# Copyright (C) 2010-2022 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ESPResSo is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
import itertools
import numpy as np
from .script_interface import ScriptInterfaceHelper, script_interface_register
from .math import CylindricalTransformationParameters
[docs]
@script_interface_register
class Observable(ScriptInterfaceHelper):
"""
Base class for all observables.
Methods
-------
shape()
Get the shape of the numpy array returned by the observable.
"""
_so_name = "Observables::Observable"
_so_bind_methods = ("shape",)
_so_creation_policy = "GLOBAL"
[docs]
def calculate(self):
return np.array(self.call_method("calculate")).reshape(self.shape())
[docs]
class ProfileObservable(Observable):
"""
Base class for histogram-based observables.
"""
[docs]
def bin_edges(self):
"""
Returns
-------
:obj:`ndarray` of :obj:`float`
Positions between the bins. If the histogram has dimensions
``(M,N,O)``, the bin edges have dimensions ``(M+1,N+1,O+1,3)``.
"""
edges = self.call_method("edges")
shape = list(map(len, edges)) + [len(edges)]
return np.array(list(itertools.product(*edges))).reshape(shape)
[docs]
def bin_centers(self):
"""
Returns
-------
:obj:`ndarray` of :obj:`float`
Positions of the bins centers. If the histogram has dimensions
``(M,N,O)``, the bin centers have dimensions ``(M,N,O,3)``.
"""
edges = self.call_method("edges")
for i, edge in enumerate(edges):
edges[i] = np.array(edge[:-1]) + (edge[1] - edge[0]) / 2
shape = list(map(len, edges)) + [len(edges)]
return np.array(list(itertools.product(*edges))).reshape(shape)
[docs]
class CylindricalProfileObservable(ProfileObservable):
"""
Base class for observables that work with cylinder coordinates
"""
def __init__(
self, transform_params=CylindricalTransformationParameters(), **kwargs):
# Provide default transformation parameters if not user-provided
kwargs['transform_params'] = transform_params
super().__init__(**kwargs)
[docs]
@script_interface_register
class ComPosition(Observable):
"""Calculates the center of mass for particles with given ids.
Note that virtual sites are not included since they do not have a meaningful mass.
Output format: :math:`\\frac{1}{\\sum_i m_i} \\left( \\sum_i m_i r^x_i, \\sum_i m_i r^y_i, \\sum_i m_i r^z_i\\right)`
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(3,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ComPosition"
[docs]
@script_interface_register
class ComVelocity(Observable):
"""Calculates the center of mass velocity for particles with given ids.
Note that virtual sites are not included since they do not have a meaningful mass.
Output format: :math:`\\frac{1}{\\sum_i m_i} \\left( \\sum_i m_i v^x_i, \\sum_i m_i v^y_i, \\sum_i m_i v^z_i\\right)`
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(3,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ComVelocity"
[docs]
@script_interface_register
class DensityProfile(ProfileObservable):
"""Calculates the particle density profile for particles with given ids.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
n_x_bins : :obj:`int`
Number of bins in ``x`` direction.
n_y_bins : :obj:`int`
Number of bins in ``y`` direction.
n_z_bins : :obj:`int`
Number of bins in ``z`` direction.
min_x : :obj:`float`
Minimum ``x`` to consider.
min_y : :obj:`float`
Minimum ``y`` to consider.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_x : :obj:`float`
Maximum ``x`` to consider.
max_y : :obj:`float`
Maximum ``y`` to consider.
max_z : :obj:`float`
Maximum ``z`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_x_bins``, ``n_y_bins``, ``n_z_bins``) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::DensityProfile"
[docs]
@script_interface_register
class DipoleMoment(Observable):
"""Calculates the electric dipole moment for particles with given ids.
