diff --git a/diceplayer/environment/atom.py b/diceplayer/environment/atom.py index a9a9801..5aeeff8 100644 --- a/diceplayer/environment/atom.py +++ b/diceplayer/environment/atom.py @@ -1,52 +1,23 @@ -from diceplayer.utils.ptable import atommass +from diceplayer.utils.ptable import PTable + +from dataclasses import dataclass +@dataclass class Atom: """ Atom class declaration. This class is used throughout the DicePlayer program to represent atoms. - - Atributes: - lbl (int): Dice derived variable used to represent atoms with identical energies and simetric positions. - na (int): Atomic number of the represented atom. - rx (float): x cartesian coordinates of the represented atom. - ry (float): y cartesian coordinates of the represented atom. - rz (float): z cartesian coordinates of the represented atom. - chg (float): charge of the represented atom. - eps (float): quantum number epsilon of the represented atom. - sig (float): quantum number sigma of the represented atom. """ - def __init__( - self, - lbl: int, - na: int, - rx: float, - ry: float, - rz: float, - chg: float, - eps: float, - sig: float, - ) -> None: - """ - The constructor function __init__ is used to create new instances of the Atom class. + lbl: int + na: int + rx: float + ry: float + rz: float + chg: float + eps: float + sig: float - Args: - lbl (int): Dice derived variable used to represent atoms with identical energies and simetric positions. - na (int): Atomic number of the represented atom. - rx (float): x cartesian coordinates of the represented atom. - ry (float): y cartesian coordinates of the represented atom. - rz (float): z cartesian coordinates of the represented atom. - chg (float): charge of the represented atom. - eps (float): quantum number epsilon of the represented atom. - sig (float): quantum number sigma of the represented atom. - """ - - self.lbl = lbl - self.na = na - self.rx = rx - self.ry = ry - self.rz = rz - self.chg = chg - self.eps = eps - self.sig = sig - self.mass = atommass[self.na] + @property + def mass(self) -> float: + return PTable.get_atomic_mass(self.na) diff --git a/diceplayer/environment/molecule.py b/diceplayer/environment/molecule.py index 24053ee..4df0409 100644 --- a/diceplayer/environment/molecule.py +++ b/diceplayer/environment/molecule.py @@ -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 diff --git a/diceplayer/interface/gaussian_interface.py b/diceplayer/interface/gaussian_interface.py index cd4bc85..641df28 100644 --- a/diceplayer/interface/gaussian_interface.py +++ b/diceplayer/interface/gaussian_interface.py @@ -2,12 +2,12 @@ from __future__ import annotations from diceplayer import logger from diceplayer.config.player_config import PlayerConfig -from diceplayer.environment.atom import Atom +from diceplayer.environment import Atom from diceplayer.environment.molecule import Molecule from diceplayer.environment.system import System from diceplayer.interface import Interface from diceplayer.utils.misc import date_time -from diceplayer.utils.ptable import atomsymb +from diceplayer.utils.ptable import PTable import numpy