def test_equality_of_sqs_objects_with_different_indexing():
"""SQS structures that are the same, but indexed differently should be equal."""
# TODO: implement this behavior in SQS.__eq__
config_1 = [['A', 'B'], ['A']]
occupancy_1 = [[0.25, 0.75], [1]]
site_ratios_1 = [3, 1]
config_2 = [['A'], ['A', 'B']]
occupancy_2 = [[1], [0.25, 0.75]]
site_ratios_2 = [1, 3]
s1 = PRLStructure(Lattice.hexagonal(1, 2), ['Mg', 'Mg'], [[0, 0, 0], [0.3333, 0.66666, 0.5]], sublattice_configuration=config_1, sublattice_occupancies=occupancy_1, sublattice_site_ratios=site_ratios_1)
s2 = PRLStructure(Lattice.hexagonal(1, 2), ['Mg', 'Mg'], [[0, 0, 0], [0.3333, 0.66666, 0.5]], sublattice_configuration=config_2, sublattice_occupancies=occupancy_2, sublattice_site_ratios=site_ratios_2)
assert s1 == s2
def test_structure(self):
quartz = self.quartz.structure
np.testing.assert_array_almost_equal(
quartz.lattice.matrix,
[[4.913400, 0, 0], [-2.456700, 4.255129, 0], [0, 0, 5.405200]])
self.assertEqual(quartz.formula, "Si3 O6")
self.assertNotIn("molecule-ID", self.quartz.atoms.columns)
ethane = self.ethane.structure
np.testing.assert_array_almost_equal(ethane.lattice.matrix,
np.diag([10.0] * 3))
lbounds = np.array(self.ethane.box.bounds)[:, 0]
coords = self.ethane.atoms[["x", "y", "z"]].values - lbounds
np.testing.assert_array_almost_equal(ethane.cart_coords, coords)
np.testing.assert_array_almost_equal(ethane.site_properties["charge"],
self.ethane.atoms["q"])
tatb = self.tatb.structure
frac_coords = tatb.frac_coords[381]
real_frac_coords = frac_coords - np.floor(frac_coords)
np.testing.assert_array_almost_equal(
real_frac_coords, [0.01553397, 0.71487872, 0.14134139])
co = Structure.from_spacegroup(194,
Lattice.hexagonal(2.50078, 4.03333),
["Co"], [[1 / 3, 2 / 3, 1 / 4]])
ld_co = LammpsData.from_structure(co)
self.assertEqual(ld_co.structure.composition.reduced_formula, "Co")
ni = Structure.from_spacegroup(225, Lattice.cubic(3.50804), ["Ni"],
[[0, 0, 0]])
ld_ni = LammpsData.from_structure(ni)
self.assertEqual(ld_ni.structure.composition.reduced_formula, "Ni")
def test_structure(self):
quartz = self.quartz.structure
np.testing.assert_array_equal(quartz.lattice.matrix,
[[4.913400, 0, 0],
[-2.456700, 4.255129, 0],
[0, 0, 5.405200]])
self.assertEqual(quartz.formula, "Si3 O6")
self.assertNotIn("molecule-ID", self.quartz.atoms.columns)
ethane = self.ethane.structure
np.testing.assert_array_equal(ethane.lattice.matrix,
np.diag([10.0] * 3))
lbounds = np.array(self.ethane.box.bounds)[:, 0]
coords = self.ethane.atoms[["x", "y", "z"]].values - lbounds
np.testing.assert_array_equal(ethane.cart_coords, coords)
np.testing.assert_array_equal(ethane.site_properties["charge"],
self.ethane.atoms["q"])
tatb = self.tatb.structure
frac_coords = tatb.frac_coords[381]
real_frac_coords = frac_coords - np.floor(frac_coords)
np.testing.assert_array_almost_equal(real_frac_coords,
[0.01553397,
0.71487872,
0.14134139])
co = Structure.from_spacegroup(194,
Lattice.hexagonal(2.50078, 4.03333),
["Co"], [[1/3, 2/3, 1/4]])
ld_co = LammpsData.from_structure(co)
self.assertEqual(ld_co.structure.composition.reduced_formula, "Co")
ni = Structure.from_spacegroup(225, Lattice.cubic(3.50804),
["Ni"], [[0, 0, 0]])
ld_ni = LammpsData.from_structure(ni)
self.assertEqual(ld_ni.structure.composition.reduced_formula, "Ni")
def test_equality_of_sqs_objects():
"""SQS structures with different underlying crystal structures are equivalent iff sublattice models are equivalent."""
