def perturb_structure(
structure: Structure, center: List[float],
cutoff: float) -> Tuple[Structure, Tuple[PerturbedSite, ...]]:
""" structure perturbation
Args:
structure: pmg Structure class object
center: Fractional coordinates of a central position.
cutoff: Radius of a sphere in which atoms are perturbed.
"""
p_structure = structure.copy()
perturbed_sites = []
cartesian_coords = structure.lattice.get_cartesian_coords(center)
neighboring_atoms: List[PeriodicNeighbor] = structure.get_sites_in_sphere(
pt=cartesian_coords, r=cutoff, include_index=True)
for p_neighbor in neighboring_atoms:
vector, distance = random_3d_vector(defaults.displace_distance)
p_structure.translate_sites(p_neighbor.index,
vector,
frac_coords=False)
s = PerturbedSite(element=str(p_neighbor.specie),
distance=p_neighbor.nn_distance,
initial_coords=tuple(p_neighbor.frac_coords),
perturbed_coords=tuple(
p_structure[p_neighbor.index].frac_coords),
displacement=distance)
perturbed_sites.append(s)
return p_structure, tuple(perturbed_sites)
def __init__(
self,
initial_structure: Structure,
task: Task,
kpt_mode: Union[KpointsMode, str, None] = None, # None for default
kpt_density: Optional[float] = None, # in Å
gamma_centered: Optional[bool] = None, # Vasp definition
only_even_num_kpts: bool = False, # If ceil kpt numbers to be even.
num_kpt_factor: Optional[int] = None, # Set NKRED to this as well.
band_ref_dist: float = defaults.band_mesh_distance,
symprec: float = defaults.symmetry_length_tolerance,
angle_tolerance: float = defaults.symmetry_angle_tolerance,
is_magnetization: bool = False): # Whether the system is magnetic.
if kpt_mode:
kpt_mode = KpointsMode.from_string(str(kpt_mode))
self._initial_structure = initial_structure.copy()
self._task = task
self._kpt_density = kpt_density or defaults.kpoint_density
logger.info(f"kpoint density is set to {self._kpt_density}")
self._is_magnetization = is_magnetization
self._num_kpt_factor = num_kpt_factor or self._task.default_kpt_factor
if self._num_kpt_factor != 1:
logger.info(f"kpoint factor is set to {self._num_kpt_factor}")
self._symmetrizer = \
StructureSymmetrizer(structure=self._initial_structure,
symprec=symprec,
angle_tolerance=angle_tolerance,
band_mesh_distance=band_ref_dist,
time_reversal=(not self._is_magnetization))
# overwrite options fixed by other options
self._gamma_centered = task.requisite_gamma_centered or gamma_centered
self._adjust_only_even_num_kpts(only_even_num_kpts)
self._adjust_kpt_mode(kpt_mode)
def refine_defect_structure(structure: Structure,
anchor_atom_index: int = None,
anchor_atom_coords: np.ndarray = None):
symmetrizer = StructureSymmetrizer(structure,
defaults.symmetry_length_tolerance,
defaults.symmetry_angle_tolerance)
result = structure.copy()
spglib_data = symmetrizer.spglib_sym_data
origin_shift = spglib_data["origin_shift"]
inv_trans_mat = inv(spglib_data["transformation_matrix"])
coords = spglib_data["std_positions"]
# This transformation is key for refinement.
new_coords = np.array([
np.dot(inv_trans_mat, (coords[i] - origin_shift))
for i in range(len(result))
])
if anchor_atom_index:
offset = new_coords[anchor_atom_index] - anchor_atom_coords
new_coords = new_coords - offset
for i, coords in zip(result, new_coords):
i.frac_coords = coords % 1
if result != structure:
logger.info(f"Structure is refined to the one with point group "
f"{symmetrizer.point_group}.")
return result
else:
logger.info(f"Refined structure is same as before, so do nothing.")
