fix io, phonon and symmetry

src/pymatgen/io/abinit/abitimer.py

@@ -114,7 +114,7 @@ def parse(self, filenames):
         read_ok = []
         for filename in filenames:
             try:
-                file = open(filename)  # noqa: SIM115
+                file = open(filename, encoding="utf-8")  # noqa: SIM115
             except OSError:
                 logger.warning(f"Cannot open file {filename}")
                 continue
@@ -684,7 +684,7 @@ def to_csv(self, fileobj=sys.stdout):
         is_str = isinstance(fileobj, str)
 
         if is_str:
-            fileobj = open(fileobj, mode="w")  # noqa: SIM115
+            fileobj = open(fileobj, mode="w", encoding="utf-8")  # noqa: SIM115
 
         for idx, section in enumerate(self.sections):
             fileobj.write(section.to_csvline(with_header=(idx == 0)))

src/pymatgen/io/abinit/inputs.py

@@ -617,7 +617,7 @@ def write(self, filepath="run.abi"):
         os.makedirs(dirname, exist_ok=True)
 
         # Write the input file.
-        with open(filepath, mode="w") as file:
+        with open(filepath, mode="w", encoding="utf-8") as file:
             file.write(str(self))
 
     def deepcopy(self):

src/pymatgen/io/adf.py

@@ -551,7 +551,7 @@ def write_file(self, molecule, inp_file):
                 unres_block = AdfKey("Unrestricted")
                 mol_blocks.append(unres_block)
 
-        with open(inp_file, "w+") as file:
+        with open(inp_file, "w+", encoding="utf-8") as file:
             for block in mol_blocks:
                 file.write(str(block) + "\n")
             file.write(str(self.task) + "\n")
@@ -656,7 +656,7 @@ def _parse_logfile(self, logfile):
                     return
                 break
 
-        with open(logfile) as file:
+        with open(logfile, encoding="utf-8") as file:
             for line in file:
                 if match := error_patt.search(line):
                     self.is_failed = True

src/pymatgen/io/aims/inputs.py

@@ -213,7 +213,7 @@ def write_file(self, directory: str | Path | None = None, overwrite: bool = Fals
         if not overwrite and file_name.exists():
             raise ValueError(f"geometry.in file exists in {directory}")
 
-        with open(f"{directory}/geometry.in", mode="w") as file:
+        with open(f"{directory}/geometry.in", mode="w", encoding="utf-8") as file:
             file.write(self.get_header(file_name.as_posix()))
             file.write(self.content)
             file.write("\n")
@@ -665,7 +665,7 @@ def write_file(
 
         content = self.get_content(structure, verbose_header)
 
-        with open(f"{directory}/control.in", mode="w") as file:
+        with open(f"{directory}/control.in", mode="w", encoding="utf-8") as file:
             file.write(f"#{'=' * 72}\n")
             file.write(f"# FHI-aims geometry file: {directory}/geometry.in\n")
             file.write("# File generated from pymatgen\n")

src/pymatgen/io/aims/parsers.py

@@ -1137,7 +1137,7 @@ def read_aims_header_info(
             with gzip.open(filename, mode="rt") as file:
                 content = file.read()
         else:
-            with open(filename) as file:
+            with open(filename, encoding="utf-8") as file:
                 content = file.read()
 
     if content is None:
@@ -1196,7 +1196,7 @@ def read_aims_output(
             with gzip.open(path, mode="rt") as file:
                 content = file.read()
         else:
-            with open(path) as file:
+            with open(path, encoding="utf-8") as file:
                 content = file.read()
 
     if content is None:

src/pymatgen/io/aims/sets/base.py

@@ -250,7 +250,7 @@ def _read_previous(
             # Should be checked with Fireworks, will not for sure work with
             # jobflow_remote)
             split_prev_dir = str(prev_dir).split(":")[-1]
-            with open(f"{split_prev_dir}/parameters.json") as param_file:
+            with open(f"{split_prev_dir}/parameters.json", encoding="utf-8") as param_file:
                 prev_params = json.load(param_file, cls=MontyDecoder)
 
             try:

src/pymatgen/io/feff/sets.py

@@ -104,10 +104,10 @@ def write_input(self, output_dir=".", make_dir_if_not_present=True):
         )
 
         for k, v in feff.items():
-            with open(os.path.join(output_dir, k), mode="w") as file:
+            with open(os.path.join(output_dir, k), mode="w", encoding="utf-8") as file:
                 file.write(str(v))
 
-        with open(f"{output_dir}/feff.inp", mode="w") as file:
+        with open(f"{output_dir}/feff.inp", mode="w", encoding="utf-8") as file:
             file.write(feff_input)
 
