From 0457c445de26e0bd5b78ac3ff77db07ad40bb1e6 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sat, 7 Dec 2024 19:08:01 +0800
Subject: [PATCH 01/14] explicit mode for zopen

---
 src/pymatgen/apps/borg/hive.py         |  2 +-
 src/pymatgen/core/structure.py         |  4 ++--
 src/pymatgen/io/cif.py                 |  2 +-
 src/pymatgen/io/common.py              |  2 +-
 src/pymatgen/io/cp2k/utils.py          |  2 +-
 src/pymatgen/io/feff/inputs.py         |  2 +-
 src/pymatgen/io/feff/outputs.py        |  6 +++---
 src/pymatgen/io/fiesta.py              | 10 +++++-----
 src/pymatgen/io/gaussian.py            | 10 +++++-----
 src/pymatgen/io/lammps/generators.py   |  2 +-
 src/pymatgen/io/lobster/inputs.py      |  2 +-
 src/pymatgen/io/nwchem.py              |  6 +++---
 src/pymatgen/io/qchem/outputs.py       |  2 ++
 src/pymatgen/io/res.py                 |  4 ++--
 src/pymatgen/io/template.py            |  2 +-
 src/pymatgen/io/vasp/outputs.py        |  2 +-
 src/pymatgen/io/zeopp.py               |  4 ++--
 tests/electronic_structure/test_dos.py |  2 +-
 tests/io/qchem/test_utils.py           |  1 +
 tests/io/vasp/test_outputs.py          |  2 +-
 20 files changed, 36 insertions(+), 33 deletions(-)

diff --git a/src/pymatgen/apps/borg/hive.py b/src/pymatgen/apps/borg/hive.py
index 932aa1ec7ce..a46f190b3b0 100644
--- a/src/pymatgen/apps/borg/hive.py
+++ b/src/pymatgen/apps/borg/hive.py
@@ -443,7 +443,7 @@ def _get_transformation_history(path: PathLike):
     """Check for a transformations.json* file and return the history."""
     if trans_json := glob(f"{path!s}/transformations.json*"):
         try:
-            with zopen(trans_json[0]) as file:
+            with zopen(trans_json[0], mode="rt") as file:
                 return json.load(file)["history"]
         except Exception:
             return None
diff --git a/src/pymatgen/core/structure.py b/src/pymatgen/core/structure.py
index 8e46793c837..2a469929e76 100644
--- a/src/pymatgen/core/structure.py
+++ b/src/pymatgen/core/structure.py
@@ -2994,7 +2994,7 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
 
             geom_in = AimsGeometryIn.from_structure(self)
             if filename:
-                with zopen(filename, mode="w") as file:
+                with zopen(filename, mode="wt") as file:
                     file.write(geom_in.get_header(filename))
                     file.write(geom_in.content)
                     file.write("\n")
@@ -4009,7 +4009,7 @@ def from_file(cls, filename: PathLike) -> Self | None:
         """
         filename = str(filename)
 
-        with zopen(filename) as file:
+        with zopen(filename, mode="rt") as file:
             contents = file.read()
         fname = filename.lower()
         if fnmatch(fname, "*.xyz*"):
diff --git a/src/pymatgen/io/cif.py b/src/pymatgen/io/cif.py
index 60377486900..235509f805b 100644
--- a/src/pymatgen/io/cif.py
+++ b/src/pymatgen/io/cif.py
@@ -1761,5 +1761,5 @@ def write_file(
         mode: Literal["w", "a", "wt", "at"] = "w",
     ) -> None:
         """Write the CIF file."""
-        with zopen(filename, mode=mode) as file:
+        with zopen(filename, mode=mode) as file:  # DEBUG: bad default value
             file.write(str(self))
diff --git a/src/pymatgen/io/common.py b/src/pymatgen/io/common.py
index b2445b9c356..a40afb7608c 100644
--- a/src/pymatgen/io/common.py
+++ b/src/pymatgen/io/common.py
@@ -526,7 +526,7 @@ def __getitem__(self, item):
             f"No parser defined for {item}. Contents are returned as a string.",
             UserWarning,
         )
-        with zopen(fpath, "rt") as f:
+        with zopen(fpath, mode="rt") as f:
             return f.read()
 
     def get_files_by_name(self, name: str) -> dict[str, Any]:
diff --git a/src/pymatgen/io/cp2k/utils.py b/src/pymatgen/io/cp2k/utils.py
index 7eca9758a73..9c800cb6803 100644
--- a/src/pymatgen/io/cp2k/utils.py
+++ b/src/pymatgen/io/cp2k/utils.py
@@ -80,7 +80,7 @@ def preprocessor(data: str, dir: str = ".") -> str:  # noqa: A002
             raise ValueError(f"length of inc should be 2, got {len(inc)}")
         inc = inc[1].strip("'")
         inc = inc.strip('"')
-        with zopen(os.path.join(dir, inc)) as file:
+        with zopen(os.path.join(dir, inc), mode="rt") as file:
             data = re.sub(rf"{incl}", file.read(), data)
     variable_sets = re.findall(r"(@SET.+)", data, re.IGNORECASE)
     for match in variable_sets:
diff --git a/src/pymatgen/io/feff/inputs.py b/src/pymatgen/io/feff/inputs.py
index 1b3a11571fc..13c2a83c4f0 100644
--- a/src/pymatgen/io/feff/inputs.py
+++ b/src/pymatgen/io/feff/inputs.py
@@ -246,7 +246,7 @@ def header_string_from_file(filename: str = "feff.inp"):
         Returns:
             Reads header string.
         """
-        with zopen(filename, mode="r") as file:
+        with zopen(filename, mode="rt") as file:
             lines = file.readlines()
             feff_header_str = []
             ln = 0
diff --git a/src/pymatgen/io/feff/outputs.py b/src/pymatgen/io/feff/outputs.py
index 16a0de3567d..9e31051ae4b 100644
--- a/src/pymatgen/io/feff/outputs.py
+++ b/src/pymatgen/io/feff/outputs.py
@@ -70,7 +70,7 @@ def from_file(cls, feff_inp_file: str = "feff.inp", ldos_file: str = "ldos") ->
             dos_index = 1
             begin = 0
 
-            with zopen(pot_inp, mode="r") as potfile:
+            with zopen(pot_inp, mode="rt") as potfile:
                 for line in potfile:
                     if len(pot_read_end.findall(line)) > 0:
                         break
@@ -95,7 +95,7 @@ def from_file(cls, feff_inp_file: str = "feff.inp", ldos_file: str = "ldos") ->
             dicts = Potential.pot_dict_from_str(pot_string)
             pot_dict = dicts[0]
 
-        with zopen(f"{ldos_file}00.dat", mode="r") as file:
+        with zopen(f"{ldos_file}00.dat", mode="rt") as file:
             lines = file.readlines()
         e_fermi = float(lines[0].split()[4])
 
@@ -172,7 +172,7 @@ def charge_transfer_from_file(feff_inp_file, ldos_file):
             pot_inp = re.sub(r"feff.inp", r"pot.inp", feff_inp_file)
             pot_readstart = re.compile(".*iz.*lmaxsc.*xnatph.*xion.*folp.*")
             pot_readend = re.compile(".*ExternalPot.*switch.*")
-            with zopen(pot_inp, mode="r") as potfile:
+            with zopen(pot_inp, mode="rt") as potfile:
                 for line in potfile:
                     if len(pot_readend.findall(line)) > 0:
                         break
diff --git a/src/pymatgen/io/fiesta.py b/src/pymatgen/io/fiesta.py
index df647a600fa..98643d16279 100644
--- a/src/pymatgen/io/fiesta.py
+++ b/src/pymatgen/io/fiesta.py
@@ -214,7 +214,7 @@ def __init__(self, filename):
         """
         self.filename = filename
 
-        with zopen(filename) as file:
+        with zopen(filename, mode="rt") as file:
             basis_set = file.read()
 
         self.data = self._parse_file(basis_set)
@@ -533,7 +533,7 @@ def write_file(self, filename: str | Path) -> None:
         Args:
             filename: Filename.
         """
-        with zopen(filename, mode="w") as file:
+        with zopen(filename, mode="wt") as file:
             file.write(str(self))
 
     def as_dict(self):
@@ -712,7 +712,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             FiestaInput object
         """
-        with zopen(filename) as file:
+        with zopen(filename, mode="rt") as file:
             return cls.from_str(file.read())
 
 
@@ -730,7 +730,7 @@ def __init__(self, filename):
         """
         self.filename = filename
 
-        with zopen(filename) as file:
+        with zopen(filename, mode="rt") as file:
             data = file.read()
 
         chunks = re.split(r"GW Driver iteration", data)
@@ -821,7 +821,7 @@ def __init__(self, filename):
         """
         self.filename = filename
 
-        with zopen(filename) as file:
+        with zopen(filename, mode="rt") as file:
             log_bse = file.read()
 
         # self.job_info = self._parse_preamble(preamble)
diff --git a/src/pymatgen/io/gaussian.py b/src/pymatgen/io/gaussian.py
index cdd98482022..8e7ac941470 100644
--- a/src/pymatgen/io/gaussian.py
+++ b/src/pymatgen/io/gaussian.py
@@ -368,7 +368,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             GaussianInput object
         """
-        with zopen(filename, mode="r") as file:
+        with zopen(filename, mode="rt") as file:
             return cls.from_str(file.read())
 
     def get_zmatrix(self):
@@ -447,9 +447,9 @@ def para_dict_to_str(para, joiner=" "):
     def write_file(self, filename, cart_coords=False):
         """Write the input string into a file.
 
-        Option: see __str__ method
+        Option: see `__str__` method
         """
-        with zopen(filename, mode="w") as file:
+        with zopen(filename, mode="wt") as file:
             file.write(self.to_str(cart_coords))
 
     def as_dict(self):
@@ -1102,7 +1102,7 @@ def read_scan(self):
         data = {"energies": [], "coords": {}}
 
         # read in file
-        with zopen(self.filename, mode="r") as file:
+        with zopen(self.filename, mode="rt") as file:
             line = file.readline()
 
             while line != "":
@@ -1188,7 +1188,7 @@ def read_excitation_energies(self):
         transitions = []
 
         # read in file
-        with zopen(self.filename, mode="r") as file:
+        with zopen(self.filename, mode="rt") as file:
             line = file.readline()
             td = False
             while line != "":
diff --git a/src/pymatgen/io/lammps/generators.py b/src/pymatgen/io/lammps/generators.py
index 143860d8764..7a4a0f0ca86 100644
--- a/src/pymatgen/io/lammps/generators.py
+++ b/src/pymatgen/io/lammps/generators.py
@@ -67,7 +67,7 @@ def get_input_set(self, structure: Structure | LammpsData | CombinedData) -> Lam
         data: LammpsData = LammpsData.from_structure(structure) if isinstance(structure, Structure) else structure
 
         # Load the template
-        with zopen(self.template, mode="r") as file:
+        with zopen(self.template, mode="rt") as file:
             template_str = file.read()
 
         # Replace all variables
diff --git a/src/pymatgen/io/lobster/inputs.py b/src/pymatgen/io/lobster/inputs.py
index a4f7902e73b..b592c27e7ed 100644
--- a/src/pymatgen/io/lobster/inputs.py
+++ b/src/pymatgen/io/lobster/inputs.py
@@ -642,7 +642,7 @@ def _get_potcar_symbols(POTCAR_input: PathLike) -> list[str]:
                 raise ValueError("Lobster only works with PAW! Use different POTCARs")
 