config = [['A', 'B'], ['A']]
occupancy = [[0.5, 0.5], [1]]
site_ratios = [3, 1]
# Use same sublattice for different underlying structures. Should be equal
s1 = PRLStructure(Lattice.hexagonal(1, 2), ['Mg', 'Mg'],
[[0, 0, 0], [0.3333, 0.66666, 0.5]],
sublattice_configuration=config,
sublattice_occupancies=occupancy,
sublattice_site_ratios=site_ratios)
s2 = PRLStructure(Lattice.cubic(1), ['Fe'], [[0, 0, 0]],
sublattice_configuration=config,
sublattice_occupancies=occupancy,
sublattice_site_ratios=site_ratios)
assert s1 == s2
# Use same underlying crystal structures, but different sublattice configurations. Should be not equal
s1.sublattice_site_ratios = [2, 1]
assert s1 != s2
s1.sublattice_site_ratios = site_ratios
s1.sublattice_occupancies = [[0.25, 0.5], [1]]
assert s1 != s2
s1.sublattice_occupancies = occupancy
s1.sublattice_configuration = [['A', 'A'], ['A']]
assert s1 != s2
s1.sublattice_configuration = config
assert s1 == s2
def setUp(self):
self.single_bond = Structure(
Lattice.cubic(10),
["H", "H", "H"], [[1, 0, 0], [0, 0, 0], [6, 0, 0]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.linear = Structure(
Lattice.cubic(10),
["H", "H", "H"], [[1, 0, 0], [0, 0, 0], [2, 0, 0]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.bent45 = Structure(
Lattice.cubic(10), ["H", "H", "H"],
[[0, 0, 0], [0.707, 0.707, 0], [0.707, 0, 0]],
validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=True,
site_properties=None)
self.cubic = Structure(
Lattice.cubic(1),
["H"], [[0, 0, 0]], validate_proximity=False,
to_unit_cell=False, coords_are_cartesian=False,
site_properties=None)
self.bcc = Structure(
Lattice.cubic(1),
["H", "H"], [[0, 0, 0], [0.5, 0.5, 0.5]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.fcc = Structure(
Lattice.cubic(1), ["H", "H", "H", "H"],
[[0, 0, 0], [0, 0.5, 0.5], [0.5, 0, 0.5], [0.5, 0.5, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.hcp = Structure(
Lattice.hexagonal(1, 1.633),
["H", "H"],
[[0.3333, 0.6667, 0.25], [0.6667, 0.3333, 0.75]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.diamond = Structure(
Lattice.cubic(1), ["H", "H", "H", "H", "H", "H", "H", "H"],
[[0, 0, 0.5], [0.75, 0.75, 0.75], [0, 0.5, 0], [0.75, 0.25, 0.25],
[0.5, 0, 0], [0.25, 0.75, 0.25], [0.5, 0.5, 0.5],
[0.25, 0.25, 0.75]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=False, site_properties=None)
self.trigonal_off_plane = Structure(
Lattice.cubic(100),
["H", "H", "H", "H"],
[[0.50, 0.50, 0.50], [0.25, 0.75, 0.25],
[0.25, 0.25, 0.75], [0.75, 0.25, 0.25]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.regular_triangle = Structure(
Lattice.cubic(30), ["H", "H", "H", "H"],
[[15, 15.28867, 15.65], [14.5, 15, 15], [15.5, 15, 15],
[15, 15.866, 15]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_planar = Structure(
Lattice.cubic(30), ["H", "H", "H", "H"],
[[15, 15.28867, 15], [14.5, 15, 15], [15.5, 15, 15],
[15, 15.866, 15]], validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_planar = Structure(
Lattice.cubic(30), ["H", "H", "H", "H", "H"],
[[15, 15, 15], [14.75, 14.75, 15], [14.75, 15.25, 15],
[15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square = Structure(
Lattice.cubic(30), ["H", "H", "H", "H", "H"],
[[15, 15, 15.707], [14.75, 14.75, 15], [14.75, 15.25, 15],
[15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.T_shape = Structure(
