pydocstyle D411

Missing blank line before section ('Args')

pymatgen/analysis/chemenv/coordination_environments/coordination_geometries.py

@@ -239,6 +239,7 @@ def safe_separation_permutations(self, ordered_plane=False, ordered_point_groups
         Simple and safe permutations for this separation plane.
 
         This is not meant to be used in production. Default configuration for ChemEnv does not use this method.
+
         Args:
             ordered_plane: Whether the order of the points in the plane can be used to reduce the
                 number of permutations.

pymatgen/analysis/chemenv/coordination_environments/structure_environments.py

@@ -1883,6 +1883,7 @@ def get_site_info_for_specie_allces(self, specie, min_fraction=0.0):
     def get_statistics(self, statistics_fields=DEFAULT_STATISTICS_FIELDS, bson_compatible=False):
         """
         Get the statistics of environments for this structure.
+
         Args:
             statistics_fields: Which statistics to get.
             bson_compatible: Whether to make the dictionary BSON-compatible.
@@ -1974,6 +1975,7 @@ def site_has_clear_environment(self, isite, conditions=None):
     def structure_has_clear_environments(self, conditions=None, skip_none=True, skip_empty=False):
         """
         Whether all sites in a structure have "clear" environments.
+
         Args:
             conditions: Conditions to be checked for an environment to be "clear".
             skip_none: Whether to skip sites for which no environments have been computed.

pymatgen/analysis/chemenv/coordination_environments/voronoi.py

@@ -860,6 +860,7 @@ def dp_func(dp):
     def get_sadf_figure(self, isite, normalized=True, figsize=None, step_function=None):
         """
         Get the Solid Angle Distribution Figure for a given site.
+
         Args:
             isite: Index of the site.
             normalized: Whether to normalize angles.