Output format: :math:`\\left(\\sum_i q_i r^x_i, \\sum_i q_i r^y_i, \\sum_i q_i r^z_i\\right)`
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(3,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::DipoleMoment"
[docs]
@script_interface_register
class FluxDensityProfile(ProfileObservable):
"""Calculates the particle flux density for particles with given ids.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
n_x_bins : :obj:`int`
Number of bins in ``x`` direction.
n_y_bins : :obj:`int`
Number of bins in ``y`` direction.
n_z_bins : :obj:`int`
Number of bins in ``z`` direction.
min_x : :obj:`float`
Minimum ``x`` to consider.
min_y : :obj:`float`
Minimum ``y`` to consider.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_x : :obj:`float`
Maximum ``x`` to consider.
max_y : :obj:`float`
Maximum ``y`` to consider.
max_z : :obj:`float`
Maximum ``z`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_x_bins``, ``n_y_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float`
The fourth dimension of the array stores the histogram for the x,
y and z components of the flux density, respectively.
"""
_so_name = "Observables::FluxDensityProfile"
[docs]
@script_interface_register
class ForceDensityProfile(ProfileObservable):
"""Calculates the force density profile for particles with given ids.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
n_x_bins : :obj:`int`
Number of bins in ``x`` direction.
n_y_bins : :obj:`int`
Number of bins in ``y`` direction.
n_z_bins : :obj:`int`
Number of bins in ``z`` direction.
min_x : :obj:`float`
Minimum ``x`` to consider.
min_y : :obj:`float`
Minimum ``y`` to consider.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_x : :obj:`float`
Maximum ``x`` to consider.
max_y : :obj:`float`
Maximum ``y`` to consider.
max_z : :obj:`float`
Maximum ``z`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_x_bins``, ``n_y_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float`
The fourth dimension of the array stores the histogram for the x,
y and z components of the force, respectively.
"""
_so_name = "Observables::ForceDensityProfile"
[docs]
@script_interface_register
class LBVelocityProfile(ProfileObservable):
"""Calculates the LB fluid velocity profile.
This observable samples the fluid in on a regular grid defined by the variables
``sampling_*``. Note that a small delta leads to a large number of sample
points and carries a performance cost.
Parameters
----------
n_x_bins : :obj:`int`
Number of bins in ``x`` direction.
n_y_bins : :obj:`int`
Number of bins in ``y`` direction.
n_z_bins : :obj:`int`
Number of bins in ``z`` direction.
min_x : :obj:`float`
Minimum ``x`` to consider.
min_y : :obj:`float`
Minimum ``y`` to consider.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_x : :obj:`float`
Maximum ``x`` to consider.
max_y : :obj:`float`
Maximum ``y`` to consider.
max_z : :obj:`float`
Maximum ``z`` to consider.
sampling_delta_x : :obj:`float`, default=1.0
Spacing for the sampling grid in ``x``-direction.
sampling_delta_y : :obj:`float`, default=1.0
Spacing for the sampling grid in ``y``-direction.
sampling_delta_z : :obj:`float`, default=1.0
Spacing for the sampling grid in ``z``-direction.
sampling_offset_x : :obj:`float`, default=0.0
Offset for the sampling grid in ``x``-direction.
sampling_offset_y : :obj:`float`, default=0.0
Offset for the sampling grid in ``y``-direction.
sampling_offset_z : :obj:`float`, default=0.0
Offset for the sampling grid in ``z``-direction.
allow_empty_bins : :obj:`bool`, default=False
Whether or not to allow bins that will not be sampled at all.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_x_bins``, ``n_y_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float`
The fourth dimension of the array stores the histogram for the x,
y and z components of the LB velocity, respectively.
"""
_so_name = "Observables::LBVelocityProfile"
[docs]
@script_interface_register
class LBFluidPressureTensor(Observable):
"""Calculates the average pressure tensor of the LB fluid for all nodes.
Parameters
----------
None
Methods
-------
calculate()
Run the observable.
Returns
-------
(3, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::LBFluidPressureTensor"
[docs]
@script_interface_register
class MagneticDipoleMoment(Observable):
"""Calculates the magnetic dipole moment for particles with given ids.
