prefer list literal over verbose coords.append

pymatgen/analysis/phase_diagram.py

@@ -1294,10 +1294,10 @@ def get_chempot_range_stability_phase(self, target_comp, open_elt):
                             min_open = test_open
                             min_mus = v
 
-        elts = [e for e in self.elements if e != open_elt]
+        elems = [e for e in self.elements if e != open_elt]
         res = {}
 
-        for i, el in enumerate(elts):
+        for i, el in enumerate(elems):
             res[el] = (min_mus[i] + muref[i], max_mus[i] + muref[i])
 
         res[open_elt] = (min_open, max_open)

pymatgen/symmetry/analyzer.py

@@ -60,7 +60,7 @@ class SpacegroupAnalyzer:
     Uses spglib to perform various symmetry finding operations.
     """
 
-    def __init__(self, structure: Structure, symprec: float | None = 0.01, angle_tolerance=5.0):
+    def __init__(self, structure: Structure, symprec: float | None = 0.01, angle_tolerance: float = 5.0) -> None:
         """
         Args:
             structure (Structure/IStructure): Structure to find symmetry
@@ -476,7 +476,7 @@ def get_conventional_to_primitive_transformation_matrix(self, international_mono
 
     @cite_conventional_cell_algo
     def get_primitive_standard_structure(self, international_monoclinic=True, keep_site_properties=False):
-        """Gives a structure with a primitive cell according to certain standards the
+        """Gives a structure with a primitive cell according to certain standards. The
         standards are defined in Setyawan, W., & Curtarolo, S. (2010). High-throughput
         electronic band structure calculations: Challenges and tools. Computational
         Materials Science, 49(2), 299-312. doi:10.1016/j.commatsci.2010.05.010.

pymatgen/transformations/advanced_transformations.py

@@ -322,7 +322,7 @@ def __init__(
             n_jobs (int): Number of parallel jobs used to compute energy criteria. This is used only when the Ewald
                 or m3gnet or callable sort_criteria is used. Default is -1, which uses all available CPUs.
         """
-        self.symm_prec = symm_prec
+        self.sym_prec = symm_prec
         self.min_cell_size = min_cell_size
         self.max_cell_size = max_cell_size
         self.refine_structure = refine_structure
@@ -362,7 +362,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
             num_to_return = 1
 
         if self.refine_structure:
-            finder = SpacegroupAnalyzer(structure, self.symm_prec)
+            finder = SpacegroupAnalyzer(structure, self.sym_prec)
             structure = finder.get_refined_structure()
 
         contains_oxidation_state = all(hasattr(sp, "oxi_state") and sp.oxi_state != 0 for sp in structure.elements)
@@ -391,7 +391,7 @@ def apply_transformation(self, structure: Structure, return_ranked_list: bool |
                 structure,
                 min_cell_size=self.min_cell_size,
                 max_cell_size=max_cell_size,
-                symm_prec=self.symm_prec,
+                symm_prec=self.sym_prec,
                 refine_structure=False,
                 enum_precision_parameter=self.enum_precision_parameter,
                 check_ordered_symmetry=self.check_ordered_symmetry,

tests/alchemy/test_materials.py

@@ -30,9 +30,7 @@ def test_append_transformation(self):
         self.trans.append_transformation(trafo)
         assert self.trans.final_structure.composition.reduced_formula == "NaMnPO4"
         assert len(self.trans.structures) == 3
-        coords = []
-        coords.append([0, 0, 0])
-        coords.append([0.75, 0.5, 0.75])
+        coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
         lattice = [
             [3.8401979337, 0, 0],
             [1.9200989668, 3.3257101909, 0],

