Reaction type for advancing a KMCDualState for Kinetic Monte Carlo. More...

#include <CD_KMCDualStateReaction.H>

Public Member Functions
	KMCDualStateReaction ()=default
	Default constructor.

	KMCDualStateReaction (const KMCDualStateReaction &)=default
	Copy constructor.

	KMCDualStateReaction (const std::list< size_t > &a_lhsReactives, const std::list< size_t > &a_rhsReactives, const std::list< size_t > &a_rhsNonReactives) noexcept
	Full constructor.

virtual	~KMCDualStateReaction ()
	Destructor.

Real &	rate () const noexcept
	Get modifiable reaction rate.

Real	propensity (const State &a_state) const noexcept
	Compute the propensity function for this reaction type.

T	computeCriticalNumberOfReactions (const State &a_state) const noexcept
	Compute the number of times the reaction can fire before exhausting one of the reactants.

const std::list< size_t > &	getReactants () const noexcept
	Get the reactants in the reaction.

std::list< size_t >	getReactiveProducts () const noexcept
	Get the products from the reaction.

std::list< size_t >	getNonReactiveProducts () const noexcept
	Get the non-reactive products from the reaction.

T	getStateChange (const size_t a_reactant) const noexcept
	Get the state change due to a change in the input reactant.

void	advanceState (State &a_state, const T &a_numReactions) const noexcept
	Advance the incoming state with the number of reactions.

Static Public Member Functions
static T	population (const size_t &a_reactant, const State &a_state) noexcept
	Get the population of the reactant in the input state.

Protected Member Functions
void	computeStateChanges () noexcept
	Compute state change vectors from the reactant/product lists.

void	sanityCheck (const State &a_state) const noexcept
	Debugging function which ensures that the class data holders do not reach out of the incoming state.

Protected Attributes
Real	m_rate
	Reaction rate.

Real	m_propensityFactor
	Factor for the case where two or more particles of the same species react.

std::list< size_t >	m_lhsReactives
	Reactive species (left-hand side).

std::list< size_t >	m_rhsReactives
	Product species (right-hand side reactive).

std::list< size_t >	m_rhsNonReactives
	Non-reactive product species.

std::map< size_t, T >	m_reactiveStateChange
	State change for reactants/products.

std::vector< T >	m_reactiveStateChangeDense
	Dense form of m_reactiveStateChange, indexed by reactive species.

std::vector< std::pair< size_t, size_t > >	m_lhsOrders
	Reactants of the left-hand side, compacted to (species, order) pairs.

std::map< size_t, T >	m_nonReactiveStateChange
	State change for non-reactive products.

Detailed Description

template<typename State = KMCDualState<long long>, typename T = long long>
class KMCDualStateReaction< State, T >

Reaction type for advancing a KMCDualState for Kinetic Monte Carlo.

Note: T is the integer type used for the state.

Constructor & Destructor Documentation

◆ KMCDualStateReaction()

template<typename State , typename T >

KMCDualStateReaction< State, T >::KMCDualStateReaction	(	const std::list< size_t > &	a_lhsReactives,
		const std::list< size_t > &	a_rhsReactives,
		const std::list< size_t > &	a_rhsNonReactives
	)

inlinenoexcept

Full constructor.

Parameters

[in]	a_lhsReactives	Reactive species on the left-hand side of the reaction (i.e., the reactants).
[in]	a_rhsReactives	Reactive species on the right-hand side of the reaction (i.e., the products).
[in]	a_rhsNonReactives	Non-reactive species on the right-hand side of the reaction (i.e., piggybacked products).

Member Function Documentation

◆ advanceState()

template<typename State , typename T >

void KMCDualStateReaction< State, T >::advanceState	(	State &	a_state,
		const T &	a_numReactions
	)		const

inlinenoexcept

Advance the incoming state with the number of reactions.

Parameters

[in,out]	a_state	State vector.
[in]	a_numReactions	Number of reactions.

◆ computeCriticalNumberOfReactions()

template<typename State , typename T >

T KMCDualStateReaction< State, T >::computeCriticalNumberOfReactions ( const State & a_state ) const

inlinenoexcept

Compute the number of times the reaction can fire before exhausting one of the reactants.

Parameters

[in] a_state State vector.

Returns: Critical number of reactions.

◆ getNonReactiveProducts()

template<typename State , typename T >

std::list< size_t > KMCDualStateReaction< State, T >::getNonReactiveProducts ( ) const

inlinenoexcept

Get the non-reactive products from the reaction.

