# coding: utf-8
# Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
# Distributed under the terms of "New BSD License", see the LICENSE file.
import numpy as np
from ase.atom import Atom as ASEAtom
from pyiron_atomistics.atomistics.structure.periodic_table import (
ChemicalElement,
PeriodicTable,
)
__author__ = "Sudarsan Surendralal"
__copyright__ = (
"Copyright 2021, Max-Planck-Institut für Eisenforschung GmbH - "
"Computational Materials Design (CM) Department"
)
__version__ = "1.0"
__maintainer__ = "Sudarsan Surendralal"
__email__ = "surendralal@mpie.de"
__status__ = "production"
__date__ = "Aug 1, 2020"
[docs]
class Atom(ASEAtom):
"""
Class for representing a single atom derived from the `ASE atom class`_.
Args:
symbol (str/pyiron_atomistics.atomistics.structure.periodic_table.ChemcicalElement): Symbol or elecment object
position (list/numpy.ndarray): Position of atom in cartesian coordinates
tag (str): Tag assigned to structure
momentum (float): Momentum
mass (float): Atomic mass in a.u.
magmom (float): Magnetic moment in Bohn Magneton
charge (float): Charge in e
atoms (ase.atoms.Atoms): Assigned atoms
index (int): Assigned index
.. _ASE atom class: https://wiki.fysik.dtu.dk/ase/ase/atom.html
"""
[docs]
def __init__(
self,
symbol="X",
position=(0, 0, 0),
tag=None,
momentum=None,
mass=None,
magmom=None,
charge=None,
atoms=None,
index=None,
pse=None,
element=None,
**qwargs,
):
if element is None:
element = symbol
if pse is None:
pse = PeriodicTable()
if element is None or element == "X":
if "Z" in qwargs:
el_symbol = pse.atomic_number_to_abbreviation(qwargs["Z"])
qwargs["element"] = pse.element(el_symbol)
else:
if isinstance(element, str):
el_symbol = element
qwargs["element"] = pse.element(el_symbol)
elif isinstance(element, ChemicalElement):
qwargs["element"] = element
else:
raise ValueError("Unknown element type")
# KeyError handling required for user defined elements
try:
ASEAtom.__init__(
self,
symbol=symbol,
position=position,
tag=tag,
momentum=momentum,
mass=mass,
magmom=magmom,
charge=charge,
atoms=atoms,
index=index,
)
except KeyError:
symbol = pse.Parent[symbol]
ASEAtom.__init__(
self,
symbol=symbol,
position=position,
tag=tag,
momentum=momentum,
mass=mass,
magmom=magmom,
charge=charge,
atoms=atoms,
index=index,
)
# ASE compatibility for tags
for key, val in qwargs.items():
self.data[key] = val
def __getattr__(self, key):
try:
return self.data[key]
except KeyError:
raise AttributeError(key)
@property
def mass(self):
"""
Gives the atomic mass of the atom
Returns:
float: The atomic mass in a.u.
"""
return float(self.element.AtomicMass)
@property
def symbol(self):
"""
The chemical symbol of the atom
Returns:
str: The chemical symbol of the atom
"""
return self.element.Abbreviation
@property
def number(self):
"""
The atomic number of the atom
Returns:
int: The atomic number according to the periodic table
"""
return self.element.AtomicNumber
def __eq__(self, other):
if not (isinstance(other, Atom)):
return False
conditions = [
np.allclose(self.position, other.position),
self.symbol == other.symbol,
]
return all(conditions)
[docs]
def ase_to_pyiron(ase_obj):
"""
Convert an ase.atom.Atom object to its equivalent pyiron structure
Args:
ase_obj(ase.atom.Atom): The ase atoms instance to convert
Returns:
pyiron.atomistics.structure.atom.Atom: The equivalent pyiron Atom
"""
return Atom(
symbol=ase_obj.symbol,
position=ase_obj.position,
tag=ase_obj.tag,
momentum=ase_obj.momentum,
mass=ase_obj.mass,
magmom=ase_obj.magmom,
charge=ase_obj.charge,
atoms=ase_obj.atoms,
index=ase_obj.index,
)
