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 test_remove_collisions(self):
ca = ChargeDensityAnalyzer(self.chg_FePO4)
ca.get_local_extrema(threshold_frac=0)
ca.remove_collisions() # should not trigger error
self.assertEqual(len(ca.extrema_df), 0)
self.ca_FePO4.get_local_extrema(find_min=False, threshold_frac=1.0)
self.ca_FePO4.remove_collisions(min_dist=0.5)
self.assertEqual(len(self.ca_FePO4.extrema_df), 0)
def test_remove_collisions(self):
ca = ChargeDensityAnalyzer(self.chg_FePO4)
ca.get_local_extrema(threshold_frac=0)
ca.remove_collisions() # should not trigger error
self.assertEqual(len(ca.extrema_df), 0)
self.ca_FePO4.get_local_extrema(find_min=False, threshold_frac=1.0)
self.ca_FePO4.remove_collisions(min_dist=0.5)
self.assertEqual(len(self.ca_FePO4.extrema_df), 0)
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")
class ChgDenAnalyzerTest(unittest.TestCase):
def setUp(self):
# This is a CHGCAR_sum file with reduced grid size
chgcar_path = os.path.join(test_dir, "CHGCAR.FePO4")
chg_FePO4 = Chgcar.from_file(chgcar_path)
self.chgcar_path = chgcar_path
self.chg_FePO4 = chg_FePO4
self.ca_FePO4 = ChargeDensityAnalyzer(chg_FePO4)
self.s_LiFePO4 = Structure.from_file(
os.path.join(test_dir, "LiFePO4.cif"))
def test_get_local_extrema(self):
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
threshold_frac = random.random()
threshold_abs_min = random.randrange(2, 14)
threshold_abs_max = random.randrange(27e2, 28e4)
# Minima test
full_list_min = self.ca_FePO4.get_local_extrema(find_min=True,
threshold_frac=1.0)
frac_list_min_frac = self.ca_FePO4.get_local_extrema(
find_min=True, threshold_frac=threshold_frac)
frac_list_min_abs = self.ca_FePO4.get_local_extrema(
find_min=True, threshold_abs=threshold_abs_min)
self.assertAlmostEqual(len(full_list_min) * threshold_frac,
len(frac_list_min_frac),
delta=1)
ca.get_local_extrema(find_min=True)
df_expected = ca.extrema_df[
ca.extrema_df["Charge Density"] <= threshold_abs_min]
self.assertEqual(len(frac_list_min_abs), len(df_expected))
# Maxima test
full_list_max = self.ca_FePO4.get_local_extrema(find_min=False,
threshold_frac=1.0)
frac_list_max = self.ca_FePO4.get_local_extrema(
find_min=False, threshold_frac=threshold_frac)
frac_list_max_abs = self.ca_FePO4.get_local_extrema(
find_min=False, threshold_abs=threshold_abs_max)
self.assertAlmostEqual(len(full_list_max) * threshold_frac,
len(frac_list_max),
delta=1)
# Local maxima should finds all center of atoms
self.assertEqual(len(self.ca_FePO4.structure), len(full_list_max))
ca.get_local_extrema(find_min=False)
df_expected = ca.extrema_df[
ca.extrema_df["Charge Density"] >= threshold_abs_max]
self.assertEqual(len(frac_list_max_abs), len(df_expected))
def test_remove_collisions(self):
ca = ChargeDensityAnalyzer(self.chg_FePO4)
ca.get_local_extrema(threshold_frac=0)
ca.remove_collisions() # should not trigger error
self.assertEqual(len(ca.extrema_df), 0)
self.ca_FePO4.get_local_extrema(find_min=False, threshold_frac=1.0)
self.ca_FePO4.remove_collisions(min_dist=0.5)
self.assertEqual(len(self.ca_FePO4.extrema_df), 0)
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_get_structure_with_nodes(self):
s_FePO4 = self.ca_FePO4.get_structure_with_nodes(find_min=True)
sites_predicted = np.array([
self.s_LiFePO4[i].frac_coords for i in range(len(self.s_LiFePO4))
if self.s_LiFePO4[i].species_string == "Li"
])
sites_guess = np.array([
s_FePO4[i].frac_coords for i in range(len(s_FePO4))
if s_FePO4[i].species_string == "X0+"
])
distances = s_FePO4.lattice.get_all_distances(sites_predicted,
sites_guess).flatten()
distances = [d for d in distances if d < 0.1]
self.assertEqual(len(distances), len(sites_predicted))
def test_from_file(self):
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
self.assertTrue(isinstance(ca, ChargeDensityAnalyzer))
def test_sort_sites_by_integrated_chg(self):
print(self.chgcar_path)
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
ca.get_local_extrema()
ca.sort_sites_by_integrated_chg()
