Base class for reaction ensemble methods. More...

#include <ReactionAlgorithm.hpp>

Inheritance diagram for ReactionMethods::ReactionAlgorithm:

Collaboration diagram for ReactionMethods::ReactionAlgorithm:

Classes
struct	ParticleChanges

Public Member Functions
	ReactionAlgorithm (boost::mpi::communicator const &comm, int seed, double kT, double exclusion_range, std::unordered_map< int, double > const &exclusion_radius_per_type)

virtual	~ReactionAlgorithm ()=default

double	get_acceptance_rate_configurational_moves () const

auto	get_kT () const

auto	get_exclusion_range () const

auto	get_volume () const

void	set_volume (double new_volume)

void	update_volume ()
	Automatically sets the volume which is used by the reaction ensemble to the volume of a cuboid box.

void	set_exclusion_radius_per_type (std::unordered_map< int, double > const &map)

void	remove_constraint ()

void	set_cyl_constraint (double center_x, double center_y, double radius)

void	set_slab_constraint (double slab_start_z, double slab_end_z)

Utils::Vector2d	get_slab_constraint_parameters () const

void	setup_bookkeeping_of_empty_pids ()
	Cleans the list of empty pids and searches for empty pid in the system.

void	delete_particle (int p_id)
	Deletes the particle with the given p_id and stores the id if the deletion created a hole in the particle id range.

void	add_reaction (std::shared_ptr< SingleReaction > const &new_reaction)
	Adds a reaction to the reaction system.

void	delete_reaction (int reaction_id)

bool	is_reaction_under_way () const

auto const &	get_old_system_state () const

std::optional< double >	create_new_trial_state (int reaction_id)
	Carry out a reaction MC move and calculate the new potential energy.

double	make_reaction_mc_move_attempt (int reaction_id, double bf, double E_pot_old, double E_pot_new)
	Accept or reject a reaction MC move made by create_new_trial_state based on a probability acceptance `bf`.

bool	make_displacement_mc_move_attempt (int type, int n_particles)
	Attempt displacement MC moves for particles of a given type.

double	calculate_potential_energy () const
	Compute the system potential energy.

int	i_random (int maxint)
	draws a random integer from the uniform distribution in the range [0,maxint-1]

Public Attributes
std::vector< std::shared_ptr< SingleReaction > >	reactions

std::unordered_map< int, double >	charges_of_types

double	kT

double	exclusion_range
	Hard sphere radius.

std::unordered_map< int, double >	exclusion_radius_per_type

double	volume

int	non_interacting_type = 100

int	m_accepted_configurational_MC_moves = 0

int	m_tried_configurational_MC_moves = 0

bool	particle_inside_exclusion_range_touched = false

bool	neighbor_search_order_n = true

Protected Member Functions
void	restore_old_system_state ()
	Restore last valid system state.

void	clear_old_system_state ()
	Clear last valid system state.

auto &	make_new_system_state ()
	Open new handle for system state tracking.

void	displacement_mc_move (int type, int n_particles)
	Carry out displacement MC moves for particles of a given type.

void	make_reaction_attempt (::ReactionMethods::SingleReaction const &reaction, ParticleChanges &bookkeeping)
	Carry out a chemical reaction and save the old system state.

bool	all_reactant_particles_exist (SingleReaction const &current_reaction) const
	Checks whether all particles exist for the provided reaction.

Utils::Vector3d	get_random_position_in_box ()
	Writes a random position inside the central box into the provided array.

Protected Attributes
std::vector< int >	m_empty_p_ids_smaller_than_max_seen_particle

std::shared_ptr< ParticleChanges >	m_system_changes

Detailed Description

Base class for reaction ensemble methods.

Definition at line 48 of file core/reaction_methods/ReactionAlgorithm.hpp.

Constructor & Destructor Documentation

◆ ReactionAlgorithm()

ReactionMethods::ReactionAlgorithm::ReactionAlgorithm	(	boost::mpi::communicator const &	comm,
		int	seed,
		double	kT,
		double	exclusion_range,
		std::unordered_map< int, double > const &	exclusion_radius_per_type
	)

inline

Definition at line 53 of file core/reaction_methods/ReactionAlgorithm.hpp.

◆ ~ReactionAlgorithm()

virtual ReactionMethods::ReactionAlgorithm::~ReactionAlgorithm ( )

virtualdefault

Member Function Documentation

◆ add_reaction()

void ReactionMethods::ReactionAlgorithm::add_reaction ( std::shared_ptr< SingleReaction > const & new_reaction )

Adds a reaction to the reaction system.