def get_111_struct(self):
lattice = Lattice( self.lattconst * np.identity(3))
species = [self.eltA, self.eltB, self.eltC,
self.eltC, self.eltC]
coords = [[0., 0., 0.], [0.5, 0.5, 0.5], [0.5, 0.5, 0.],
[0.5, 0., 0.5], [0., 0.5, 0.5]]
struct = Structure(lattice, species, coords,
coords_are_cartesian=False)
return struct.copy()
def test_coloring_with_fixed_species():
lattice = Lattice(3.945 * np.eye(3))
species = ["Sr", "Ti", "O", "O", "O"]
frac_coords = np.array([[0, 0, 0], [0.5, 0.5, 0.5], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.5, 0.0]])
aristo = Structure(lattice, species, frac_coords)
base_structure = aristo.copy()
base_structure.remove_species(["Sr", "Ti"])
additional_species = species[:2]
additional_frac_coords = frac_coords[:2]
mapping_color_species = [DummySpecie("X"), "O"]
num_types = len(mapping_color_species)
index = 2
se = StructureEnumerator(
base_structure,
index,
num_types,
mapping_color_species=mapping_color_species,
color_exchange=False,
leave_superperiodic=False,
use_all_colors=False,
)
list_dstructs = se.generate(additional_species=additional_species,
additional_frac_coords=additional_frac_coords)
# with base_site_constraints
mapping_color_species2 = [DummySpecie("X"), "O", "Sr", "Ti"]
num_types2 = len(mapping_color_species2)
base_site_constraints = [
[2], # Sr site
[3], # Cu site
[0, 1], # O or V
[0, 1], # O or V
[0, 1], # O or V
]
se2 = StructureEnumerator(
aristo,
index,
num_types2,
mapping_color_species=mapping_color_species2,
base_site_constraints=base_site_constraints,
color_exchange=False,
leave_superperiodic=False,
use_all_colors=False,
)
list_dstructs2 = se2.generate()
# check uniqueness by StructureMatcher
stm = StructureMatcher(ltol=1e-4, stol=1e-4)
grouped = stm.group_structures(list_dstructs + list_dstructs2)
assert len(grouped) == len(list_dstructs)
assert all([(len(matched) == 2) for matched in grouped])
def structure(self):
strained_lattice = perform_strain( self.base.lattice.matrix, self.strain_tensor)
species, coords = [], []
for ind, perturb in enumerate(self.atomic_perturbations):
species.append( self.base.species[ind])
coords.append( self.base.cart_coords[ind] + np.array(perturb) )
struct = Structure(strained_lattice, species, coords,
coords_are_cartesian=True)
return struct.copy()
def test_coloring_with_fixed_species(sto_perovskite: Structure):
base_structure = sto_perovskite.copy()
base_structure.remove_species(["Sr", "Ti"])
additional_species = sto_perovskite.species[:2]
additional_frac_coords = sto_perovskite.frac_coords[:2]
mapping_color_species = [DummySpecie("X"), "O"]
num_types = len(mapping_color_species)
index = 2
se = StructureEnumerator(
base_structure,
index,
num_types,
mapping_color_species=mapping_color_species,
color_exchange=False,
remove_superperiodic=True,
remove_incomplete=False,
)
list_dstructs = se.generate(additional_species=additional_species,
additional_frac_coords=additional_frac_coords)
# with base_site_constraints
mapping_color_species2 = [DummySpecie("X"), "O", "Sr", "Ti"]
num_types2 = len(mapping_color_species2)
base_site_constraints = [
[2], # Sr site
[3], # Cu site
[0, 1], # O or V
[0, 1], # O or V
[0, 1], # O or V
]
se2 = StructureEnumerator(
sto_perovskite,
index,
num_types2,
mapping_color_species=mapping_color_species2,
base_site_constraints=base_site_constraints,
color_exchange=False,
remove_superperiodic=True,
remove_incomplete=False,
)
list_dstructs2 = se2.generate()
# check uniqueness by StructureMatcher
stm = StructureMatcher(ltol=1e-4, stol=1e-4)
grouped = stm.group_structures(list_dstructs +
list_dstructs2) # type: ignore
assert len(grouped) == len(list_dstructs)
assert all([(len(matched) == 2) for matched in grouped])
def __init__(self,
perfect: Structure,
initial: Structure,
final: Structure,
symprec: float,
dist_tol: float,
neighbor_cutoff_factor: float = None):
self.cutoff = neighbor_cutoff_factor or defaults.cutoff_distance_factor
self.symprec = symprec
self.perfect, self.initial, self.final = perfect, initial, final
self.dist_tol = dist_tol
assert perfect.lattice == initial.lattice == final.lattice
self.lattice = perfect.lattice
self._orig_comp = DefectStructureComparator(final, perfect, dist_tol)
self._orig_center = self._orig_comp.defect_center_coord
self._calc_drift()
self.shifted_final = final.copy()
self.center = tuple(self._orig_center - self._drift_vector)
for site in self.shifted_final:
site.frac_coords -= np.array(self._drift_vector)
self.comp_w_perf = DefectStructureComparator(self.shifted_final,
perfect, dist_tol)
self.comp_w_init = DefectStructureComparator(self.shifted_final,
initial, dist_tol)
self.defect_structure_info = DefectStructureInfo(
shifted_final_structure=self.shifted_final,
initial_site_sym=self.initial_site_sym,
final_site_sym=self.final_site_sym,
site_diff=self.comp_w_perf.make_site_diff(),
site_diff_from_initial=self.comp_w_init.make_site_diff(),
symprec=symprec,
dist_tol=dist_tol,
anchor_atom_idx=self._anchor_atom_idx,
neighbor_atom_indices=self._neighbor_atom_indices,
neighbor_cutoff_factor=self.cutoff,
drift_vector=self._drift_vector,
drift_dist=self._drift_distance,
center=self.center,
displacements=self.calc_displacements())
def __init__(self,
structure: Structure,
symprec: float = defaults.symmetry_length_tolerance,
angle_tolerance: float = defaults.symmetry_angle_tolerance,
time_reversal: bool = True,
band_mesh_distance: float = defaults.band_mesh_distance):
"""Get full information of seekpath band path.
