# -*- coding: utf-8 -*-
"""
Created on 2020-05-11
@author: Vincent Michaud-Rioux
"""
from nanotools.base import Base
from nanotools.energy import Energy
from nanotools.io.calculators import solve_generic
from nanotools.solver import Solver
from nanotools.system import System
from nanotools.totalenergy import TotalEnergy
from nanotools.utils import dict_converter
import attr
import numpy as np
[docs]
@attr.s
class MullikenData(Base):
"""``Mulliken`` class' data holder.
Args:
Returns:
"""
atom_populations: np.ndarray = attr.ib(
default=[],
converter=attr.converters.optional(np.array),
validator=attr.validators.optional(attr.validators.instance_of(np.ndarray)),
)
orbital_populations: np.ndarray = attr.ib(
default=[],
converter=attr.converters.optional(np.array),
validator=attr.validators.optional(attr.validators.instance_of(np.ndarray)),
)
orbital_atom: np.ndarray = attr.ib(
default=[],
converter=attr.converters.optional(np.array),
validator=attr.validators.optional(attr.validators.instance_of(np.ndarray)),
)
orbital_index: np.ndarray = attr.ib(
default=[],
converter=attr.converters.optional(np.array),
validator=attr.validators.optional(attr.validators.instance_of(np.ndarray)),
)
orbital_l: np.ndarray = attr.ib(
default=[],
converter=attr.converters.optional(np.array),
validator=attr.validators.optional(attr.validators.instance_of(np.ndarray)),
)
orbital_m: np.ndarray = attr.ib(
default=[],
converter=attr.converters.optional(np.array),
validator=attr.validators.optional(attr.validators.instance_of(np.ndarray)),
)
orbital_species: np.ndarray = attr.ib(
default=[],
converter=attr.converters.optional(np.array),
validator=attr.validators.optional(attr.validators.instance_of(np.ndarray)),
)
[docs]
@attr.s
class Mulliken(Base):
"""``Mulliken`` class.
Examples::
from nanotools import Mulliken
import numpy as np
calc = Mulliken.from_totalenergy("nano_scf_out.json")
calc.solve()
Attributes:
system:
Object containing system related parameters.
energy:
Object containing the total energy and its derivatives (force, stress, etc.).
mulliken:
Object containing the Mulliken population data.
solver:
Object containing solver related parameters.
"""
# input is dictionary with default constructor
system: System = attr.ib(
converter=lambda d: dict_converter(d, System),
validator=attr.validators.instance_of(System),
)
# optional
energy: Energy = attr.ib(
factory=Energy,
converter=lambda d: dict_converter(d, Energy),
validator=attr.validators.instance_of(Energy),
)
mulliken: MullikenData = attr.ib(
factory=MullikenData,
converter=lambda d: dict_converter(d, MullikenData),
validator=attr.validators.instance_of(MullikenData),
)
solver: Solver = attr.ib(
factory=Solver,
converter=lambda d: dict_converter(d, Solver),
validator=attr.validators.instance_of(Solver),
)
classname: str = attr.ib()
@classname.default
def _classname_default_value(self):
return self.__class__.__name__
def __attrs_post_init__(self):
pass
@classmethod
def from_totalenergy(cls, totalenergy, **kwargs):
if isinstance(totalenergy, TotalEnergy):
pass
else:
totalenergy = TotalEnergy.read(totalenergy)
sys = totalenergy.system.copy()
calc = cls(sys, solver=totalenergy.solver, **kwargs)
calc.energy = totalenergy.energy.copy()
return calc
[docs]
def solve(self, input="nano_mul_in", output="nano_mul_out"):
"""Performs a non.self-consistent calculation calling ``rescuplus``.
Args:
filename (str):
The object is saved to an input file ``filename`` which is read by ``rescuplus``.
output (str):
The results (with various extensions) are moved to files ``output`` and the results are
loaded to the object.
"""
self._check_mul()
output = solve_generic(self, "mul", input, output)
self._update(output + ".json")
def _check_mul(self):
return