Reference documentation for deal.II version Git 4acf23c 2019-01-19 09:47:04 +0100
\(\newcommand{\dealcoloneq}{\mathrel{\vcenter{:}}=}\)
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
Particles::ParticleHandler< dim, spacedim > Class Template Reference

#include <deal.II/particles/particle_handler.h>

Inheritance diagram for Particles::ParticleHandler< dim, spacedim >:
[legend]

Public Types

using particle_iterator = ParticleIterator< dim, spacedim >
 
using particle_iterator_range = boost::iterator_range< particle_iterator >
 

Public Member Functions

 ParticleHandler ()
 
 ParticleHandler (const parallel::distributed::Triangulation< dim, spacedim > &tria, const Mapping< dim, spacedim > &mapping, const unsigned int n_properties=0)
 
 ~ParticleHandler () override
 
void initialize (const parallel::distributed::Triangulation< dim, spacedim > &tria, const Mapping< dim, spacedim > &mapping, const unsigned int n_properties=0)
 
void clear ()
 
void clear_particles ()
 
void update_cached_numbers ()
 
particle_iterator begin () const
 
particle_iterator begin ()
 
particle_iterator end () const
 
particle_iterator end ()
 
particle_iterator begin_ghost () const
 
particle_iterator begin_ghost ()
 
particle_iterator end_ghost () const
 
particle_iterator end_ghost ()
 
particle_iterator_range particles_in_cell (const typename Triangulation< dim, spacedim >::active_cell_iterator &cell)
 
particle_iterator_range particles_in_cell (const typename Triangulation< dim, spacedim >::active_cell_iterator &cell) const
 
void remove_particle (const particle_iterator &particle)
 
particle_iterator insert_particle (const Particle< dim, spacedim > &particle, const typename Triangulation< dim, spacedim >::active_cell_iterator &cell)
 
void insert_particles (const std::multimap< typename Triangulation< dim, spacedim >::active_cell_iterator, Particle< dim, spacedim >> &particles)
 
void insert_particles (const std::vector< Point< spacedim >> &positions)
 
void register_additional_store_load_functions (const std::function< std::size_t()> &size_callback, const std::function< void *(const particle_iterator &, void *)> &store_callback, const std::function< const void *(const particle_iterator &, const void *)> &load_callback)
 
types::particle_index n_global_particles () const
 
types::particle_index n_global_max_particles_per_cell () const
 
types::particle_index n_locally_owned_particles () const
 
types::particle_index get_next_free_particle_index () const
 
unsigned int n_properties_per_particle () const
 
PropertyPoolget_property_pool () const
 
unsigned int n_particles_in_cell (const typename Triangulation< dim, spacedim >::active_cell_iterator &cell) const
 
void sort_particles_into_subdomains_and_cells ()
 
void exchange_ghost_particles ()
 
void register_store_callback_function ()
 
void register_load_callback_function (const bool serialization)
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 
- Public Member Functions inherited from Subscriptor
 Subscriptor ()
 
 Subscriptor (const Subscriptor &)
 
 Subscriptor (Subscriptor &&) noexcept
 
virtual ~Subscriptor ()
 
Subscriptoroperator= (const Subscriptor &)
 
Subscriptoroperator= (Subscriptor &&) noexcept
 
template<typename ConstCharStar = const char *>
std::enable_if< std::is_same< ConstCharStar, const char * >::value >::type subscribe (std::atomic< bool > *const validity, ConstCharStar identifier=nullptr) const
 
void subscribe (std::atomic< bool > *const validity, const char *&&identifier) const =delete
 
void unsubscribe (std::atomic< bool > *const validity, const char *identifier=nullptr) const
 
unsigned int n_subscriptions () const
 
template<typename StreamType >
void list_subscribers (StreamType &stream) const
 
void list_subscribers () const
 
template<class Archive >
void serialize (Archive &ar, const unsigned int version)
 

Private Member Functions

void send_recv_particles (const std::map< types::subdomain_id, std::vector< particle_iterator >> &particles_to_send, std::multimap< internal::LevelInd, Particle< dim, spacedim >> &received_particles, const std::map< types::subdomain_id, std::vector< typename Triangulation< dim, spacedim >::active_cell_iterator >> &new_cells_for_particles=std::map< types::subdomain_id, std::vector< typename Triangulation< dim, spacedim >::active_cell_iterator >>())
 
std::vector< char > store_particles (const typename Triangulation< dim, spacedim >::cell_iterator &cell, const typename Triangulation< dim, spacedim >::CellStatus status) const
 
void load_particles (const typename Triangulation< dim, spacedim >::cell_iterator &cell, const typename Triangulation< dim, spacedim >::CellStatus status, const boost::iterator_range< std::vector< char >::const_iterator > &data_range)
 

