def handle_unparsablespecies(cif_string):
"""
Handles CIF parsing errors arising from unrecognizable species
:param cif_string: (str) cif file
:return: pymatgen structure object with appended unparsable species
"""
cif_string_new = ''
symbols = []
coords = []
occupancies = []
cif = CifFile.from_string(cif_string).data
for block in cif:
if 'standardized' in block:
cif_stdblock = cif[block]
break
for i, sym in enumerate(cif_stdblock['_atom_site_type_symbol']):
if 'OH' in sym:
symbols.append(sym)
coords.append([
float(cif_stdblock['_atom_site_fract_x'][i]),
float(cif_stdblock['_atom_site_fract_y'][i]),
float(cif_stdblock['_atom_site_fract_z'][i])
])
occupancies.append(float(cif_stdblock['_atom_site_occupancy'][i]))
for key in cif:
cif_string_new += str(cif[key]) + '\n'
cif_string_new += '\n'
new_struct = CifParser.from_string(cif_string_new).get_structures()[0]
for specie_no in range(len(symbols)):
new_struct.append({DummySpecie('X'): occupancies[specie_no]},
coords[specie_no],
properties={"molecule": [symbols[specie_no]]})
return new_struct
def get_scene_and_legend(self) -> Tuple[Scene, Dict[str, str]]:
legend = Legend(self.graph.structure,
color_scheme="VESTA",
cmap_range=None)
legend.uniform_radius = 0.3
scene = get_structure_graph_scene(
self.graph,
draw_image_atoms=True,
bonded_sites_outside_unit_cell=False,
hide_incomplete_edges=True,
explicitly_calculate_polyhedra_hull=False,
group_by_symmetry=True,
draw_polyhedra=False,
legend=legend)
scene.name = "DefectStructureComponentScene"
lattice: Lattice = self.graph.structure.lattice
origin = -self.graph.structure.lattice.get_cartesian_coords(
[0.5, 0.5, 0.5])
scene_json = scene.to_json()
for idx, i in enumerate(self.interstitials, 1):
site = Site(species=DummySpecie(),
coords=lattice.get_cartesian_coords(i.frac_coords))
interstitial_scene = site.get_scene(origin=origin)
interstitial_scene.name = f"i{idx}"
interstitial_scene.contents[0].contents[0].tooltip = f"i{idx}"
scene_json["contents"].append(interstitial_scene.to_json())
return scene_json, legend.get_legend()
def test_specie_cifwriter(self):
si4 = Specie("Si", 4)
si3 = Specie("Si", 3)
n = DummySpecie("X", -3)
coords = list()
coords.append(np.array([0.5, 0.5, 0.5]))
coords.append(np.array([0.75, 0.5, 0.75]))
coords.append(np.array([0, 0, 0]))
lattice = Lattice(
np.array([[3.8401979337, 0.00, 0.00],
[1.9200989668, 3.3257101909, 0.00],
[0.00, -2.2171384943, 3.1355090603]]))
struct = Structure(lattice, [n, {si3: 0.5, n: 0.5}, si4], coords)
writer = CifWriter(struct)
ans = """# generated using pymatgen
data_X1.5Si1.5
_symmetry_space_group_name_H-M 'P 1'
_cell_length_a 3.84019793
_cell_length_b 3.84019899
_cell_length_c 3.84019793
_cell_angle_alpha 119.99999086
_cell_angle_beta 90.00000000
_cell_angle_gamma 60.00000914
_symmetry_Int_Tables_number 1
_chemical_formula_structural X1.5Si1.5
_chemical_formula_sum 'X1.5 Si1.5'
_cell_volume 40.04479464
_cell_formula_units_Z 1
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 'x, y, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
X3- -3.0
Si3+ 3.0
Si4+ 4.0
loop_
_atom_site_type_symbol
_atom_site_label
_atom_site_symmetry_multiplicity
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
_atom_site_occupancy
X3- X1 1 0.500000 0.500000 0.500000 1
X3- X2 1 0.750000 0.500000 0.750000 0.5
