def test_from_cod(self):
""" Test building a Crystal object from the COD """
# revision = None and latest revision should give the same Crystal
c = Crystal.from_cod(1521124)
c2 = Crystal.from_cod(1521124, revision=176429)
self.assertEqual(c, c2)
def gen_xyz(file, n=[0, 0, 1], rep=[1, 1, 1], pad=0, xyz='', **kwargs):
''' convert cif file into autoslic .xyz input file
- file : cif_file
- rep : super cell repeat
- n : reorient of the z axis into n
- pad : amount of padding on each side (in unit of super cell size)
'''
if isinstance(file, str):
tail = ''.join(np.array(n, dtype=str)) + '.xyz'
if file.split('.')[-1] == 'cif':
crys = Crystal.from_cif(file)
if not xyz: xyz = file.replace('.cif', tail)
elif sum(np.array(list(Crystal.builtins)) == file):
crys = Crystal.from_database(file)
if not xyz: xyz = file + tail
lat_vec = np.array(crys.lattice_vectors)
lat_params = crys.lattice_parameters[:3]
pattern = np.array([[a.atomic_number] + list(a.coords_cartesian) +
[a.occupancy, 1.0] for a in crys.atoms])
else:
if not xyz: raise Exception('xyz filename required')
pattern = file
pattern, lat = make_xyz(xyz,
pattern,
lat_vec,
lat_params,
n=n,
pad=pad,
rep=rep,
**kwargs)
npy_file = xyz.replace('.xyz', '.npy')
np.save(npy_file, [lat, pattern])
print(colors.green + 'binary coords file saved :' + colors.yellow +
npy_file + colors.black)
def test_equality(self):
""" Test that __eq__ works as expected """
c1 = Crystal.from_database("Pu-alpha")
c2 = deepcopy(c1)
self.assertEqual(c1, c2)
c3 = Crystal.from_database("Pu-epsilon")
self.assertNotEqual(c1, c3)
def test_equality():
"""Test that __eq__ works as expected"""
c1 = Crystal.from_database("Pu-alpha")
c2 = deepcopy(c1)
assert c1 == c2
c3 = Crystal.from_database("Pu-epsilon")
assert c1 != c3
def import_crys(file):
if file.split('.')[-1] == 'cif':
crys = Crystal.from_cif(file)
elif sum(np.array(list(Crystal.builtins)) == file):
crys = Crystal.from_database(file)
else:
raise Exception('cannot import %s' % file)
return crys
def test_reciprocal_matrix1(self):
c = Crystal("quartz")
c.lattice_angles_deg = np.fromstring("90.0 90.0 120.0", sep=' ')
c.lattice_lengths = np.fromstring("4.913 4.913 5.400", sep=' ')
c.calculate_reciprocal()
isaw_rec = np.fromstring(""" 1.278890 0.000000 0.000000
0.738367 1.476735 -0.000000
-0.000000 -0.000000 1.163553""", sep=' ').reshape(3,3)
assert np.allclose(isaw_rec, c.reciprocal_lattice), "Reciprocal lattice of %s matches ISAW lattice." % c.name
def test_reciprocal_matrix2(self):
c = Crystal("oxalic acid")
c.lattice_angles_deg = np.fromstring("90.0 103.2 90.0", sep=' ')
c.lattice_lengths = np.fromstring("6.094 3.601 11.915", sep=' ')
c.calculate_reciprocal()
isaw_rec = np.fromstring(""" 1.031045 0.000000 0.000000
-0.000000 1.744845 0.000000
0.241829 -0.000000 0.54164""", sep=' ').reshape(3,3)
assert np.allclose(isaw_rec, c.reciprocal_lattice), "Reciprocal lattice of %s matches ISAW lattice." % c.name
def __init__(self, unitCell, latticeVectors):
self._unitCell = [Atom(atom[0], coords=atom[1]) for atom in unitCell]
Crystal.__init__(self, self._unitCell, latticeVectors)
self.atomsPerUnitCell = len(unitCell)
self.atomicWeights = [atom.mass for atom in self._unitCell]
self.atomLabels = [
f'{inx}_{atom.element}'
for atom, inx in zip(self._unitCell, range(self.atomsPerUnitCell))
]
def test_reciprocal_matrix4(self):
c = Crystal("Natrolite(conventional orthorhombic cell)")
