include DataConatiner check

pyiron_atomistics/atomistics/master/murnaghan.py

@@ -31,7 +31,7 @@
 
 
 def _debye_kernel(xi):
-    return xi ** 3 / (np.exp(xi) - 1)
+    return xi**3 / (np.exp(xi) - 1)
 
 
 def debye_integral(x):
@@ -40,16 +40,16 @@ def debye_integral(x):
 
 def debye_function(x):
     if hasattr(x, "__len__"):
-        return np.array([3 / xx ** 3 * debye_integral(xx) for xx in x])
-    return 3 / x ** 3 * debye_integral(x)
+        return np.array([3 / xx**3 * debye_integral(xx) for xx in x])
+    return 3 / x**3 * debye_integral(x)
 
 
 # https://gitlab.com/ase/ase/blob/master/ase/eos.py
 def birchmurnaghan_energy(V, E0, B0, BP, V0):
     "BirchMurnaghan equation from PRB 70, 224107"
     eta = (V0 / V) ** (1 / 3)
-    return E0 + 9 * B0 * V0 / 16 * (eta ** 2 - 1) ** 2 * (
-        6 + BP * (eta ** 2 - 1) - 4 * eta ** 2
+    return E0 + 9 * B0 * V0 / 16 * (eta**2 - 1) ** 2 * (
+        6 + BP * (eta**2 - 1) - 4 * eta**2
     )
 
 
@@ -88,7 +88,7 @@ def pouriertarantola(V, E0, B0, BP, V0):
     eta = (V / V0) ** (1 / 3)
     squiggle = -3 * np.log(eta)
 
-    E = E0 + B0 * V0 * squiggle ** 2 / 6 * (3 + squiggle * (BP - 2))
+    E = E0 + B0 * V0 * squiggle**2 / 6 * (3 + squiggle * (BP - 2))
     return E
 
 
@@ -235,7 +235,7 @@ def debye_temperature(self):
 
         GPaTokBar = 10
         Ang3_to_Bohr3 = (
-            scipy.constants.angstrom ** 3
+            scipy.constants.angstrom**3
             / scipy.constants.physical_constants["Bohr radius"][0] ** 3
         )
         convert = 67.48  # conversion factor, Moruzzi Eq. (4)
@@ -505,7 +505,7 @@ def _fit_leastsq(self, volume_lst, energy_lst, fittype="birchmurnaghan"):
         a, b, c = np.polyfit(vol_lst, eng_lst, 2)
         v0 = -b / (2 * a)
         pfit_leastsq, perr_leastsq = fit_leastsq(
-            [a * v0 ** 2 + b * v0 + c, 2 * a * v0 * eV_div_A3_to_GPa, 4, v0],
+            [a * v0**2 + b * v0 + c, 2 * a * v0 * eV_div_A3_to_GPa, 4, v0],
             vol_lst,
             eng_lst,
             fittype,

pyiron_atomistics/atomistics/master/phonopy.py

@@ -339,7 +339,7 @@ def get_hesse_matrix(self):
         unit_conversion = (
             scipy.constants.physical_constants["Hartree energy in eV"][0]
             / scipy.constants.physical_constants["Bohr radius"][0] ** 2
-            * scipy.constants.angstrom ** 2
+            * scipy.constants.angstrom**2
         )
         force_shape = np.shape(self.phonopy.force_constants)
         force_reshape = force_shape[0] * force_shape[2]

pyiron_atomistics/atomistics/structure/atoms.py

@@ -1939,7 +1939,7 @@ def get_distance(self, a0, a1, mic=True, vector=False):
         if mic:
             distance, d_len = find_mic(distance, self.cell, self.pbc)
         else:
-            d_len = np.array([np.sqrt((distance ** 2).sum())])
+            d_len = np.array([np.sqrt((distance**2).sum())])
         if vector:
             return distance[0]
 

pyiron_atomistics/atomistics/structure/neighbors.py

@@ -354,7 +354,7 @@ def _estimate_num_neighbors(
             volume = self._ref_structure.get_volume(per_atom=True)
             width_buffer = 1 + width_buffer
             width_buffer *= get_volume_of_n_sphere_in_p_norm(3, self.norm_order)
-            num_neighbors = max(14, int(width_buffer * cutoff_radius ** 3 / volume))
+            num_neighbors = max(14, int(width_buffer * cutoff_radius**3 / volume))
         elif num_neighbors is None:
             num_neighbors = self.num_neighbors
         if self.num_neighbors is None:
@@ -575,7 +575,7 @@ def centrosymmetry(self):
         indices = np.indices((len(self.vecs),) + all_arr.shape[:-1])
         v = self.vecs[indices[0], all_arr[np.newaxis, :, :, 0]]
         v += self.vecs[indices[0], all_arr[np.newaxis, :, :, 1]]
-        return np.sum(v ** 2, axis=-1).sum(axis=-1).min(axis=-1)
+        return np.sum(v**2, axis=-1).sum(axis=-1).min(axis=-1)
 
     def __getattr__(self, name):
         """Attributes for the mode. Same as setting `neigh.mode`."""

