ESPResSo
Extensible Simulation Package for Research on Soft Matter Systems
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core/cluster_analysis/ClusterStructure.hpp
Go to the documentation of this file.
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/*
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* Copyright (C) 2010-2022 The ESPResSo project
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*
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* This file is part of ESPResSo.
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*
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* ESPResSo is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation, either version 3 of the License, or
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* (at your option) any later version.
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*
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* ESPResSo is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public License
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* along with this program. If not, see <http://www.gnu.org/licenses/>.
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*/
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#pragma once
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#include "
BoxGeometry.hpp
"
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#include "pair_criteria/PairCriterion.hpp"
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#include "
Cluster.hpp
"
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#include "
Particle.hpp
"
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#include <map>
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#include <memory>
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namespace
ClusterAnalysis
{
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/** @brief Holds the result and parameters of a cluster analysis */
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class
ClusterStructure
{
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public
:
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ClusterStructure
();
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/** @brief Map holding the individual clusters. The key is an integer cluster
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* id */
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std::map<int, std::shared_ptr<Cluster>>
clusters
;
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/** @brief Map between particle ids and corresponding cluster ids */
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std::map<int, int>
cluster_id
;
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/** @brief Clear data structures */
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void
clear
();
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/** @brief Run cluster analysis, consider all particle pairs */
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void
run_for_all_pairs
();
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/** @brief Run cluster analysis, consider pairs of particles connected by a
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* bonded interaction */
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void
run_for_bonded_particles
();
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/** Is particle p part of a cluster */
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bool
part_of_cluster
(
const
Particle
&p);
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/** Sets the pair criterion which decides if two particles are neighbors */
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void
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set_pair_criterion
(std::shared_ptr<PairCriteria::PairCriterion>
const
&c) {
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m_pair_criterion = c;
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}
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PairCriteria::PairCriterion
const
&
pair_criterion
()
const
{
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return
*m_pair_criterion;
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}
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void
attach
(std::weak_ptr<BoxGeometry const>
const
&box_geo) {
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m_box_geo = box_geo;
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}
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private
:
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/** @brief Clusters that turn out to be the same during the analysis process
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* (i.e., if two particles are neighbors that already belong to different
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* clusters
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*/
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std::map<int, int> m_cluster_identities;
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/** @brief pair criterion which decides whether two particles are neighbors */
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std::shared_ptr<PairCriteria::PairCriterion> m_pair_criterion;
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/** @brief Consider an individual pair of particles during cluster analysis */
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void
add_pair(
const
Particle
&p1,
const
Particle
&p2);
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/** Merge clusters and populate their structures */
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void
merge_clusters();
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/** @brief Follow a chain of cluster identities during analysis */
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inline
int
find_id_for(
int
x);
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/** @brief Get next free cluster id */
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inline
int
get_next_free_cluster_id();
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void
sanity_checks()
const
;
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auto
get_box_geo()
const
{
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auto
ptr = m_box_geo.lock();
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assert(ptr);
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return
ptr;
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}
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mutable
std::weak_ptr<BoxGeometry const> m_box_geo;
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};
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}
// namespace ClusterAnalysis
BoxGeometry.hpp
Particle.hpp
ClusterAnalysis::ClusterStructure
Holds the result and parameters of a cluster analysis.
Definition
core/cluster_analysis/ClusterStructure.hpp:34
ClusterAnalysis::ClusterStructure::cluster_id
std::map< int, int > cluster_id
Map between particle ids and corresponding cluster ids.
Definition
core/cluster_analysis/ClusterStructure.hpp:41
ClusterAnalysis::ClusterStructure::ClusterStructure
ClusterStructure()
Definition
ClusterStructure.cpp:37
ClusterAnalysis::ClusterStructure::clear
void clear()
Clear data structures.
Definition
ClusterStructure.cpp:39
ClusterAnalysis::ClusterStructure::part_of_cluster
bool part_of_cluster(const Particle &p)
Is particle p part of a cluster.
Definition
ClusterStructure.cpp:45
ClusterAnalysis::ClusterStructure::run_for_bonded_particles
void run_for_bonded_particles()
Run cluster analysis, consider pairs of particles connected by a bonded interaction.
Definition
ClusterStructure.cpp:66
ClusterAnalysis::ClusterStructure::pair_criterion
PairCriteria::PairCriterion const & pair_criterion() const
Definition
core/cluster_analysis/ClusterStructure.hpp:57
ClusterAnalysis::ClusterStructure::run_for_all_pairs
void run_for_all_pairs()
Run cluster analysis, consider all particle pairs.
Definition
ClusterStructure.cpp:50
ClusterAnalysis::ClusterStructure::clusters
std::map< int, std::shared_ptr< Cluster > > clusters
Map holding the individual clusters.
Definition
core/cluster_analysis/ClusterStructure.hpp:39
ClusterAnalysis::ClusterStructure::attach
void attach(std::weak_ptr< BoxGeometry const > const &box_geo)
Definition
core/cluster_analysis/ClusterStructure.hpp:61
ClusterAnalysis::ClusterStructure::set_pair_criterion
void set_pair_criterion(std::shared_ptr< PairCriteria::PairCriterion > const &c)
Sets the pair criterion which decides if two particles are neighbors.
Definition
core/cluster_analysis/ClusterStructure.hpp:53
PairCriteria::PairCriterion
Criterion which returns a true/false value for a pair of particles.
Definition
core/pair_criteria/PairCriterion.hpp:29
ClusterAnalysis
Definition
Cluster.cpp:43
Cluster.hpp
Particle
Struct holding all information for one particle.
Definition
Particle.hpp:395
src
core
cluster_analysis
ClusterStructure.hpp
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