tests/analysis/test_structure_analyzer.py

@@ -110,34 +110,35 @@ def test_oxide_type(self):
         el_li = Element("Li")
         el_o = Element("O")
         latt = Lattice([[3.985034, 0, 0], [0, 4.881506, 0], [0, 0, 2.959824]])
-        elts = [el_li, el_li, el_o, el_o, el_o, el_o]
-        coords = []
-        coords.append([0.500000, 0.500000, 0.500000])
-        coords.append([0, 0, 0])
-        coords.append([0.632568, 0.085090, 0.500000])
-        coords.append([0.367432, 0.914910, 0.500000])
-        coords.append([0.132568, 0.414910, 0.000000])
-        coords.append([0.867432, 0.585090, 0.000000])
-        struct = Structure(latt, elts, coords)
+        elems = [el_li, el_li, el_o, el_o, el_o, el_o]
+        coords = [
+            [0.5, 0.5, 0.5],
+            [0, 0, 0],
+            [0.632568, 0.085090, 0.5],
+            [0.367432, 0.914910, 0.5],
+            [0.132568, 0.414910, 0],
+            [0.867432, 0.585090, 0],
+        ]
+        struct = Structure(latt, elems, coords)
         assert oxide_type(struct, 1.1) == "superoxide"
 
         el_li = Element("Li")
         el_o = Element("O")
-        elts = [el_li, el_o, el_o, el_o]
+        elems = [el_li, el_o, el_o, el_o]
         latt = Lattice.from_parameters(3.999911, 3.999911, 3.999911, 133.847504, 102.228244, 95.477342)
         coords = [
             [0.513004, 0.513004, 1.000000],
             [0.017616, 0.017616, 0.000000],
             [0.649993, 0.874790, 0.775203],
             [0.099587, 0.874790, 0.224797],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         assert oxide_type(struct, 1.1) == "ozonide"
 
         latt = Lattice.from_parameters(3.159597, 3.159572, 7.685205, 89.999884, 89.999674, 60.000510)
         el_li = Element("Li")
         el_o = Element("O")
-        elts = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
+        elems = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
         coords = [
             [0.666656, 0.666705, 0.750001],
             [0.333342, 0.333378, 0.250001],
@@ -148,14 +149,14 @@ def test_oxide_type(self):
             [0.666666, 0.666686, 0.350813],
             [0.666665, 0.666684, 0.149189],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         assert oxide_type(struct, 1.1) == "peroxide"
 
         el_li = Element("Li")
         el_o = Element("O")
         el_h = Element("H")
         latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
-        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
+        elems = [el_h, el_h, el_li, el_li, el_o, el_o]
         coords = [
             [0.000000, 0.500000, 0.413969],
             [0.500000, 0.000000, 0.586031],
@@ -164,14 +165,14 @@ def test_oxide_type(self):
             [0.000000, 0.500000, 0.192672],
             [0.500000, 0.000000, 0.807328],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         assert oxide_type(struct, 1.1) == "hydroxide"
 
         el_li = Element("Li")
         el_n = Element("N")
         el_h = Element("H")
         latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
-        elts = [el_h, el_h, el_li, el_li, el_n, el_n]
+        elems = [el_h, el_h, el_li, el_li, el_n, el_n]
         coords = [
             [0.000000, 0.500000, 0.413969],
             [0.500000, 0.000000, 0.586031],
@@ -180,12 +181,12 @@ def test_oxide_type(self):
             [0.000000, 0.500000, 0.192672],
             [0.500000, 0.000000, 0.807328],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         assert oxide_type(struct, 1.1) == "None"
 
         el_o = Element("O")
         latt = Lattice.from_parameters(4.389828, 5.369789, 5.369789, 70.786622, 69.244828, 69.244828)
-        elts = [el_o, el_o, el_o, el_o, el_o, el_o, el_o, el_o]
+        elems = [el_o, el_o, el_o, el_o, el_o, el_o, el_o, el_o]
         coords = [
             [0.844609, 0.273459, 0.786089],
             [0.155391, 0.213911, 0.726541],
@@ -196,7 +197,7 @@ def test_oxide_type(self):
             [0.132641, 0.148222, 0.148222],
             [0.867359, 0.851778, 0.851778],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         assert oxide_type(struct, 1.1) == "None"
 
