Add mode: Literal["w", "a", "wt", "at"] = "w" keyword to `CifWriter…

….write_file()` (#3399)

* add mode: Literal["w", "a", "wt", "at"] = "w" keyword to CifWriter.write_file()

* add test_cif_writer_write_file

* cif to CIF in comments

pymatgen/analysis/chemenv/utils/scripts_utils.py

@@ -238,7 +238,7 @@ def compute_environments(chemenv_configuration):
             input_source = test
         if source_type == "cif":
             if not found:
-                input_source = input("Enter path to cif file : ")
+                input_source = input("Enter path to CIF file : ")
             parser = CifParser(input_source)
             structure = parser.get_structures()[0]
         elif source_type == "mp":

pymatgen/command_line/mcsqs_caller.py

@@ -81,8 +81,7 @@ def run_mcsqs(
         instances = os.cpu_count()
 
     original_directory = os.getcwd()
-    if not directory:
-        directory = tempfile.mkdtemp()
+    directory = directory or tempfile.mkdtemp()
     os.chdir(directory)
 
     if isinstance(scaling, (int, float)):
@@ -109,13 +108,7 @@ def run_mcsqs(
         process.communicate()
 
     # Generate SQS structures
-    add_ons = [
-        f"-T {temperature}",
-        f"-wr {wr}",
-        f"-wn {wn}",
-        f"-wd {wd}",
-        f"-tol {tol}",
-    ]
+    add_ons = [f"-T {temperature}", f"-wr {wr}", f"-wn {wn}", f"-wd {wd}", f"-tol {tol}"]
 
     mcsqs_find_sqs_processes = []
     if instances and instances > 1:
@@ -181,7 +174,7 @@ def _parse_sqs_path(path) -> Sqs:
     # detected instances will be 0 if mcsqs was run in series, or number of instances
     detected_instances = len(list(path.glob("bestsqs*[0-9]*.out")))
 
-    # Convert best SQS structure to cif file and pymatgen Structure
+    # Convert best SQS structure to CIF file and pymatgen Structure
     with Popen("str2cif < bestsqs.out > bestsqs.cif", shell=True, cwd=path) as p:
         p.communicate()
 
@@ -198,7 +191,7 @@ def _parse_sqs_path(path) -> Sqs:
     objective_function = float(objective_function_str) if objective_function_str != "Perfect_match" else "Perfect_match"
 
     # Get all SQS structures and objective functions
-    allsqs = []
+    all_sqs = []
 
     for i in range(detected_instances):
         sqs_out = f"bestsqs{i + 1}.out"
@@ -213,14 +206,14 @@ def _parse_sqs_path(path) -> Sqs:
         objective_function_str = lines[-1].split("=")[-1].strip()
         obj: float | str
         obj = float(objective_function_str) if objective_function_str != "Perfect_match" else "Perfect_match"
-        allsqs.append({"structure": sqs, "objective_function": obj})
+        all_sqs.append({"structure": sqs, "objective_function": obj})
 
     clusters = _parse_clusters(path / "clusters.out")
 
     return Sqs(
         bestsqs=best_sqs,
         objective_function=objective_function,
-        allsqs=allsqs,
+        allsqs=all_sqs,
         directory=str(path.resolve()),
         clusters=clusters,
     )

pymatgen/io/cif.py

@@ -65,7 +65,7 @@ def __init__(self, data, loops, header):
         """
         self.loops = loops
         self.data = data
-        # AJ says: CIF Block names cannot be more than 75 characters or you
+        # AJ (@computron) says: CIF Block names cannot be more than 75 characters or you
         # get an Exception
         self.header = header[:74]
 
@@ -246,26 +246,27 @@ def from_string(cls, *args, **kwargs):
         return cls.from_str(*args, **kwargs)
 
     @classmethod
-    def from_str(cls, string):
-        """
-        Reads CifFile from a string.
+    def from_str(cls, string) -> CifFile:
+        """Reads CifFile from a string.
 
         :param string: String representation.
 
         Returns:
             CifFile
         """
         dct = {}
-        for x in re.split(r"^\s*data_", f"x\n{string}", flags=re.MULTILINE | re.DOTALL)[1:]:
+
+        for block_str in re.split(r"^\s*data_", f"x\n{string}", flags=re.MULTILINE | re.DOTALL)[1:]:
             # Skip over Cif block that contains powder diffraction data.
             # Some elements in this block were missing from CIF files in
             # Springer materials/Pauling file DBs.
-            # This block anyway does not contain any structure information, and
+            # This block does not contain any structure information anyway, and
             # CifParser was also not parsing it.
-            if "powder_pattern" in re.split(r"\n", x, maxsplit=1)[0]:
+            if "powder_pattern" in re.split(r"\n", block_str, maxsplit=1)[0]:
                 continue
-            c = CifBlock.from_str("data_" + x)
-            dct[c.header] = c
+            block = CifBlock.from_str("data_" + block_str)
+            dct[block.header] = block
+
         return cls(dct, string)
 
