--- /dev/null
+New: ParticleHandler::get_particle_positions() and ParticleHandler::set_particle_positions() allow
+to set and get particle positions from various types of sources.
+<br>
+(Bruno Blais, Luca Heltai, 2020/01/10)
#include <deal.II/base/array_view.h>
#include <deal.II/base/bounding_box.h>
+#include <deal.II/base/function.h>
#include <deal.II/base/mpi.h>
#include <deal.II/base/smartpointer.h>
#include <deal.II/base/subscriptor.h>
& global_bounding_boxes,
const std::vector<std::vector<double>> &properties = {});
+ /**
+ * Set the position of the particles by using the values contained in the
+ * vector @p input_vector.
+ *
+ * The vector @p input_vector should have read access to the indices
+ * created by extracting the locally relevant ids with
+ * locally_relevant_ids(), and taking its tensor
+ * product with the index set representing the range `[0, spacedim)`, i.e.:
+ * @code
+ * IndexSet ids = particle_handler.locally_relevant_ids().
+ * tensor_product(complete_index_set(spacedim));
+ * @endcode
+ *
+ * The position of the particle with global index `id` is read from
+ * spacedim consecutive entries starting from
+ * `input_vector[id*spacedim]`.
+ *
+ * If the argument @p displace_particles is set to false, then the new
+ * position is computed by setting it to the values contained in
+ * @p input_vector. By default, the particles are displaced of the
+ * amount contained in the @p input_vector.
+ *
+ * After setting the new position, this function calls internally the method
+ * sort_particles_into_subdomains_and_cells(). You should
+ * make sure you satisfy the requirements of that function.
+ *
+ * @param[in] input_vector A parallel distributed vector containing
+ * the displacement to apply to each particle, or their new absolute
+ * position.
+ *
+ * @param[in] displace_particles Control if the @p input_vector should
+ * be interpreted as a displacement vector, or a vector of absolute
+ * positions.
+ *
+ * @authors Luca Heltai, Bruno Blais, 2019.
+ */
+ template <class VectorType>
+ void
+ set_particle_positions(const VectorType &input_vector,
+ const bool displace_particles = true);
+
+ /**
+ * Set the position of the particles within the particle handler using a
+ * vector of points. The new set of point defined by the
+ * vector has to be sufficiently close to the original one to ensure that
+ * the sort_particles_into_subdomains_and_cells() function manages to find
+ * the new cells in which the particles belong
+ *
+ * @param [in] new_positions A vector of points of dimension
+ * particle_handler.n_locally_owned_particles()
+ *
+ * @param [in] displace_particles When true, this add the value of the
+ * vector of points to the
+ * current position of the particle, thus displacing them by the
+ * amount given by the function. When false, the position of the
+ * particle is replaced by the value in the vector
+ *
+ * @authors Bruno Blais, Luca Heltai (2019)
+ */
+ void
+ set_particle_positions(const std::vector<Point<spacedim>> &new_positions,
+ const bool displace_particles = true);
+
+
+ /**
+ * Set the position of the particles within the particle handler using a
+ * function with spacedim components. The new set of point defined by the
+ * fuction has to be sufficiently close to the original one to ensure that
+ * the sort_particles_into_subdomains_and_cells algorithm manages to find
+ * the new cells in which the particles belong.
+ *
+ * @param [in] function A function that has n_components==spacedim that
+ * describes either the displacement or the new position of the particles
+ *
+ * @param [in] displace_particles When true, this add the results of the
+ * function to the current position of the particle, thus displacing them by
+ * the amount given by the function. When false, the position of the
+ * particle is is replaced by the value of the function
+ *
+ * @authors Bruno Blais, Luca Heltai (2019)
+ */
+ void
+ set_particle_positions(const Function<spacedim> &function,
+ const bool displace_particles = true);
+
+ /**
+ * Read the position of the particles and store them into the distributed
+ * vector @p output_vector. By default the
+ * @p output_vector is overwritten by this operation, but you can add to
+ * its entries by setting @p add_to_output_vector to `true`.
+ *
+ * This is the reverse operation of the set_particle_positions() function.
+ * The position of the particle with global index `id` is written to
+ * spacedim consecutive entries starting from
+ * `output_vector[id*spacedim]`.
+ *
+ * @param[out] output_vector A parallel distributed vector containing
+ * the positions of the particles, or updated with the positions of the
+ * particles.
+ *
+ * @param[in] add_to_output_vector Control if the function should set the
+ * entries of the @p output_vector or if should add to them.
+ *
+ * @author Luca Heltai, Bruno Blais, 2019.
