Merge pull request #1300 from pyiron/dependabot/pip/spglib-2.3.0

Bump spglib from 2.2.0 to 2.3.0

.ci_support/environment.yml

@@ -3,7 +3,7 @@ channels:
 dependencies:
 - aimsgb =1.1.0
 - ase =3.22.1
-- atomistics =0.1.21
+- atomistics =0.1.22
 - coverage
 - codacy-coverage
 - defusedxml =0.7.1
@@ -21,5 +21,5 @@ dependencies:
 - scikit-learn =1.4.0
 - scipy =1.12.0
 - seekpath =2.1.0
-- spglib =2.2.0
+- spglib =2.3.0
 - structuretoolkit =0.0.18

pyiron_atomistics/atomistics/job/atomistic.py

@@ -259,15 +259,15 @@ def calc_md(
         self._generic_input["temperature"] = temperature
         self._generic_input["n_ionic_steps"] = n_ionic_steps
         self._generic_input["n_print"] = n_print
-        self._generic_input[
-            "temperature_damping_timescale"
-        ] = temperature_damping_timescale
+        self._generic_input["temperature_damping_timescale"] = (
+            temperature_damping_timescale
+        )
         if pressure is not None:
             self._generic_input["pressure"] = pressure
         if pressure_damping_timescale is not None:
-            self._generic_input[
-                "pressure_damping_timescale"
-            ] = pressure_damping_timescale
+            self._generic_input["pressure_damping_timescale"] = (
+                pressure_damping_timescale
+            )
         if time_step is not None:
             self._generic_input["time_step"] = time_step
         self._generic_input.remove_keys(["max_iter"])

pyiron_atomistics/atomistics/master/phonopy.py

@@ -277,9 +277,9 @@ def collect_output(self):
             hdf5_out["qpoints"] = mesh_dict["qpoints"]
             hdf5_out["supercell_matrix"] = self._phonopy_supercell_matrix()
             hdf5_out["displacement_dataset"] = self.phonopy.get_displacement_dataset()
-            hdf5_out[
-                "dynamical_matrix"
-            ] = self.phonopy.dynamical_matrix.get_dynamical_matrix()
+            hdf5_out["dynamical_matrix"] = (
+                self.phonopy.dynamical_matrix.get_dynamical_matrix()
+            )
             hdf5_out["force_constants"] = self.phonopy.force_constants
 
     def write_phonopy_force_constants(self, file_name="FORCE_CONSTANTS", cwd=None):

pyiron_atomistics/atomistics/structure/atoms.py

@@ -2444,15 +2444,17 @@ def get_initial_magnetic_moments(self):
                 ):
                     return np.array(
                         [
-                            [
-                                float(spin_dir)
-                                for spin_dir in spin.replace("[", "")
-                                .replace("]", "")
-                                .replace(",", "")
-                                .split()
-                            ]
-                            if spin
-                            else [0.0, 0.0, 0.0]
+                            (
+                                [
+                                    float(spin_dir)
+                                    for spin_dir in spin.replace("[", "")
+                                    .replace("]", "")
+                                    .replace(",", "")
+                                    .split()
+                                ]
+                                if spin
+                                else [0.0, 0.0, 0.0]
+                            )
                             for spin in spin_lst
                         ]
                     )
@@ -3131,9 +3133,9 @@ def ase_to_pyiron(ase_obj):
             elif constraint_dict["name"] == "FixScaled":
                 if "selective_dynamics" not in pyiron_atoms.arrays.keys():
                     pyiron_atoms.add_tag(selective_dynamics=[True, True, True])
-                pyiron_atoms.selective_dynamics[
-                    constraint_dict["kwargs"]["a"]
-                ] = constraint_dict["kwargs"]["mask"]
+                pyiron_atoms.selective_dynamics[constraint_dict["kwargs"]["a"]] = (
+                    constraint_dict["kwargs"]["mask"]
+                )
             else:
                 warnings.warn("Unsupported ASE constraint: " + constraint_dict["name"])
     return pyiron_atoms
@@ -3402,7 +3404,6 @@ def default(data, dflt):
 
 
 class Symbols(ASESymbols):
-
     """
     Derived from the ase symbols class which has the following docs:
 

pyiron_atomistics/dft/bader.py

@@ -19,7 +19,6 @@
 
 
 class Bader:
-
     """
     Module to apply the Bader charge partitioning scheme to finished DFT jobs. This module is interfaced with the
     `Bader code`_ from the Greame Henkelmann group.

pyiron_atomistics/dft/waves/dos.py

@@ -18,7 +18,6 @@
 
 
 class Dos(object):
-
     """
     The DOS class stores all information to store and retrieve the total and resolved density of states from an
     electronic structure calculation.

pyiron_atomistics/dft/waves/electronic.py

@@ -462,9 +462,9 @@ def grand_dos_matrix(self):
             for spin in range(self.n_spins):
                 for i, kpt in enumerate(self.kpoints):
                     for j, band in enumerate(kpt.bands):
-                        self._grand_dos_matrix[
-                            spin, i, j, :, :
-                        ] = band.resolved_dos_matrix
+                        self._grand_dos_matrix[spin, i, j, :, :] = (
+                            band.resolved_dos_matrix
+                        )
         return self._grand_dos_matrix
 
