#include "rattle.hpp"
#include "BoxGeometry.hpp"
#include "Particle.hpp"
#include "ParticleRange.hpp"
#include "bonded_interactions/bonded_interaction_data.hpp"
#include "bonded_interactions/rigid_bond.hpp"
#include "cell_system/CellStructure.hpp"
#include "communication.hpp"
#include "errorhandling.hpp"
#include <utils/Vector.hpp>
#include <utils/math/tensor_product.hpp>
#include <utils/matrix.hpp>
#include <boost/mpi/collectives/all_reduce.hpp>
#include <boost/range/algorithm.hpp>
#include <cmath>
#include <cstddef>
#include <functional>
#include <span>
#include <variant>
#include <vector>

Include dependency graph for rattle.cpp:

Functions
static void	check_convergence (int cnt, char const *const name)

void	save_old_position (const ParticleRange &particles, const ParticleRange &ghost_particles)
	copy current position

static void	init_correction_vector (const ParticleRange &particles, const ParticleRange &ghost_particles)
	reset correction vectors to zero

static bool	calculate_positional_correction (RigidBond const &ia_params, BoxGeometry const &box_geo, Particle &p1, Particle &p2, int bond_id, std::vector< Utils::Vector9d > &rigid_bond_virial)
	Calculate the positional correction for the particles.

template<typename Kernel >
static bool	compute_correction_vector (CellStructure &cs, BoxGeometry const &box_geo, BondedInteractionsMap const &bonded_ias, Kernel kernel)
	Compute the correction vectors using given kernel.

static void	apply_positional_correction (const ParticleRange &particles)
	Apply positional corrections.

void	correct_position_shake (CellStructure &cs, BoxGeometry const &box_geo, BondedInteractionsMap &bonded_ias)
	Propagate velocity and position while using SHAKE algorithm for bond constraint.

static bool	calculate_velocity_correction (RigidBond const &ia_params, BoxGeometry const &box_geo, Particle &p1, Particle &p2)
	Calculate the velocity correction for the particles.

static void	apply_velocity_correction (ParticleRange const &particles)
	Apply velocity corrections.

void	correct_velocity_shake (CellStructure &cs, BoxGeometry const &box_geo, BondedInteractionsMap const &bonded_ias)
	Correction of current velocities using RATTLE algorithm.

Variables
static constexpr auto	shake_max_iterations = 1000
	Maximal number of iterations before the RATTLE algorithm bails out.

Function Documentation

◆ apply_positional_correction()

static void apply_positional_correction ( const ParticleRange & particles )

static

Apply positional corrections.

Parameters

particles particle range

Definition at line 172 of file rattle.cpp.

References Particle::pos(), Particle::rattle_params(), and Particle::v().

Referenced by correct_position_shake().

◆ apply_velocity_correction()

static void apply_velocity_correction ( ParticleRange const & particles )

static

Apply velocity corrections.

Parameters

particles particle range

Definition at line 256 of file rattle.cpp.

References Particle::rattle_params(), and Particle::v().

Referenced by correct_velocity_shake().

◆ calculate_positional_correction()

static bool calculate_positional_correction	(	RigidBond const &	ia_params,
		BoxGeometry const &	box_geo,
		Particle &	p1,
		Particle &	p2,
		int	bond_id,
		std::vector< Utils::Vector9d > &	rigid_bond_virial
	)

static

Calculate the positional correction for the particles.

Parameters

ia_params	Parameters
box_geo	Box geometry.
p1	First particle.
p2	Second particle.
bond_id	Bonded interaction id of this specific bond.
rigid_bond_virial	Per-bond-type RATTLE constraint virial accumulator, indexed by `bond_id`.

Returns: True if there was a correction.

Definition at line 99 of file rattle.cpp.

References Utils::flatten(), BoxGeometry::get_mi_vector(), stream, and Utils::tensor_product().

Referenced by correct_position_shake().

◆ calculate_velocity_correction()

static bool calculate_velocity_correction	(	RigidBond const &	ia_params,
		BoxGeometry const &	box_geo,
		Particle &	p1,
		Particle &	p2
	)

static

Calculate the velocity correction for the particles.

Parameters

ia_params	Parameters
box_geo	Box geometry.
p1	First particle.
p2	Second particle.

Returns: True if there was a correction.

Definition at line 230 of file rattle.cpp.

References BoxGeometry::get_mi_vector(), and stream.