Note: site properties such as magmom are removed.
The structures of aP (SG:1, 2), mC (5, 8, 9, 12, 15) and
oA (38, 39, 40, 41) can be different between spglib and seekpath.
see Y. Hinuma et al. Comput. Mater. Sci. 128 (2017) 140–184
-- spglib mC
6.048759 -3.479491 0.000000
6.048759 3.479491 0.000000
-4.030758 0.000000 6.044512
-- seekpath mC
6.048759 3.479491 0.000000
-6.048759 3.479491 0.000000
-4.030758 0.000000 6.044512
"""
self.structure = structure.copy()
if structure.site_properties:
logger.warning(
f"Site property {structure.site_properties.keys()} "
f"removed in primitive and conventional structures.")
self.symprec = symprec
self.angle_tolerance = angle_tolerance
self.time_reversal = time_reversal
self.ref_distance = band_mesh_distance
lattice_matrix = structure.lattice.matrix
positions = structure.frac_coords.tolist()
atomic_numbers = [i.specie.number for i in structure.sites]
self.cell = (lattice_matrix, positions, atomic_numbers)
# evaluated lazily
self._spglib_sym_data = None
self._conventional = None
self._primitive = None
self._second_primitive = None
self._seekpath_data = None
self._band_primitive = None
self._irreducible_kpoints = None
def quick_view(
structure: Structure,
*args,
conventional: bool = False,
supercell: list = [1, 1, 1],
symprec: float = 0.01,
angle_tolerance: float = 5.0
) -> JsmolView:
"""A function to visualize pymatgen Structure objects in jupyter notebook using jupyter_jsmol package.
Args:
structure: pymatgen Structure object.
*args: Extra arguments for JSmol's load command. Eg. "{2 2 2}", "packed"
conventional: use conventional cell. Defaults to False.
supercell: can be used to make supercells with pymatgen.Structure.make_supercell method.
symprec: If not none, finds the symmetry of the structure
and writes the cif with symmetry information. Passes symprec
to the SpacegroupAnalyzer.
angle_tolerance: Angle tolerance for symmetry finding. Passes
angle_tolerance to the SpacegroupAnalyzer. Used only if symprec
is not None.
Returns:
A jupyter widget object.
"""
s = structure.copy()
if conventional:
spga = SpacegroupAnalyzer(s, symprec=symprec, angle_tolerance=angle_tolerance)
s = spga.get_conventional_standard_structure()
cif = CifWriter(
s, symprec=symprec, angle_tolerance=angle_tolerance, refine_struct=False
)
supercell_str = "{" + " ".join(map(str, supercell)) + "}"
return JsmolView.from_str(str(cif), supercell_str, *args)
def get_sqrt2_1_struct(self):
"""Setup a sqrt 2 x sqrt 2 x 1 structure"""
orig_scaled_mat = np.array([[self.lattconst * np.sqrt(2), 0., 0.],
[0., self.lattconst * np.sqrt(2), 0.],
[0., 0., self.lattconst]])
rotation = np.array([[np.cos(45. * np.pi / 180.), -np.sin(45. * np.pi / 180.), 0],
[np.sin(45. * np.pi / 180.), np.cos(45. * np.pi / 180.), 0],
[0., 0., 1.]])
rotated_mat = np.dot(orig_scaled_mat, rotation)
lattice = Lattice(rotated_mat)
species = [self.eltA, self.eltA,
self.eltB, self.eltB,
self.eltC, self.eltC, self.eltC,
self.eltC, self.eltC, self.eltC]
coords = [[0.5, 0., 0.5], [0., 0.5, 0.5],
[0., 0., 0.], [0.5, 0.5, 0.],
[0.25, 0.25, 0.], [0.75, 0.75, 0.], [0.25, 0.75, 0.],
[0.75, 0.25, 0.], [0., 0., 0.5], [0.5, 0.5, 0.5]]
struct = Structure(lattice, species, coords,
coords_are_cartesian=False)
return struct.copy()
class CollinearMagneticStructureAnalyzerTest(unittest.TestCase):
def setUp(self):
parser = CifParser(os.path.join(PymatgenTest.TEST_FILES_DIR, "Fe.cif"))
self.Fe = parser.get_structures()[0]
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "LiFePO4.cif"))
self.LiFePO4 = parser.get_structures()[0]
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR, "Fe3O4.cif"))
self.Fe3O4 = parser.get_structures()[0]
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"magnetic.ncl.example.GdB4.mcif"))
self.GdB4 = parser.get_structures()[0]
parser = CifParser(
os.path.join(PymatgenTest.TEST_FILES_DIR,
"magnetic.example.NiO.mcif"))
self.NiO_expt = parser.get_structures()[0]
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords)
latt = Lattice([[2.085, 2.085, 0.0], [0.0, -2.085, -2.085],
[-2.085, 2.085, -4.17]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0, 0.5], [0, 0, 0], [0.25, 0.5, 0.25],
[0.75, 0.5, 0.75]]
self.NiO_AFM_111 = Structure(latt,
species,
coords,
site_properties={"magmom": [-5, 5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0], [0, 0, -4.17], [-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5], [0, 0, 0], [0, 0.5, 0], [0.5, 0, 0.5]]