pymatgen/analysis/diffraction/tem.py

@@ -83,6 +83,7 @@ def wavelength_rel(self) -> float:
         """
         Calculates the wavelength of the electron beam with relativistic kinematic effects taken
             into account.
+
         Args:
             none
         Returns:
@@ -101,6 +102,7 @@ def wavelength_rel(self) -> float:
     def generate_points(coord_left: int = -10, coord_right: int = 10) -> np.ndarray:
         """
         Generates a bunch of 3D points that span a cube.
+
         Args:
             coord_left (int): The minimum coordinate value.
             coord_right (int): The maximum coordinate value.
@@ -119,6 +121,7 @@ def zone_axis_filter(
     ) -> list[tuple[int, int, int]]:
         """
         Filters out all points that exist within the specified Laue zone according to the zone axis rule.
+
         Args:
             points (np.ndarray): The list of points to be filtered.
             laue_zone (int): The desired Laue zone.
@@ -156,6 +159,7 @@ def bragg_angles(
     ) -> dict[tuple[int, int, int], float]:
         """
         Gets the Bragg angles for every hkl point passed in (where n = 1).
+
         Args:
             interplanar_spacings (dict): dictionary of hkl to interplanar spacing
         Returns:
@@ -170,6 +174,7 @@ def bragg_angles(
     def get_s2(self, bragg_angles: dict[tuple[int, int, int], float]) -> dict[tuple[int, int, int], float]:
         """
         Calculates the s squared parameter (= square of sin theta over lambda) for each hkl plane.
+
         Args:
             bragg_angles (dict): The bragg angles for each hkl plane.
         Returns:
@@ -188,6 +193,7 @@ def x_ray_factors(
         """
         Calculates x-ray factors, which are required to calculate atomic scattering factors. Method partially inspired
         by the equivalent process in the xrd module.
+
         Args:
             structure (Structure): The input structure.
             bragg_angles (dict): Dictionary of hkl plane to Bragg angle.
@@ -214,6 +220,7 @@ def electron_scattering_factors(
     ) -> dict[str, dict[tuple[int, int, int], float]]:
         """
         Calculates atomic scattering factors for electrons using the Mott-Bethe formula (1st order Born approximation).
+
         Args:
             structure (Structure): The input structure.
             bragg_angles (dict of 3-tuple to float): The Bragg angles for each hkl plane.
@@ -239,6 +246,7 @@ def cell_scattering_factors(
     ) -> dict[tuple[int, int, int], int]:
         """
         Calculates the scattering factor for the whole cell.
+
         Args:
             structure (Structure): The input structure.
             bragg_angles (dict of 3-tuple to float): The Bragg angles for each hkl plane.
@@ -264,6 +272,7 @@ def cell_intensity(
     ) -> dict[tuple[int, int, int], float]:
         """
         Calculates cell intensity for each hkl plane. For simplicity's sake, take I = |F|**2.
+
         Args:
             structure (Structure): The input structure.
             bragg_angles (dict of 3-tuple to float): The Bragg angles for each hkl plane.
@@ -285,6 +294,7 @@ def get_pattern(
     ) -> pd.DataFrame:
         """
         Returns all relevant TEM DP info in a pandas dataframe.
+
         Args:
             structure (Structure): The input structure.
             scaled (boolean): Required value for inheritance, does nothing in TEM pattern
@@ -322,6 +332,7 @@ def normalized_cell_intensity(
     ) -> dict[tuple[int, int, int], float]:
         """
         Normalizes the cell_intensity dict to 1, for use in plotting.
+
         Args:
             structure (Structure): The input structure.
             bragg_angles (dict of 3-tuple to float): The Bragg angles for each hkl plane.
@@ -344,6 +355,7 @@ def is_parallel(
     ) -> bool:
         """
         Checks if two hkl planes are parallel in reciprocal space.
+
         Args:
             structure (Structure): The input structure.
             plane (3-tuple): The first plane to be compared.
@@ -357,6 +369,7 @@ def is_parallel(
     def get_first_point(self, structure: Structure, points: list) -> dict[tuple[int, int, int], float]:
         """
         Gets the first point to be plotted in the 2D DP, corresponding to maximum d/minimum R.
+
         Args:
             structure (Structure): The input structure.
             points (list): All points to be checked.
@@ -378,6 +391,7 @@ def get_interplanar_angle(structure: Structure, p1: tuple[int, int, int], p2: tu
         """
         Returns the interplanar angle (in degrees) between the normal of two crystal planes.
         Formulas from International Tables for Crystallography Volume C pp. 2-9.
+
         Args:
             structure (Structure): The input structure.
             p1 (3-tuple): plane 1
@@ -434,6 +448,7 @@ def get_plot_coeffs(
         """
         Calculates coefficients of the vector addition required to generate positions for each DP point
         by the Moore-Penrose inverse method.
+
         Args:
             p1 (3-tuple): The first point. Fixed.
             p2 (3-tuple): The second point. Fixed.
@@ -451,6 +466,7 @@ def get_positions(self, structure: Structure, points: list) -> dict[tuple[int, i
         """
         Calculates all the positions of each hkl point in the 2D diffraction pattern by vector addition.
         Distance in centimeters.
+
         Args:
             structure (Structure): The input structure.
             points (list): All points to be checked.
@@ -501,6 +517,7 @@ def get_positions(self, structure: Structure, points: list) -> dict[tuple[int, i
     def tem_dots(self, structure: Structure, points) -> list:
         """
         Generates all TEM_dot as named tuples that will appear on the 2D diffraction pattern.
+
         Args:
             structure (Structure): The input structure.
             points (list): All points to be checked.
@@ -524,6 +541,7 @@ def tem_dots(self, structure: Structure, points) -> list:
     def get_plot_2d(self, structure: Structure) -> go.Figure:
         """
         Generates the 2D diffraction pattern of the input structure.
+
         Args:
             structure (Structure): The input structure.
         Returns:
@@ -602,6 +620,7 @@ def get_plot_2d_concise(self, structure: Structure) -> go.Figure:
         """
         Generates the concise 2D diffraction pattern of the input structure of a smaller size and without layout.
         Does not display.
+
         Args:
             structure (Structure): The input structure.
         Returns:

