CosPersistenceAngles.hpp

Go to the documentation of this file.

/*
 * Copyright (C) 2019-2022 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/>.
 */
#ifndef OBSERVABLES_PERSISTENCEANGLES_HPP
#define OBSERVABLES_PERSISTENCEANGLES_HPP
 
#include "BoxGeometry.hpp"
#include "PidObservable.hpp"
#include "system/System.hpp"
 
#include <utils/Vector.hpp>
 
#include <cassert>
#include <cmath>
#include <cstddef>
#include <stdexcept>
#include <utility>
#include <vector>
 
namespace Observables {
 
/** Calculate bond angles in a polymer.
 *  The \a ith entry in the result vector corresponds to the
 *  averaged cosine of the angle between bonds that are \a i bonds apart.
 */
class CosPersistenceAngles : public PidObservable {
public:
  using PidObservable::PidObservable;
  explicit CosPersistenceAngles(std::vector<int> ids)
      : PidObservable(std::move(ids)) {
    if (this->ids().size() < 3)
      throw std::runtime_error("At least 3 particles are required");
  }
  explicit CosPersistenceAngles(std::vector<int> ids) {…}
 
  std::vector<double>
  evaluate(boost::mpi::communicator const &comm,
           ParticleReferenceRange const &local_particles,
           const ParticleObservables::traits<Particle> &traits) const override {
 
    auto const positions_sorted = detail::get_all_particle_positions(
        comm, local_particles, ids(), traits, false);
 
    if (comm.rank() != 0) {
      return {};
    }
 
    auto const &box_geo = *System::get_system().box_geo;
    auto const no_of_angles = n_values();
    auto const no_of_bonds = no_of_angles + 1;
    std::vector<double> angles(no_of_angles);
    std::vector<Utils::Vector3d> bond_vectors(no_of_bonds);
    auto get_bond_vector = [&](auto index) {
      return box_geo.get_mi_vector(positions_sorted[index + 1],
                                   positions_sorted[index]);
    };
    for (std::size_t i = 0; i < no_of_bonds; ++i) {
      auto const tmp = get_bond_vector(i);
      bond_vectors[i] = tmp / tmp.norm();
    }
    // calculate angles between neighbouring bonds, next neighbours, etc...
    for (std::size_t i = 0; i < no_of_angles; ++i) {
      auto average = 0.0;
      for (std::size_t j = 0; j < no_of_angles - i; ++j) {
        average += bond_vectors[j] * bond_vectors[j + i + 1];
      }
      angles[i] = average / static_cast<double>(no_of_angles - i);
    }
 
    return angles;
  }
  evaluate(boost::mpi::communicator const &comm, {…}
  std::vector<std::size_t> shape() const override {
    assert(ids().size() >= 2);
    return {ids().size() - 2};
  }
  std::vector<std::size_t> shape() const override  {…}
};
class CosPersistenceAngles : public PidObservable {…};
 
} // Namespace Observables
 
#endif