self.NiO_AFM_001 = Structure(latt,
species,
coords,
site_properties={"magmom": [-5, 5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0], [0, 0, -4.17], [-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5], [0, 0, 0], [0, 0.5, 0], [0.5, 0, 0.5]]
self.NiO_AFM_001_opposite = Structure(
latt, species, coords, site_properties={"magmom": [5, -5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0], [0, 0, -4.17], [-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5], [0, 0, 0], [0, 0.5, 0], [0.5, 0, 0.5]]
self.NiO_unphysical = Structure(
latt, species, coords, site_properties={"magmom": [-3, 0, 0, 0]})
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
def test_get_representations(self):
# tests to convert between storing magnetic moment information
# on site_properties or on Species 'spin' property
# test we store magnetic moments on site properties
self.Fe.add_site_property("magmom", [5])
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertEqual(msa.structure.site_properties["magmom"][0], 5)
# and that we can retrieve a spin representation
Fe_spin = msa.get_structure_with_spin()
self.assertFalse("magmom" in Fe_spin.site_properties)
self.assertEqual(Fe_spin[0].specie.spin, 5)
# test we can remove magnetic moment information
msa.get_nonmagnetic_structure()
self.assertFalse("magmom" in Fe_spin.site_properties)
# test with disorder on magnetic site
self.Fe[0] = {
Species("Fe", oxidation_state=0, properties={"spin": 5}): 0.5,
"Ni": 0.5,
}
self.assertRaises(NotImplementedError,
CollinearMagneticStructureAnalyzer, self.Fe)
def test_matches(self):
self.assertTrue(self.NiO.matches(self.NiO_AFM_111))
self.assertTrue(self.NiO.matches(self.NiO_AFM_001))
# MSA adds magmoms to Structure, so not equal
msa = CollinearMagneticStructureAnalyzer(
self.NiO, overwrite_magmom_mode="replace_all")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_111))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001))
msa = CollinearMagneticStructureAnalyzer(
self.NiO_AFM_001, overwrite_magmom_mode="respect_sign")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_111))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_001))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_001_opposite))
msa = CollinearMagneticStructureAnalyzer(
self.NiO_AFM_111, overwrite_magmom_mode="respect_sign")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_111))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001_opposite))
def test_modes(self):
mode = "none"
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties["magmom"]
self.assertEqual(magmoms, [0, 0])
mode = "respect_sign"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties["magmom"]
self.assertEqual(magmoms, [-5, 0, 0, 0])
mode = "respect_zeros"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties["magmom"]
self.assertEqual(magmoms, [5, 0, 0, 0])
mode = "replace_all"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode,
make_primitive=False)
magmoms = msa.structure.site_properties["magmom"]
self.assertEqual(magmoms, [5, 5, 0, 0])
mode = "replace_all_if_undefined"
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties["magmom"]
self.assertEqual(magmoms, [5, 0])
mode = "normalize"
msa = CollinearMagneticStructureAnalyzer(
msa.structure, overwrite_magmom_mode="normalize")
magmoms = msa.structure.site_properties["magmom"]
self.assertEqual(magmoms, [1, 0])
def test_net_positive(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical)
magmoms = msa.structure.site_properties["magmom"]
self.assertEqual(magmoms, [3, 0, 0, 0])
def test_get_ferromagnetic_structure(self):
msa = CollinearMagneticStructureAnalyzer(
self.NiO, overwrite_magmom_mode="replace_all_if_undefined")
s1 = msa.get_ferromagnetic_structure()
s1_magmoms = [float(m) for m in s1.site_properties["magmom"]]
s1_magmoms_ref = [5.0, 0.0]
self.assertListEqual(s1_magmoms, s1_magmoms_ref)
_ = CollinearMagneticStructureAnalyzer(
self.NiO_AFM_111, overwrite_magmom_mode="replace_all_if_undefined")
s2 = msa.get_ferromagnetic_structure(make_primitive=False)
s2_magmoms = [float(m) for m in s2.site_properties["magmom"]]
s2_magmoms_ref = [5.0, 0.0]
self.assertListEqual(s2_magmoms, s2_magmoms_ref)
s2_prim = msa.get_ferromagnetic_structure(make_primitive=True)
self.assertTrue(
CollinearMagneticStructureAnalyzer(s1).matches_ordering(s2_prim))