c.lattice_angles_deg = np.fromstring("90.0 90.0 90.0", sep=' ')
c.lattice_lengths = np.fromstring("18.328 18.585 6.597", sep=' ')
c.calculate_reciprocal()
isaw_rec = np.fromstring(""" 0.342819 0.000000 0.000000
-0.000000 0.338078 0.000000
-0.000000 -0.000000 0.952431 """, sep=' ').reshape(3,3)
#print c.reciprocal_lattice, "\n\n\n"
assert np.allclose(isaw_rec, c.reciprocal_lattice, atol=1e-5), "Reciprocal lattice of %s matches ISAW lattice." % c.name
def test_reciprocal_matrix3(self):
c = Crystal("Natrolite(reduced cell)")
c.lattice_angles_deg = np.fromstring("83.5 70.5 70.2", sep=' ')
c.lattice_lengths = np.fromstring("6.601 9.739 9.893", sep=' ')
c.calculate_reciprocal()
isaw_rec = np.fromstring(""" 0.951854 -0.000000 0.000000
-0.342876 0.685738 0.000000
-0.336898 0.000033 0.673719 """, sep=' ').reshape(3,3)
#print c.reciprocal_lattice, "\n\n\n"
assert np.allclose(isaw_rec, c.reciprocal_lattice, atol=1e-3), "Reciprocal lattice of %s matches ISAW lattice." % c.name
def test_ase_atoms_back_and_forth(name):
""" Test conversion to and from ase Atoms """
crystal = Crystal.from_database(name)
to_ase = crystal.to_ase()
crystal2 = Crystal.from_ase(to_ase)
# ase has different handling of coordinates which can lead to
# rounding beyond 1e-3. Therefore, we cannot compare directly sets
# assertSetEqual(set(crystal), set(crystal2))
assert len(crystal) == len(crystal2)
def test_cif_writer_idempotence(name):
""" Test that conversion to CIF of a structure loaded from CIF is idempotent. """
# Testing on all built-in structure assures us that corner cases
# are taken care of.
cryst = Crystal.from_database(name)
with tempfile.TemporaryDirectory() as temp_dir:
f = Path(temp_dir) / "temp.cif"
cryst.to_cif(f)
cryst2 = Crystal.from_cif(f)
assert cryst == cryst2
def test_powdersim_peak_alignment():
""" Test that the diffraction peaks align with what is expected. """
crystal = Crystal.from_database("C")
for reflection in [(0, 1, 1), (1, 2, 0), (-1, 2, 0)]:
qknown = np.linalg.norm(crystal.scattering_vector((0, 1, 1)))
# Range of scattering vectors is tightly centered around a particular reflection
# So that the maximum of the diffraction pattern MUST be at reflection (010)
q = np.linspace(qknown - 0.1, qknown + 0.1, 256)
pattern = powdersim(Crystal.from_database("C"), q)
assert abs(q[np.argmax(pattern)] - qknown) < q[1] - q[0]
def test_idempotence(self):
""" Test that conversion to CIF of a structure loaded from CIF is idempotent. """
# Testing on all built-in structure assures us that corner cases
# are taken care of.
for name in Crystal.builtins:
with self.subTest(f"CIF idempotence {name}"):
cryst = Crystal.from_database(name)
with tempfile.TemporaryDirectory() as temp_dir:
f = Path(temp_dir) / "temp.cif"
cryst.to_cif(f)
cryst2 = Crystal.from_cif(f)
self.assertEqual(cryst, cryst2)
def test_constructors(self):
""" Test Supercell constructors for varyous 'builtin' structures """
for name in islice(Crystal.builtins, 20):
with self.subTest(name):
s = Crystal.from_database(name).supercell(2, 2, 2)
self.assertEqual(len(s), 8 * len(s.crystal))
def load_datagrid_sim(folder, arr, x):
'''
Load cif files from folder into ase crystal objects, simulate crystal
diffraction and represent data in timeseries
Args:
folder (string): Where we load the data from.
arr (list): List of cif filenames in folder.
x (nparray): representation of 1/angström for powder simulation.