pymatgen/analysis/ferroelectricity/polarization.py

@@ -96,7 +96,6 @@ def get_total_ionic_dipole(structure, zval_dict):
     center (np.array with shape [3,1]) : dipole center used by VASP
     tiny (float) : tolerance for determining boundary of calculation.
     """
-
     tot_ionic = []
     for site in structure:
         zval = zval_dict[str(site.specie)]
@@ -112,6 +111,7 @@ class PolarizationLattice(Structure):
     def get_nearest_site(self, coords, site, r=None):
         """
         Given coords and a site, find closet site to coords.
+
         Args:
             coords (3x1 array): Cartesian coords of center of sphere
             site: site to find closest to coords

pymatgen/analysis/gb/grain.py

@@ -162,6 +162,7 @@ def get_sorted_structure(self, key=None, reverse=False):
         meaning as in list.sort. By default, sites are sorted by the
         electronegativity of the species. Note that Slab has to override this
         because of the different __init__ args.
+
         Args:
             key: Specifies a function of one argument that is used to extract
                 a comparison key from each list element: key=str.lower. The
@@ -811,6 +812,7 @@ def gb_from_parameters(
     def get_ratio(self, max_denominator=5, index_none=None):
         """
         find the axial ratio needed for GB generator input.
+
         Args:
             max_denominator (int): the maximum denominator for
                 the computed ratio, default to be 5.

pymatgen/analysis/interfaces/zsl.py

@@ -175,6 +175,7 @@ def get_equiv_transformations(self, transformation_sets, film_vectors, substrate
         Applies the transformation_sets to the film and substrate vectors
         to generate super-lattices and checks if they matches.
         Returns all matching vectors sets.
+
         Args:
             transformation_sets(array): an array of transformation sets:
                 each transformation set is an array with the (i,j)

pymatgen/analysis/local_env.py

@@ -3856,6 +3856,7 @@ def molecules_allowed(self):
     def get_nn_info(self, structure: Structure, n: int) -> list[dict]:
         """
         Get all near-neighbor information.
+
         Args:
             structure: (Structure) pymatgen Structure
             n: (int) index of target site
@@ -4071,6 +4072,7 @@ def _semicircle_integral(dist_bins, idx):
         """
         An internal method to get an integral between two bounds of a unit
         semicircle. Used in algorithm to determine bond probabilities.
+
         Args:
             dist_bins: (float) list of all possible bond weights
             idx: (float) index of starting bond weight

pymatgen/analysis/structure_matcher.py

@@ -903,6 +903,7 @@ def _anonymous_match(
     ):
         """
         Tries all permutations of matching struct1 to struct2.
+
         Args:
             struct1, struct2 (Structure): Preprocessed input structures
         Returns:

pymatgen/analysis/structure_prediction/volume_predictor.py

@@ -124,6 +124,7 @@ def get_predicted_structure(self, structure: Structure, ref_structure):
         """
         Given a structure, returns back the structure scaled to predicted
         volume.
+
         Args:
             structure (Structure): structure w/unknown volume
             ref_structure (Structure): A reference structure with a similar
@@ -237,6 +238,7 @@ def get_predicted_structure(self, structure: Structure, icsd_vol=False):
         """
         Given a structure, returns back the structure scaled to predicted
         volume.
+
         Args:
             structure (Structure): structure w/unknown volume
 