Definition at line 65 of file core/reaction_methods/ReactionAlgorithm.cpp.

References init_type_map(), non_interacting_type, and reactions.

◆ all_reactant_particles_exist()

bool ReactionMethods::ReactionAlgorithm::all_reactant_particles_exist ( SingleReaction const & current_reaction ) const

protected

Checks whether all particles exist for the provided reaction.

Definition at line 137 of file core/reaction_methods/ReactionAlgorithm.cpp.

References number_of_particles_with_type(), ReactionMethods::SingleReaction::reactant_coefficients, and ReactionMethods::SingleReaction::reactant_types.

Referenced by ReactionMethods::WidomInsertion::calculate_particle_insertion_potential_energy(), and create_new_trial_state().

◆ calculate_potential_energy()

double ReactionMethods::ReactionAlgorithm::calculate_potential_energy ( ) const

Compute the system potential energy.

Definition at line 626 of file core/reaction_methods/ReactionAlgorithm.cpp.

References System::get_system().

Referenced by ReactionMethods::WidomInsertion::calculate_particle_insertion_potential_energy(), create_new_trial_state(), and make_displacement_mc_move_attempt().

◆ clear_old_system_state()

void ReactionMethods::ReactionAlgorithm::clear_old_system_state ( )

inlineprotected

Clear last valid system state.

Definition at line 166 of file core/reaction_methods/ReactionAlgorithm.hpp.

References is_reaction_under_way(), and m_system_changes.

Referenced by make_displacement_mc_move_attempt(), make_reaction_mc_move_attempt(), and restore_old_system_state().

◆ create_new_trial_state()

std::optional< double > ReactionMethods::ReactionAlgorithm::create_new_trial_state ( int reaction_id )

Carry out a reaction MC move and calculate the new potential energy.

Particles are selected without replacement. The previous state of the system is cached.

Returns: Potential energy of the system after the move.

Definition at line 253 of file core/reaction_methods/ReactionAlgorithm.cpp.

References all_reactant_particles_exist(), calculate_potential_energy(), make_new_system_state(), make_reaction_attempt(), particle_inside_exclusion_range_touched, and reactions.

◆ delete_particle()

void ReactionMethods::ReactionAlgorithm::delete_particle ( int p_id )

Deletes the particle with the given p_id and stores the id if the deletion created a hole in the particle id range.

This method is intended to only delete unbonded particles since bonds are coupled to ids. This is used to avoid the id range becoming excessively huge.

Definition at line 398 of file core/reaction_methods/ReactionAlgorithm.cpp.

References get_maximal_particle_id(), m_empty_p_ids_smaller_than_max_seen_particle, and remove_particle().

Referenced by make_reaction_mc_move_attempt(), and restore_old_system_state().

◆ delete_reaction()

void ReactionMethods::ReactionAlgorithm::delete_reaction ( int reaction_id )

inline

Definition at line 134 of file core/reaction_methods/ReactionAlgorithm.hpp.

References reactions.

◆ displacement_mc_move()

void ReactionMethods::ReactionAlgorithm::displacement_mc_move	(	int	type,
		int	n_particles
	)

protected

Carry out displacement MC moves for particles of a given type.

Particles are selected without replacement.

Parameters

type	Type of particles to move.
n_particles	Number of particles of that type to move.

Definition at line 516 of file core/reaction_methods/ReactionAlgorithm.cpp.

References Utils::contains(), get_random_p_id(), get_random_position_in_box(), i_random(), kT, make_new_system_state(), ReactionMethods::ReactionAlgorithm::ParticleChanges::moved, number_of_particles_with_type(), particle_inside_exclusion_range_touched, and set_particle_pos().

Referenced by make_displacement_mc_move_attempt().

◆ get_acceptance_rate_configurational_moves()

double ReactionMethods::ReactionAlgorithm::get_acceptance_rate_configurational_moves ( ) const

inline

Definition at line 88 of file core/reaction_methods/ReactionAlgorithm.hpp.

References m_accepted_configurational_MC_moves, and m_tried_configurational_MC_moves.

◆ get_exclusion_range()

auto ReactionMethods::ReactionAlgorithm::get_exclusion_range ( ) const

inline

Definition at line 94 of file core/reaction_methods/ReactionAlgorithm.hpp.

References exclusion_range.

◆ get_kT()

auto ReactionMethods::ReactionAlgorithm::get_kT ( ) const

inline

Definition at line 93 of file core/reaction_methods/ReactionAlgorithm.hpp.