def test_magnetic_properties(self):
msa = CollinearMagneticStructureAnalyzer(self.GdB4)
self.assertFalse(msa.is_collinear)
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertFalse(msa.is_magnetic)
self.Fe.add_site_property("magmom", [5])
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertTrue(msa.is_magnetic)
self.assertTrue(msa.is_collinear)
self.assertEqual(msa.ordering, Ordering.FM)
msa = CollinearMagneticStructureAnalyzer(
self.NiO,
make_primitive=False,
overwrite_magmom_mode="replace_all_if_undefined",
)
self.assertEqual(msa.number_of_magnetic_sites, 4)
self.assertEqual(msa.number_of_unique_magnetic_sites(), 1)
self.assertEqual(msa.types_of_magnetic_species, (Element.Ni, ))
self.assertEqual(msa.get_exchange_group_info(), ("Fm-3m", 225))
def test_str(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO_AFM_001)
ref_msa_str = """Structure Summary
Lattice
abc : 2.948635277547903 4.17 2.948635277547903
angles : 90.0 90.0 90.0
volume : 36.2558565
A : 2.085 2.085 0.0
B : 0.0 0.0 -4.17
C : -2.085 2.085 0.0
Magmoms Sites
+5.00 PeriodicSite: Ni (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: O (0.0000, 0.0000, -2.0850) [0.0000, 0.5000, 0.0000]
PeriodicSite: O (0.0000, 2.0850, 0.0000) [0.5000, 0.0000, 0.5000]
-5.00 PeriodicSite: Ni (0.0000, 2.0850, -2.0850) [0.5000, 0.5000, 0.5000]"""
# just compare lines form 'Magmoms Sites',
# since lattice param string can vary based on machine precision
self.assertEqual(
"\n".join(str(msa).split("\n")[-5:-1]),
"\n".join(ref_msa_str.split("\n")[-5:-1]),
)
def test_round_magmoms(self):
struct = self.NiO_AFM_001.copy()
struct.add_site_property("magmom", [-5.0143, -5.02, 0.147, 0.146])
msa = CollinearMagneticStructureAnalyzer(struct,
round_magmoms=0.001,
make_primitive=False)
self.assertTrue(
np.allclose(msa.magmoms, [5.0171, 5.0171, -0.1465, -0.1465]))
self.assertAlmostEqual(msa.magnetic_species_and_magmoms["Ni"], 5.0171)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms["O"], 0.1465)
struct.add_site_property("magmom", [-5.0143, 4.5, 0.147, 0.146])
msa = CollinearMagneticStructureAnalyzer(struct,
round_magmoms=0.001,
make_primitive=False)
self.assertTrue(
np.allclose(msa.magmoms, [5.0143, -4.5, -0.1465, -0.1465]))
self.assertAlmostEqual(msa.magnetic_species_and_magmoms["Ni"][0], 4.5)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms["Ni"][1],
5.0143)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms["O"], 0.1465)
def get_start_end_structures(
isite: PeriodicSite,
esite: PeriodicSite,
base_struct: Structure,
sc_mat: List[List[Union[int, float]]],
vac_mode: bool,
debug: bool = False,
) -> Tuple[Structure, Structure, Structure]:
"""
Obtain the starting and terminating structures in a supercell for NEB calculations.
Args:
hop: object presenting the migration event
base_struct: unit cell representation of the structure
sc_mat: supercell transformation to create the simulation cell for the NEB calc
Returns:
initial structure, final structure, empty structure all in the supercell
"""
def remove_site_at_pos(structure: Structure, site: PeriodicSite):
new_struct_sites = []
for isite in structure:
if not vac_mode or (isite.distance(site) <= 1e-8):
continue
new_struct_sites.append(isite)
return Structure.from_sites(new_struct_sites)
base_sc = base_struct.copy() * sc_mat
start_struct = base_struct.copy() * sc_mat
end_struct = base_struct.copy() * sc_mat
sc_mat_inv = np.linalg.inv(sc_mat)
if not vac_mode:
# insertion the endpoints
start_struct.insert(
0,
esite.species_string,
np.dot(isite.frac_coords, sc_mat_inv),
properties={"magmom": 0},
)
end_struct.insert(
0,
esite.species_string,
np.dot(esite.frac_coords, sc_mat_inv),
properties={"magmom": 0},
)
else:
# remove the other endpoint
ipos_sc = np.dot(isite.frac_coords, sc_mat_inv)
epos_sc = np.dot(esite.frac_coords, sc_mat_inv)
if debug:
icart = base_sc.lattice.get_cartesian_coords(ipos_sc)
ecart = base_sc.lattice.get_cartesian_coords(epos_sc)
assert abs(
np.linalg.norm(icart - ecart) -
np.linalg.norm(isite.coords - esite.coords)) < 1e-5
i_ref_ = PeriodicSite(species=esite.species_string,
coords=ipos_sc,
lattice=base_sc.lattice)
e_ref_ = PeriodicSite(species=esite.species_string,
coords=epos_sc,
lattice=base_sc.lattice)
start_struct = remove_site_at_pos(start_struct, e_ref_)
end_struct = remove_site_at_pos(end_struct, i_ref_)
return start_struct, end_struct, base_sc
