def test_calc_max_sphere_radius():
lattice_vectors_1 = np.array([[5, 0, 0], [0, 10, 0], [0, 0, 20]])
lattice_vectors_2 = np.array([[10, 0, 0], [0, 10, 0], [10, 10, 10]])
radius_1 = calc_max_sphere_radius(lattice_vectors_1)
radius_2 = calc_max_sphere_radius(lattice_vectors_2)
assert radius_1 == 10.0
assert radius_2 == 5.0
def __init__(self, parchg: Chgcar, center_coords: List[float]):
self.data = parchg.spin_data
self.dim = parchg.dim
self.lattice = parchg.structure.lattice
self.center = center_coords
self.radius = calc_max_sphere_radius(self.lattice.matrix)
self._distances_data = None
def spherical_dist(self, data: np.ndarray, center: List[int],
distance_bins: np.ndarray):
assert distance_bins[-1] <= calc_max_sphere_radius(self.lattice.matrix)
shifted_dist = self.shifted_distance_data(center)
_sum, _ = np.histogram(shifted_dist, distance_bins, weights=data)
counts, _ = np.histogram(shifted_dist, distance_bins)
histogram = _sum / counts / self.lattice.volume
return histogram.tolist()
def make_defect_charge_info(parchgs: List[Chgcar], band_idxs: List[int],
bin_interval: float, grids: Grids):
radius = calc_max_sphere_radius(parchgs[0].structure.lattice.matrix)
num_bins = int(np.ceil(radius / bin_interval))
distance_bins = np.array([bin_interval * i
for i in range(num_bins)] + [radius])
ave_charge_density = 1.0 / parchgs[0].structure.volume
charge_dists = []
for parchg in parchgs:
charge_dists.append(make_charge_dist(parchg, grids, distance_bins))
return DefectChargeInfo(distance_bins.tolist(), band_idxs, charge_dists,
ave_charge_density)