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refactor: unify and modernize periodic table utilities and typing

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- Replace atomsymb and atommass tuples with AtomInfo dataclass and PTable enum for atomic data
- Refactor all usages to access atomic symbol and mass via PTable methods
- Remove nptyping dependency, switch to numpy.typing for type annotations
- Update molecule and atom classes to use new typing and atomic data access
- Bump numpy version to 2.x and remove nptyping from dependencies
This commit is contained in:
Vitor Hideyoshi
2026-02-27 17:56:11 -03:00
parent b6e57bc1c5
commit d400970e8f
8 changed files with 242 additions and 356 deletions
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45
diceplayer/environment/molecule.py
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@@ -7,11 +7,12 @@ if TYPE_CHECKING:
from nptyping import Float, NDArray, Shape
from diceplayer import logger
from diceplayer.environment.atom import Atom
from diceplayer.environment import Atom
from diceplayer.utils.misc import BOHR2ANG
from diceplayer.utils.ptable import ghost_number
from diceplayer.utils.ptable import GHOST_NUMBER
import numpy as np
import numpy.typing as npt
from numpy.linalg import linalg
from typing_extensions import Any, List, Tuple, Union
@@ -26,12 +27,12 @@ class Molecule:
Atributes:
molname (str): The name of the represented molecule
atom (List[Atom]): List of atoms of the represented molecule
position (NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule
energy (NDArray[Any, Any]): The energy of the represented molecule
gradient (NDArray[Any, Any]): The first derivative of the energy relative to the position
hessian (NDArray[Any, Any]): The second derivative of the energy relative to the position
position (npt.NDArray[np.float64]): The position relative to the internal atoms of the represented molecule
energy (npt.NDArray[np.float64]): The energy of the represented molecule
gradient (npt.NDArray[np.float64]): The first derivative of the energy relative to the position
hessian (npt.NDArray[np.float64]): The second derivative of the energy relative to the position
total_mass (int): The total mass of the molecule
com (NDArray[Any, Any]): The center of mass of the molecule
com (npt.NDArray[np.float64]): The center of mass of the molecule
"""
def __init__(self, molname: str) -> None:
@@ -44,16 +45,16 @@ class Molecule:
self.molname: str = molname
self.atom: List[Atom] = []
self.position: NDArray[Any, Any]
self.energy: NDArray[Any, Any]
self.gradient: NDArray[Any, Any]
self.hessian: NDArray[Any, Any]
self.position: npt.NDArray[np.float64]
self.energy: npt.NDArray[np.float64]
self.gradient: npt.NDArray[np.float64]
self.hessian: npt.NDArray[np.float64]
self.ghost_atoms: List[Atom] = []
self.lp_atoms: List[Atom] = []
self.total_mass: int = 0
self.com: Union[None, NDArray[Any, Any]] = None
self.com: Union[None, npt.NDArray[np.float64]] = None
def add_atom(self, a: Atom) -> None:
"""
@@ -68,7 +69,7 @@ class Molecule:
self.center_of_mass()
def center_of_mass(self) -> NDArray[Any, Any]:
def center_of_mass(self) -> npt.NDArray[np.float64]:
"""
Calculates the center of mass of the molecule
"""
@@ -115,7 +116,7 @@ class Molecule:
return [charge, dipole[0], dipole[1], dipole[2], total_dipole]
def distances_between_atoms(self) -> NDArray[Shape["Any,Any"], Float]:
def distances_between_atoms(self) -> npt.NDArray[np.float64]:
"""
Calculates distances between the atoms of the molecule
@@ -135,16 +136,22 @@ class Molecule:
return np.array(distances).reshape(dim, dim - 1)
def inertia_tensor(self) -> NDArray[Shape["3, 3"], Float]:
def inertia_tensor(self) -> npt.NDArray[np.float64]:
"""
Calculates the inertia tensor of the molecule.
Returns:
NDArray[Shape["3, 3"], Float]: inertia tensor of the molecule.
npt.NDArray[np.float64]: inertia tensor of the molecule.
"""
self.center_of_mass()
Ixx = Ixy = Ixz = Iyy = Iyz = Izz = 0.0
Ixx = 0.0
Ixy = 0.0
Ixz = 0.0
Iyy = 0.0
Iyz = 0.0
Izz = 0.0
for atom in self.atom:
dx = atom.rx - self.com[0]
@@ -374,9 +381,9 @@ class Molecule:
distances = []
for atom1 in self.atom:
if atom1.na != ghost_number:
if atom1.na != GHOST_NUMBER:
for atom2 in molec.atom:
if atom2.na != ghost_number:
if atom2.na != GHOST_NUMBER:
dx = atom1.rx - atom2.rx
dy = atom1.ry - atom2.ry
dz = atom1.rz - atom2.rz