         # Warning about a bug in LOBSTER-4.1.0
-        with zopen(POTCAR_input, mode="r") as file:
+        with zopen(POTCAR_input, mode="rt") as file:
             data = file.read()
 
         if isinstance(data, bytes):
diff --git a/src/pymatgen/io/nwchem.py b/src/pymatgen/io/nwchem.py
index 5aa772591af..5d3ca9bf6f5 100644
--- a/src/pymatgen/io/nwchem.py
+++ b/src/pymatgen/io/nwchem.py
@@ -391,7 +391,7 @@ def write_file(self, filename):
         Args:
             filename (str): Filename.
         """
-        with zopen(filename, mode="w") as file:
+        with zopen(filename, mode="wt") as file:
             file.write(str(self))
 
     def as_dict(self):
@@ -531,7 +531,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             NwInput object
         """
-        with zopen(filename) as file:
+        with zopen(filename, mode="rt") as file:
             return cls.from_str(file.read())
 
 
@@ -554,7 +554,7 @@ def __init__(self, filename):
         """
         self.filename = filename
 
-        with zopen(filename) as file:
+        with zopen(filename, mode="rt") as file:
             data = file.read()
 
         chunks = re.split(r"NWChem Input Module", data)
diff --git a/src/pymatgen/io/qchem/outputs.py b/src/pymatgen/io/qchem/outputs.py
index d7525a52ccd..ec00c50d9c1 100644
--- a/src/pymatgen/io/qchem/outputs.py
+++ b/src/pymatgen/io/qchem/outputs.py
@@ -58,6 +58,7 @@ def __init__(self, filename: str):
         self.data["errors"] = []
         self.data["warnings"] = {}
         self.text = ""
+        # TODO: why not utf-8 encoding?
         with zopen(filename, mode="rt", encoding="ISO-8859-1") as file:
             self.text = file.read()
 
@@ -2951,6 +2952,7 @@ def nbo_parser(filename: str) -> dict[str, list[pd.DataFrame]]:
         RuntimeError: If a section cannot be found.
     """
     # Open the lines
+    # TODO: why not utf-8 encoding?
     with zopen(filename, mode="rt", encoding="ISO-8859-1") as file:
         lines = file.readlines()
 
diff --git a/src/pymatgen/io/res.py b/src/pymatgen/io/res.py
index 9a45a3b9dc2..9f5226a4aa0 100644
--- a/src/pymatgen/io/res.py
+++ b/src/pymatgen/io/res.py
@@ -249,7 +249,7 @@ def _parse_str(cls, source: str) -> Res:
     def _parse_file(cls, filename: str | Path) -> Res:
         """Parse the res file as a file."""
         self = cls()
-        with zopen(filename, mode="r") as file:
+        with zopen(filename, mode="rt") as file:
             self.source = file.read()
             return self._parse_txt()
 
@@ -335,7 +335,7 @@ def string(self) -> str:
 
     def write(self, filename: str) -> None:
         """Write the res data to a file."""
-        with zopen(filename, mode="w") as file:
+        with zopen(filename, mode="wt") as file:
             file.write(str(self))
 
 
diff --git a/src/pymatgen/io/template.py b/src/pymatgen/io/template.py
index 2ee08031ede..de4759b06d3 100644
--- a/src/pymatgen/io/template.py
+++ b/src/pymatgen/io/template.py
@@ -52,7 +52,7 @@ def get_input_set(
         self.filename = str(filename)
 
         # Load the template
-        with zopen(self.template, mode="r") as file:
+        with zopen(self.template, mode="rt") as file:
             template_str = file.read()
 
         # Replace all variables
diff --git a/src/pymatgen/io/vasp/outputs.py b/src/pymatgen/io/vasp/outputs.py
index 14b116ffcbf..436652dbbd7 100644
--- a/src/pymatgen/io/vasp/outputs.py
+++ b/src/pymatgen/io/vasp/outputs.py
@@ -5394,7 +5394,7 @@ def __init__(
         self.occu_tol = occu_tol
         self.separate_spins = separate_spins
 
-        with zopen(filename, mode="r") as file:
+        with zopen(filename, mode="rt") as file:
             self.ispin = int(file.readline().split()[-1])
 
             # Remove useless header information
diff --git a/src/pymatgen/io/zeopp.py b/src/pymatgen/io/zeopp.py
index 55a1506dc44..56cf1d8b1c8 100644
--- a/src/pymatgen/io/zeopp.py
+++ b/src/pymatgen/io/zeopp.py
@@ -146,7 +146,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             ZeoCssr object.
         """
-        with zopen(filename, mode="r") as file:
+        with zopen(filename, mode="rt") as file:
             return cls.from_str(file.read())
 
 
@@ -200,7 +200,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             XYZ object
         """
-        with zopen(filename) as file:
+        with zopen(filename, mode="rt") as file:
             return cls.from_str(file.read())
 
     def __str__(self) -> str:
diff --git a/tests/electronic_structure/test_dos.py b/tests/electronic_structure/test_dos.py
index a7c8dec41b1..5206baca6e5 100644
--- a/tests/electronic_structure/test_dos.py
+++ b/tests/electronic_structure/test_dos.py
@@ -108,7 +108,7 @@ class TestCompleteDos(TestCase):
     def setUp(self):
         with open(f"{TEST_DIR}/complete_dos.json") as file:
             self.dos = CompleteDos.from_dict(json.load(file))
-        with zopen(f"{TEST_DIR}/pdag3_complete_dos.json.gz") as file:
+        with zopen(f"{TEST_DIR}/pdag3_complete_dos.json.gz", mode="rt") as file:
             self.dos_pdag3 = CompleteDos.from_dict(json.load(file))
 
     def test_get_gap(self):
diff --git a/tests/io/qchem/test_utils.py b/tests/io/qchem/test_utils.py
index 4ad091b8242..f90e819a410 100644
--- a/tests/io/qchem/test_utils.py
+++ b/tests/io/qchem/test_utils.py
@@ -36,6 +36,7 @@ def test_process_parsed_hess(self):
             binary = file.read()
             data_132 = [struct.unpack("d", binary[ii * 8 : (ii + 1) * 8])[0] for ii in range(len(binary) // 8)]
 
+        # TODO: why not utf-8 encoding?
         with zopen(f"{TEST_DIR}/parse_hess/HESS", mode="rt", encoding="ISO-8859-1") as file:
             data_hess = file.readlines()
 
diff --git a/tests/io/vasp/test_outputs.py b/tests/io/vasp/test_outputs.py
index e02b9ac027a..51966e239b1 100644
--- a/tests/io/vasp/test_outputs.py
+++ b/tests/io/vasp/test_outputs.py
@@ -2148,7 +2148,7 @@ def test_consistency(self):
         wder_ref = np.loadtxt(f"{VASP_OUT_DIR}/WAVEDERF.Si.gz", skiprows=1)
 
         def _check(wder):
-            with zopen(f"{VASP_OUT_DIR}/WAVEDERF.Si.gz") as file:
+            with zopen(f"{VASP_OUT_DIR}/WAVEDERF.Si.gz", mode="rt") as file:
                 first_line = [int(a) for a in file.readline().split()]
             assert wder.nkpoints == first_line[1]
             assert wder.nbands == first_line[2]

From 4fccd593130484724ede4be6355352a4f84dd88e Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sat, 7 Dec 2024 19:32:24 +0800
Subject: [PATCH 02/14] fix bad mode for cifwrite

---
 src/pymatgen/io/cif.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/pymatgen/io/cif.py b/src/pymatgen/io/cif.py
index 235509f805b..16cd66ef9b1 100644
--- a/src/pymatgen/io/cif.py
+++ b/src/pymatgen/io/cif.py
@@ -1757,9 +1757,9 @@ def cif_file(self) -> CifFile:
 
     def write_file(
         self,
-        filename: str | Path,
-        mode: Literal["w", "a", "wt", "at"] = "w",
+        filename: PathLike,
+        mode: Literal["wt", "at"] = "wt",
     ) -> None:
         """Write the CIF file."""
-        with zopen(filename, mode=mode) as file:  # DEBUG: bad default value
+        with zopen(filename, mode=mode) as file:
             file.write(str(self))

From 88c13595a8c388f01d3bc4bab82e7666d73d6188 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sat, 7 Dec 2024 19:37:18 +0800
Subject: [PATCH 03/14] remove tag

---
 src/pymatgen/io/qchem/outputs.py | 2 --
 tests/io/qchem/test_utils.py     | 1 -
 2 files changed, 3 deletions(-)

diff --git a/src/pymatgen/io/qchem/outputs.py b/src/pymatgen/io/qchem/outputs.py
index ec00c50d9c1..d7525a52ccd 100644
--- a/src/pymatgen/io/qchem/outputs.py
+++ b/src/pymatgen/io/qchem/outputs.py
@@ -58,7 +58,6 @@ def __init__(self, filename: str):
         self.data["errors"] = []
         self.data["warnings"] = {}
         self.text = ""
-        # TODO: why not utf-8 encoding?
         with zopen(filename, mode="rt", encoding="ISO-8859-1") as file:
             self.text = file.read()
 
@@ -2952,7 +2951,6 @@ def nbo_parser(filename: str) -> dict[str, list[pd.DataFrame]]:
         RuntimeError: If a section cannot be found.
     """
     # Open the lines
-    # TODO: why not utf-8 encoding?
     with zopen(filename, mode="rt", encoding="ISO-8859-1") as file:
         lines = file.readlines()
 
diff --git a/tests/io/qchem/test_utils.py b/tests/io/qchem/test_utils.py
index f90e819a410..4ad091b8242 100644
--- a/tests/io/qchem/test_utils.py
+++ b/tests/io/qchem/test_utils.py
@@ -36,7 +36,6 @@ def test_process_parsed_hess(self):
             binary = file.read()
             data_132 = [struct.unpack("d", binary[ii * 8 : (ii + 1) * 8])[0] for ii in range(len(binary) // 8)]
 
-        # TODO: why not utf-8 encoding?
         with zopen(f"{TEST_DIR}/parse_hess/HESS", mode="rt", encoding="ISO-8859-1") as file:
             data_hess = file.readlines()
 

From 7df79b55ac7616b7e0e5b9a439bf4dabf12980d9 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sat, 7 Dec 2024 22:09:17 +0800
Subject: [PATCH 04/14] remove an unnecessary cast to int

---
 src/pymatgen/transformations/site_transformations.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/pymatgen/transformations/site_transformations.py b/src/pymatgen/transformations/site_transformations.py
index 4672bad1183..6b1bede1f2a 100644
--- a/src/pymatgen/transformations/site_transformations.py
+++ b/src/pymatgen/transformations/site_transformations.py
@@ -431,9 +431,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
             n_to_remove = round(n_to_remove)
             num_remove_dict[tuple(idx)] = n_to_remove
             n = len(idx)
-            total_combos += int(
-                round(math.factorial(n) / math.factorial(n_to_remove) / math.factorial(n - n_to_remove))
-            )
+            total_combos += round(math.factorial(n) / math.factorial(n_to_remove) / math.factorial(n - n_to_remove))
 
         self.logger.debug(f"Total combinations = {total_combos}")
 

From c9bf970928e7e1d235a835e3cb4ad45a149ce010 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 17:59:12 +0800
Subject: [PATCH 05/14] TODO: test monty zopen change

---
 .github/workflows/test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 852fa8719f0..4bf09b475bd 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -92,6 +92,9 @@ jobs:
           uv pip install dist/*.whl
           uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
 
+          # TODO: test monty change on zopen
+          uv pip install git+https://github.com/DanielYang59/monty.git@zopen-encoding
+
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |

From 4925a3e6bd29283fb13134d22b9ad86db1ae20b9 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 18:08:29 +0800
Subject: [PATCH 06/14] fix implicit mode