as np from nptyping import NDArray @@ -161,9 +161,9 @@ class GaussianInterface(Interface): if ( line[0].title() - != atomsymb[ + != PTable.get_atomic_symbol( self.system.molecule[type].atom[site].na - ].strip() + ).strip() ): raise SyntaxError( "Error: Invalid Dice Output. Atom type does not match." @@ -188,7 +188,7 @@ class GaussianInterface(Interface): for atom in new_molecule.atom: asec_charges.append( { - "lbl": atomsymb[atom.na], + "lbl": PTable.get_atomic_symbol(atom.na), "rx": atom.rx, "ry": atom.ry, "rz": atom.rz, @@ -258,7 +258,7 @@ class GaussianInterface(Interface): ) for atom in self.system.molecule[0].atom: - symbol = atomsymb[atom.na] + symbol = PTable.get_atomic_symbol(atom.na) gaussian_input.append( "{:<2s} {:>10.5f} {:>10.5f} {:>10.5f}\n".format( symbol, atom.rx, atom.ry, atom.rz diff --git a/diceplayer/player.py b/diceplayer/player.py index f711088..75ee643 100644 --- a/diceplayer/player.py +++ b/diceplayer/player.py @@ -2,7 +2,7 @@ from diceplayer import VERSION, logger from diceplayer.config.player_config import PlayerConfig from diceplayer.environment import Atom, Molecule, System from diceplayer.interface import DiceInterface, GaussianInterface -from diceplayer.utils import atomsymb, weekday_date_time +from diceplayer.utils import PTable, weekday_date_time import yaml from pydantic import BaseModel @@ -289,7 +289,7 @@ class Player: file.write(f"Cycle # {cycle}\n") for atom in self.system.molecule[0].atom: - symbol = atomsymb[atom.na] + symbol = PTable.get_atomic_symbol(atom.na) file.write( f"{symbol:<2s} {atom.rx:>10.6f} {atom.ry:>10.6f} {atom.rz:>10.6f}\n" ) diff --git a/diceplayer/utils/__init__.py b/diceplayer/utils/__init__.py index c5d280c..ecd350f 100644 --- a/diceplayer/utils/__init__.py +++ b/diceplayer/utils/__init__.py @@ -6,14 +6,14 @@ from .misc import ( make_step_dir, weekday_date_time, ) -from .ptable import atommass, atomsymb +from .ptable import AtomInfo, PTable __all__ = [ "Logger", "valid_logger", - "atomsymb", - "atommass", + "PTable", + "AtomInfo", "weekday_date_time", "date_time", "compress_files_1mb", diff --git a/diceplayer/utils/ptable.py b/diceplayer/utils/ptable.py index 158bfdb..b5983fc 100644 --- a/diceplayer/utils/ptable.py +++ b/diceplayer/utils/ptable.py @@ -1,223 +1,143 @@ -#### Label used in Dice for a ghost atom -dice_ghost_label = "Xx" +from dataclasses import dataclass +from enum import Enum -#### Tuple of atom symbols -atomsymb = ( - "00", - "H ", - "He", - "Li", - "Be", - "B ", - "C ", - "N ", - "O ", - "F ", - "Ne", - "Na", - "Mg", - "Al", - "Si", - "P ", - "S ", - "Cl", - "Ar", - "K ", - "Ca", - "Sc", - "Ti", - "V ", - "Cr", - "Mn", - "Fe", - "Co", - "Ni", - "Cu", - "Zn", - "Ga", - "Ge", - "As", - "Se", - "Br", - "Kr", - "Rb", - "Sr", - "Y ", - "Zr", - "Nb", - "Mo", - "Tc", - "Ru", - "Rh", - "Pd", - "Ag", - "Cd", - "In", - "Sn", - "Sb", - "Te", - "I ", - "Xe", - "Cs", - "Ba", - "La", - "Ce", - "Pr", - "Nd", - "Pm", - "Sm", - "Eu", - "Gd", - "Tb", - "Dy", - "Ho", - "Er", - "Tm", - "Yb", - "Lu", - "Hf", - "Ta", - "W ", - "Re", - "Os", - "Ir", - "Pt", - "Au", - "Hg", - "Ti", - "Pb", - "Bi", - "Po", - "At", - "Rn", - "Fr", - "Ra", - "Ac", - "Th", - "Pa", - "U ", - "Np", - "Pu", - "Am", - "Cm", - "Bk", - "Cf", - "Es", - "Fm", - "Md", - "No", - "Lr", - dice_ghost_label, -) -#### Tuple of atom masses -atommass = ( - 0.0, - 1.0079, - 4.0026, - 6.9410, - 9.0122, - 10.811, - 12.011, - 14.007, - 15.999, - 18.998, - 20.180, - 22.990, - 24.305, - 26.982, - 28.086, - 30.974, - 32.065, - 35.453, - 39.948, - 39.098, - 40.078, - 44.956, - 47.867, - 50.942, - 51.996, - 54.938, - 55.845, - 58.933, - 58.693, - 63.546, - 65.409, - 69.723, - 72.640, - 74.922, - 78.960, - 79.904, - 83.798, - 85.468, - 87.620, - 88.906, - 91.224, - 92.906, - 95.940, - 98.000, - 101.07, - 102.91, - 106.42, - 107.87, - 112.41, - 114.82, - 118.71, - 121.76, - 127.60, - 126.90, - 131.29, - 132.91, - 137.33, - 138.91, - 140.12, - 140.91, - 144.24, - 145.00, - 150.36, - 151.96, - 157.25, - 158.93, - 162.50, - 164.93, - 167.26, - 168.93, - 173.04, - 174.97, - 178.49, - 180.95, - 183.84, - 186.21, - 190.23, - 192.22, - 195.08, - 196.97, - 200.59, - 204.38, - 207.20, - 208.98, - 209.00, - 210.00, - 222.00, - 223.00, - 226.00, - 227.00, - 232.04, - 231.04, - 238.03, - 237.00, - 244.00, - 243.00, - 247.00, - 247.00, - 251.00, - 252.00, - 257.00, - 258.00, - 259.00, - 262.00, - 0.000, -) +DICE_GHOST_LABEL = "Xx" #### Number of the ghost atom -ghost_number = len(atomsymb) - 1 +GHOST_NUMBER = 0 + + +@dataclass(frozen=True, slots=True) +class AtomInfo: + atomic_number: int + symbol: str + mass: float + + +class PTable(Enum): + Xx = AtomInfo(GHOST_NUMBER, DICE_GHOST_LABEL, 0.0) + H = AtomInfo(1, "H", 1.0079) + He = AtomInfo(2, "He", 4.0026) + Li = AtomInfo(3, "Li", 6.9410) + Be = AtomInfo(4, "Be", 9.0122) + B = AtomInfo(5, "B", 10.811) + C = AtomInfo(6, "C", 12.011) + N = AtomInfo(7, "N", 14.007) + O = AtomInfo(8, "O", 15.999) + F = AtomInfo(9, "F", 18.998) + Ne = AtomInfo(10, "Ne", 20.180) + Na = AtomInfo(11, "Na", 22.990) + Mg = AtomInfo(12, "Mg", 24.305) + Al = AtomInfo(13, "Al", 26.982) + Si = AtomInfo(14, "Si", 28.086) + P = AtomInfo(15, "P", 30.974) + S = AtomInfo(16, "S", 32.065) + Cl = AtomInfo(17, "Cl", 35.453) + Ar = AtomInfo(18, "Ar", 39.948) + K = AtomInfo(19, "K", 39.098) + Ca = AtomInfo(20, "Ca", 40.078) + Sc = AtomInfo(21, "Sc", 44.956) + Ti = AtomInfo(22, "Ti", 47.867) + V = AtomInfo(23, "V", 50.942) + Cr = AtomInfo(24, "Cr", 51.996) + Mn = AtomInfo(25, "Mn", 54.938) + Fe = AtomInfo(26, "Fe", 55.845) + Co = AtomInfo(27, "Co", 58.933) + Ni = AtomInfo(28, "Ni", 58.693) + Cu = AtomInfo(29, "Cu", 63.546) + Zn = AtomInfo(30, "Zn", 65.409) + Ga = AtomInfo(31, "Ga", 69.723) + Ge = AtomInfo(32, "Ge", 72.640) + As = AtomInfo(33, "As", 74.922) + Se = AtomInfo(34, "Se", 78.960) + Br = AtomInfo(35, "Br", 79.904) + Kr = AtomInfo(36, "Kr", 83.798) + Rb = AtomInfo(37, "Rb", 85.468) + Sr = AtomInfo(38, "Sr", 87.620) + Y = AtomInfo(39, "Y", 88.906) + Zr = AtomInfo(40, "Zr", 91.224) + Nb = AtomInfo(41, "Nb", 92.906) + Mo = AtomInfo(42, "Mo", 95.940) + Tc = AtomInfo(43, "Tc", 98.000) + Ru = AtomInfo(44, "Ru", 101.07) + Rh = AtomInfo(45, "Rh", 102.91) + Pd = AtomInfo(46, "Pd", 