# -*- coding: utf-8 -*-
"""
Created on 2020-05-12
@author: Vincent Michaud-Rioux
"""
from nptyping import NDArray
from nanotools.base import Base
from nanotools.utils import load_dcal, load_dcal_parameter, load_dcal_var
from scipy.special import spherical_jn as jn
import attr
import numpy as np
# TODO: what to do with vfld
[docs]
@attr.s(auto_detect=True, eq=False)
class RadFunc(Base):
"""
radFunc class.
Attributes:
"""
path: str = attr.ib(validator=attr.validators.instance_of(str))
varname: str = attr.ib(validator=attr.validators.instance_of(str))
ecut: float = attr.ib(
default=36.75, converter=float, validator=attr.validators.instance_of(float)
)
index: int = attr.ib(
default=0,
converter=int,
validator=attr.validators.instance_of(int),
)
rgrid: NDArray = attr.ib(
factory=lambda: np.zeros((0)),
converter=attr.converters.optional(np.array),
# validator=attr.validators.optional(attr.validators.instance_of(NDArray)),
)
rwght: NDArray = attr.ib(
factory=lambda: np.zeros((0)),
converter=attr.converters.optional(np.array),
# validator=attr.validators.optional(attr.validators.instance_of(NDArray)),
)
rvals: NDArray = attr.ib(
factory=lambda: np.zeros((0)),
converter=attr.converters.optional(np.array),
# validator=attr.validators.optional(attr.validators.instance_of(NDArray)),
)
qgrid: NDArray = attr.ib(
factory=lambda: np.zeros((0)),
converter=attr.converters.optional(np.array),
# validator=attr.validators.optional(attr.validators.instance_of(NDArray)),
)
qwght: NDArray = attr.ib(
factory=lambda: np.zeros((0)),
converter=attr.converters.optional(np.array),
# validator=attr.validators.optional(attr.validators.instance_of(NDArray)),
)
qvals: NDArray = attr.ib(
factory=lambda: np.zeros((0)),
converter=attr.converters.optional(np.array),
# validator=attr.validators.optional(attr.validators.instance_of(NDArray)),
)
def __attrs_post_init__(self):
sizes = [
getattr(self, a).size
for a in ["rgrid", "rwght", "rvals", "qgrid", "qwght", "qvals"]
]
if np.all(np.array(sizes) > 0):
return
varname = self.varname
if varname in ["Vna", "Vlocal", "Vnl"]:
vfld = "vvData"
if varname in ["VnlSO"]:
vfld = "vsoData"
if varname in ["Rna", "Rlocal", "Rpc"]:
vfld = "rhoData"
if varname in ["OrbitalSet"]:
vfld = "frData"
if varname in ["Vna", "Vlocal", "Rna", "Rlocal", "Rpc"]:
i = None
else:
i = self.index
data, fmt = load_dcal(self.path, varname)
if data is None or len(data) == 0:
self.rgrid = np.linspace(0, 5, 11)
self.rwght = np.zeros((11))
self.rvals = np.zeros((11))
self.qgrid = np.linspace(0, 5, 11)
self.qwght = np.zeros((11))
self.qvals = np.zeros((11))
self.ecut = max(self.qgrid)
return
self.rgrid = load_dcal_var(data, "rrData", fmt, i)
self.rwght = load_dcal_var(data, "drData", fmt, i)
self.rvals = load_dcal_var(data, vfld, fmt, i)
try:
self.qgrid = load_dcal_var(data, "qqData", fmt, i)
self.qwght = load_dcal_var(data, "qwData", fmt, i)
self.qvals = load_dcal_var(data, "fqData", fmt, i)
except:
# self.qgrid, self.qwght = leggauss(int(ecut*10))
# self.qgrid = (0 * (1 - self.qgrid) + ecut * (1 + self.qgrid)) / 2
nq = int(self.ecut * 30)
if type(self) is RadFunc:
l = 0
else:
l = self.l
self.qgrid = np.linspace(0, self.ecut, num=nq + 1)
self.qwght = np.ones((nq + 1)) / nq * self.ecut
self.qwght[0] *= 0.5