+ */
+ template <class VectorType>
+ void
+ get_particle_positions(VectorType &output_vector,
+ const bool add_to_output_vector = false);
+
+ /**
+ * Gather the position of the particles within the particle handler in
+ * a vector of points.
+ *
+ * @param [in,out] positions A vector preallocated at size
+ * (particle_handler.n_locally_owned_articles) and whose points will become
+ * the positions of the locally owned particles
+ *
+ * @param [in] add_to_output_vector When true, the value of the point of
+ * the particles is added to the positions vector. When false,
+ * the value of the points in the positions vector are replaced by the
+ * position of the particles.
+ *
+ * @authors Bruno Blais, Luca Heltai (2019)
+ *
+ */
+ void
+ get_particle_positions(std::vector<Point<spacedim>> &positions,
+ const bool add_to_output_vector = false);
+
/**
* This function allows to register three additional functions that are
* called every time a particle is transferred to another process
&global_number_of_particles &global_max_particles_per_cell
& next_free_particle_index;
}
+
+
+
+ template <int dim, int spacedim>
+ template <class VectorType>
+ void
+ ParticleHandler<dim, spacedim>::set_particle_positions(
+ const VectorType &input_vector,
+ const bool displace_particles)
+ {
+ AssertDimension(input_vector.size(),
+ get_next_free_particle_index() * spacedim);
+ for (auto &p : *this)
+ {
+ const auto &point = p.get_location();
+ auto new_point = point * (displace_particles ? 1.0 : 0.0);
+ const auto id = p.get_id();
+ for (unsigned int i = 0; i < spacedim; ++i)
+ new_point[i] += input_vector[id * spacedim + i];
+ p.set_location(new_point);
+ }
+ sort_particles_into_subdomains_and_cells();
+ }
+
+
+
+ template <int dim, int spacedim>
+ template <class VectorType>
+ void
+ ParticleHandler<dim, spacedim>::get_particle_positions(
+ VectorType &output_vector,
+ const bool add_to_output_vector)
+ {
+ AssertDimension(output_vector.size(),
+ get_next_free_particle_index() * spacedim);
+ for (const auto &p : *this)
+ {
+ auto & point = p.get_location();
+ const auto id = p.get_id();
+ if (add_to_output_vector)
+ for (unsigned int i = 0; i < spacedim; ++i)
+ output_vector[id * spacedim + i] += point[i];
+ else
+ for (unsigned int i = 0; i < spacedim; ++i)
+ output_vector[id * spacedim + i] = point[i];
+ }
+ if (add_to_output_vector)
+ output_vector.compress(VectorOperation::add);
+ else
+ output_vector.compress(VectorOperation::insert);
+ }
+
} // namespace Particles
DEAL_II_NAMESPACE_CLOSE
+ template <int dim, int spacedim>
+ void
+ ParticleHandler<dim, spacedim>::get_particle_positions(
+ std::vector<Point<spacedim>> &positions,
+ const bool add_to_output_vector)
+ {
+ // There should be one point per particle to gather
+ AssertDimension(positions.size(), n_locally_owned_particles());
+
+ unsigned int i = 0;
+ for (auto it = begin(); it != end(); ++it, ++i)
+ {
+ if (add_to_output_vector)
+ positions[i] = positions[i] + it->get_location();
+ else
+ positions[i] = it->get_location();
+ }
+ }
+
+
+
+ template <int dim, int spacedim>
+ void
+ ParticleHandler<dim, spacedim>::set_particle_positions(
+ const std::vector<Point<spacedim>> &new_positions,
+ const bool displace_particles)
+ {
+ // There should be one point per particle to fix the new position
+ AssertDimension(new_positions.size(), n_locally_owned_particles());
+
+ unsigned int i = 0;
+ for (auto it = begin(); it != end(); ++it, ++i)
+ {
+ if (displace_particles)
+ it->set_location(it->get_location() + new_positions[i]);
+ else
+ it->set_location(new_positions[i]);
+ }
+ sort_particles_into_subdomains_and_cells();
+ }
+
+
+
+ template <int dim, int spacedim>
+ void
+ ParticleHandler<dim, spacedim>::set_particle_positions(
+ const Function<spacedim> &function,
+ const bool displace_particles)
+ {
+ // The function should have sufficient components to displace the
+ // particles
+ AssertDimension(function.n_components, spacedim);
+