Returns: m_rhsNonReactives

◆ getReactants()

template<typename State , typename T >

const std::list< size_t > & KMCDualStateReaction< State, T >::getReactants ( ) const

inlinenoexcept

Get the reactants in the reaction.

Returned by reference because KMCSolver walks this list once per reaction per grid cell when it assembles the reactant set for the time step calculation; returning by value deep-copied the list, and with it one heap allocation per element, on every one of those walks.

Returns: m_lhsReactives

◆ getReactiveProducts()

template<typename State , typename T >

std::list< size_t > KMCDualStateReaction< State, T >::getReactiveProducts ( ) const

inlinenoexcept

Get the products from the reaction.

Returns: m_rhsReactives

◆ getStateChange()

template<typename State , typename T >

T KMCDualStateReaction< State, T >::getStateChange ( const size_t a_reactant ) const

inlinenoexcept

Get the state change due to a change in the input reactant.

Parameters

[in] a_reactant Reactive species.

Returns: State change for the reactant.

◆ population()

template<typename State , typename T >

T KMCDualStateReaction< State, T >::population	(	const size_t &	a_reactant,
		const State &	a_state
	)

inlinestaticnoexcept

Get the population of the reactant in the input state.

Parameters

[in]	a_reactant	Reactive species.
[in]	a_state	State vector.

Returns: Population of the reactant.

◆ propensity()

template<typename State , typename T >

Real KMCDualStateReaction< State, T >::propensity ( const State & a_state ) const

inlinenoexcept

Compute the propensity function for this reaction type.

Parameters

[in] a_state State vector.

Returns: Reaction propensity.

Note: User should set the rate before calling this routine.

◆ rate()

template<typename State , typename T >

Real & KMCDualStateReaction< State, T >::rate ( ) const

inlinenoexcept

Get modifiable reaction rate.

Returns: m_rate

◆ sanityCheck()

template<typename State , typename T >

void KMCDualStateReaction< State, T >::sanityCheck ( const State & a_state ) const

inlineprotectednoexcept

Debugging function which ensures that the class data holders do not reach out of the incoming state.

This is necessary because PlasmaReaction does not have compile-time size restrictions on the incoming state. The internals of this method uses Chombo assertions so the compiler should be able to take this function out of the executable if compiling with the correct flags.

Parameters

[in] a_state State vector.

Member Data Documentation

◆ m_lhsOrders

template<typename State = KMCDualState<long long>, typename T = long long>

std::vector<std::pair<size_t, size_t> > KMCDualStateReaction< State, T >::m_lhsOrders

protected

Reactants of the left-hand side, compacted to (species, order) pairs.

Built once in computeStateChanges() from the same reactant tally that fixes m_propensityFactor. propensity() uses it to form the falling factorial directly from the incoming state; without it the reaction has to copy the whole state vector on every call so that it can decrement its own copy while multiplying.

◆ m_propensityFactor

template<typename State = KMCDualState<long long>, typename T = long long>

Real KMCDualStateReaction< State, T >::m_propensityFactor

protected

Factor for the case where two or more particles of the same species react.

For reactions X + X -> null the propensity is k * X * (X-1)/2 because there are X * (X-1)/2 unique pairs of particles in the cell.

◆ m_reactiveStateChangeDense

template<typename State = KMCDualState<long long>, typename T = long long>

std::vector<T> KMCDualStateReaction< State, T >::m_reactiveStateChangeDense

protected

Dense form of m_reactiveStateChange, indexed by reactive species.

Built once in computeStateChanges() and holding the same values as m_reactiveStateChange, with zero for species the reaction does not touch. It exists because getStateChange() sits in the innermost loop of KMCSolver::computeDt and KMCSolver::getNonCriticalTimeStep, which run once per reactant per reaction per grid cell. Serving those from the map cost two red-black-tree walks (find followed by at) per lookup. Species indices at or beyond the vector's length are not involved in the reaction and their state change is zero.

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

Source/KineticMonteCarlo/CD_KMCDualStateReaction.H
Source/KineticMonteCarlo/CD_KMCDualStateReactionImplem.H

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ KMCDualStateReaction()

Member Function Documentation

◆ advanceState()

◆ computeCriticalNumberOfReactions()

◆ getNonReactiveProducts()

◆ getReactants()

◆ getReactiveProducts()

◆ getStateChange()

◆ population()

◆ propensity()

◆ rate()

◆ sanityCheck()

Member Data Documentation

◆ m_lhsOrders

◆ m_propensityFactor

◆ m_reactiveStateChangeDense