def test_new_with_structure(self):
"""Testing new_with_structure."""
si2_inp = AbinitInput(structure=abidata.cif_file("si.cif"), pseudos=abidata.pseudos("14si.pspnc"),
abi_kwargs={"ecut": 4, "toldfe": 1e-10, "nband": 6, "ngkpt": [12, 12, 12]})
# Build new input with same parameters and compressed unit cell.
new_vol = 0.9 * si2_inp.structure.volume
new_lattice = si2_inp.structure.lattice.scale(new_vol)
new_structure = abilab.Structure(new_lattice, si2_inp.structure.species, si2_inp.structure.frac_coords)
new_inp = si2_inp.new_with_structure(new_structure, scdims=None)
assert new_inp.structure.volume == new_vol
assert new_inp["ecut"] == 4
#al2_structure = abilab.Structure.from_file(abidata.cif_file("al.cif"))
# Let's build an input file for a (2, 3, 4) supercell
#super_structure = si2_inp.structure.make_supercell
scdims = np.array((2, 3, 4))
# Note: This will return a pymatgen structure, not an Abipy structure.
super_structure = si2_inp.structure * scdims
sc_inp = si2_inp.new_with_structure(super_structure, scdims=scdims)
assert isinstance(sc_inp.structure, abilab.Structure)
assert len(sc_inp.structure) == 2 * scdims.prod()
self.assert_almost_equal(sc_inp.structure.volume, si2_inp.structure.volume * scdims.prod())
assert sc_inp["chkprim"] == 0
assert sc_inp["nband"] == si2_inp["nband"] * scdims.prod()
self.assert_equal(sc_inp["ngkpt"], [6, 4, 3])
self.abivalidate_input(sc_inp)
def special_positions(lattice, u):
"""Construct the crystalline `Structure` for given value of the internal parameter u."""
frac_coords = {}
frac_coords["Si"] = [
[1/2 + u, 1/2 - u, 0],
[u, -u, u],
]
frac_coords["O"] = [ [0, 0, u] ]
species, coords = [], []
for symbol, positions in frac_coords.items():
species += len(positions) * [symbol]
coords += positions
return abilab.Structure(lattice, species, coords, validate_proximity=True, coords_are_cartesian=False)