Constant-pH Ensemble, for derivation see [35]. More...

#include <ConstantpHEnsemble.hpp>

Inheritance diagram for ReactionMethods::ConstantpHEnsemble:

Collaboration diagram for ReactionMethods::ConstantpHEnsemble:

Public Member Functions
	ConstantpHEnsemble (boost::mpi::communicator const &comm, int seed, double kT, double exclusion_range, double constant_pH, 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]

Public Attributes
double	m_constant_pH

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

Additional Inherited Members
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

Constant-pH Ensemble, for derivation see [35].

For the constant pH reactions you need to provide the deprotonation and afterwards the corresponding protonation reaction (in this order). If you want to deal with multiple reactions do it multiple times. Note that there is a difference in the usecase of the constant pH reactions and the above reaction ensemble. For the constant pH simulation directily the apparent equilibrium constant which carries a unit needs to be provided – this is equivalent to the gamma of the reaction ensemble above, where the dimensionless reaction constant needs to be provided. Again: For the constant-pH algorithm not the dimensionless reaction constant needs to be provided here, but the apparent reaction constant.

Definition at line 41 of file core/reaction_methods/ConstantpHEnsemble.hpp.

Constructor & Destructor Documentation

◆ ConstantpHEnsemble()

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

inline

Definition at line 43 of file core/reaction_methods/ConstantpHEnsemble.hpp.

Member Data Documentation

◆ m_constant_pH

double ReactionMethods::ConstantpHEnsemble::m_constant_pH

Definition at line 50 of file core/reaction_methods/ConstantpHEnsemble.hpp.

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

core/reaction_methods/ConstantpHEnsemble.hpp

Public Member Functions

Public Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ConstantpHEnsemble()

Member Data Documentation

◆ m_constant_pH