def get_cc_structures(ground: Structure,
excited: Structure,
displacements: np.ndarray,
remove_zero: bool = True) -> Tuple[List, List]:
"""Generate the structures for a CC diagram.
Parameters
----------
ground : pymatgen.core.structure.Structure
pymatgen structure corresponding to the ground (final) state
excited : pymatgen.core.structure.Structure
pymatgen structure corresponding to the excited (initial) state
displacements : list(float)
list of displacements to compute the perturbed structures. Note: the
displacements are for only one potential energy surface and will be
applied to both (e.g. displacements=np.linspace(-0.1, 0.1, 5)) will
return 10 structures 5 of the ground state displaced at +-10%, +-5%,
and 0% and 5 of the excited state displaced similarly)
remove_zero : bool
remove 0% displacement from list (default is True)
Returns
-------
ground_structs = list(pymatgen.core.structure.Struture)
a list of structures corresponding to the displaced ground state
excited_structs = list(pymatgen.core.structure.Structure)
a list of structures corresponding to the displaced excited state
"""
displacements = np.array(displacements)
if remove_zero:
displacements = displacements[displacements != 0.]
ground_structs = ground.interpolate(excited, nimages=displacements)
excited_structs = ground.interpolate(excited, nimages=(displacements + 1.))
return ground_structs, excited_structs
def setUp(self):
c1 = [[0.5] * 3, [0.9] * 3]
c2 = [[0.5] * 3, [0.9, 0.1, 0.1]]
s1 = Structure(Lattice.cubic(5), ['Si', 'Si'], c1)
s2 = Structure(Lattice.cubic(5), ['Si', 'Si'], c2)
structs = []
for s in s1.interpolate(s2, 3, pbc=True):
structs.append(Structure.from_sites(s.sites, to_unit_cell=True))
self.structures = structs
self.vis = MITNEBSet(self.structures)
def setUp(self):
c1 = [[0.5] * 3, [0.9] * 3]
c2 = [[0.5] * 3, [0.9, 0.1, 0.1]]
s1 = Structure(Lattice.cubic(5), ['Si', 'Si'], c1)
s2 = Structure(Lattice.cubic(5), ['Si', 'Si'], c2)
structs = []
for s in s1.interpolate(s2, 3, pbc=True):
structs.append(Structure.from_sites(s.sites, to_unit_cell=True))
self.structures = structs
self.vis = MITNEBSet(self.structures)
def test_write_inputs(self):
c1 = [[0.5] * 3, [0.9] * 3]
c2 = [[0.5] * 3, [0.9, 0.1, 0.1]]
s1 = Structure(Lattice.cubic(5), ['Si', 'Si'], c1)
s2 = Structure(Lattice.cubic(5), ['Si', 'Si'], c2)
structs = []
for s in s1.interpolate(s2, 3, pbc=True):
structs.append(Structure.from_sites(s.sites, to_unit_cell=True))
fc = self.vis._process_structures(structs)[2].frac_coords
self.assertTrue(np.allclose(fc, [[0.5]*3,[0.9, 1.033333, 1.0333333]]))
def test_write_inputs(self):
c1 = [[0.5] * 3, [0.9] * 3]
c2 = [[0.5] * 3, [0.9, 0.1, 0.1]]
s1 = Structure(Lattice.cubic(5), ['Si', 'Si'], c1)
s2 = Structure(Lattice.cubic(5), ['Si', 'Si'], c2)
structs = []
for s in s1.interpolate(s2, 3, pbc=True):
structs.append(Structure.from_sites(s.sites, to_unit_cell=True))
fc = self.vis._process_structures(structs)[2].frac_coords
self.assertTrue(
np.allclose(fc, [[0.5] * 3, [0.9, 1.033333, 1.0333333]]))
