# -*- coding: utf-8 -*-
"""This module defines the ``Energy`` class."""
from attr import field
from pint import Quantity
from nanotools.base import Base
from nanotools.system import System
from nanotools.utils import to_quantity
import attr
import numpy as np
def converter_energy(x):
return to_quantity(x, "eV")
def converter_forces(x):
return to_quantity(x, "eV / angstrom", shape=(-1, 3))
def converter_stress(x):
return to_quantity(x, "eV / angstrom ** 3", shape=(3, 3))
[docs]
@attr.s(auto_detect=True, eq=False)
class Energy(Base):
"""``Energy`` class.
The ``Energy`` class stores energy data. It is typically empty before a calculation.
It gets overwritten during a calculation.
Attributes:
esr:
esr is the short-range energy.
Example::
esr = energy.esr
ebs:
ebs is the band structure energy.
Example::
ebs = energy.ebs
edh:
edh is the delta Hartree energy.
Example::
edh = energy.edh
efermi:
efermi is the Fermi energy.
Example::
efermi = energy.efermi
etot:
etot is the total energy.
Example::
etot = energy.etot
evxc:
evxc is the exchange-correlation potential energy.
Example::
evxc = energy.evxc
exc:
exc is the exchange-correlation energy.
Example::
exc = energy.exc
eigenvalues:
eigenvalues is a three-dimensional array containing the Kohn-Sham energies (the eigenvalues of the Kohn-Sham equation). The dimensions are the following: bands, k-point, spin.
Example::
eigenvalues = energy.eigenvalues
forces:
forces is a two-dimensional array containing the atomic forces (as calculated by the Hellman-Feynman theorem).
Example::
forces = energy.forces
forces_return:
If True, the forces are computed and written to energy.forces. They are not computed otherwise.
Example::
energy.forces_return = True
stress:
stress is a two-dimensional array containing the stress tensor (as calculated by the Hellman-Feynman theorem).
Example::
stress = energy.stress
stress_return:
If True, the stress tensor is computed and written to energy.stress. It is not computed otherwise.
Example::
energy.stress_return = True
edftd3:
Grimme's DFT-D3 energy.
It is evaluated with ASE's
`DFTD3 calculator <https://wiki.fysik.dtu.dk/ase/ase/calculators/dftd3.html>`_.
For additional details on the methods, please visit the Mulliken Center's
`website <https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dft-d3/>`_.
frc_dftd3:
Grimme's DFT-D3 forces.
stress_dftd3:
Grimme's DFT-D3 stress.
include_dftd3:
Grimme's DFT-D3 switch.
If True, include D3 dispersion corrections in energy, forces and stress.
Do nothing otherwise.
"""
esr: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
ebg: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
ebs: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
edh: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
exc: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
evxc: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
etot: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
efermi: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
eigenvalues: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
efree: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
entropy: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
forces: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
forces_return: bool = field(
default=False,
converter=bool,
validator=attr.validators.instance_of(bool),
)
stress: Quantity = field(
default=None,
converter=attr.converters.optional(converter_stress),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
stress_return: bool = field(
default=False,
converter=bool,
validator=attr.validators.instance_of(bool),
)
frc_t: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
frc_s: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
frc_vnl: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
frc_veff: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
frc_sr: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
frc_vna: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
