Merge branch 'master' into dependabot/pip/ase-3.22.1

pymatgen/analysis/diffusion/aimd/clustering.py

@@ -80,7 +80,7 @@ def get_labels(points, centroids):
         """
         dists = all_distances(points, centroids)
         min_dists = np.min(dists, axis=1)
-        return np.where(dists == min_dists[:, None])[1], np.sum(min_dists ** 2)
+        return np.where(dists == min_dists[:, None])[1], np.sum(min_dists**2)
 
     @staticmethod
     def get_centroids(points, labels, k, centroids):
@@ -149,7 +149,7 @@ def get_labels(self, points, centroids):
         """
         dists = self.lattice.get_all_distances(points, centroids)
         min_dists = np.min(dists, axis=1)
-        return np.where(dists == min_dists[:, None])[1], np.sum(min_dists ** 2)
+        return np.where(dists == min_dists[:, None])[1], np.sum(min_dists**2)
 
     def get_centroids(self, points, labels, k, centroids):
         """

pymatgen/analysis/diffusion/aimd/pathway.py

@@ -226,7 +226,7 @@ def to_chgcar(self, filename="CHGCAR.vasp"):
         """
 
         count = 1
-        VolinAu = self.structure.lattice.volume / 0.5291772083 ** 3
+        VolinAu = self.structure.lattice.volume / 0.5291772083**3
         symbols = self.structure.symbol_set
         natoms = [str(int(self.structure.composition[symbol])) for symbol in symbols]
         init_fcoords = np.array(self.structure.frac_coords)

pymatgen/analysis/diffusion/aimd/rdf.py

@@ -77,7 +77,7 @@ def __init__(
         images = images.reshape((len(r) ** 3, 3))
 
         # Find the zero image vector
-        zd = np.sum(images ** 2, axis=1)
+        zd = np.sum(images**2, axis=1)
         indx0 = np.argmin(zd)
 
         for s in structures:
@@ -95,7 +95,7 @@ def __init__(
         for fcoords, ref_fcoords, latt in zip(fcoords_list, ref_fcoords_list, lattices):
             dcf = fcoords[:, None, None, :] + images[None, None, :, :] - ref_fcoords[None, :, None, :]
             dcc = latt.get_cartesian_coords(dcf)
-            d2 = np.sum(dcc ** 2, axis=3)
+            d2 = np.sum(dcc**2, axis=3)
             dists = [
                 d2[u, v, j] ** 0.5
                 for u in range(len(indices))
@@ -356,7 +356,7 @@ def __init__(
             for i, j in natoms.items():
                 self.density[s_index][i] = j / self.structures[s_index].volume
 
-        self.volumes = 4.0 * np.pi * self.r ** 2 * self.dr
+        self.volumes = 4.0 * np.pi * self.r**2 * self.dr
         self.volumes[self.volumes < 1e-8] = 1e8  # avoid divide by zero
         self.n_structures = len(self.structures)
         self.sigma = ceil(sigma / self.dr)
@@ -468,7 +468,7 @@ def get_coordination_number(self, ref_species, species, is_average=True):
         if isinstance(species, str):
             species = [species]
         density = [sum(i[j] for j in species) for i in self.density]
-        cn = [np.cumsum(rdf * density[i] * 4.0 * np.pi * self.r ** 2 * self.dr) for i, rdf in enumerate(all_rdf)]
+        cn = [np.cumsum(rdf * density[i] * 4.0 * np.pi * self.r**2 * self.dr) for i, rdf in enumerate(all_rdf)]
         if is_average:
             cn = np.mean(cn, axis=0)
         return self.r, cn

pymatgen/analysis/diffusion/aimd/van_hove.py

@@ -119,8 +119,8 @@ def __init__(
         ref_ions = []  # type: ArrayLike
 
         # auxiliary factor for 4*\pi*r^2
-        aux_factor = 4.0 * np.pi * interval ** 2
-        aux_factor[0] = np.pi * dr ** 2
+        aux_factor = 4.0 * np.pi * interval**2
+        aux_factor[0] = np.pi * dr**2
 
         for i, ss in enumerate(diffusion_analyzer.get_drift_corrected_structures()):
             all_fcoords = np.array(ss.frac_coords)
@@ -158,7 +158,7 @@ def __init__(
         images = images.reshape((len(r) ** 3, 3))
 
