# -*- coding: utf-8 -*-
"""
===============================================================================
Atom classes with a dipole moment (:mod:`sknano.core.atoms.dipole_atoms`)
===============================================================================
.. currentmodule:: sknano.core.atoms.dipole_atoms
"""
from __future__ import absolute_import, division, print_function
from __future__ import unicode_literals
__docformat__ = 'restructuredtext en'
from operator import attrgetter
import numbers
# import numpy as np
from sknano.core.math import Vector, Vectors
from .atoms import Atom, Atoms
__all__ = ['DipoleAtom', 'DipoleAtoms']
[docs]class DipoleAtom(Atom):
"""An `Atom` sub-class with electric dipole moment attributes.
Parameters
----------
element : {str, int}, optional
A string representation of the element symbol or an integer specifying
an element atomic number.
px, py, pz : float, optional
:math:`p_x, p_y, p_z` components of `DipoleAtom` dipole moment.
"""
def __init__(self, *args, px=None, py=None, pz=None, **kwargs):
super().__init__(*args, **kwargs)
self._p = Vector([px, py, pz])
self.fmtstr = super().fmtstr + \
", px={px:.6f}, py={py:.6f}, pz={pz:.6f}"
# def __lt__(self, other):
# return (self.p < other.p and super().__le__(other)) or \
# (self.p <= other.p and super().__lt__(other))
def __eq__(self, other):
if not self._is_valid_operand(other):
return NotImplemented
return self.p == other.p and super().__eq__(other)
def __le__(self, other):
if not self._is_valid_operand(other):
return NotImplemented
if self.p > other.p or not super().__le__(other):
return False
return True
def __lt__(self, other):
if not self._is_valid_operand(other):
return NotImplemented
if self.p >= other.p or not super().__lt__(other):
return False
return True
def __ge__(self, other):
if not self._is_valid_operand(other):
return NotImplemented
if self.p < other.p or not super().__ge__(other):
return False
return True
def __gt__(self, other):
if not self._is_valid_operand(other):
return NotImplemented
if self.p <= other.p or not super().__gt__(other):
return False
return True
def __dir__(self):
attrs = super().__dir__()
attrs.extend(['px', 'py', 'pz'])
return attrs
@property
def px(self):
""":math:`x` component of `DipoleAtom` dipole moment vector"""
return self._p.x
@px.setter
def px(self, value):
"""Set :math:`p_x`.
Set :math:`p_x`, the :math:`x` component of `DipoleAtom` dipole moment
vector.
Parameters
----------
value : float
:math:`p_x` component of dipole moment
"""
if not isinstance(value, numbers.Number):
raise TypeError('Expected a number')
self._p.x = value
@property
def py(self):
""":math:`x` component of `DipoleAtom` dipole moment vector"""
return self._p.y
@py.setter
def py(self, value):
"""Set :math:`p_y`.
Set :math:`p_y`, the :math:`y` component of `DipoleAtom` dipole moment
vector.
Parameters
----------
value : float
:math:`p_y` component of dipole moment
"""
if not isinstance(value, numbers.Number):
raise TypeError('Expected a number')
self._p.y = value
@property
def pz(self):
""":math:`z` component of `DipoleAtom` dipole moment vector"""
return self._p.z
@pz.setter
def pz(self, value):
"""Set :math:`p_z`.
Set :math:`p_z`, the :math:`z` component of `DipoleAtom` dipole moment
vector.
Parameters
----------
value : float
:math:`p_z` component of dipole moment
"""
if not isinstance(value, numbers.Number):
raise TypeError('Expected a number')
self._p.z = value
@property
def p(self):
"""Dipole moment :math:`\\mathbf{p}=q\\mathbf{d}`."""
return self._p
@p.setter
def p(self, value):
"""Set `DipoleAtom` dipole moment :math:`\\mathbf{p}=q\\mathbf{d}`.
Parameters
----------
value : array_like
electric dipole moment vector
"""
self._p[:] = Vector(value, nd=3)
[docs] def rezero(self, epsilon=1.0e-10):
"""Re-zero dipole moment vector components.
Set dipole moment vector components with absolute value less than
`epsilon` to zero.
Parameters
----------
epsilon : float
smallest allowed absolute value of any :math:`x,y,z` component.
"""
self.p.rezero(epsilon)
super().rezero(epsilon)
[docs] def rotate(self, **kwargs):
"""Rotate `Atom` dipole moment vector.
Parameters
----------
angle : float
axis : :class:`~sknano.core.math.Vector`, optional
anchor_point : :class:`~sknano.core.math.Point`, optional
rot_point : :class:`~sknano.core.math.Point`, optional
from_vector, to_vector : :class:`~sknano.core.math.Vector`, optional
degrees : bool, optional
transform_matrix : :class:`~numpy:numpy.ndarray`
"""
self.p.rotate(**kwargs)
super().rotate(**kwargs)
[docs] def todict(self):
"""Return :class:`~python:dict` of constructor parameters."""
super_dict = super().todict()
super_dict.update(dict(px=self.px, py=self.py, pz=self.pz))
return super_dict
[docs]class DipoleAtoms(Atoms):
"""An `Atoms` sub-class for `DipoleAtom`\ s.
A container class for `DipoleAtom` objects.
Parameters
----------
atoms : {None, sequence, `DipoleAtoms`}, optional
if not `None`, then a list of `DipoleAtom` instance objects or an
existing `DipoleAtoms` instance object.
"""
@property
def __atom_class__(self):
return DipoleAtom
def sort(self, key=attrgetter('p'), reverse=False):
super().sort(key=key, reverse=reverse)
@property
def p(self):
""":class:`Vectors` of :attr:`DipoleAtom.p` :class:`Vector`\ s."""
return Vectors([atom.p for atom in self])
@property
def dipole_moments(self):
"""An alias for :attr:`DipoleAtoms.p"""
return self.p
@property
def px(self):
""":class:`~numpy:numpy.ndarray` of :attr:`DipoleAtom.px` \
components."""
return self.p.x
@property
def py(self):
""":class:`~numpy:numpy.ndarray` of :attr:`DipoleAtom.py` \
components."""
return self.p.y
@property
def pz(self):
""":class:`~numpy:numpy.ndarray` of :attr:`DipoleAtom.pz` \
components."""
return self.p.z
@property
def P(self):
"""Return the total net dipole moment vector of `DipoleAtoms`."""
return Vector(self.dipole_moments.sum(axis=1))
