Convert kpts in Kpoints to Sequence[tuple] and set it as property (#3758)

* convert some types

* make real tuple

* remove unnecessary `int` before `math.floor/ceil`

* Revert remove unnecessary int to avoid diff pollute

This reverts commit f8f43a2.

* fix some tests

* fix more tests

* relocate type Vector3D Matrix3D SitePropsType

* fix some Kpoint types

* fix some type

* relocate dunder methods to the head

* fix some type errors

* revert unneeded cast to tuple

* pre-commit auto-fixes

* revert unneeded cast to tuple

* revert unneeded cast to tuple

* pre-commit auto-fixes

* use Union over |

* remove unnecessary wrapping

* fix some types

* fix direct float str to int conversion

* use float for Kpoint

* fix type

* increase msg verbosity

* fix types

* remove debug print

* add missing types

* handle nparray

* fix/suppress mypy error

* change kpt weight to float in doc

* add type for typealias

* fix typealias import

* remove type annotation for types

* add unit test for property kpts

Author: DanielYang59

pymatgen/core/interface.py

@@ -29,8 +29,7 @@
     from numpy.typing import ArrayLike
     from typing_extensions import Self
 
-    from pymatgen.core.trajectory import Vector3D
-    from pymatgen.util.typing import CompositionLike
+    from pymatgen.util.typing import CompositionLike, Vector3D
 
 # This module implements representations of grain boundaries, as well as
 # algorithms for generating them.

pymatgen/core/lattice.py

@@ -25,8 +25,7 @@
     from numpy.typing import ArrayLike
     from typing_extensions import Self
 
-    from pymatgen.core.trajectory import Vector3D
-    from pymatgen.util.typing import PbcLike
+    from pymatgen.util.typing import PbcLike, Vector3D
 
 __author__ = "Shyue Ping Ong, Michael Kocher"
 __copyright__ = "Copyright 2011, The Materials Project"

pymatgen/core/trajectory.py

@@ -6,10 +6,9 @@
 
 import itertools
 import warnings
-from collections.abc import Iterator, Sequence
 from fnmatch import fnmatch
 from pathlib import Path
-from typing import TYPE_CHECKING, Any, Union
+from typing import TYPE_CHECKING
 
 import numpy as np
 from monty.io import zopen
@@ -20,17 +19,17 @@
 from pymatgen.io.vasp.outputs import Vasprun, Xdatcar
 
 if TYPE_CHECKING:
+    from collections.abc import Iterator
+
     from typing_extensions import Self
 
+    from pymatgen.util.typing import Matrix3D, SitePropsType, Vector3D
+
 
 __author__ = "Eric Sivonxay, Shyam Dwaraknath, Mingjian Wen, Evan Spotte-Smith"
 __version__ = "0.1"
 __date__ = "Jun 29, 2022"
 
-Vector3D = tuple[float, float, float]
-Matrix3D = tuple[Vector3D, Vector3D, Vector3D]
-SitePropsType = Union[list[dict[Any, Sequence[Any]]], dict[Any, Sequence[Any]]]
-
 
 class Trajectory(MSONable):
     """Trajectory of a geometry optimization or molecular dynamics simulation.

pymatgen/io/aims/outputs.py

@@ -18,10 +18,10 @@
     from collections.abc import Sequence
     from pathlib import Path
 
-    from emmet.core.math import Matrix3D, Vector3D
     from typing_extensions import Self
 
     from pymatgen.core import Molecule, Structure
+    from pymatgen.util.typing import Matrix3D, Vector3D
 
 __author__ = "Andrey Sobolev and Thomas A. R. Purcell"
 __version__ = "1.0"

pymatgen/io/aims/parsers.py

@@ -5,7 +5,7 @@
 import gzip
 from dataclasses import dataclass, field
 from pathlib import Path
-from typing import TYPE_CHECKING, Any
+from typing import TYPE_CHECKING, Any, cast
 
 import numpy as np
 
@@ -16,7 +16,7 @@
     from collections.abc import Generator, Sequence
     from io import TextIOWrapper
 
-    from emmet.core.math import Matrix3D, Vector3D
+    from pymatgen.util.typing import Matrix3D, Vector3D
 
 __author__ = "Thomas A. R. Purcell and Andrey Sobolev"
 __version__ = "1.0"
@@ -566,9 +566,9 @@ def _parse_lattice_atom_pos(
             elif "atom   " in line:
                 line_split = line.split()
                 species.append(line_split[4])
-                coords.append([float(inp) for inp in line_split[1:4]])
+                coords.append(cast(tuple[float, float, float], tuple(float(inp) for inp in line_split[1:4])))
             elif "velocity   " in line:
-                velocities.append([float(inp) for inp in line.split()[1:]])
+                velocities.append(cast(tuple[float, float, float], tuple(float(inp) for inp in line.split()[1:4])))
 
         lattice = Lattice(lattice_vectors) if len(lattice_vectors) == 3 else None
         return species, coords, velocities, lattice

pymatgen/io/cif.py

@@ -32,7 +32,7 @@
 if TYPE_CHECKING:
     from typing_extensions import Self
 
-    from pymatgen.core.trajectory import Vector3D
+    from pymatgen.util.typing import Vector3D
 