Output format: :math:`\\left(\\sum_i \\mu^x_i, \\sum_i \\mu^y_i, \\sum_i \\mu^z_i\\right)`
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(3,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::MagneticDipoleMoment"
[docs]
@script_interface_register
class ParticleAngularVelocities(Observable):
"""Calculates the angular velocity (omega) in the spaced-fixed frame of reference
Output format: :math:`(\\omega^x_1,\\ \\omega^y_1,\\ \\omega^z_1),\\ (\\omega^x_2,\\ \\omega^y_2,\\ \\omega^z_2), \\dots,\\ (\\omega^x_n,\\ \\omega^y_n,\\ \\omega^z_n)`.
The particles are ordered according to the list of ids passed to the observable.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticleAngularVelocities"
[docs]
@script_interface_register
class ParticleBodyAngularVelocities(Observable):
"""Calculates the angular velocity (omega) in the particles' body-fixed frame of reference.
For each particle, the body-fixed frame of reference is obtained from the particle's
orientation stored in the quaternions.
Output format: :math:`(\\omega^x_1,\\ \\omega^y_1,\\ \\omega^z_1),\\ (\\omega^x_2,\\ \\omega^y_2,\\ \\omega^z_2), \\dots,\\ (\\omega^x_n,\\ \\omega^y_n,\\ \\omega^z_n)`.
The particles are ordered according to the list of ids passed to the observable.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticleBodyAngularVelocities"
[docs]
@script_interface_register
class ParticleBodyVelocities(Observable):
"""Calculates the particle velocity in the particles' body-fixed frame of reference.
For each particle, the body-fixed frame of reference is obtained from the particle's
orientation stored in the quaternions.
Output format: :math:`(v^x_1,\\ v^y_1,\\ v^z_1),\\ (v^x_2,\\ v^y_2,\\ v^z_2),\\ \\dots,\\ (v^x_n,\\ v^y_n,\\ v^z_n)`.
The particles are ordered according to the list of ids passed to the observable.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticleBodyVelocities"
[docs]
@script_interface_register
class ParticleForces(Observable):
"""Calculates the particle forces for particles with given ids.
Output format: :math:`(f^x_1,\\ f^y_1,\\ f^z_1),\\ (f^x_2,\\ f^y_2,\\ f^z_2),\\ \\dots,\\ (f^x_n,\\ f^y_n,\\ f^z_n)`.
The particles are ordered according to the list of ids passed to the observable.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticleForces"
[docs]
@script_interface_register
class ParticlePositions(Observable):
"""Calculates the particle positions for particles with given ids.
Output format: :math:`(x_1,\\ y_1,\\ z_1),\\ (x_2,\\ y_2,\\ z_2),\\ \\dots,\\ (x_n,\\ y_n,\\ z_n)`.
The particles are ordered according to the list of ids passed to the observable.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticlePositions"
[docs]
@script_interface_register
class ParticleVelocities(Observable):
"""Calculates the particle velocities for particles with given ids.
Output format: :math:`(v^x_1,\\ v^y_1,\\ v^z_1),\\ (v^x_2,\\ v^y_2,\\ v^z_2),\\ \\dots,\\ (v^x_n,\\ v^y_n,\\ v^z_n)`.
The particles are ordered according to the list of ids passed to the observable.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticleVelocities"
[docs]
@script_interface_register
class ParticleDirectors(Observable):
"""Calculates the particle directors for particles with given ids.
Output format: :math:`(d^x_1,\\ d^y_1,\\ d^z_1),\\ (d^x_2,\\ d^y_2,\\ d^z_2),\\ \\dots,\\ (d^x_n,\\ d^y_n,\\ d^z_n)`.
The particles are ordered according to the list of ids passed to the observable.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticleDirectors"
[docs]
@script_interface_register
class ParticleDipoleFields(Observable):
"""Calculates the particle dipole fields for particles with given ids.
Output format: :math:`(h^x_1,\\ h^y_1,\\ h^z_1),\\ (h^x_2,\\ h^y_2,\\ h^z_2),\\ \\dots,\\ (h^x_n,\\ h^y_n,\\ h^z_n)`.