Si3+ Si3 1 0.750000 0.500000 0.750000 0.5
Si4+ Si4 1 0.000000 0.000000 0.000000 1
"""
for l1, l2 in zip(str(writer).split("\n"), ans.split("\n")):
self.assertEqual(l1.strip(), l2.strip())
# test that mixed valence works properly
s2 = Structure.from_str(ans, "cif")
self.assertEqual(struct.composition, s2.composition)
def get_scene_and_legend(self,
scene_additions=None
) -> Tuple[Scene, Dict[str, str]]:
legend = Legend(self.graph.structure,
color_scheme="VESTA",
radius_scheme="uniform",
cmap_range=None)
legend.uniform_radius = 0.2
scene = get_structure_graph_scene(
self.graph,
draw_image_atoms=True,
bonded_sites_outside_unit_cell=False,
hide_incomplete_edges=True,
explicitly_calculate_polyhedra_hull=False,
group_by_symmetry=False,
legend=legend)
scene.name = "DefectStructureComponentScene"
# axes = graph.structure.lattice._axes_from_lattice()
# axes.visible = True
# scene.contents.append(axes)
scene = scene.to_json()
if scene_additions:
scene["contents"].append(scene_additions)
lattice = self.graph.structure.lattice
origin = -self.graph.structure.lattice.get_cartesian_coords(
[0.5, 0.5, 0.5])
for name, frac_coords in self.vacancy_sites:
site = Site(species=DummySpecie(name),
coords=lattice.get_cartesian_coords(frac_coords))
vac_scene = site.get_scene(origin=origin)
vac_scene.name = f"{name}_{frac_coords}"
vac_scene.contents[0].contents[0].tooltip = name
scene["contents"].append(vac_scene.to_json())
return scene, legend.get_legend()
def structure_from_string(data):
"""
Parses a rndstr.in or lat.in file into pymatgen's
Structure format.
:param data: contents of a rndstr.in or lat.in file
:return: Structure object
"""
data = data.splitlines()
data = [x.split() for x in data if x] # remove empty lines
# following specification/terminology given in manual
if len(data[0]) == 6: # lattice parameters
a, b, c, alpha, beta, gamma = map(float, data[0])
coord_system = Lattice.from_parameters(a, b, c,
alpha, beta, gamma).matrix
lattice_vecs = np.array([
[data[1][0], data[1][1], data[1][2]],
[data[2][0], data[2][1], data[2][2]],
[data[3][0], data[3][1], data[3][2]]
], dtype=float)
first_species_line = 4
else:
coord_system = np.array([
[data[0][0], data[0][1], data[0][2]],
[data[1][0], data[1][1], data[1][2]],
[data[2][0], data[2][1], data[2][2]]
], dtype=float)
lattice_vecs = np.array([
[data[3][0], data[3][1], data[3][2]],
[data[4][0], data[4][1], data[4][2]],
[data[5][0], data[5][1], data[5][2]]
], dtype=float)
first_species_line = 6
scaled_matrix = np.matmul(coord_system, lattice_vecs)
lattice = Lattice(scaled_matrix)
all_coords = []
all_species = []
for l in data[first_species_line:]:
all_coords.append(np.array([l[0], l[1], l[2]], dtype=float))
species_strs = "".join(l[3:]) # join multiple strings back together
species_strs = species_strs.replace(" ", "") # trim any white space
species_strs = species_strs.split(",") # comma-delimited
species = {}
for species_str in species_strs:
species_str = species_str.split('=')
if len(species_str) == 1:
# assume occupancy is 1.0
species_str = [species_str[0], 1.0]
try:
species[Specie(species_str[0])] = float(species_str[1])
except Exception:
species[DummySpecie(species_str[0])] = float(species_str[1])
all_species.append(species)
return Structure(lattice, all_species, all_coords)