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chore: removes nptyping and updates dependencies

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This commit is contained in:
Vitor Hideyoshi
2025-09-23 05:07:39 -03:00
parent 57be666129
commit 7ef6f8b0b8
4 changed files with 103 additions and 111 deletions
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77
diceplayer/shared/environment/molecule.py
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@@ -1,9 +1,6 @@
from __future__ import annotations # from __future__ import annotations
from typing import TYPE_CHECKING import numpy.typing as npt
if TYPE_CHECKING:
from nptyping import Float, NDArray, Shape
from diceplayer import logger from diceplayer import logger
from diceplayer.shared.environment.atom import Atom from diceplayer.shared.environment.atom import Atom
@@ -25,12 +22,12 @@ class Molecule:
Atributes: Atributes:
molname (str): The name of the represented molecule molname (str): The name of the represented molecule
atom (List[Atom]): List of atoms 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 position (npt.NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule
energy (NDArray[Any, Any]): The energy of the represented molecule energy (npt.NDArray[Any, Any]): The energy of the represented molecule
gradient (NDArray[Any, Any]): The first derivative of the energy relative to the position gradient (npt.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 hessian (npt.NDArray[Any, Any]): The second derivative of the energy relative to the position
total_mass (int): The total mass of the molecule total_mass (int): The total mass of the molecule
com (NDArray[Any, Any]): The center of mass of the molecule com (npt.NDArray[Any, Any]): The center of mass of the molecule
""" """
def __init__(self, molname: str) -> None: def __init__(self, molname: str) -> None:
@@ -43,16 +40,16 @@ class Molecule:
self.molname: str = molname self.molname: str = molname
self.atom: List[Atom] = [] self.atom: List[Atom] = []
self.position: NDArray[Any, Any] self.position: npt.NDArray[Any, Any]
self.energy: NDArray[Any, Any] self.energy: npt.NDArray[Any, Any]
self.gradient: NDArray[Any, Any] self.gradient: npt.NDArray[Any, Any]
self.hessian: NDArray[Any, Any] self.hessian: npt.NDArray[Any, Any]
self.ghost_atoms: List[Atom] = [] self.ghost_atoms: List[Atom] = []
self.lp_atoms: List[Atom] = [] self.lp_atoms: List[Atom] = []
self.total_mass: int = 0 self.total_mass: int = 0
self.com: Union[None, NDArray[Any, Any]] = None self.com: Union[None, npt.NDArray[Any, Any]] = None
def add_atom(self, a: Atom) -> None: def add_atom(self, a: Atom) -> None:
""" """
@@ -67,7 +64,7 @@ class Molecule:
self.center_of_mass() self.center_of_mass()
def center_of_mass(self) -> NDArray[Any, Any]: def center_of_mass(self) -> npt.NDArray[Any]:
""" """
Calculates the center of mass of the molecule Calculates the center of mass of the molecule
""" """
@@ -97,7 +94,7 @@ class Molecule:
Calculates the charges and dipole of the molecule atoms Calculates the charges and dipole of the molecule atoms
Returns: Returns:
List[float]: Respectivly magnitude of the: charge magnitude, first dipole, List[npt.Float]: Respectivly magnitude of the: charge magnitude, first dipole,
second dipole, third dipole and total dipole. second dipole, third dipole and total dipole.
""" """
@@ -114,12 +111,12 @@ class Molecule:
return [charge, dipole[0], dipole[1], dipole[2], total_dipole] 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 Calculates distances between the atoms of the molecule
Returns: Returns:
NDArray[Shape["Any,Any"],Float]: distances between the atoms. npt.NDArray[npt.Shape["Any,Any"],npt.Float]: distances between the atoms.
""" """
distances = [] distances = []
@@ -134,12 +131,12 @@ class Molecule:
return np.array(distances).reshape(dim, dim - 1) 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. Calculates the inertia tensor of the molecule.
Returns: Returns:
NDArray[Shape["3, 3"], Float]: inertia tensor of the molecule. npt.NDArray[npt.Shape["3, 3"], npt.Float]: inertia tensor of the molecule.
""" """
self.center_of_mass() self.center_of_mass()
