Fix usage of strict=True for zip in cp2k.outputs

src/pymatgen/io/cp2k/outputs.py

@@ -297,7 +297,7 @@ def parse_structures(self, trajectory_file=None, lattice_file=None):
             self.structures = []
             gs = self.initial_structure.site_properties.get("ghost")
             if not self.is_molecule:
-                for mol, latt in zip(mols, lattices, strict=True):
+                for mol, latt in zip(mols, lattices, strict=False):
                     self.structures.append(
                         Structure(
                             lattice=latt,
@@ -520,7 +520,7 @@ def parse_ionic_steps(self):
         if not self.data.get("stress_tensor"):
             self.parse_stresses()
 
-        for i, (structure, energy) in enumerate(zip(self.structures, self.data.get("total_energy"), strict=True)):
+        for i, (structure, energy) in enumerate(zip(self.structures, self.data.get("total_energy"), strict=False)):
             self.ionic_steps.append(
                 {
                     "structure": structure,
@@ -627,8 +627,8 @@ def parse_dft_params(self):
             suffix = ""
             for ll in self.data.get("vdw"):
                 for _possible, _name in zip(
-                    ["RVV10", "LMKLL", "DRSLL", "DFT-D3", "DFT-D2"],
-                    ["RVV10", "LMKLL", "DRSLL", "D3", "D2"],
+                    ("RVV10", "LMKLL", "DRSLL", "DFT-D3", "DFT-D2"),
+                    ("RVV10", "LMKLL", "DRSLL", "D3", "D2"),
                     strict=True,
                 ):
                     if _possible in ll[0]:
@@ -1463,7 +1463,7 @@ def _gauss_smear(densities, energies, npts, width):
         dct = np.zeros(npts)
         e_s = np.linspace(min(energies), max(energies), npts)
 
-        for e, _pd in zip(energies, densities, strict=True):
+        for e, _pd in zip(energies, densities, strict=False):
             weight = np.exp(-(((e_s - e) / width) ** 2)) / (np.sqrt(np.pi) * width)
             dct += _pd * weight
 

tests/io/cp2k/test_inputs.py

@@ -26,19 +26,6 @@
 
 TEST_DIR = f"{TEST_FILES_DIR}/io/cp2k"
 
-si_struct = Structure(
-    lattice=[[0, 2.734364, 2.734364], [2.734364, 0, 2.734364], [2.734364, 2.734364, 0]],
-    species=["Si", "Si"],
-    coords=[[0, 0, 0], [0.25, 0.25, 0.25]],
-)
-
-nonsense_struct = Structure(
-    lattice=[[-1.0, -10.0, -100.0], [0.1, 0.01, 0.001], [7.0, 11.0, 21.0]],
-    species=["H"],
-    coords=[[-1, -1, -1]],
-)
-
-ch_mol = Molecule(species=["C", "H"], coords=[[0, 0, 0], [1, 1, 1]])
 
 BASIS_FILE_STR = """
  H  SZV-MOLOPT-GTH SZV-MOLOPT-GTH-q1
@@ -52,26 +39,9 @@
       0.066918004004  0.037148121400
       0.021708243634 -0.001125195500
 """
-ALL_HYDROGEN_STR = """
-H ALLELECTRON ALL
-    1    0    0
-     0.20000000    0
-"""
-POT_HYDROGEN_STR = """
-H GTH-PBE-q1 GTH-PBE
-    1
-     0.20000000    2    -4.17890044     0.72446331
-    0
-"""
-CP2K_INPUT_STR = """
-&GLOBAL
-    RUN_TYPE ENERGY
-    PROJECT_NAME CP2K ! default name
-&END
-"""
 
 
-class TestBasisAndPotential(PymatgenTest):
+class TestBasis(PymatgenTest):
     def test_basis_info(self):
         # Ensure basis metadata can be read from string
         basis_info = BasisInfo.from_str("cc-pc-DZVP-MOLOPT-q1-SCAN")
@@ -93,25 +63,13 @@ def test_basis_info(self):
         assert basis_info3.polarization == 1
         assert basis_info3.contracted, True
 
-    def test_potential_info(self):
-        # Ensure potential metadata can be read from string
-        pot_info = PotentialInfo.from_str("GTH-PBE-q1-NLCC")
-        assert pot_info.potential_type == "GTH"
-        assert pot_info.xc == "PBE"
-        assert pot_info.nlcc
-
-        # Ensure one-way soft-matching works
-        pot_info2 = PotentialInfo.from_str("GTH-q1-NLCC")
-        assert pot_info2.softmatch(pot_info)
-        assert not pot_info.softmatch(pot_info2)
-
     def test_basis(self):
         # Ensure cp2k formatted string can be read for data correctly
         mol_opt = GaussianTypeOrbitalBasisSet.from_str(BASIS_FILE_STR)
         assert mol_opt.nexp == [7]
         # Basis file can read from strings
         bf = BasisFile.from_str(BASIS_FILE_STR)
-        for obj in [mol_opt, bf.objects[0]]:
+        for obj in (mol_opt, bf.objects[0]):
             assert_allclose(
                 obj.exponents[0],
                 [
@@ -133,22 +91,49 @@ def test_basis(self):
         assert_array_equal(kw.values, ["AUX_FIT", "SZV-MOLOPT-GTH"])
         mol_opt.info.admm = False
 
