HideyoshiNakazone/DicePlayer
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Adds Formatter to Project

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This commit is contained in:
Vitor Hideyoshi
2023-06-11 16:04:25 -03:00
parent 82f3092f3e
commit c4dae5e8d1
29 changed files with 1151 additions and 721 deletions
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32
diceplayer/shared/environment/molecule.py
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@@ -1,18 +1,18 @@
from __future__ import annotations
from diceplayer.shared.utils.ptable import ghost_number
from diceplayer import logger
from diceplayer.shared.environment.atom import Atom
from diceplayer.shared.utils.misc import BOHR2ANG
from diceplayer import logger
from diceplayer.shared.utils.ptable import ghost_number
from nptyping import NDArray, Shape, Float
from numpy.linalg import linalg
import numpy as np
from nptyping import Float, NDArray, Shape
from numpy.linalg import linalg
from typing import List, Any, Tuple, Union
from copy import deepcopy
import logging
import math
from copy import deepcopy
from typing import Any, List, Tuple, Union
class Molecule:
@@ -127,9 +127,9 @@ class Molecule:
dx = atom1.rx - atom2.rx
dy = atom1.ry - atom2.ry
dz = atom1.rz - atom2.rz
distances.append(math.sqrt(dx ** 2 + dy ** 2 + dz ** 2))
distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
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]:
"""
@@ -147,9 +147,9 @@ class Molecule:
dy = atom.ry - self.com[1]
dz = atom.rz - self.com[2]
Ixx += atom.mass * (dy ** 2 + dz ** 2)
Iyy += atom.mass * (dz ** 2 + dx ** 2)
Izz += atom.mass * (dx ** 2 + dy ** 2)
Ixx += atom.mass * (dy**2 + dz**2)
Iyy += atom.mass * (dz**2 + dx**2)
Izz += atom.mass * (dx**2 + dy**2)
Ixy += atom.mass * dx * dy * -1
Ixz += atom.mass * dx * dz * -1
@@ -169,7 +169,9 @@ class Molecule:
try:
evals, evecs = linalg.eigh(self.inertia_tensor())
except ValueError:
raise RuntimeError("Error: diagonalization of inertia tensor did not converge")
raise RuntimeError(
"Error: diagonalization of inertia tensor did not converge"
)
return evals, evecs
@@ -355,7 +357,7 @@ class Molecule:
)
)
def minimum_distance(self, molec: 'Molecule') -> float:
def minimum_distance(self, molec: "Molecule") -> float:
"""
Return the minimum distance between two molecules
@@ -374,6 +376,6 @@ class Molecule:
dx = atom1.rx - atom2.rx
dy = atom1.ry - atom2.ry
dz = atom1.rz - atom2.rz
distances.append(math.sqrt(dx ** 2 + dy ** 2 + dz ** 2))
distances.append(math.sqrt(dx**2 + dy**2 + dz**2))
return min(distances)
return min(distances)