#!/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
"""Base class for cylindrical analysis."""
import logging
from typing import Callable, Dict, Optional, Union
import MDAnalysis as mda
import numpy as np
from ..lib.math import transform_cylinder
from ..lib.util import render_docs
from .base import ProfileBase
from .planar import PlanarBase
logger = logging.getLogger(__name__)
[docs]
@render_docs
class CylinderBase(PlanarBase):
r"""Analysis class providing options and attributes for a cylinder system.
Provide the results attribute `r`.
Parameters
----------
${ATOMGROUP_PARAMETER}
${CYLINDER_CLASS_PARAMETERS}
${WRAP_COMPOUND_PARAMETER}
Attributes
----------
${CYLINDER_CLASS_ATTRIBUTES}
pos_cyl : numpy.ndarray
positions in cylinder coordinats (r, phi, z)
_obs.R : float
Average length (in Å) along the radial dimension in the current frame.
_obs.bin_pos : numpy.ndarray, (n_bins)
Central bin position of each bin (in Å) in the current frame.
_obs.bin_width : float
Bin width (in Å) in the current frame
_obs.bin_edges : numpy.ndarray, (n_bins + 1)
Edges of the bins (in Å) in the current frame.
_obs.bin_area : numpy.ndarray, (n_bins)
Area of the annulus pf the each bin in the current frame. Calculated via
:math:`\pi \left( r_{i+1}^2 - r_i^2 \right)` where `i` is the index of the bin.
_obs.bin_volume : numpy.ndarray, (n_bins)
Volume of an hollow cylinder of each bin (in Å^3) in the current frame.
Calculated via :math:`\pi L \left( r_{i+1}^2 - r_i^2 \right)` where `i` is the
index of the bin.
"""
def __init__(
self,
atomgroup: mda.AtomGroup,
unwrap: bool,
refgroup: Optional[mda.AtomGroup],
jitter: float,
concfreq: int,
dim: int,
zmin: Union[None, float],
zmax: Union[None, float],
bin_width: float,
rmin: float,
rmax: Union[None, float],
wrap_compound: str,
):
super().__init__(
atomgroup=atomgroup,
unwrap=unwrap,
refgroup=refgroup,
jitter=jitter,
concfreq=concfreq,
wrap_compound=wrap_compound,
dim=dim,
zmin=zmin,
zmax=zmax,
bin_width=bin_width,
)
self.rmin = rmin
self._rmax = rmax
def _compute_lab_frame_cylinder(self):
"""Compute lab limit `rmax`."""
box_half = self._universe.dimensions[self.odims].min() / 2
if self._rmax is None:
self.rmax = box_half
elif self._rmax <= box_half:
self.rmax = self._rmax
else:
logger.warn(
f"`rmax` is bigger than half the smallest box vector ({box_half:.2f}) "
"in the radial direction. This will lead to artifacts at the edges."
)
self.rmax = self._rmax
# Transform into cylinder coordinates
self.pos_cyl = transform_cylinder(
self._universe.atoms.positions, origin=self.box_center, dim=self.dim
)
def _prepare(self):
"""Prepare the cylinder analysis."""
super()._prepare()
self._compute_lab_frame_cylinder()
if self.rmin < 0:
raise ValueError("Only values for `rmin` larger or equal 0 are " "allowed.")
if self._rmax is not None and self._rmax <= self.rmin:
raise ValueError("`rmax` can not be smaller than or equal " "to `rmin`!")
try:
if self._bin_width > 0:
R = self.rmax - self.rmin
self.n_bins = int(np.ceil(R / self._bin_width))
else:
raise ValueError("Binwidth must be a positive number.")
except TypeError:
raise ValueError("Binwidth must be a number.")
def _single_frame(self):
"""Single frame for the cylinder analysis."""
super()._single_frame()
self._compute_lab_frame_cylinder()
self._obs.R = self.rmax - self.rmin
self._obs.bin_edges = np.linspace(
self.rmin, self.rmax, self.n_bins + 1, endpoint=True
)
self._obs.bin_width = self._obs.R / self.n_bins
self._obs.bin_pos = self._obs.bin_edges[1:] - self._obs.bin_width / 2
self._obs.bin_area = np.pi * np.diff(self._obs.bin_edges**2)
self._obs.bin_volume = self._obs.bin_area * self._obs.L
def _conclude(self):
"""Results calculations for the cylinder analysis."""
super()._conclude()
self.results.bin_pos = self.means.bin_pos
[docs]
@render_docs
class ProfileCylinderBase(CylinderBase, ProfileBase):
"""Base class for computing radial profiles in a cylindrical geometry.
${CORRELATION_INFO_RADIAL}
Parameters
----------
${PROFILE_CYLINDER_CLASS_PARAMETERS}
${PROFILE_CLASS_PARAMETERS_PRIVATE}
Attributes
----------
${PROFILE_CYLINDER_CLASS_ATTRIBUTES}
"""
def __init__(
self,
atomgroup: mda.AtomGroup,
unwrap: bool,
refgroup: Optional[mda.AtomGroup],
jitter: float,
concfreq: int,
dim: int,
zmin: Union[None, float],
zmax: Union[None, float],
bin_width: float,
rmin: float,
rmax: Union[None, float],
grouping: str,
bin_method: str,
output: str,
weighting_function: Callable,
weighting_function_kwargs: Union[None, Dict],
normalization: str,
):
CylinderBase.__init__(
self,
atomgroup=atomgroup,
unwrap=unwrap,
refgroup=refgroup,
jitter=jitter,
concfreq=concfreq,
dim=dim,
zmin=zmin,
zmax=zmax,
bin_width=bin_width,
rmin=rmin,
rmax=rmax,
wrap_compound=grouping, # same as grouping to avoid broken compounds
)
# `AnalysisBase` performs conversions on `atomgroup`. Take converted
# `atomgroup` and not the user provided ones.
ProfileBase.__init__(
self,
atomgroup=self.atomgroup,
grouping=grouping,
bin_method=bin_method,
output=output,
weighting_function=weighting_function,
weighting_function_kwargs=weighting_function_kwargs,
normalization=normalization,
)
def _prepare(self):
CylinderBase._prepare(self)
ProfileBase._prepare(self)
logger.info(
f"Computing {self.grouping} radial profile along "
f"{'XYZ'[self.dim]}-axes."
)
def _compute_histogram(
self, positions: np.ndarray, weights: Optional[np.ndarray] = None
) -> np.ndarray:
positions = transform_cylinder(positions, self.box_center, self.dim)
# Use the 2D histogram function to perform the selection in the z dimension.
hist, _, _ = np.histogram2d(
positions[:, 0],
positions[:, 2],
bins=(self.n_bins, 1),
range=((self.rmin, self.rmax), (self.zmin, self.zmax)),
weights=weights,
)
# Reshape into 1D array
hist = hist[:, 0]
return hist
def _single_frame(self) -> float:
CylinderBase._single_frame(self)
ProfileBase._single_frame(self)
# Take the center bin of the zeroth group for correlation analysis.
return self._obs.profile[0]
def _conclude(self):
CylinderBase._conclude(self)
ProfileBase._conclude(self)