Returns:
fd (datagrid): representation of intensity values and 1/angström
values in datagrid object.
'''
filename_arr = []
crys_arr = []
for file in arr:
filename = os.sep.join([folder, file])
filename_arr.append(file)
crys = read(filename)
crys = Crystal.from_ase(crys)
diff = powdersim(crys, x)
diff_norm = diff / diff.max()
crys_arr.append(diff_norm)
crys_arr = np.array(crys_arr)
print(crys_arr)
return crys_arr
def test_side_effects():
""" Test that mesh arrays are not written to in pelectrostatic """
crystal = Crystal.from_database("C")
xx, yy = np.meshgrid(np.linspace(-10, 10, 32), np.linspace(-10, 10, 32))
xx.setflags(write=False)
yy.setflags(write=False)
potential = pelectrostatic(crystal, xx, yy)
def test_return_shape():
""" Test that the return shape of pelectrostatic is the same as input arrays """
crystal = Crystal.from_database("C")
xx, yy = np.meshgrid(np.linspace(-10, 10, 32), np.linspace(-10, 10, 32))
potential = pelectrostatic(crystal, xx, yy)
assert xx.shape == potential.shape
def test_simulation_3_peaks(self):
"""
Test calibration from simulation, down to 1% error . Peaks (200) and (220) from monoclinic VO2 are used,
"""
s = np.linspace(0.11, 0.8, 1024)
q = 4 * np.pi * s
c = Crystal.from_database("vo2-m1")
I = powdersim(c, s)
peak1 = (2, 0, 0)
Gx1, Gy1, Gz1 = c.scattering_vector(peak1)
q1 = np.sqrt(Gx1 ** 2 + Gy1 ** 2 + Gz1 ** 2)
arr_index1 = np.argmin(np.abs(q - q1))
peak2 = (2, 2, 0)
Gx2, Gy2, Gz2 = c.scattering_vector(peak2)
q2 = np.sqrt(Gx2 ** 2 + Gy2 ** 2 + Gz2 ** 2)
arr_index2 = np.argmin(np.abs(q - q2))
peak3 = (3, 0, -2)
Gx2, Gy2, Gz2 = c.scattering_vector(peak3)
q3 = np.sqrt(Gx2 ** 2 + Gy2 ** 2 + Gz2 ** 2)
arr_index3 = np.argmin(np.abs(q - q3))
calibrated = powder_calq(
I,
c,
peak_indices=(arr_index1, arr_index2, arr_index3),
miller_indices=(peak1, peak2, peak3),
)
self.assertTupleEqual(I.shape, calibrated.shape)
self.assertTrue(np.allclose(q, calibrated, rtol=0.01))
def pow_sim(path1):
filename1 = Path(path1).name
#filename2 = Path(path2).name
# load cif file to an ase object
cry1 = read(path1)
#cry2 = read(path2)
# crystal object for powdersim in skued lib
crys1 = Crystal.from_ase(cry1)
#crys2 = Crystal.from_ase(cry2)
# powder simulation with range of q
q = np.linspace(1, 7, 512)
diff1 = powdersim(crys1, q, fwhm_g = 0.01, fwhm_l=0.03)
#diff2 = powdersim(crys2, q)
# matplotlib config
plt.figure()
plt.plot(q, diff1/diff1.max(), '-b', label=filename1, alpha= 0.3)
#plt.plot(q, diff2/diff2.max(), '-r', label=filename2, alpha= 0.3)
plt.legend()
plt.xlim([q.min(), q.max()])
plt.xlabel('$q (1/\AA)$')
plt.ylabel('Diffracted intensity (A.u.)')
