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core.py
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core.py
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"""Utility functions for dealing with Atoms."""
from __future__ import annotations
import hashlib
import logging
from copy import deepcopy
from typing import TYPE_CHECKING
import numpy as np
from ase.filters import Filter
from ase.io.jsonio import encode
from pymatgen.io.ase import AseAtomsAdaptor
if TYPE_CHECKING:
from ase.atoms import Atoms
from ase.optimize.optimize import Dynamics
from numpy.typing import NDArray
logger = logging.getLogger(__name__)
def get_atoms_id(atoms: Atoms) -> str:
"""
Returns a unique ID for the Atoms object. Note: The .info dict and calculator is
excluded from the hash generation.
Parameters
----------
atoms
Atoms object
Returns
-------
str
MD5 hash of the Atoms object
"""
atoms = copy_atoms(atoms)
atoms.info = {}
atoms.calc = None
encoded_atoms = encode(atoms)
# This is a hack to avoid int32/int64 and float32/float64 differences
# between machines.
encoded_atoms = (
encoded_atoms.replace("int64", "int")
.replace("int32", "int")
.replace("float64", "float")
.replace("float32", "float")
)
return hashlib.md5(encoded_atoms.encode("utf-8")).hexdigest()
def check_is_metal(atoms: Atoms) -> bool:
"""
Checks if a structure is a likely metal.
Parameters
----------
atoms
Atoms object
Returns
-------
bool
True if the structure is likely a metal; False otherwise
"""
struct = (
AseAtomsAdaptor().get_structure(atoms)
if atoms.pbc.any()
else AseAtomsAdaptor().get_molecule(atoms, charge_spin_check=False)
)
return all(k.is_metal for k in struct.composition)
def copy_atoms(atoms: Atoms) -> Atoms:
"""
Simple function to copy an atoms object to prevent mutability.
Parameters
----------
atoms
Atoms object
Returns
-------
atoms
Atoms object
"""
try:
atoms = deepcopy(atoms)
except Exception:
# Needed because of ASE issue #1084
calc = atoms.calc
atoms = atoms.copy()
atoms.calc = calc
return atoms
def get_charge_attribute(atoms: Atoms) -> int | None:
"""
Get the charge of an Atoms object.
Parameters
----------
atoms
Atoms object
Returns
-------
int | None
Charge of the Atoms object
"""
return (
atoms.charge
if getattr(atoms, "charge", None)
else (
round(atoms.get_initial_charges().sum())
if atoms.has("initial_charges")
else None
)
)
def get_spin_multiplicity_attribute(atoms: Atoms) -> int | None:
"""
Get the spin multiplicity of an Atoms object.
Parameters
----------
atoms
Atoms object
Returns
-------
int | None
Spin multiplicity of the Atoms object
"""
return (
atoms.spin_multiplicity
if getattr(atoms, "spin_multiplicity", None)
else (
round(np.abs(atoms.get_initial_magnetic_moments().sum()) + 1)
if atoms.has("initial_magmoms")
else None
)
)
def check_charge_and_spin(
atoms: Atoms, charge: int | None = None, spin_multiplicity: int | None = None
) -> tuple[int, int]:
"""
Check the validity of a given `charge` and `multiplicity`. If they are `None`, then
set the charge and/or spin multiplicity of a molecule using the following routine,
raising a `ValueError` if there is an incompatibility.
Charges:
1. If `charge` is specified, that is the charge.
2. If `atoms.charge` is present, that is the charge.
3. If `atoms.has("initial_charges")`, then
`atoms.get_initial_charges.sum()` is the charge.
4. If `spin_multiplicity` is set, set the charge to the smallest physically
possible value.
5. Otherwise, set to 0.
Spin multiplicity:
1. If `spin_multiplicity` is specified, that is the spin multiplicity.
2. If `atoms.spin_multiplicity` is present, that is the spin multiplicity.
3. If `atoms.has("initial_magmoms")`, then
`np.abs(atoms.get_initial_magnetic_moments().sum())+1` is the spin
multiplicity.
4. If none of the above, use Pymatgen to identify the lowest physically
possible spin multiplicity given the number of electrons and the charge, if
set.
Parameters
----------
atoms
Atoms object
charge
Molecular charge
spin_multiplicity
Molecular multiplicity
Returns
-------
charge, multiplicity
"""
charge = charge if charge is not None else get_charge_attribute(atoms)
spin_multiplicity = (
spin_multiplicity
if spin_multiplicity is not None
else get_spin_multiplicity_attribute(atoms)
)
if charge is None and spin_multiplicity is not None:
charge = 0
try:
mol = AseAtomsAdaptor.get_molecule(atoms)
if charge is not None:
if spin_multiplicity is not None:
mol.set_charge_and_spin(charge, spin_multiplicity)
else:
mol.set_charge_and_spin(charge)
except ValueError:
mol = AseAtomsAdaptor.get_molecule(atoms, charge_spin_check=False)
nelectrons = mol.nelectrons - charge if charge else mol.nelectrons
default_spin_multiplicity = 1 if nelectrons % 2 == 0 else 2
mol.set_charge_and_spin(
charge if charge is not None else mol.charge,
(
spin_multiplicity
if spin_multiplicity is not None
else default_spin_multiplicity
),
)
if (mol.nelectrons + mol.spin_multiplicity) % 2 != 1:
raise ValueError(
f"Charge of {mol.charge} and spin multiplicity of {mol.spin_multiplicity} is"
" not possible for this molecule."
)
logger.debug(
f"Setting charge to {mol.charge} and spin multiplicity to {mol.spin_multiplicity}"
)
return mol.charge, mol.spin_multiplicity
def get_final_atoms_from_dynamics(dynamics: Dynamics) -> Atoms:
"""
Get the final atoms object from a dynamics run.
Parameters
----------
dynamics
ASE dynamics object
Returns
-------
Atoms
Atoms object
"""
return (
dynamics.atoms.atoms if isinstance(dynamics.atoms, Filter) else dynamics.atoms
)
def perturb(mol: Atoms, matrix: list[list[float]] | NDArray, scale: float) -> Atoms:
"""
Perturb each atom in a molecule by a (scaled) 1x3 vector, reflecting e.g. a vibrational normal mode.
Parameters
----------
mol
ASE Atoms object representing a molecule
matrix
Nx3 matrix, where N is the number of atoms. This means that there is potentially a different translation
vector for each atom in the molecule.
scale
Scaling factor for perturbation
Returns
-------
Atoms
The input molecule after perturbation
"""
mol_copy = copy_atoms(mol)
mode = np.asarray(matrix)
orig_pos = mol_copy.get_positions()
pos = orig_pos + mode * scale
mol_copy.set_positions(pos)
return mol_copy