pyiron_atomistics/atomistics/structure/sparse_list.py

@@ -111,7 +111,7 @@ def to_hdf(self, hdf, key):
             my_dict["index"] = self.keys()
             if data_type == "list_bool":
                 my_dict["values"] = [
-                    sum([2 ** i * int(v) for i, v in enumerate(val)])
+                    sum([2**i * int(v) for i, v in enumerate(val)])
                     for val in self.values()
                 ]
             else:

pyiron_atomistics/atomistics/volumetric/generic.py

@@ -85,7 +85,7 @@ def gauss_f(d, fwhm=0.529177):
         """
         sigma = fwhm / (2 * np.sqrt(2 * np.log(2)))
         d2 = d * d
-        return np.exp(-1 / (2 * sigma ** 2) * d2)
+        return np.exp(-1 / (2 * sigma**2) * d2)
 
     @staticmethod
     def dist_between_two_grid_points(

pyiron_atomistics/dft/job/generic.py

@@ -494,11 +494,11 @@ def get_density_of_states(self, sigma=0.1, shift_by_fermi_energy=True, grid=None
             - grid[np.newaxis, np.newaxis, np.newaxis, :]
         )
         hist = (
-            np.exp(-((hist) ** 2) / (2 * sigma ** 2))
+            np.exp(-((hist) ** 2) / (2 * sigma**2))
             * k_weights[np.newaxis, :, np.newaxis, np.newaxis]
         )
         hist = np.sum(hist, axis=(1, 2))
-        hist *= 2 / len(eigen_values) / np.sqrt(2 * np.pi * sigma ** 2)
+        hist *= 2 / len(eigen_values) / np.sqrt(2 * np.pi * sigma**2)
         return {"grid": grid, "dos": hist}
 
 

pyiron_atomistics/interactive/sxextoptint.py

@@ -164,13 +164,16 @@ def _write_input(
         selective_dynamics=False,
     ):
         with open(os.path.join(working_directory, "optim.sx"), "w") as f:
-            content = "main { ricQN { ric { maxDist = %f; withAngles; } maxSteps = %i; dEnergy = %f; dF = %f; maxStepLength = %f; softModeDamping = %f;}}" % (
-                maxDist,
-                ionic_steps,
-                ionic_energy_tolerance,
-                ionic_force_tolerance,
-                max_step_length,
-                soft_mode_damping,
+            content = (
+                "main { ricQN { ric { maxDist = %f; withAngles; } maxSteps = %i; dEnergy = %f; dF = %f; maxStepLength = %f; softModeDamping = %f;}}"
+                % (
+                    maxDist,
+                    ionic_steps,
+                    ionic_energy_tolerance,
+                    ionic_force_tolerance,
+                    max_step_length,
+                    soft_mode_damping,
+                )
             )
             if selective_dynamics:
                 content += "structure { include <structure.sx>; }"

pyiron_atomistics/lammps/interactive.py

@@ -722,7 +722,7 @@ def interactive_stress_getter(self):
             ss[:, ind].reshape(len(self.structure), 3, 3)
             / constants.eV
             * constants.bar
-            * constants.angstrom ** 3
+            * constants.angstrom**3
         )
         if np.matrix.trace(self._prism.R) != 3:
             ss = np.einsum("ij,njk->nik", self._prism.R, ss)

pyiron_atomistics/lammps/structure.py

@@ -70,7 +70,7 @@ def __init__(self, cell, pbc=(True, True, True), digits=10):
         yhi = np.sin(gamma) * bn
         xzp = np.cos(beta) * cn
         yzp = (bn * cn * np.cos(alpha) - xyp * xzp) / yhi
-        zhi = np.sqrt(cn ** 2 - xzp ** 2 - yzp ** 2)
+        zhi = np.sqrt(cn**2 - xzp**2 - yzp**2)
 