         # write the structure to CIF file

src/pymatgen/io/lammps/utils.py

@@ -305,7 +305,7 @@ def run(self, site_property: str | None = None) -> Molecule:
         with tempfile.TemporaryDirectory() as scratch_dir:
             self._write_input(input_dir=scratch_dir)
             with (
-                open(os.path.join(scratch_dir, self.input_file)) as packmol_input,
+                open(os.path.join(scratch_dir, self.input_file), encoding="utf-8") as packmol_input,
                 Popen(self.packmol_bin, stdin=packmol_input, stdout=PIPE, stderr=PIPE) as proc,
             ):
                 stdout, stderr = proc.communicate()

src/pymatgen/io/multiwfn.py

@@ -180,7 +180,7 @@ def get_qtaim_descs(file: PathLike) -> dict[str, dict[str, Any]]:
     cp_sections = list()
     descriptors = dict()
 
-    with open(file) as f:
+    with open(file, encoding="utf-8") as f:
         lines = f.readlines()
         lines = [line[:-1] for line in lines]
 

src/pymatgen/io/pwmat/inputs.py

@@ -136,7 +136,7 @@ def get_types(self) -> np.ndarray:
         """
         content = "POSITION"
         idx_row = LineLocator.locate_all_lines(file_path=self.atom_config_path, content=content)[0]
-        with open(self.atom_config_path) as file:
+        with open(self.atom_config_path, encoding="utf-8") as file:
             atom_config_content = file.readlines()
         atomic_numbers_content = atom_config_content[idx_row : idx_row + self.n_atoms]
         atomic_numbers_lst = [int(row.split()[0]) for row in atomic_numbers_content]  # convert str to int
@@ -151,7 +151,7 @@ def get_coords(self) -> np.ndarray:
         coords_lst: list[np.ndarray] = []
         content: str = "POSITION"
         idx_row: int = LineLocator.locate_all_lines(file_path=self.atom_config_path, content=content)[0]
-        with open(self.atom_config_path) as file:
+        with open(self.atom_config_path, encoding="utf-8") as file:
             atom_config_content = file.readlines()
         """
         row_content:
@@ -174,7 +174,7 @@ def get_magmoms(self) -> np.ndarray:
         try:  # Error: not containing magmoms info.
             idx_row = LineLocator.locate_all_lines(file_path=self.atom_config_path, content=content)[-1]
 
-            with open(self.atom_config_path) as file:
+            with open(self.atom_config_path, encoding="utf-8") as file:
                 atom_config_content = file.readlines()
 
             magnetic_moments_content = atom_config_content[idx_row : idx_row + self.n_atoms]

src/pymatgen/io/qchem/outputs.py

@@ -666,7 +666,7 @@ def multiple_outputs_from_file(filename, keep_sub_files=True):
         if text[0] == "":
             text = text[1:]
         for i, sub_text in enumerate(text):
-            with open(f"{filename}.{i}", mode="w") as temp:
+            with open(f"{filename}.{i}", mode="w", encoding="utf-8") as temp:
                 temp.write(sub_text)
             tempOutput = QCOutput(f"{filename}.{i}")
             to_return.append(tempOutput)

src/pymatgen/io/xtb/inputs.py

@@ -56,7 +56,7 @@ def write_input_files(self):
                 reference_fnm=self.coords_filename,
                 constraints=self.constraints,
             )
-            with open(".constrains", mode="w") as file:
+            with open(".constrains", mode="w", encoding="utf-8") as file:
                 file.write(constrains_string)
 
     @staticmethod

src/pymatgen/phonon/thermal_displacements.py

@@ -220,7 +220,7 @@ def write_cif(self, filename: str) -> None:
         writer.write_file(filename)
         # This will simply append the thermal displacement part to the CIF from the CifWriter
         # In the long run, CifWriter could be extended to handle thermal displacement matrices
-        with open(filename, mode="a") as file:
+        with open(filename, mode="a", encoding="utf-8") as file:
             file.write("loop_ \n")
             file.write("_atom_site_aniso_label\n")
             file.write("_atom_site_aniso_U_11\n")

src/pymatgen/symmetry/maggroups.py

@@ -560,5 +560,5 @@ def _write_all_magnetic_space_groups_to_file(filename):
     all_msgs = list(map(MagneticSpaceGroup, range(1, 1652)))
     for msg in all_msgs:
         out += f"\n{msg.data_str()}\n\n--------\n"
-    with open(filename, mode="w") as file:
+    with open(filename, mode="w", encoding="utf-8") as file:
         file.write(out)