class CollinearMagneticStructureAnalyzerTest(unittest.TestCase):
def setUp(self):
parser = CifParser(os.path.join(test_dir, 'Fe.cif'))
self.Fe = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'LiFePO4.cif'))
self.LiFePO4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'Fe3O4.cif'))
self.Fe3O4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'magnetic.ncl.example.GdB4.mcif'))
self.GdB4 = parser.get_structures()[0]
parser = CifParser(os.path.join(test_dir, 'magnetic.example.NiO.mcif'))
self.NiO_expt = parser.get_structures()[0]
latt = Lattice.cubic(4.17)
species = ["Ni", "O"]
coords = [[0, 0, 0],
[0.5, 0.5, 0.5]]
self.NiO = Structure.from_spacegroup(225, latt, species, coords)
latt = Lattice([[2.085, 2.085, 0.0],
[0.0, -2.085, -2.085],
[-2.085, 2.085, -4.17]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0, 0.5],
[0, 0, 0],
[0.25, 0.5, 0.25],
[0.75, 0.5, 0.75]]
self.NiO_AFM_111 = Structure(latt, species, coords,
site_properties={'magmom': [-5, 5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_AFM_001 = Structure(latt, species, coords,
site_properties={'magmom': [-5, 5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_AFM_001_opposite = Structure(latt, species, coords,
site_properties={'magmom': [5, -5, 0, 0]})
latt = Lattice([[2.085, 2.085, 0],
[0, 0, -4.17],
[-2.085, 2.085, 0]])
species = ["Ni", "Ni", "O", "O"]
coords = [[0.5, 0.5, 0.5],
[0, 0, 0],
[0, 0.5, 0],
[0.5, 0, 0.5]]
self.NiO_unphysical = Structure(latt, species, coords,
site_properties={'magmom': [-3, 0, 0, 0]})
warnings.simplefilter("ignore")
def tearDown(self):
warnings.simplefilter("default")
def test_get_representations(self):
# tests to convert between storing magnetic moment information
# on site_properties or on Specie 'spin' property
# test we store magnetic moments on site properties
self.Fe.add_site_property('magmom', [5])
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertEqual(msa.structure.site_properties['magmom'][0], 5)
# and that we can retrieve a spin representaiton
Fe_spin = msa.get_structure_with_spin()
self.assertFalse('magmom' in Fe_spin.site_properties)
self.assertEqual(Fe_spin[0].specie.spin, 5)
# test we can remove magnetic moment information
Fe_none = msa.get_nonmagnetic_structure()
self.assertFalse('magmom' in Fe_spin.site_properties)
# test with disorder on magnetic site
self.Fe[0] = {Specie('Fe', oxidation_state=0, properties={'spin': 5}): 0.5, 'Ni': 0.5}
self.assertRaises(NotImplementedError, CollinearMagneticStructureAnalyzer, self.Fe)
def test_matches(self):
self.assertTrue(self.NiO.matches(self.NiO_AFM_111))
self.assertTrue(self.NiO.matches(self.NiO_AFM_001))
# MSA adds magmoms to Structure, so not equal
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode="replace_all")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_111))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001))
msa = CollinearMagneticStructureAnalyzer(self.NiO_AFM_001,
overwrite_magmom_mode="respect_sign")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_111))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_001))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_001_opposite))
msa = CollinearMagneticStructureAnalyzer(self.NiO_AFM_111,
overwrite_magmom_mode="respect_sign")
self.assertFalse(msa.matches_ordering(self.NiO))
self.assertTrue(msa.matches_ordering(self.NiO_AFM_111))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001))
self.assertFalse(msa.matches_ordering(self.NiO_AFM_001_opposite))
def test_modes(self):
mode = "none"
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [0, 0])
mode = "respect_sign"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [-5, 0, 0, 0])
mode = "respect_zeros"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [5, 0, 0, 0])
mode = "replace_all"
msa = CollinearMagneticStructureAnalyzer(self.NiO_unphysical,
overwrite_magmom_mode=mode,
make_primitive=False)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [5, 5, 0, 0])
mode = "replace_all_if_undefined"
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode=mode)
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [5, 0])
mode = "normalize"
msa = CollinearMagneticStructureAnalyzer(msa.structure,
overwrite_magmom_mode='normalize')
magmoms = msa.structure.site_properties['magmom']
self.assertEqual(magmoms, [1, 0])
def test_get_ferromagnetic_structure(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO,
