G4DNAMolecularReactionData Class Reference

#include <G4DNAMolecularReactionTable.hh>

Public Types
using	Reactant = const G4MolecularConfiguration
using	ReactantPair = std::pair<Reactant*, Reactant*>
using	ReactionProducts = std::vector<Reactant*>
using	RateParam = std::function<double (double)>

Public Member Functions
	G4DNAMolecularReactionData (G4double reactionRate, const G4MolecularConfiguration *reactive1, const G4MolecularConfiguration *reactive2)
	G4DNAMolecularReactionData (G4double reactionRate, const G4String &reactive1, const G4String &reactive2)
	~G4DNAMolecularReactionData ()
int	GetReactionID () const
void	SetReactionID (int ID)
ReactantPair	GetReactants ()
Reactant *	GetReactant1 () const
Reactant *	GetReactant2 () const
void	SetObservedReactionRateConstant (G4double rate)
G4double	GetObservedReactionRateConstant () const
G4double	GetActivationRateConstant () const
G4double	GetDiffusionRateConstant () const
void	SetReactionRadius (G4double radius)
G4double	GetReactionRadius () const
void	SetEffectiveReactionRadius (G4double radius)
G4double	GetEffectiveReactionRadius () const
G4double	GetOnsagerRadius () const
void	SetProbability (G4double prob)
G4double	GetProbability () const
void	SetReactionType (G4int type)
G4int	GetReactionType () const
void	SetReactant1 (Reactant *reactive)
void	SetReactant2 (Reactant *reactive)
void	SetReactants (Reactant *reactive1, Reactant *reactive2)
void	AddProduct (Reactant *molecule)
void	SetReactant1 (const G4String &reactive)
void	SetReactant2 (const G4String &reactive)
void	SetReactants (const G4String &reactive1, const G4String &reactive2)
void	AddProduct (const G4String &molecule)
G4int	GetNbProducts () const
Reactant *	GetProduct (G4int i) const
const ReactionProducts *	GetProducts () const
void	RemoveProducts ()
void	SetPolynomialParameterization (const std::vector< double > &P)
void	SetArrehniusParameterization (double A0, double E_R)
void	SetScaledParameterization (double temperature_K, double rateCste)
void	ScaleForNewTemperature (double temp_K)
void	ComputeEffectiveRadius ()

Static Public Member Functions
static double	PolynomialParam (double temp_K, std::vector< double > P)
static double	ArrehniusParam (double temp_K, std::vector< double > P)
static double	ScaledParameterization (double temp_K, double temp_init, double rateCste_init)

Protected Member Functions
	G4DNAMolecularReactionData ()

Protected Attributes
Reactant *	fpReactant1
Reactant *	fpReactant2
G4double	fObservedReactionRate
G4double	fActivationRate
G4double	fDiffusionRate
G4double	fOnsagerRadius
G4double	fReactionRadius
G4double	fEffectiveReactionRadius
G4double	fProbability
G4int	fType
ReactionProducts	fProducts
RateParam	fRateParam
int	fReactionID

Detailed Description

G4DNAMolecularReactionData contains the information relative to a given reaction (eg : °OH + °OH -> H2O2)

Definition at line 65 of file G4DNAMolecularReactionTable.hh.

Member Typedef Documentation

RateParam

using G4DNAMolecularReactionData::RateParam = std::function<double (double)>

Definition at line 130 of file G4DNAMolecularReactionTable.hh.

Reactant

using G4DNAMolecularReactionData::Reactant = const G4MolecularConfiguration

Definition at line 79 of file G4DNAMolecularReactionTable.hh.

ReactantPair

using G4DNAMolecularReactionData::ReactantPair = std::pair<Reactant*, Reactant*>

Definition at line 80 of file G4DNAMolecularReactionTable.hh.

ReactionProducts

using G4DNAMolecularReactionData::ReactionProducts = std::vector<Reactant*>

Definition at line 81 of file G4DNAMolecularReactionTable.hh.

Constructor & Destructor Documentation

G4DNAMolecularReactionData() [1/3]

G4DNAMolecularReactionData::G4DNAMolecularReactionData	(	G4double	reactionRate,
		const G4MolecularConfiguration *	reactive1,
		const G4MolecularConfiguration *	reactive2 )

G4DNAMolecularReactionData() [2/3]

G4DNAMolecularReactionData::G4DNAMolecularReactionData	(	G4double	reactionRate,
		const G4String &	reactive1,
		const G4String &	reactive2 )

Definition at line 89 of file G4DNAMolecularReactionTable.cc.

