87 lines
2.5 KiB
Python
87 lines
2.5 KiB
Python
from crystalpol.shared.system.atom import Atom
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from crystalpol.shared.utils.ptable import atom_symbol
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from typing import Final, List, TextIO
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import math
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""" Constants of unit conversion """
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BOHR2ANG: Final[float] = 0.52917721092
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ANG2BOHR: Final[float] = 1 / BOHR2ANG
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class Molecule:
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"""
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Molecule class declaration. This class is used throughout the DicePlayer program to represent molecules.
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Atributes:
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molname (str): The name of the represented molecule
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atom (List[Atom]): List of atoms of the represented molecule
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position (NDArray[Any, Any]): The position relative to the internal atoms of the represented molecule
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energy (NDArray[Any, Any]): The energy of the represented molecule
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gradient (NDArray[Any, Any]): The first derivative of the energy relative to the position
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hessian (NDArray[Any, Any]): The second derivative of the energy relative to the position
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total_mass (int): The total mass of the molecule
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com (NDArray[Any, Any]): The center of mass of the molecule
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"""
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__slots__ = (
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'mol_name',
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'atoms',
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'position'
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)
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def __init__(self, mol_name: str) -> None:
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"""
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The constructor function __init__ is used to create new instances of the Molecule class.
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Args:
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mol_name (str): Molecule name
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"""
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self.mol_name: str = mol_name
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self.atoms: List[Atom] = []
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def __iter__(self):
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for atom in self.atoms:
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yield atom
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def __len__(self):
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return len(self.atoms)
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def add_atom(self, a: Atom) -> None:
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"""
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Adds Atom instance to the molecule.
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Args:
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a (Atom): Atom instance to be added to atom list.
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"""
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self.atoms.append(a)
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def update_charges(self, charges: List[float]) -> None:
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if len(charges) != len(self.atoms):
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raise ValueError(
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f"The number of charges ({len(charges)}) does not match the number of atoms ({len(self.atoms)})"
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)
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for i, atom in enumerate(self.atoms):
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atom.chg = charges[i]
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def print_mol_info(self, fh: TextIO) -> None:
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"""
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Prints the Molecule information into a Output File
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Args:
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fh (TextIO): Output File
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"""
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fh.write("-"*80)
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fh.write(f"Molecule Name: {self.mol_name}\n")
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fh.write("\n")
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for atom in self.atoms:
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fh.write(f"{atom_symbol[atom.na]} r: [{atom.rx}, {atom.ry}, {atom.rz}] charge: {atom.chg}")
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