def extrema_coords(volumetric_data: VolumetricData,
find_min: bool,
params: VolumetricDataAnalyzeParams) -> DataFrame:
result = ChargeDensityAnalyzer(chgcar=volumetric_data)
result.get_local_extrema(threshold_frac=params.threshold_frac,
threshold_abs=params.threshold_abs,
find_min=find_min)
if params.min_dist:
# Remove sites near host atoms.
result.remove_collisions(params.min_dist)
if params.tol:
try:
# Cluster interstitials that are too close together using a tol.
result.cluster_nodes(tol=params.tol)
except ValueError:
# error raised when only a single local extreme point.
pass
if params.radius:
result.sort_sites_by_integrated_chg(r=params.radius)
result = result.extrema_df
if "avg_charge_den" in result.columns:
result.rename(columns={'avg_charge_den': 'ave_value'}, inplace=True)
result.rename(columns={'Charge Density': 'value'}, inplace=True)
logger.info("\n" + result.__str__())
return result
def interstitials_from_volumetric_data(volumetric_data: VolumetricData,
find_min: bool = True,
threshold_frac: float = None,
threshold_abs: float = None,
min_dist: float = 0.5,
tol: float = 0.5,
radius: float = 0.4) -> None:
cda = ChargeDensityAnalyzer(chgcar=volumetric_data)
cda.get_local_extrema(threshold_frac=threshold_frac,
threshold_abs=threshold_abs,
find_min=find_min)
cda.sort_sites_by_integrated_chg(r=radius)
# Remove sites near host atoms.
cda.remove_collisions(min_dist)
# Cluster interstitials that are too close together using a tol.
try:
cda.cluster_nodes(tol=tol)
except ValueError:
# error raised when only a single local extreme point.
pass
print(cda.extrema_df)
structure: Structure = volumetric_data.structure.copy()
start_index = len(structure)
end_index = len(structure) + len(cda.extrema_coords)
interstitial_indices = [i for i in range(start_index, end_index)]
for coords in cda.extrema_coords:
structure.append(Element.H, coords)
symmetrizer = StructureSymmetrizer(structure)
equiv_atoms = symmetrizer.spglib_sym_data["equivalent_atoms"]
print(f"Host symmetry {symmetrizer.spglib_sym_data['international']}")
print("++ Inequivalent indices and site symmetries ++")
orig_num_atoms = len(volumetric_data.structure)
structure_for_visualize: Structure = volumetric_data.structure.copy()
for i, ii in enumerate(interstitial_indices):
if ii == equiv_atoms[ii]:
idx = orig_num_atoms + i
coords = structure[idx].frac_coords
def element():
for z in range(1, 100):
e = Element.from_Z(z)
if e not in structure_for_visualize.composition:
yield e
structure_for_visualize.append(next(element()), coords)
idx_coords = \
f"{i:>3} {coords[0]:8.4f} {coords[1]:8.4f} {coords[2]:8.4f}"
print(idx_coords,
symmetrizer.spglib_sym_data["site_symmetry_symbols"][ii])
structure_for_visualize.to(filename="POSCAR-w-interstitials")
def test_cluster_nodes(self):
ca = ChargeDensityAnalyzer(self.chg_FePO4)
ca.get_local_extrema()
ca.cluster_nodes(tol=20)
self.assertEqual(len(ca.extrema_df), 1)
def test_cluster_nodes(self):
ca = ChargeDensityAnalyzer(self.chg_FePO4)
ca.get_local_extrema()
ca.cluster_nodes(tol=20)
self.assertEqual(len(ca.extrema_df), 1)