The particles are ordered according to the list of ids passed to the observable.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticleDipoleFields"
[docs]
@script_interface_register
class ParticleDistances(Observable):
"""Calculates the distances between particles with given ids along a
polymer chain.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N - 1,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::ParticleDistances"
[docs]
@script_interface_register
class TotalForce(Observable):
"""Calculates the total force on particles with given ids.
Note that virtual sites are not included since forces on them do not enter the equation of motion directly.
Output format: :math:`\\left(\\sum_i f^x_i, \\sum_i f^y_i, \\sum_i f^z_i\\right)`
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(3,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::TotalForce"
[docs]
@script_interface_register
class BondAngles(Observable):
"""Calculates the angles between bonds of particles with given ids along a
polymer chain.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N - 2,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::BondAngles"
[docs]
@script_interface_register
class CosPersistenceAngles(Observable):
"""Calculates the cosine of mutual bond angles for chained particles with given ids.
The *i*-th value of the result contains the cosine of the angle between bonds that
are separated by *i* bonds. The values are averaged over the chain.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N - 2,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::CosPersistenceAngles"
[docs]
@script_interface_register
class BondDihedrals(Observable):
"""Calculates the dihedrals between particles with given ids along a
polymer chain.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
Methods
-------
calculate()
Run the observable.
Returns
-------
(N - 3,) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::BondDihedrals"
[docs]
@script_interface_register
class Energy(Observable):
"""Calculates the total energy.
Methods
-------
calculate()
Run the observable.
Returns
-------
:obj:`float`
"""
_so_name = "Observables::Energy"
[docs]
@script_interface_register
class Pressure(Observable):
"""Calculates the total scalar pressure.
Methods
-------
calculate()
Run the observable.
Returns
-------
:obj:`float`
"""
_so_name = "Observables::Pressure"
[docs]
@script_interface_register
class PressureTensor(Observable):
"""Calculates the total pressure tensor.
Methods
-------
calculate()
Run the observable.
Returns
-------
(3, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::PressureTensor"
[docs]
@script_interface_register
class DPDStress(Observable):
"""Calculates the non-equilibrium contribution of the DPD interaction
to the stress tensor.
Parameters
----------
None
Methods
-------
calculate()
Run the observable.
Returns
-------
(3, 3) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::DPDStress"
[docs]
@script_interface_register
class CylindricalDensityProfile(CylindricalProfileObservable):
"""Calculates the particle density in cylindrical coordinates.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
transform_params : :class:`espressomd.math.CylindricalTransformationParameters`, optional
Parameters of the cylinder transformation. Defaults to the default of :class:`espressomd.math.CylindricalTransformationParameters`
n_r_bins : :obj:`int`, default = 1
Number of bins in radial direction.
n_phi_bins : :obj:`int`, default = 1
Number of bins for the azimuthal direction.
n_z_bins : :obj:`int`, default = 1
Number of bins in ``z`` direction.
min_r : :obj:`float`, default = 0
Minimum ``r`` to consider.
min_phi : :obj:`float`, default = :math:`-\\pi`
Minimum ``phi`` to consider. Must be in :math:`[-\\pi,\\pi)`.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_r : :obj:`float`
Maximum ``r`` to consider.
max_phi : :obj:`float`, default = :math:`\\pi`
Maximum ``phi`` to consider. Must be in :math:`(-\\pi,\\pi]`.
max_z : :obj:`float`
Maximum ``z`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_r_bins``, ``n_phi_bins``, ``n_z_bins``) :obj:`ndarray` of :obj:`float`
"""
_so_name = "Observables::CylindricalDensityProfile"
[docs]
@script_interface_register
class CylindricalFluxDensityProfile(CylindricalProfileObservable):
"""Calculates the particle flux density in cylindrical coordinates.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
transform_params : :class:`espressomd.math.CylindricalTransformationParameters`, optional
Parameters of the cylinder transformation. Defaults to the default of :class:`espressomd.math.CylindricalTransformationParameters`
n_r_bins : :obj:`int`, default = 1
Number of bins in radial direction.
