def setUp(self):
unittest.TestCase.setUp(self)
self.atoms = atomsites.AtomSites()
self.atom1 = atomsite.AtomSite(13, 0, 0, 0)
self.atom2 = atomsite.AtomSite(13, 0, 0.5, 0.5)
self.atom3 = atomsite.AtomSite(13, 0.5, 0, 0.5)
self.atom4 = atomsite.AtomSite(13, 0, 0.5, 0.5)
def __call__(self, atom):
"""
Return the symmetry operation on an *atomsite*.
:math:`= RV + T`
:arg atom: atomsite to apply the symmetry operation
:type atom: :class:`atomsite.AtomSite`
"""
position = atom.position
atomicnumber = atom.atomicnumber
newposition = self.r * position + self.t
return atomsite.AtomSite(atomicnumber, newposition)
def get_atomsites(self):
"""
Return a :class:`list` of :class:`atomsite.AtomSite` from the cif.
:rtype: : keyword:`list`
"""
atoms = atomsites.AtomSites()
symmetry_equiv_pos_as_xyz = self.get(SYMMETRY_EQUIV_POS_AS_XYZ)
atom_site_labels = self.get(ATOM_SITE_LABEL)
atom_site_fract_xs = self.get(ATOM_SITE_FRACT_X)
atom_site_fract_ys = self.get(ATOM_SITE_FRACT_Y)
atom_site_fract_zs = self.get(ATOM_SITE_FRACT_Z)
for i, atom_site_label in enumerate(atom_site_labels):
# Remove digits after the chemical symbol
if len(atom_site_label) > 1 and atom_site_label[1].isdigit():
symbol = atom_site_label[0]
else:
symbol = atom_site_label[:2]
atomicnumber = ElementProperties.getAtomicNumberBySymbol(symbol)
atom = atomsite.AtomSite(atomicnumber, atom_site_fract_xs[i][0],
atom_site_fract_ys[i][0],
atom_site_fract_zs[i][0])
atoms.append(atom)
# Apply symmetry equivalent positions
for atom in atoms:
x, y, z = tuple(atom.position)
atomicnumber = atom.atomicnumber
for equiv_pos in symmetry_equiv_pos_as_xyz:
equiv_x, equiv_y, equiv_z = equiv_pos
# Allow float division
equiv_x = equiv_x.replace('1/', '1.0/').replace(
'2/', '2.0/').replace('3/', '3.0/').replace(
'4/', '4.0/').replace('6/', '6.0/')
equiv_y = equiv_y.replace('1/', '1.0/').replace(
'2/', '2.0/').replace('3/', '3.0/').replace(
'4/', '4.0/').replace('6/', '6.0/')
equiv_z = equiv_z.replace('1/', '1.0/').replace(
'2/', '2.0/').replace('3/', '3.0/').replace(
'4/', '4.0/').replace('6/', '6.0/')
# Replace x, y, z by the value
newx = eval(
equiv_x.replace('x', str(x)).replace('y', str(y)).replace(
'z', str(z)))
newy = eval(
equiv_y.replace('x', str(x)).replace('y', str(y)).replace(
'z', str(z)))
newz = eval(
equiv_z.replace('x', str(x)).replace('y', str(y)).replace(
'z', str(z)))
# Add if new position
newatom = atomsite.AtomSite(atomicnumber, newx, newy, newz)
try:
atoms.append(newatom)
except atomsites.AtomSitePositionError:
pass
return atoms
def setUp(self):
unittest.TestCase.setUp(self)
self.atom1 = atomsite.AtomSite(13, 0, 0.5, 1.5)
self.atom2 = atomsite.AtomSite(14, (0.3, -0.8, 0.1))
def setUp(self):
unittest.TestCase.setUp(self)
# Manual testing
self.cubic = unitcell.create_cubic_unitcell(2)
self.tetragonal = unitcell.create_tetragonal_unitcell(2, 3)
self.orthorhombic = unitcell.create_orthorhombic_unitcell(1, 2, 3)
self.trigonal = unitcell.create_trigonal_unitcell(2, 35.0 / 180 * pi)
self.hexagonal = unitcell.create_hexagonal_unitcell(2, 3)
self.monoclinic = unitcell.create_monoclinic_unitcell(
1, 2, 3, 55.0 / 180 * pi)
self.triclinic = \
unitcell.create_triclinic_unitcell(1, 2, 3,
75.0 / 180 * pi, 55.0 / 180 * pi, 35.0 / 180 * pi)
self.planes = [
plane.Plane(1, 0, 0),
plane.Plane(1, 1, 0),
plane.Plane(1, 1, 1),
plane.Plane(2, 0, 2),
plane.Plane(1, 2, 3),
plane.Plane(4, 5, 6),
plane.Plane(0, 9, 2)
]
# Example 1.13 from Mathematical Crystallography (p.31-33)
self.L1 = unitcell.create_hexagonal_unitcell(4.914, 5.409)
self.atom1 = atomsite.AtomSite(8, (0.4141, 0.2681, 0.1188))
self.atom2 = atomsite.AtomSite(14, (0.4699, 0.0, 0.0))
self.atom3 = atomsite.AtomSite(14, (0.5301, 0.5301, 0.3333))
# Problem 1.13 from Mathematical Crystallography (p.34)
alpha = 93.11 / 180.0 * pi
beta = 115.91 / 180.0 * pi
gamma = 91.26 / 180.0 * pi
self.L2 = unitcell.create_triclinic_unitcell(8.173, 12.869, 14.165,
alpha, beta, gamma)
self.atom4 = atomsite.AtomSite(8, (0.3419, 0.3587, 0.1333))
self.atom5 = atomsite.AtomSite(14, (0.5041, 0.3204, 0.1099))
self.atom6 = atomsite.AtomSite(13, (0.1852, 0.3775, 0.1816))
# Example 2.16 and Problem 2.9 from Mathematical Crystallography (p.64-65)
alpha = 114.27 / 180.0 * pi
beta = 82.68 / 180.0 * pi
gamma = 94.58 / 180.0 * pi
self.L3 = unitcell.create_triclinic_unitcell(6.621, 7.551, 17.381,
alpha, beta, gamma)
# Problem 2.15 from Mathematical Crystallography (p.79)
alpha = 113.97 / 180.0 * pi
beta = 98.64 / 180.0 * pi
gamma = 67.25 / 180.0 * pi
self.L4 = unitcell.create_triclinic_unitcell(5.148, 7.251, 5.060,
alpha, beta, gamma)
# Scattering factors
relativepath = os.path.join('..', 'testdata', 'goodconfiguration.cfg')
configurationfilepath = Files.getCurrentModulePath(
__file__, relativepath)
self.scatter = scatteringfactors.XrayScatteringFactors(
configurationfilepath)
# Atom sites
self.atomsfcc = atomsites.AtomSites([
atomsite.AtomSite(14, 0.5, 0.5, 0.0),
atomsite.AtomSite(14, 0.5, 0.0, 0.5),
atomsite.AtomSite(14, 0.0, 0.5, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)
])
self.atomsbcc = atomsites.AtomSites([
atomsite.AtomSite(14, 0.5, 0.5, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)
])
self.atomshcp = atomsites.AtomSites([
atomsite.AtomSite(14, 1 / 3.0, 2 / 3.0, 0.5),
atomsite.AtomSite(14, 0.0, 0.0, 0.0)
])
def setUp(self):
unittest.TestCase.setUp(self)
self.sg = spacegroups.sg25
self.atom1 = atomsite.AtomSite(13, 1, 0, 0)
self.atom2 = atomsite.AtomSite(13, 0.1, 0.1, 0.1)