Cluster.cpp

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/*
 * 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/>.
 */
 
#include "config/config.hpp"
 
#ifdef GSL
#include "gsl/gsl_fit.h"
#endif
 
#include "Cluster.hpp"
 
#include "BoxGeometry.hpp"
#include "Particle.hpp"
#include "errorhandling.hpp"
#include "particle_node.hpp"
 
#include <utils/Vector.hpp>
 
#include <algorithm>
#include <cmath>
#include <cstddef>
#include <numeric>
#include <stdexcept>
#include <utility>
#include <vector>
 
namespace ClusterAnalysis {
 
// Center of mass of an aggregate
Utils::Vector3d Cluster::center_of_mass() {
  return center_of_mass_subcluster(particles);
}
Utils::Vector3d Cluster::center_of_mass() {…}
 
// Center of mass of an aggregate
Utils::Vector3d
Cluster::center_of_mass_subcluster(std::vector<int> const &particle_ids) {
  sanity_checks();
  auto const box_geo_handle = get_box_geo();
  auto const &box_geo = *box_geo_handle;
  Utils::Vector3d com{};
 
  // The distances between the particles are "folded", such that all distances
  // are smaller than box_l/2 in a periodic system. The 1st particle
  // of the cluster is arbitrarily chosen as reference.
 
  auto const reference_position =
      box_geo.folded_position(get_particle_data(particles[0]).pos());
  double total_mass = 0.;
  for (int pid : particle_ids) {
    auto const folded_pos =
        box_geo.folded_position(get_particle_data(pid).pos());
    auto const dist_to_reference =
        box_geo.get_mi_vector(folded_pos, reference_position);
    com += dist_to_reference * get_particle_data(pid).mass();
    total_mass += get_particle_data(pid).mass();
  }
 
  // Normalize by number of particles
  com /= total_mass;
 
  // Re-add reference position
  com += reference_position;
 
  // Fold into simulation box
  return box_geo.folded_position(com);
}
Cluster::center_of_mass_subcluster(std::vector<int> const &particle_ids) {…}
 
double Cluster::longest_distance() {
  sanity_checks();
  auto const box_geo_handle = get_box_geo();
  auto const &box_geo = *box_geo_handle;
  double ld = 0.;
  for (auto a = particles.begin(); a != particles.end(); a++) {
    for (auto b = a; ++b != particles.end();) {
      auto const dist = box_geo
                            .get_mi_vector(get_particle_data(*a).pos(),
                                           get_particle_data(*b).pos())
                            .norm();
 
      // Larger than previous largest distance?
      ld = std::max(ld, dist);
    }
  }
  return ld;
}
double Cluster::longest_distance() {…}
 
// Radius of gyration
double Cluster::radius_of_gyration() {
  return radius_of_gyration_subcluster(particles);
}
double Cluster::radius_of_gyration() {…}
 
double
Cluster::radius_of_gyration_subcluster(std::vector<int> const &particle_ids) {
  sanity_checks();
  auto const box_geo_handle = get_box_geo();
  auto const &box_geo = *box_geo_handle;
  // Center of mass
  Utils::Vector3d com = center_of_mass_subcluster(particle_ids);
  double sum_sq_dist = 0.;
  for (auto const pid : particle_ids) {
    // calculate square length of this distance
    sum_sq_dist +=
        box_geo.get_mi_vector(com, get_particle_data(pid).pos()).norm2();
  }
 
  return sqrt(sum_sq_dist / static_cast<double>(particle_ids.size()));
}
Cluster::radius_of_gyration_subcluster(std::vector<int> const &particle_ids) {…}
 
template <typename T>
std::vector<std::size_t> sort_indices(const std::vector<T> &v) {
 
  // Unsorted for unsorted vector (0..n-1)
  std::vector<std::size_t> idx(v.size());
  std::iota(idx.begin(), idx.end(), std::size_t{0u});
 
  // sort indices based on comparing values in v
  std::ranges::sort(
      idx, [&v](std::size_t i1, std::size_t i2) { return v[i1] < v[i2]; });
  return idx;
}
std::vector<std::size_t> sort_indices(const std::vector<T> &v) {…}
 
std::pair<double, double> Cluster::fractal_dimension(double dr) {
#ifdef GSL
  sanity_checks();
  auto const box_geo_handle = get_box_geo();
  auto const &box_geo = *box_geo_handle;
  Utils::Vector3d com = center_of_mass();
  // calculate Df using linear regression on the logarithms of the radii of
  // gyration against the number of particles in sub-clusters. Particles are
  // included step by step from the center of mass outwards
 
  // Distances of particles from the center of mass
  std::vector<double> distances;
 
  for (auto const &it : particles) {
    distances.push_back(box_geo.get_mi_vector(com, get_particle_data(it).pos())
                            .norm()); // add distance from the current particle
                                      // to the com in the distances vectors
  }
 
  // Get particle indices in the cluster which yield distances  sorted in
  // ascending order from center of mass.
  auto particle_indices = sort_indices(distances);
 
  // Particle ids in the current sub-cluster
  std::vector<int> subcluster_ids;
 
  std::vector<double> log_pcounts;   // particle count
  std::vector<double> log_diameters; // corresponding radii of gyration
  double last_dist = 0;
  for (auto const idx : particle_indices) {
    subcluster_ids.push_back(particles[idx]);
    if (distances[idx] < last_dist + dr)
      continue;
 
    last_dist = distances[idx];
    if (subcluster_ids.size() == 1)
      continue;
    auto const current_rg = radius_of_gyration_subcluster(subcluster_ids);
    log_pcounts.push_back(log(static_cast<double>(subcluster_ids.size())));
    log_diameters.push_back(log(current_rg * 2.0));
  }
  double c0, c1, cov00, cov01, cov11, sumsq;
  gsl_fit_linear(log_diameters.data(), 1, log_pcounts.data(), 1,
                 log_pcounts.size(), &c0, &c1, &cov00, &cov01, &cov11, &sumsq);
  double mean_sq_residual = sumsq / static_cast<double>(log_diameters.size());
  return {c1, mean_sq_residual};
#else
  runtimeErrorMsg() << "GSL (gnu scientific library) is required for fractal "
                       "dimension calculation.";
  return {0, 0};
#endif
}
std::pair<double, double> Cluster::fractal_dimension(double dr) {…}
 
void Cluster::sanity_checks() const {
  auto const box_geo_handle = get_box_geo();
  auto const &box_geo = *box_geo_handle;
  if (box_geo.type() != BoxType::CUBOID) {
    throw std::runtime_error(
        "Cluster analysis is not compatible with non-cuboid box types");
  }
}
 
} // namespace ClusterAnalysis
namespace ClusterAnalysis {…}