print(ca._extrema_df.iloc[0], 0.5)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['a'], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['b'], 0.5)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['c'], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['Charge Density'],
1.65288944124)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['Int. Charge Density'],
0.0018375161626331743)
class ChgDenAnalyzerTest(unittest.TestCase):
def setUp(self):
# This is a CHGCAR_sum file with reduced grid size
chgcar_path = os.path.join(test_dir, "CHGCAR.FePO4")
chg_FePO4 = Chgcar.from_file(chgcar_path)
self.chgcar_path = chgcar_path
self.chg_FePO4 = chg_FePO4
self.ca_FePO4 = ChargeDensityAnalyzer(chg_FePO4)
self.s_LiFePO4 = Structure.from_file(
os.path.join(test_dir, "LiFePO4.cif"))
def test_get_local_extrema(self):
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
threshold_frac = random.random()
threshold_abs_min = random.randrange(2, 14)
threshold_abs_max = random.randrange(27e2, 28e4)
# Minima test
full_list_min = self.ca_FePO4.get_local_extrema(find_min=True,
threshold_frac=1.0)
frac_list_min_frac = self.ca_FePO4.get_local_extrema(find_min=True,
threshold_frac=threshold_frac)
frac_list_min_abs = self.ca_FePO4.get_local_extrema(find_min=True,
threshold_abs=threshold_abs_min)
self.assertAlmostEqual(len(full_list_min) * threshold_frac,
len(frac_list_min_frac), delta=1)
ca.get_local_extrema(find_min=True)
df_expected = ca.extrema_df[
ca.extrema_df["Charge Density"] <= threshold_abs_min]
self.assertEqual(len(frac_list_min_abs), len(df_expected))
# Maxima test
full_list_max = self.ca_FePO4.get_local_extrema(find_min=False,
threshold_frac=1.0)
frac_list_max = self.ca_FePO4.get_local_extrema(find_min=False,
threshold_frac=threshold_frac)
frac_list_max_abs = self.ca_FePO4.get_local_extrema(find_min=False,
threshold_abs=threshold_abs_max)
self.assertAlmostEqual(len(full_list_max) * threshold_frac,
len(frac_list_max), delta=1)
# Local maxima should finds all center of atoms
self.assertEqual(len(self.ca_FePO4.structure), len(full_list_max))
ca.get_local_extrema(find_min=False)
df_expected = ca.extrema_df[
ca.extrema_df["Charge Density"] >= threshold_abs_max]
self.assertEqual(len(frac_list_max_abs), len(df_expected))
def test_remove_collisions(self):
ca = ChargeDensityAnalyzer(self.chg_FePO4)
ca.get_local_extrema(threshold_frac=0)
ca.remove_collisions() # should not trigger error
self.assertEqual(len(ca.extrema_df), 0)
self.ca_FePO4.get_local_extrema(find_min=False, threshold_frac=1.0)
self.ca_FePO4.remove_collisions(min_dist=0.5)
self.assertEqual(len(self.ca_FePO4.extrema_df), 0)
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_get_structure_with_nodes(self):
s_FePO4 = self.ca_FePO4.get_structure_with_nodes(find_min=True)
sites_predicted = np.array([
self.s_LiFePO4[i].frac_coords
for i in range(len(self.s_LiFePO4))
if self.s_LiFePO4[i].species_string == "Li"
])
sites_guess = np.array(
[s_FePO4[i].frac_coords for i in range(len(s_FePO4)) if
s_FePO4[i].species_string == "X0+"])
distances = s_FePO4.lattice.get_all_distances(sites_predicted,
sites_guess).flatten()
distances = [d for d in distances if d < 0.1]
self.assertEqual(len(distances), len(sites_predicted))
def test_from_file(self):
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
self.assertTrue(isinstance(ca, ChargeDensityAnalyzer))
def test_sort_sites_by_integrated_chg(self):
print(self.chgcar_path)
ca = ChargeDensityAnalyzer.from_file(self.chgcar_path)
ca.get_local_extrema()
ca.sort_sites_by_integrated_chg()
print(ca._extrema_df.iloc[0], 0.5)
print(ca._extrema_df.iloc[0]['avg_charge_den'])
self.assertAlmostEqual(ca._extrema_df.iloc[0]['a'], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['b'], 0.5)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['c'], 0.0)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['Charge Density'],
1.65288944124)
self.assertAlmostEqual(ca._extrema_df.iloc[0]['avg_charge_den'],
0.006831484178753711)