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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
View File

@@ -1,9 +1,6 @@
from __future__ import annotations
# from __future__ import annotations
from typing import TYPE_CHECKING
if TYPE_CHECKING:
from nptyping import Float, NDArray, Shape
import numpy.typing as npt
from diceplayer import logger
from diceplayer.shared.environment.atom import Atom
@@ -25,12 +22,12 @@ 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[Any, Any]): The position relative to the internal atoms of the represented molecule
energy (npt.NDArray[Any, Any]): The energy of the represented molecule
gradient (npt.NDArray[Any, Any]): The first 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
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:
@@ -43,16 +40,16 @@ 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[Any, Any]
self.energy: npt.NDArray[Any, Any]
self.gradient: npt.NDArray[Any, Any]
self.hessian: npt.NDArray[Any, Any]
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[Any, Any]] = None
def add_atom(self, a: Atom) -> None:
"""
@@ -67,7 +64,7 @@ class Molecule:
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
"""
@@ -97,7 +94,7 @@ class Molecule:
Calculates the charges and dipole of the molecule atoms
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.
"""
@@ -114,12 +111,12 @@ 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
Returns:
NDArray[Shape["Any,Any"],Float]: distances between the atoms.
npt.NDArray[npt.Shape["Any,Any"],npt.Float]: distances between the atoms.
"""
distances = []
@@ -134,12 +131,12 @@ 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[npt.Shape["3, 3"], npt.Float]: inertia tensor of the molecule.
"""
self.center_of_mass()
@@ -160,12 +157,12 @@ class Molecule:
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
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.
"""
@@ -178,11 +175,11 @@ class Molecule:
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
Returns:
np.ndarray: internal position relative to atoms of the molecule
npt.NDArray: internal position relative to atoms of the molecule
"""
position_list = []
@@ -193,7 +190,7 @@ class Molecule:
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
returns the max difference between the new and old charges
@@ -207,22 +204,22 @@ class Molecule:
# @staticmethod
# def update_hessian(
# step: np.ndarray,
# cur_gradient: np.ndarray,
# old_gradient: np.ndarray,
# hessian: np.ndarray,
# ) -> np.ndarray:
# step: npt.NDArray,
# cur_gradient: npt.NDArray,
# old_gradient: npt.NDArray,
# hessian: npt.NDArray,
# ) -> npt.NDArray:
# """
# Updates the Hessian of the molecule based on the current hessian, the current gradient and the previous gradient
#
# Args:
# step (np.ndarray): step value of the iteration
# cur_gradient (np.ndarray): current gradient
# old_gradient (np.ndarray): previous gradient
# hessian (np.ndarray): current hessian
# step (npt.NDArray): step value of the iteration
# cur_gradient (npt.NDArray): current gradient
# old_gradient (npt.NDArray): previous gradient
# hessian (npt.NDArray): current hessian
#
# Returns:
# np.ndarray: updated hessian of the molecule
# npt.NDArray: updated hessian of the molecule
# """
#
# dif_gradient = cur_gradient - old_gradient
@@ -238,7 +235,7 @@ class Molecule:
Calculates sides of the smallest box that the molecule could fit
Returns:
List[float]: list of the sizes of the molecule
List[npt.Float]: list of the sizes of the molecule
"""
x_list = []
@@ -289,12 +286,12 @@ class Molecule:
atom.ry = new_position[1]
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
Args:
vector (np.ndarray): translation vector
vector (npt.NDArray): translation vector
Returns:
Molecule: new Molecule object translated by a vector
@@ -368,7 +365,7 @@ class Molecule:
molec (Molecule): Molecule object to be compared
Returns:
float: minimum distance between the two molecules
npt.Float: minimum distance between the two molecules
"""
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
import numpy as np
from nptyping import NDArray
import numpy.typing as npt
import os
import shutil
@@ -25,7 +25,7 @@ class GaussianInterface(Interface):
self.system = system
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)
if cycle > 1:

126
poetry.lock generated
View File

@@ -294,73 +294,69 @@ files = [
{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]]
name = "numpy"
version = "1.26.4"
version = "2.2.6"
description = "Fundamental package for array computing in Python"
optional = false
python-versions = ">=3.9"
python-versions = ">=3.10"
groups = ["main"]
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[[package]]
@@ -675,12 +671,12 @@ version = "4.15.0"
description = "Backported and Experimental Type Hints for Python 3.9+"
optional = false
python-versions = ">=3.9"
groups = ["main", "dev"]
groups = ["dev"]
markers = "python_version == \"3.10\""
files = [
{file = "typing_extensions-4.15.0-py3-none-any.whl", hash = "sha256:f0fa19c6845758ab08074a0cfa8b7aecb71c999ca73d62883bc25cc018c4e548"},
{file = "typing_extensions-4.15.0.tar.gz", hash = "sha256:0cea48d173cc12fa28ecabc3b837ea3cf6f38c6d1136f85cbaaf598984861466"},
]
markers = {main = "python_version == \"3.9\"", dev = "python_version < \"3.11\""}
[[package]]
name = "virtualenv"
@@ -706,5 +702,5 @@ test = ["covdefaults (>=2.3)", "coverage (>=7.2.7)", "coverage-enable-subprocess
[metadata]
lock-version = "2.1"
python-versions = ">=3.9,<4.0"
content-hash = "80ecbda1b826475e5eef19c940136c907a9687c7f4a6a0577a65ddd9b8a3343b"
python-versions = ">=3.10,<4.0"
content-hash = "f90241137e4e1197ca6a78485387f4227bbcb8ab61f83955c23cb2479ad3c8c4"

7
pyproject.toml
View File

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