     def test_sulfide_type(self):

tests/entries/test_compatibility.py

@@ -1321,15 +1321,15 @@ def test_process_entry_superoxide(self):
         el_li = Element("Li")
         el_o = Element("O")
         latt = Lattice([[3.985034, 0.0, 0.0], [0.0, 4.881506, 0.0], [0.0, 0.0, 2.959824]])
-        elts = [el_li, el_li, el_o, el_o, el_o, el_o]
+        elems = [el_li, el_li, el_o, el_o, el_o, el_o]
         coords = []
         coords.append([0.500000, 0.500000, 0.500000])
         coords.append([0.0, 0.0, 0.0])
         coords.append([0.632568, 0.085090, 0.500000])
         coords.append([0.367432, 0.914910, 0.500000])
         coords.append([0.132568, 0.414910, 0.000000])
         coords.append([0.867432, 0.585090, 0.000000])
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         lio2_entry = ComputedStructureEntry(
             struct,
             -3,
@@ -1351,7 +1351,7 @@ def test_process_entry_peroxide(self):
         latt = Lattice.from_parameters(3.159597, 3.159572, 7.685205, 89.999884, 89.999674, 60.000510)
         el_li = Element("Li")
         el_o = Element("O")
-        elts = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
+        elems = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
         coords = [
             [0.666656, 0.666705, 0.750001],
             [0.333342, 0.333378, 0.250001],
@@ -1362,7 +1362,7 @@ def test_process_entry_peroxide(self):
             [0.666666, 0.666686, 0.350813],
             [0.666665, 0.666684, 0.149189],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         li2o2_entry = ComputedStructureEntry(
             struct,
             -3,
@@ -1383,15 +1383,15 @@ def test_process_entry_peroxide(self):
     def test_process_entry_ozonide(self):
         el_li = Element("Li")
         el_o = Element("O")
-        elts = [el_li, el_o, el_o, el_o]
+        elems = [el_li, el_o, el_o, el_o]
         latt = Lattice.from_parameters(3.999911, 3.999911, 3.999911, 133.847504, 102.228244, 95.477342)
         coords = [
             [0.513004, 0.513004, 1.000000],
             [0.017616, 0.017616, 0.000000],
             [0.649993, 0.874790, 0.775203],
             [0.099587, 0.874790, 0.224797],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         lio3_entry = ComputedStructureEntry(
             struct,
             -3,
@@ -1412,10 +1412,10 @@ def test_process_entry_ozonide(self):
     def test_process_entry_oxide(self):
         el_li = Element("Li")
         el_o = Element("O")
-        elts = [el_li, el_li, el_o]
+        elems = [el_li, el_li, el_o]
         latt = Lattice.from_parameters(3.278, 3.278, 3.278, 60, 60, 60)
         coords = [[0.25, 0.25, 0.25], [0.75, 0.75, 0.75], [0.0, 0.0, 0.0]]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         li2o_entry = ComputedStructureEntry(
             struct,
             -3,
@@ -1602,10 +1602,10 @@ def setUp(self):
     def test_oxide_energy_corr(self):
         el_li = Element("Li")
         el_o = Element("O")
-        elts = [el_li, el_li, el_o]
+        elems = [el_li, el_li, el_o]
         latt = Lattice.from_parameters(3.278, 3.278, 3.278, 60, 60, 60)
         coords = [[0.25, 0.25, 0.25], [0.75, 0.75, 0.75], [0.0, 0.0, 0.0]]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         li2o_entry = ComputedStructureEntry(
             struct,
             -3,
@@ -1627,7 +1627,7 @@ def test_peroxide_energy_corr(self):
         latt = Lattice.from_parameters(3.159597, 3.159572, 7.685205, 89.999884, 89.999674, 60.000510)
         el_li = Element("Li")
         el_o = Element("O")
-        elts = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
+        elems = [el_li, el_li, el_li, el_li, el_o, el_o, el_o, el_o]
         coords = [
             [0.666656, 0.666705, 0.750001],
             [0.333342, 0.333378, 0.250001],
@@ -1638,7 +1638,7 @@ def test_peroxide_energy_corr(self):
             [0.666666, 0.666686, 0.350813],
             [0.666665, 0.666684, 0.149189],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         cse_params = {
             "is_hubbard": False,
             "hubbards": None,
@@ -1656,15 +1656,15 @@ def test_peroxide_energy_corr(self):
     def test_ozonide(self):
         el_li = Element("Li")
         el_o = Element("O")
-        elts = [el_li, el_o, el_o, el_o]
+        elems = [el_li, el_o, el_o, el_o]
         latt = Lattice.from_parameters(3.999911, 3.999911, 3.999911, 133.847504, 102.228244, 95.477342)
         coords = [
             [0.513004, 0.513004, 1.000000],
             [0.017616, 0.017616, 0.000000],
             [0.649993, 0.874790, 0.775203],
             [0.099587, 0.874790, 0.224797],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         lio3_entry = ComputedStructureEntry(
             struct,
             -3,
@@ -1867,7 +1867,7 @@ def test_aqueous_compat(self):
         el_o = Element("O")
         el_h = Element("H")
         latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
-        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
+        elems = [el_h, el_h, el_li, el_li, el_o, el_o]
         coords = [
             [0.000000, 0.500000, 0.413969],
             [0.500000, 0.000000, 0.586031],
@@ -1876,7 +1876,7 @@ def test_aqueous_compat(self):
             [0.000000, 0.500000, 0.192672],
             [0.500000, 0.000000, 0.807328],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
         lioh_entry = ComputedStructureEntry(
             struct,
             -3,
@@ -1902,7 +1902,7 @@ def test_potcar_doenst_match_structure(self):
         el_o = Element("O")
         el_h = Element("H")
         latt = Lattice.from_parameters(3.565276, 3.565276, 4.384277, 90.000000, 90.000000, 90.000000)
-        elts = [el_h, el_h, el_li, el_li, el_o, el_o]
+        elems = [el_h, el_h, el_li, el_li, el_o, el_o]
         coords = [
             [0.000000, 0.500000, 0.413969],
             [0.500000, 0.000000, 0.586031],
@@ -1911,7 +1911,7 @@ def test_potcar_doenst_match_structure(self):
             [0.000000, 0.500000, 0.192672],
             [0.500000, 0.000000, 0.807328],
         ]
-        struct = Structure(latt, elts, coords)
+        struct = Structure(latt, elems, coords)
 
