ESPResSo
Extensible Simulation Package for Research on Soft Matter Systems
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ParticleDistances.hpp
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1/*
2 * Copyright (C) 2019-2022 The ESPResSo project
3 *
4 * This file is part of ESPResSo.
5 *
6 * ESPResSo is free software: you can redistribute it and/or modify
7 * it under the terms of the GNU General Public License as published by
8 * the Free Software Foundation, either version 3 of the License, or
9 * (at your option) any later version.
10 *
11 * ESPResSo is distributed in the hope that it will be useful,
12 * but WITHOUT ANY WARRANTY; without even the implied warranty of
13 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
14 * GNU General Public License for more details.
15 *
16 * You should have received a copy of the GNU General Public License
17 * along with this program. If not, see <http://www.gnu.org/licenses/>.
18 */
19#ifndef OBSERVABLES_PARTICLEDISTANCES_HPP
20#define OBSERVABLES_PARTICLEDISTANCES_HPP
21
22#include "BoxGeometry.hpp"
23#include "PidObservable.hpp"
24#include "system/System.hpp"
25
26#include <cassert>
27#include <cstddef>
28#include <stdexcept>
29#include <utility>
30#include <vector>
31
32namespace Observables {
33
34/** Calculate distances between particles in a polymer.
35 * For @f$ n @f$ bonded particles, return the @f$ n-1 @f$ distances separating
36 * them.
37 */
39public:
41 explicit ParticleDistances(std::vector<int> ids)
42 : PidObservable(std::move(ids)) {
43 if (this->ids().size() < 2)
44 throw std::runtime_error("At least 2 particles are required");
45 }
46
47 std::vector<double>
48 evaluate(boost::mpi::communicator const &comm,
49 ParticleReferenceRange const &local_particles,
50 const ParticleObservables::traits<Particle> &traits) const override {
51 auto const positions_sorted = detail::get_all_particle_positions(
52 comm, local_particles, ids(), traits, false);
53
54 if (comm.rank() != 0) {
55 return {};
56 }
57
58 auto const &box_geo = *System::get_system().box_geo;
59 std::vector<double> res(n_values());
60
61 for (std::size_t i = 0, end = n_values(); i < end; i++) {
62 auto const v =
63 box_geo.get_mi_vector(positions_sorted[i], positions_sorted[i + 1]);
64 res[i] = v.norm();
65 }
66 return res;
67 }
68 std::vector<std::size_t> shape() const override {
69 assert(!ids().empty());
70 return {ids().size() - 1};
71 }
72};
73
74} // namespace Observables
75
76#endif
std::size_t n_values() const
Size of the flat array returned by the observable.
Calculate distances between particles in a polymer.
std::vector< std::size_t > shape() const override
std::vector< double > evaluate(boost::mpi::communicator const &comm, ParticleReferenceRange const &local_particles, const ParticleObservables::traits< Particle > &traits) const override
ParticleDistances(std::vector< int > ids)
std::vector< int > const & ids() const
std::shared_ptr< BoxGeometry > box_geo
std::vector< std::reference_wrapper< Particle const > > ParticleReferenceRange
System & get_system()