def setUp(self):
self.maxDiff = None
# trivial example, simple square lattice for testing
structure = Structure(Lattice.tetragonal(5.0, 50.0), ["H"], [[0, 0, 0]])
self.square_sg = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
# TODO: decorating still fails because the structure graph gives a CN of 8 for this square lattice
# self.square_sg.decorate_structure_with_ce_info()
# body-centered square lattice for testing
structure = Structure(Lattice.tetragonal(5.0, 50.0), ["H", "He"], [[0, 0, 0], [0.5, 0.5, 0.5]])
self.bc_square_sg = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.bc_square_sg.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(-1, -1, 0))
self.bc_square_sg.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
# body-centered square lattice for testing
# directions reversed, should be equivalent to bc_square
structure = Structure(Lattice.tetragonal(5.0, 50.0), ["H", "He"], [[0, 0, 0], [0.5, 0.5, 0.5]])
self.bc_square_sg_r = StructureGraph.with_empty_graph(structure, edge_weight_name="", edge_weight_units="")
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(1, 0, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(-1, 0, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, 1, 0))
self.bc_square_sg_r.add_edge(0, 0, from_jimage=(0, 0, 0), to_jimage=(0, -1, 0))
self.bc_square_sg_r.add_edge(0, 1, from_jimage=(0, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(-1, 0, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(-1, -1, 0), to_jimage=(0, 0, 0))
self.bc_square_sg_r.add_edge(1, 0, from_jimage=(0, -1, 0), to_jimage=(0, 0, 0))
# MoS2 example, structure graph obtained from critic2
# (not ground state, from mp-1023924, single layer)
stdout_file = os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2_critic2_stdout.txt")
with open(stdout_file) as f:
reference_stdout = f.read()
self.structure = Structure.from_file(os.path.join(PymatgenTest.TEST_FILES_DIR, "critic2/MoS2.cif"))
c2o = Critic2Analysis(self.structure, reference_stdout)
self.mos2_sg = c2o.structure_graph(include_critical_points=False)
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).get_primitive_structure()
# BCC example.
self.bcc = Structure(Lattice.cubic(5.0), ["He", "He"], [[0, 0, 0], [0.5, 0.5, 0.5]])
warnings.simplefilter("ignore")
def test_from_edges(self):
edges = {
(0, 0, (0, 0, 0), (1, 0, 0)): None,
(0, 0, (0, 0, 0), (-1, 0, 0)): None,
(0, 0, (0, 0, 0), (0, 1, 0)): None,
(0, 0, (0, 0, 0), (0, -1, 0)): None,
}
structure = Structure(Lattice.tetragonal(5.0, 50.0), ["H"], [[0, 0, 0]])
sg = StructureGraph.with_edges(structure, edges)
self.assertEqual(sg, self.square_sg)
def structures():
coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
lattice = [[3.8, 0, 0], [1.9, 3.3, 0], [0, -2.2, 3.1]]
Si2 = Structure(lattice, ["Si4+", "Si4+"], coords)
coords = [
[0.25, 0.25, 0.173],
[0.75, 0.75, 0.827],
[0.75, 0.25, 0],
[0.25, 0.75, 0],
[0.25, 0.25, 0.676],
[0.75, 0.75, 0.324],
]
lattice = Lattice.tetragonal(4.192, 6.88)
Si2Ru2Pr2 = Structure(lattice, ["Si", "Si", "Ru", "Ru", "Pr", "Pr"],
coords)
return [Si2, Si2Ru2Pr2]
def elongated_tetragonal():
lattice = Lattice.tetragonal(a=1, c=3 * sqrt(2))
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)
def tetra_close_to_cubic():
lattice = Lattice.tetragonal(1.001 * 10 / sqrt(2), 10)
coords = [[0.0, 0.0, 0.0]]
return IStructure(lattice=lattice, species=["H"], coords=coords)