Merge branch 'master' into symmetrized_structure_as_dict_monsable

src/pymatgen/analysis/local_env.py

@@ -3745,23 +3745,23 @@ def get_nn_info(self, structure: Structure, n: int):
 
         if self.use_fictive_radius:
             # calculate fictive ionic radii
-            firs = [_get_fictive_ionic_radius(site, neighbor) for neighbor in neighbors]
+            fict_ionic_radii = [_get_fictive_ionic_radius(site, neighbor) for neighbor in neighbors]
         else:
             # just use the bond distance
-            firs = [neighbor.nn_distance for neighbor in neighbors]
+            fict_ionic_radii = [neighbor.nn_distance for neighbor in neighbors]
 
         # calculate mean fictive ionic radius
-        mefir = _get_mean_fictive_ionic_radius(firs)
+        mefir = _get_mean_fictive_ionic_radius(fict_ionic_radii)
 
         # iteratively solve MEFIR; follows equation 4 in Hoppe's EconN paper
         prev_mefir = float("inf")
         while abs(prev_mefir - mefir) > 1e-4:
             # this is guaranteed to converge
             prev_mefir = mefir
-            mefir = _get_mean_fictive_ionic_radius(firs, minimum_fir=mefir)
+            mefir = _get_mean_fictive_ionic_radius(fict_ionic_radii, minimum_fir=mefir)
 
         siw = []
-        for nn, fir in zip(neighbors, firs, strict=True):
+        for nn, fir in zip(neighbors, fict_ionic_radii, strict=True):
             if nn.nn_distance < self.cutoff:
                 w = math.exp(1 - (fir / mefir) ** 6)
                 if w > self.tol:

src/pymatgen/electronic_structure/dos.py

@@ -107,9 +107,12 @@ def get_interpolated_gap(
         energies = self.x
         below_fermi = [i for i in range(len(energies)) if energies[i] < self.efermi and tdos[i] > tol]
         above_fermi = [i for i in range(len(energies)) if energies[i] > self.efermi and tdos[i] > tol]
+        if not below_fermi or not above_fermi:
+            return 0.0, self.efermi, self.efermi
+
         vbm_start = max(below_fermi)
         cbm_start = min(above_fermi)
-        if vbm_start == cbm_start:
+        if vbm_start in [cbm_start, cbm_start - 1]:
             return 0.0, self.efermi, self.efermi
 
         # Interpolate between adjacent values
@@ -311,7 +314,7 @@ def get_interpolated_gap(
 
         vbm_start = max(below_fermi)
         cbm_start = min(above_fermi)
-        if vbm_start == cbm_start:
+        if vbm_start in [cbm_start, cbm_start - 1]:
             return 0.0, self.efermi, self.efermi
 
         # Interpolate between adjacent values

src/pymatgen/io/vasp/sets.py

@@ -2663,7 +2663,8 @@ def kpoints_updates(self) -> Kpoints:
 
 
 class NEBSet(VaspInputSet):
-    """Write NEB inputs.
+    """An input set for NEB calculations. These are based on NEB parameters that have been extensively tested by the
+    Materials Virtual Lab.
 
     Note that EDIFF is not on a per atom basis for this input set.
     """
@@ -2695,11 +2696,19 @@ def __init__(
 
         # NEB specific defaults
         defaults = {
+            "EDIFF": 5e-5,
+            "EDIFFG": -0.02,
             "IMAGES": len(structures) - 2,
-            "IBRION": 1,
             "ISYM": 0,
+            "ISIF": 2,
             "LCHARG": False,
             "LDAU": False,
+            "LORBIT": 0,
+            "NSW": 200,
+            "ALGO": "Normal",
+            "IBRION": 3,
+            "IOPT": 1,
+            "POTIM": 0,
         }
         self._config_dict["INCAR"].update(defaults)
         self.parent_set = parent_set
@@ -2799,24 +2808,11 @@ def __init__(self, structures: list[Structure], **kwargs) -> None:
         """
         user_incar_settings = kwargs.get("user_incar_settings", {})
 
-        # CI-NEB settings
+        # Additional CI-NEB settings
         defaults = {
-            "EDIFF": 5e-5,
-            "EDIFFG": -0.02,
-            "IBRION": 3,
             "ICHAIN": 0,
-            "IOPT": 1,
-            "ISIF": 2,
-            "ISMEAR": 0,
-            "ISPIN": 2,
-            "LCHARG": False,
             "LCLIMB": True,
-            "LDAU": False,
-            "LORBIT": 0,
-            "NSW": 200,
-            "POTIM": 0,
             "SPRING": -5,
-            "ALGO": "Normal",
         }
         if user_incar_settings != {}:
             defaults.update(user_incar_settings)

src/pymatgen/util/coord.py

@@ -135,7 +135,7 @@ def get_linear_interpolated_value(x_values: ArrayLike, y_values: ArrayLike, x: f
     """
     arr = np.array(sorted(zip(x_values, y_values, strict=True), key=lambda d: d[0]))
 
-    indices = np.where(arr[:, 0] >= x)[0]
+    indices = np.where(arr[:, 0] > x)[0]
 
     if len(indices) == 0 or indices[0] == 0:
         raise ValueError(f"{x=} is out of range of provided x_values ({min(x_values)}, {max(x_values)})")

tests/io/vasp/test_sets.py

@@ -1342,7 +1342,9 @@ def test_incar(self):
         incar = self.vis.incar
         assert "LDAUU" not in incar
         assert incar["EDIFF"] == approx(0.00005)
-        assert self.vis_MIT.incar["EDIFF"] == approx(0.00001)
+        assert self.vis_MIT.incar["EDIFF"] == approx(0.00005)
+        assert incar["NSW"] == 200
+        assert incar["IBRION"] == 3
         assert "LCLIMB" in self.vis_cineb.incar
 
     def test_kpoints(self):

tests/util/test_coord.py

@@ -19,6 +19,11 @@ def test_get_linear_interpolated_value(self):
         with pytest.raises(ValueError, match=r"x=6 is out of range of provided x_values \(0, 5\)"):
             coord.get_linear_interpolated_value(x_vals, y_vals, 6)
 
+        # test when x is equal to first value in x_vals (previously broke, fixed in #4299):
+        assert coord.get_linear_interpolated_value(x_vals, y_vals, 0) == approx(3)
+        with pytest.raises(ValueError, match=r"x=-0.5 is out of range of provided x_values \(0, 5\)"):
+            coord.get_linear_interpolated_value(x_vals, y_vals, -0.5)
+
     def test_in_coord_list(self):
         coords = [[0, 0, 0], [0.5, 0.5, 0.5]]
         test_coord = [0.1, 0.1, 0.1]