overwrite_magmom_mode="replace_all_if_undefined")
s1 = msa.get_ferromagnetic_structure()
s1_magmoms = [float(m) for m in s1.site_properties['magmom']]
s1_magmoms_ref = [5.0, 0.0]
self.assertListEqual(s1_magmoms, s1_magmoms_ref)
msa2 = CollinearMagneticStructureAnalyzer(self.NiO_AFM_111,
overwrite_magmom_mode="replace_all_if_undefined")
s2 = msa.get_ferromagnetic_structure(make_primitive=False)
s2_magmoms = [float(m) for m in s2.site_properties['magmom']]
s2_magmoms_ref = [5.0, 0.0]
self.assertListEqual(s2_magmoms, s2_magmoms_ref)
s2_prim = msa.get_ferromagnetic_structure(make_primitive=True)
self.assertTrue(CollinearMagneticStructureAnalyzer(s1).matches_ordering(s2_prim))
def test_magnetic_properties(self):
msa = CollinearMagneticStructureAnalyzer(self.GdB4)
self.assertFalse(msa.is_collinear)
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertFalse(msa.is_magnetic)
self.Fe.add_site_property('magmom', [5])
msa = CollinearMagneticStructureAnalyzer(self.Fe)
self.assertTrue(msa.is_magnetic)
self.assertTrue(msa.is_collinear)
self.assertEqual(msa.ordering, Ordering.FM)
msa = CollinearMagneticStructureAnalyzer(self.NiO, make_primitive=False,
overwrite_magmom_mode="replace_all_if_undefined")
self.assertEqual(msa.number_of_magnetic_sites, 4)
self.assertEqual(msa.number_of_unique_magnetic_sites(), 1)
self.assertEqual(msa.types_of_magnetic_specie, [Element('Ni')])
self.assertEqual(msa.get_exchange_group_info(), ('Fm-3m', 225))
def test_str(self):
msa = CollinearMagneticStructureAnalyzer(self.NiO_AFM_001)
ref_msa_str = """Structure Summary
Lattice
abc : 2.948635277547903 4.17 2.948635277547903
angles : 90.0 90.0 90.0
volume : 36.2558565
A : 2.085 2.085 0.0
B : 0.0 0.0 -4.17
C : -2.085 2.085 0.0
Magmoms Sites
+5.00 PeriodicSite: Ni (0.0000, 0.0000, 0.0000) [0.0000, 0.0000, 0.0000]
PeriodicSite: O (0.0000, 0.0000, -2.0850) [0.0000, 0.5000, 0.0000]
PeriodicSite: O (0.0000, 2.0850, 0.0000) [0.5000, 0.0000, 0.5000]
-5.00 PeriodicSite: Ni (0.0000, 2.0850, -2.0850) [0.5000, 0.5000, 0.5000]"""
# just compare lines form 'Magmoms Sites',
# since lattice param string can vary based on machine precision
self.assertEqual("\n".join(str(msa).split("\n")[-5:-1]),
"\n".join(ref_msa_str.split("\n")[-5:-1]))
def test_round_magmoms(self):
struct = self.NiO_AFM_001.copy()
struct.add_site_property('magmom', [-5.0143, -5.02, 0.147, 0.146])
msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
self.assertTrue(np.allclose(msa.magmoms, [-5.0171, -5.0171, 0.1465, 0.1465]))
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'], 5.0171)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['O'], 0.1465)
struct.add_site_property('magmom', [-5.0143, 4.5, 0.147, 0.146])
msa = CollinearMagneticStructureAnalyzer(struct, round_magmoms=0.001, make_primitive=False)
self.assertTrue(np.allclose(msa.magmoms, [-5.0143, 4.5, 0.1465, 0.1465]))
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'][0], 4.5)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['Ni'][1], 5.0143)
self.assertAlmostEqual(msa.magnetic_species_and_magmoms['O'], 0.1465)
def test_supercell_subsets(self):
sm = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=False,
scale=True,
attempt_supercell=True,
allow_subset=True,
supercell_size='volume')
sm_no_s = StructureMatcher(ltol=0.2,
stol=0.3,
angle_tol=5,
primitive_cell=False,
scale=True,
attempt_supercell=True,
allow_subset=False,
supercell_size='volume')
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Ag', 'Si', 'Si'],
[[.7, .4, .5], [0, 0, 0.1], [0, 0, 0.2]])
s1.make_supercell([2, 1, 1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0, 0.1, -0.95], [0, 0.1, 0], [-.7, .5, .375]])
shuffle = [0, 2, 1, 3, 4, 5]
s1 = Structure.from_sites([s1[i] for i in shuffle])
#test when s1 is exact supercell of s2
result = sm.get_s2_like_s1(s1, s2)
for a, b in zip(s1, result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(s1, s2))
self.assertTrue(sm.fit(s2, s1))
self.assertTrue(sm_no_s.fit(s1, s2))
self.assertTrue(sm_no_s.fit(s2, s1))
rms = (0.048604032430991401, 0.059527539448807391)
self.assertTrue(np.allclose(sm.get_rms_dist(s1, s2), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2, s1), rms))
#test when the supercell is a subset of s2
subset_supercell = s1.copy()
del subset_supercell[0]
result = sm.get_s2_like_s1(subset_supercell, s2)
self.assertEqual(len(result), 6)