plt.title('Crystal diffraction ')
plt.show()
def test_reciprocal_symmetry_operations(name):
"""Test that the reciprocal symmetry operations output makes sense"""
identity = np.eye(4)
c = Crystal.from_database(name)
symops = c.reciprocal_symmetry_operations()
assert np.allclose(identity, symops[0])
def setUp(self):
self.crystal = Crystal.from_database("C")
self.reflections = list(combinations_with_replacement(range(-3, 4), 3))
self.intensities = [
np.abs(structure_factor(self.crystal, *reflection))**2
for reflection in self.reflections
]
def test_from_cod_new_dir():
"""Test that a cache dir is created by Crystal.from_cod"""
with tempfile.TemporaryDirectory() as temp_dir:
download_dir = Path(temp_dir) / "test_cod"
assert not download_dir.exists()
c = Crystal.from_cod(1521124, download_dir=download_dir)
assert download_dir.exists()
def test_from_cod_new_dir(self):
""" Test that a cache dir is created by Crystal.from_cod """
with tempfile.TemporaryDirectory() as temp_dir:
download_dir = Path(temp_dir) / "test_cod"
self.assertFalse(download_dir.exists())
c = Crystal.from_cod(1521124, download_dir=download_dir)
self.assertTrue(download_dir.exists())
def load_datagrid_sim(folder, arr, x):
'''
Load cif files from folder into ase crystal objects, simulate crystal
diffraction and represent data in timeseries
Args:
folder (string): Where we load the data from.
arr (list): List of cif filenames in folder.
x (nparray): representation of 1/angström for powder simulation.
Returns:
fd (datagrid): representation of intensity values and 1/angström
values in datagrid object.
'''
filename_arr = []
crys_arr = []
for file in arr:
filename = os.sep.join([folder, file])
filename_arr.append(file)
crys = read(filename)
crys = Crystal.from_ase(crys)
diff = powdersim(crys, x, fwhm_l=50)
diff_norm = diff / diff.max()
crys_arr.append(diff_norm)
crys_arr = np.array(crys_arr)
fd = FDataGrid(crys_arr,
x,
dataset_name='Diffraction Curves',
argument_names=[r'$q (1/\AA)$'],
coordinate_names=['Diffracted intensity (A.u.)'])
print(fd)
return fd
def Li_rots():
crys = Crystal.from_database('Li')
coords = np.array([a.coords_cartesian for a in crys.atoms])
# files = rcc.rotate_xyz(crys,Nrot=8,name='dat/Lithium/rots/',opt='p')
files = rcc.orient_crystal(coords,ez=[0,0,1],n_u=[0,,1])
for file in files[:4] : rcc.show_grid(file,title=file,equal=1)#,xyTicks=3.49,xylims=[0,100,0,100])
def test_primitive_for_builtins(self):
""" Test that all built-in crystal have a primitive cell """
for name in Crystal.builtins:
with self.subTest(name):
c = Crystal.from_database(name)
prim = c.primitive(symprec=0.1)
self.assertLessEqual(len(prim), len(c))
def get_pendulossung(name='Si', miller=[0, 0, 0], keV=200, opt='p'):
''' give the theorertical 2-beam approximation Pendullosung thickness
- `name` : compound
- `miller` : [h,k,l]
- `keV` : wavelength (keV)
RETURN
- xi : Pendullosung thickness (A)
'''
# compute structure factor
from crystals import Crystal
crys = Crystal.from_database(name)
lat_vec = crys.reciprocal_vectors
pattern = np.array(
[list(a.coords_fractional) + [a.atomic_number] for a in crys.atoms])
hkl, Fhkl = structure_factor3D(pattern,
lat_vec,
hklMax=max(miller),
sym=0,
v='')
ax, by, cz = crys.lattice_parameters[:3]
Vcell = crys.volume
# compute Pendullosung
h, k, l = miller
Ug, K = np.abs(Fhkl[h, k, l]) / Vcell, 1 / scatf.wavelength(keV)
xi = K / Ug
if 'p' in opt:
print(green + "\tPendullosung thickness " + name + '[%d%d%d]' %
(h, k, l) + black)