     @classmethod
@@ -675,7 +676,7 @@ def get_symops(self, data):
         operations are parsed. If the symops are not present, the space
         group symbol is parsed, and symops are generated.
         """
-        symops = []
+        sym_ops = []
         for symmetry_label in [
             "_symmetry_equiv_pos_as_xyz",
             "_symmetry_equiv_pos_as_xyz_",
@@ -690,11 +691,11 @@ def get_symops(self, data):
                     self.warnings.append(msg)
                     xyz = [xyz]
                 try:
-                    symops = [SymmOp.from_xyz_str(s) for s in xyz]
+                    sym_ops = [SymmOp.from_xyz_str(s) for s in xyz]
                     break
                 except ValueError:
                     continue
-        if not symops:
+        if not sym_ops:
             # Try to parse symbol
             for symmetry_label in [
                 "_symmetry_space_group_name_H-M",
@@ -718,7 +719,7 @@ def get_symops(self, data):
                     try:
                         spg = space_groups.get(sg)
                         if spg:
-                            symops = SpaceGroup(spg).symmetry_ops
+                            sym_ops = SpaceGroup(spg).symmetry_ops
                             msg = msg_template.format(symmetry_label)
                             warnings.warn(msg)
                             self.warnings.append(msg)
@@ -734,17 +735,17 @@ def get_symops(self, data):
                         for d in cod_data:
                             if sg == re.sub(r"\s+", "", d["hermann_mauguin"]):
                                 xyz = d["symops"]
-                                symops = [SymmOp.from_xyz_str(s) for s in xyz]
+                                sym_ops = [SymmOp.from_xyz_str(s) for s in xyz]
                                 msg = msg_template.format(symmetry_label)
                                 warnings.warn(msg)
                                 self.warnings.append(msg)
                                 break
                     except Exception:
                         continue
 
-                    if symops:
+                    if sym_ops:
                         break
-        if not symops:
+        if not sym_ops:
             # Try to parse International number
             for symmetry_label in [
                 "_space_group_IT_number",
@@ -755,18 +756,18 @@ def get_symops(self, data):
                 if data.data.get(symmetry_label):
                     try:
                         i = int(str2float(data.data.get(symmetry_label)))
-                        symops = SpaceGroup.from_int_number(i).symmetry_ops
+                        sym_ops = SpaceGroup.from_int_number(i).symmetry_ops
                         break
                     except ValueError:
                         continue
 
-        if not symops:
+        if not sym_ops:
             msg = "No _symmetry_equiv_pos_as_xyz type key found. Defaulting to P1."
             warnings.warn(msg)
             self.warnings.append(msg)
-            symops = [SymmOp.from_xyz_str(s) for s in ["x", "y", "z"]]
+            sym_ops = [SymmOp.from_xyz_str(s) for s in ["x", "y", "z"]]
 
-        return symops
+        return sym_ops
 
     def get_magsymops(self, data):
         """
@@ -1165,6 +1166,8 @@ def get_structures(
         Returns:
             list[Structure]: All structures in CIF file.
         """
+        print(len(self._cif.data))
+
         if not check_occu:  # added in https://github.com/materialsproject/pymatgen/pull/2836
             warnings.warn("Structures with unphysical site occupancies are not compatible with many pymatgen features.")
         if primitive and symmetrized:
@@ -1478,18 +1481,20 @@ def __init__(
         self._cf = CifFile(dct)
 
     @property
-    def ciffile(self):
+    def cif_file(self):
         """Returns: CifFile associated with the CifWriter."""
         return self._cf
 
     def __str__(self):
-        """Returns the cif as a string."""
+        """Returns the CIF as a string."""
         return str(self._cf)
 
-    def write_file(self, filename):
-        """Write the cif file."""
-        with zopen(filename, "wt") as f:
-            f.write(str(self))
+    def write_file(self, filename: str | Path, mode: Literal["w", "a", "wt", "at"] = "w") -> None:
+        """Write the CIF file."""
+        with zopen(filename, mode=mode) as file:
+            file.write(str(self))
+            if mode in ["a", "at"]:
+                file.write("\n\n")
 
 
 def str2float(text):

pymatgen/io/feff/sets.py

@@ -105,7 +105,7 @@ def write_input(self, output_dir=".", make_dir_if_not_present=True):
         with open(f"{output_dir}/feff.inp", "w") as f:
             f.write(feff_input)
 
