v2.9.8 release.

Former-commit-id: b4c3fe59195799373fe7e99f9260c09794eb1e2c [formerly 8825973]
Former-commit-id: 469a22220bc99b4f381328983226b8e366a74923

Author: shyuep

docs/pymatgen.analysis.diffraction.rst

@@ -0,0 +1,28 @@
+pymatgen.analysis.diffraction package
+=====================================
+
+Subpackages
+-----------
+
+.. toctree::
+
+
+Submodules
+----------
+
+pymatgen.analysis.diffraction.xrd module
+----------------------------------------
+
+.. automodule:: pymatgen.analysis.diffraction.xrd
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pymatgen.analysis.diffraction
+    :members:
+    :undoc-members:
+    :show-inheritance:

pymatgen/analysis/diffraction/xrd.py

@@ -93,9 +93,7 @@ def get_xrd_data(self, structure):
             structure: Input structure
 
         Returns:
-            {XRD data} in the form of [
-                [two_theta, scaled_intensity, [h, k, l]]
-            ]
+            {XRD data} in the form of [[two_theta, scaled_intensity, [h, k, l]]]
         """
         if self.symprec:
             finder = SymmetryFinder(structure, symprec=self.symprec)

pymatgen/analysis/diffusion_analyzer.py

@@ -271,7 +271,7 @@ def from_structures(cls, structures, specie, temperature,
                 MSD vs dt. Weights are proportional to 1/dt, since the
                 number of observations are also proportional to 1/dt (and
                 hence the variance is proportional to dt)
-            """
+        """
         structure = structures[0]
 
         p = [np.array(s.frac_coords)[:, None] for s in structures]
@@ -446,7 +446,7 @@ def _get_vasprun(args):
 def get_extrapolated_diffusivity(temps, diffusivities, new_temp):
     """
     Returns (Arrhenius) extrapolated diffusivity at new_temp
-    
+
     Args:
         temps ([float]): A sequence of temperatures. units: K
         diffusivities ([float]): A sequence of diffusivities (e.g.,
@@ -468,13 +468,13 @@ def get_extrapolated_conductivity(temps, diffusivities, new_temp, structure,
                                   species):
     """
     Returns extrapolated mS/cm conductivity.
-    
+
     Args:
         temps ([float]): A sequence of temperatures. units: K
         diffusivities ([float]): A sequence of diffusivities (e.g.,
             from DiffusionAnalyzer.diffusivity). units: cm^2/s
         new_temp (float): desired temperature. units: K
-        structure (structure): structure used for the diffusivity calculation 
+        structure (structure): structure used for the diffusivity calculation
         species (string/Specie): conducting species
 
     Returns:
@@ -513,7 +513,7 @@ def get_arrhenius_plot(temps, diffusivities, **kwargs):
     # out in base 10 for easier reading of the diffusivity scale,
     # but the Arrhenius relationship is in base e).
     actv_energy = - w[0] * phyc.k_b / phyc.e * 1e6 * math.log(10)
-    plt.text(0.6, 0.85, "E$_a$ = {:.0f} meV".format(actv_energy), 
+    plt.text(0.6, 0.85, "E$_a$ = {:.0f} meV".format(actv_energy),
              fontsize=30, transform=plt.axes().transAxes)
     plt.ylabel("log(D (cm$^2$/s))")
     plt.xlabel("1000/T (K$^{-1}$)")

pymatgen/electronic_structure/bandstructure.py

@@ -480,10 +480,9 @@ def get_band_gap(self):
 
         Returns:
             A dict {"energy","direct","transition"}:
-            - "energy": band gap energy
-            - "direct": A boolean telling if the gap is direct (True)
-              or not (False)
-            - "transition": kpoint labels of the transition (e.g., "\Gamma-X")
+            "energy": band gap energy
+            "direct": A boolean telling if the gap is direct or not
+            "transition": kpoint labels of the transition (e.g., "\Gamma-X")
         """
         if self.is_metal():
             return {"energy": 0.0, "direct": False, "transition": None}

pymatgen/io/vaspio/vasp_output.py

@@ -129,6 +129,7 @@ class Vasprun(object):
         in VASP).
 
     .. attribute:: dielectric
+
         The real and imaginary part of the dielectric constant (e.g., computed
         by RPA) in function of the energy (frequency). Optical properties (e.g.
         absorption coefficient) can be obtained through this.
@@ -138,11 +139,13 @@ class Vasprun(object):
         real_partyz,real_partxz]],[[imag_partxx,imag_partyy,imag_partzz,
         imag_partxy, imag_partyz, imag_partxz]])
 
-    .. atribute:: epsilon_static
+    .. attribute:: epsilon_static
+
         The static part of the dielectric constant. Present when it's a DFPT run
         (LEPSILON=TRUE)
 
     .. attribute:: nionic_steps
+
         The total number of ionic steps. This number is always equal
         to the total number of steps in the actual run even if
         ionic_step_skip is used.

pymatgen/io/vaspio_set.py

@@ -853,15 +853,17 @@ def __init__(self, user_incar_settings=None, ionic=True):
 class MPBSHSEVaspInputSet(DictVaspInputSet):
     """
     Implementation of a VaspInputSet for HSE band structure computations
-    Remember that HSE band structures cannot be non-self consistent. So, a band structure
-    along syymetry lines for instance needs a uniform grid with appropriate weights + weight 0
-    path in reciprocal space
+    Remember that HSE band structures cannot be non-self consistent. So, a band
+    structure along syymetry lines for instance needs a uniform grid with
+    appropriate weights + weight 0 path in reciprocal space
+
     Args:
         user_incar_settings(dict): A dict specifying additional incar
             settings
-        added_kpoints: a list of kpoints (list of 3 number list) with weight 0 added to the run.
-            The k-points are in fractional coordinates
-        kpoints_density: the kpoint density of the uniform grid used for the band structure run
+        added_kpoints: a list of kpoints (list of 3 number list) with weight 0
+            added to the run. The k-points are in fractional coordinates
+        kpoints_density: the kpoint density of the uniform grid used for the
+            band structure run
         mode: Line: Generate k-points along symmetry lines for
             bandstructure. Uniform: Generate uniform k-points grid