print('%-5s= %.2f\n%-5s= %.2f\n%-5s= %.2f' %
('K', K, 'Ug', Ug, 'xi', xi))
return xi
def import_cif(file,
xyz='',
n=[0, 0, 1],
rep=[1, 1, 1],
pad=0,
dopt='s',
lfact=1.0,
tail=''):
''' convert cif file into autoslic .xyz input file
- file : cif_file
- rep : super cell repeat
- n : reorient of the z axis into n
- pad : amount of padding on each side (in unit of super cell size)
'''
crys = Crystal.from_cif(file)
lat_vec = np.array(crys.lattice_vectors)
lat_params = crys.lattice_parameters[:3]
pattern = np.array([[a.atomic_number] + list(lfact * a.coords_cartesian) +
[a.occupancy, 1.0] for a in crys.atoms])
if xyz:
make_xyz(xyz,
pattern,
lat_vec,
lat_params,
n=n,
pad=pad,
rep=rep,
fmt='%.4f',
dopt=dopt)
pattern[:,
1:4] = rcc.orient_crystal(pattern[:, 1:4],
n_u=n) #,lat_params #pattern,crys # file
return pattern
def test_substructure_preservation():
"""Test that initializing a crystal with substructures preserves the substructures"""
atoms = [Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])]
substructures = [AtomicStructure(atoms=[Atom("U", [0, 0, 0])])]
c = Crystal(unitcell=atoms + substructures, lattice_vectors=np.eye(3))
assert len(c) == 3
assert substructures[0] in c.substructures
def test_builtins(self):
""" Test that all names in Crystal.builtins build without errors,
and that Crystal.source is correctly recorded. """
for name in Crystal.builtins:
with self.subTest(name):
c = Crystal.from_database(name)
self.assertIn(name, c.source)
def test_substructure_preservation(self):
""" Test that initializing a crystal with substructures preserves the substructures """
atoms = [Atom("Ag", [0, 0, 0]), Atom("Ag", [1, 1, 1])]
substructures = [AtomicStructure(atoms=[Atom("U", [0, 0, 0])])]
c = Crystal(unitcell=atoms + substructures, lattice_vectors=np.eye(3))
self.assertEqual(len(c), 3)
self.assertIn(substructures[0], c.substructures)
def test_chemical_composition_add_to_unity(self):
""" Test that AtomicStructure.chemical_composition always adds up to 1 """
# Faster to create a large atomic structure from a Crystal object
# Testing for 10 crystal structures only
for name in islice(Crystal.builtins, 10):
with self.subTest("Chemical composition: " + name):
structure = AtomicStructure(atoms=Crystal.from_database(name))
self.assertAlmostEqual(sum(structure.chemical_composition.values()), 1)
def test_back_and_forth(self):
""" Test conversion to and from ase Atoms """
to_ase = self.crystal.to_ase()
crystal2 = Crystal.from_ase(to_ase)
# ase has different handling of coordinates which can lead to
# rounding beyond 1e-3. Therefore, we cannot compare directly sets
# self.assertSetEqual(set(self.crystal), set(crystal2))
self.assertEqual(len(self.crystal), len(crystal2))
def dont_test_compare_ubs(self):
"""ISAWev does not take into account the goniometer angles when outputting the
UB matrix file. ISAW does. This compares the U and B matrices obtained from both.
"""
#0, np.pi/4, 0
c = Crystal("oxalic acid")
c.read_ISAW_ubmatrix_file("data/TOPAZ_1204.mat", angles=[0, np.pi/4, 0])
c2 = Crystal("oxalic acid from EV")
c2.read_ISAW_ubmatrix_file("data/TOPAZ_1204_ev.mat", angles=[0, 0, 0])
assert np.allclose(c.reciprocal_lattice, c2.reciprocal_lattice, atol=0.05), "B matrices match, roughly. %s vs %s" % (c.reciprocal_lattice, c2.reciprocal_lattice)
assert np.allclose(c.u_matrix, c2.u_matrix, atol=0.02), "U matrices match, roughly. %s vs %s" % (c.u_matrix, c2.u_matrix)
print "\n\n\n"
print c.u_matrix
print c2.u_matrix