---
 tests/io/vasp/test_inputs.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/io/vasp/test_inputs.py b/tests/io/vasp/test_inputs.py
index 1616ff4e5e7..5b572d44acd 100644
--- a/tests/io/vasp/test_inputs.py
+++ b/tests/io/vasp/test_inputs.py
@@ -1560,7 +1560,7 @@ def test_from_file(self):
         }
 
     def test_potcar_map(self):
-        fe_potcar = zopen(f"{FAKE_POTCAR_DIR}/POT_GGA_PAW_PBE/POTCAR.Fe_pv.gz").read().decode("utf-8")
+        fe_potcar = zopen(f"{FAKE_POTCAR_DIR}/POT_GGA_PAW_PBE/POTCAR.Fe_pv.gz", mode="rt", encoding="utf-8").read()
         # specify V instead of Fe - this makes sure the test won't pass if the
         # code just grabs the POTCAR from the config file (the config file would
         # grab the V POTCAR)

From be411a0f9d13bb3ebf77ecd5997ce5b21af81910 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 18:18:19 +0800
Subject: [PATCH 07/14] Revert "TODO: test monty zopen change"

This reverts commit c9bf970928e7e1d235a835e3cb4ad45a149ce010.
---
 .github/workflows/test.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4bf09b475bd..852fa8719f0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -92,9 +92,6 @@ jobs:
           uv pip install dist/*.whl
           uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
 
-          # TODO: test monty change on zopen
-          uv pip install git+https://github.com/DanielYang59/monty.git@zopen-encoding
-
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |

From e75c196d47c614022e534741178eabd1316f9efe Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 22:06:15 +0800
Subject: [PATCH 08/14] Revert "Revert "TODO: test monty zopen change""

This reverts commit be411a0f9d13bb3ebf77ecd5997ce5b21af81910.
---
 .github/workflows/test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 852fa8719f0..4bf09b475bd 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -92,6 +92,9 @@ jobs:
           uv pip install dist/*.whl
           uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
 
+          # TODO: test monty change on zopen
+          uv pip install git+https://github.com/DanielYang59/monty.git@zopen-encoding
+
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |

From 4d699d700b0e00aaa16969b6a517b031bda5dd08 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 22:12:24 +0800
Subject: [PATCH 09/14] Revert "Revert "Revert "TODO: test monty zopen
 change"""

This reverts commit e75c196d47c614022e534741178eabd1316f9efe.
---
 .github/workflows/test.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4bf09b475bd..852fa8719f0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -92,9 +92,6 @@ jobs:
           uv pip install dist/*.whl
           uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
 
-          # TODO: test monty change on zopen
-          uv pip install git+https://github.com/DanielYang59/monty.git@zopen-encoding
-
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |

From 14d501a6ed3f303d21c3568cfa4226e8faa7182f Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 22:29:44 +0800
Subject: [PATCH 10/14] explicit text mode for stout

---
 src/pymatgen/io/fiesta.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/pymatgen/io/fiesta.py b/src/pymatgen/io/fiesta.py
index 98643d16279..5f7bc4fc03f 100644
--- a/src/pymatgen/io/fiesta.py
+++ b/src/pymatgen/io/fiesta.py
@@ -63,7 +63,7 @@ def run(self):
         init_folder = os.getcwd()
         os.chdir(self.folder)
 
-        with zopen(self.log_file, mode="w") as fout:
+        with zopen(self.log_file, mode="wt") as fout:
             subprocess.call(
                 [
                     self._NWCHEM2FIESTA_cmd,
@@ -138,7 +138,7 @@ def _gw_run(self):
         if self.folder != init_folder:
             os.chdir(self.folder)
 
-        with zopen(self.log_file, mode="w") as fout:
+        with zopen(self.log_file, mode="wt") as fout:
             subprocess.call(
                 [
                     "mpirun",
@@ -161,7 +161,7 @@ def bse_run(self):
         if self.folder != init_folder:
             os.chdir(self.folder)
 
-        with zopen(self.log_file, mode="w") as fout:
+        with zopen(self.log_file, mode="wt") as fout:
             subprocess.call(
                 [
                     "mpirun",

From 3fdf8cb64f206bf180e54ecf04da97319ceea836 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 22:56:55 +0800
Subject: [PATCH 11/14] some explicit utf-8 for zopen

---
 dev_scripts/potcar_scrambler.py      |  2 +-
 src/pymatgen/apps/borg/hive.py       |  2 +-
 src/pymatgen/apps/borg/queen.py      |  4 ++--
 src/pymatgen/core/structure.py       | 18 ++++++++---------
 src/pymatgen/core/trajectory.py      |  2 +-
 src/pymatgen/io/adf.py               |  2 +-
 src/pymatgen/io/aims/inputs.py       |  4 ++--
 src/pymatgen/io/cif.py               |  4 ++--
 src/pymatgen/io/common.py            |  6 +++---
 src/pymatgen/io/core.py              |  6 +++---
 src/pymatgen/io/cp2k/inputs.py       |  2 +-
 src/pymatgen/io/cp2k/outputs.py      | 16 +++++++--------
 src/pymatgen/io/cp2k/utils.py        |  2 +-
 src/pymatgen/io/cssr.py              |  4 ++--
 src/pymatgen/io/exciting/inputs.py   |  2 +-
 src/pymatgen/io/feff/inputs.py       | 20 +++++++++----------
 src/pymatgen/io/feff/outputs.py      | 10 +++++-----
 src/pymatgen/io/fiesta.py            | 16 +++++++--------
 src/pymatgen/io/gaussian.py          | 10 +++++-----
 src/pymatgen/io/lammps/data.py       |  4 ++--
 src/pymatgen/io/lammps/generators.py |  2 +-
 src/pymatgen/io/lammps/inputs.py     |  4 ++--
 src/pymatgen/io/lammps/outputs.py    |  4 ++--
 src/pymatgen/io/lmto.py              |  6 +++---
 src/pymatgen/io/lobster/inputs.py    |  4 ++--
 src/pymatgen/io/lobster/outputs.py   | 30 ++++++++++++++--------------
 src/pymatgen/io/nwchem.py            |  6 +++---
 src/pymatgen/io/pwscf.py             |  2 +-
 src/pymatgen/io/res.py               |  4 ++--
 src/pymatgen/io/template.py          |  2 +-
 src/pymatgen/io/xr.py                |  4 ++--
 src/pymatgen/io/xyz.py               |  4 ++--
 src/pymatgen/io/zeopp.py             |  4 ++--
 33 files changed, 106 insertions(+), 106 deletions(-)

diff --git a/dev_scripts/potcar_scrambler.py b/dev_scripts/potcar_scrambler.py
index f7115f1996a..7e1aa2579f9 100644
--- a/dev_scripts/potcar_scrambler.py
+++ b/dev_scripts/potcar_scrambler.py
@@ -124,7 +124,7 @@ def scramble_single_potcar(self, potcar: PotcarSingle) -> str:
         return scrambled_potcar_str
 
     def to_file(self, filename: str) -> None:
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.scrambled_potcars_str)
 
     @classmethod
diff --git a/src/pymatgen/apps/borg/hive.py b/src/pymatgen/apps/borg/hive.py
index a46f190b3b0..2ea8a1be63b 100644
--- a/src/pymatgen/apps/borg/hive.py
+++ b/src/pymatgen/apps/borg/hive.py
@@ -443,7 +443,7 @@ def _get_transformation_history(path: PathLike):
     """Check for a transformations.json* file and return the history."""
     if trans_json := glob(f"{path!s}/transformations.json*"):
         try:
-            with zopen(trans_json[0], mode="rt") as file:
+            with zopen(trans_json[0], mode="rt", encoding="utf-8") as file:
                 return json.load(file)["history"]
         except Exception:
             return None
diff --git a/src/pymatgen/apps/borg/queen.py b/src/pymatgen/apps/borg/queen.py
index 2dd4d74e03a..bfa47b39432 100644
--- a/src/pymatgen/apps/borg/queen.py
+++ b/src/pymatgen/apps/borg/queen.py
@@ -103,12 +103,12 @@ def save_data(self, filename: PathLike) -> None:
                 that if the filename ends with gz or bz2, the relevant gzip
                 or bz2 compression will be applied.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             json.dump(list(self._data), file, cls=MontyEncoder)
 
     def load_data(self, filename: PathLike) -> None:
         """Load assimilated data from a file."""
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             self._data = json.load(file, cls=MontyDecoder)
 
 
diff --git a/src/pymatgen/core/structure.py b/src/pymatgen/core/structure.py
index 2a469929e76..8f9fc7f7321 100644
--- a/src/pymatgen/core/structure.py
+++ b/src/pymatgen/core/structure.py
@@ -2952,7 +2952,7 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
         elif fmt == "json" or fnmatch(filename.lower(), "*.json*"):
             json_str = json.dumps(self.as_dict())
             if filename:
-                with zopen(filename, mode="wt") as file:
+                with zopen(filename, mode="wt", encoding="utf-8") as file:
                     file.write(json_str)
             return json_str
         elif fmt == "xsf" or fnmatch(filename.lower(), "*.xsf*"):
@@ -2960,7 +2960,7 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
 
             res_str = XSF(self).to_str()
             if filename:
-                with zopen(filename, mode="wt", encoding="utf8") as file:
+                with zopen(filename, mode="wt", encoding="utf-8") as file:
                     file.write(res_str)
             return res_str
         elif (
@@ -2986,7 +2986,7 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
             yaml.dump(self.as_dict(), str_io)
             yaml_str = str_io.getvalue()
             if filename:
-                with zopen(filename, mode="wt") as file:
+                with zopen(filename, mode="wt", encoding="utf-8") as file:
                     file.write(yaml_str)
             return yaml_str
         elif fmt == "aims" or fnmatch(filename, "geometry.in"):
@@ -2994,7 +2994,7 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
 
             geom_in = AimsGeometryIn.from_structure(self)
             if filename:
-                with zopen(filename, mode="wt") as file:
+                with zopen(filename, mode="wt", encoding="utf-8") as file:
                     file.write(geom_in.get_header(filename))
                     file.write(geom_in.content)
                     file.write("\n")
@@ -3009,7 +3009,7 @@ def to(self, filename: PathLike = "", fmt: FileFormats = "", **kwargs) -> str:
 
             res_str = ResIO.structure_to_str(self)
             if filename:
-                with zopen(filename, mode="wt", encoding="utf8") as file:
+                with zopen(filename, mode="wt", encoding="utf-8") as file:
                     file.write(res_str)
             return res_str
         elif fmt == "pwmat" or fnmatch(filename.lower(), "*.pwmat") or fnmatch(filename.lower(), "*.config"):
@@ -3172,7 +3172,7 @@ def from_file(
             return struct
 
         fname = os.path.basename(filename)
-        with zopen(filename, mode="rt", errors="replace") as file:
+        with zopen(filename, mode="rt", errors="replace", encoding="utf-8") as file:
             contents = file.read()
         if fnmatch(fname.lower(), "*.cif*") or fnmatch(fname.lower(), "*.mcif*"):
             return cls.from_str(
@@ -3918,7 +3918,7 @@ def to(self, filename: str = "", fmt: str = "") -> str | None:
         elif fmt == "json" or fnmatch(filename, "*.json*") or fnmatch(filename, "*.mson*"):
             json_str = json.dumps(self.as_dict())
             if filename:
-                with zopen(filename, mode="wt", encoding="utf8") as file:
+                with zopen(filename, mode="wt", encoding="utf-8") as file:
                     file.write(json_str)
             return json_str
         elif fmt in {"yaml", "yml"} or fnmatch(filename, "*.yaml*") or fnmatch(filename, "*.yml*"):
@@ -3927,7 +3927,7 @@ def to(self, filename: str = "", fmt: str = "") -> str | None:
             yaml.dump(self.as_dict(), str_io)
             yaml_str = str_io.getvalue()
             if filename:
-                with zopen(filename, mode="wt", encoding="utf8") as file:
+                with zopen(filename, mode="wt", encoding="utf-8") as file:
                     file.write(yaml_str)
             return yaml_str
         else:
@@ -4009,7 +4009,7 @@ def from_file(cls, filename: PathLike) -> Self | None:
         """
         filename = str(filename)
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             contents = file.read()
         fname = filename.lower()
         if fnmatch(fname, "*.xyz*"):
diff --git a/src/pymatgen/core/trajectory.py b/src/pymatgen/core/trajectory.py
index a7bc74ac2d6..53a02ffb063 100644
--- a/src/pymatgen/core/trajectory.py
+++ b/src/pymatgen/core/trajectory.py
@@ -465,7 +465,7 @@ def write_Xdatcar(
 
         xdatcar_str = "\n".join(lines) + "\n"
 
