Merge pull request #91 from materialsproject/master

sync

Author: benrich37

src/pymatgen/core/lattice.py

@@ -10,7 +10,7 @@
 import warnings
 from collections import defaultdict
 from fractions import Fraction
-from functools import reduce
+from functools import cached_property, reduce
 from typing import TYPE_CHECKING
 
 import numpy as np
@@ -22,6 +22,7 @@
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
+    from typing import Literal
 
     from numpy.typing import ArrayLike, NDArray
     from typing_extensions import Self
@@ -74,17 +75,6 @@ def __init__(
 
         self.pbc = pbc
 
-    @property
-    def pbc(self) -> tuple[bool, bool, bool]:
-        """Tuple defining the periodicity of the Lattice."""
-        return self._pbc  # type:ignore[return-value]
-
-    @pbc.setter
-    def pbc(self, pbc: tuple[bool, bool, bool]) -> None:
-        if len(pbc) != 3 or any(item not in {True, False} for item in pbc):
-            raise ValueError(f"pbc must be a tuple of three True/False values, got {pbc}")
-        self._pbc = tuple(bool(item) for item in pbc)
-
     def __repr__(self) -> str:
         return "\n".join(
             [
@@ -148,6 +138,22 @@ def __format__(self, fmt_spec: str = "") -> str:
         return fmt.format(*(format(c, fmt_spec) for row in matrix for c in row))
 
     @property
+    def pbc(self) -> tuple[bool, bool, bool]:
+        """Tuple defining the periodicity of the Lattice."""
+        return self._pbc  # type:ignore[return-value]
+
+    @pbc.setter
+    def pbc(self, pbc: tuple[bool, bool, bool]) -> None:
+        if len(pbc) != 3 or any(item not in {True, False} for item in pbc):
+            raise ValueError(f"pbc must be a tuple of three True/False values, got {pbc}")
+        self._pbc = tuple(bool(item) for item in pbc)
+
+    @property
+    def matrix(self) -> NDArray[np.float64]:
+        """Copy of matrix representing the Lattice."""
+        return self._matrix
+
+    @cached_property
     def lengths(self) -> tuple[float, float, float]:
         """Lattice lengths.
 
@@ -156,7 +162,7 @@ def lengths(self) -> tuple[float, float, float]:
         """
         return tuple(np.sqrt(np.sum(self._matrix**2, axis=1)).tolist())  # type: ignore[return-value]
 
-    @property
+    @cached_property
     def angles(self) -> tuple[float, float, float]:
         """Lattice angles.
 
@@ -172,16 +178,17 @@ def angles(self) -> tuple[float, float, float]:
         angles = np.arccos(angles) * 180.0 / np.pi  # type: ignore[assignment]
         return tuple(angles.tolist())  # type: ignore[return-value]
 
+    @cached_property
+    def volume(self) -> float:
+        """Volume of the unit cell in Angstrom^3."""
+        matrix = self._matrix
+        return float(abs(np.dot(np.cross(matrix[0], matrix[1]), matrix[2])))
+
     @property
     def is_orthogonal(self) -> bool:
         """Whether all angles are 90 degrees."""
         return all(abs(a - 90) < 1e-5 for a in self.angles)
 
-    @property
-    def matrix(self) -> NDArray[np.float64]:
-        """Copy of matrix representing the Lattice."""
-        return self._matrix
-
     @property
     def is_3d_periodic(self) -> bool:
         """True if the Lattice is periodic in all directions."""
@@ -507,12 +514,6 @@ def gamma(self) -> float:
         """Angle gamma of lattice in degrees."""
         return self.angles[2]
 
-    @property
-    def volume(self) -> float:
-        """Volume of the unit cell in Angstrom^3."""
-        matrix = self._matrix
-        return float(abs(np.dot(np.cross(matrix[0], matrix[1]), matrix[2])))
-
     @property
     def parameters(self) -> tuple[float, float, float, float, float, float]:
         """6-tuple of floats (a, b, c, alpha, beta, gamma)."""
@@ -521,7 +522,7 @@ def parameters(self) -> tuple[float, float, float, float, float, float]:
     @property
     def params_dict(self) -> dict[str, float]:
         """Dictionary of lattice parameters."""
-        return dict(zip("a b c alpha beta gamma".split(), self.parameters, strict=True))
+        return dict(zip(("a", "b", "c", "alpha", "beta", "gamma"), self.parameters, strict=True))
 
     @property
     def reciprocal_lattice(self) -> Self:
@@ -897,11 +898,11 @@ def selling_dist(self, other: Self) -> float:
 
         return min(np.linalg.norm(reflection - selling2) for reflection in all_reflections)  # type: ignore[return-value, type-var]
 
-    def as_dict(self, verbosity: int = 0) -> dict:
+    def as_dict(self, verbosity: Literal[0, 1] = 0) -> dict:
         """MSONable dict representation of the Lattice.
 