-        # write the structure to cif file
+        # write the structure to CIF file
         if "ATOMS" not in feff:
             self.atoms.struct.to(fmt="cif", filename=os.path.join(output_dir, feff["PARAMETERS"]["CIF"]))
 

tests/files/.pytest-split-durations

@@ -1895,7 +1895,7 @@
     "tests/io/test_cif.py::TestCifIO::test_replacing_finite_precision_frac_coords": 0.01487579196691513,
     "tests/io/test_cif.py::TestCifIO::test_site_labels": 0.022716625011526048,
     "tests/io/test_cif.py::TestCifIO::test_site_symbol_preference": 0.013636041956488043,
-    "tests/io/test_cif.py::TestCifIO::test_specie_cifwriter": 0.0027243339573033154,
+    "tests/io/test_cif.py::TestCifIO::test_specie_cif_writer": 0.0027243339573033154,
     "tests/io/test_cif.py::TestCifIO::test_symmetrized": 0.11127212399151176,
     "tests/io/test_cif.py::TestMagCif::test_bibtex": 0.0052501659956760705,
     "tests/io/test_cif.py::TestMagCif::test_get_structures": 0.0418014990282245,

tests/io/test_atat.py

@@ -86,7 +86,7 @@ def test_mcsqs_export(self):
         assert Mcsqs(struct).to_str() == ref_string
 
     def test_mcsqs_cif_nacl(self):
-        # cif file from str2cif (utility distributed with atat)
+        # CIF file from str2cif (utility distributed with atat)
         struc_from_cif = Structure.from_file(f"{test_dir}/bestsqs_nacl.cif")
 
         # output file directly from mcsqs
@@ -100,7 +100,7 @@ def test_mcsqs_cif_nacl(self):
         )
 
     def test_mcsqs_cif_pzt(self):
-        # cif file from str2cif (utility distributed with atat)
+        # CIF file from str2cif (utility distributed with atat)
         struc_from_cif = Structure.from_file(f"{test_dir}/bestsqs_pzt.cif")
 
         # output file directly from mcsqs

tests/io/test_cif.py

@@ -350,7 +350,7 @@ def test_cif_parser_springer_pauling(self):
             assert struct.formula == "Zn1.29 Fe0.69 As2 Pb1.02 O8"
 
     def test_cif_parser_cod(self):
-        """Parsing problematic cif files from the COD database."""
+        """Parsing problematic CIF files from the COD database."""
         # Symbol in capital letters
         parser = CifParser(f"{TEST_FILES_DIR}/Cod_2100513.cif")
         for struct in parser.get_structures():
@@ -491,11 +491,11 @@ def test_symmetrized(self):
         # test angle tolerance.
         struct = Structure.from_file(f"{TEST_FILES_DIR}/LiFePO4.cif")
         writer = CifWriter(struct, symprec=0.1, angle_tolerance=0)
-        d = next(iter(writer.ciffile.data.values()))
+        d = next(iter(writer.cif_file.data.values()))
         assert d["_symmetry_Int_Tables_number"] == 14
         struct = Structure.from_file(f"{TEST_FILES_DIR}/LiFePO4.cif")
         writer = CifWriter(struct, symprec=0.1, angle_tolerance=2)
-        d = next(iter(writer.ciffile.data.values()))
+        d = next(iter(writer.cif_file.data.values()))
         assert d["_symmetry_Int_Tables_number"] == 62
 
     def test_disordered(self):
@@ -554,7 +554,7 @@ def test_cif_writer_without_refinement(self):
         same_si2 = CifParser.from_str(cif_str).get_structures()[0]
         assert len(si2) == len(same_si2)
 
-    def test_specie_cifwriter(self):
+    def test_specie_cif_writer(self):
         si4 = Species("Si", 4)
         si3 = Species("Si", 3)
         n = DummySpecies("X", -3)
@@ -620,9 +620,9 @@ def test_primes(self):
 
     def test_missing_atom_site_type_with_oxi_states(self):
         parser = CifParser(f"{TEST_FILES_DIR}/P24Ru4H252C296S24N16.cif")
-        c = Composition({"S0+": 24, "Ru0+": 4, "H0+": 252, "C0+": 296, "N0+": 16, "P0+": 24})
+        comp = Composition({"S0+": 24, "Ru0+": 4, "H0+": 252, "C0+": 296, "N0+": 16, "P0+": 24})
         for struct in parser.get_structures(primitive=False):
-            assert struct.composition == c
+            assert struct.composition == comp
 
     def test_no_coords_or_species(self):
         string = """#generated using pymatgen
@@ -855,6 +855,22 @@ def test_no_check_occu(self):
             structs = parser.get_structures(primitive=False, check_occu=False)[0]
             assert structs[0].species.as_dict()["Te"] == 1.5
 
+    def test_cif_writer_write_file(self):
+        struct1 = Structure.from_file(f"{TEST_FILES_DIR}/POSCAR")
+        out_path = f"{self.tmp_path}/test.cif"
+        CifWriter(struct1).write_file(out_path)
+        read_structs = CifParser(out_path).get_structures()
+        assert len(read_structs) == 1
+        assert struct1.matches(read_structs[0])
+
+        # test write_file append mode='a'
+        struct2 = Structure.from_file(f"{TEST_FILES_DIR}/Graphite.cif")
+        CifWriter(struct2).write_file(out_path, mode="a")
+
+        read_structs = CifParser(out_path).get_structures()
+        assert len(read_structs) == 2
+        assert [x.formula for x in read_structs] == ["Fe4 P4 O16", "C4"]
+
 
 class TestMagCif(PymatgenTest):
     def setUp(self):