def setUp(self):
self.cif_file_names = [
os.path.abspath(file_name)
for file_name in glob.glob(os.path.join(TEST_FILES, 'cifs/*.cif'))
]
space_group = SpaceGroup('C 1 2/m 1')
lattice = Lattice(4.0, 5.0, 6.0, 90.0, 109.10, 90.0)
sites = []
sites.append(Site(label="Li", abc=(0.25, 0.0, 0.0), occupancy=0.80))
sites.append(Site(label="Mn", abc=(0.25, 0.0, 0.0), occupancy=0.20))
sites.append(Site(label="O", abc=(0.5, 0.5, 0.5)))
self.crystal = Crystal(sites=sites,
space_group=space_group,
lattice=lattice)
def setUp(self):
self.crystals = []
for file_name in glob.glob('data/cifs/*.cif'):
#file_name = 'test_cifs/icsd-12301.cif'
c = Crystal.from_cif(file_name)
c.print_summary
self.crystals.append(c)
def setUp(self):
self.cif_file_names = [os.path.abspath(file_name) for file_name in glob.glob(os.path.join(TEST_FILES, 'cifs/*.cif'))]
space_group = SpaceGroup('C 1 2/m 1')
lattice = Lattice(4.0, 5.0, 6.0, 90.0, 109.10, 90.0)
sites = []
sites.append(Site(label="Li", abc=(0.25, 0.0, 0.0), occupancy=0.80))
sites.append(Site(label="Mn", abc=(0.25, 0.0, 0.0), occupancy=0.20))
sites.append(Site(label="O", abc=(0.5, 0.5, 0.5)))
self.crystal = Crystal(sites=sites, space_group=space_group, lattice=lattice)
def test_assign_coordination_number(self):
print "Test assign coordination number."
file_name = os.path.join(TEST_FILES, 'cifs', 'icsd-12301.cif')
current_crystal = Crystal.from_cif(file_name)
passed = True
for sca in current_crystal.crystal_structure.scatterers():
label = sca.label
coord_num = current_crystal.get_coordination_number(sca)
self.assertEqual(coord_num, 4.0)
'''
def test_assign_coordination_number(self):
print "Test assign coordination number."
file_name = os.path.join(TEST_FILES, 'cifs', 'icsd-12301.cif')
current_crystal = Crystal.from_cif(file_name)
passed = True
for sca in current_crystal.crystal_structure.scatterers():
label = sca.label
coord_num = current_crystal.get_coordination_number(sca)
self.assertEqual(coord_num, 4.0)
'''
def test_multiple_transforms(self):
"""docstring for test_to_niggli"""
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_standard()
ssg = n.space_group.raw_cctbx_name
f = n.to_niggli()
ssf = f.space_group.raw_cctbx_name
#self.assertEqual(ssg, ssf)
print ssg + " *** " + ssf
#f.print_summary()
print f.to_dict()
#transform_names = [t["name"] for t in f.transforms]
#print transform_names
#print f.transforms
cry = c.to_standard().to_niggli()
print c.to_standard().to_niggli().to_dict()
def test_multiple_transforms(self):
"""docstring for test_to_niggli"""
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_standard()
ssg = n.space_group.raw_cctbx_name
f = n.to_niggli()
ssf = f.space_group.raw_cctbx_name
#self.assertEqual(ssg, ssf)
print ssg + " *** " + ssf
#f.print_summary()
print f.to_dict()
#transform_names = [t["name"] for t in f.transforms]
#print transform_names
#print f.transforms
cry = c.to_standard().to_niggli()
print c.to_standard().to_niggli().to_dict()
def test_to_standard(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_standard()
n.print_summary()
print n.to_dict()
def test_crystal(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
c.print_summary()
for site in c.sites:
print site.to_dict()
def test_load_cif(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
c.print_summary
class TestCrystal(unittest.TestCase):
def setUp(self):
self.cif_file_names = [os.path.abspath(file_name) for file_name in glob.glob(os.path.join(TEST_FILES, 'cifs/*.cif'))]
space_group = SpaceGroup('C 1 2/m 1')
lattice = Lattice(4.0, 5.0, 6.0, 90.0, 109.10, 90.0)
sites = []
sites.append(Site(label="Li", abc=(0.25, 0.0, 0.0), occupancy=0.80))
sites.append(Site(label="Mn", abc=(0.25, 0.0, 0.0), occupancy=0.20))
sites.append(Site(label="O", abc=(0.5, 0.5, 0.5)))
self.crystal = Crystal(sites=sites, space_group=space_group, lattice=lattice)
def test_load_cif(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
c.print_summary
def test_crystal(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
c.print_summary()
for site in c.sites:
print site.to_dict()
def test_to_niggli(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_niggli()
n.print_summary()
print n.to_dict()
def test_to_standard(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_standard()
n.print_summary()
print n.to_dict()
def test_multiple_transforms(self):
"""docstring for test_to_niggli"""
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_standard()
ssg = n.space_group.raw_cctbx_name
f = n.to_niggli()
ssf = f.space_group.raw_cctbx_name
#self.assertEqual(ssg, ssf)
print ssg + " *** " + ssf
#f.print_summary()
print f.to_dict()
#transform_names = [t["name"] for t in f.transforms]
#print transform_names
#print f.transforms
cry = c.to_standard().to_niggli()
print c.to_standard().to_niggli().to_dict()
def test_assign_coordination_number(self):
print "Test assign coordination number."