Private Attributes

SmartPointer< const parallel::distributed::Triangulation< dim, spacedim >, ParticleHandler< dim, spacedim > > triangulation
 
SmartPointer< const Mapping< dim, spacedim >, ParticleHandler< dim, spacedim > > mapping
 
std::multimap< internal::LevelInd, Particle< dim, spacedim > > particles
 
std::multimap< internal::LevelInd, Particle< dim, spacedim > > ghost_particles
 
types::particle_index global_number_of_particles
 
unsigned int global_max_particles_per_cell
 
types::particle_index next_free_particle_index
 
std::unique_ptr< PropertyPoolproperty_pool
 
std::function< std::size_t()> size_callback
 
std::function< void *(const particle_iterator &, void *)> store_callback
 
std::function< const void *(const particle_iterator &, const void *)> load_callback
 
unsigned int handle
 

Additional Inherited Members

- Static Public Member Functions inherited from Subscriptor
static::ExceptionBase & ExcInUse (int arg1, std::string arg2, std::string arg3)
 
static::ExceptionBase & ExcNoSubscriber (std::string arg1, std::string arg2)
 

Detailed Description

template<int dim, int spacedim = dim>
class Particles::ParticleHandler< dim, spacedim >

This class manages the storage and handling of particles. It provides the data structures necessary to store particles efficiently, accessor functions to iterate over particles and find particles, and algorithms to distribute particles in parallel domains. Note that the class is designed in a similar way as the triangulation class. In particular, we call particles in the domain of the local process local particles, and particles that belong to neighbor processes and live in the ghost cells around the locally owned domain "ghost particles".

Definition at line 32 of file particle_accessor.h.

Member Typedef Documentation

template<int dim, int spacedim = dim>
using Particles::ParticleHandler< dim, spacedim >::particle_iterator = ParticleIterator<dim, spacedim>

A type that can be used to iterate over all particles in the domain.

Definition at line 60 of file particle_handler.h.

template<int dim, int spacedim = dim>
using Particles::ParticleHandler< dim, spacedim >::particle_iterator_range = boost::iterator_range<particle_iterator>

A type that represents a range of particles.

Definition at line 65 of file particle_handler.h.

Constructor & Destructor Documentation

template<int dim, int spacedim>
Particles::ParticleHandler< dim, spacedim >::ParticleHandler ( )

Default constructor.

Definition at line 32 of file particle_handler.cc.

template<int dim, int spacedim>
Particles::ParticleHandler< dim, spacedim >::ParticleHandler ( const parallel::distributed::Triangulation< dim, spacedim > &  tria,
const Mapping< dim, spacedim > &  mapping,
const unsigned int  n_properties = 0 
)

Constructor that initializes the particle handler with a given triangulation and mapping. Since particles are stored in respect to their surrounding cells this information is necessary to correctly organize the particle collection. This constructor is equivalent to calling the default constructor and the initialize function.

Definition at line 49 of file particle_handler.cc.

template<int dim, int spacedim>
Particles::ParticleHandler< dim, spacedim >::~ParticleHandler ( )
override

Destructor.

Definition at line 70 of file particle_handler.cc.

Member Function Documentation

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::initialize ( const parallel::distributed::Triangulation< dim, spacedim > &  tria,
const Mapping< dim, spacedim > &  mapping,
const unsigned int  n_properties = 0 
)

Initialize the particle handler. This function does not clear the internal data structures, it just sets the connections to the MPI communicator and the triangulation.

Definition at line 77 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::clear ( )

Clear all particle related data.

Definition at line 93 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::clear_particles ( )

Only clear particle data, but keep cache information about number of particles. This is useful during reorganization of particle data between processes.

Definition at line 105 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::update_cached_numbers ( )

Update all internally cached numbers. Note that all functions that modify internal data structures and act on multiple particles will call this function automatically (e.g. insert_particles), while functions that act on single particles will not call this function (e.g. insert_particle). This is done because the update is expensive compared to single operations.

Definition at line 114 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::begin ( ) const

Return an iterator to the first particle.

Definition at line 154 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::begin ( )

Return an iterator to the first particle.