References kT.

◆ get_old_system_state()

auto const & ReactionMethods::ReactionAlgorithm::get_old_system_state ( ) const

inline

Definition at line 155 of file core/reaction_methods/ReactionAlgorithm.hpp.

References is_reaction_under_way(), and m_system_changes.

Referenced by make_reaction_mc_move_attempt(), and restore_old_system_state().

◆ get_random_position_in_box()

Utils::Vector3d ReactionMethods::ReactionAlgorithm::get_random_position_in_box ( )

protected

Writes a random position inside the central box into the provided array.

Definition at line 457 of file core/reaction_methods/ReactionAlgorithm.cpp.

References System::System::box_geo, and System::get_system().

Referenced by displacement_mc_move().

◆ get_slab_constraint_parameters()

Utils::Vector2d ReactionMethods::ReactionAlgorithm::get_slab_constraint_parameters ( ) const

inline

Definition at line 124 of file core/reaction_methods/ReactionAlgorithm.hpp.

◆ get_volume()

auto ReactionMethods::ReactionAlgorithm::get_volume ( ) const

inline

Definition at line 95 of file core/reaction_methods/ReactionAlgorithm.hpp.

References volume.

◆ i_random()

int ReactionMethods::ReactionAlgorithm::i_random ( int maxint )

inline

draws a random integer from the uniform distribution in the range [0,maxint-1]

Parameters

maxint range.

Definition at line 228 of file core/reaction_methods/ReactionAlgorithm.hpp.

Referenced by displacement_mc_move(), and make_reaction_attempt().

◆ is_reaction_under_way()

bool ReactionMethods::ReactionAlgorithm::is_reaction_under_way ( ) const

inline

Definition at line 154 of file core/reaction_methods/ReactionAlgorithm.hpp.

References m_system_changes.

Referenced by clear_old_system_state(), get_old_system_state(), and make_new_system_state().

◆ make_displacement_mc_move_attempt()

bool ReactionMethods::ReactionAlgorithm::make_displacement_mc_move_attempt	(	int	type,
		int	n_particles
	)

Attempt displacement MC moves for particles of a given type.

Particles are selected without replacement.

Parameters

type	Type of particles to move.
n_particles	Number of particles of that type to move.

Returns: true if all moves were accepted.

Definition at line 552 of file core/reaction_methods/ReactionAlgorithm.cpp.

References calculate_potential_energy(), clear_old_system_state(), displacement_mc_move(), kT, m_accepted_configurational_MC_moves, m_tried_configurational_MC_moves, number_of_particles_with_type(), particle_inside_exclusion_range_touched, and restore_old_system_state().

◆ make_new_system_state()

auto & ReactionMethods::ReactionAlgorithm::make_new_system_state ( )

inlineprotected

Open new handle for system state tracking.

Definition at line 171 of file core/reaction_methods/ReactionAlgorithm.hpp.

References is_reaction_under_way(), and m_system_changes.

Referenced by ReactionMethods::WidomInsertion::calculate_particle_insertion_potential_energy(), create_new_trial_state(), and displacement_mc_move().

◆ make_reaction_attempt()

void ReactionMethods::ReactionAlgorithm::make_reaction_attempt	(	::ReactionMethods::SingleReaction const &	reaction,
		ParticleChanges &	bookkeeping
	)

protected

Carry out a chemical reaction and save the old system state.

Definition at line 151 of file core/reaction_methods/ReactionAlgorithm.cpp.

References ReactionMethods::ReactionAlgorithm::ParticleChanges::changed, charges_of_types, ReactionMethods::ReactionAlgorithm::ParticleChanges::created, get_random_p_id(), System::get_system(), ReactionMethods::ReactionAlgorithm::ParticleChanges::hidden, i_random(), number_of_particles_with_type(), System::System::on_particle_change(), System::System::on_particle_local_change(), on_particle_type_change(), ReactionMethods::SingleReaction::product_coefficients, ReactionMethods::SingleReaction::product_types, ReactionMethods::SingleReaction::reactant_coefficients, and ReactionMethods::SingleReaction::reactant_types.

Referenced by ReactionMethods::WidomInsertion::calculate_particle_insertion_potential_energy(), and create_new_trial_state().

◆ make_reaction_mc_move_attempt()

double ReactionMethods::ReactionAlgorithm::make_reaction_mc_move_attempt	(	int	reaction_id,
		double	bf,
		double	E_pot_old,
		double	E_pot_new
	)

Accept or reject a reaction MC move made by create_new_trial_state based on a probability acceptance bf.