         Args:
-            verbosity (int): Default of 0 only includes the matrix representation.
+            verbosity (0 | 1): Default of 0 only includes the matrix representation.
                 Set to 1 to include the lattice parameters.
         """
         dct = {
@@ -910,7 +911,15 @@ def as_dict(self, verbosity: int = 0) -> dict:
             "matrix": self._matrix.tolist(),
             "pbc": self.pbc,
         }
-        if verbosity > 0:
+
+        if verbosity not in {0, 1}:
+            warnings.warn(
+                f"`verbosity={verbosity}` is deprecated and will be disallowed in a future version. "
+                "Please use 0 (silent) or 1 (verbose) explicitly.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+        if verbosity > 0:  # TODO: explicit check `verbosity == 1`
             dct |= self.params_dict
             dct["volume"] = self.volume
 
@@ -1282,11 +1291,11 @@ def scale(self, new_volume: float) -> Self:
         Returns:
             New lattice with desired volume.
         """
-        versors = self.matrix / self.abc
+        versors = self.matrix / self.lengths
 
         geo_factor = abs(np.dot(np.cross(versors[0], versors[1]), versors[2]))
 
-        ratios = np.array(self.abc) / self.c
+        ratios = np.array(self.lengths) / self.c
 
         new_c = (new_volume / (geo_factor * np.prod(ratios))) ** (1 / 3.0)
 
@@ -1541,7 +1550,7 @@ def get_points_in_sphere_old(
         # TODO: refactor to use lll matrix (nmax will be smaller)
         # Determine the maximum number of supercells in each direction
         # required to contain a sphere of radius n
-        recp_len = np.array(self.reciprocal_lattice.abc) / (2 * np.pi)
+        recp_len = np.array(self.reciprocal_lattice.lengths) / (2 * np.pi)
         nmax = float(r) * recp_len + 0.01
 
         # Get the fractional coordinates of the center of the sphere
@@ -1849,7 +1858,7 @@ def get_points_in_spheres(
     if np.any(_pbc):
         if lattice is None:
             raise ValueError("Lattice needs to be supplied when considering periodic boundary")
-        recp_len = np.array(lattice.reciprocal_lattice.abc)
+        recp_len = np.array(lattice.reciprocal_lattice.lengths)
         maxr = np.ceil((r + 0.15) * recp_len / (2 * math.pi))
         frac_coords = lattice.get_fractional_coords(center_coords)
         nmin_temp = np.floor(np.min(frac_coords, axis=0)) - maxr

src/pymatgen/core/sites.py

@@ -4,6 +4,7 @@
 
 import collections
 import json
+import warnings
 from typing import TYPE_CHECKING, cast
 
 import numpy as np
@@ -16,7 +17,7 @@
 from pymatgen.util.misc import is_np_dict_equal
 
 if TYPE_CHECKING:
-    from typing import Any
+    from typing import Any, Literal
 
     from numpy.typing import ArrayLike, NDArray
     from typing_extensions import Self
@@ -254,7 +255,7 @@ def as_dict(self) -> dict:
         dct = {
             "name": self.species_string,
             "species": species,
-            "xyz": [float(c) for c in self.coords],
+            "xyz": self.coords.astype(float).tolist(),
             "properties": self.properties,
             "@module": type(self).__module__,
             "@class": type(self).__name__,
@@ -531,7 +532,7 @@ def distance_and_image_from_frac_coords(
         Args:
             fcoords (3x1 array): fractional coordinates to get distance from.
             jimage (3x1 array): Specific periodic image in terms of
-                lattice translations, e.g. [1,0,0] implies to take periodic
+                lattice translations, e.g. [1, 0, 0] implies to take periodic
                 image that is one a-lattice vector away. If jimage is None,
                 the image that is nearest to the site is found.
 
