Source code for maicos.modules.densitycylinder

#!/usr/bin/env python
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
#
# Copyright (c) 2023 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 cylindrical density profiles."""

import logging
from typing import List, Optional, Union

import MDAnalysis as mda

from ..core import ProfileCylinderBase
from ..lib.util import render_docs
from ..lib.weights import density_weights


logger = logging.getLogger(__name__)


[docs] @render_docs class DensityCylinder(ProfileCylinderBase): r"""Cylindrical partial density profiles. ${DENSITY_DESCRIPTION} ${CORRELATION_INFO_RADIAL} Parameters ---------- ${PROFILE_CYLINDER_CLASS_PARAMETERS} ${DENS_PARAMETER} Attributes ---------- ${PROFILE_CYLINDER_CLASS_ATTRIBUTES} """ def __init__( self, atomgroups: Union[mda.AtomGroup, List[mda.AtomGroup]], dens: str = "mass", dim: int = 2, zmin: Optional[float] = None, zmax: Optional[float] = None, 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, ): self._locals = locals() super().__init__( weighting_function=density_weights, f_kwargs={"dens": dens}, normalization="volume", atomgroups=atomgroups, dim=dim, zmin=zmin, zmax=zmax, bin_width=bin_width, rmin=rmin, rmax=rmax, refgroup=refgroup, grouping=grouping, unwrap=unwrap, bin_method=bin_method, output=output, concfreq=concfreq, jitter=jitter, )