fix pmg paper readme badge

add NthOrderElasticTensor types

Author: janosh

README.md

@@ -13,7 +13,7 @@ height="70">
 [![PyPI Downloads](https://img.shields.io/pypi/dm/pymatgen?logo=pypi&logoColor=white&color=blue&label=PyPI)](https://pypi.org/project/pymatgen)
 [![Conda Downloads](https://img.shields.io/conda/dn/conda-forge/pymatgen?logo=condaforge&color=blue&label=Conda)](https://anaconda.org/conda-forge/pymatgen)
 [![Requires Python 3.9+](https://img.shields.io/badge/Python-3.9+-blue.svg?logo=python&logoColor=white)](https://python.org/downloads)
-[![arXiv](https://img.shields.io/badge/J.ComMatSci-2012.10.028-blue)](https://doi.org/10.1016/j.commatsci.2012.10.028)
+[![Paper](https://img.shields.io/badge/J.ComMatSci-2012.10.028-blue?logo=elsevier&logoColor=white)](https://doi.org/10.1016/j.commatsci.2012.10.028)
 
 </h4>
 

dev_scripts/potcar_scrambler.py

@@ -93,8 +93,8 @@ def scramble_single_potcar(self, potcar: PotcarSingle):
         return scrambled_potcar_str
 
     def to_file(self, filename: str):
-        with zopen(filename, "wt") as f:
-            f.write(self.scrambled_potcars_str)
+        with zopen(filename, "wt") as file:
+            file.write(self.scrambled_potcars_str)
 
     @classmethod
     def from_file(cls, input_filename: str, output_filename: str | None = None):

docs/index.md

@@ -320,8 +320,7 @@ def snyder_total(self, structure: Structure) -> float:
 
     @raise_if_unphysical
     def clarke_thermalcond(self, structure: Structure) -> float:
-        """
-        Calculates Clarke's thermal conductivity (in SI units).
+        """Calculates Clarke's thermal conductivity.
 
         Args:
             structure: pymatgen structure object
@@ -339,8 +338,7 @@ def clarke_thermalcond(self, structure: Structure) -> float:
 
     @raise_if_unphysical
     def cahill_thermalcond(self, structure: Structure) -> float:
-        """
-        Calculates Cahill's thermal conductivity (in SI units).
+        """Calculate Cahill's thermal conductivity.
 
         Args:
             structure: pymatgen structure object
@@ -354,12 +352,11 @@ def cahill_thermalcond(self, structure: Structure) -> float:
 
     @due.dcite(
         Doi("10.1039/C7EE03256K"),
-        description="Minimum thermal conductivity in the context of diffuson-mediated thermal transport",
+        description="Minimum thermal conductivity in the context of diffusion-mediated thermal transport",
     )
     @raise_if_unphysical
     def agne_diffusive_thermalcond(self, structure: Structure) -> float:
-        """
-        Calculates Agne's diffusive thermal conductivity (in SI units).
+        """Calculates Agne's diffusive thermal conductivity.
 
         Please cite the original authors if using this method
         M. T. Agne, R. Hanus, G. J. Snyder, Energy Environ. Sci. 2018, 11, 609-616.
@@ -397,23 +394,23 @@ def debye_temperature(self, structure: Structure) -> float:
         return 1.05457e-34 / 1.38065e-23 * vm * (6 * np.pi**2 / v0) ** (1 / 3)
 
     @property
-    def universal_anisotropy(self):
+    def universal_anisotropy(self) -> float:
         """Returns the universal anisotropy value."""
         return 5 * self.g_voigt / self.g_reuss + self.k_voigt / self.k_reuss - 6.0
 
     @property
-    def homogeneous_poisson(self):
+    def homogeneous_poisson(self) -> float:
         """Returns the homogeneous poisson ratio."""
         return (1 - 2 / 3 * self.g_vrh / self.k_vrh) / (2 + 2 / 3 * self.g_vrh / self.k_vrh)
 
-    def green_kristoffel(self, u):
+    def green_kristoffel(self, u) -> float:
         """Returns the Green-Kristoffel tensor for a second-order tensor."""
         return self.einsum_sequence([u, u], "ijkl,i,l")
 