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(xdatcar_str)
 
     def as_dict(self) -> dict:
diff --git a/src/pymatgen/io/adf.py b/src/pymatgen/io/adf.py
index f5fbf52d9a2..6725c89beb6 100644
--- a/src/pymatgen/io/adf.py
+++ b/src/pymatgen/io/adf.py
@@ -645,7 +645,7 @@ def _parse_logfile(self, logfile):
         # The last non-empty line of the logfile must match the end pattern.
         # Otherwise the job has some internal failure. The TAPE13 part of the
         # ADF manual has a detailed explanation.
-        with zopen(logfile, mode="rt") as file:
+        with zopen(logfile, mode="rt", encoding="utf-8") as file:
             for line in reverse_readline(file):
                 if line == "":
                     continue
diff --git a/src/pymatgen/io/aims/inputs.py b/src/pymatgen/io/aims/inputs.py
index 9b7ff838bc3..0997601f750 100644
--- a/src/pymatgen/io/aims/inputs.py
+++ b/src/pymatgen/io/aims/inputs.py
@@ -133,7 +133,7 @@ def from_file(cls, filepath: str | Path) -> Self:
         Returns:
             AimsGeometryIn: The input object represented in the file
         """
-        with zopen(filepath, mode="rt") as in_file:
+        with zopen(filepath, mode="rt", encoding="utf-8") as in_file:
             content = in_file.read()
         return cls.from_str(content)
 
@@ -752,7 +752,7 @@ def from_file(cls, filename: str, label: str | None = None) -> Self:
         Returns:
             AimsSpeciesFile
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls(data=file.read(), label=label)
 
     @classmethod
diff --git a/src/pymatgen/io/cif.py b/src/pymatgen/io/cif.py
index 16cd66ef9b1..27164fdaf7f 100644
--- a/src/pymatgen/io/cif.py
+++ b/src/pymatgen/io/cif.py
@@ -299,7 +299,7 @@ def from_file(cls, filename: PathLike) -> Self:
         Returns:
             CifFile
         """
-        with zopen(filename, mode="rt", errors="replace") as file:
+        with zopen(filename, mode="rt", errors="replace", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
 
@@ -1761,5 +1761,5 @@ def write_file(
         mode: Literal["wt", "at"] = "wt",
     ) -> None:
         """Write the CIF file."""
-        with zopen(filename, mode=mode) as file:
+        with zopen(filename, mode=mode, encoding="utf-8") as file:
             file.write(str(self))
diff --git a/src/pymatgen/io/common.py b/src/pymatgen/io/common.py
index a40afb7608c..44b4045a424 100644
--- a/src/pymatgen/io/common.py
+++ b/src/pymatgen/io/common.py
@@ -351,7 +351,7 @@ def to_cube(self, filename, comment: str = ""):
             filename (str): Name of the cube file to be written.
             comment (str): If provided, this will be added to the second comment line
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(f"# Cube file for {self.structure.formula} generated by Pymatgen\n")
             file.write(f"# {comment}\n")
             file.write(f"\t {len(self.structure)} 0.000000 0.000000 0.000000\n")
@@ -383,7 +383,7 @@ def from_cube(cls, filename: str | Path) -> Self:
         Args:
             filename (str): of the cube to read
         """
-        file = zopen(filename, mode="rt")
+        file = zopen(filename, mode="rt", encoding="utf-8")
 
         # skip header lines
         file.readline()
@@ -526,7 +526,7 @@ def __getitem__(self, item):
             f"No parser defined for {item}. Contents are returned as a string.",
             UserWarning,
         )
-        with zopen(fpath, mode="rt") as f:
+        with zopen(fpath, mode="rt", encoding="utf-8") as f:
             return f.read()
 
     def get_files_by_name(self, name: str) -> dict[str, Any]:
diff --git a/src/pymatgen/io/core.py b/src/pymatgen/io/core.py
index 5484954afe1..e81cd7a026e 100644
--- a/src/pymatgen/io/core.py
+++ b/src/pymatgen/io/core.py
@@ -74,7 +74,7 @@ def write_file(self, filename: PathLike) -> None:
         Args:
             filename: The filename to output to, including path.
         """
-        with zopen(Path(filename), mode="wt") as file:
+        with zopen(Path(filename), mode="wt", encoding="utf-8") as file:
             file.write(self.get_str())
 
     @classmethod
@@ -102,7 +102,7 @@ def from_file(cls, path: PathLike) -> None:
         Returns:
             InputFile
         """
-        with zopen(Path(path), mode="rt") as file:
+        with zopen(Path(path), mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())  # from_str not implemented
 
 
@@ -218,7 +218,7 @@ def write_input(
             if isinstance(contents, InputFile):
                 contents.write_file(file_path)
             else:
-                with zopen(file_path, mode="wt") as file:
+                with zopen(file_path, mode="wt", encoding="utf-8") as file:
                     file.write(str(contents))
 
         if zip_inputs:
diff --git a/src/pymatgen/io/cp2k/inputs.py b/src/pymatgen/io/cp2k/inputs.py
index aa68870f100..488cd016771 100644
--- a/src/pymatgen/io/cp2k/inputs.py
+++ b/src/pymatgen/io/cp2k/inputs.py
@@ -692,7 +692,7 @@ def _from_dict(cls, dct: dict):
     @classmethod
     def from_file(cls, filename: str | Path) -> Self:
         """Initialize from a file."""
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             txt = preprocessor(file.read(), os.path.dirname(file.name))
             return cls.from_str(txt)
 
diff --git a/src/pymatgen/io/cp2k/outputs.py b/src/pymatgen/io/cp2k/outputs.py
index ee01c1db302..3885b640e67 100644
--- a/src/pymatgen/io/cp2k/outputs.py
+++ b/src/pymatgen/io/cp2k/outputs.py
@@ -327,7 +327,7 @@ def parse_initial_structure(self):
         )
 
         coord_table = []
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             while True:
                 line = file.readline()
                 if re.search(r"Atom\s+Kind\s+Element\s+X\s+Y\s+Z\s+Z\(eff\)\s+Mass", line):
@@ -788,7 +788,7 @@ def parse_atomic_kind_info(self):
             except (TypeError, IndexError, ValueError):
                 atomic_kind_info[kind]["total_pseudopotential_energy"] = None
 
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             j = -1
             lines = file.readlines()
             for k, line in enumerate(lines):
@@ -1009,7 +1009,7 @@ def parse_mo_eigenvalues(self):
         eigenvalues = []
         efermi = []
 
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             lines = iter(file.readlines())
             for line in lines:
                 try:
@@ -1346,7 +1346,7 @@ def parse_hyperfine(self, hyperfine_filename=None):
             else:
                 return None
 
-        with zopen(hyperfine_filename, mode="rt") as file:
+        with zopen(hyperfine_filename, mode="rt", encoding="utf-8") as file:
             lines = [line for line in file.read().split("\n") if line]
 
         hyperfine = [[] for _ in self.ionic_steps]
@@ -1367,7 +1367,7 @@ def parse_gtensor(self, gtensor_filename=None):
             else:
                 return None
 
-        with zopen(gtensor_filename, mode="rt") as file:
+        with zopen(gtensor_filename, mode="rt", encoding="utf-8") as file:
             lines = [line for line in file.read().split("\n") if line]
 
         data = {}
@@ -1404,7 +1404,7 @@ def parse_chi_tensor(self, chi_filename=None):
             else:
                 return None
 
-        with zopen(chi_filename, mode="rt") as file:
+        with zopen(chi_filename, mode="rt", encoding="utf-8") as file:
             lines = [line for line in file.read().split("\n") if line]
 
         data = {k: [] for k in "chi_soft chi_local chi_total chi_total_ppm_cgs PV1 PV2 PV3 ISO ANISO".split()}
@@ -1551,7 +1551,7 @@ def read_table_pattern(
             row_pattern, or a dict in case that named capturing groups are defined by
             row_pattern.
         """
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             if strip:
                 lines = file.readlines()
                 text = "".join(
@@ -1688,7 +1688,7 @@ def parse_pdos(dos_file=None, spin_channel=None, total=False):
     """
     spin = Spin(spin_channel) if spin_channel else Spin.down if "BETA" in os.path.split(dos_file)[-1] else Spin.up
 
-    with zopen(dos_file, mode="rt") as file:
+    with zopen(dos_file, mode="rt", encoding="utf-8") as file:
         lines = file.readlines()
         kind = re.search(r"atomic kind\s(.*)\sat iter", lines[0]) or re.search(r"list\s(\d+)\s(.*)\sat iter", lines[0])
         kind = kind.groups()[0]
diff --git a/src/pymatgen/io/cp2k/utils.py b/src/pymatgen/io/cp2k/utils.py
index 9c800cb6803..9566ce45fbe 100644
--- a/src/pymatgen/io/cp2k/utils.py
+++ b/src/pymatgen/io/cp2k/utils.py
@@ -80,7 +80,7 @@ def preprocessor(data: str, dir: str = ".") -> str:  # noqa: A002
             raise ValueError(f"length of inc should be 2, got {len(inc)}")
         inc = inc[1].strip("'")
         inc = inc.strip('"')
-        with zopen(os.path.join(dir, inc), mode="rt") as file:
+        with zopen(os.path.join(dir, inc), mode="rt", encoding="utf-8") as file:
             data = re.sub(rf"{incl}", file.read(), data)
     variable_sets = re.findall(r"(@SET.+)", data, re.IGNORECASE)
     for match in variable_sets:
diff --git a/src/pymatgen/io/cssr.py b/src/pymatgen/io/cssr.py
index c5a4fa4ab82..1068396e14b 100644
--- a/src/pymatgen/io/cssr.py
+++ b/src/pymatgen/io/cssr.py
@@ -57,7 +57,7 @@ def write_file(self, filename):
         Args:
             filename (str): Filename to write to.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self) + "\n")
 
     @classmethod
@@ -98,5 +98,5 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             Cssr object.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
diff --git a/src/pymatgen/io/exciting/inputs.py b/src/pymatgen/io/exciting/inputs.py
index 7ef99482b03..5213c8f622a 100644
--- a/src/pymatgen/io/exciting/inputs.py
+++ b/src/pymatgen/io/exciting/inputs.py
@@ -172,7 +172,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             ExcitingInput
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             data = file.read().replace("\n", "")
         return cls.from_str(data)
 
diff --git a/src/pymatgen/io/feff/inputs.py b/src/pymatgen/io/feff/inputs.py
index 13c2a83c4f0..f9321eb0881 100644
--- a/src/pymatgen/io/feff/inputs.py
+++ b/src/pymatgen/io/feff/inputs.py
@@ -246,7 +246,7 @@ def header_string_from_file(filename: str = "feff.inp"):
         Returns:
             Reads header string.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             lines = file.readlines()
             feff_header_str = []
             ln = 0
@@ -434,8 +434,8 @@ def atoms_string_from_file(filename):
         Returns:
             Atoms string.
         """
-        with zopen(filename, mode="rt") as fobject:
-            f = fobject.readlines()
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
+            f = file.readlines()
             coords = 0
             atoms_str = []
 