frc_vdh: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
frc_rpc: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
edftd3: Quantity = field(
default=None,
converter=attr.converters.optional(converter_energy),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
frc_dftd3: Quantity = field(
default=None,
converter=attr.converters.optional(converter_forces),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
stress_dftd3: Quantity = field(
default=None,
converter=attr.converters.optional(converter_stress),
validator=attr.validators.optional(attr.validators.instance_of(Quantity)),
)
include_dftd3: bool = attr.ib(
default=False,
converter=bool,
validator=attr.validators.instance_of(bool),
)
dftd3_kwargs: dict = attr.ib(default=attr.Factory(dict))
def __attrs_post_init__(self):
pass
def __eq__(self, other):
if other.__class__ is not self.__class__:
return NotImplemented
valid = True
for at in (
"eigenvalues", # arrays of floats
"forces",
"stress",
"esr", # floats
"ebg",
"ebs",
"edh",
"exc",
"evxc",
"etot",
"efermi",
"efree",
"entropy",
):
if getattr(self, at) is None:
valid = valid and getattr(self, at) == getattr(other, at)
else:
valid = valid and np.allclose(getattr(self, at), getattr(other, at))
return valid and (
self.esr.u,
self.ebg.u,
self.ebs.u,
self.edh.u,
self.exc.u,
self.evxc.u,
self.etot.u,
self.efermi.u,
self.eigenvalues.u,
self.efree.u,
self.entropy.u,
self.forces.u,
self.forces_return,
self.stress.u,
self.stress_return,
) == (
other.esr.u,
other.ebg.u,
other.ebs.u,
other.edh.u,
other.exc.u,
other.evxc.u,
other.etot.u,
other.efermi.u,
other.eigenvalues.u,
other.efree.u,
other.entropy.u,
other.forces.u,
other.forces_return,
other.stress.u,
other.stress_return,
)
def get_band_edges(self):
emin = np.min(self.eigenvalues)
emax = np.max(self.eigenvalues)
return emin - 1, emax + 1
[docs]
def get_cbm(self):
"""
Returns the conduction band maximum.
If partially occupied bands are detected, as in metals, then the function returns ``None``.
Returns:
float: conduction band maximum
"""
if self.ismetal():
return None
ev = self.eigenvalues
return np.min(ev[ev > self.efermi])
[docs]
def get_free_energy(self):
"""Returns the free energy."""
return self.efree
[docs]
def get_total_energy(self):
"""Returns the total energy."""
return self.etot
[docs]
def get_vbm(self):
"""
Returns the valence band maximum.
If partially occupied bands are detected, as in metals, then the function returns ``None``.
Returns:
float: valence band maximum
"""
if self.ismetal():
return None
ev = self.eigenvalues
return np.max(ev[ev < self.efermi])
[docs]
def set_stress_return(self, stress_return):
"""Sets stress_return attribute.
If stress_return is True, then forces_return is also set to True.
Args:
stress_return (bool): stress_return value
"""
if not isinstance(stress_return, bool):
raise Exception(
f"Invalid class {stress_return.__class__} for arg stress_return."
)
self.stress_return = stress_return
if self.stress_return:
self.forces_return = True
def set_dftd3_energy(self, atoms, include_dftd3=True, **kwargs):
from ase.calculators.dftd3 import DFTD3
if isinstance(atoms, System):
atoms = atoms.to_ase_atoms()
elif isinstance(atoms, Atoms):
pass
else:
raise Exception("Argument atoms must be of class System or ASE Atoms.")
self.dftd3_kwargs.update(kwargs)
self.include_dftd3 = include_dftd3
d3 = DFTD3(**self.dftd3_kwargs)
atoms.calc = d3
self.edftd3 = to_quantity(atoms.get_potential_energy(), "eV")
self.frc_dftd3 = to_quantity(atoms.get_forces(), "eV / angstrom", shape=(-1, 3))
self.stress_dftd3 = to_quantity(
atoms.get_stress(voigt=False), "eV / angstrom ** 3", shape=(3, 3)
)
self._update_energy_forces_stress()
set_dftd3_forces = set_dftd3_stress = set_dftd3_energy
def _update_energy_forces_stress(self):
if not self.include_dftd3:
return
ats = ["etot", "efree", "forces", "stress"]
d3s = ["edftd3", "edftd3", "frc_dftd3", "stress_dftd3"]
for a, d in zip(ats, d3s):
frc = getattr(self, a)
dfr = getattr(self, d)
if frc is None:
setattr(self, a, dfr)
else:
setattr(self, a, frc + dfr)