106.42) + Ag = AtomInfo(47, "Ag", 107.87) + Cd = AtomInfo(48, "Cd", 112.41) + In = AtomInfo(49, "In", 114.82) + Sn = AtomInfo(50, "Sn", 118.71) + Sb = AtomInfo(51, "Sb", 121.76) + Te = AtomInfo(52, "Te", 127.60) + I = AtomInfo(53, "I", 126.90) + Xe = AtomInfo(54, "Xe", 131.29) + Cs = AtomInfo(55, "Cs", 132.91) + Ba = AtomInfo(56, "Ba", 137.33) + La = AtomInfo(57, "La", 138.91) + Ce = AtomInfo(58, "Ce", 140.12) + Pr = AtomInfo(59, "Pr", 140.91) + Nd = AtomInfo(60, "Nd", 144.24) + Pm = AtomInfo(61, "Pm", 145.00) + Sm = AtomInfo(62, "Sm", 150.36) + Eu = AtomInfo(63, "Eu", 151.96) + Gd = AtomInfo(64, "Gd", 157.25) + Tb = AtomInfo(65, "Tb", 158.93) + Dy = AtomInfo(66, "Dy", 162.50) + Ho = AtomInfo(67, "Ho", 164.93) + Er = AtomInfo(68, "Er", 167.26) + Tm = AtomInfo(69, "Tm", 168.93) + Yb = AtomInfo(70, "Yb", 173.04) + Lu = AtomInfo(71, "Lu", 174.97) + Hf = AtomInfo(72, "Hf", 178.49) + Ta = AtomInfo(73, "Ta", 180.95) + W = AtomInfo(74, "W", 183.84) + Re = AtomInfo(75, "Re", 186.21) + Os = AtomInfo(76, "Os", 190.23) + Ir = AtomInfo(77, "Ir", 192.22) + Pt = AtomInfo(78, "Pt", 195.08) + Au = AtomInfo(79, "Au", 196.97) + Hg = AtomInfo(80, "Hg", 200.59) + Tl = AtomInfo(81, "Tl", 204.38) + Pb = AtomInfo(82, "Pb", 207.20) + Bi = AtomInfo(83, "Bi", 208.98) + Po = AtomInfo(84, "Po", 209.00) + At = AtomInfo(85, "At", 210.00) + Rn = AtomInfo(86, "Rn", 222.00) + Fr = AtomInfo(87, "Fr", 223.00) + Ra = AtomInfo(88, "Ra", 226.00) + Ac = AtomInfo(89, "Ac", 227.00) + Th = AtomInfo(90, "Th", 232.04) + Pa = AtomInfo(91, "Pa", 231.04) + U = AtomInfo(92, "U", 238.03) + Np = AtomInfo(93, "Np", 237.00) + Pu = AtomInfo(94, "Pu", 244.00) + Am = AtomInfo(95, "Am", 243.00) + Cm = AtomInfo(96, "Cm", 247.00) + Bk = AtomInfo(97, "Bk", 247.00) + Cf = AtomInfo(98, "Cf", 251.00) + Es = AtomInfo(99, "Es", 252.00) + Fm = AtomInfo(100, "Fm", 257.00) + Md = AtomInfo(101, "Md", 258.00) + No = AtomInfo(102, "No", 259.00) + Lr = AtomInfo(103, "Lr", 262.00) + + @classmethod + def get_atomic_symbol(cls, atomic_number: int) -> str: + for element in cls: + if element.value.atomic_number == atomic_number: + return element.value.symbol + raise ValueError(f"Atomic number {atomic_number} not found in PTable.") + + @classmethod + def get_atomic_mass(cls, atomic_number: int) -> float: + for element in cls: + if element.value.atomic_number == atomic_number: + return element.value.mass + raise ValueError(f"Atomic number {atomic_number} not found in PTable.") + + @classmethod + def get_from_atomic_number(cls, atomic_number: int) -> AtomInfo: + for element in cls: + if element.value.atomic_number == atomic_number: + return element.value + raise ValueError(f"Atomic number {atomic_number} not found in PTable.") diff --git a/poetry.lock b/poetry.lock index 0506b30..b9541e3 100644 --- a/poetry.lock +++ b/poetry.lock @@ -259,73 +259,59 @@ files = [ {file = "nodeenv-1.9.1.tar.gz", hash = "sha256:6ec12890a2dab7946721edbfbcd91f3319c6ccc9aec47be7c7e6b7011ee6645f"}, ] -[[package]] -name = "nptyping" -version = "2.5.0" -description = "Type hints for NumPy." 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