         # Set precision
         self.car_prec = dec.Decimal("10.0") ** int(

pyiron_atomistics/sphinx/base.py

@@ -117,7 +117,11 @@ def __getitem__(self, item):
                     result = super().__getitem__(tag)
                 else:
                     result = result[tag]
-                if hasattr(result, "list_nodes") and "TYPE" in result.list_nodes():
+                if (
+                    isinstance(result, HasGroups)
+                    and "NAME" in result.list_nodes()
+                    and result["NAME"] == "DataContainer"
+                ):
                     result = result.to_object()
             except (ValueError, KeyError):
                 return None
@@ -2046,7 +2050,7 @@ def get_volume(self):
         volume = re.findall("Omega:.*$", self.log_file, re.MULTILINE)
         if len(volume) > 0:
             volume = float(volume[0].split()[1])
-            volume *= BOHR_TO_ANGSTROM ** 3
+            volume *= BOHR_TO_ANGSTROM**3
         else:
             volume = 0
         return np.array(self.n_steps * [volume])

pyiron_atomistics/testing/randomatomistic.py

@@ -468,7 +468,7 @@ def _s_r(self):
 
     def interactive_energy_pot_getter(self):
         return self.input["epsilon"] * (
-            np.sum(self._s_r ** 12) - np.sum(self._s_r ** 6)
+            np.sum(self._s_r**12) - np.sum(self._s_r**6)
         )
 
     def interactive_energy_tot_getter(self):
@@ -477,12 +477,12 @@ def interactive_energy_tot_getter(self):
         )
 
     def interadtive_energy_kin_getter(self):
-        v = np.einsum("ni,n->", self._velocity ** 2, self.structure.get_masses()) / 2
+        v = np.einsum("ni,n->", self._velocity**2, self.structure.get_masses()) / 2
         return (
             (
                 v
-                * self._unit.angstrom ** 2
-                / self._unit.second ** 2
+                * self._unit.angstrom**2
+                / self._unit.second**2
                 / 1e-30
                 * self._unit.amu
             )
@@ -494,8 +494,8 @@ def interactive_forces_getter(self):
         all_values = self.input["epsilon"] * np.einsum(
             "ni,n,n->ni",
             self.neigh.flattened.vecs,
-            1 / self.neigh.flattened.distances ** 2,
-            12 * self._s_r ** 12 - 6 * self._s_r ** 6,
+            1 / self.neigh.flattened.distances**2,
+            12 * self._s_r**12 - 6 * self._s_r**6,
         )
         forces = np.zeros_like(self.structure.positions)
         np.add.at(forces, self.neigh.flattened.atom_numbers, all_values)
@@ -511,8 +511,8 @@ def interactive_pressures_getter(self):
                 "ni,nj,n,n->ij",
                 self.neigh.flattened.vecs,
                 self.neigh.flattened.vecs,
-                1 / self.neigh.flattened.distances ** 2,
-                12 * self._s_r ** 12 - 6 * self._s_r ** 6,
+                1 / self.neigh.flattened.distances**2,
+                12 * self._s_r**12 - 6 * self._s_r**6,
             )
             * self._unit.electron_volt
         )
@@ -523,15 +523,15 @@ def interactive_pressures_getter(self):
                 self._velocity,
                 self.structure.get_masses(),
             )
-            * self._unit.angstrom ** 2
-            / self._unit.second ** 2
+            * self._unit.angstrom**2
+            / self._unit.second**2
             / 1e-30
             * self._unit.amu
         )
         return (
             (pot_part + kin_part)
             / self.structure.get_volume()
-            / self._unit.angstrom ** 3
+            / self._unit.angstrom**3
         ).to(self._unit.pascal).magnitude / 1e9
 
     def interactive_stress_getter(self):

pyiron_atomistics/thermodynamics/hessian.py

@@ -126,14 +126,11 @@ def interactive_pressures_getter(self):
 
     def interactive_cells_setter(self, cell):
         if np.sum(self._stiffness_tensor) != 0:
-            epsilon = (
-                np.einsum(
-                    "ij,jk->ik",
-                    self.structure.cell,
-                    np.linalg.inv(self._reference_structure.cell),
-                )
-                - np.eye(3)
-            )
+            epsilon = np.einsum(
+                "ij,jk->ik",
+                self.structure.cell,
+                np.linalg.inv(self._reference_structure.cell),
+            ) - np.eye(3)
             epsilon = (epsilon + epsilon.T) * 0.5
             epsilon = np.append(
                 epsilon.diagonal(), np.roll(epsilon, -1, axis=0).diagonal()