    : fpReactant1(nullptr)
    , fpReactant2(nullptr)
    , fObservedReactionRate(reactionRate)
    , fActivationRate(0.)
    , fDiffusionRate(0.)
    , fOnsagerRadius(0.)
    , fReactionRadius(0.)
    , fEffectiveReactionRadius(0.)
    , fProbability(0.)
    , fType(0)
    , fReactionID(0)
{
    SetReactant1(reactant1);
    SetReactant2(reactant2);
    ComputeEffectiveRadius();
}

~G4DNAMolecularReactionData()

G4DNAMolecularReactionData::~G4DNAMolecularReactionData

(

)

Definition at line 109 of file G4DNAMolecularReactionTable.cc.

{
     fProducts.clear();
}

G4DNAMolecularReactionData() [3/3]

G4DNAMolecularReactionData::G4DNAMolecularReactionData ( )

protected

Definition at line 56 of file G4DNAMolecularReactionTable.cc.

    : fpReactant1(nullptr)
    , fpReactant2(nullptr)
    , fObservedReactionRate(0.)
    , fActivationRate(0.)
    , fDiffusionRate(0.)
    , fOnsagerRadius(0.)
    , fReactionRadius(0.)
    , fEffectiveReactionRadius(0.)
    , fProbability(0.)
    , fType(0)
    , fReactionID(0)
{
}

Member Function Documentation

AddProduct() [1/2]

void G4DNAMolecularReactionData::AddProduct

(

const G4String &

molecule

)

Definition at line 315 of file G4DNAMolecularReactionTable.cc.

{
    fProducts.push_back(G4MoleculeTable::Instance()->GetConfiguration(molecule));
}

AddProduct() [2/2]

void G4DNAMolecularReactionData::AddProduct

(

Reactant *

molecule

)

Definition at line 164 of file G4DNAMolecularReactionTable.cc.

{
    fProducts.push_back(pMolecule);
}

Referenced by G4EmDNAChemistry::ConstructReactionTable(), G4EmDNAChemistry_option1::ConstructReactionTable(), G4EmDNAChemistry_option2::ConstructReactionTable(), and G4EmDNAChemistry_option3::ConstructReactionTable().

ArrehniusParam()

double G4DNAMolecularReactionData::ArrehniusParam ( double temp_K, std::vector< double > P )

static

Definition at line 330 of file G4DNAMolecularReactionTable.cc.

{
    return P[0] * G4Exp(P[1] / temp_K)*
        (1e-3 * CLHEP::m3 / (CLHEP::mole * CLHEP::s));
}

Referenced by SetArrehniusParameterization().

ComputeEffectiveRadius()

void G4DNAMolecularReactionData::ComputeEffectiveRadius

(

)

Definition at line 114 of file G4DNAMolecularReactionTable.cc.

{
    G4double sumDiffCoeff = 0.;
 
    if (fpReactant1 == fpReactant2)
    {
        sumDiffCoeff = fpReactant1->GetDiffusionCoefficient();
        fEffectiveReactionRadius = fObservedReactionRate / (4. * CLHEP::pi * sumDiffCoeff * CLHEP::Avogadro);
    }
    else
    {
        sumDiffCoeff = fpReactant1->GetDiffusionCoefficient()
                     + fpReactant2->GetDiffusionCoefficient();
        fEffectiveReactionRadius = fObservedReactionRate / (4. * CLHEP::pi * sumDiffCoeff * CLHEP::Avogadro);
    }
 
    fReactionID = 0;
    fReactionRadius = fEffectiveReactionRadius;
    fOnsagerRadius = (fpReactant1->GetCharge() * fpReactant2->GetCharge())/(4*pi*epsilon0*k_Boltzmann) / (293.15 * 80.1) ;
    fProbability = 1;
 
}

Referenced by G4DNAMolecularReactionData().

GetActivationRateConstant()

G4double G4DNAMolecularReactionData::GetActivationRateConstant

(

)

const

Definition at line 229 of file G4DNAMolecularReactionTable.cc.

{
    return fActivationRate;
}

GetDiffusionRateConstant()

G4double G4DNAMolecularReactionData::GetDiffusionRateConstant

(

)

const

Definition at line 234 of file G4DNAMolecularReactionTable.cc.

{
    return fDiffusionRate;
}

GetEffectiveReactionRadius()

G4double G4DNAMolecularReactionData::GetEffectiveReactionRadius

(

)

const

Definition at line 255 of file G4DNAMolecularReactionTable.cc.

{
    return fEffectiveReactionRadius;
}

Referenced by G4DiffusionControlledReactionModel::GetReactionRadius(), G4DNASmoluchowskiReactionModel::GetReactionRadius(), and G4DNAGillespieDirectMethod::PropensityFunction().

