Ghost particles and particle exchange. More...

#include "ghosts.hpp"
#include "BoxGeometry.hpp"
#include "Particle.hpp"
#include "system/System.hpp"
#include <utils/serialization/memcpy_archive.hpp>
#include <boost/archive/binary_iarchive.hpp>
#include <boost/archive/binary_oarchive.hpp>
#include <boost/iostreams/device/array.hpp>
#include <boost/iostreams/device/back_inserter.hpp>
#include <boost/iostreams/stream.hpp>
#include <boost/mpi/collectives.hpp>
#include <boost/range/numeric.hpp>
#include <boost/serialization/vector.hpp>
#include <algorithm>
#include <cassert>
#include <cstddef>
#include <functional>
#include <iterator>
#include <limits>
#include <span>
#include <vector>

Include dependency graph for ghosts.cpp:

Go to the source code of this file.

Classes
class	CommBuf
	Class that stores marshalled data for ghost communications. More...

class	SerializationSizeCalculator
	Pseudo-archive to calculate the size of the serialization buffer. More...

Macros
#define	REQ_GHOST_SEND 100
	Tag for ghosts communications.

Enumerations
enum class	ReductionPolicy { MOVE , UPDATE }
	Type of reduction to carry out during serialization. More...

enum class	SerializationDirection { SAVE , LOAD }
	Whether to save the state to or load the state from the archive. More...

Functions
template<class Archive >
static void	serialize_and_reduce (Archive &ar, Particle &p, unsigned int data_parts, ReductionPolicy policy, SerializationDirection direction, BoxGeometry const &box_geo, Utils::Vector3d const *ghost_shift)
	Serialize particle data, possibly with reduction.

static auto	calc_transmit_size (BoxGeometry const &box_geo, unsigned data_parts)

static auto	calc_transmit_size (GhostCommunication const &ghost_comm, BoxGeometry const &box_geo, unsigned int data_parts)

static void	prepare_send_buffer (CommBuf &send_buffer, GhostCommunication const &ghost_comm, BoxGeometry const &box_geo, unsigned int data_parts)

static void	prepare_ghost_cell (ParticleList *cell, std::size_t size)

static void	prepare_recv_buffer (CommBuf &recv_buffer, GhostCommunication const &ghost_comm, BoxGeometry const &box_geo, unsigned int data_parts)

static void	put_recv_buffer (CommBuf &recv_buffer, GhostCommunication const &ghost_comm, BoxGeometry const &box_geo, unsigned int data_parts)

static void	add_rattle_correction_from_recv_buffer (CommBuf &recv_buffer, const GhostCommunication &ghost_comm)

static void	add_forces_from_recv_buffer (CommBuf &recv_buffer, const GhostCommunication &ghost_comm)

static void	cell_cell_transfer (GhostCommunication const &ghost_comm, BoxGeometry const &box_geo, unsigned int data_parts)

static bool	is_send_op (int comm_type, int node, int this_node)

static bool	is_recv_op (int comm_type, int node, int this_node)

static bool	is_prefetchable (GhostCommunication const &ghost_comm, int this_node)

static bool	is_poststorable (GhostCommunication const &ghost_comm, int this_node)

void	ghost_communicator (GhostCommunicator const &gcr, BoxGeometry const &box_geo, unsigned int data_parts)
	Do a ghost communication with the specified data parts.

Detailed Description

Ghost particles and particle exchange.

For more information on ghosts, see ghosts.hpp

Note on variable naming:

a "GhostCommunicator" is always named "gcr",
a "GhostCommunication" is always named "ghost_comm".

Definition in file ghosts.cpp.

Macro Definition Documentation

◆ REQ_GHOST_SEND

#define REQ_GHOST_SEND 100

Tag for ghosts communications.

Definition at line 58 of file ghosts.cpp.

Enumeration Type Documentation

◆ ReductionPolicy

enum class ReductionPolicy

strong

Type of reduction to carry out during serialization.

Enumerator
MOVE	Reduction for domain-to-domain particle communication.
UPDATE	Reduction for cell-to-cell particle update.

Definition at line 109 of file ghosts.cpp.

◆ SerializationDirection

enum class SerializationDirection

strong

Whether to save the state to or load the state from the archive.