+
+class TestPotential(PymatgenTest):
+    all_hydrogen_str = """
+H ALLELECTRON ALL
+    1    0    0
+    0.20000000    0
+"""
+
+    pot_hydrogen_str = """
+H GTH-PBE-q1 GTH-PBE
+    1
+    0.20000000    2    -4.17890044     0.72446331
+    0
+"""
+
+    def test_potential_info(self):
+        # Ensure potential metadata can be read from string
+        pot_info = PotentialInfo.from_str("GTH-PBE-q1-NLCC")
+        assert pot_info.potential_type == "GTH"
+        assert pot_info.xc == "PBE"
+        assert pot_info.nlcc
+
+        # Ensure one-way soft-matching works
+        pot_info2 = PotentialInfo.from_str("GTH-q1-NLCC")
+        assert pot_info2.softmatch(pot_info)
+        assert not pot_info.softmatch(pot_info2)
+
     def test_potentials(self):
         # Ensure cp2k formatted string can be read for data correctly
-        h_all_elec = GthPotential.from_str(ALL_HYDROGEN_STR)
+        h_all_elec = GthPotential.from_str(self.all_hydrogen_str)
         assert h_all_elec.potential == "All Electron"
-        pot = GthPotential.from_str(POT_HYDROGEN_STR)
+        pot = GthPotential.from_str(self.pot_hydrogen_str)
         assert pot.potential == "Pseudopotential"
         assert pot.r_loc == approx(0.2)
         assert pot.nexp_ppl == approx(2)
         assert_allclose(pot.c_exp_ppl, [-4.17890044, 0.72446331])
 
         # Basis file can read from strings
-        pot_file = PotentialFile.from_str(POT_HYDROGEN_STR)
+        pot_file = PotentialFile.from_str(self.pot_hydrogen_str)
         assert pot_file.objects[0] == pot
 
         pot_file_path = self.tmp_path / "potential-file"
-        pot_file_path.write_text(POT_HYDROGEN_STR)
+        pot_file_path.write_text(self.pot_hydrogen_str)
         pot_from_file = PotentialFile.from_file(pot_file_path)
         assert pot_file != pot_from_file  # unequal because pot_from_file has filename != None
 
@@ -159,12 +144,33 @@ def test_potentials(self):
         assert kw.values[0] == "ALL"
 
 
-class TestInput(PymatgenTest):
+class TestCp2kInput(PymatgenTest):
+    si_struct = Structure(
+        lattice=[[0, 2.734364, 2.734364], [2.734364, 0, 2.734364], [2.734364, 2.734364, 0]],
+        species=["Si", "Si"],
+        coords=[[0, 0, 0], [0.25, 0.25, 0.25]],
+    )
+
+    invalid_struct = Structure(
+        lattice=[[-1.0, -10.0, -100.0], [0.1, 0.01, 0.001], [7.0, 11.0, 21.0]],
+        species=["H"],
+        coords=[[-1, -1, -1]],
+    )
+
+    ch_mol = Molecule(species=["C", "H"], coords=[[0, 0, 0], [1, 1, 1]])
+
+    cp2k_input_str = """
+&GLOBAL
+    RUN_TYPE ENERGY
+    PROJECT_NAME CP2K ! default name
+&END
+"""
+
     def setUp(self):
         self.ci = Cp2kInput.from_file(f"{TEST_DIR}/cp2k.inp")
 
     def test_basic_sections(self):
-        cp2k_input = Cp2kInput.from_str(CP2K_INPUT_STR)
+        cp2k_input = Cp2kInput.from_str(self.cp2k_input_str)
         assert cp2k_input["GLOBAL"]["RUN_TYPE"] == Keyword("RUN_TYPE", "energy")
         assert cp2k_input["GLOBAL"]["PROJECT_NAME"].description == "default name"
         self.assert_msonable(cp2k_input)
@@ -190,13 +196,13 @@ def test_basic_keywords(self):
         assert "[Ha]" in kwd.get_str()
 
     def test_coords(self):
-        for struct in [nonsense_struct, si_struct, ch_mol]:
+        for struct in (self.invalid_struct, self.si_struct, self.ch_mol):
             coords = Coord(struct)
             for val in coords.keywords.values():
                 assert isinstance(val, Keyword | KeywordList)
 
     def test_kind(self):
-        for struct in [nonsense_struct, si_struct, ch_mol]:
+        for struct in (self.invalid_struct, self.si_struct, self.ch_mol):
             for spec in struct.species:
                 assert spec == Kind(spec).specie
 
@@ -246,7 +252,7 @@ def test_preprocessor(self):
         assert self.ci["FORCE_EVAL"]["DFT"]["SCF"]["MAX_SCF"] == Keyword("MAX_SCF", 1)
 
     def test_mongo(self):
-        cp2k_input = Cp2kInput.from_str(CP2K_INPUT_STR)
+        cp2k_input = Cp2kInput.from_str(self.cp2k_input_str)
         cp2k_input.inc({"GLOBAL": {"TEST": 1}})
         assert cp2k_input["global"]["test"] == Keyword("TEST", 1)
 

tests/io/cp2k/test_outputs.py

@@ -12,7 +12,7 @@
 TEST_DIR = f"{TEST_FILES_DIR}/io/cp2k"
 
 
-class TestSet(TestCase):
+class TestCp2kOutput(TestCase):
     def setUp(self):
         self.out = Cp2kOutput(f"{TEST_DIR}/cp2k.out", auto_load=True)