def test_from_seed(self):
from pymatgen import Lattice, Structure
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice.from_parameters(a=3.84,
b=3.84,
c=3.84,
alpha=120,
beta=90,
gamma=60)
struct = Structure(lattice, ["Si", "C"], coords)
s1 = pyxtal()
s1.from_seed(struct)
s2 = s1.subgroup(once=True)
pmg_s1 = s1.to_pymatgen()
pmg_s2 = s2.to_pymatgen()
self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_s2))
def test_from_seed(self):
from pymatgen import Lattice, Structure
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice.from_parameters(a=3.84,
b=3.84,
c=3.84,
alpha=120,
beta=90,
gamma=60)
struct = Structure(lattice, ["Si", "C"], coords)
s1 = random_crystal(seed=struct)
s2 = s1.subgroup(once=True)
pmg_s1 = s1.to_pymatgen()
pmg_s2 = s2.to_pymatgen()
#sga1 = SpacegroupAnalyzer(pmg_s1).get_space_group_symbol()
#sga2 = SpacegroupAnalyzer(pmg_s2).get_space_group_symbol()
self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_s2))
def test_from_seed(self):
from pymatgen import Lattice, Structure
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = Lattice.from_parameters(a=3.84,
b=3.84,
c=3.84,
alpha=120,
beta=90,
gamma=60)
struct = Structure(lattice, ["Si", "C"], coords)
s1 = pyxtal()
s1.from_seed(struct)
s2 = s1.subgroup_once(eps=0)
pmg_s1 = s1.to_pymatgen()
pmg_s2 = s2.to_pymatgen()
self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_s2))
pmg_s1 = Structure.from_file(cif_path + "B28.vasp")
struc = pyxtal()
struc.from_seed(seed=cif_path + "B28.vasp")
pmg_s2 = struc.to_pymatgen()
self.assertTrue(sm.StructureMatcher().fit(pmg_s1, pmg_s2))
permutation = {"B": "C"}
struc.subgroup_once(0.01, None, permutation, max_cell=2)