Source code for espressomd.cluster_analysis
#
# 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/>.
#
from .script_interface import ScriptInterfaceHelper, script_interface_register
from .particle_data import ParticleHandle
[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()
Get particles in the cluster
size()
Returns the number of particles in the cluster
center_of_mass()
Center of mass of the cluster (folded coordinates)
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.
.. note::
Requires ``GSL`` external feature, enabled with
``-D ESPRESSO_BUILD_WITH_GSL=ON``.
Parameters
----------
dr: :obj:`float`
Minimum increment for the radius of the spheres.
Returns
-------
:obj:`tuple`:
Fractal dimension and mean square residual.
"""
_so_name = "ClusterAnalysis::Cluster"
_so_checkpointable = False
_so_bind_methods = ("particle_ids", "particles", "size", "longest_distance",
"radius_of_gyration", "fractal_dimension", "center_of_mass")
_so_creation_policy = "LOCAL"
[docs]
@script_interface_register
class ClusterStructure(ScriptInterfaceHelper):
"""Cluster structure of a simulation system, and access to cluster analysis
Parameters
----------
pair_criterion: :class:`espressomd.pair_criteria._PairCriterion`
Criterion to decide whether two particles are neighbors.
system: :class:`espressomd.system.System`
System to run the cluster analysis on.
"""
_so_name = "ClusterAnalysis::ClusterStructure"
_so_checkpointable = False
_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.
Parameters
----------
p : :obj:`espressomd.particle_data.ParticleHandle` or :obj:`int` containing the particle id
Particle.
"""
if isinstance(p, ParticleHandle):
return self.call_method("cid_for_particle", pid=p.id)
if isinstance(p, int):
return self.call_method("cid_for_particle", pid=p)
raise TypeError(
"The particle has to be passed as instance of ParticleHandle or as an integer particle id")
@property
def clusters(self):
"""Gives access to the clusters in the cluster structure via an
instance of :class:`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 (yields ``(id, cluster)`` tuples)
Example::
>>> for cluster_id, cluster in clusters:
... print(f"{cluster_id=} CoM={cluster.center_of_mass()}")
cluster_id=1 CoM=[1.71834061 1.54988961 1.54734631]
"""
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")