ESPResSo
Extensible Simulation Package for Research on Soft Matter Systems
Loading...
Searching...
No Matches
BindAtPointOfCollision.cpp
Go to the documentation of this file.
1/*
2 * Copyright (C) 2011-2024 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
20#include <config/config.hpp>
21
22#ifdef COLLISION_DETECTION
23#ifdef VIRTUAL_SITES_RELATIVE
24
26#include "CollisionPair.hpp"
27#include "utils.hpp"
28
29#include "BoxGeometry.hpp"
30#include "Particle.hpp"
32#include "cell_system/Cell.hpp"
34#include "communication.hpp"
36#include "system/System.hpp"
37#include "virtual_sites.hpp"
38
39#include <utils/Vector.hpp>
40#include <utils/math/sqr.hpp>
42
43#include <boost/mpi/collectives.hpp>
44#include <boost/mpi/operations.hpp>
45
46#include <cassert>
47#include <stdexcept>
48#include <utility>
49#include <vector>
50
51namespace CollisionDetection {
52
54 // Validate distance
55 if (distance <= 0.) {
56 throw std::domain_error("Parameter 'distance' must be > 0");
57 }
58 // Cache square of cutoff
60
61 // Check vs placement parameter
62 if (vs_placement < 0. or vs_placement > 1.) {
63 throw std::domain_error("Parameter 'vs_placement' must be between 0 and 1");
64 }
65
66 // Check if bond exists
67 assert(system.bonded_ias->contains(bond_vs));
68 // The bond between the virtual sites can be pair or triple
69 auto const n_partners = number_of_partners(*system.bonded_ias->at(bond_vs));
70 if (n_partners != 1 and n_partners != 2) {
71 throw std::runtime_error("The bond type to be used for binding virtual "
72 "sites needs to be a pair bond");
73 }
74
75 // Create particle types
76 if (part_type_vs < 0) {
77 throw std::domain_error("Collision detection particle type for virtual "
78 "sites needs to be >=0");
79 }
80 system.nonbonded_ias->make_particle_type_exist(part_type_vs);
81}
82
84 System::System &system, std::vector<CollisionPair> &local_collision_queue) {
85 auto &cell_structure = *system.cell_structure;
86 auto const min_global_cut = system.get_min_global_cut();
87 auto const &box_geo = *system.box_geo;
88
89 add_bind_centers(local_collision_queue, cell_structure, bond_centers);
90
91 // Gather the global collision queue, because only one node has a collision
92 // across node boundaries in its queue.
93 // The other node might still have to change particle properties on its
94 // non-ghost particle
95 auto global_collision_queue = gather_collision_queue(local_collision_queue);
96
97 // Synchornize max_seen_part
98 auto const global_max_seen_particle = boost::mpi::all_reduce(
99 ::comm_cart, cell_structure.get_max_local_particle_id(),
100 boost::mpi::maximum<int>());
101
102 int current_vs_pid = global_max_seen_particle + 1;
103
104 // Iterate over global collision queue
105 for (auto &c : global_collision_queue) {
106
107 // Get particle pointers
108 Particle *p1 = cell_structure.get_local_particle(c.first);
109 Particle *p2 = cell_structure.get_local_particle(c.second);
110
111 // Only nodes take part in particle creation and binding
112 // that see both particles
113
114 // If we cannot access both particles, both are ghosts,
115 // or one is ghost and one is not accessible
116 // we only increase the counter for the ext id to use based on the
117 // number of particles created by other nodes
118 if (((!p1 or p1->is_ghost()) and (!p2 or p2->is_ghost())) or !p1 or !p2) {
119 // Increase local counters
120 current_vs_pid += 2;
121 continue;
122 }
123 // We consider the pair because one particle is local to the node and
124 // the other is local or ghost.