for a, b in zip(subset_supercell, result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(subset_supercell, s2))
self.assertTrue(sm.fit(s2, subset_supercell))
self.assertFalse(sm_no_s.fit(subset_supercell, s2))
self.assertFalse(sm_no_s.fit(s2, subset_supercell))
rms = (0.053243049896333279, 0.059527539448807336)
self.assertTrue(np.allclose(sm.get_rms_dist(subset_supercell, s2),
rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2, subset_supercell),
rms))
#test when s2 (once made a supercell) is a subset of s1
s2_missing_site = s2.copy()
del s2_missing_site[1]
result = sm.get_s2_like_s1(s1, s2_missing_site)
for a, b in zip((s1[i] for i in (0, 2, 4, 5)), result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(s1, s2_missing_site))
self.assertTrue(sm.fit(s2_missing_site, s1))
self.assertFalse(sm_no_s.fit(s1, s2_missing_site))
self.assertFalse(sm_no_s.fit(s2_missing_site, s1))
rms = (0.029763769724403633, 0.029763769724403987)
self.assertTrue(np.allclose(sm.get_rms_dist(s1, s2_missing_site), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2_missing_site, s1), rms))
def test_supercell_subsets(self):
sm = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=True, allow_subset=True,
supercell_size='volume')
sm_no_s = StructureMatcher(ltol=0.2, stol=0.3, angle_tol=5,
primitive_cell=False, scale=True,
attempt_supercell=True, allow_subset=False,
supercell_size='volume')
l = Lattice.orthorhombic(1, 2, 3)
s1 = Structure(l, ['Ag', 'Si', 'Si'],
[[.7,.4,.5],[0,0,0.1],[0,0,0.2]])
s1.make_supercell([2,1,1])
s2 = Structure(l, ['Si', 'Si', 'Ag'],
[[0,0.1,-0.95],[0,0.1,0],[-.7,.5,.375]])
shuffle = [0,2,1,3,4,5]
s1 = Structure.from_sites([s1[i] for i in shuffle])
#test when s1 is exact supercell of s2
result = sm.get_s2_like_s1(s1, s2)
for a, b in zip(s1, result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(s1, s2))
self.assertTrue(sm.fit(s2, s1))
self.assertTrue(sm_no_s.fit(s1, s2))
self.assertTrue(sm_no_s.fit(s2, s1))
rms = (0.048604032430991401, 0.059527539448807391)
self.assertTrue(np.allclose(sm.get_rms_dist(s1, s2), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2, s1), rms))
#test when the supercell is a subset of s2
subset_supercell = s1.copy()
del subset_supercell[0]
result = sm.get_s2_like_s1(subset_supercell, s2)
self.assertEqual(len(result), 6)
for a, b in zip(subset_supercell, result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(subset_supercell, s2))
self.assertTrue(sm.fit(s2, subset_supercell))
self.assertFalse(sm_no_s.fit(subset_supercell, s2))
self.assertFalse(sm_no_s.fit(s2, subset_supercell))
rms = (0.053243049896333279, 0.059527539448807336)
self.assertTrue(np.allclose(sm.get_rms_dist(subset_supercell, s2), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2, subset_supercell), rms))
#test when s2 (once made a supercell) is a subset of s1
s2_missing_site = s2.copy()
del s2_missing_site[1]
result = sm.get_s2_like_s1(s1, s2_missing_site)
for a, b in zip((s1[i] for i in (0, 2, 4, 5)), result):
self.assertTrue(a.distance(b) < 0.08)
self.assertEqual(a.species_and_occu, b.species_and_occu)
self.assertTrue(sm.fit(s1, s2_missing_site))
self.assertTrue(sm.fit(s2_missing_site, s1))
self.assertFalse(sm_no_s.fit(s1, s2_missing_site))
self.assertFalse(sm_no_s.fit(s2_missing_site, s1))
rms = (0.029763769724403633, 0.029763769724403987)
self.assertTrue(np.allclose(sm.get_rms_dist(s1, s2_missing_site), rms))
self.assertTrue(np.allclose(sm.get_rms_dist(s2_missing_site, s1), rms))
import numpy as np
from pymatgen.core import Lattice, Structure
from pymatgen.core.periodic_table import Specie, DummySpecie
from pymatgen.analysis.structure_matcher import StructureMatcher
from dsenum import StructureEnumerator
from dsenum.utils import write_cif, refine_and_resize_structure
if __name__ == "__main__":
lattice = Lattice(3.945 * np.eye(3))
species = ["Sr", "Ti", "O", "O", "O"]
frac_coords = np.array([[0, 0, 0], [0.5, 0.5, 0.5], [0.0, 0.5, 0.5],
[0.5, 0.0, 0.5], [0.5, 0.5, 0.0]])
aristo = Structure(lattice, species, frac_coords)
base_structure = aristo.copy()
base_structure.remove_species(["Sr", "Ti"])
additional_species = species[:2]
additional_frac_coords = frac_coords[:2]
mapping_color_species = [DummySpecie("X"), "O"]
num_types = len(mapping_color_species)
index = 2
se = StructureEnumerator(
base_structure,
index,
num_types,
mapping_color_species=mapping_color_species,
color_exchange=False,
leave_superperiodic=False,