#!/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 velocity profiles."""
from typing import List, Optional, Union
import MDAnalysis as mda
from ..core import ProfileCylinderBase
from ..lib.util import render_docs
from ..lib.weights import velocity_weights
[docs]
@render_docs
class VelocityCylinder(ProfileCylinderBase):
r"""Cartesian velocity profile across a cylinder.
Reads in coordinates and velocities from a trajectory and calculates a velocity
:math:`[\mathrm{Å/ps}]` or a flux per unit area :math:`[\mathrm{Å^{-2}\,ps^{-1}}]`
profile along a given axis.
The ``grouping`` keyword gives you fine control over the velocity profile, e.g. you
can choose atomar or molecular velocities. Note that if the first one is employed
for complex compounds, usually a contribution corresponding to the vorticity appears
in the profile.
${CORRELATION_INFO_RADIAL}
Parameters
----------
${PROFILE_CYLINDER_CLASS_PARAMETERS}
${VDIM_PARAMETER}
${FLUX_PARAMETER}
Attributes
----------
${PROFILE_CYLINDER_CLASS_ATTRIBUTES}
"""
def __init__(
self,
atomgroups: Union[mda.AtomGroup, List[mda.AtomGroup]],
dim: int = 2,
zmin: Optional[float] = None,
zmax: Optional[float] = None,
bin_width: int = 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 = "velocity.dat",
concfreq: int = 0,
jitter: float = 0.0,
vdim: int = 0,
flux: bool = False,
):
self._locals = locals()
if vdim not in [0, 1, 2]:
raise ValueError("Velocity dimension can only be x=0, y=1 or z=2.")
if flux:
normalization = "volume"
else:
normalization = "number"
super(VelocityCylinder, self).__init__(
weighting_function=velocity_weights,
f_kwargs={"vdim": vdim},
normalization=normalization,
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,
)