125
126 // Enable rotation on the particles to which vs will be attached
129
130 // Positions of the virtual sites
131 auto const vec21 = box_geo.get_mi_vector(p1->pos(), p2->pos());
132 auto const pos1 = p1->pos() - vec21 * vs_placement;
133 auto const pos2 = p1->pos() - vec21 * (1. - vs_placement);
134
135 auto handle_particle = [&](Particle *p, Utils::Vector3d const &pos) {
136 if (not p->is_ghost()) {
137 place_vs_and_relate_to_particle(cell_structure, box_geo, part_type_vs,
138 min_global_cut, current_vs_pid, pos,
139 p->id());
140 // Particle storage locations may have changed due to
141 // added particle
142 p1 = cell_structure.get_local_particle(c.first);
143 p2 = cell_structure.get_local_particle(c.second);
144 }
145 };
146
147 // place virtual sites on the node where the base particle is not a ghost
148 handle_particle(p1, pos1);
149 // Increment counter
150 current_vs_pid++;
151
152 handle_particle(p2, pos2);
153 // Increment counter
154 current_vs_pid++;
155
156 // Create bonds
157 auto const n_partners = number_of_partners(*system.bonded_ias->at(bond_vs));
158 if (n_partners == 1) {
159 // Create bond between the virtual particles
160 const int bondG[] = {current_vs_pid - 2};
161 // Only add bond if vs was created on this node
162 if (auto p = cell_structure.get_local_particle(current_vs_pid - 1))
163 p->bonds().insert({bond_vs, bondG});
164 }
165 if (n_partners == 2) {
166 // Create 1st bond between the virtual particles
167 const int bondG[] = {c.first, c.second};
168 // Only add bond if vs was created on this node
169 if (auto p = cell_structure.get_local_particle(current_vs_pid - 1))
170 p->bonds().insert({bond_vs, bondG});
171 if (auto p = cell_structure.get_local_particle(current_vs_pid - 2))
172 p->bonds().insert({bond_vs, bondG});
173 }
174 } // Loop over all collisions in the queue
175
176#ifdef ADDITIONAL_CHECKS
177 assert(Utils::Mpi::all_compare(::comm_cart, current_vs_pid) &&
178 "Nodes disagree about current_vs_pid");
179#endif
180
181 // If any node had a collision, all nodes need to resort
182 if (not global_collision_queue.empty()) {
183 cell_structure.set_resort_particles(Cells::RESORT_GLOBAL);
184 cell_structure.update_ghosts_and_resort_particle(
187 }
188}
189
190} // namespace CollisionDetection
191
192#endif // VIRTUAL_SITES_RELATIVE
193#endif // COLLISION_DETECTION
Vector implementation and trait types for boost qvm interoperability.
Data structures for bonded interactions.
int number_of_partners(Bonded_IA_Parameters const &iaparams)
Get the number of bonded partners for the specified bond.
void handle_collisions(System::System &system, std::vector< CollisionPair > &local_collision_queue)
int part_type_vs
particle type for virtual sites created on collision
int bond_centers
bond type used between centers of colliding particles
double distance_sq
Square of distance at which particle are bound.
Main system class.
void update_used_propagations()
Update the global propagation bitmask.
std::shared_ptr< BondedInteractionsMap > bonded_ias
auto get_min_global_cut() const
Get min_global_cut.
std::shared_ptr< CellStructure > cell_structure
std::shared_ptr< BoxGeometry > box_geo
std::shared_ptr< InteractionsNonBonded > nonbonded_ias
boost::mpi::communicator comm_cart
The communicator.
This file contains the defaults for ESPResSo.
@ DATA_PART_PROPERTIES
Particle::p.
@ DATA_PART_BONDS
Particle::bonds.
void place_vs_and_relate_to_particle(CellStructure &cell_structure, BoxGeometry const &box_geo, int const part_type_vs, double const min_global_cut, int const current_vs_pid, Utils::Vector3d const &pos, int const relate_to)
auto gather_collision_queue(std::vector< CollisionPair > const &local)
void add_bind_centers(std::vector< CollisionPair > &collision_queue, CellStructure &cell_structure, int bond_centers)
bool all_compare(boost::mpi::communicator const &comm, T const &value)
Compare values on all nodes.
DEVICE_QUALIFIER constexpr T sqr(T x)
Calculates the SQuaRe of x.
Definition sqr.hpp:28
Various procedures concerning interactions between particles.
Struct holding all information for one particle.
Definition Particle.hpp:395
auto const & bonds() const
Definition Particle.hpp:428
bool is_ghost() const
Definition Particle.hpp:440
auto const & pos() const
Definition Particle.hpp:431
void set_can_rotate_all_axes()
Definition Particle.hpp:473
auto const & id() const
Definition Particle.hpp:414