         lioh_entry = ComputedStructureEntry(
             struct,

tests/io/test_xcrysden.py

@@ -8,9 +8,7 @@
 
 class TestXSF(PymatgenTest):
     def test_xsf(self):
-        coords = []
-        coords.append([0, 0, 0])
-        coords.append([0.75, 0.5, 0.75])
+        coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
         lattice = Lattice(
             [
                 [3.8401979337, 0.00, 0.00],

tests/io/vasp/test_inputs.py

@@ -186,9 +186,7 @@ def test_cart_scale(self):
 
     def test_significant_figures(self):
         si = 14
-        coords = []
-        coords.append([0, 0, 0])
-        coords.append([0.75, 0.5, 0.75])
+        coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
 
         # Silicon structure for testing.
         latt = [
@@ -215,9 +213,7 @@ def test_significant_figures(self):
 
     def test_str(self):
         si = 14
-        coords = []
-        coords.append([0, 0, 0])
-        coords.append([0.75, 0.5, 0.75])
+        coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
 
         # Silicon structure for testing.
         latt = [
@@ -335,9 +331,7 @@ def test_setattr(self):
 
     def test_velocities(self):
         si = 14
-        coords = []
-        coords.append([0, 0, 0])
-        coords.append([0.75, 0.5, 0.75])
+        coords = [[0, 0, 0], [0.75, 0.5, 0.75]]
 
         # Silicon structure for testing.
         latt = [