ReactionMethods Namespace Reference

Classes
class	ConstantpHEnsemble
	Constant-pH Ensemble, for derivation see [38]. More...
class	ReactionAlgorithm
	Base class for reaction ensemble methods. More...
class	ReactionEnsemble
	Reaction ensemble method. More...
struct	SingleReaction
class	WidomInsertion
	Widom insertion method. More...

Functions
double	ln_factorial_Ni0_divided_by_factorial_Ni0_plus_nu_i (int Ni0, int nu_i)
	Calculates the logaritm of factorial expression which occurs in the reaction ensemble acceptance probability.
double	calculate_factorial_expression (SingleReaction const &reaction, std::unordered_map< int, int > const &particle_numbers)
	Calculates the logarithm of whole product of factorial expressions which occur in the reaction ensemble acceptance probability.
double	calculate_factorial_expression_cpH (SingleReaction const &reaction, std::unordered_map< int, int > const &particle_numbers)
	Calculates the logarithm of factorial expression which occurs in the constant pH method with symmetric proposal probability.

Function Documentation

calculate_factorial_expression()

double ReactionMethods::calculate_factorial_expression	(	SingleReaction const &	reaction,
		std::unordered_map< int, int > const &	particle_numbers
	)

Calculates the logarithm of whole product of factorial expressions which occur in the reaction ensemble acceptance probability.

See [41].

Definition at line 49 of file utils.cpp.

References ln_factorial_Ni0_divided_by_factorial_Ni0_plus_nu_i(), ReactionMethods::SingleReaction::product_coefficients, ReactionMethods::SingleReaction::product_types, ReactionMethods::SingleReaction::reactant_coefficients, and ReactionMethods::SingleReaction::reactant_types.

calculate_factorial_expression_cpH()

double ReactionMethods::calculate_factorial_expression_cpH	(	SingleReaction const &	reaction,
		std::unordered_map< int, int > const &	particle_numbers
	)

Calculates the logarithm of factorial expression which occurs in the constant pH method with symmetric proposal probability.

See [29] for details. zeta = 1 (see [41]) since we only perform one reaction at one call of the function.

Definition at line 68 of file utils.cpp.

References ln_factorial_Ni0_divided_by_factorial_Ni0_plus_nu_i(), ReactionMethods::SingleReaction::product_coefficients, ReactionMethods::SingleReaction::product_types, ReactionMethods::SingleReaction::reactant_coefficients, and ReactionMethods::SingleReaction::reactant_types.

ln_factorial_Ni0_divided_by_factorial_Ni0_plus_nu_i()

double ReactionMethods::ln_factorial_Ni0_divided_by_factorial_Ni0_plus_nu_i	(	int	Ni0,
		int	nu_i
	)

Calculates the logaritm of factorial expression which occurs in the reaction ensemble acceptance probability.

Definition at line 29 of file utils.cpp.

Referenced by calculate_factorial_expression(), and calculate_factorial_expression_cpH().