Lattice.cubic(30), ["H", "H", "H", "H"],
[[15, 15, 15], [15, 15, 15.5], [15, 15.5, 15],
[15, 14.5, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.square_pyramid = Structure(
Lattice.cubic(30), ["H", "H", "H", "H", "H", "H"],
[[15, 15, 15], [15, 15, 15.3535], [14.75, 14.75, 15],
[14.75, 15.25, 15], [15.25, 14.75, 15], [15.25, 15.25, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.pentagonal_planar = Structure(
Lattice.cubic(30), ["Xe", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [1.17969, 0, 0], [-1.17969, 0, 0],
[1.90877, -2.24389, 0], [-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.pentagonal_pyramid = Structure(
Lattice.cubic(30), ["Xe", "F", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [0, -1.6237, 1.17969], [1.17969, 0, 0],
[-1.17969, 0, 0], [1.90877, -2.24389, 0],
[-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.pentagonal_bipyramid = Structure(
Lattice.cubic(30),
["Xe", "F", "F", "F", "F", "F", "F", "F"],
[[0, -1.6237, 0], [0, -1.6237, -1.17969],
[0, -1.6237, 1.17969], [1.17969, 0, 0],
[-1.17969, 0, 0], [1.90877, -2.24389, 0],
[-1.90877, -2.24389, 0], [0, -3.6307, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.hexagonal_planar = Structure(
Lattice.cubic(30),
["H", "C", "C", "C", "C", "C", "C"],
[[0, 0, 0], [0.71, 1.2298, 0],
[-0.71, 1.2298, 0], [0.71, -1.2298, 0], [-0.71, -1.2298, 0],
[1.4199, 0, 0], [-1.4199, 0, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.hexagonal_pyramid = Structure(
Lattice.cubic(30),
["H", "Li", "C", "C", "C", "C", "C", "C"],
[[0, 0, 0], [0, 0, 1.675], [0.71, 1.2298, 0],
[-0.71, 1.2298, 0], [0.71, -1.2298, 0], [-0.71, -1.2298, 0],
[1.4199, 0, 0], [-1.4199, 0, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.hexagonal_bipyramid = Structure(
Lattice.cubic(30),
["H", "Li", "Li", "C", "C", "C", "C", "C", "C"],
[[0, 0, 0], [0, 0, 1.675], [0, 0, -1.675],
[0.71, 1.2298, 0], [-0.71, 1.2298, 0],
[0.71, -1.2298, 0], [-0.71, -1.2298, 0],
[1.4199, 0, 0], [-1.4199, 0, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_pyramid = Structure(
Lattice.cubic(30),
["P", "Cl", "Cl", "Cl", "Cl"],
[[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0],
[1.74937, -1.01, 0], [-1.74937, -1.01, 0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.trigonal_bipyramidal = Structure(
Lattice.cubic(30), ["P", "Cl", "Cl", "Cl", "Cl", "Cl"],
[[0, 0, 0], [0, 0, 2.14], [0, 2.02, 0],
[1.74937, -1.01, 0], [-1.74937, -1.01, 0], [0, 0, -2.14]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.cuboctahedron = Structure(
Lattice.cubic(30),
["H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H", "H"],
[[15, 15, 15], [15, 14.5, 14.5], [15, 14.5, 15.5],
[15, 15.5, 14.5], [15, 15.5, 15.5],
[14.5, 15, 14.5], [14.5, 15, 15.5], [15.5, 15, 14.5], [15.5, 15, 15.5],
[14.5, 14.5, 15], [14.5, 15.5, 15], [15.5, 14.5, 15], [15.5, 15.5, 15]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.see_saw_rect = Structure(
Lattice.cubic(30),
["H", "H", "H", "H", "H"],
[[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [0.0, -1.0, 0.0],
[0.0, 0.0, -1.0], [-1.0, 0.0, 0.0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
self.sq_face_capped_trig_pris = Structure(
Lattice.cubic(30),
["H", "H", "H", "H", "H", "H", "H", "H"],
[[0, 0, 0], [-0.6546536707079771, -0.37796447300922725, 0.6546536707079771],