GetNbProducts()

G4int G4DNAMolecularReactionData::GetNbProducts

(

)

const

Definition at line 169 of file G4DNAMolecularReactionTable.cc.

{
    return (G4int)fProducts.size();
}

Referenced by G4DNAMakeReaction::MakeReaction(), G4DNAMolecularReaction::MakeReaction(), G4DNAMolecularReactionTable::PrintTable(), G4ChemEquilibrium::SetEquilibrium(), and G4DNAUpdateSystemModel::UpdateSystem().

GetObservedReactionRateConstant()

G4double G4DNAMolecularReactionData::GetObservedReactionRateConstant

(

)

const

Definition at line 224 of file G4DNAMolecularReactionTable.cc.

{
    return fObservedReactionRate;
}

Referenced by G4DiffusionControlledReactionModel::GetTimeToEncounter(), G4DNAMolecularReactionTable::PrintTable(), and G4DNAGillespieDirectMethod::PropensityFunction().

GetOnsagerRadius()

G4double G4DNAMolecularReactionData::GetOnsagerRadius

(

)

const

Definition at line 260 of file G4DNAMolecularReactionTable.cc.

{
    return fOnsagerRadius;
}

GetProbability()

G4double G4DNAMolecularReactionData::GetProbability

(

)

const

Definition at line 265 of file G4DNAMolecularReactionTable.cc.

{
    return fProbability;
}

GetProduct()

G4DNAMolecularReactionData::Reactant * G4DNAMolecularReactionData::GetProduct

(

G4int

i

)

const

Definition at line 174 of file G4DNAMolecularReactionTable.cc.

{
    return fProducts[i];
}

Referenced by G4DNAMolecularReactionTable::PrintTable(), G4ChemEquilibrium::SetEquilibrium(), and G4DNAUpdateSystemModel::UpdateSystem().

GetProducts()

const G4DNAMolecularReactionData::ReactionProducts * G4DNAMolecularReactionData::GetProducts

(

)

const

Definition at line 179 of file G4DNAMolecularReactionTable.cc.

{
    return &fProducts;
}

GetReactant1()

G4DNAMolecularReactionData::Reactant * G4DNAMolecularReactionData::GetReactant1

(

)

const

Definition at line 209 of file G4DNAMolecularReactionTable.cc.

{
    return fpReactant1;
}

Referenced by G4DNAGillespieDirectMethod::PropensityFunction(), G4ChemEquilibrium::SetEquilibrium(), G4DNAMolecularReactionTable::SetReaction(), G4DNAScavengerProcess::SetReaction(), and G4DNAUpdateSystemModel::UpdateSystem().

GetReactant2()

G4DNAMolecularReactionData::Reactant * G4DNAMolecularReactionData::GetReactant2

(

)

const

Definition at line 214 of file G4DNAMolecularReactionTable.cc.

{
    return fpReactant2;
}

Referenced by G4DNAGillespieDirectMethod::PropensityFunction(), G4ChemEquilibrium::SetEquilibrium(), G4DNAMolecularReactionTable::SetReaction(), G4DNAScavengerProcess::SetReaction(), and G4DNAUpdateSystemModel::UpdateSystem().

GetReactants()

G4DNAMolecularReactionData::ReactantPair G4DNAMolecularReactionData::GetReactants

(

)

Definition at line 204 of file G4DNAMolecularReactionTable.cc.

{
    return std::make_pair(fpReactant1, fpReactant2);
}

GetReactionID()

int G4DNAMolecularReactionData::GetReactionID

(

)

const

Definition at line 137 of file G4DNAMolecularReactionTable.cc.

{
    return fReactionID;
}

GetReactionRadius()

G4double G4DNAMolecularReactionData::GetReactionRadius

(

)

const

Definition at line 245 of file G4DNAMolecularReactionTable.cc.

{
    return fReactionRadius;
}

GetReactionType()

G4int G4DNAMolecularReactionData::GetReactionType

(

)

const

Definition at line 310 of file G4DNAMolecularReactionTable.cc.

{
    return fType;
}

Referenced by G4DNAIRT::GetIndependentReactionTime(), and G4ChemEquilibrium::SetEquilibrium().

PolynomialParam()

double G4DNAMolecularReactionData::PolynomialParam ( double temp_K, std::vector< double > P )

static

Definition at line 320 of file G4DNAMolecularReactionTable.cc.

{
    double inv_temp = 1. / temp_K;
 
    return pow(10,
               P[0] + P[1] * inv_temp + P[2] * pow(inv_temp, 2)
               + P[3] * pow(inv_temp, 3) + P[4] * pow(inv_temp, 4))
        * (1e-3 * CLHEP::m3 / (CLHEP::mole * CLHEP::s));
}

Referenced by SetPolynomialParameterization().

