Fix bad use of enumerate(start).

src/pymatgen/analysis/graphs.py

@@ -2419,8 +2419,8 @@ def find_rings(self, including=None) -> list[list[tuple[int, int]]]:
 
         for cycle in cycles_nodes:
             edges = []
-            for _, itm in enumerate(cycle, start=-1):
-                edges.append((itm, itm))
+            for idx, itm in enumerate(cycle):
+                edges.append((itm, cycle[idx - 1]))
             cycles_edges.append(edges)
 
         return cycles_edges

src/pymatgen/core/structure.py

@@ -3460,12 +3460,13 @@ def find_nn_pos_before_site(site_idx: int):
         output = []
         output_var = []
         for idx, site in enumerate(self):
+            sp = site.specie
             if idx == 0:
-                output.append(f"{site.specie}")
+                output.append(f"{sp}")
             elif idx == 1:
                 nn = find_nn_pos_before_site(idx)
                 bond_length = self.get_distance(idx, nn[0])
-                output.append(f"{site.specie} {nn[0] + 1} B{idx}")
+                output.append(f"{sp} {nn[0] + 1} B{idx}")
                 output_var.append(f"B{idx}={bond_length:.6f}")
             elif idx == 2:
                 nn = find_nn_pos_before_site(idx)
@@ -3478,7 +3479,7 @@ def find_nn_pos_before_site(site_idx: int):
                 bond_length = self.get_distance(idx, nn[0])
                 angle = self.get_angle(idx, nn[0], nn[1])
                 dih = self.get_dihedral(idx, nn[0], nn[1], nn[2])
-                output.append(f"{site.specie} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx} {nn[2] + 1} D{idx}")
+                output.append(f"{sp} {nn[0] + 1} B{idx} {nn[1] + 1} A{idx} {nn[2] + 1} D{idx}")
                 output_var.extend((f"B{idx}={bond_length:.6f}", f"A{idx}={angle:.6f}", f"D{idx}={dih:.6f}"))
         return "\n".join(output) + "\n\n" + "\n".join(output_var)
 

src/pymatgen/io/cp2k/inputs.py

@@ -2530,9 +2530,9 @@ def from_str(cls, string: str) -> Self:
             data["nlcc"] = True
         if "GTH" in string:
             data["potential_type"] = "GTH"
-        for idx, char in enumerate(string, start=1):
-            if char == "Q" and char.isnumeric():
-                data["electrons"] = int("".join(_ for _ in string[idx:] if _.isnumeric()))
+        for idx, char in enumerate(string):
+            if char == "Q" and string[idx + 1].isnumeric():
+                data["electrons"] = int("".join(_ for _ in string[(idx + 1) :] if _.isnumeric()))
 
         for x in ("LDA", "PADA", "MGGA", "GGA", "HF", "PBE0", "PBE", "BP", "BLYP", "B3LYP", "SCAN"):
             if x in string:

src/pymatgen/io/lmto.py

@@ -181,13 +181,13 @@ def from_str(cls, data: str, sigfigs: int = 8) -> Self:
 
         for cat in ["STRUC", "CLASS", "SITE"]:
             fields = struct_lines[cat].split("=")
-            for idx, field in enumerate(fields, start=1):
+            for idx, field in enumerate(fields):
                 token = field.split()[-1]
                 if token == "ALAT":
-                    a_lat = round(float(fields[idx].split()[0]), sigfigs)
+                    a_lat = round(float(fields[idx + 1].split()[0]), sigfigs)
                     structure_tokens["ALAT"] = a_lat
                 elif token == "ATOM":
-                    atom = fields[idx].split()[0]
+                    atom = fields[idx + 1].split()[0]
                     if not bool(re.match("E[0-9]*$", atom)):
                         if cat == "CLASS":
                             structure_tokens["CLASS"].append(atom)
@@ -197,9 +197,9 @@ def from_str(cls, data: str, sigfigs: int = 8) -> Self:
                         pass
                 elif token in ["PLAT", "POS"]:
                     try:
-                        arr = np.array([round(float(i), sigfigs) for i in field.split()])
+                        arr = np.array([round(float(i), sigfigs) for i in fields[idx + 1].split()])
                     except ValueError:
-                        arr = np.array([round(float(i), sigfigs) for i in fields[idx].split()[:-1]])
+                        arr = np.array([round(float(i), sigfigs) for i in fields[idx + 1].split()[:-1]])
                     if token == "PLAT":
                         structure_tokens["PLAT"] = arr.reshape([3, 3])
                     elif not bool(re.match("E[0-9]*$", atom)):

src/pymatgen/io/xtb/inputs.py

@@ -80,11 +80,11 @@ def constrains_template(molecule, reference_fnm, constraints) -> str:
         atoms_for_mtd = [idx for idx in range(1, len(mol) + 1) if idx not in atoms_to_constrain]
         # Write as 1-3,5 instead of 1,2,3,5
         interval_list = [atoms_for_mtd[0]]
-        for idx, val in enumerate(atoms_for_mtd, start=1):
+        for idx, val in enumerate(atoms_for_mtd):
             if val + 1 not in atoms_for_mtd:
                 interval_list.append(val)
                 if idx != len(atoms_for_mtd):
-                    interval_list.append(val)
+                    interval_list.append(atoms_for_mtd[idx + 1])
         allowed_mtd_string = ",".join(
             [f"{interval_list[i]}-{interval_list[i + 1]}" for i in range(len(interval_list)) if i % 2 == 0]
         )

src/pymatgen/symmetry/kpath.py

@@ -1480,15 +1480,15 @@ def _get_key_lines(key_points, bz_as_key_point_inds):
             # not the face center point (don't need to check it since it's not
             # shared with other facets)
             face_center_ind = facet_as_key_point_inds[-1]
-            for j, ind in enumerate(facet_as_key_point_inds_bndy, start=-1):
+            for j, ind in enumerate(facet_as_key_point_inds_bndy):
                 if (
-                    min(ind, ind),
-                    max(ind, ind),
+                    min(ind, facet_as_key_point_inds_bndy[j - 1]),
+                    max(ind, facet_as_key_point_inds_bndy[j - 1]),
                 ) not in key_lines:
                     key_lines.append(
                         (
-                            min(ind, ind),
-                            max(ind, ind),
+                            min(ind, facet_as_key_point_inds_bndy[j - 1]),
+                            max(ind, facet_as_key_point_inds_bndy[j - 1]),
                         )
                     )
                 k = j + 2 if j != len(facet_as_key_point_inds_bndy) - 2 else 0