self.qwght[-1] *= 0.5
self.qvals = radialFT(self.rgrid, self.rwght, self.rvals, self.qgrid, l)
self.ecut = max(self.qgrid)
def __eq__(self, other):
if other.__class__ is not self.__class__:
return NotImplemented
return (
self.path,
self.varname,
self.ecut,
self.index,
) == (
other.path,
other.varname,
other.ecut,
other.index,
) and (
np.allclose(self.rgrid, other.rgrid)
and np.allclose(self.rwght, other.rwght)
and np.allclose(self.rvals, other.rvals)
and np.allclose(self.qgrid, other.qgrid)
and np.allclose(self.qwght, other.qwght)
and np.allclose(self.qvals, other.qvals)
)
def zero_out(self):
self.rvals[:] = 0.0
self.qvals[:] = 0.0
[docs]
@attr.s
class Orb(RadFunc):
l: int = attr.ib(default=None)
n: int = attr.ib(default=-1)
def __attrs_post_init__(self):
if self.l is None:
i = self.index
data, fmt = load_dcal(self.path, self.varname)
try:
tmp = load_dcal_parameter(data, "L", fmt, i)
assert len(tmp) == 1
self.l = tmp.astype(int).item()
except ValueError:
raise Exception(
"Couldn't find parameter 'l' in file " + self.path + "."
)
try:
tmp = load_dcal_parameter(data, "N", fmt, i)
assert len(tmp) == 1
self.n = tmp.astype(int).item()
except:
pass
super().__attrs_post_init__()
[docs]
@attr.s
class KbOrb(Orb):
j: int = attr.ib(default=None)
energy = attr.ib(default=None)
kbcos = attr.ib(default=None)
kbnrg = attr.ib(default=None)
def __attrs_post_init__(self):
if self.kbnrg is None:
i = self.index
data, fmt = load_dcal(self.path, self.varname)
try:
tmp = load_dcal_parameter(data, "halfLxEkbso", fmt, i)
if tmp is None:
tmp = load_dcal_parameter(data, "KBenergy", fmt, i)
else:
j = load_dcal_parameter(data, "J", fmt, i)
self.j = int(j)
assert len(tmp) == 1
self.kbnrg = tmp.astype(float).item()
except ValueError:
raise Exception(
"Couldn't find parameter 'KBenergy' in file " + self.path + "."
)
super().__attrs_post_init__()
[docs]
@attr.s
class AoOrb(Orb):
zeta = attr.ib(default=-1)
energy = attr.ib(default=None)
coulombU = attr.ib(default=None)
exchangeJ = attr.ib(default=None)
population = attr.ib(default=None)
def __attrs_post_init__(self):
if self.population is None:
i = self.index
data, fmt = load_dcal(self.path, self.varname)
try:
tmp = load_dcal_parameter(data, "Population", fmt, i)
assert len(tmp) == 1
self.population = tmp.astype(float).item()
except ValueError:
raise Exception(
"Couldn't find parameter 'Population' in file " + self.path + "."
)
super().__attrs_post_init__()
def to_vacuum(self):
self.path = ""
self.energy = 0.0
self.coulombU = 0.0
self.exchangeJ = 0.0
self.population = 0.0
[docs]
def radialFT(r, fr, dr, q, l=0):
"""
Description
Computes the radial Fourier transform.
Args:
r (1D array):
Radial grid.
fr (1D array):
Radial values.
dr (1D array):
Radial integration weights.
q (1D array):
Fourier grid.
l (1D array):
Principal angular momentum.
Returns:
fq (1D array):
Radial Fourier transform.
"""
if l < 0:
l = 0
fq = r.reshape((-1, 1)) * q.reshape((1, -1))
fq = jn(l, fq)
fq = r.reshape((-1, 1)) ** 2 * fr.reshape((-1, 1)) * fq
fq = np.sqrt(2 / np.pi) * np.matmul(dr.reshape((1, -1)), fq).flatten()
return fq
# reference MATLAB code
# fq = bsxfun(@times,r(:),q(:)');
# fq = bsxfun(@times,r(:).^2.*fr(:),calcSphericalBessel(l,fq));
# fq = sqrt(2/pi)*dr*fq;