The previous state of the system is either restored from the cache if the move is rejected, or cleared from the cache if the move is accepted.

Returns: Potential energy of the system after the move was accepted or rejected.

Definition at line 273 of file core/reaction_methods/ReactionAlgorithm.cpp.

References clear_old_system_state(), delete_particle(), get_old_system_state(), kT, reactions, and restore_old_system_state().

◆ remove_constraint()

void ReactionMethods::ReactionAlgorithm::remove_constraint ( )

inline

Definition at line 121 of file core/reaction_methods/ReactionAlgorithm.hpp.

◆ restore_old_system_state()

void ReactionMethods::ReactionAlgorithm::restore_old_system_state ( )

protected

Restore last valid system state.

This method tries to keep the cell system overhead to a minimum. Event callbacks are only called once after all particles are updated, except for particle deletion (the cell structure is still reinitialized after each deletion).

Definition at line 85 of file core/reaction_methods/ReactionAlgorithm.cpp.

References type_tracking::any_type, charges_of_types, clear_old_system_state(), delete_particle(), get_old_system_state(), System::get_system(), on_particle_type_change(), and Cells::RESORT_GLOBAL.

Referenced by ReactionMethods::WidomInsertion::calculate_particle_insertion_potential_energy(), make_displacement_mc_move_attempt(), and make_reaction_mc_move_attempt().

◆ set_cyl_constraint()

void ReactionMethods::ReactionAlgorithm::set_cyl_constraint	(	double	center_x,
		double	center_y,
		double	radius
	)

Definition at line 425 of file core/reaction_methods/ReactionAlgorithm.cpp.

References System::System::box_geo, and System::get_system().

◆ set_exclusion_radius_per_type()

void ReactionMethods::ReactionAlgorithm::set_exclusion_radius_per_type ( std::unordered_map< int, double > const & map )

inline

Definition at line 104 of file core/reaction_methods/ReactionAlgorithm.hpp.

References exclusion_radius_per_type, and exclusion_range.

◆ set_slab_constraint()

void ReactionMethods::ReactionAlgorithm::set_slab_constraint	(	double	slab_start_z,
		double	slab_end_z
	)

Definition at line 440 of file core/reaction_methods/ReactionAlgorithm.cpp.

References System::System::box_geo, and System::get_system().

◆ set_volume()

void ReactionMethods::ReactionAlgorithm::set_volume ( double new_volume )

inline

Definition at line 96 of file core/reaction_methods/ReactionAlgorithm.hpp.

References volume.

◆ setup_bookkeeping_of_empty_pids()

void ReactionMethods::ReactionAlgorithm::setup_bookkeeping_of_empty_pids ( )

Cleans the list of empty pids and searches for empty pid in the system.

Definition at line 611 of file core/reaction_methods/ReactionAlgorithm.cpp.

References get_particle_ids_parallel(), and m_empty_p_ids_smaller_than_max_seen_particle.

Referenced by ReactionMethods::WidomInsertion::calculate_particle_insertion_potential_energy().

◆ update_volume()

void ReactionMethods::ReactionAlgorithm::update_volume ( )

Automatically sets the volume which is used by the reaction ensemble to the volume of a cuboid box.

Definition at line 129 of file core/reaction_methods/ReactionAlgorithm.cpp.

References System::System::box_geo, System::get_system(), and volume.

Member Data Documentation

◆ charges_of_types

std::unordered_map<int, double> ReactionMethods::ReactionAlgorithm::charges_of_types

Definition at line 73 of file core/reaction_methods/ReactionAlgorithm.hpp.

Referenced by make_reaction_attempt(), and restore_old_system_state().

◆ exclusion_radius_per_type

std::unordered_map<int, double> ReactionMethods::ReactionAlgorithm::exclusion_radius_per_type

Definition at line 82 of file core/reaction_methods/ReactionAlgorithm.hpp.

Referenced by set_exclusion_radius_per_type().

◆ exclusion_range

double ReactionMethods::ReactionAlgorithm::exclusion_range

Hard sphere radius.

If particles are closer than this value, it is assumed that their interaction energy gets approximately infinite, therefore these configurations do not contribute to the partition function and ensemble averages.

Definition at line 81 of file core/reaction_methods/ReactionAlgorithm.hpp.

Referenced by get_exclusion_range(), and set_exclusion_radius_per_type().