Fix test_valid_magmom_struct() error message regex (#3276)

* psps->PSPs in doc strings

* fix typo

* try fix test_valid_magmom_struct() err msg regex

* revert pymatgen/io/abinit/pseudos.py

Author: janosh

pymatgen/analysis/piezo_sensitivity.py

@@ -51,7 +51,7 @@ def __init__(self, structure: Structure, bec, pointops, tol: float = 1e-3):
         if np.sum(self.bec) >= tol:
             warnings.warn("Input born effective charge tensor does not satisfy charge neutrality")
 
-    def get_BEC_operations(self, eigtol=1e-05, opstol=1e-03):
+    def get_BEC_operations(self, eigtol=1e-5, opstol=1e-3):
         """
         Returns the symmetry operations which maps the tensors
         belonging to equivalent sites onto each other in the form
@@ -187,7 +187,7 @@ def __init__(self, structure: Structure, ist, pointops, tol: float = 1e-3):
         if not (obj - np.transpose(obj, (0, 1, 3, 2)) < tol).all():
             warnings.warn("Input internal strain tensor does not satisfy standard symmetries")
 
-    def get_IST_operations(self, opstol=1e-03):
+    def get_IST_operations(self, opstol=1e-3):
         """
         Returns the symmetry operations which maps the tensors
         belonging to equivalent sites onto each other in the form
@@ -278,7 +278,7 @@ def __init__(self, structure: Structure, fcm, pointops, sharedops, tol: float =
         self.sharedops = sharedops
         self.FCM_operations = None
 
-    def get_FCM_operations(self, eigtol=1e-05, opstol=1e-05):
+    def get_FCM_operations(self, eigtol=1e-5, opstol=1e-5):
         """
         Returns the symmetry operations which maps the tensors
         belonging to equivalent sites onto each other in the form
@@ -497,7 +497,7 @@ def get_stable_FCM(self, fcm, fcmasum=10):
             maxeig = np.max(-1 * eigs)
             eigsort = np.argsort(np.abs(eigs))
             for i in range(3, len(eigs)):
-                if eigs[eigsort[i]] > 1e-06:
+                if eigs[eigsort[i]] > 1e-6:
                     eigs[eigsort[i]] = -1 * maxeig * np.random.rand()
             diag = np.real(np.eye(len(fcm)) * eigs)
 
@@ -508,7 +508,7 @@ def get_stable_FCM(self, fcm, fcmasum=10):
             unstable_modes = 0
             eigsort = np.argsort(np.abs(eigs))
             for i in range(3, len(eigs)):
-                if eigs[eigsort[i]] > 1e-06:
+                if eigs[eigsort[i]] > 1e-6:
                     unstable_modes = 1
             if unstable_modes == 1:
                 count = count + 1

pymatgen/analysis/structure_prediction/volume_predictor.py

@@ -171,13 +171,12 @@ def predict(self, structure: Structure, icsd_vol=False):
 
         Args:
             structure (Structure) : a crystal structure with an unknown volume.
-            icsd_vol (bool) : True if the input structure's volume comes from
-                ICSD.
+            icsd_vol (bool) : True if the input structure's volume comes from ICSD.
 
         Returns:
             a float value of the predicted volume.
         """
-        # Get standard deviation of electronnegativity in the structure.
+        # Get standard deviation of electronegativity in the structure.
         std_x = np.std([site.specie.X for site in structure])
         # Sites that have atomic radii
         sub_sites = []

pymatgen/cli/pmg.py

@@ -123,7 +123,7 @@ def main():
         "--add",
         dest="var_spec",
         nargs="+",
-        help="Variables to add in the form of space separated key value pairs. E.g., PMG_VASP_PSP_DIR ~/psps",
+        help="Variables to add in the form of space separated key value pairs. E.g., PMG_VASP_PSP_DIR ~/PSPs",
     )
 
     groups.add_argument(

pymatgen/core/structure.py

@@ -2553,7 +2553,7 @@ def as_dataframe(self):
         Example:
             Species    a    b             c    x             y             z  magmom
             0    (Si)  0.0  0.0  0.000000e+00  0.0  0.000000e+00  0.000000e+00       5
-            1    (Si)  0.0  0.0  1.000000e-07  0.0 -2.217138e-07  3.135509e-07      -5
+            1    (Si)  0.0  0.0  1.000000e-7  0.0 -2.217138e-7  3.135509e-7      -5
         """
         data = []
         site_properties = self.site_properties

pymatgen/electronic_structure/boltztrap.py

@@ -862,7 +862,7 @@ def get_symm_bands(self, structure: Structure, efermi, kpt_line=None, labels_dic
             _idx_list: list[tuple[int, ArrayLike]] = []
             for idx, kp in enumerate(kpt_line):
                 w: list[bool] = []
-                prec = 1e-05
+                prec = 1e-5
                 while len(w) == 0:
                     w = np.where(np.all(np.abs(kp - self._bz_kpoints) < [prec] * 3, axis=1))[0]  # type: ignore
                     prec *= 10

pymatgen/io/abinit/netcdf.py

@@ -368,7 +368,7 @@ def __init__(self, name, doc, etsf_name=None):
     _H("ntypat", "input variable", etsf_name="number_of_atom_species"),
     _H("occopt", "input variable"),
     _H("pertcase", "the index of the perturbation, 0 if GS calculation"),
-    _H("usepaw", "input variable (0=norm-conserving psps, 1=paw)"),
+    _H("usepaw", "input variable (0=norm-conserving PSPs, 1=paw)"),
     _H("usewvl", "input variable (0=plane-waves, 1=wavelets)"),
     _H("kptopt", "input variable (defines symmetries used for k-point sampling)"),
     _H("pawcpxocc", "input variable"),
@@ -379,7 +379,7 @@ def __init__(self, name, doc, etsf_name=None):
     _H("nshiftk", "number of shifts after inkpts."),
     _H("icoulomb", "input variable."),
     _H("ecut", "input variable", etsf_name="kinetic_energy_cutoff"),
-    _H("ecutdg", "input variable (ecut for NC psps, pawecutdg for paw)"),
+    _H("ecutdg", "input variable (ecut for NC PSPs, pawecutdg for paw)"),
     _H("ecutsm", "input variable"),
     _H("ecut_eff", "ecut*dilatmx**2 (dilatmx is an input variable)"),
     _H("etot", "EVOLVING variable"),
@@ -398,17 +398,17 @@ def __init__(self, name, doc, etsf_name=None):
     _H("kptrlatt_orig", "kptrlatt_orig(3,3) Original kptrlatt"),
     _H("kptrlatt", "kptrlatt(3,3) kptrlatt after inkpts."),
     _H("istwfk", "input variable istwfk(nkpt)"),
-    _H("lmn_size", "lmn_size(npsp) from psps"),
+    _H("lmn_size", "lmn_size(npsp) from PSPs"),
     _H("nband", "input variable nband(nkpt*nsppol)", etsf_name="number_of_states"),
     _H(
         "npwarr",
         "npwarr(nkpt) array holding npw for each k point",
         etsf_name="number_of_coefficients",
     ),
-    _H("pspcod", "pscod(npsp) from psps"),
-    _H("pspdat", "psdat(npsp) from psps"),
-    _H("pspso", "pspso(npsp) from psps"),
-    _H("pspxc", "pspxc(npsp) from psps"),
+    _H("pspcod", "pscod(npsp) from PSPs"),
+    _H("pspdat", "psdat(npsp) from PSPs"),
+    _H("pspso", "pspso(npsp) from PSPs"),
+    _H("pspxc", "pspxc(npsp) from PSPs"),
     _H("so_psp", "input variable so_psp(npsp)"),
     _H("symafm", "input variable symafm(nsym)"),
     # _H(symrel="input variable symrel(3,3,nsym)",  etsf_name="reduced_symmetry_matrices"),
@@ -429,14 +429,14 @@ def __init__(self, name, doc, etsf_name=None):
     _H("shiftk", "shiftk(3,nshiftk), shiftks after inkpts"),
     _H("amu", "amu(ntypat) ! EVOLVING variable"),
     # _H("xred", "EVOLVING variable xred(3,natom)", etsf_name="reduced_atom_positions"),
-    _H("zionpsp", "zionpsp(npsp) from psps"),
+    _H("zionpsp", "zionpsp(npsp) from PSPs"),
     _H(
         "znuclpsp",
-        "znuclpsp(npsp) from psps. Note the difference between (znucl|znucltypat) and znuclpsp",
+        "znuclpsp(npsp) from PSPs. Note the difference between (znucl|znucltypat) and znuclpsp",
     ),
     _H("znucltypat", "znucltypat(ntypat) from alchemy", etsf_name="atomic_numbers"),
     _H("codvsn", "version of the code"),
-    _H("title", "title(npsp) from psps"),
+    _H("title", "title(npsp) from PSPs"),
     _H(
         "md5_pseudos",
         "md5pseudos(npsp), md5 checksums associated to pseudos (read from file)",

pymatgen/io/vasp/outputs.py

@@ -248,7 +248,7 @@ class Vasprun(MSONable):
                     'e_wo_entrp': -525.07195568,
                     'kinetic': 3.17809233,
                     'lattice kinetic': 0.0,
-                    'nosekinetic': 1.323e-05,
+                    'nosekinetic': 1.323e-5,
                     'nosepot': 0.0,
                     'total': -521.89385012
                     },
@@ -2241,10 +2241,12 @@ def _parse_sci_notation(line):
         Method to parse lines with values in scientific notation and potentially
         without spaces in between the values. This assumes that the scientific
         notation always lists two digits for the exponent, e.g. 3.535E-02
+
         Args:
             line: line to parse.
 
-        Returns: an array of numbers if found, or empty array if not
+        Returns:
+            list[float]: numbers if found, empty ist if not
         """
         m = re.findall(r"[\.\-\d]+E[\+\-]\d{2}", line)
         if m:

pymatgen/io/vasp/sets.py

@@ -870,7 +870,7 @@ class MPRelaxSet(DictSet):
     Implementation of VaspInputSet utilizing parameters in the public
     Materials Project. Typically, the pseudopotentials chosen contain more
     electrons than the MIT parameters, and the k-point grid is ~50% more dense.
-    The LDAUU parameters are also different due to the different psps used,
+    The LDAUU parameters are also different due to the different PSPs used,
     which result in different fitted values.
     """
 
@@ -1264,8 +1264,7 @@ def __init__(self, structure: Structure, bandgap=0, prev_incar=None, lepsilon=Fa
         Args:
             structure (Structure): Structure from previous run.
             bandgap (float): Bandgap of the structure in eV. The bandgap is used to
-                    compute the appropriate k-point density and determine the
-                    smearing settings.
+                compute the appropriate k-point density and determine the smearing settings.
             prev_incar (Incar): Incar file from previous run.
             lepsilon (bool): Whether to add static dielectric calculation
             lcalcpol (bool): Whether to turn on evaluation of the Berry phase approximations
@@ -2742,7 +2741,7 @@ def __init__(self, structure: Structure, **kwargs):
 
         updates = {
             "ADDGRID": True,
-            "EDIFF": 1e-05,
+            "EDIFF": 1e-5,
             "EDIFFG": -0.05,
             "LASPH": True,
             "LDAU": False,

tests/analysis/test_interface_reactions.py

@@ -169,42 +169,42 @@ def test_get_entry_energy(self):
         ) as warns:
             energy = InterfacialReactivity._get_entry_energy(self.pd, comp)
         assert len(warns) == 1
-        test1 = np.isclose(energy, -30, atol=1e-03)
+        test1 = np.isclose(energy, -30, atol=1e-3)
         assert test1, f"_get_entry_energy: energy for {comp.reduced_formula} is wrong!"
         # Test normal functionality
         comp = Composition("MnO2")
-        test2 = np.isclose(InterfacialReactivity._get_entry_energy(self.pd, comp), -30, atol=1e-03)
+        test2 = np.isclose(InterfacialReactivity._get_entry_energy(self.pd, comp), -30, atol=1e-3)
         assert test2, f"_get_entry_energy: energy for {comp.reduced_formula} is wrong!"
 
     def test_get_grand_potential(self):
         comp = Composition("LiMnO2")
         # Test non-normalized case
-        test1 = np.isclose(self.irs[1]._get_grand_potential(comp), -27, atol=1e-03)
+        test1 = np.isclose(self.irs[1]._get_grand_potential(comp), -27, atol=1e-3)
         assert test1, "_get_grand_potential: Non-normalized case gets error!"
 
         # Test normalized case
-        test2 = np.isclose(self.irs[2]._get_grand_potential(comp), -9, atol=1e-03)
+        test2 = np.isclose(self.irs[2]._get_grand_potential(comp), -9, atol=1e-3)
         assert test2, "_get_grand_potential: Normalized case gets error!"
 
         comp2 = Composition("Li2O2")
         # Test use_hull_energy option.
-        test3 = np.isclose(self.irs[8]._get_grand_potential(comp2), -4, atol=1e-03)
+        test3 = np.isclose(self.irs[8]._get_grand_potential(comp2), -4, atol=1e-3)
         assert test3, "_get_grand_potential: get hull energy gets error!"
 
-        test4 = np.isclose(self.irs[9]._get_grand_potential(comp2), -2, atol=1e-03)
+        test4 = np.isclose(self.irs[9]._get_grand_potential(comp2), -2, atol=1e-3)
         assert test4, f"_get_grand_potential: gets error for {comp2.reduced_formula}!"
 
     def test_get_energy(self):
-        test1 = np.isclose(self.irs[0]._get_energy(0.5), -15, atol=1e-03)
+        test1 = np.isclose(self.irs[0]._get_energy(0.5), -15, atol=1e-3)
         assert test1, "_get_energy: phase diagram gets error!"
 
-        test2 = np.isclose(self.irs[3]._get_energy(0.6666666), -7.333333, atol=1e-03)
+        test2 = np.isclose(self.irs[3]._get_energy(0.6666666), -7.333333, atol=1e-3)
         assert test2, "_get_energy: grand canonical phase diagram gets error!"
 
-        test3 = np.isclose(self.irs[6]._get_energy(0.3333333), -3.333333, atol=1e-03)
+        test3 = np.isclose(self.irs[6]._get_energy(0.3333333), -3.333333, atol=1e-3)
         assert test3, "_get_energy: convex hull energy gets error. "
 
-        test4 = np.isclose(self.irs[7]._get_energy(0.3333333), -4, atol=1e-03)
+        test4 = np.isclose(self.irs[7]._get_energy(0.3333333), -4, atol=1e-3)
         assert test4, "_get_energy: gets error. "
 
     def test_get_reaction(self):

tests/analysis/test_molecule_matcher.py

@@ -392,14 +392,14 @@ def test_fit(self):
         mm = HungarianOrderMatcher(mol1)
 
         _, rmsd = mm.fit(mol2)
-        assert rmsd == approx(1.4171601659148593e-05, abs=1e-6)
+        assert rmsd == approx(1.4171601659148593e-5, abs=1e-6)
 
         mol1 = Molecule.from_file(f"{test_dir}/c1.xyz")
         mol2 = Molecule.from_file(f"{test_dir}/c2.xyz")
         mm = HungarianOrderMatcher(mol1)
 
         _, rmsd = mm.fit(mol2)
-        assert rmsd == approx(9.479012116064961e-05, abs=1e-6)
+        assert rmsd == approx(9.479012116064961e-5, abs=1e-6)
 
         mol1 = Molecule.from_file(f"{test_dir}/t3.xyz")
         mol2 = Molecule.from_file(f"{test_dir}/t4.xyz")
@@ -413,7 +413,7 @@ def test_fit(self):
         mm = HungarianOrderMatcher(mol1)
 
         _, rmsd = mm.fit(mol2)
-        assert rmsd == approx(9.28245597473488e-05, abs=1e-6)
+        assert rmsd == approx(9.28245597473488e-5, abs=1e-6)
 
         mol1 = Molecule.from_file(f"{test_dir}/ethene1.xyz")
         mol2 = Molecule.from_file(f"{test_dir}/ethene2.xyz")
@@ -497,14 +497,14 @@ def test_fit(self):
         mm = GeneticOrderMatcher(mol1, threshold=0.01)
 
         _, rmsd = mm.fit(mol2)[0]
-        assert rmsd == approx(7.061017534055039e-05, abs=1e-6)
+        assert rmsd == approx(7.061017534055039e-5, abs=1e-6)
 
         mol1 = Molecule.from_file(f"{test_dir}/c1.xyz")
         mol2 = Molecule.from_file(f"{test_dir}/c2.xyz")
         mm = GeneticOrderMatcher(mol1, threshold=0.01)
 
         _, rmsd = mm.fit(mol2)[0]
-        assert rmsd == approx(9.459575146593829e-05, abs=1e-6)
+        assert rmsd == approx(9.459575146593829e-5, abs=1e-6)
 
         mol1 = Molecule.from_file(f"{test_dir}/t3.xyz")
         mol2 = Molecule.from_file(f"{test_dir}/t4.xyz")
@@ -518,7 +518,7 @@ def test_fit(self):
         mm = GeneticOrderMatcher(mol1, threshold=0.01)
 
         _, rmsd = mm.fit(mol2)[0]
-        assert rmsd == approx(9.28245597473488e-05, abs=1e-6)
+        assert rmsd == approx(9.28245597473488e-5, abs=1e-6)
 
         mol1 = Molecule.from_file(f"{test_dir}/ethene1.xyz")
         mol2 = Molecule.from_file(f"{test_dir}/ethene2.xyz")