file_name = os.path.join(TEST_FILES, 'cifs', 'icsd-12301.cif')
current_crystal = Crystal.from_cif(file_name)
passed = True
for sca in current_crystal.crystal_structure.scatterers():
label = sca.label
coord_num = current_crystal.get_coordination_number(sca)
self.assertEqual(coord_num, 4.0)
'''
# make sure labels match cctbx output
# not the most rigorous test but alright for now
if label == "Li-0":
if coord_num != 6:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 6."
passed = False
elif label == "Fe-1":
if coord_num != 6:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 6."
passed = False
elif label == "P-2":
if coord_num != 4:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 4."
passed = False
elif label == "O-3":
if coord_num != 4:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 4."
passed = False
elif label == "O-4":
if coord_num != 6:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 6."
passed = False
elif label == "O-5":
if coord_num != 6:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 6."
passed = False
else:
print "Unknown atom found for this test. Test Failed."
passed = False
'''
def test_assign_wyckoff(self):
"""docstring for test_assign_wyckoff"""
abc = [0.25, 0.25, 0.5]
letter = self.crystal.assign_wyckoff(abc)
self.assertEqual(letter, 'f')
def test_symmetry_error(self):
space_group = SpaceGroup('F d d 2')
lattice = Lattice(4.0, 5.0, 6.0, 88.0, 91.0, 95.0)
sites = []
sites.append(Site(label="Li", abc=(0.25, 0.0, 0.0), occupancy=0.80))
#crystal = Crystal(sites=sites, space_group=space_group, lattice=lattice)
pass
def test_to_standard(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_standard()
n.print_summary()
print n.to_dict()
def test_crystal(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
c.print_summary()
for site in c.sites:
print site.to_dict()
def test_load_cif(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
c.print_summary
class TestCrystal(unittest.TestCase):
def setUp(self):
self.cif_file_names = [
os.path.abspath(file_name)
for file_name in glob.glob(os.path.join(TEST_FILES, 'cifs/*.cif'))
]
space_group = SpaceGroup('C 1 2/m 1')
lattice = Lattice(4.0, 5.0, 6.0, 90.0, 109.10, 90.0)
sites = []
sites.append(Site(label="Li", abc=(0.25, 0.0, 0.0), occupancy=0.80))
sites.append(Site(label="Mn", abc=(0.25, 0.0, 0.0), occupancy=0.20))
sites.append(Site(label="O", abc=(0.5, 0.5, 0.5)))
self.crystal = Crystal(sites=sites,
space_group=space_group,
lattice=lattice)
def test_load_cif(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
c.print_summary
def test_crystal(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
c.print_summary()
for site in c.sites:
print site.to_dict()
def test_to_niggli(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_niggli()
n.print_summary()
print n.to_dict()
def test_to_standard(self):
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_standard()
n.print_summary()
print n.to_dict()
def test_multiple_transforms(self):
"""docstring for test_to_niggli"""
for file_name in self.cif_file_names:
c = Crystal.from_cif(file_name)
n = c.to_standard()
ssg = n.space_group.raw_cctbx_name
f = n.to_niggli()
ssf = f.space_group.raw_cctbx_name
#self.assertEqual(ssg, ssf)
print ssg + " *** " + ssf
#f.print_summary()
print f.to_dict()
#transform_names = [t["name"] for t in f.transforms]
#print transform_names
#print f.transforms
cry = c.to_standard().to_niggli()
print c.to_standard().to_niggli().to_dict()
def test_assign_coordination_number(self):
print "Test assign coordination number."
file_name = os.path.join(TEST_FILES, 'cifs', 'icsd-12301.cif')
current_crystal = Crystal.from_cif(file_name)
passed = True
for sca in current_crystal.crystal_structure.scatterers():
label = sca.label
coord_num = current_crystal.get_coordination_number(sca)
self.assertEqual(coord_num, 4.0)
'''
# make sure labels match cctbx output
# not the most rigorous test but alright for now
if label == "Li-0":
if coord_num != 6:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 6."
passed = False
elif label == "Fe-1":
if coord_num != 6:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 6."
passed = False
elif label == "P-2":
if coord_num != 4:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 4."
passed = False
elif label == "O-3":
if coord_num != 4:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 4."
passed = False
elif label == "O-4":
if coord_num != 6:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 6."
passed = False
elif label == "O-5":
if coord_num != 6:
print "Coordination number test failed on label = " + label
print "Number is", coord_num, "and should be 6."
passed = False
else:
print "Unknown atom found for this test. Test Failed."
passed = False
'''
def test_assign_wyckoff(self):
"""docstring for test_assign_wyckoff"""
abc = [0.25, 0.25, 0.5]
letter = self.crystal.assign_wyckoff(abc)
self.assertEqual(letter, 'f')
def test_symmetry_error(self):
space_group = SpaceGroup('F d d 2')
lattice = Lattice(4.0, 5.0, 6.0, 88.0, 91.0, 95.0)
sites = []
sites.append(Site(label="Li", abc=(0.25, 0.0, 0.0), occupancy=0.80))
#crystal = Crystal(sites=sites, space_group=space_group, lattice=lattice)
pass