         # find the zero image vector
-        zd = np.sum(images ** 2, axis=1)
+        zd = np.sum(images**2, axis=1)
         indx0 = np.argmin(zd)
 
         for it in range(reduced_nt):
@@ -172,7 +172,7 @@ def __init__(
                     - ref_ions[it1, None, :, None, :]
                 )
                 dcc = lattice.get_cartesian_coords(dcf)
-                d2 = np.sum(dcc ** 2, axis=3)
+                d2 = np.sum(dcc**2, axis=3)
                 dists = [
                     d2[u, v, j] ** 0.5
                     for u in range(len(indices))

pymatgen/analysis/diffusion/analyzer.py

@@ -269,7 +269,7 @@ def __init__(
                     dcomponents = dc[:, n:, :] - dc[:, :-n, :]
 
                 # Get msd
-                sq_disp = dx ** 2
+                sq_disp = dx**2
                 sq_disp_ions[:, i] = np.average(np.sum(sq_disp, axis=2), axis=1)
                 msd[i] = np.average(sq_disp_ions[:, i][indices])
 
@@ -335,7 +335,7 @@ def weighted_lstsq(a, b):
             # Drift and displacement information.
             self.drift = drift
             self.corrected_displacements = dc
-            self.max_ion_displacements = np.max(np.sum(dc ** 2, axis=-1) ** 0.5, axis=1)
+            self.max_ion_displacements = np.max(np.sum(dc**2, axis=-1) ** 0.5, axis=1)
             self.max_framework_displacement = np.max(self.max_ion_displacements[framework_indices])
             self.msd = msd
             self.mscd = mscd
@@ -802,7 +802,7 @@ def get_conversion_factor(structure, species, temperature):
     n = structure.composition[species]
 
     vol = structure.volume * 1e-24  # units cm^3
-    return 1000 * n / (vol * const.N_A) * z ** 2 * (const.N_A * const.e) ** 2 / (const.R * temperature)
+    return 1000 * n / (vol * const.N_A) * z**2 * (const.N_A * const.e) ** 2 / (const.R * temperature)
 
 
 def _get_vasprun(args):

pymatgen/analysis/diffusion/neb/pathfinder.py

@@ -78,7 +78,7 @@ def __init__(self, structures):
         weights = np.zeros_like(target_dists, dtype=np.float64)
         for ni in range(nimages):
             avg_dist = (target_dists[ni] + structures[ni + 1].distance_matrix) / 2.0
-            weights[ni] = 1.0 / (avg_dist ** 4 + np.eye(natoms, dtype=np.float64) * 1e-8)
+            weights[ni] = 1.0 / (avg_dist**4 + np.eye(natoms, dtype=np.float64) * 1e-8)
 
         for ni, i in itertools.product(range(nimages + 2), range(natoms)):
             frac_coords = structures[ni][i].frac_coords
@@ -255,7 +255,7 @@ def get_unit_vector(vec):
         Args:
             vec: Vector.
         """
-        return vec / np.sqrt(np.sum(vec ** 2))
+        return vec / np.sqrt(np.sum(vec**2))
 
     def _get_total_forces(self, x, true_forces, spring_const):
         """

requirements-ci.txt

@@ -1,4 +1,4 @@
-pytest==6.2.5
+pytest==7.0.0
 pytest-cov==3.0.0
 coveralls==3.3.1
 mypy==0.931
@@ -7,4 +7,4 @@ flake8==4.0.1
 pylint==2.12.2
 black==22.1.0
 treon==0.1.3
-maggma==0.29.0
+maggma==0.39.1