@@ -160,12 +157,12 @@ class Molecule:
return np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]]) return np.array([[Ixx, Ixy, Ixz], [Ixy, Iyy, Iyz], [Ixz, Iyz, Izz]])
def principal_axes(self) -> Tuple[np.ndarray, np.ndarray]: def principal_axes(self) -> Tuple[npt.NDArray, npt.NDArray]:
""" """
Calculates the principal axes of the molecule Calculates the principal axes of the molecule
Returns: Returns:
Tuple[np.ndarray, np.ndarray]: Tuple where the first value is the Eigen Values and the second is the Eigen Vectors, Tuple[npt.NDArray, npt.NDArray]: Tuple where the first value is the Eigen Values and the second is the Eigen Vectors,
representing the principal axes of the molecule. representing the principal axes of the molecule.
""" """
@@ -178,11 +175,11 @@ class Molecule:
return evals, evecs return evals, evecs
def read_position(self) -> np.ndarray: def read_position(self) -> npt.NDArray:
"""Reads the position of the molecule from the position values of the atoms """Reads the position of the molecule from the position values of the atoms
Returns: Returns:
np.ndarray: internal position relative to atoms of the molecule npt.NDArray: internal position relative to atoms of the molecule
""" """
position_list = [] position_list = []
@@ -193,7 +190,7 @@ class Molecule:
return position return position
def update_charges(self, charges: NDArray) -> int: def update_charges(self, charges: npt.NDArray) -> int:
""" """
Updates the charges of the atoms of the molecule and Updates the charges of the atoms of the molecule and
returns the max difference between the new and old charges returns the max difference between the new and old charges
@@ -207,22 +204,22 @@ class Molecule:
# @staticmethod # @staticmethod
# def update_hessian( # def update_hessian(
# step: np.ndarray, # step: npt.NDArray,
# cur_gradient: np.ndarray, # cur_gradient: npt.NDArray,
# old_gradient: np.ndarray, # old_gradient: npt.NDArray,
# hessian: np.ndarray, # hessian: npt.NDArray,
# ) -> np.ndarray: # ) -> npt.NDArray:
# """ # """
# Updates the Hessian of the molecule based on the current hessian, the current gradient and the previous gradient # Updates the Hessian of the molecule based on the current hessian, the current gradient and the previous gradient
# #
# Args: # Args:
# step (np.ndarray): step value of the iteration # step (npt.NDArray): step value of the iteration
# cur_gradient (np.ndarray): current gradient # cur_gradient (npt.NDArray): current gradient
# old_gradient (np.ndarray): previous gradient # old_gradient (npt.NDArray): previous gradient
# hessian (np.ndarray): current hessian # hessian (npt.NDArray): current hessian
# #
# Returns: # Returns:
# np.ndarray: updated hessian of the molecule # npt.NDArray: updated hessian of the molecule
# """ # """
# #
# dif_gradient = cur_gradient - old_gradient # dif_gradient = cur_gradient - old_gradient
@@ -238,7 +235,7 @@ class Molecule:
Calculates sides of the smallest box that the molecule could fit Calculates sides of the smallest box that the molecule could fit
Returns: Returns:
List[float]: list of the sizes of the molecule List[npt.Float]: list of the sizes of the molecule
""" """
x_list = [] x_list = []
@@ -289,12 +286,12 @@ class Molecule:
atom.ry = new_position[1] atom.ry = new_position[1]
atom.rz = new_position[2] atom.rz = new_position[2]
def translate(self, vector: np.ndarray) -> "Molecule": def translate(self, vector: npt.NDArray) -> "Molecule":
""" """
Creates a new Molecule object where its' atoms has been translated by a vector Creates a new Molecule object where its' atoms has been translated by a vector
Args: Args:
vector (np.ndarray): translation vector vector (npt.NDArray): translation vector
Returns: Returns:
Molecule: new Molecule object translated by a vector Molecule: new Molecule object translated by a vector
@@ -368,7 +365,7 @@ class Molecule:
molec (Molecule): Molecule object to be compared molec (Molecule): Molecule object to be compared
Returns: Returns:
float: minimum distance between the two molecules npt.Float: minimum distance between the two molecules
""" """
distances = [] distances = []