Enumerator
SAVE
LOAD

Definition at line 117 of file ghosts.cpp.

Function Documentation

◆ add_forces_from_recv_buffer()

static void add_forces_from_recv_buffer	(	CommBuf &	recv_buffer,
		const GhostCommunication &	ghost_comm
	)

static

Definition at line 365 of file ghosts.cpp.

References stream.

Referenced by ghost_communicator().

◆ add_rattle_correction_from_recv_buffer()

static void add_rattle_correction_from_recv_buffer	(	CommBuf &	recv_buffer,
		const GhostCommunication &	ghost_comm
	)

static

Definition at line 351 of file ghosts.cpp.

References stream.

Referenced by ghost_communicator().

◆ calc_transmit_size() [1/2]

static auto calc_transmit_size	(	BoxGeometry const &	box_geo,
		unsigned	data_parts
	)

static

Definition at line 230 of file ghosts.cpp.

References MOVE, SAVE, serialize_and_reduce(), and stream.

Referenced by calc_transmit_size(), cell_cell_transfer(), ghost_communicator(), prepare_recv_buffer(), and prepare_send_buffer().

◆ calc_transmit_size() [2/2]

static auto calc_transmit_size	(	GhostCommunication const &	ghost_comm,
		BoxGeometry const &	box_geo,
		unsigned int	data_parts
	)

static

Definition at line 239 of file ghosts.cpp.

References calc_transmit_size(), GHOSTTRANS_PARTNUM, and stream.

◆ cell_cell_transfer()

static void cell_cell_transfer	(	GhostCommunication const &	ghost_comm,
		BoxGeometry const &	box_geo,
		unsigned int	data_parts
	)

static

Definition at line 378 of file ghosts.cpp.

References calc_transmit_size(), GHOSTTRANS_BONDS, GHOSTTRANS_PARTNUM, LOAD, CommBuf::make_span(), prepare_ghost_cell(), CommBuf::resize(), SAVE, serialize_and_reduce(), stream, and UPDATE.

Referenced by ghost_communicator().

◆ ghost_communicator()

void ghost_communicator	(	GhostCommunicator const &	gcr,
		BoxGeometry const &	box_geo,
		unsigned int	data_parts
	)

Do a ghost communication with the specified data parts.

Definition at line 443 of file ghosts.cpp.

References add_forces_from_recv_buffer(), add_rattle_correction_from_recv_buffer(), calc_transmit_size(), cell_cell_transfer(), GHOST_BCST, GHOST_JOBMASK, GHOST_LOCL, GHOST_PREFETCH, GHOST_PSTSTORE, GHOST_RDCE, GHOST_RECV, GHOST_SEND, GHOSTTRANS_FORCE, GHOSTTRANS_NONE, GHOSTTRANS_RATTLE, is_recv_op(), is_send_op(), prepare_recv_buffer(), prepare_send_buffer(), put_recv_buffer(), REQ_GHOST_SEND, stream, and this_node.

Referenced by CellStructure::ghosts_count(), CellStructure::ghosts_reduce_forces(), CellStructure::ghosts_reduce_rattle_correction(), CellStructure::ghosts_update(), and HybridDecomposition::resort().

◆ is_poststorable()

static bool is_poststorable	(	GhostCommunication const &	ghost_comm,
		int	this_node
	)

static

Definition at line 435 of file ghosts.cpp.

References GHOST_JOBMASK, GHOST_PSTSTORE, is_recv_op(), stream, and this_node.

◆ is_prefetchable()

static bool is_prefetchable	(	GhostCommunication const &	ghost_comm,
		int	this_node
	)

static

Definition at line 427 of file ghosts.cpp.

References GHOST_JOBMASK, GHOST_PREFETCH, is_send_op(), stream, and this_node.

◆ is_recv_op()

static bool is_recv_op	(	int	comm_type,
		int	node,
		int	this_node
	)

static

Definition at line 421 of file ghosts.cpp.

References GHOST_BCST, GHOST_RDCE, GHOST_RECV, stream, and this_node.

Referenced by ghost_communicator(), and is_poststorable().

◆ is_send_op()

static bool is_send_op	(	int	comm_type,
		int	node,
		int	this_node
	)

static

Definition at line 416 of file ghosts.cpp.

