Box(position_type const& position = position_type())
: position_(position),
units_(array_gen(
create_vector<position_type>(1., 0., 0.),
create_vector<position_type>(0., 1., 0.),
create_vector<position_type>(0., 0., 1.))),
half_extent_(array_gen<length_type>(0.5, 0.5, 0.5)) {}
Plane(position_type const& position,
position_type const& vx,
position_type const& vy,
length_type const& half_lx,
length_type const& half_ly)
: position_(position), units_(array_gen(vx, vy, cross_product(vx, vy))),
half_extent_(array_gen<length_type>(half_lx, half_ly)) {}
Box(position_type const& position,
position_type const& vx,
position_type const& vy,
position_type const& vz,
length_type const& half_lx,
length_type const& half_ly,
length_type const& half_lz)
: position_(position), units_(array_gen(vx, vy, vz)),
half_extent_(array_gen<length_type>(half_lx, half_ly, half_lz)) {}
Plane(position_type const& position,
position_type const& vx,
position_type const& vy,
Tarray_ const& half_extent = array_gen<length_type>(0.5, 0.5))
: position_(position), units_(array_gen(vx, vy, cross_product(vx, vy)))
{
std::copy(boost::begin(half_extent), boost::end(half_extent),
boost::begin(half_extent_));
}
Box(position_type const& position,
position_type const& vx,
position_type const& vy,
position_type const& vz,
Tarray_ const& half_extent = array_gen<length_type>(0.5, 0.5, 0.5))
: position_(position), units_(array_gen(vx, vy, vz))
{
std::copy(boost::begin(half_extent), boost::end(half_extent),
boost::begin(half_extent_));
}
Box(position_type const& position, Tarray_ const& half_extent)
: position_(position),
units_(array_gen(
create_vector<position_type>(1., 0., 0.),
create_vector<position_type>(0., 1., 0.),
create_vector<position_type>(0., 0., 1.)))
{
std::copy(boost::begin(half_extent), boost::end(half_extent),
boost::begin(half_extent_));
}
void do_benchmark(Real volume, std::size_t n, Traits::time_type t, Real dt_factor)
{
typedef Traits::world_type::species_id_type species_id;
typedef Traits::world_type::particle_id_type particle_id;
typedef Traits::world_type::species_type species;
typedef Traits::world_type::length_type length_type;
typedef Traits::world_type::particle_id_pair_generator particle_id_pair_generator;
typedef Traits::network_rules_type::reaction_rule_type reaction_rule_type;
typedef Traits::world_type::position_type position_type;
SerialIDGenerator<species_id> sidgen;
Traits::world_type::traits_type::rng_type rng;
BasicNetworkRulesImpl nr;
Traits::network_rules_type nrw(nr);
length_type const world_size(std::pow(volume, 1. / 3.));
std::size_t const matrix_size(
std::max(static_cast<std::size_t>(3u),
static_cast<std::size_t>(std::pow(3. * n, 1. / 3.))));
Traits::world_type w(world_size, matrix_size);
species A(sidgen(), 1e-12, 2.5e-9, "default");
w.add_species(A);
boost::shared_ptr<Traits::world_type::structure_type> default_surface(
new Traits::cuboidal_region_type("default",
Traits::box_type(
position_type(world_size / 2, world_size / 2, world_size / 2),
array_gen(world_size / 2, world_size / 2, world_size / 2))));
w.add_structure(default_surface);
std::vector<particle_id> A_particles;
inject_particles(w, rng, A_particles, A.id(), n);
std::cout << "T: " << t << std::endl;
std::cout << "V: " << volume << std::endl;
std::cout << "N: " << n << std::endl;
std::cout << "world size: " << world_size << std::endl;
std::cout << "matrix size: " << matrix_size << std::endl;
{
std::cout << "stir" << std::endl;
BDSimulator<Traits> s(w, nrw, rng, dt_factor);
std::cout << "dt: " << s.dt() << std::endl;
Traits::time_type const stir_time(t * .1);
while (s.step(stir_time));
}
{
std::cout << "run" << std::endl;
BDSimulator<Traits> s(w, nrw, rng, dt_factor);
boost::timer timer;
while (s.step(t));
std::cout << "t: " << s.t() << "=" << t << std::endl;
std::cout << "dt: " << s.dt() << std::endl;
std::cout << "steps (total): " << s.num_steps() << std::endl;
std::cout << "elapsed: " << timer.elapsed() << std::endl;
std::cout << "steps per second: "
<< (static_cast<double>(s.num_steps()) / timer.elapsed())
<< std::endl;
std::cout << "steps/N: "
<< (static_cast<double>(s.num_steps()) / n)
<< std::endl;
}
}
virtual particle_id_pair_and_distance_list* check_overlap(particle_shape_type const& s, particle_id_type const& ignore1, particle_id_type const& ignore2) const
{
return check_overlap(s, array_gen(ignore1, ignore2));
}