Referenced by correct_velocity_shake().

◆ check_convergence()

static void check_convergence	(	int	cnt,
		char const *const	name
	)

static

Definition at line 52 of file rattle.cpp.

References runtimeErrorMsg, shake_max_iterations, and stream.

Referenced by correct_position_shake(), and correct_velocity_shake().

◆ compute_correction_vector()

template<typename Kernel >

static bool compute_correction_vector	(	CellStructure &	cs,
		BoxGeometry const &	box_geo,
		BondedInteractionsMap const &	bonded_ias,
		Kernel	kernel
	)

static

Compute the correction vectors using given kernel.

Parameters

cs	cell structure
box_geo	Box geometry
bonded_ias	Bonded interactions
kernel	kernel function

Returns: True if correction is necessary

Definition at line 145 of file rattle.cpp.

References BondedInteractionsMap::at(), CellStructure::bond_loop(), and stream.

Referenced by correct_position_shake(), and correct_velocity_shake().

◆ correct_position_shake()

void correct_position_shake	(	CellStructure &	cs,
		BoxGeometry const &	box_geo,
		BondedInteractionsMap &	bonded_ias
	)

Propagate velocity and position while using SHAKE algorithm for bond constraint.

Accumulate the per-bond-type RATTLE constraint virial into bonded_ias.rigid_bond_virial.

Definition at line 179 of file rattle.cpp.

References apply_positional_correction(), Utils::Vector< T, N >::broadcast(), calculate_positional_correction(), check_convergence(), CellStructure::check_resort_required(), comm_cart, compute_correction_vector(), Cells::DATA_PART_MOMENTUM, Cells::DATA_PART_POSITION, Cells::DATA_PART_PROPERTIES, BondedInteractionsMap::get_next_key(), CellStructure::ghost_particles(), CellStructure::ghosts_reduce_rattle_correction(), CellStructure::ghosts_update(), init_correction_vector(), CellStructure::local_particles(), Cells::RESORT_LOCAL, Cells::RESORT_NONE, BondedInteractionsMap::rigid_bond_virial, CellStructure::set_resort_particles(), shake_max_iterations, stream, and CellStructure::update_ghosts_and_resort_particle().

Referenced by System::System::integrate().

◆ correct_velocity_shake()

void correct_velocity_shake	(	CellStructure &	cs,
		BoxGeometry const &	box_geo,
		BondedInteractionsMap const &	bonded_ias
	)

Correction of current velocities using RATTLE algorithm.

Definition at line 261 of file rattle.cpp.

References apply_velocity_correction(), calculate_velocity_correction(), check_convergence(), comm_cart, compute_correction_vector(), Cells::DATA_PART_MOMENTUM, Cells::DATA_PART_POSITION, CellStructure::ghost_particles(), CellStructure::ghosts_reduce_rattle_correction(), CellStructure::ghosts_update(), init_correction_vector(), CellStructure::local_particles(), shake_max_iterations, and stream.

Referenced by System::System::integrate().

◆ init_correction_vector()

static void init_correction_vector	(	const ParticleRange &	particles,
		const ParticleRange &	ghost_particles
	)

static

reset correction vectors to zero

Parameters

particles	particle range
ghost_particles	ghost particle range

Definition at line 79 of file rattle.cpp.

Referenced by correct_position_shake(), and correct_velocity_shake().

◆ save_old_position()

void save_old_position	(	const ParticleRange &	particles,
		const ParticleRange &	ghost_particles
	)

copy current position

Transfer the current particle positions from Particle::pos to Particle::pos_last_time_step.

Parameters

particles	particle range
ghost_particles	ghost particle range

Definition at line 65 of file rattle.cpp.

References stream.

Referenced by System::System::integrate().

Variable Documentation

◆ shake_max_iterations

constexpr auto shake_max_iterations = 1000

staticconstexpr

Maximal number of iterations before the RATTLE algorithm bails out.

Definition at line 50 of file rattle.cpp.

Referenced by check_convergence(), correct_position_shake(), and correct_velocity_shake().

Functions

Variables

Function Documentation

◆ apply_positional_correction()

◆ apply_velocity_correction()

◆ calculate_positional_correction()

◆ calculate_velocity_correction()

◆ check_convergence()

◆ compute_correction_vector()

◆ correct_position_shake()

◆ correct_velocity_shake()

◆ init_correction_vector()

◆ save_old_position()

Variable Documentation

◆ shake_max_iterations