ghosts.cpp File Reference

Ghost particles and particle exchange. More...

#include "ghosts.hpp"
#include "BoxGeometry.hpp"
#include "Particle.hpp"
#include "system/System.hpp"
#include <utils/Span.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 <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 57 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 106 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 114 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 362 of file ghosts.cpp.

References Utils::make_span(), and GhostCommunication::part_lists.

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 348 of file ghosts.cpp.

References Utils::make_span(), and GhostCommunication::part_lists.

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 227 of file ghosts.cpp.

References MOVE, SAVE, serialize_and_reduce(), and SerializationSizeCalculator::size().

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 236 of file ghosts.cpp.

References calc_transmit_size(), GHOSTTRANS_PARTNUM, GhostCommunication::part_lists, and sum.

cell_cell_transfer()

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

static

Definition at line 375 of file ghosts.cpp.

References calc_transmit_size(), GHOSTTRANS_BONDS, GHOSTTRANS_PARTNUM, LOAD, Utils::make_span(), GhostCommunication::part_lists, prepare_ghost_cell(), CommBuf::resize(), SAVE, serialize_and_reduce(), GhostCommunication::shift, 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 440 of file ghosts.cpp.

References add_forces_from_recv_buffer(), add_rattle_correction_from_recv_buffer(), CommBuf::bonds(), calc_transmit_size(), cell_cell_transfer(), GhostCommunicator::communications, CommBuf::data(), 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(), GhostCommunicator::mpi_comm, GhostCommunication::node, node, prepare_recv_buffer(), prepare_send_buffer(), put_recv_buffer(), REQ_GHOST_SEND, CommBuf::size(), this_node, and GhostCommunication::type.

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 432 of file ghosts.cpp.

References GHOST_JOBMASK, GHOST_PSTSTORE, is_recv_op(), GhostCommunication::node, node, this_node, and GhostCommunication::type.

is_prefetchable()

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

static

Definition at line 424 of file ghosts.cpp.

References GHOST_JOBMASK, GHOST_PREFETCH, is_send_op(), GhostCommunication::node, node, this_node, and GhostCommunication::type.

is_recv_op()

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

static

Definition at line 418 of file ghosts.cpp.

References GHOST_BCST, GHOST_RDCE, GHOST_RECV, node, 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 413 of file ghosts.cpp.

References GHOST_BCST, GHOST_RDCE, GHOST_SEND, node, 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 287 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 297 of file ghosts.cpp.

References CommBuf::bonds(), calc_transmit_size(), and CommBuf::resize().

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 249 of file ghosts.cpp.

References CommBuf::bonds(), calc_transmit_size(), GHOSTTRANS_BONDS, GHOSTTRANS_PARTNUM, Utils::make_span(), MOVE, GhostCommunication::part_lists, CommBuf::resize(), SAVE, serialize_and_reduce(), GhostCommunication::shift, and CommBuf::size().

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 307 of file ghosts.cpp.

References CommBuf::bonds(), GHOSTTRANS_BONDS, GHOSTTRANS_PARTNUM, LOAD, Utils::make_span(), MOVE, GhostCommunication::part_lists, prepare_ghost_cell(), serialize_and_reduce(), and CommBuf::size().

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 124 of file ghosts.cpp.

References Particle::dipm(), Particle::ext_force(), Particle::ext_torque(), Particle::fixed(), BoxGeometry::fold_position(), force, 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(), pos, Particle::pos_last_time_step(), Particle::propagation(), Particle::q(), Particle::quat(), Particle::rattle_correction(), Particle::rinertia(), Particle::rotation(), SAVE, Particle::swimming(), torque, 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().