Definition at line 163 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::end ( ) const

Return an iterator past the end of the particles.

Definition at line 172 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::end ( )

Return an iterator past the end of the particles.

Definition at line 181 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::begin_ghost ( ) const

Return an iterator to the first ghost particle.

Definition at line 190 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::begin_ghost ( )

Return an iterator to the first ghost particle.

Definition at line 199 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::end_ghost ( ) const

Return an iterator past the end of the ghost particles.

Definition at line 208 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::end_ghost ( )

Return an iterator past the end of the ghost particles.

Definition at line 217 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator_range Particles::ParticleHandler< dim, spacedim >::particles_in_cell ( const typename Triangulation< dim, spacedim >::active_cell_iterator &  cell)

Return a pair of particle iterators that mark the begin and end of the particles in a particular cell. The last iterator is the first particle that is no longer in the cell.

Definition at line 238 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator_range Particles::ParticleHandler< dim, spacedim >::particles_in_cell ( const typename Triangulation< dim, spacedim >::active_cell_iterator &  cell) const

Return a pair of particle iterators that mark the begin and end of the particles in a particular cell. The last iterator is the first particle that is no longer in the cell.

Definition at line 226 of file particle_handler.cc.

template<int dim, int spacedim = dim>
void Particles::ParticleHandler< dim, spacedim >::remove_particle ( const particle_iterator particle)

Remove a particle pointed to by the iterator.

Definition at line 262 of file particle_handler.cc.

template<int dim, int spacedim>
ParticleHandler< dim, spacedim >::particle_iterator Particles::ParticleHandler< dim, spacedim >::insert_particle ( const Particle< dim, spacedim > &  particle,
const typename Triangulation< dim, spacedim >::active_cell_iterator &  cell 
)

Insert a particle into the collection of particles. Return an iterator to the new position of the particle. This function involves a copy of the particle and its properties. Note that this function is of \(O(N \log N)\) complexity for \(N\) particles.

Definition at line 272 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::insert_particles ( const std::multimap< typename Triangulation< dim, spacedim >::active_cell_iterator, Particle< dim, spacedim >> &  particles)

Insert a number of particles into the collection of particles. This function involves a copy of the particles and their properties. Note that this function is of O(n_existing_particles + n_particles) complexity.

Definition at line 296 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::insert_particles ( const std::vector< Point< spacedim >> &  positions)

Create and insert a number of particles into the collection of particles. This function takes a list of positions and creates a set of particles at these positions, which are then added to the local particle collection. Note that this function currently uses GridTools::compute_point_locations, which assumes all positions are within the local part of the triangulation. If one of them is not in the local domain this function will throw an exception.

Definition at line 316 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::register_additional_store_load_functions ( const std::function< std::size_t()> &  size_callback,
const std::function< void *(const particle_iterator &, void *)> &  store_callback,
const std::function< const void *(const particle_iterator &, const void *)> &  load_callback 
)

This function allows to register three additional functions that are called every time a particle is transferred to another process (i.e. during sorting into cells, during ghost particle transfer, or during serialization of all particles).

Parameters
size_callbackA function that is called when serializing particle data. The function gets no arguments and is expected to return the size of the additional data that is serialized per particle. Note that this currently implies the data size has to be the same for every particle.
store_callbackA function that is called once per particle when serializing particle data. Arguments to the function are a particle iterator that identifies the current particle and a void pointer that points to a data block of size size_callback() in which the function can store additional data. The function is expected to return a void pointer pointing to a position right after its data block.
load_callbackA function that is called once per particle when deserializing particle data. Arguments to the function are a particle iterator that identifies the current particle and a void pointer that points to a data block of size size_callback() in which additional data was stored by the store_callback function. The function is expected to return a void pointer pointing to a position right after its data block.

Definition at line 999 of file particle_handler.cc.

template<int dim, int spacedim>
types::particle_index Particles::ParticleHandler< dim, spacedim >::n_global_particles ( ) const

Return the total number of particles that were managed by this class the last time the update_cached_numbers() function was called. The actual number of particles may have changed since then if particles have been added or removed.

Returns
Total number of particles in simulation.

Definition at line 377 of file particle_handler.cc.

template<int dim, int spacedim>
types::particle_index Particles::ParticleHandler< dim, spacedim >::n_global_max_particles_per_cell ( ) const

Return the maximum number of particles per cell the last time the update_cached_numbers() function was called.

Returns
Maximum number of particles in one cell in simulation.