@@ -527,7 +527,7 @@ def write_file(self, filename="ATOMS"):
         Args:
             filename: path for file to be written
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(f"{self}\n")
 
 
@@ -651,7 +651,7 @@ def write_file(self, filename="PARAMETERS"):
         Args:
             filename: filename and path to write to.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(f"{self}\n")
 
     @classmethod
@@ -665,7 +665,7 @@ def from_file(cls, filename: str = "feff.inp") -> Self:
         Returns:
             Tags
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             lines = list(clean_lines(file.readlines()))
         params = {}
         eels_params = []
@@ -825,8 +825,8 @@ def pot_string_from_file(filename="feff.inp"):
         Returns:
             FEFFPOT string.
         """
-        with zopen(filename, mode="rt") as f_object:
-            f = f_object.readlines()
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
+            f = file.readlines()
             ln = -1
             pot_str = ["POTENTIALS\n"]
             pot_tag = -1
@@ -931,7 +931,7 @@ def write_file(self, filename="POTENTIALS"):
         Args:
             filename: filename and path to write potential file to.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self) + "\n")
 
 
@@ -973,7 +973,7 @@ def __str__(self):
 
     def write_file(self, filename="paths.dat"):
         """Write paths.dat."""
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self) + "\n")
 
 
diff --git a/src/pymatgen/io/feff/outputs.py b/src/pymatgen/io/feff/outputs.py
index 9e31051ae4b..8357fdfd357 100644
--- a/src/pymatgen/io/feff/outputs.py
+++ b/src/pymatgen/io/feff/outputs.py
@@ -70,7 +70,7 @@ def from_file(cls, feff_inp_file: str = "feff.inp", ldos_file: str = "ldos") ->
             dos_index = 1
             begin = 0
 
-            with zopen(pot_inp, mode="rt") as potfile:
+            with zopen(pot_inp, mode="rt", encoding="utf-8") as potfile:
                 for line in potfile:
                     if len(pot_read_end.findall(line)) > 0:
                         break
@@ -95,7 +95,7 @@ def from_file(cls, feff_inp_file: str = "feff.inp", ldos_file: str = "ldos") ->
             dicts = Potential.pot_dict_from_str(pot_string)
             pot_dict = dicts[0]
 
-        with zopen(f"{ldos_file}00.dat", mode="rt") as file:
+        with zopen(f"{ldos_file}00.dat", mode="rt", encoding="utf-8") as file:
             lines = file.readlines()
         e_fermi = float(lines[0].split()[4])
 
@@ -172,7 +172,7 @@ def charge_transfer_from_file(feff_inp_file, ldos_file):
             pot_inp = re.sub(r"feff.inp", r"pot.inp", feff_inp_file)
             pot_readstart = re.compile(".*iz.*lmaxsc.*xnatph.*xion.*folp.*")
             pot_readend = re.compile(".*ExternalPot.*switch.*")
-            with zopen(pot_inp, mode="rt") as potfile:
+            with zopen(pot_inp, mode="rt", encoding="utf-8") as potfile:
                 for line in potfile:
                     if len(pot_readend.findall(line)) > 0:
                         break
@@ -203,7 +203,7 @@ def charge_transfer_from_file(feff_inp_file, ldos_file):
 
         for idx in range(len(dicts[0]) + 1):
             if len(str(idx)) == 1:
-                with zopen(f"{ldos_file}0{idx}.dat", mode="rt") as file:
+                with zopen(f"{ldos_file}0{idx}.dat", mode="rt", encoding="utf-8") as file:
                     lines = file.readlines()
                     s = float(lines[3].split()[2])
                     p = float(lines[4].split()[2])
@@ -212,7 +212,7 @@ def charge_transfer_from_file(feff_inp_file, ldos_file):
                     tot = float(lines[1].split()[4])
                     cht[str(idx)] = {pot_dict[idx]: {"s": s, "p": p, "d": d, "f": f1, "tot": tot}}
             else:
-                with zopen(f"{ldos_file}{idx}.dat", mode="rt") as file:
+                with zopen(f"{ldos_file}{idx}.dat", mode="rt", encoding="utf-8") as file:
                     lines = file.readlines()
                     s = float(lines[3].split()[2])
                     p = float(lines[4].split()[2])
diff --git a/src/pymatgen/io/fiesta.py b/src/pymatgen/io/fiesta.py
index 5f7bc4fc03f..5ed94ac3e69 100644
--- a/src/pymatgen/io/fiesta.py
+++ b/src/pymatgen/io/fiesta.py
@@ -63,7 +63,7 @@ def run(self):
         init_folder = os.getcwd()
         os.chdir(self.folder)
 
-        with zopen(self.log_file, mode="wt") as fout:
+        with zopen(self.log_file, mode="wt", encoding="utf-8") as fout:
             subprocess.call(
                 [
                     self._NWCHEM2FIESTA_cmd,
@@ -138,7 +138,7 @@ def _gw_run(self):
         if self.folder != init_folder:
             os.chdir(self.folder)
 
-        with zopen(self.log_file, mode="wt") as fout:
+        with zopen(self.log_file, mode="wt", encoding="utf-8") as fout:
             subprocess.call(
                 [
                     "mpirun",
@@ -161,7 +161,7 @@ def bse_run(self):
         if self.folder != init_folder:
             os.chdir(self.folder)
 
-        with zopen(self.log_file, mode="wt") as fout:
+        with zopen(self.log_file, mode="wt", encoding="utf-8") as fout:
             subprocess.call(
                 [
                     "mpirun",
@@ -214,7 +214,7 @@ def __init__(self, filename):
         """
         self.filename = filename
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             basis_set = file.read()
 
         self.data = self._parse_file(basis_set)
@@ -533,7 +533,7 @@ def write_file(self, filename: str | Path) -> None:
         Args:
             filename: Filename.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self))
 
     def as_dict(self):
@@ -712,7 +712,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             FiestaInput object
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
 
@@ -730,7 +730,7 @@ def __init__(self, filename):
         """
         self.filename = filename
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             data = file.read()
 
         chunks = re.split(r"GW Driver iteration", data)
@@ -821,7 +821,7 @@ def __init__(self, filename):
         """
         self.filename = filename
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             log_bse = file.read()
 
         # self.job_info = self._parse_preamble(preamble)
diff --git a/src/pymatgen/io/gaussian.py b/src/pymatgen/io/gaussian.py
index 8e7ac941470..c74c9354406 100644
--- a/src/pymatgen/io/gaussian.py
+++ b/src/pymatgen/io/gaussian.py
@@ -368,7 +368,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             GaussianInput object
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
     def get_zmatrix(self):
@@ -449,7 +449,7 @@ def write_file(self, filename, cart_coords=False):
 
         Option: see `__str__` method
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.to_str(cart_coords))
 
     def as_dict(self):
@@ -661,7 +661,7 @@ def _parse(self, filename):
         opt_structures = []
         route_lower = {}
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             for line in file:
                 if parse_stage == 0:
                     if start_patt.search(line):
@@ -1102,7 +1102,7 @@ def read_scan(self):
         data = {"energies": [], "coords": {}}
 
         # read in file
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             line = file.readline()
 
             while line != "":
@@ -1188,7 +1188,7 @@ def read_excitation_energies(self):
         transitions = []
 
         # read in file
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             line = file.readline()
             td = False
             while line != "":
diff --git a/src/pymatgen/io/lammps/data.py b/src/pymatgen/io/lammps/data.py
index 13514acd8c2..d241f6c41bf 100644
--- a/src/pymatgen/io/lammps/data.py
+++ b/src/pymatgen/io/lammps/data.py
@@ -647,7 +647,7 @@ def from_file(cls, filename: str, atom_style: str = "full", sort_id: bool = Fals
             sort_id (bool): Whether sort each section by id. Default to
                 True.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             lines = file.readlines()
         kw_pattern = r"|".join(itertools.chain(*SECTION_KEYWORDS.values()))
         section_marks = [idx for idx, line in enumerate(lines) if re.search(kw_pattern, line)]
@@ -1436,7 +1436,7 @@ def parse_xyz(cls, filename: str | Path) -> pd.DataFrame:
         Returns:
             pandas.DataFrame
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             lines = file.readlines()
 
         str_io = StringIO("".join(lines[2:]))  # skip the 2nd line
diff --git a/src/pymatgen/io/lammps/generators.py b/src/pymatgen/io/lammps/generators.py
index 7a4a0f0ca86..d541dd1adf4 100644
--- a/src/pymatgen/io/lammps/generators.py
+++ b/src/pymatgen/io/lammps/generators.py
@@ -67,7 +67,7 @@ def get_input_set(self, structure: Structure | LammpsData | CombinedData) -> Lam
         data: LammpsData = LammpsData.from_structure(structure) if isinstance(structure, Structure) else structure
 
         # Load the template
-        with zopen(self.template, mode="rt") as file:
+        with zopen(self.template, mode="rt", encoding="utf-8") as file:
             template_str = file.read()
 
         # Replace all variables
diff --git a/src/pymatgen/io/lammps/inputs.py b/src/pymatgen/io/lammps/inputs.py
index bcb421354c2..5b473a16a28 100644
--- a/src/pymatgen/io/lammps/inputs.py
+++ b/src/pymatgen/io/lammps/inputs.py
@@ -549,7 +549,7 @@ def write_file(
                 If False, a single block is assumed.
         """
         filename = filename if isinstance(filename, Path) else Path(filename)
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.get_str(ignore_comments=ignore_comments, keep_stages=keep_stages))
 
     @classmethod
@@ -649,7 +649,7 @@ def from_file(cls, path: str | Path, ignore_comments: bool = False, keep_stages:
             LammpsInputFile
         """
         filename = path if isinstance(path, Path) else Path(path)
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read(), ignore_comments=ignore_comments, keep_stages=keep_stages)
 
     def __repr__(self) -> str:
diff --git a/src/pymatgen/io/lammps/outputs.py b/src/pymatgen/io/lammps/outputs.py
index 216cc458c66..4efc01fc934 100644
--- a/src/pymatgen/io/lammps/outputs.py
+++ b/src/pymatgen/io/lammps/outputs.py
@@ -115,7 +115,7 @@ def parse_lammps_dumps(file_pattern):
         files = sorted(files, key=lambda f: int(re.match(pattern, f)[1]))
 
     for filename in files:
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             dump_cache = []
             for line in file:
                 if line.startswith("ITEM: TIMESTEP"):
@@ -144,7 +144,7 @@ def parse_lammps_log(filename: str = "log.lammps") -> list[pd.DataFrame]:
     Returns:
         [pd.DataFrame] containing thermo data for each completed run.
     """
-    with zopen(filename, mode="rt") as file:
+    with zopen(filename, mode="rt", encoding="utf-8") as file:
         lines = file.readlines()
     begin_flag = (
         "Memory usage per processor =",
diff --git a/src/pymatgen/io/lmto.py b/src/pymatgen/io/lmto.py
index 1a5d669d4bc..a660ee12510 100644
--- a/src/pymatgen/io/lmto.py
+++ b/src/pymatgen/io/lmto.py
@@ -139,7 +139,7 @@ def write_file(self, filename="CTRL", **kwargs):
         """Write a CTRL file with structure, HEADER, and VERS that can be
         used as input for lmhart.run.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.get_str(**kwargs))
 
