Faunus::ReactionData Class Reference

General properties of reactionsEnd of class. More...

#include <molecule.h>

Public Types
enum	Direction : char { LEFT = 0, RIGHT = 1 }
using	StoichiometryMap = std::map< int, int >
	key = id; value = stoichiometic coeff.
using	AtomicAndMolecularPair = std::pair< const StoichiometryMap &, const StoichiometryMap & >
using	StoichiometryPair = StoichiometryMap::value_type
	first = id; second = stoichiometic coeff.
using	MapFilter = std::function< bool(const ReactionData::StoichiometryPair &)>

Public Member Functions
void	setDirection (Direction)
	Set directions of the process.
void	setRandomDirection (Random &random)
	Set random direction (left or right)
Direction	getDirection () const
	Get direction of the process.
void	reverseDirection ()
	Reverse direction of reaction.
AtomicAndMolecularPair	getProducts () const
	Pair with atomic and molecular products.
AtomicAndMolecularPair	getReactants () const
	Pair with atomic and molecular reactants.
double	freeEnergy () const
	Free energy of reaction in current direction (kT) More...
bool	containsAtomicSwap () const
	True if a swap move is detected, i.e. atom_a <-> atom_b.
const std::string &	getReactionString () const
	Reaction string.
std::pair< std::set< int >, std::set< int > >	participatingAtomsAndMolecules () const
	Atom and molecule id's affected. More...

Public Attributes
bool	only_neutral_molecules = false
	Only neutral molecules are involved in the reaction.

Static Public Attributes
static const MapFilter	is_implicit_group
static const MapFilter	not_implicit_group
static const MapFilter	not_implicit_atom
static const MapFilter	is_atomic_group
static const MapFilter	is_molecular_group

Friends
void	from_json (const json &, ReactionData &)
void	to_json (json &, const ReactionData &)

Detailed Description

General properties of reactionsEnd of class.

Placeholder for chemical reactions used in the RCMC move. A reaction has two sides, left and right, each contained one or more atomic / molecular reactants and products. The reaction is associated with an equilibrium constant, lnK or pK. If the direction is RIGHT, the right-hand side species are products and the left-hand side are reactants. Vice versa if the direction is LEFT. The direction can be changed with setDirection() which also handles sign changes of lnK and pK. The functions getProducts() and getReactants() returns a pair with atomic and molecular reactants/products, always reflecting the current direction.

Todo:

• [x] Enable canonic and reservoir_size
• [ ] Enable reservoir size to be given as molarity and number
• [ ] Merge products and reactant structures using signed stoichiometric numbers
• [x] reservoir_size should ideally be associated with an implicit molecule
• [ ] direction should be a member of ReactionData due to possible data races

Member Function Documentation

freeEnergy()

double Faunus::ReactionData::freeEnergy

(

)

const

Free energy of reaction in current direction (kT)

Returns

Reaction free energy in the current direction, i.e. products minus reactants (kT)

participatingAtomsAndMolecules()

std::pair< std::set< int >, std::set< int > > Faunus::ReactionData::participatingAtomsAndMolecules

(

)

const

Atom and molecule id's affected.

Returns

Pair of sets with id's for atoms and molecules participating in the reaction (i.e. reactants & products)

Member Data Documentation

is_atomic_group

const ReactionData::MapFilter Faunus::ReactionData::is_atomic_group

static

Initial value:

= [](const auto& pair) {
    return Faunus::molecules.at(pair.first).isAtomic();
}

is_implicit_group

const ReactionData::MapFilter Faunus::ReactionData::is_implicit_group

static

Initial value:

= [](const auto& pair) {
    return Faunus::molecules.at(pair.first).isImplicit();
}

is_molecular_group

const ReactionData::MapFilter Faunus::ReactionData::is_molecular_group

static

Initial value:

= [](const auto& pair) {
    return Faunus::molecules.at(pair.first).isMolecular();
}

not_implicit_atom

const ReactionData::MapFilter Faunus::ReactionData::not_implicit_atom

static

Initial value:

= [](const auto& pair) {
    return !Faunus::atoms.at(pair.first).implicit;
}

not_implicit_group

const ReactionData::MapFilter Faunus::ReactionData::not_implicit_group

static

Initial value:

= [](const auto& pair) {
    return !Faunus::molecules.at(pair.first).isImplicit();
}

---

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

• src/molecule.h
• src/molecule.cpp