Definition at line 386 of file particle_handler.cc.

template<int dim, int spacedim>
types::particle_index Particles::ParticleHandler< dim, spacedim >::n_locally_owned_particles ( ) const

Return the number of particles in the local part of the triangulation.

Definition at line 395 of file particle_handler.cc.

template<int dim, int spacedim>
types::particle_index Particles::ParticleHandler< dim, spacedim >::get_next_free_particle_index ( ) const

Return the next free particle index in the global set of particles the last time the update_cached_numbers() function was called.

Definition at line 434 of file particle_handler.cc.

template<int dim, int spacedim>
unsigned int Particles::ParticleHandler< dim, spacedim >::n_properties_per_particle ( ) const

Return the number of properties each particle has.

Definition at line 404 of file particle_handler.cc.

template<int dim, int spacedim>
PropertyPool & Particles::ParticleHandler< dim, spacedim >::get_property_pool ( ) const

Return a reference to the property pool that owns all particle properties, and organizes them physically.

Definition at line 443 of file particle_handler.cc.

template<int dim, int spacedim>
unsigned int Particles::ParticleHandler< dim, spacedim >::n_particles_in_cell ( const typename Triangulation< dim, spacedim >::active_cell_iterator &  cell) const

Return the number of particles in the given cell.

Definition at line 413 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::sort_particles_into_subdomains_and_cells ( )

Find and update the cells containing each particle for all locally owned particles. If particles moved out of the local subdomain they will be sent to their new process and inserted there. After this function call every particle is either on its current process and in its current cell, or deleted (if it could not find its new process or cell).

Definition at line 483 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::exchange_ghost_particles ( )

Exchange all particles that live in cells that are ghost cells to other processes. Clears and re-populates the ghost_neighbors member variable.

Definition at line 709 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::register_store_callback_function ( )

Callback function that should be called before every refinement and when writing checkpoints. This function is used to register store_particles() with the triangulation.

Definition at line 1014 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::register_load_callback_function ( const bool  serialization)

Callback function that should be called after every refinement and after resuming from a checkpoint. This function is used to register load_particles() with the triangulation.

Definition at line 1045 of file particle_handler.cc.

template<int dim, int spacedim>
template<class Archive >
void Particles::ParticleHandler< dim, spacedim >::serialize ( Archive &  ar,
const unsigned int  version 
)

Serialize the contents of this class.

Definition at line 532 of file particle_handler.h.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::send_recv_particles ( const std::map< types::subdomain_id, std::vector< particle_iterator >> &  particles_to_send,
std::multimap< internal::LevelInd, Particle< dim, spacedim >> &  received_particles,
const std::map< types::subdomain_id, std::vector< typename Triangulation< dim, spacedim >::active_cell_iterator >> &  new_cells_for_particles = std::map< types::subdomain_id, std::vector< typename Triangulation<dim, spacedim>::active_cell_iterator>>() 
)
private

Transfer particles that have crossed subdomain boundaries to other processors. All received particles and their new cells will be appended to the received_particles vector.

Parameters
[in]particles_to_sendAll particles that should be sent and their new subdomain_ids are in this map.
[in,out]received_particlesVector that stores all received particles. Note that it is not required nor checked that the list is empty, received particles are simply attached to the end of the vector.
[in]new_cells_for_particlesOptional vector of cell iterators with the same structure as particles_to_send. If this parameter is given it should contain the cell iterator for every particle to be send in which the particle belongs. This parameter is necessary if the cell information of the particle iterator is outdated (e.g. after particle movement).

Definition at line 781 of file particle_handler.cc.

template<int dim, int spacedim>
std::vector< char > Particles::ParticleHandler< dim, spacedim >::store_particles ( const typename Triangulation< dim, spacedim >::cell_iterator &  cell,
const typename Triangulation< dim, spacedim >::CellStatus  status 
) const
private

Called by listener functions from Triangulation for every cell before a refinement step. All particles have to be attached to their cell to be sent around to the new processes.

Definition at line 1104 of file particle_handler.cc.

template<int dim, int spacedim>
void Particles::ParticleHandler< dim, spacedim >::load_particles ( const typename Triangulation< dim, spacedim >::cell_iterator &  cell,
const typename Triangulation< dim, spacedim >::CellStatus  status,
const boost::iterator_range< std::vector< char >::const_iterator > &  data_range 
)
private

Called by listener functions after a refinement step. The local map of particles has to be read from the triangulation user_pointer.