pymatgen/analysis/surface_analysis.py

@@ -176,6 +176,7 @@ def gibbs_binding_energy(self, eads=False):
     def surface_energy(self, ucell_entry, ref_entries=None):
         """
         Calculates the surface energy of this SlabEntry.
+
         Args:
             ucell_entry (entry): An entry object for the bulk
             ref_entries (list: [entry]): A list of entries for each type
@@ -419,6 +420,7 @@ def __init__(self, all_slab_entries, ucell_entry, ref_entries=None):
         """
         Object for plotting surface energy in different ways for clean and
             adsorbed surfaces.
+
         Args:
             all_slab_entries (dict or list): Dictionary or list containing
                 all entries for slab calculations. See attributes.
@@ -660,6 +662,7 @@ def get_surface_equilibrium(self, slab_entries, delu_dict=None):
             building surface phase diagrams. Note that to solve for x equations
             (x slab_entries), there must be x free variables (chemical potentials).
             Adjust delu_dict as need be to get the correct number of free variables.
+
         Args:
             slab_entries (array): The coefficients of the first equation
             delu_dict (dict): Dictionary of the chemical potentials to be set as
@@ -1137,6 +1140,7 @@ def BE_vs_clean_SE(
         """
         For each facet, plot the clean surface energy against the most
             stable binding energy.
+
         Args:
             delu_dict (dict): Dictionary of the chemical potentials to be set as
                 constant. Note the key should be a sympy Symbol object of the
@@ -1199,6 +1203,7 @@ def surface_chempot_range_map(
             and determines the chempot rangeo fht e second element for each
             SlabEntry. Future implementation will determine the chempot range
             map first by solving systems of equations up to 3 instead of 2.
+
         Args:
             elements (list): Sequence of elements to be considered as independent
                 variables. E.g., if you want to show the stability ranges of
@@ -1644,6 +1649,7 @@ def is_converged(self, min_points_frac=0.015, tol: float = 0.0025):
             potential within some distance (min_point) about where the peak
             electrostatic potential is found along the c direction of the
             slab. This is dependent on the size of the slab.
+
         Args:
             min_point (fractional coordinates): The number of data points
                 +/- the point of where the electrostatic potential is at

pymatgen/analysis/topological/spillage.py

@@ -20,6 +20,7 @@ class SOCSpillage:
     def __init__(self, wf_noso="", wf_so=""):
         """
         Requires path to WAVECAR files with and without LSORBIT = .TRUE.
+
         Args:
             wf_noso : WAVECAR without spin-orbit coupling
             wf_so : WAVECAR with spin-orbit coupling

pymatgen/apps/battery/battery_abc.py

@@ -246,6 +246,7 @@ def get_sub_electrodes(self, adjacent_only=True):
         If this electrode contains multiple voltage steps, then it is possible
         to use only a subset of the voltage steps to define other electrodes.
         Must be implemented for each electrode object.
+
         Args:
             adjacent_only: Only return electrodes from compounds that are
                 adjacent on the convex hull, i.e. no electrodes returned

pymatgen/command_line/critic2_caller.py

@@ -489,6 +489,7 @@ def structure_graph(self, include_critical_points=("bond", "ring", "cage")):
         """
         A StructureGraph object describing bonding information
         in the crystal.
+
         Args:
             include_critical_points: add DummySpecies for
             the critical points themselves, a list of

pymatgen/core/bonds.py

@@ -80,6 +80,7 @@ def get_bond_order(self, tol: float = 0.2, default_bl: float | None = None) -> f
     def is_bonded(site1, site2, tol: float = 0.2, bond_order: float | None = None, default_bl: float | None = None):
         """
         Test if two sites are bonded, up to a certain limit.
+
         Args:
             site1 (Site): First site
             site2 (Site): Second site

pymatgen/electronic_structure/dos.py

@@ -1255,6 +1255,7 @@ def get_site_orbital_dos(self, site: PeriodicSite, orbital: str) -> Dos:  # type
     def get_site_t2g_eg_resolved_dos(self, site: PeriodicSite) -> dict[str, Dos]:
         """
         Get the t2g, eg projected DOS for a particular site.
+
         Args:
             site: Site in Structure associated with CompleteDos.
 

pymatgen/electronic_structure/plotter.py

@@ -2286,6 +2286,7 @@ def __init__(
     def get_plot(self, bs: BandStructureSymmLine, dos: Dos | CompleteDos | None = None):
         """
         Get a matplotlib plot object.
+
         Args:
             bs (BandStructureSymmLine): the bandstructure to plot. Projection
                 data must exist for projected plots.

pymatgen/io/cif.py

@@ -645,6 +645,7 @@ def get_lattice_no_exception(
     ):
         """
         Generate the lattice from the provided lattice parameters.
+
         Args:
             data:
             length_strings:

pymatgen/io/packmol.py

@@ -44,6 +44,7 @@ class PackmolSet(InputSet):
 
     def run(self, path: str | Path, timeout=30):
         """Run packmol and write out the packed structure.
+
         Args:
             path: The path in which packmol input files are located.
             timeout: Timeout in seconds.