Source code for espressomd.cluster_analysis

# Copyright (C) 2010-2019 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
# 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 <>.
from .script_interface import ScriptInterfaceHelper, script_interface_register
from .particle_data import ParticleHandle, ParticleSlice

[docs]@script_interface_register class Cluster(ScriptInterfaceHelper): """Class representing a cluster of particles Methods ------- particle_ids(): Returns list of particle ids in the cluster particles(): Returns an instance of ParticleSlice containing the particles in the cluster size(): Returns the number of particles in the cluster center_of_mass(): center of mass of the cluster longest_distance(): Longest distance between any combination of two particles in the cluster fractal_dimension(dr=None): estimates the cluster's fractal dimension by fitting the number of particles :math:`n` in spheres of growing radius around the center of mass to :math:`c*r_g^d`, where :math:`r_g` is the radius of gyration of the particles within the sphere, and :math:`d` is the fractal dimension. Parameters ---------- dr: Minimum increment for the radius of the spheres. Returns ------- :obj:`tuple`: Fractal_dimension, mean_square_residual. """ _so_name = "ClusterAnalysis::Cluster" _so_bind_methods = ("particle_ids", "size", "longest_distance", "radius_of_gyration", "fractal_dimension", "center_of_mass") _so_creation_policy = "LOCAL"
[docs] def particles(self): return ParticleSlice(self.particle_ids())
[docs]@script_interface_register class ClusterStructure(ScriptInterfaceHelper): """Cluster structure of a simulation system, and access to cluster analysis Attributes ---------- pair_criterion: classes derived from ``_PairCriterion`` Criterion to decide whether two particles are neighbors. clusters: behaves like a read-only dictionary Access to individual clusters in the cluster structure either via ``cluster[i]``, where ``i`` is a (non-consecutive) integer cluster id or via iteration:: for pair in clusters: where pair contains the numeric id and the corresponding cluster object. """ _so_name = "ClusterAnalysis::ClusterStructure" _so_creation_policy = "LOCAL" def __init__(self, *args, **kwargs): super().__init__(*args, **kwargs) self._clusters = Clusters(self)
[docs] def run_for_all_pairs(self): """ Runs the cluster analysis, considering all pairs of particles in the system """ return self.call_method("run_for_all_pairs")
[docs] def run_for_bonded_particles(self): """ Runs the cluster analysis, considering only pairs of particles connected by a pair-bond. """ return self.call_method("run_for_bonded_particles")
[docs] def clear(self): """ Clears the cluster structure. """ return self.call_method("clear")
[docs] def cluster_ids(self): """ Returns a list of all cluster ids of the clusters in the structure. """ return self.call_method("cluster_ids")
[docs] def cid_for_particle(self, p): """Returns cluster id for the particle (passed as ParticleHandle or particle id)""" if isinstance(p, ParticleHandle): return self.call_method("cid_for_particle", if isinstance(p, int): return self.call_method("cid_for_particle", pid=p) else: raise TypeError( "The particle has to be passed as instance of Particle handle or as an integer particle id")
@property def clusters(self): """Gives access to the clusters in the cluster structure via an instance of :any:`Clusters`.""" return self._clusters
[docs]class Clusters: """Access to the clusters in the cluster structure. Access is as follows: * Number of clusters: len(clusters) * Access a cluster via its id: clusters[id] * Iterate over clusters:: for c in clusters: where c will be a tuple containing the cluster id and the cluster object """ def __init__(self, cluster_structure): self.cluster_structure = cluster_structure def __getitem__(self, cluster_id): return self.cluster_structure.call_method("get_cluster", id=cluster_id) def __iter__(self): for cid in self.cluster_structure.cluster_ids(): yield (cid, self.cluster_structure.call_method("get_cluster", id=cid)) def __len__(self): return self.cluster_structure.call_method("n_clusters")