Reaction ensemble method. More...

#include <ReactionEnsemble.hpp>

Inheritance diagram for ReactionMethods::ReactionEnsemble:

Collaboration diagram for ReactionMethods::ReactionEnsemble:

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

Public Member Functions inherited from 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)

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]

Additional Inherited Members
Public Attributes inherited from ReactionMethods::ReactionAlgorithm
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 inherited from ReactionMethods::ReactionAlgorithm
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 inherited from ReactionMethods::ReactionAlgorithm
std::vector< int >	m_empty_p_ids_smaller_than_max_seen_particle

std::shared_ptr< ParticleChanges >	m_system_changes

Detailed Description

Reaction ensemble method.

Works for the reaction ensemble at constant volume and temperature. For the reaction ensemble at constant pressure, additionally employ a barostat! NOTE: a chemical reaction consists of a forward and backward reaction. Here both reactions have to be defined separately. The extent of the reaction is here chosen to be +1. If the reaction trial move for a dissociation of HA is accepted then there is one more dissociated ion pair H+ and A-. Implementation of [40].

Definition at line 37 of file core/reaction_methods/ReactionEnsemble.hpp.

Constructor & Destructor Documentation

◆ ReactionEnsemble()

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

inline

Definition at line 39 of file core/reaction_methods/ReactionEnsemble.hpp.

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

core/reaction_methods/ReactionEnsemble.hpp

Public Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ReactionEnsemble()