@@ -556,7 +557,7 @@ def distance_and_image(
         Args:
             other (PeriodicSite): Other site to get distance from.
             jimage (3x1 array): Specific periodic image in terms of lattice
-                translations, e.g. [1,0,0] implies to take periodic image
+                translations, e.g. [1, 0, 0] implies to take periodic image
                 that is one a-lattice vector away. If jimage is None,
                 the image that is nearest to the site is found.
 
@@ -576,7 +577,7 @@ def distance(
         Args:
             other (PeriodicSite): Other site to get distance from.
             jimage (3x1 array): Specific periodic image in terms of lattice
-                translations, e.g. [1,0,0] implies to take periodic image
+                translations, e.g. [1, 0, 0] implies to take periodic image
                 that is one a-lattice vector away. If jimage is None,
                 the image that is nearest to the site is found.
 
@@ -585,11 +586,11 @@ def distance(
         """
         return self.distance_and_image(other, jimage)[0]
 
-    def as_dict(self, verbosity: int = 0) -> dict:
+    def as_dict(self, verbosity: Literal[0, 1] = 0) -> dict:
         """JSON-serializable dict representation of PeriodicSite.
 
         Args:
-            verbosity (int): Verbosity level. Default of 0 only includes the matrix
+            verbosity (0 | 1): Verbosity level. Default of 0 only includes the matrix
                 representation. Set to 1 for more details such as Cartesian coordinates, etc.
         """
         species = []
@@ -602,16 +603,23 @@ def as_dict(self, verbosity: int = 0) -> dict:
 
         dct = {
             "species": species,
-            "abc": [float(c) for c in self._frac_coords],
+            "abc": self._frac_coords.astype(float).tolist(),
             "lattice": self._lattice.as_dict(verbosity=verbosity),
             "@module": type(self).__module__,
             "@class": type(self).__name__,
             "properties": self.properties,
             "label": self.label,
         }
 
-        if verbosity > 0:
-            dct["xyz"] = [float(c) for c in self.coords]
+        if verbosity not in {0, 1}:
+            warnings.warn(
+                f"`verbosity={verbosity}` is deprecated and will be disallowed in a future version. "
+                "Please use 0 (silent) or 1 (verbose) explicitly.",
+                DeprecationWarning,
+                stacklevel=2,
+            )
+        if verbosity > 0:  # TODO: explicitly check `verbosity == 1`
+            dct["xyz"] = self.coords.astype(float).tolist()
 
         return dct
 

src/pymatgen/core/structure.py

@@ -2813,14 +2813,14 @@ def get_orderings(
 
     def as_dict(
         self,
-        verbosity: int = 1,
+        verbosity: Literal[0, 1] = 1,
         fmt: Literal["abivars"] | None = None,
         **kwargs,
     ) -> dict[str, Any]:
         """Dict representation of Structure.
 
         Args:
-            verbosity (int): Verbosity level. Default of 1 includes both
+            verbosity (0 | 1): Verbosity level. Default of 1 includes both
                 direct and Cartesian coordinates for all sites, lattice
                 parameters, etc. Useful for reading and for insertion into a
                 database. Set to 0 for an extremely lightweight version
@@ -2857,7 +2857,10 @@ def as_dict(
             del site_dict["lattice"]
             del site_dict["@module"]
             del site_dict["@class"]
+            if verbosity == 0:
+                del site_dict["label"]
             sites.append(site_dict)
+
         dct["sites"] = sites
         return dct
 

tests/core/test_lattice.py

@@ -148,7 +148,6 @@ def test_static_methods(self):
         assert lattice.angles == approx(expected_angles)
 
     def test_attributes(self):
-        """Docstring for test_attributes."""
         lattice = Lattice.cubic(10.0)
         assert lattice.a == approx(10)
         assert lattice.b == approx(10)

tests/core/test_structure.py

@@ -268,6 +268,7 @@ def test_as_dict(self):
         dct = struct.as_dict(0)
         assert "volume" not in dct["lattice"]
         assert "xyz" not in dct["sites"][0]
+        assert "label" not in dct["sites"][0]
 
     def test_from_dict(self):
         dct = self.propertied_structure.as_dict()