma)]
cell = ibrav2cell(ibrav, celldm)
np.testing.assert_array_almost_equal(cell,
crys.cc2cell(crys.celldm2cc(celldm)))