+ Vector<double> new_position(spacedim);
+ for (auto &particle : *this)
+ {
+ Point<spacedim> particle_location = particle.get_location();
+ function.vector_value(particle_location, new_position);
+ if (displace_particles)
+ for (unsigned int d = 0; d < spacedim; ++d)
+ particle_location[d] = particle_location[d] + new_position[d];
+ else
+ for (unsigned int d = 0; d < spacedim; ++d)
+ particle_location[d] = new_position[d];
+ particle.set_location(particle_location);
+ }
+ sort_particles_into_subdomains_and_cells();
+ }
+
+
+
template <int dim, int spacedim>
PropertyPool &
ParticleHandler<dim, spacedim>::get_property_pool() const
--- /dev/null
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2017 - 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// Test get and set particle positions
+
+#include <deal.II/base/mpi.h>
+#include <deal.II/base/utilities.h>
+
+#include <deal.II/distributed/tria.h>
+
+#include <deal.II/fe/mapping_q.h>
+
+#include <deal.II/grid/filtered_iterator.h>
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/grid_tools.h>
+
+#include <deal.II/lac/trilinos_vector.h>
+
+#include <deal.II/particles/particle_handler.h>
+
+#include "../tests.h"
+
+template <int dim, int spacedim>
+void
+test()
+{
+ parallel::distributed::Triangulation<dim, spacedim> tr(MPI_COMM_WORLD);
+
+ GridGenerator::hyper_cube(tr);
+ tr.refine_global(2);
+
+ MappingQ<dim, spacedim> mapping(1);
+
+ Particles::ParticleHandler<dim, spacedim> particle_handler(tr, mapping);
+
+ const unsigned int n_points = 10;
+ const unsigned int my_cpu = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD);
+ const unsigned int n_cpus = Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD);
+ Testing::srand(my_cpu + 1);
+
+ // Distribute the local points to the processor that owns them
+ // on the triangulation
+ auto my_bounding_box = GridTools::compute_mesh_predicate_bounding_box(
+ tr, IteratorFilters::LocallyOwnedCell());
+
+ auto global_bounding_boxes =
+ Utilities::MPI::all_gather(MPI_COMM_WORLD, my_bounding_box);
+
+ std::vector<Point<spacedim>> points(n_points);
+ for (auto &p : points)
+ p = random_point<spacedim>();
+
+ auto cpu_to_index =
+ particle_handler.insert_global_particles(points, global_bounding_boxes);
+
+ const auto set = particle_handler.locally_relevant_ids().tensor_product(
+ complete_index_set(spacedim));
+
+ TrilinosWrappers::MPI::Vector vector(set, MPI_COMM_WORLD);
+ particle_handler.get_particle_positions(vector);
+ deallog << "Local set: ";
+ set.print(deallog);
+ deallog << std::endl
+ << "Local vector norm: " << vector.linfty_norm() << std::endl;
+
+ // With this we know we don't get out of the domain
+ vector *= 1e-3;
+ particle_handler.set_particle_positions(vector);
+
+ // Make sure we have a new index set
+
+ const auto new_set = particle_handler.locally_relevant_ids().tensor_product(
+ complete_index_set(spacedim));
+
+ TrilinosWrappers::MPI::Vector new_vector(new_set, MPI_COMM_WORLD);
+
+ particle_handler.get_particle_positions(new_vector);
+ deallog << "New position norm: " << vector.linfty_norm() << std::endl;
+}
+
+
+
+int
+main(int argc, char *argv[])
+{
+ Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+ MPILogInitAll all;
+
+ deallog.push("2d/2d");
+ test<2, 2>();
+ deallog.pop();
+ deallog.push("3d/3d");
+ test<3, 3>();
+ deallog.pop();
+}
--- /dev/null
+
+DEAL:0:2d/2d::Local set: {[0,19]}
+DEAL:0:2d/2d::
+DEAL:0:2d/2d::Local vector norm: 0.952230
+DEAL:0:2d/2d::New position norm: 0.000952230
+DEAL:0:3d/3d::Local set: {[0,29]}
+DEAL:0:3d/3d::
+DEAL:0:3d/3d::Local vector norm: 0.998925
+DEAL:0:3d/3d::New position norm: 0.000998925
--- /dev/null
+
+DEAL:0:2d/2d::Local set: {[0,1], [4,5], [22,27], [30,35], [38,39]}
+DEAL:0:2d/2d::
+DEAL:0:2d/2d::Local vector norm: 0.990603
+DEAL:0:2d/2d::New position norm: 0.000990603
+DEAL:0:3d/3d::Local set: {[3,8], [18,20], [24,35], [39,41], [51,53], [57,59]}
+DEAL:0:3d/3d::
+DEAL:0:3d/3d::Local vector norm: 0.998925