     @classmethod
@@ -153,7 +153,7 @@ def from_file(cls, filename: str | Path = "CTRL", **kwargs) -> Self:
         Returns:
             An LMTOCtrl object.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             contents = file.read()
         return cls.from_str(contents, **kwargs)
 
@@ -322,7 +322,7 @@ def __init__(self, filename="COPL", to_eV=False):
               eV, set to True. Defaults to False for energies in Ry.
         """
         # COPL files have an extra trailing blank line
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             contents = file.read().split("\n")[:-1]
         # The parameters line is the second line in a COPL file. It
         # contains all parameters that are needed to map the file.
diff --git a/src/pymatgen/io/lobster/inputs.py b/src/pymatgen/io/lobster/inputs.py
index b592c27e7ed..3bbe0518a11 100644
--- a/src/pymatgen/io/lobster/inputs.py
+++ b/src/pymatgen/io/lobster/inputs.py
@@ -585,7 +585,7 @@ def from_file(cls, lobsterin: PathLike) -> Self:
         Returns:
             Lobsterin object
         """
-        with zopen(lobsterin, mode="rt") as file:
+        with zopen(lobsterin, mode="rt", encoding="utf-8") as file:
             lines = file.read().split("\n")
         if not lines:
             raise RuntimeError("lobsterin file contains no data.")
@@ -642,7 +642,7 @@ def _get_potcar_symbols(POTCAR_input: PathLike) -> list[str]:
                 raise ValueError("Lobster only works with PAW! Use different POTCARs")
 
         # Warning about a bug in LOBSTER-4.1.0
-        with zopen(POTCAR_input, mode="rt") as file:
+        with zopen(POTCAR_input, mode="rt", encoding="utf-8") as file:
             data = file.read()
 
         if isinstance(data, bytes):
diff --git a/src/pymatgen/io/lobster/outputs.py b/src/pymatgen/io/lobster/outputs.py
index 300e2f68c90..78946c1fc51 100644
--- a/src/pymatgen/io/lobster/outputs.py
+++ b/src/pymatgen/io/lobster/outputs.py
@@ -121,7 +121,7 @@ def __init__(
             else:
                 self._filename = "COHPCAR.lobster"
 
-        with zopen(self._filename, mode="rt") as file:
+        with zopen(self._filename, mode="rt", encoding="utf-8") as file:
             lines = file.read().split("\n")
 
         # The parameters line is the second line in a COHPCAR file.
@@ -405,7 +405,7 @@ def __init__(
         # LOBSTER list files have an extra trailing blank line
         # and we don't need the header.
         if self._icohpcollection is None:
-            with zopen(self._filename, mode="rt") as file:
+            with zopen(self._filename, mode="rt", encoding="utf-8") as file:
                 all_lines = file.read().split("\n")
                 lines = all_lines[1:-1] if "spin" not in all_lines[1] else all_lines[2:-1]
             if len(lines) == 0:
@@ -622,7 +622,7 @@ def __init__(self, filename: PathLike | None = "NcICOBILIST.lobster") -> None:
 
         # LOBSTER list files have an extra trailing blank line
         # and we don't need the header
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             lines = file.read().split("\n")[1:-1]
         if len(lines) == 0:
             raise RuntimeError("NcICOBILIST file contains no data.")
@@ -753,7 +753,7 @@ def _parse_doscar(self):
 
         tdensities = {}
         itdensities = {}
-        with zopen(doscar, mode="rt") as file:
+        with zopen(doscar, mode="rt", encoding="utf-8") as file:
             file.readline()  # Skip the first line
             efermi = float([file.readline() for nn in range(4)][3].split()[17])
             dos = []
@@ -912,7 +912,7 @@ def __init__(
         self.loewdin = [] if loewdin is None else loewdin
 
         if self.num_atoms is None:
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")[3:-3]
             if len(lines) == 0:
                 raise RuntimeError("CHARGES file contains no data.")
@@ -1046,7 +1046,7 @@ def __init__(self, filename: PathLike | None, **kwargs) -> None:
                 else:
                     raise ValueError(f"{attr}={val} is not a valid attribute for Lobsterout")
         elif filename:
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")
             if len(lines) == 0:
                 raise RuntimeError("lobsterout does not contain any data")
@@ -1438,7 +1438,7 @@ def __init__(
             raise ValueError("No FATBAND files in folder or given")
 
         for fname in filenames:
-            with zopen(fname, mode="rt") as file:
+            with zopen(fname, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")
 
             atom_names.append(os.path.split(fname)[1].split("_")[1].capitalize())
@@ -1472,7 +1472,7 @@ def __init__(
         eigenvals: dict = {}
         p_eigenvals: dict = {}
         for ifilename, filename in enumerate(filenames):
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")
 
             if ifilename == 0:
@@ -1620,7 +1620,7 @@ def __init__(
         self.max_deviation = [] if max_deviation is None else max_deviation
 
         if not self.band_overlaps_dict:
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")
 
             spin_numbers = [0, 1] if lines[0].split()[-1] == "0" else [1, 2]
@@ -1760,7 +1760,7 @@ def __init__(
         self.is_lcfo = is_lcfo
         self.list_dict_grosspop = [] if list_dict_grosspop is None else list_dict_grosspop
         if not self.list_dict_grosspop:
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")
 
             # Read file to list of dict
@@ -1890,7 +1890,7 @@ def _parse_file(
             imaginary (list[float]): Imaginary parts of wave function.
             distance (list[float]): Distances to the first point in wave function file.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             lines = file.read().split("\n")
 
         points = []
@@ -2060,7 +2060,7 @@ def __init__(
         self.madelungenergies_mulliken = None if madelungenergies_mulliken is None else madelungenergies_mulliken
 
         if self.ewald_splitting is None:
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")[5]
             if len(lines) == 0:
                 raise RuntimeError("MadelungEnergies file contains no data.")
@@ -2131,7 +2131,7 @@ def __init__(
         self.madelungenergies_mulliken: list | float = madelungenergies_mulliken or []
 
         if self.num_atoms is None:
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")
             if len(lines) == 0:
                 raise RuntimeError("SitePotentials file contains no data.")
@@ -2284,7 +2284,7 @@ def __init__(
         """
 
         self._filename = str(filename)
-        with zopen(self._filename, mode="rt") as file:
+        with zopen(self._filename, mode="rt", encoding="utf-8") as file:
             lines = file.readlines()
         if len(lines) == 0:
             raise RuntimeError("Please check provided input file, it seems to be empty")
@@ -2472,7 +2472,7 @@ def __init__(
         self.bin_width = 0.0 if bin_width is None else bin_width
 
         if not self.bwdf:
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 lines = file.read().split("\n")
             if len(lines) == 0:
                 raise RuntimeError("BWDF file contains no data.")
diff --git a/src/pymatgen/io/nwchem.py b/src/pymatgen/io/nwchem.py
index 5d3ca9bf6f5..2e7e9f22efd 100644
--- a/src/pymatgen/io/nwchem.py
+++ b/src/pymatgen/io/nwchem.py
@@ -391,7 +391,7 @@ def write_file(self, filename):
         Args:
             filename (str): Filename.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self))
 
     def as_dict(self):
@@ -531,7 +531,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             NwInput object
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
 
@@ -554,7 +554,7 @@ def __init__(self, filename):
         """
         self.filename = filename
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             data = file.read()
 
         chunks = re.split(r"NWChem Input Module", data)
diff --git a/src/pymatgen/io/pwscf.py b/src/pymatgen/io/pwscf.py
index 2f32c0c346a..03f7e7d456e 100644
--- a/src/pymatgen/io/pwscf.py
+++ b/src/pymatgen/io/pwscf.py
@@ -275,7 +275,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             PWInput object
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
     @classmethod
diff --git a/src/pymatgen/io/res.py b/src/pymatgen/io/res.py
index 9f5226a4aa0..cfc81f3d649 100644
--- a/src/pymatgen/io/res.py
+++ b/src/pymatgen/io/res.py
@@ -249,7 +249,7 @@ def _parse_str(cls, source: str) -> Res:
     def _parse_file(cls, filename: str | Path) -> Res:
         """Parse the res file as a file."""
         self = cls()
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             self.source = file.read()
             return self._parse_txt()
 
@@ -335,7 +335,7 @@ def string(self) -> str:
 
     def write(self, filename: str) -> None:
         """Write the res data to a file."""
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self))
 
 
diff --git a/src/pymatgen/io/template.py b/src/pymatgen/io/template.py
index de4759b06d3..bacfd661e97 100644
--- a/src/pymatgen/io/template.py
+++ b/src/pymatgen/io/template.py
@@ -52,7 +52,7 @@ def get_input_set(
         self.filename = str(filename)
 
         # Load the template
-        with zopen(self.template, mode="rt") as file:
+        with zopen(self.template, mode="rt", encoding="utf-8") as file:
             template_str = file.read()
 
         # Replace all variables
diff --git a/src/pymatgen/io/xr.py b/src/pymatgen/io/xr.py
index 834b8d6d797..e86554a83be 100644
--- a/src/pymatgen/io/xr.py
+++ b/src/pymatgen/io/xr.py
@@ -68,7 +68,7 @@ def write_file(self, filename: str | Path) -> None:
         Args:
             filename (str): name of the file to write to.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self) + "\n")
 
     @classmethod
@@ -155,5 +155,5 @@ def from_file(cls, filename: str | Path, use_cores: bool = True, thresh: float =
             xr (Xr): Xr object corresponding to the input
                     file.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read(), use_cores=use_cores, thresh=thresh)
diff --git a/src/pymatgen/io/xyz.py b/src/pymatgen/io/xyz.py
index 98078baa63c..4f44f66e552 100644
--- a/src/pymatgen/io/xyz.py
+++ b/src/pymatgen/io/xyz.py
@@ -111,7 +111,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             XYZ object
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
     def as_dataframe(self):
@@ -151,5 +151,5 @@ def write_file(self, filename: str) -> None:
         Args:
             filename (str): File name of output file.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self))
diff --git a/src/pymatgen/io/zeopp.py b/src/pymatgen/io/zeopp.py
index 56cf1d8b1c8..64f1557f4d1 100644
--- a/src/pymatgen/io/zeopp.py
+++ b/src/pymatgen/io/zeopp.py
@@ -146,7 +146,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             ZeoCssr object.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
 
@@ -200,7 +200,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             XYZ object
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
     def __str__(self) -> str:

From d899c87e60e58b5719f1123a60f992a9428d0e51 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 23:03:10 +0800
Subject: [PATCH 12/14] TO BE REVERTED: test monty pr

---
 .github/workflows/test.yml | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 852fa8719f0..4bf09b475bd 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -92,6 +92,9 @@ jobs:
           uv pip install dist/*.whl
           uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
 
+          # TODO: test monty change on zopen
+          uv pip install git+https://github.com/DanielYang59/monty.git@zopen-encoding
+
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |

From 0ece310bea9fa1be9a47a424e1a07ef883f9c741 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 23:07:02 +0800
Subject: [PATCH 13/14] add the rest encoding