n_phi_bins : :obj:`int`, default = 1
Number of bins for the azimuthal direction.
n_z_bins : :obj:`int`, default = 1
Number of bins in ``z`` direction.
min_r : :obj:`float`, default = 0
Minimum ``r`` to consider.
min_phi : :obj:`float`, default = :math:`-\\pi`
Minimum ``phi`` to consider. Must be in :math:`[-\\pi,\\pi)`.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_r : :obj:`float`
Maximum ``r`` to consider.
max_phi : :obj:`float`, default = :math:`\\pi`
Maximum ``phi`` to consider. Must be in :math:`(-\\pi,\\pi]`.
max_z : :obj:`float`
Maximum ``z`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float`
The fourth dimension of the array stores the histogram for the
radial distance, azimuth and axial coordinate of the particle
flux density field, respectively.
"""
_so_name = "Observables::CylindricalFluxDensityProfile"
[docs]
@script_interface_register
class CylindricalLBFluxDensityProfileAtParticlePositions(
CylindricalProfileObservable):
"""Calculates the LB fluid flux density at the particle positions in
cylindrical coordinates.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
transform_params : :class:`espressomd.math.CylindricalTransformationParameters`, optional
Parameters of the cylinder transformation. Defaults to the default of :class:`espressomd.math.CylindricalTransformationParameters`
n_r_bins : :obj:`int`, default = 1
Number of bins in radial direction.
n_phi_bins : :obj:`int`, default = 1
Number of bins for the azimuthal direction.
n_z_bins : :obj:`int`, default = 1
Number of bins in ``z`` direction.
min_r : :obj:`float`, default = 0
Minimum ``r`` to consider.
min_phi : :obj:`float`, default = :math:`-\\pi`
Minimum ``phi`` to consider. Must be in :math:`[-\\pi,\\pi)`.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_r : :obj:`float`
Maximum ``r`` to consider.
max_phi : :obj:`float`, default = :math:`\\pi`
Maximum ``phi`` to consider. Must be in :math:`(-\\pi,\\pi]`.
max_z : :obj:`float`
Maximum ``z`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float`
The fourth dimension of the array stores the histogram for the
radial distance, azimuth and axial coordinate of the LB flux
density field, respectively.
"""
_so_name = "Observables::CylindricalLBFluxDensityProfileAtParticlePositions"
[docs]
@script_interface_register
class CylindricalLBVelocityProfileAtParticlePositions(
CylindricalProfileObservable):
"""Calculates the LB fluid velocity at the particle positions in
cylindrical coordinates.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
transform_params : :class:`espressomd.math.CylindricalTransformationParameters`, optional
Parameters of the cylinder transformation. Defaults to the default of :class:`espressomd.math.CylindricalTransformationParameters`
n_r_bins : :obj:`int`, default = 1
Number of bins in radial direction.
n_phi_bins : :obj:`int`, default = 1
Number of bins for the azimuthal direction.
n_z_bins : :obj:`int`, default = 1
Number of bins in ``z`` direction.
min_r : :obj:`float`, default = 0
Minimum ``r`` to consider.
min_phi : :obj:`float`, default = :math:`-\\pi`
Minimum ``phi`` to consider. Must be in :math:`[-\\pi,\\pi)`.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_r : :obj:`float`
Maximum ``r`` to consider.
max_phi : :obj:`float`, default = :math:`\\pi`
Maximum ``phi`` to consider. Must be in :math:`(-\\pi,\\pi]`.
max_z : :obj:`float`
Maximum ``z`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float`
The fourth dimension of the array stores the histogram for the
radial distance, azimuth and axial coordinate of the LB velocity
field, respectively.
"""
_so_name = "Observables::CylindricalLBVelocityProfileAtParticlePositions"
[docs]
@script_interface_register
class CylindricalVelocityProfile(CylindricalProfileObservable):
"""Calculates the particle velocity profile in cylindrical coordinates.
Parameters
----------
ids : array_like of :obj:`int`
The ids of (existing) particles to take into account.
transform_params : :class:`espressomd.math.CylindricalTransformationParameters`, optional
Parameters of the cylinder transformation. Defaults to the default of :class:`espressomd.math.CylindricalTransformationParameters`
n_r_bins : :obj:`int`, default = 1
Number of bins in radial direction.
n_phi_bins : :obj:`int`, default = 1
Number of bins for the azimuthal direction.
n_z_bins : :obj:`int`, default = 1
Number of bins in ``z`` direction.
min_r : :obj:`float`, default = 0
Minimum ``r`` to consider.
min_phi : :obj:`float`, default = :math:`-\\pi`
Minimum ``phi`` to consider. Must be in :math:`[-\\pi,\\pi)`.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_r : :obj:`float`
Maximum ``r`` to consider.
max_phi : :obj:`float`, default = :math:`\\pi`
Maximum ``phi`` to consider. Must be in :math:`(-\\pi,\\pi]`.
max_z : :obj:`float`
Maximum ``z`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float`
The fourth dimension of the array stores the histogram for the
radial distance, azimuth and axial coordinate of the particle
velocity field, respectively.
"""
_so_name = "Observables::CylindricalVelocityProfile"
[docs]
@script_interface_register
class CylindricalLBVelocityProfile(CylindricalProfileObservable):
"""Calculates the LB fluid velocity profile in cylindrical coordinates.
This observable samples the fluid in on a regular grid defined by variable
``sampling_density``. Note that a small delta leads to a large number of
sample points and carries a performance cost.
Parameters
----------
transform_params : :class:`espressomd.math.CylindricalTransformationParameters`, optional
Parameters of the cylinder transformation. Defaults to the default of :class:`espressomd.math.CylindricalTransformationParameters`
n_r_bins : :obj:`int`, default = 1
Number of bins in radial direction.
n_phi_bins : :obj:`int`, default = 1
Number of bins for the azimuthal direction.
n_z_bins : :obj:`int`, default = 1
Number of bins in ``z`` direction.
min_r : :obj:`float`, default = 0
Minimum ``r`` to consider.
min_phi : :obj:`float`, default = :math:`-\\pi`
Minimum ``phi`` to consider. Must be in :math:`[-\\pi,\\pi)`.
min_z : :obj:`float`
Minimum ``z`` to consider.
max_r : :obj:`float`
Maximum ``r`` to consider.
max_phi : :obj:`float`, default = :math:`\\pi`
Maximum ``phi`` to consider. Must be in :math:`(-\\pi,\\pi]`.
max_z : :obj:`float`
Maximum ``z`` to consider.
sampling_density : :obj:`float`
Samples per unit volume for the LB velocity interpolation.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float`
The fourth dimension of the array stores the histogram for the
radial distance, azimuth and axial coordinate of the LB velocity
field, respectively.
"""
_so_name = "Observables::CylindricalLBVelocityProfile"
[docs]
@script_interface_register
class RDF(Observable):
"""Calculates a radial distribution function.
The result is normalized by the bulk concentration.
Parameters
----------
ids1 : array_like of :obj:`int`
The ids of (existing) particles to calculate the distance from.
ids2 : array_like of :obj:`int`, optional
The ids of (existing) particles to calculate the distance to.
If not provided, use ``ids1``.
n_r_bins : :obj:`int`
Number of bins in radial direction.
min_r : :obj:`float`
Minimum ``r`` to consider.
max_r : :obj:`float`
Maximum ``r`` to consider.
Methods
-------
calculate()
Run the observable.
Returns
-------
(``n_r_bins``,) :obj:`ndarray` of :obj:`float`
The RDF.
"""
_so_name = "Observables::RDF"
def __init__(self, **kwargs):
if "ids2" not in kwargs:
kwargs["ids2"] = []
super().__init__(**kwargs)
[docs]
def bin_centers(self):
bin_width = (self.max_r - self.min_r) / self.n_r_bins
return self.min_r + (np.arange(self.n_r_bins) + 0.5) * bin_width