#!/usr/bin/env python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
#
# Copyright (c) 2024 Authors and contributors
# (see the AUTHORS.rst file for the full list of names)
#
# Released under the GNU Public Licence, v3 or any higher version
# SPDX-License-Identifier: GPL-3.0-or-later
"""Module for computing spherical density profiles."""
import logging
from typing import Optional
import MDAnalysis as mda
from ..core import ProfileSphereBase
from ..lib.util import render_docs
from ..lib.weights import density_weights
logger = logging.getLogger(__name__)
[docs]
@render_docs
class DensitySphere(ProfileSphereBase):
r"""Spherical partial density profiles.
${DENSITY_DESCRIPTION}
${CORRELATION_INFO_RADIAL}
Parameters
----------
${PROFILE_SPHERE_CLASS_PARAMETERS}
${DENS_PARAMETER}
Attributes
----------
${PROFILE_SPHERE_CLASS_ATTRIBUTES}
"""
def __init__(
self,
atomgroup: mda.AtomGroup,
dens: str = "mass",
bin_width: float = 1,
rmin: float = 0,
rmax: Optional[float] = None,
refgroup: Optional[mda.AtomGroup] = None,
grouping: str = "atoms",
unwrap: bool = True,
bin_method: str = "com",
output: str = "density.dat",
concfreq: int = 0,
jitter: float = 0.0,
) -> None:
self._locals = locals()
super().__init__(
atomgroup=atomgroup,
unwrap=unwrap,
refgroup=refgroup,
jitter=jitter,
concfreq=concfreq,
rmin=rmin,
rmax=rmax,
bin_width=bin_width,
grouping=grouping,
bin_method=bin_method,
output=output,
weighting_function=density_weights,
weighting_function_kwargs={"dens": dens},
normalization="volume",
)