26#include "system/System.hpp"
43 m_cluster_identities.clear();
60 this->add_pair(p1, p2);
69 for (
const auto &p : partCfg) {
70 for (
auto const bond : p.bonds()) {
71 if (bond.partner_ids().size() == 1) {
89 if (!m_pair_criterion) {
94 if (m_pair_criterion->decide(p1, p2)) {
99 const int cid = get_next_free_cluster_id();
121 m_cluster_identities[cid1] = cid2;
122 }
else if (cid1 < cid2) {
123 m_cluster_identities[cid2] = cid1;
133void ClusterStructure::merge_clusters() {
139 std::vector<std::pair<int, int>> to_be_changed;
145 const int cid = find_id_for(it.second);
148 to_be_changed.emplace_back(it.first, cid);
151 clusters[cid] = std::make_shared<Cluster>();
156 for (
auto it : to_be_changed) {
167 clusters[it.second] = std::make_shared<Cluster>();
169 clusters[it.second]->particles.push_back(it.first);
174 std::sort(c.second->particles.begin(), c.second->particles.end());
178int ClusterStructure::find_id_for(
int x) {
180 while (m_cluster_identities.find(tmp) != m_cluster_identities.end()) {
181 tmp = m_cluster_identities[tmp];
186int ClusterStructure::get_next_free_cluster_id() {
188 int max_seen_cluster = 0;
191 if (max_seen_cluster < cid) {
192 max_seen_cluster = cid;
195 return max_seen_cluster + 1;
198void ClusterStructure::sanity_checks()
const {
200 throw std::runtime_error(
201 "Cluster analysis is not compatible with non-cuboid box types");
std::map< int, int > cluster_id
Map between particle ids and corresponding cluster ids.
void clear()
Clear data structures.
bool part_of_cluster(const Particle &p)
Is particle p part of a cluster.
void run_for_bonded_particles()
Run cluster analysis, consider pairs of particles connected by a bonded interaction.
void run_for_all_pairs()
Run cluster analysis, consider all particle pairs.
std::map< int, std::shared_ptr< Cluster > > clusters
Map holding the individual clusters.
Particle cache on the head node.
std::shared_ptr< BoxGeometry > box_geo
This file contains the errorhandling code for severe errors, like a broken bond or illegal parameter ...
#define runtimeErrorMsg()
void for_each_pair(ForwardIterator first, ForwardIterator last, BinaryOp op)
Execute op for each pair of elements in [first, last) once.
const Particle & get_particle_data(int p_id)
Get particle data.
Particles creation and deletion.
Struct holding all information for one particle.