def read_cif(filename):
"""
read the cif, mainly for pyxtal cif output
Be cautious in using it to read other cif files
Args:
filename: path of the structure file
Return:
pyxtal structure
"""
species = []
coords = []
with open(filename, 'r') as f:
lines = f.readlines()
for i, line in enumerate(lines):
if line.startswith('_symmetry_Int_Tables_number'):
sg = int(line.split()[-1])
elif line.startswith('_cell_length_a'):
a = float(lines[i].split()[-1])
b = float(lines[i+1].split()[-1])
c = float(lines[i+2].split()[-1])
alpha = float(lines[i+3].split()[-1])
beta = float(lines[i+4].split()[-1])
gamma = float(lines[i+5].split()[-1])
elif line.startswith('_symmetry_cell_setting'):
lat_type = line.split()[-1]
elif line.startswith('_symmetry_space_group_name_H-M '):
symbol = line.split()[-1]
if eval(symbol) in ["Pn", "P21/n", "C2/n"]:
diag = True
else:
diag = False
elif line.find('_atom_site') >= 0:
s = i
while True:
s += 1
if lines[s].find('_atom_site') >= 0:
pass
elif len(lines[s].split()) <= 3:
break
else:
tmp = lines[s].split()
pos = [float(tmp[-4]), float(tmp[-3]), float(tmp[-2])]
species.append(tmp[0])
coords.append(pos)
break
wp0 = Group(sg)[0]
lattice = Lattice.from_para(a, b, c, alpha, beta, gamma, lat_type)
sites = []
for specie, coord in zip(species, coords):
pt, wp, _ = WP_merge(coord, lattice.matrix, wp0, tol=0.1)
sites.append(atom_site(wp, pt, specie, diag))
return lattice, sites
from pymatgen.core.structure import Molecule
import pymatgen.analysis.structure_matcher as sm
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from pymatgen.core.operations import SymmOp
from pyxtal import pyxtal
from pyxtal.lattice import Lattice
from pyxtal.symmetry import Group, Wyckoff_position, get_wyckoffs
from pyxtal.wyckoff_site import WP_merge
from pyxtal.XRD import Similarity
from pyxtal.operations import get_inverse
cif_path = resource_filename("pyxtal", "database/cifs/")
l0 = Lattice.from_matrix([[4.08, 0, 0], [0, 9.13, 0], [0, 0, 5.50]])
l1 = Lattice.from_matrix([[4.08, 0, 0], [0, 9.13, 0], [0, 0, 5.50]])
l2 = Lattice.from_para(4.08, 9.13, 5.50, 90, 90, 90)
l3 = Lattice.from_para(4.08, 7.13, 5.50, 90, 38, 90, ltype="monoclinic")
wp1 = Wyckoff_position.from_group_and_index(36, 0)
wp2 = Wyckoff_position.from_group_and_index(36, "4a")
class TestGroup(unittest.TestCase):
def test_list_wyckoff_combinations(self):
g = Group(64)
a1, _ = g.list_wyckoff_combinations([4, 2])
self.assertTrue(a1 is None)
a2, _ = g.list_wyckoff_combinations([4, 8], quick=False)
self.assertTrue(len(a2) == 8)
class TestOptLat(unittest.TestCase):