+DEAL:0:3d/3d::New position norm: 0.000998925
+
+DEAL:1:2d/2d::Local set: {[2,3], [6,21], [28,29], [36,37]}
+DEAL:1:2d/2d::
+DEAL:1:2d/2d::Local vector norm: 0.990603
+DEAL:1:2d/2d::New position norm: 0.000990603
+DEAL:1:3d/3d::Local set: {[0,2], [9,17], [21,23], [36,38], [42,50], [54,56]}
+DEAL:1:3d/3d::
+DEAL:1:3d/3d::Local vector norm: 0.998925
+DEAL:1:3d/3d::New position norm: 0.000998925
+
--- /dev/null
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2017 - 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// Test insert_global_particles. Make sure we don't lose particles
+// along the way
+
+#include <deal.II/base/mpi.h>
+#include <deal.II/base/utilities.h>
+
+#include <deal.II/distributed/tria.h>
+
+#include <deal.II/fe/mapping_q.h>
+
+#include <deal.II/grid/filtered_iterator.h>
+#include <deal.II/grid/grid_generator.h>
+#include <deal.II/grid/grid_tools.h>
+
+#include <deal.II/particles/particle_handler.h>
+
+#include "../tests.h"
+
+template <int dim, int spacedim>
+void
+test()
+{
+ parallel::distributed::Triangulation<dim, spacedim> tr(MPI_COMM_WORLD);
+
+ GridGenerator::hyper_cube(tr);
+ tr.refine_global(2);
+
+ MappingQ<dim, spacedim> mapping(1);
+
+ Particles::ParticleHandler<dim, spacedim> particle_handler(tr, mapping);
+
+ const unsigned int n_points = 2;
+ const unsigned int my_cpu = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD);
+ const unsigned int n_cpus = Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD);
+ Testing::srand(my_cpu + 1);
+
+ // Create the bounding boxes for the global insertion
+ auto my_bounding_box = GridTools::compute_mesh_predicate_bounding_box(
+ tr, IteratorFilters::LocallyOwnedCell());
+
+ auto global_bounding_boxes =
+ Utilities::MPI::all_gather(MPI_COMM_WORLD, my_bounding_box);
+
+ std::vector<Point<spacedim>> points(n_points);
+ for (auto &p : points)
+ p = random_point<spacedim>(0.1, 0.2);
+
+ auto cpu_to_index =
+ particle_handler.insert_global_particles(points, global_bounding_boxes);
+
+ for (const auto &particle : particle_handler)
+ {
+ deallog << "Particle id : " << particle.get_id();
+ deallog << " Particle location: " << particle.get_location() << std::endl;
+ }
+
+ Tensor<1, spacedim> displacement;
+ displacement[0] = 0.1;
+ std::vector<Point<spacedim>> new_particle_positions(
+ particle_handler.n_locally_owned_particles());
+
+ std::vector<Point<spacedim>> old_particle_positions(
+ particle_handler.n_locally_owned_particles());
+ particle_handler.get_particle_positions(old_particle_positions);
+
+ for (unsigned int i = 0; i < old_particle_positions.size(); ++i)
+ new_particle_positions[i] = old_particle_positions[i] + displacement;
+
+ particle_handler.set_particle_positions(new_particle_positions, false);
+
+ deallog << "Displacement" << std::endl;
+ for (const auto &particle : particle_handler)
+ {
+ deallog << "Particle id : " << particle.get_id();
+ deallog << " Particle location: " << particle.get_location() << std::endl;
+ }
+}
+
+
+
+int
+main(int argc, char *argv[])
+{
+ Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+ MPILogInitAll all;
+
+ deallog.push("2d/2d");
+ test<2, 2>();
+ deallog.pop();
+ deallog << "---" << std::endl;
+ deallog.push("3d/3d");
+ test<3, 3>();
+ deallog.pop();
+}
--- /dev/null
+
+DEAL:0:2d/2d::Particle id : 0 Particle location: 0.184019 0.139438
+DEAL:0:2d/2d::Particle id : 1 Particle location: 0.178310 0.179844
+DEAL:0:2d/2d::Displacement
+DEAL:0:2d/2d::Particle id : 0 Particle location: 0.284019 0.139438
+DEAL:0:2d/2d::Particle id : 1 Particle location: 0.278310 0.179844
+DEAL:0::---
+DEAL:0:3d/3d::Particle id : 0 Particle location: 0.184019 0.139438 0.178310
+DEAL:0:3d/3d::Particle id : 1 Particle location: 0.179844 0.191165 0.119755
+DEAL:0:3d/3d::Displacement
+DEAL:0:3d/3d::Particle id : 0 Particle location: 0.284019 0.139438 0.178310
+DEAL:0:3d/3d::Particle id : 1 Particle location: 0.279844 0.191165 0.119755
projects / dealii.git / commitdiff