Definition at line 1196 of file particle_handler.cc.

Member Data Documentation

template<int dim, int spacedim = dim>
SmartPointer<const parallel::distributed::Triangulation<dim, spacedim>, ParticleHandler<dim, spacedim> > Particles::ParticleHandler< dim, spacedim >::triangulation
private

Address of the triangulation to work on.

Definition at line 372 of file particle_handler.h.

template<int dim, int spacedim = dim>
SmartPointer<const Mapping<dim, spacedim>, ParticleHandler<dim, spacedim> > Particles::ParticleHandler< dim, spacedim >::mapping
private

Address of the mapping to work on.

Definition at line 378 of file particle_handler.h.

template<int dim, int spacedim = dim>
std::multimap<internal::LevelInd, Particle<dim, spacedim> > Particles::ParticleHandler< dim, spacedim >::particles
private

Set of particles currently living in the local domain, organized by the level/index of the cell they are in.

Definition at line 384 of file particle_handler.h.

template<int dim, int spacedim = dim>
std::multimap<internal::LevelInd, Particle<dim, spacedim> > Particles::ParticleHandler< dim, spacedim >::ghost_particles
private

Set of particles that currently live in the ghost cells of the local domain, organized by the level/index of the cell they are in. These particles are equivalent to the ghost entries in distributed vectors.

Definition at line 391 of file particle_handler.h.

template<int dim, int spacedim = dim>
types::particle_index Particles::ParticleHandler< dim, spacedim >::global_number_of_particles
private

This variable stores how many particles are stored globally. It is calculated by update_cached_numbers().

Definition at line 397 of file particle_handler.h.

template<int dim, int spacedim = dim>
unsigned int Particles::ParticleHandler< dim, spacedim >::global_max_particles_per_cell
private

The maximum number of particles per cell in the global domain. This variable is important to store and load particle data during repartition and serialization of the solution. Note that the variable is only updated when it is needed, e.g. after particle movement, before/after mesh refinement, before creating a checkpoint and after resuming from a checkpoint.

Definition at line 407 of file particle_handler.h.

template<int dim, int spacedim = dim>
types::particle_index Particles::ParticleHandler< dim, spacedim >::next_free_particle_index
private

This variable stores the next free particle index that is available globally in case new particles need to be generated.

Definition at line 413 of file particle_handler.h.

template<int dim, int spacedim = dim>
std::unique_ptr<PropertyPool> Particles::ParticleHandler< dim, spacedim >::property_pool
private

This object owns and organizes the memory for all particle properties.

Definition at line 419 of file particle_handler.h.

template<int dim, int spacedim = dim>
std::function<std::size_t()> Particles::ParticleHandler< dim, spacedim >::size_callback
private

A function that can be registered by calling register_additional_store_load_functions. It is called when serializing particle data. The function gets no arguments and is expected to return the size of the additional data that is serialized per particle. Note that this currently implies the data size has to be the same for every particle, but it does not have to be the same for every serialization process (e.g. a serialization during particle movement might include temporary data, while a serialization after movement was finished does not need to transfer this data).

Definition at line 432 of file particle_handler.h.

template<int dim, int spacedim = dim>
std::function<void *(const particle_iterator &, void *)> Particles::ParticleHandler< dim, spacedim >::store_callback
private

A function that can be registered by calling register_additional_store_load_functions. It is called once per particle when serializing particle data. Arguments to the function are a particle iterator that identifies the current particle and a void pointer that points to a data block of size size_callback() in which the function can store additional data. The function is expected to return a void pointer pointing to a position right after its data block.

Definition at line 444 of file particle_handler.h.

template<int dim, int spacedim = dim>
std::function<const void *(const particle_iterator &, const void *)> Particles::ParticleHandler< dim, spacedim >::load_callback
private

A function that is called once per particle when deserializing particle data. Arguments to the function are a particle iterator that identifies the current particle and a void pointer that points to a data block of size size_callback() from which the function can load additional data. This block was filled by the store_callback function during serialization. This function is expected to return a void pointer pointing to a position right after its data block.

Definition at line 457 of file particle_handler.h.

template<int dim, int spacedim = dim>
unsigned int Particles::ParticleHandler< dim, spacedim >::handle
private

This variable is set by the register_store_callback_function() function and used by the register_load_callback_function() function to check where the particle data was registered in the corresponding triangulation object.

Definition at line 465 of file particle_handler.h.


The documentation for this class was generated from the following files: