Source code for espressomd.observables

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import itertools
import numpy as np
from .script_interface import ScriptInterfaceHelper, script_interface_register


[docs]@script_interface_register class Observable(ScriptInterfaceHelper): """ Base class for all observables. Methods ------- shape() Return the shape of the observable. """ _so_name = "Observables::Observable" _so_bind_methods = ("shape",) _so_creation_policy = "LOCAL"
[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]@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. 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. Returns ------- (3,) :obj:`ndarray` of :obj:`float` """ _so_name = "Observables::ComVelocity"
[docs]@script_interface_register class Current(Observable): """Calculates the electric current for particles with given ids. Output format: :math:`\\left(\\sum_i q_i v^x_i, \\sum_i q_i v^y_i, \\sum_i q_i v^z_i, \\right)` Parameters ---------- ids : array_like of :obj:`int` The ids of (existing) particles to take into account. Returns ------- (3,) :obj:`ndarray` of :obj:`float` """ _so_name = "Observables::Current"
[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. Returns ------- (3,) :obj:`ndarray` of :obj:`float` """ _so_name = "Observables::DensityProfile"
[docs]@script_interface_register class DipoleMoment(Observable): """Calculates the 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. 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. Returns ------- (``n_x_bins``, ``n_y_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float` The fourth component contains the histogram for the x, y and z components of the flux density. """ _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. Returns ------- (``n_x_bins``, ``n_y_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float` The fourth component contains the histogram for the x, y and z components of the force. """ _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. .. WARNING:: In case of the CPU version of the LB fluid implementation, this observable currently only works for a single core. 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. Returns ------- (``n_x_bins``, ``n_y_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float` The fourth component contains the histogram for the x, y and z components of the LB velocity. """ _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 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. 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. 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. 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. 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. 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. 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. Returns ------- (N, 3) :obj:`ndarray` of :obj:`float` """ _so_name = "Observables::ParticleVelocities"
[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. 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. 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. 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. 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. Returns ------- (N - 3,) :obj:`ndarray` of :obj:`float` """ _so_name = "Observables::BondDihedrals"
[docs]@script_interface_register class Energy(Observable): """Calculates the total energy. Returns ------- :obj:`float` """ _so_name = "Observables::Energy"
[docs]@script_interface_register class Pressure(Observable): """Calculates the total scalar pressure. Returns ------- :obj:`float` """ _so_name = "Observables::Pressure"
[docs]@script_interface_register class PressureTensor(Observable): """Calculates the total pressure tensor. 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 Returns ------- (3, 3) :obj:`ndarray` of :obj:`float` """ _so_name = "Observables::DPDStress"
[docs]@script_interface_register class CylindricalDensityProfile(ProfileObservable): """Calculates the particle density in cylindrical coordinates. Parameters ---------- ids : array_like of :obj:`int` The ids of (existing) particles to take into account. center : (3,) array_like of :obj:`float` Position of the center of the cylindrical coordinate system for the histogram. axis : (3,) array_like of :obj:`float` Orientation vector of the ``z``-axis of the cylindrical coordinate system for the histogram. n_r_bins : :obj:`int` Number of bins in radial direction. n_phi_bins : :obj:`int` Number of bins for the azimuthal direction. n_z_bins : :obj:`int` Number of bins in ``z`` direction. min_r : :obj:`float` Minimum ``r`` to consider. min_phi : :obj:`float` Minimum ``phi`` to consider. min_z : :obj:`float` Minimum ``z`` to consider. max_r : :obj:`float` Maximum ``r`` to consider. max_phi : :obj:`float` Maximum ``phi`` to consider. max_z : :obj:`float` Maximum ``z`` to consider. 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(ProfileObservable): """Calculates the particle flux density in cylindrical coordinates. Parameters ---------- ids : array_like of :obj:`int` The ids of (existing) particles to take into account. center : (3,) array_like of :obj:`float` Position of the center of the cylindrical coordinate system for the histogram. axis : (3,) array_like of :obj:`float` Orientation vector of the ``z``-axis of the cylindrical coordinate system for the histogram. n_r_bins : :obj:`int` Number of bins in radial direction. n_phi_bins : :obj:`int` Number of bins for the azimuthal direction. n_z_bins : :obj:`int` Number of bins in ``z`` direction. min_r : :obj:`float` Minimum ``r`` to consider. min_phi : :obj:`float` Minimum ``phi`` to consider. min_z : :obj:`float` Minimum ``z`` to consider. max_r : :obj:`float` Maximum ``r`` to consider. max_phi : :obj:`float` Maximum ``phi`` to consider. max_z : :obj:`float` Maximum ``z`` to consider. Returns ------- (``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float` The fourth component contains the histogram for the radial distance, azimuth and axial coordinate of the particle flux density field. """ _so_name = "Observables::CylindricalFluxDensityProfile"
[docs]@script_interface_register class CylindricalLBFluxDensityProfileAtParticlePositions(ProfileObservable): """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. center : (3,) array_like of :obj:`float` Position of the center of the cylindrical coordinate system for the histogram. axis : (3,) array_like of :obj:`float` Orientation vector of the ``z``-axis of the cylindrical coordinate system for the histogram. n_r_bins : :obj:`int` Number of bins in radial direction. n_phi_bins : :obj:`int` Number of bins for the azimuthal direction. n_z_bins : :obj:`int` Number of bins in ``z`` direction. min_r : :obj:`float` Minimum ``r`` to consider. min_phi : :obj:`float` Minimum ``phi`` to consider. min_z : :obj:`float` Minimum ``z`` to consider. max_r : :obj:`float` Maximum ``r`` to consider. max_phi : :obj:`float` Maximum ``phi`` to consider. max_z : :obj:`float` Maximum ``z`` to consider. Returns ------- (``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float` The fourth component contains the histogram for the radial distance, azimuth and axial coordinate of the LB flux density field. """ _so_name = "Observables::CylindricalLBFluxDensityProfileAtParticlePositions"
[docs]@script_interface_register class CylindricalLBVelocityProfileAtParticlePositions(ProfileObservable): """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. center : (3,) array_like of :obj:`float` Position of the center of the cylindrical coordinate system for the histogram. axis : (3,) array_like of :obj:`float` Orientation vector of the ``z``-axis of the cylindrical coordinate system for the histogram. n_r_bins : :obj:`int` Number of bins in radial direction. n_phi_bins : :obj:`int` Number of bins for the azimuthal direction. n_z_bins : :obj:`int` Number of bins in ``z`` direction. min_r : :obj:`float` Minimum ``r`` to consider. min_phi : :obj:`float` Minimum ``phi`` to consider. min_z : :obj:`float` Minimum ``z`` to consider. max_r : :obj:`float` Maximum ``r`` to consider. max_phi : :obj:`float` Maximum ``phi`` to consider. max_z : :obj:`float` Maximum ``z`` to consider. Returns ------- (``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float` The fourth component contains the histogram for the radial distance, azimuth and axial coordinate of the LB velocity field. """ _so_name = "Observables::CylindricalLBVelocityProfileAtParticlePositions"
[docs]@script_interface_register class CylindricalVelocityProfile(ProfileObservable): """Calculates the particle velocity profile in cylindrical coordinates. Parameters ---------- ids : array_like of :obj:`int` The ids of (existing) particles to take into account. center : (3,) array_like of :obj:`float` Position of the center of the cylindrical coordinate system for the histogram. axis : (3,) array_like of :obj:`float` Orientation vector of the ``z``-axis of the cylindrical coordinate system for the histogram. n_r_bins : :obj:`int` Number of bins in radial direction. n_phi_bins : :obj:`int` Number of bins for the azimuthal direction. n_z_bins : :obj:`int` Number of bins in ``z`` direction. min_r : :obj:`float` Minimum ``r`` to consider. min_phi : :obj:`float` Minimum ``phi`` to consider. min_z : :obj:`float` Minimum ``z`` to consider. max_r : :obj:`float` Maximum ``r`` to consider. max_phi : :obj:`float` Maximum ``phi`` to consider. max_z : :obj:`float` Maximum ``z`` to consider. Returns ------- (``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float` The fourth component contains the histogram for the radial distance, azimuth and axial coordinate of the particle velocity field. """ _so_name = "Observables::CylindricalVelocityProfile"
[docs]@script_interface_register class CylindricalLBVelocityProfile(ProfileObservable): """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 ---------- center : (3,) array_like of :obj:`float` Position of the center of the cylindrical coordinate system for the histogram. axis : (3,) array_like of :obj:`float` Orientation vector of the ``z``-axis of the cylindrical coordinate system for the histogram. n_r_bins : :obj:`int` Number of bins in radial direction. n_phi_bins : :obj:`int` Number of bins for the azimuthal direction. n_z_bins : :obj:`int` Number of bins in ``z`` direction. min_r : :obj:`float` Minimum ``r`` to consider. min_phi : :obj:`float` Minimum ``phi`` to consider. min_z : :obj:`float` Minimum ``z`` to consider. max_r : :obj:`float` Maximum ``r`` to consider. max_phi : :obj:`float` Maximum ``phi`` to consider. max_z : :obj:`float` Maximum ``z`` to consider. sampling_density : :obj:`float` Samples per unit volume for the LB velocity interpolation. Returns ------- (``n_r_bins``, ``n_phi_bins``, ``n_z_bins``, 3) :obj:`ndarray` of :obj:`float` The fourth component contains the histogram for the radial distance, azimuth and axial coordinate of the LB velocity field. """ _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. Returns ------- (``n_r_bins``,) :obj:`ndarray` of :obj:`float` The RDF. """ _so_name = "Observables::RDF" def __init__(self, **kwargs): if "oid" not in kwargs and "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