 __author__ = "Shyue Ping Ong, Will Richards, Matthew Horton"
 

pymatgen/io/cp2k/inputs.py

@@ -50,6 +50,7 @@
 
     from pymatgen.core.lattice import Lattice
     from pymatgen.core.structure import Molecule, Structure
+    from pymatgen.util.typing import Kpoint
 
 __author__ = "Nicholas Winner"
 __version__ = "2.0"
@@ -2031,37 +2032,44 @@ def from_kpoints(cls, kpoints: VaspKpoints, structure=None) -> Self:
         weights = kpoints.kpts_weights
 
         if kpoints.style == KpointsSupportedModes.Monkhorst:
-            k = kpts[0]
-            x, y, z = (k, k, k) if isinstance(k, (int, float)) else k
+            kpt: Kpoint = kpts[0]  # type: ignore[assignment]
+            x, y, z = (kpt, kpt, kpt) if isinstance(kpt, (int, float)) else kpt  # type: ignore[misc]
             scheme = f"MONKHORST-PACK {x} {y} {z}"
             units = "B_VECTOR"
+
         elif kpoints.style == KpointsSupportedModes.Reciprocal:
             units = "B_VECTOR"
             scheme = "GENERAL"
+
         elif kpoints.style == KpointsSupportedModes.Cartesian:
             units = "CART_ANGSTROM"
             scheme = "GENERAL"
+
         elif kpoints.style == KpointsSupportedModes.Gamma:
+            if not structure:
+                raise ValueError(
+                    "No cp2k automatic gamma constructor. A structure is required to construct from spglib"
+                )
+
             if (isinstance(kpts[0], Iterable) and tuple(kpts[0]) == (1, 1, 1)) or (
                 isinstance(kpts[0], (float, int)) and int(kpts[0]) == 1
             ):
                 scheme = "GAMMA"
-                units = "B_VECTOR"
-            elif not structure:
-                raise ValueError(
-                    "No cp2k automatic gamma constructor. A structure is required to construct from spglib"
-                )
             else:
                 sga = SpacegroupAnalyzer(structure)
-                _kpts, weights = zip(*sga.get_ir_reciprocal_mesh(mesh=kpts))
-                kpts = list(itertools.chain.from_iterable(_kpts))
+                _kpts, weights = zip(*sga.get_ir_reciprocal_mesh(mesh=kpts))  # type: ignore[assignment]
+                kpts = tuple(itertools.chain.from_iterable(_kpts))
                 scheme = "GENERAL"
-                units = "B_VECTOR"
+
+            units = "B_VECTOR"
+
         elif kpoints.style == KpointsSupportedModes.Line_mode:
             scheme = "GENERAL"
             units = "B_VECTOR"
+
         else:
             raise ValueError("Unrecognized k-point style")
+
         return Kpoints(kpts=kpts, weights=weights, scheme=scheme, units=units)
 
 

pymatgen/io/lobster/inputs.py

@@ -30,8 +30,6 @@
 from pymatgen.util.due import Doi, due
 
 if TYPE_CHECKING:
-    from collections.abc import Sequence
-
     from typing_extensions import Self
 
     from pymatgen.core.composition import Composition
@@ -431,7 +429,7 @@ def write_KPOINTS(
         reciprocal_density: int = 100,
         isym: int = -1,
         from_grid: bool = False,
-        input_grid: Sequence[int] = (5, 5, 5),
+        input_grid: tuple[int, int, int] = (5, 5, 5),
         line_mode: bool = True,
         kpoints_line_density: int = 20,
         symprec: float = 0.01,
@@ -446,7 +444,7 @@ def write_KPOINTS(
             isym (int): either -1 or 0. Current Lobster versions only allow -1.
             from_grid (bool): If True KPOINTS will be generated with the help of a grid given in input_grid.
                 Otherwise, they will be generated from the reciprocal_density
-            input_grid (list): grid to generate the KPOINTS file
+            input_grid (tuple): grid to generate the KPOINTS file
             line_mode (bool): If True, band structure will be generated
             kpoints_line_density (int): density of the lines in the band structure
             symprec (float): precision to determine symmetry
@@ -543,7 +541,7 @@ def write_KPOINTS(
             comment=comment,
             style=Kpoints.supported_modes.Reciprocal,
             num_kpts=len(kpts),
-            kpts=kpts,
+            kpts=tuple(kpts),
             kpts_weights=weights,
             labels=all_labels,
         )

pymatgen/io/lobster/outputs.py

@@ -1407,9 +1407,10 @@ def __init__(
         self.p_eigenvals = p_eigenvals
 
         label_dict = {}
-        for idx, label in enumerate(kpoints_object.labels[-self.number_kpts :], start=0):
-            if label is not None:
-                label_dict[label] = kpoints_array[idx]
+        if kpoints_object.labels is not None:
+            for idx, label in enumerate(kpoints_object.labels[-self.number_kpts :], start=0):
+                if label is not None:
+                    label_dict[label] = kpoints_array[idx]
 
         self.label_dict = label_dict
 

pymatgen/io/res.py

@@ -29,7 +29,7 @@
 
     from typing_extensions import Self
 
-    from pymatgen.core.trajectory import Vector3D
+    from pymatgen.util.typing import Vector3D
 
 
 @dataclass(frozen=True)