References GHOST_BCST, GHOST_RDCE, GHOST_SEND, stream, and this_node.

Referenced by ghost_communicator(), and is_prefetchable().

◆ prepare_ghost_cell()

static void prepare_ghost_cell	(	ParticleList *	cell,
		std::size_t	size
	)

static

Definition at line 290 of file ghosts.cpp.

References Utils::Bag< T >::resize().

Referenced by cell_cell_transfer(), and put_recv_buffer().

◆ prepare_recv_buffer()

static void prepare_recv_buffer	(	CommBuf &	recv_buffer,
		GhostCommunication const &	ghost_comm,
		BoxGeometry const &	box_geo,
		unsigned int	data_parts
	)

static

Definition at line 300 of file ghosts.cpp.

References calc_transmit_size(), and stream.

Referenced by ghost_communicator().

◆ prepare_send_buffer()

static void prepare_send_buffer	(	CommBuf &	send_buffer,
		GhostCommunication const &	ghost_comm,
		BoxGeometry const &	box_geo,
		unsigned int	data_parts
	)

static

Definition at line 252 of file ghosts.cpp.

References calc_transmit_size(), GHOSTTRANS_BONDS, GHOSTTRANS_PARTNUM, MOVE, SAVE, serialize_and_reduce(), and stream.

Referenced by ghost_communicator().

◆ put_recv_buffer()

static void put_recv_buffer	(	CommBuf &	recv_buffer,
		GhostCommunication const &	ghost_comm,
		BoxGeometry const &	box_geo,
		unsigned int	data_parts
	)

static

Definition at line 310 of file ghosts.cpp.

References GHOSTTRANS_BONDS, GHOSTTRANS_PARTNUM, LOAD, MOVE, prepare_ghost_cell(), serialize_and_reduce(), and stream.

Referenced by ghost_communicator().

◆ serialize_and_reduce()

template<class Archive >

static void serialize_and_reduce	(	Archive &	ar,
		Particle &	p,
		unsigned int	data_parts,
		ReductionPolicy	policy,
		SerializationDirection	direction,
		BoxGeometry const &	box_geo,
		Utils::Vector3d const *	ghost_shift
	)

static

Serialize particle data, possibly with reduction.

The reduction can take place during the save stage, e.g. to apply a ghost shift to the particle position, or during the load stage, e.g. to transfer momentum between particles in two local cells.

Definition at line 127 of file ghosts.cpp.

References Particle::dipm(), Particle::ext_force(), Particle::ext_torque(), Particle::fixed(), BoxGeometry::fold_position(), Particle::force(), Particle::gamma(), Particle::gamma_rot(), GHOSTTRANS_FORCE, GHOSTTRANS_MOMENTUM, GHOSTTRANS_POSITION, GHOSTTRANS_PROPRTS, GHOSTTRANS_RATTLE, Particle::id(), Particle::image_box(), LOAD, Particle::mass(), Particle::mol_id(), Particle::mu_E(), Particle::omega(), Particle::pos(), Particle::pos_last_time_step(), Particle::propagation(), Particle::q(), Particle::quat(), Particle::rattle_correction(), Particle::rinertia(), Particle::rotation(), SAVE, stream, Particle::swimming(), Particle::torque(), Particle::type(), UPDATE, Particle::v(), and Particle::vs_relative().

Referenced by calc_transmit_size(), cell_cell_transfer(), prepare_send_buffer(), and put_recv_buffer().

Classes

Macros

Enumerations

Functions

Detailed Description

Macro Definition Documentation

◆ REQ_GHOST_SEND

Enumeration Type Documentation

◆ ReductionPolicy

◆ SerializationDirection

Function Documentation

◆ add_forces_from_recv_buffer()

◆ add_rattle_correction_from_recv_buffer()

◆ calc_transmit_size() [1/2]

◆ calc_transmit_size() [2/2]

◆ cell_cell_transfer()

◆ ghost_communicator()

◆ is_poststorable()

◆ is_prefetchable()

◆ is_recv_op()

◆ is_send_op()

◆ prepare_ghost_cell()

◆ prepare_recv_buffer()

◆ prepare_send_buffer()

◆ put_recv_buffer()

◆ serialize_and_reduce()