     @property
     def property_dict(self):
         """Returns a dictionary of properties derived from the elastic tensor."""
-        props = [
+        props = (
             "k_voigt",
             "k_reuss",
             "k_vrh",
@@ -423,7 +420,7 @@ def property_dict(self):
             "universal_anisotropy",
             "homogeneous_poisson",
             "y_mod",
-        ]
+        )
         return {prop: getattr(self, prop) for prop in props}
 
     def get_structure_property_dict(
@@ -441,7 +438,7 @@ def get_structure_property_dict(
             ignore_errors (bool): if set to true, will set problem properties
                 that depend on a physical tensor to None, defaults to False
         """
-        s_props = [
+        s_props = (
             "trans_v",
             "long_v",
             "snyder_ac",
@@ -450,7 +447,7 @@ def get_structure_property_dict(
             "clarke_thermalcond",
             "cahill_thermalcond",
             "debye_temperature",
-        ]
+        )
         sp_dict: dict[str, float | Structure | None]
         if ignore_errors and (self.k_vrh < 0 or self.g_vrh < 0):
             sp_dict = {prop: None for prop in s_props}
@@ -514,8 +511,8 @@ def from_independent_strains(cls, strains, stresses, eq_stress=None, vasp=False,
                 c_ij[ii, jj] = np.polyfit(strains[:, ii], stresses[:, jj], 1)[0]
         if vasp:
             c_ij *= -0.1  # Convert units/sign convention of vasp stress tensor
-        c = cls.from_voigt(c_ij)
-        return c.zeroed(tol)
+        instance = cls.from_voigt(c_ij)
+        return instance.zeroed(tol)
 
 
 class ComplianceTensor(Tensor):

pymatgen/analysis/elasticity/elastic.py

@@ -10,39 +10,39 @@
 
 class TestTemplateInputGen(PymatgenTest):
     def test_write_inputs(self):
-        tis = TemplateInputGen().get_input_set(
+        input_set = TemplateInputGen().get_input_set(
             template=f"{TEST_FILES_DIR}/template_input_file.txt",
             variables={"TEMPERATURE": 298},
             filename="hello_world.in",
         )
-        tis.write_input(self.tmp_path)
-        with open(os.path.join(self.tmp_path, "hello_world.in")) as f:
-            assert "298" in f.read()
+        input_set.write_input(self.tmp_path)
+        with open(os.path.join(self.tmp_path, "hello_world.in")) as file:
+            assert "298" in file.read()
 
         with pytest.raises(FileNotFoundError, match="No such file or directory:"):
-            tis.write_input(os.path.join(self.tmp_path, "temp"), make_dir=False)
+            input_set.write_input(os.path.join(self.tmp_path, "temp"), make_dir=False)
 
-        tis.write_input(os.path.join(self.tmp_path, "temp"), make_dir=True)
+        input_set.write_input(os.path.join(self.tmp_path, "temp"), make_dir=True)
 
-        tis = TemplateInputGen().get_input_set(
+        input_set = TemplateInputGen().get_input_set(
             template=f"{TEST_FILES_DIR}/template_input_file.txt",
             variables={"TEMPERATURE": 400},
             filename="hello_world.in",
         )
 
         # test len, iter, getitem
-        assert len(tis.inputs) == 1
-        assert len(list(tis.inputs)) == 1
-        assert isinstance(tis.inputs["hello_world.in"], str)
+        assert len(input_set.inputs) == 1
+        assert len(list(input_set.inputs)) == 1
+        assert isinstance(input_set.inputs["hello_world.in"], str)
 
         with pytest.raises(FileExistsError, match="hello_world.in"):
-            tis.write_input(self.tmp_path, overwrite=False)
+            input_set.write_input(self.tmp_path, overwrite=False)
 
-        tis.write_input(self.tmp_path, overwrite=True)
+        input_set.write_input(self.tmp_path, overwrite=True)
 
-        with open(os.path.join(self.tmp_path, "hello_world.in")) as f:
-            assert "400" in f.read()
+        with open(os.path.join(self.tmp_path, "hello_world.in")) as file:
+            assert "400" in file.read()
 
-        tis.write_input(self.tmp_path, zip_inputs=True)
+        input_set.write_input(self.tmp_path, zip_inputs=True)
 
         assert "InputSet.zip" in list(os.listdir(self.tmp_path))