---
 src/pymatgen/io/pwmat/inputs.py        | 10 +++---
 src/pymatgen/io/pwmat/outputs.py       |  6 ++--
 src/pymatgen/io/qchem/inputs.py        |  6 ++--
 src/pymatgen/io/qchem/outputs.py       |  2 +-
 src/pymatgen/io/qchem/sets.py          |  2 +-
 src/pymatgen/io/vasp/inputs.py         | 28 ++++++++--------
 src/pymatgen/io/vasp/outputs.py        | 46 +++++++++++++-------------
 src/pymatgen/util/io_utils.py          |  2 +-
 tests/electronic_structure/test_dos.py |  2 +-
 tests/io/aims/conftest.py              |  2 +-
 tests/io/pwmat/test_inputs.py          |  6 ++--
 tests/io/vasp/test_outputs.py          |  2 +-
 12 files changed, 57 insertions(+), 57 deletions(-)

diff --git a/src/pymatgen/io/pwmat/inputs.py b/src/pymatgen/io/pwmat/inputs.py
index aa60c1737cd..92bd77e0374 100644
--- a/src/pymatgen/io/pwmat/inputs.py
+++ b/src/pymatgen/io/pwmat/inputs.py
@@ -36,7 +36,7 @@ def locate_all_lines(file_path: PathLike, content: str, exclusion: str = "") ->
         """
         row_idxs: list[int] = []  # starts from 1 to be compatible with linecache package
         row_no: int = 0
-        with zopen(file_path, mode="rt") as file:
+        with zopen(file_path, mode="rt", encoding="utf-8") as file:
             for row_content in file:
                 row_no += 1
                 if content.upper() in row_content.upper() and (
@@ -418,7 +418,7 @@ def from_file(cls, filename: PathLike, mag: bool = False) -> Self:
         Returns:
             AtomConfig object.
         """
-        with zopen(filename, "rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(data=file.read(), mag=mag)
 
     @classmethod
@@ -466,7 +466,7 @@ def get_str(self) -> str:
 
     def write_file(self, filename: PathLike, **kwargs):
         """Write AtomConfig to a file."""
-        with zopen(filename, "wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.get_str(**kwargs))
 
     def as_dict(self):
@@ -588,7 +588,7 @@ def write_file(self, filename: PathLike):
         Args:
             filename (PathLike): The absolute path of file to be written.
         """
-        with zopen(filename, "wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.get_str())
 
 
@@ -694,5 +694,5 @@ def get_hsp_row_str(label: str, index: int, coordinate: float) -> str:
 
     def write_file(self, filename: PathLike):
         """Write HighSymmetryPoint to a file."""
-        with zopen(filename, "wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.get_str())
diff --git a/src/pymatgen/io/pwmat/outputs.py b/src/pymatgen/io/pwmat/outputs.py
index 9389e82befb..0183be0bab7 100644
--- a/src/pymatgen/io/pwmat/outputs.py
+++ b/src/pymatgen/io/pwmat/outputs.py
@@ -135,7 +135,7 @@ def _parse_sefv(self) -> list[dict]:
                 'atom_forces' and 'virial'.
         """
         ionic_steps: list[dict] = []
-        with zopen(self.filename, "rt") as mvt:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as mvt:
             tmp_step: dict = {}
             for ii in range(self.n_ionic_steps):
                 tmp_chunk: str = ""
@@ -168,7 +168,7 @@ def __init__(self, filename: PathLike):
             filename (PathLike): The absolute path of OUT.FERMI file.
         """
         self.filename: PathLike = filename
-        with zopen(self.filename, "rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             self._e_fermi: float = np.round(float(file.readline().split()[-2].strip()), 3)
 
     @property
@@ -346,7 +346,7 @@ def _parse(self):
         labels: list[str] = []
         labels = linecache.getline(str(self.filename), 1).split()[1:]
         dos_str: str = ""
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             file.readline()
             dos_str = file.read()
         dos: np.ndarray = np.loadtxt(StringIO(dos_str))
diff --git a/src/pymatgen/io/qchem/inputs.py b/src/pymatgen/io/qchem/inputs.py
index d350a84ba55..7ff5be8487e 100644
--- a/src/pymatgen/io/qchem/inputs.py
+++ b/src/pymatgen/io/qchem/inputs.py
@@ -373,7 +373,7 @@ def write_multi_job_file(job_list: list[QCInput], filename: str):
             job_list (list[QCInput]): List of QChem jobs.
             filename (str): Name of the file to write.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(QCInput.multi_job_string(job_list))
 
     @classmethod
@@ -387,7 +387,7 @@ def from_file(cls, filename: str | Path) -> Self:
         Returns:
             QcInput
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
     @classmethod
@@ -401,7 +401,7 @@ def from_multi_jobs_file(cls, filename: str) -> list[Self]:
         Returns:
             List of QCInput objects
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             # the delimiter between QChem jobs is @@@
             multi_job_strings = file.read().split("@@@")
             # list of individual QChem jobs
diff --git a/src/pymatgen/io/qchem/outputs.py b/src/pymatgen/io/qchem/outputs.py
index d7525a52ccd..f9cc304c72f 100644
--- a/src/pymatgen/io/qchem/outputs.py
+++ b/src/pymatgen/io/qchem/outputs.py
@@ -661,7 +661,7 @@ def multiple_outputs_from_file(filename, keep_sub_files=True):
         2.) Creates separate QCCalcs for each one from the sub-files.
         """
         to_return = []
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             text = re.split(r"\s*(?:Running\s+)*Job\s+\d+\s+of\s+\d+\s+", file.read())
         if text[0] == "":
             text = text[1:]
diff --git a/src/pymatgen/io/qchem/sets.py b/src/pymatgen/io/qchem/sets.py
index 31c5b8fc321..c3321d150d6 100644
--- a/src/pymatgen/io/qchem/sets.py
+++ b/src/pymatgen/io/qchem/sets.py
@@ -643,7 +643,7 @@ def write(self, input_file: PathLike) -> None:
         """
         self.write_file(input_file)
         if self.smd_solvent in {"custom", "other"} and self.qchem_version == 5:
-            with zopen(os.path.join(os.path.dirname(input_file), "solvent_data"), mode="wt") as file:
+            with zopen(os.path.join(os.path.dirname(input_file), "solvent_data"), mode="wt", encoding="utf-8") as file:
                 file.write(self.custom_smd)
 
 
diff --git a/src/pymatgen/io/vasp/inputs.py b/src/pymatgen/io/vasp/inputs.py
index 6fa0f690df2..af0390b0064 100644
--- a/src/pymatgen/io/vasp/inputs.py
+++ b/src/pymatgen/io/vasp/inputs.py
@@ -284,7 +284,7 @@ def from_file(
             except Exception:
                 names = None
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read(), names, read_velocities=read_velocities)
 
     @classmethod
@@ -657,7 +657,7 @@ def write_file(self, filename: PathLike, **kwargs) -> None:
         """Write POSCAR to a file. The supported kwargs are the same as those for
         the Poscar.get_str method and are passed through directly.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.get_str(**kwargs))
 
     def as_dict(self) -> dict:
@@ -892,7 +892,7 @@ def write_file(self, filename: PathLike) -> None:
         Args:
             filename (str): filename to write to.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self))
 
     @classmethod
@@ -905,7 +905,7 @@ def from_file(cls, filename: PathLike) -> Self:
         Returns:
             Incar object
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
     @classmethod
@@ -1645,7 +1645,7 @@ def from_file(cls, filename: PathLike) -> Self:
         Returns:
             Kpoints object
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             return cls.from_str(file.read())
 
     @classmethod
@@ -1786,7 +1786,7 @@ def write_file(self, filename: PathLike) -> None:
         Args:
             filename (PathLike): Filename to write to.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self))
 
     def as_dict(self) -> dict[str, Any]:
@@ -2390,9 +2390,9 @@ def write_file(self, filename: str) -> None:
         """Write PotcarSingle to a file.
 
         Args:
-            filename (str): Filename to write to.
+            filename (str): File to write to.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self))
 
     def copy(self) -> Self:
@@ -2417,7 +2417,7 @@ def from_file(cls, filename: PathLike) -> Self:
         symbol = match[0] if match else ""
 
         try:
-            with zopen(filename, mode="rt") as file:
+            with zopen(filename, mode="rt", encoding="utf-8") as file:
                 return cls(file.read(), symbol=symbol or None)
 
         except UnicodeDecodeError:
@@ -2823,7 +2823,7 @@ def from_file(cls, filename: PathLike) -> Self:
         Returns:
             Potcar
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             fdata = file.read()
 
         potcar = cls()
@@ -2846,7 +2846,7 @@ def write_file(self, filename: PathLike) -> None:
         Args:
             filename (PathLike): filename to write to.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(str(self))
 
     def set_symbols(
@@ -2982,7 +2982,7 @@ def write_input(
 
         for key, value in self.items():
             if value is not None:
-                with zopen(os.path.join(output_dir, key), mode="wt") as file:
+                with zopen(os.path.join(output_dir, key), mode="wt", encoding="utf-8") as file:
                     file.write(str(value))
 
         if cif_name:
@@ -3005,8 +3005,8 @@ def write_input(
         files_to_transfer = files_to_transfer or {}
         for key, val in files_to_transfer.items():
             with (
-                zopen(val, "rb") as fin,
-                zopen(str(Path(output_dir) / key), "wb") as fout,
+                zopen(val, mode="rb") as fin,
+                zopen(str(Path(output_dir) / key), mode="wb") as fout,
             ):
                 copyfileobj(fin, fout)
 
diff --git a/src/pymatgen/io/vasp/outputs.py b/src/pymatgen/io/vasp/outputs.py
index 436652dbbd7..ba23c9c9f11 100644
--- a/src/pymatgen/io/vasp/outputs.py
+++ b/src/pymatgen/io/vasp/outputs.py
@@ -309,7 +309,7 @@ def __init__(
         self.separate_spins = separate_spins
         self.exception_on_bad_xml = exception_on_bad_xml
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             if ionic_step_skip or ionic_step_offset:
                 # Remove parts of the xml file and parse the string
                 content: str = file.read()
@@ -1759,7 +1759,7 @@ def __init__(
         self.occu_tol = occu_tol
         self.separate_spins = separate_spins
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             self.efermi = None
             parsed_header = False
             in_kpoints_opt = False
@@ -2111,7 +2111,7 @@ def __init__(self, filename: PathLike) -> None:
 
         # Data from beginning of OUTCAR
         run_stats["cores"] = None
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             for line in file:
                 if "serial" in line:
                     # Activate serial parallelization
@@ -2362,7 +2362,7 @@ def read_table_pattern(
         if last_one_only and first_one_only:
             raise ValueError("last_one_only and first_one_only options are incompatible")
 
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             text = file.read()
         table_pattern_text = header_pattern + r"\s*^(?P<table_body>(?:\s+" + row_pattern + r")+)\s+" + footer_pattern
         table_pattern = re.compile(table_pattern_text, re.MULTILINE | re.DOTALL)
@@ -2448,7 +2448,7 @@ def read_freq_dielectric(self) -> None:
         data: dict[str, Any] = {"REAL": [], "IMAGINARY": []}
         count = 0
         component = "IMAGINARY"
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             for line in file:
                 line = line.strip()
                 if re.match(plasma_pattern, line):
@@ -2574,7 +2574,7 @@ def read_cs_raw_symmetrized_tensors(self) -> None:
         row_pattern = r"\s+".join([r"([-]?\d+\.\d+)"] * 3)
         unsym_footer_pattern = r"^\s+SYMMETRIZED TENSORS\s+$"
 
-        with zopen(self.filename, mode="rt") as file:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as file:
             text = file.read()
         unsym_table_pattern_text = header_pattern + first_part_pattern + r"(?P<table_body>.+)" + unsym_footer_pattern
         table_pattern = re.compile(unsym_table_pattern_text, re.MULTILINE | re.DOTALL)
@@ -3357,7 +3357,7 @@ def read_core_state_eigen(self) -> list[dict]:
             The core state eigenenergie of the 2s AO of the 6th atom of the
             structure at the last ionic step is [5]["2s"][-1].
         """
-        with zopen(self.filename, mode="rt") as foutcar:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as foutcar:
             line = foutcar.readline()
             cl: list[dict] = []
 