     @grand_dos_matrix.setter
@@ -624,9 +624,9 @@ def generate_from_matrices(self):
                     occ = self.occupancy_matrix[spin][i][j]
                     self.kpoints[-1].add_band(eigenvalue=val, occupancy=occ, spin=spin)
                     if self._grand_dos_matrix is not None:
-                        self.kpoints[-1].bands[spin][
-                            -1
-                        ].resolved_dos_matrix = self.grand_dos_matrix[spin, i, j, :, :]
+                        self.kpoints[-1].bands[spin][-1].resolved_dos_matrix = (
+                            self.grand_dos_matrix[spin, i, j, :, :]
+                        )
 
     def get_spin_resolved_dos(self, spin_indices=0):
         """
@@ -751,7 +751,6 @@ def __repr__(self):
 
 
 class Kpoint(object):
-
     """
     All data related to a single k-point is stored in this module
 

pyiron_atomistics/interactive/quasi_newton.py

@@ -137,8 +137,7 @@ def inv_hessian(self):
             return np.einsum(
                 "ik,k,jk->ij",
                 self.eigenvectors,
-                self.eigenvalues
-                / (self.eigenvalues**2 + np.exp(self.regularization)),
+                self.eigenvalues / (self.eigenvalues**2 + np.exp(self.regularization)),
                 self.eigenvectors,
             )
         else:
@@ -277,7 +276,6 @@ def run_qn(
 
 
 class QuasiNewton(InteractiveWrapper):
-
     """
     Structure optimization scheme via Quasi-Newton algorithm.
 

pyiron_atomistics/lammps/base.py

@@ -366,9 +366,9 @@ def enable_h5md(self):
         """
         del self.input.control["dump_modify___1"]
         del self.input.control["dump___1"]
-        self.input.control[
-            "dump___1"
-        ] = "all h5md ${dumptime} dump.h5 position force create_group yes"
+        self.input.control["dump___1"] = (
+            "all h5md ${dumptime} dump.h5 position force create_group yes"
+        )
 
     def write_input(self):
         """
@@ -897,79 +897,79 @@ def _set_selective_dynamics(self):
                     self.input.control["group___constraintxyz"] = "id " + " ".join(
                         [str(ind) for ind in constraint_xyz]
                     )
-                    self.input.control[
-                        "fix___constraintxyz"
-                    ] = "constraintxyz setforce 0.0 0.0 0.0"
+                    self.input.control["fix___constraintxyz"] = (
+                        "constraintxyz setforce 0.0 0.0 0.0"
+                    )
                     if self._generic_input["calc_mode"] == "md":
-                        self.input.control[
-                            "velocity___constraintxyz"
-                        ] = "set 0.0 0.0 0.0"
+                        self.input.control["velocity___constraintxyz"] = (
+                            "set 0.0 0.0 0.0"
+                        )
                 if len(constraint_xy) > 0:
                     self.input.control["group___constraintxy"] = "id " + " ".join(
                         [str(ind) for ind in constraint_xy]
                     )
-                    self.input.control[
-                        "fix___constraintxy"
-                    ] = "constraintxy setforce 0.0 0.0 NULL"
+                    self.input.control["fix___constraintxy"] = (
+                        "constraintxy setforce 0.0 0.0 NULL"
+                    )
                     if self._generic_input["calc_mode"] == "md":
-                        self.input.control[
-                            "velocity___constraintxy"
-                        ] = "set 0.0 0.0 NULL"
+                        self.input.control["velocity___constraintxy"] = (
+                            "set 0.0 0.0 NULL"
+                        )
                 if len(constraint_yz) > 0:
                     self.input.control["group___constraintyz"] = "id " + " ".join(
                         [str(ind) for ind in constraint_yz]
                     )
-                    self.input.control[
-                        "fix___constraintyz"
-                    ] = "constraintyz setforce NULL 0.0 0.0"
+                    self.input.control["fix___constraintyz"] = (
+                        "constraintyz setforce NULL 0.0 0.0"
+                    )
                     if self._generic_input["calc_mode"] == "md":
-                        self.input.control[
-                            "velocity___constraintyz"
-                        ] = "set NULL 0.0 0.0"
+                        self.input.control["velocity___constraintyz"] = (
+                            "set NULL 0.0 0.0"
+                        )
                 if len(constraint_zx) > 0:
                     self.input.control["group___constraintxz"] = "id " + " ".join(
                         [str(ind) for ind in constraint_zx]
                     )
-                    self.input.control[
-                        "fix___constraintxz"
-                    ] = "constraintxz setforce 0.0 NULL 0.0"
+                    self.input.control["fix___constraintxz"] = (
+                        "constraintxz setforce 0.0 NULL 0.0"
+                    )
                     if self._generic_input["calc_mode"] == "md":
-                        self.input.control[
-                            "velocity___constraintxz"
-                        ] = "set 0.0 NULL 0.0"
+                        self.input.control["velocity___constraintxz"] = (
+                            "set 0.0 NULL 0.0"
+                        )
                 if len(constraint_x) > 0:
                     self.input.control["group___constraintx"] = "id " + " ".join(
                         [str(ind) for ind in constraint_x]
                     )
-                    self.input.control[
-                        "fix___constraintx"
-                    ] = "constraintx setforce 0.0 NULL NULL"
+                    self.input.control["fix___constraintx"] = (
+                        "constraintx setforce 0.0 NULL NULL"
+                    )
                     if self._generic_input["calc_mode"] == "md":
-                        self.input.control[
-                            "velocity___constraintx"
-                        ] = "set 0.0 NULL NULL"
+                        self.input.control["velocity___constraintx"] = (
+                            "set 0.0 NULL NULL"
+                        )
                 if len(constraint_y) > 0:
                     self.input.control["group___constrainty"] = "id " + " ".join(
                         [str(ind) for ind in constraint_y]
                     )
-                    self.input.control[
-                        "fix___constrainty"
-                    ] = "constrainty setforce NULL 0.0 NULL"
+                    self.input.control["fix___constrainty"] = (
+                        "constrainty setforce NULL 0.0 NULL"
+                    )
                     if self._generic_input["calc_mode"] == "md":
-                        self.input.control[
-                            "velocity___constrainty"
-                        ] = "set NULL 0.0 NULL"
+                        self.input.control["velocity___constrainty"] = (
+                            "set NULL 0.0 NULL"
+                        )
                 if len(constraint_z) > 0:
                     self.input.control["group___constraintz"] = "id " + " ".join(
                         [str(ind) for ind in constraint_z]
                     )
-                    self.input.control[
-                        "fix___constraintz"
-                    ] = "constraintz setforce NULL NULL 0.0"
+                    self.input.control["fix___constraintz"] = (
+                        "constraintz setforce NULL NULL 0.0"
+                    )
                     if self._generic_input["calc_mode"] == "md":
-                        self.input.control[
-                            "velocity___constraintz"
-                        ] = "set NULL NULL 0.0"
+                        self.input.control["velocity___constraintz"] = (
+                            "set NULL NULL 0.0"
+                        )
 