4
diceplayer/shared/interface/gaussian_interface.py
View File

@@ -10,7 +10,7 @@ from diceplayer.shared.utils.misc import date_time
from diceplayer.shared.utils.ptable import atomsymb from diceplayer.shared.utils.ptable import atomsymb
import numpy as np import numpy as np
from nptyping import NDArray import numpy.typing as npt
import os import os
import shutil import shutil
@@ -25,7 +25,7 @@ class GaussianInterface(Interface):
self.system = system self.system = system
self.step = step_dto self.step = step_dto
def start(self, cycle: int) -> Dict[str, NDArray]: def start(self, cycle: int) -> Dict[str, npt.NDArray]:
self._make_qm_dir(cycle) self._make_qm_dir(cycle)
if cycle > 1: if cycle > 1:

126
poetry.lock generated
View File

@@ -294,73 +294,69 @@ files = [
{file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"},
] ]
[[package]]
name = "nptyping"
version = "2.5.0"
description = "Type hints for NumPy."
optional = false
python-versions = ">=3.7"
groups = ["main"]
files = [
{file = "nptyping-2.5.0-py3-none-any.whl", hash = "sha256:764e51836faae33a7ae2e928af574cfb701355647accadcc89f2ad793630b7c8"},
{file = "nptyping-2.5.0.tar.gz", hash = "sha256:e3d35b53af967e6fb407c3016ff9abae954d3a0568f7cc13a461084224e8e20a"},
]
[package.dependencies]
numpy = {version = ">=1.20.0,<2.0.0", markers = "python_version >= \"3.8\""}
typing-extensions = {version = ">=4.0.0,<5.0.0", markers = "python_version < \"3.10\""}
[package.extras]
build = ["invoke (>=1.6.0)", "pip-tools (>=6.5.0)"]
complete = ["pandas", "pandas-stubs-fork ; python_version >= \"3.8\""]
dev = ["autoflake", "beartype (<0.10.0) ; python_version < \"3.10\"", "beartype (>=0.10.0) ; python_version >= \"3.10\"", "black", "codecov (>=2.1.0)", "coverage", "feedparser", "invoke (>=1.6.0)", "isort", "mypy", "pandas", "pandas-stubs-fork ; python_version >= \"3.8\"", "pip-tools (>=6.5.0)", "pylint", "pyright", "setuptools", "typeguard", "wheel"]
pandas = ["pandas", "pandas-stubs-fork ; python_version >= \"3.8\""]
qa = ["autoflake", "beartype (<0.10.0) ; python_version < \"3.10\"", "beartype (>=0.10.0) ; python_version >= \"3.10\"", "black", "codecov (>=2.1.0)", "coverage", "feedparser", "isort", "mypy", "pylint", "pyright", "setuptools", "typeguard", "wheel"]
[[package]] [[package]]
name = "numpy" name = "numpy"
version = "1.26.4" version = "2.2.6"
description = "Fundamental package for array computing in Python" description = "Fundamental package for array computing in Python"
optional = false optional = false
python-versions = ">=3.9" python-versions = ">=3.10"
groups = ["main"] groups = ["main"]
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[[package]] [[package]]
@@ -675,12 +671,12 @@ version = "4.15.0"
description = "Backported and Experimental Type Hints for Python 3.9+" description = "Backported and Experimental Type Hints for Python 3.9+"
optional = false optional = false
python-versions = ">=3.9" python-versions = ">=3.9"
groups = ["main", "dev"] groups = ["dev"]
markers = "python_version == \"3.10\""
files = [ files = [
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] ]
markers = {main = "python_version == \"3.9\"", dev = "python_version < \"3.11\""}
[[package]] [[package]]
name = "virtualenv" name = "virtualenv"
@@ -706,5 +702,5 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
[metadata] [metadata]
lock-version = "2.1" lock-version = "2.1"
python-versions = ">=3.9,<4.0" python-versions = ">=3.10,<4.0"
content-hash = "80ecbda1b826475e5eef19c940136c907a9687c7f4a6a0577a65ddd9b8a3343b" content-hash = "f90241137e4e1197ca6a78485387f4227bbcb8ab61f83955c23cb2479ad3c8c4"

7
pyproject.toml
View File

@@ -19,18 +19,17 @@ diceplayer = "diceplayer.__main__:main"
# POETRY # POETRY
[tool.poetry] [tool.poetry]
version = "0.0.0"
packages = [ packages = [
{ include = "diceplayer" } { include = "diceplayer" }
] ]
version = "0.0.0"
[tool.poetry.dependencies] [tool.poetry.dependencies]
python = ">=3.9,<4.0" python = ">=3.10,<4.0"
numpy = "^1.26.4" numpy = "^2.2.6"
argparse = "^1.4.0" argparse = "^1.4.0"
setproctitle = "^1.3.2" setproctitle = "^1.3.2"
pyyaml = "^6.0" pyyaml = "^6.0"
nptyping = "^2.5.0"
[tool.poetry.group.dev.dependencies] [tool.poetry.group.dev.dependencies]
coverage = "^7.2.7" coverage = "^7.2.7"