@@ -3399,7 +3399,7 @@ def read_avg_core_poten(self) -> list[list]:
             The average core potential of the 2nd atom of the structure at the
             last ionic step is: [-1][1]
         """
-        with zopen(self.filename, mode="rt") as foutcar:
+        with zopen(self.filename, mode="rt", encoding="utf-8") as foutcar:
             line = foutcar.readline()
             aps: list[list[float]] = []
             while line != "":
@@ -3595,7 +3595,7 @@ def parse_file(filename: PathLike) -> tuple[Poscar, dict, dict]:
         ngrid_pts = 0
         data_count = 0
         poscar = None
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             for line in file:
                 original_line = line
                 line = line.strip()
@@ -3729,7 +3729,7 @@ def write_spin(data_type: str) -> None:
             if isinstance(data, Iterable):
                 file.write("".join(data))
 
-        with zopen(file_name, mode="wt") as file:
+        with zopen(file_name, mode="wt", encoding="utf-8") as file:
             poscar = Poscar(self.structure)
 
             # Use original name if it's been set (e.g. from Chgcar)
@@ -4062,7 +4062,7 @@ def _read(self, filename: PathLike, parsed_kpoints: set[tuple[Kpoint]] | None =
         if parsed_kpoints is None:
             parsed_kpoints = set()
 
-        with zopen(filename, mode="rt") as file_handle:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             preamble_expr = re.compile(r"# of k-points:\s*(\d+)\s+# of bands:\s*(\d+)\s+# of ions:\s*(\d+)")
             kpoint_expr = re.compile(r"^k-point\s+(\d+).*weight = ([0-9\.]+)")
             band_expr = re.compile(r"^band\s+(\d+)")
@@ -4093,7 +4093,7 @@ def _read(self, filename: PathLike, parsed_kpoints: set[tuple[Kpoint]] | None =
             # total and x,y,z) for each band, while non-SOC have only 1 list of projections:
             tot_count = 0
             band_count = 0
-            for line in file_handle:
+            for line in file:
                 if total_expr.match(line):
                     tot_count += 1
                 elif band_expr.match(line):
@@ -4101,7 +4101,7 @@ def _read(self, filename: PathLike, parsed_kpoints: set[tuple[Kpoint]] | None =
                 if band_count == 2:
                     break
 
-            file_handle.seek(0)  # reset file handle to beginning
+            file.seek(0)  # reset file handle to beginning
             if tot_count == 1:
                 is_soc = False
             elif tot_count == 4:
@@ -4118,7 +4118,7 @@ def _read(self, filename: PathLike, parsed_kpoints: set[tuple[Kpoint]] | None =
             skipping_kpoint = False  # true when skipping projections for a previously-parsed kpoint
             ion_line_count = 0  # printed twice when phase factors present
             proj_data_parsed_for_band = 0  # 0 for non-SOC, 1-4 for SOC/phase factors
-            for line in file_handle:
+            for line in file:
                 line = line.strip()
                 if ion_expr.match(line):
                     ion_line_count += 1
@@ -4353,8 +4353,8 @@ def smart_convert(header: str, num: float | str) -> float | str:
         electronic_pattern = re.compile(r"\s*\w+\s*:(.*)")
 
         header: list = []
-        with zopen(filename, mode="rt") as fid:
-            for line in fid:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
+            for line in file:
                 if match := electronic_pattern.match(line.strip()):
                     tokens = match[1].split()
                     data = {header[idx]: smart_convert(header[idx], tokens[idx]) for idx in range(len(tokens))}
@@ -4493,10 +4493,10 @@ def __init__(
         if ionicstep_end is not None and ionicstep_end < 1:
             raise ValueError("End ionic step cannot be less than 1")
 
-        file_len = sum(1 for _ in zopen(filename, mode="rt"))
+        file_len = sum(1 for _ in zopen(filename, mode="rt", encoding="utf-8"))
         ionicstep_cnt = 1
         ionicstep_start = ionicstep_start or 0
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             title = None
             for iline, line in enumerate(file):
                 line = line.strip()
@@ -4592,7 +4592,7 @@ def concatenate(
             raise ValueError("End ionic step cannot be less than 1")
 
         ionicstep_cnt = 1
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             for line in file:
                 line = line.strip()
                 if preamble is None:
@@ -4680,7 +4680,7 @@ def write_file(self, filename: PathLike, **kwargs) -> None:
             **kwargs: The same as those for the Xdatcar.get_str
                 method and are passed through directly.
         """
-        with zopen(filename, mode="wt") as file:
+        with zopen(filename, mode="wt", encoding="utf-8") as file:
             file.write(self.get_str(**kwargs))
 
 
@@ -4702,7 +4702,7 @@ def __init__(self, filename: PathLike) -> None:
         Args:
             filename: Name of file containing DYNMAT.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             lines = list(clean_lines(file.readlines()))
             self._nspecs, self._natoms, self._ndisps = map(int, lines[0].split())
             self._masses = map(float, lines[1].split())
@@ -5394,7 +5394,7 @@ def __init__(
         self.occu_tol = occu_tol
         self.separate_spins = separate_spins
 
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             self.ispin = int(file.readline().split()[-1])
 
             # Remove useless header information
@@ -5545,7 +5545,7 @@ def from_formatted(cls, filename: PathLike) -> Self:
         Returns:
             A Waveder object.
         """
-        with zopen(filename, mode="rt") as file:
+        with zopen(filename, mode="rt", encoding="utf-8") as file:
             nspin, nkpts, nbands = file.readline().split()
         # 1 and 4 are the eigenvalues of the bands (this data is missing in the WAVEDER file)
         # 6:12 are the complex matrix elements in each cartesian direction.
diff --git a/src/pymatgen/util/io_utils.py b/src/pymatgen/util/io_utils.py
index f8c7d268f43..7bf4efdc2f4 100644
--- a/src/pymatgen/util/io_utils.py
+++ b/src/pymatgen/util/io_utils.py
@@ -81,7 +81,7 @@ def micro_pyawk(filename, search, results=None, debug=None, postdebug=None):
     for entry in search:
         entry[0] = re.compile(entry[0])
 
-    with zopen(filename, mode="rt") as file:
+    with zopen(filename, mode="rt", encoding="utf-8") as file:
         for line in file:
             for entry in search:
                 match = re.search(entry[0], line)
diff --git a/tests/electronic_structure/test_dos.py b/tests/electronic_structure/test_dos.py
index 5206baca6e5..edf2c6957ae 100644
--- a/tests/electronic_structure/test_dos.py
+++ b/tests/electronic_structure/test_dos.py
@@ -108,7 +108,7 @@ class TestCompleteDos(TestCase):
     def setUp(self):
         with open(f"{TEST_DIR}/complete_dos.json") as file:
             self.dos = CompleteDos.from_dict(json.load(file))
-        with zopen(f"{TEST_DIR}/pdag3_complete_dos.json.gz", mode="rt") as file:
+        with zopen(f"{TEST_DIR}/pdag3_complete_dos.json.gz", mode="rt", encoding="utf-8") as file:
             self.dos_pdag3 = CompleteDos.from_dict(json.load(file))
 
     def test_get_gap(self):
diff --git a/tests/io/aims/conftest.py b/tests/io/aims/conftest.py
index 3cabe2b3ca8..b2ac971c904 100644
--- a/tests/io/aims/conftest.py
+++ b/tests/io/aims/conftest.py
@@ -150,7 +150,7 @@ def compare_single_files(ref_file: PathLike, test_file: PathLike) -> None:
     with open(test_file) as tf:
         test_lines = tf.readlines()[5:]
 
-    with zopen(f"{ref_file}.gz", mode="rt") as rf:
+    with zopen(f"{ref_file}.gz", mode="rt", encoding="utf-8") as rf:
         ref_lines = rf.readlines()[5:]
 
     for test_line, ref_line in zip(test_lines, ref_lines, strict=True):
diff --git a/tests/io/pwmat/test_inputs.py b/tests/io/pwmat/test_inputs.py
index 7618e7ecdf6..e1438482623 100644
--- a/tests/io/pwmat/test_inputs.py
+++ b/tests/io/pwmat/test_inputs.py
@@ -47,7 +47,7 @@ class TestACstrExtractor(PymatgenTest):
     def test_extract(self):
         filepath = f"{TEST_DIR}/atom.config"
         ac_extractor = ACExtractor(file_path=filepath)
-        with zopen(filepath, mode="rt") as file:
+        with zopen(filepath, mode="rt", encoding="utf-8") as file:
             ac_str_extractor = ACstrExtractor(atom_config_str="".join(file.readlines()))
         assert ac_extractor.n_atoms == ac_str_extractor.get_n_atoms()
         for idx in range(9):
@@ -102,7 +102,7 @@ def test_write_file(self):
         tmp_file = f"{self.tmp_path}/gen.kpt.testing.lzma"
         gen_kpt.write_file(tmp_file)
         tmp_gen_kpt_str = ""
-        with zopen(tmp_file, mode="rt") as file:
+        with zopen(tmp_file, mode="rt", encoding="utf-8") as file:
             tmp_gen_kpt_str = file.read()
         assert gen_kpt.get_str() == tmp_gen_kpt_str
 
@@ -128,7 +128,7 @@ def test_write_file(self):
         tmp_filepath = f"{self.tmp_path}/HIGH_SYMMETRY_POINTS.testing.lzma"
         high_symmetry_points.write_file(tmp_filepath)
         tmp_high_symmetry_points_str = ""
-        with zopen(tmp_filepath, "rt") as file:
+        with zopen(tmp_filepath, "rt", encoding="utf-8") as file:
             tmp_high_symmetry_points_str = file.read()
         assert tmp_high_symmetry_points_str == high_symmetry_points.get_str()
 
diff --git a/tests/io/vasp/test_outputs.py b/tests/io/vasp/test_outputs.py
index 51966e239b1..e459bec8919 100644
--- a/tests/io/vasp/test_outputs.py
+++ b/tests/io/vasp/test_outputs.py
@@ -2148,7 +2148,7 @@ def test_consistency(self):
         wder_ref = np.loadtxt(f"{VASP_OUT_DIR}/WAVEDERF.Si.gz", skiprows=1)
 
         def _check(wder):
-            with zopen(f"{VASP_OUT_DIR}/WAVEDERF.Si.gz", mode="rt") as file:
+            with zopen(f"{VASP_OUT_DIR}/WAVEDERF.Si.gz", mode="rt", encoding="utf-8") as file:
                 first_line = [int(a) for a in file.readline().split()]
             assert wder.nkpoints == first_line[1]
             assert wder.nbands == first_line[2]

From caee02af3313c11b5282507eee55fbadd5eba547 Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Sun, 8 Dec 2024 23:35:04 +0800
Subject: [PATCH 14/14] Revert "TO BE REVERTED: test monty pr"

This reverts commit d899c87e60e58b5719f1123a60f992a9428d0e51.
---
 .github/workflows/test.yml | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 4bf09b475bd..852fa8719f0 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -92,9 +92,6 @@ jobs:
           uv pip install dist/*.whl
           uv pip install pymatgen[${{ matrix.config.extras }}] --resolution=${{ matrix.config.resolution }}
 
-          # TODO: test monty change on zopen
-          uv pip install git+https://github.com/DanielYang59/monty.git@zopen-encoding
-
       - name: Install optional Ubuntu dependencies
         if: matrix.config.os == 'ubuntu-latest'
         run: |