     @staticmethod
     def _modify_structure_to_allow_requested_deformation(

pyiron_atomistics/lammps/control.py

@@ -816,9 +816,9 @@ def _fix_with_three_vector(self, ids, vector, fix_string, conversion):
                 vector[i] = str(v * conversion)
         name = str(hash(tuple(ids))).replace("-", "m")  # A unique name for the group
         self._set_group_by_id(name, ids)
-        self[
-            "fix___{}_{}".format(fix_string.replace(" ", "_"), name)
-        ] = "{} {} {}".format(name, fix_string, " ".join(vector))
+        self["fix___{}_{}".format(fix_string.replace(" ", "_"), name)] = (
+            "{} {} {}".format(name, fix_string, " ".join(vector))
+        )
 
     def fix_move_linear_by_id(self, ids, velocity):
         """

pyiron_atomistics/lammps/interactive.py

@@ -274,9 +274,9 @@ def function(ptr, timestep, nlocal, ids, x, fexternal):
         if not self.server.run_mode.interactive:
             raise AssertionError("Callback works only in interactive mode")
         self._user_fix_external = _FixExternal(function)
-        self.input.control[
-            "fix___fix_external"
-        ] = "all external pf/callback {} {}".format(n_call, n_apply)
+        self.input.control["fix___fix_external"] = (
+            "all external pf/callback {} {}".format(n_call, n_apply)
+        )
         if overload_internal_fix_external:
             self._user_fix_external.fix_external = function
 

pyiron_atomistics/lammps/potential.py

@@ -26,7 +26,6 @@
 
 
 class LammpsPotential(GenericParameters):
-
     """
     This module helps write commands which help in the control of parameters related to the potential used in LAMMPS
     simulations

pyiron_atomistics/testing/randomatomistic.py

@@ -467,9 +467,7 @@ def _s_r(self):
         return self.input["sigma"] / self.neigh.flattened.distances
 
     def interactive_energy_pot_getter(self):
-        return self.input["epsilon"] * (
-            np.sum(self._s_r**12) - np.sum(self._s_r**6)
-        )
+        return self.input["epsilon"] * (np.sum(self._s_r**12) - np.sum(self._s_r**6))
 
     def interactive_energy_tot_getter(self):
         return (
@@ -479,13 +477,7 @@ 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
         return (
-            (
-                v
-                * self._unit.angstrom**2
-                / self._unit.second**2
-                / 1e-30
-                * self._unit.amu
-            )
+            (v * self._unit.angstrom**2 / self._unit.second**2 / 1e-30 * self._unit.amu)
             .to("eV")
             .magnitude
         )
@@ -529,9 +521,7 @@ def interactive_pressures_getter(self):
             * self._unit.amu
         )
         return (
-            (pot_part + kin_part)
-            / self.structure.get_volume()
-            / self._unit.angstrom**3
+            (pot_part + kin_part) / self.structure.get_volume() / self._unit.angstrom**3
         ).to(self._unit.pascal).magnitude / 1e9
 
     def interactive_stress_getter(self):