def test_comp():
comp = {"Li": 2, "O": 4}
cc = Composition(comp)
assert (
cc.prototype,
cc.formula,
cc.reduced_formula,
round(cc.weight, 4),
cc.to_dict(),
) == ("AB2", "Li2O4", "LiO2", 77.8796, comp)
c = Composition.from_string("Al2O3Al5Co6O1")
td = c.to_dict()
fd = Composition.from_dict(td)
assert c.formula == "Al7Co6O4"
def composition(self):
"""Get composition of the atoms object."""
comp = {}
for i in self.elements:
comp[i] = comp.setdefault(i, 0) + 1
return Composition(OrderedDict(comp))
def from_cif(filename="atoms.cif"):
"""Read .cif format file."""
# Warnings:
# May not work for:
# system with partial occupancy
# cif file with multiple blocks
# _atom_site_U_iso, instead of fractn_x, cartn_x
# with non-zero _atom_site_attached_hydrogens
f = open(filename, "r")
lines = f.read().splitlines()
f.close()
lat_a = ""
lat_b = ""
lat_c = ""
lat_alpha = ""
lat_beta = ""
lat_gamma = ""
# TODO: check if chemical_formula_sum
# matches Atoms.compsotion.reduced_formula
# chemical_formula_structural = ""
# chemical_formula_sum = ""
# chemical_name_mineral = ""
sym_xyz_line = ""
for ii, i in enumerate(lines):
if "_cell_length_a" in i:
lat_a = float(i.split()[1].split("(")[0])
if "_cell_length_b" in i:
lat_b = float(i.split()[1].split("(")[0])
if "_cell_length_c" in i:
lat_c = float(i.split()[1].split("(")[0])
if "_cell_angle_alpha" in i:
lat_alpha = float(i.split()[1].split("(")[0])
if "_cell_angle_beta" in i:
lat_beta = float(i.split()[1].split("(")[0])
if "_cell_angle_gamma" in i:
lat_gamma = float(i.split()[1].split("(")[0])
# if "_chemical_formula_structural" in i:
# chemical_formula_structural = i.split()[1]
# if "_chemical_formula_sum" in i:
# chemical_formula_sum = i.split()[1]
# if "_chemical_name_mineral" in i:
# chemical_name_mineral = i.split()[1]
if "_symmetry_equiv_pos_as_xyz" in i:
sym_xyz_line = ii
if "_symmetry_equiv_pos_as_xyz_" in i:
sym_xyz_line = ii
if "_symmetry_equiv_pos_as_xyz_" in i:
sym_xyz_line = ii
if "_space_group_symop_operation_xyz_" in i:
sym_xyz_line = ii
if "_space_group_symop_operation_xyz" in i:
sym_xyz_line = ii
symm_ops = []
terminate = False
count = 0
while not terminate:
print("sym_xyz_line", sym_xyz_line)
tmp = lines[sym_xyz_line + count + 1]
if "x" in tmp and "y" in tmp and "z" in tmp:
# print("tmp", tmp)
symm_ops.append(tmp)
count += 1
else:
terminate = True
tmp_arr = [lat_a, lat_b, lat_c, lat_alpha, lat_beta, lat_gamma]
if any(ele == "" for ele in tmp_arr):
raise ValueError("Lattice information is incomplete.", tmp_arr)
lat = Lattice.from_parameters(
lat_a, lat_b, lat_c, lat_alpha, lat_beta, lat_gamma
)
terminate = False
atom_features = []
count = 0
beginning_atom_info_line = 0
for ii, i in enumerate(lines):
if "loop_" in i and "_atom_site" in lines[ii + count + 1]:
beginning_atom_info_line = ii
while not terminate:
if "_atom" in lines[beginning_atom_info_line + count + 1]:
atom_features.append(
lines[beginning_atom_info_line + count + 1]
)
count += 1
if "_atom" not in lines[beginning_atom_info_line + count]:
terminate = True
terminate = False
count = 1
atom_liines = []
while not terminate:
number = beginning_atom_info_line + len(atom_features) + count
if number == len(lines):
terminate = True
break
line = lines[number]
# print ('tis line',line)
if len(line.split()) == len(atom_features):
atom_liines.append(line)
count += 1
else:
terminate = True
label_index = ""
fract_x_index = ""
fract_y_index = ""
fract_z_index = ""
cartn_x_index = ""
cartn_y_index = ""
cartn_z_index = ""
occupancy_index = ""
for ii, i in enumerate(atom_features):
if "_atom_site_label" in i:
label_index = ii
if "fract_x" in i:
fract_x_index = ii
if "fract_y" in i:
fract_y_index = ii
if "fract_z" in i:
fract_z_index = ii
if "cartn_x" in i:
cartn_x_index = ii
if "cartn_y" in i:
cartn_y_index = ii
if "cartn_z" in i:
cartn_z_index = ii
if "occupancy" in i:
occupancy_index = ii
if fract_x_index == "" and cartn_x_index == "":
raise ValueError("Cannot find atomic coordinate info.")