[0.6546536707079771, -0.37796447300922725, 0.6546536707079771],
[0.0, 0.7559289460184545, 0.6546536707079771],
[-0.6546536707079771, -0.37796447300922725, -0.6546536707079771],
[0.6546536707079771, -0.37796447300922725, -0.6546536707079771],
[0.0, 0.7559289460184545, -0.6546536707079771], [0.0, -1.0, 0.0]],
validate_proximity=False, to_unit_cell=False,
coords_are_cartesian=True, site_properties=None)
from pymatgen import Structure, Lattice
from crystal_toolkit.helpers.asymptote import write_asy_file
from crystal_toolkit.components.structure import StructureMoleculeComponent
import os
example_struct = Structure.from_spacegroup(
"P6_3mc",
Lattice.hexagonal(3.22, 5.24),
["Ga", "N"],
[[1 / 3, 2 / 3, 0], [1 / 3, 2 / 3, 3 / 8]],
)
smc = StructureMoleculeComponent(example_struct, hide_incomplete_bonds=True)
file_name = "./asy_test/single/GaN.asy"
write_asy_file(smc, file_name)
write_asy_file(smc, "./asy_test/multi/GaN.asy")
example_struct = Structure.from_spacegroup(
"P6_3mc",
Lattice.hexagonal(3.22, 5.24),
["In", "N"],
[[1 / 3, 2 / 3, 0], [1 / 3, 2 / 3, 3 / 8]],
)
smc = StructureMoleculeComponent(example_struct, hide_incomplete_bonds=True)
write_asy_file(smc, "./asy_test/multi/InN.asy")
example_struct = Structure.from_spacegroup(
"P6_3mc",
Lattice.hexagonal(3.22, 5.24),
["Al", "N"],
[[1 / 3, 2 / 3, 0], [1 / 3, 2 / 3, 3 / 8]],
)
write_structure(f,'POSCAR_F1expected')
write_structure(final,'POSCAR_F1')
#Test 2 - Test in all 3 dimensions
ssize=[5,5,5]
fsize=[8,8,8]
psize=[1,1,1]
primordialstructure = primf.copy()
primordialstructure.make_supercell(psize)
f = primf.copy()
f.make_supercell(fsize)
write_structure(primordialstructure, 'POSCAR_prim2')
final = finite_size_scale('POSCAR_Fdefect', ssize, 'POSCAR_prim2', fsize, psize)
write_structure(f,'POSCAR_F2expected')
write_structure(final,'POSCAR_F2')
#Test 3 - Test for non-cubic lattice
ssize = [4,4,4]
fsize=[8,8,8]
psize=[1,1,1]
mglat = Lattice.hexagonal(3.21,5.21)
primmg = Structure(mglat,["Mg","Mg"],[[1./3.,2./3.,3./4.],[2./3.,1./3.,1./4.]])
primordialstructure = primmg.copy()
primordialstructure.make_supercell(psize)
f = primmg.copy()
f.make_supercell(fsize)
write_structure(primordialstructure,'POSCAR_prim3')
final = finite_size_scale('POSCAR_Mdefect', ssize, 'POSCAR_prim3', fsize, psize)
write_structure(f,'POSCAR_Mg3expected')
write_structure(final,'POSCAR_Mg3')
ssize = [5, 5, 5]
fsize = [8, 8, 8]
psize = [1, 1, 1]
primordialstructure = primf.copy()
primordialstructure.make_supercell(psize)
f = primf.copy()
f.make_supercell(fsize)
write_structure(primordialstructure, 'POSCAR_prim2')
final = finite_size_scale('POSCAR_Fdefect', ssize, 'POSCAR_prim2', fsize,
psize)
write_structure(f, 'POSCAR_F2expected')
write_structure(final, 'POSCAR_F2')
#Test 3 - Test for non-cubic lattice
ssize = [4, 4, 4]
fsize = [8, 8, 8]
psize = [1, 1, 1]
mglat = Lattice.hexagonal(3.21, 5.21)
primmg = Structure(
mglat, ["Mg", "Mg"],
[[1. / 3., 2. / 3., 3. / 4.], [2. / 3., 1. / 3., 1. / 4.]])
primordialstructure = primmg.copy()
primordialstructure.make_supercell(psize)
f = primmg.copy()
f.make_supercell(fsize)
write_structure(primordialstructure, 'POSCAR_prim3')
final = finite_size_scale('POSCAR_Mdefect', ssize, 'POSCAR_prim3', fsize,
psize)
write_structure(f, 'POSCAR_Mg3expected')
write_structure(final, 'POSCAR_Mg3')
