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# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding: utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under the Lesser GNU Public Licence, v2.1 or any higher version
#
# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
#
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
#
r"""
Dielectric --- :mod:`MDAnalysis.analysis.dielectric`
===========================================================
:Authors: Mattia Felice Palermo, Philip Loche
:Year: 2022
:Copyright: Lesser GNU Public License v2.1+
"""
import numpy as np
from MDAnalysis.units import constants, convert
from MDAnalysis.analysis.base import AnalysisBase
from MDAnalysis.due import due, Doi
from MDAnalysis.exceptions import NoDataError
due.cite(
Doi("10.1080/00268978300102721"),
description="Dielectric analysis",
path="MDAnalysis.analysis.dielectric",
cite_module=True,
)
del Doi
class DielectricConstant(AnalysisBase):
r"""
Computes the average dipole moment
.. math::
\boldsymbol M = \sum_i q_i \boldsymbol r_i
where :math:`q_i` is the charge and :math:`\boldsymbol r_i` the position of
atom :math:`i` in the given :class:`MDAnalysis.core.groups.AtomGroup`.
Also, the static dielectric constant
.. math::
\varepsilon = 1 + \frac{\langle M^2 \rangle - \langle M \rangle^2}
{3 \varepsilon_ 0 V k_B T}
is calculated for a system in tin foil boundary conditions, which is
the usual case if electrostatics are handled with a Ewald summation
technique. See [Neumann1983]_ for details on the derivation.
.. warning::
Applying this class requires that no free charges, such as ions or
charged fragments, are present in the simulation.
Parameters
----------
atomgroup : MDAnalysis.core.groups.AtomGroup
Atomgroup on which the analysis is executed
temperature : float
Temperature (Kelvin) at which the system has been simulated
make_whole : bool
Make molecules whole; If the input already contains whole molecules
this can be disabled to gain speedup
verbose : bool
Show detailed progress of the calculation
Attributes
----------
results.M : numpy.ndarray
Directional dependant dipole moment
:math:`\langle \boldsymbol M \rangle` in :math:`eÅ`.
results.M2 : numpy.ndarray
Directional dependant squared dipole moment
:math:`\langle \boldsymbol M^2 \rangle` in :math:`(eÅ)^2`
results.fluct : float
Directional dependant dipole moment fluctuation
:math:`\langle \boldsymbol M^2 \rangle - \langle \boldsymbol M \rangle^2`
in :math:`(eÅ)^2`
results.eps : numpy.ndarray
Directional dependant static dielectric constant
results.eps_mean : float
Static dielectric constant
Example
-------
Create a :class:`DielectricConstant` instance by supplying an
:class:`~MDAnalysis.core.groups.AtomGroup`,
then use the :meth:`run` method::
import MDAnalysis as mda
from MDAnalysis.analysis.dielectric import DielectricConstant
from MDAnalysisTests.datafiles import PSF_TRICLINIC, DCD_TRICLINIC
# Load a pure water system
universe = mda.Universe(PSF_TRICLINIC, DCD_TRICLINIC)
diel = DielectricConstant(universe.atoms)
diel.run()
print(diel.results)
The static dielectric constant of the provided atomgroup is saved
within the :class:`~MDAnalysis.analysis.base.Results` attribute.
.. versionadded:: 2.1.0
"""
def __init__(self, atomgroup, temperature=300, make_whole=True, **kwargs):
super(DielectricConstant, self).__init__(
atomgroup.universe.trajectory, **kwargs
)
self.atomgroup = atomgroup
self.temperature = temperature
self.make_whole = make_whole
def _prepare(self):
if not hasattr(self.atomgroup, "charges"):
raise NoDataError("No charges defined given atomgroup.")
if not np.allclose(
self.atomgroup.total_charge(compound="fragments"), 0.0, atol=1e-5
):
raise NotImplementedError(
"Analysis for non-neutral systems or"
" systems with free charges are not"
" available."
)
self.volume = 0
self.results.M = np.zeros(3)
self.results.M2 = np.zeros(3)
self.results.fluct = np.zeros(3)
self.results.eps = np.zeros(3)
self.results.eps_mean = 0
def _single_frame(self):
if self.make_whole:
self.atomgroup.unwrap()
self.volume += self.atomgroup.universe.trajectory.ts.volume
M = np.dot(self.atomgroup.charges, self.atomgroup.positions)
self.results.M += M
self.results.M2 += M * M
def _conclude(self):
self.results.M /= self.n_frames
self.results.M2 /= self.n_frames
self.volume /= self.n_frames
self.results.fluct = self.results.M2 - self.results.M * self.results.M
self.results.eps = self.results.fluct / (
convert(constants["Boltzmann_constant"], "kJ/mol", "eV")
* self.temperature
* self.volume
* constants["electric_constant"]
)
self.results.eps_mean = self.results.eps.mean()
self.results.eps += 1
self.results.eps_mean += 1
|