elements = []
coords = []
cif_atoms = None
if fract_x_index != "":
for ii, i in enumerate(atom_liines):
tmp = i.split()
tmp_lbl = list(
Composition.from_string(tmp[label_index]).to_dict().keys()
)
elem = tmp_lbl[0]
coord = [
float(tmp[fract_x_index].split("(")[0]),
float(tmp[fract_y_index].split("(")[0]),
float(tmp[fract_z_index].split("(")[0]),
]
if len(tmp_lbl) > 1:
raise ValueError("Check if labesl are correct.", tmp_lbl)
if (
occupancy_index != ""
and not float(
tmp[occupancy_index].split("(")[0]
).is_integer()
):
raise ValueError(
"Fractional occupancy is not supported.",
float(tmp[occupancy_index].split("(")[0]),
elem,
)
elements.append(elem)
coords.append(coord)
cif_atoms = Atoms(
lattice_mat=lat.matrix,
elements=elements,
coords=coords,
cartesian=False,
)
elif cartn_x_index != "":
for ii, i in enumerate(atom_liines):
tmp = i.split()
tmp_lbl = list(
Composition.from_string(tmp[label_index]).to_dict().keys()
)
elem = tmp_lbl[0]
coord = [
float(tmp[cartn_x_index].split("(")[0]),
float(tmp[cartn_y_index].split("(")[0]),
float(tmp[cartn_z_index].split("(")[0]),
]
if len(tmp_lbl) > 1:
raise ValueError("Check if labesl are correct.", tmp_lbl)
if (
occupancy_index != ""
and not float(
tmp[occupancy_index].split("(")[0]
).is_integer()
):
raise ValueError(
"Fractional occupancy is not supported.",
float(tmp[occupancy_index].split("(")[0]),
elem,
)
elements.append(elem)
coords.append(coord)
cif_atoms = Atoms(
lattice_mat=lat.matrix,
elements=elements,
coords=coords,
cartesian=True,
)
else:
raise ValueError(
"Cannot find atomic coordinate info from cart or frac."
)
# frac_coords=list(cif_atoms.frac_coords)
cif_elements = cif_atoms.elements
lat = cif_atoms.lattice.matrix
if len(symm_ops) > 1:
frac_coords = list(cif_atoms.frac_coords)
for i in symm_ops:
for jj, j in enumerate(frac_coords):
new_c_coord = get_new_coord_for_xyz_sym(
xyz_string=i, frac_coord=j
)
new_frac_coord = [new_c_coord][0]
if not check_duplicate_coords(frac_coords, new_frac_coord):
frac_coords.append(new_frac_coord)
cif_elements.append(cif_elements[jj])
new_atoms = Atoms(
lattice_mat=lat,
coords=frac_coords,
elements=cif_elements,
cartesian=False,
)
cif_atoms = new_atoms
return cif_atoms