RemoveProducts()

void G4DNAMolecularReactionData::RemoveProducts

(

)

Definition at line 184 of file G4DNAMolecularReactionTable.cc.

{
    fProducts.clear();
}

ScaledParameterization()

double G4DNAMolecularReactionData::ScaledParameterization ( double temp_K, double temp_init, double rateCste_init )

static

Definition at line 336 of file G4DNAMolecularReactionTable.cc.

{
    double D0 = G4MolecularConfiguration::DiffCoeffWater(temp_init);
    double Df = G4MolecularConfiguration::DiffCoeffWater(temp_K);
    return Df * rateCste_init / D0;
}

Referenced by SetScaledParameterization().

ScaleForNewTemperature()

void G4DNAMolecularReactionData::ScaleForNewTemperature

(

double

temp_K

)

Definition at line 809 of file G4DNAMolecularReactionTable.cc.

{
    if (fRateParam)
    {
        SetObservedReactionRateConstant(fRateParam(temp_K));
    }
}

Referenced by G4DNAMolecularReactionTable::ScaleReactionRateForNewTemperature().

SetArrehniusParameterization()

void G4DNAMolecularReactionData::SetArrehniusParameterization	(	double	A0,
		double	E_R )

Definition at line 779 of file G4DNAMolecularReactionTable.cc.

{
    std::vector<double> P = { A0, E_R };
    fRateParam = std::bind(ArrehniusParam, std::placeholders::_1, P);
}

SetEffectiveReactionRadius()

void G4DNAMolecularReactionData::SetEffectiveReactionRadius

(

G4double

radius

)

Definition at line 250 of file G4DNAMolecularReactionTable.cc.

{
    fEffectiveReactionRadius = radius;
}

Referenced by G4EmDNAChemistry_option2::ConstructReactionTable().

SetObservedReactionRateConstant()

void G4DNAMolecularReactionData::SetObservedReactionRateConstant

(

G4double

rate

)

Definition at line 219 of file G4DNAMolecularReactionTable.cc.

{
    fObservedReactionRate = rate;
}

Referenced by ScaleForNewTemperature().

SetPolynomialParameterization()

void G4DNAMolecularReactionData::SetPolynomialParameterization

(

const std::vector< double > &

P

)

Definition at line 772 of file G4DNAMolecularReactionTable.cc.

{
    fRateParam = std::bind(PolynomialParam, std::placeholders::_1, P);
}

SetProbability()

void G4DNAMolecularReactionData::SetProbability

(

G4double

prob

)

Definition at line 270 of file G4DNAMolecularReactionTable.cc.

{
    fProbability = prob;
}

SetReactant1() [1/2]

void G4DNAMolecularReactionData::SetReactant1

(

const G4String &

reactive

)

Definition at line 189 of file G4DNAMolecularReactionTable.cc.

{
    fpReactant1 = G4MoleculeTable::Instance()->GetConfiguration(reactive);
}

SetReactant1() [2/2]

void G4DNAMolecularReactionData::SetReactant1

(

Reactant *

reactive

)

Definition at line 147 of file G4DNAMolecularReactionTable.cc.

{
    fpReactant1 = pReactive;
}

Referenced by G4DNAMolecularReactionData().

SetReactant2() [1/2]

void G4DNAMolecularReactionData::SetReactant2

(

const G4String &

reactive

)

Definition at line 193 of file G4DNAMolecularReactionTable.cc.

{
    fpReactant2 = G4MoleculeTable::Instance()->GetConfiguration(reactive);
}

SetReactant2() [2/2]

void G4DNAMolecularReactionData::SetReactant2

(

Reactant *

reactive

)

Definition at line 152 of file G4DNAMolecularReactionTable.cc.

{
    fpReactant2 = pReactive;
}

Referenced by G4DNAMolecularReactionData().

SetReactants() [1/2]

void G4DNAMolecularReactionData::SetReactants	(	const G4String &	reactive1,
		const G4String &	reactive2 )

Definition at line 197 of file G4DNAMolecularReactionTable.cc.

{
    fpReactant1 = G4MoleculeTable::Instance()->GetConfiguration(reactant1);
    fpReactant2 = G4MoleculeTable::Instance()->GetConfiguration(reactant2);
}

SetReactants() [2/2]

void G4DNAMolecularReactionData::SetReactants	(	Reactant *	reactive1,
		Reactant *	reactive2 )

Definition at line 157 of file G4DNAMolecularReactionTable.cc.

{
    fpReactant1 = pReactant1;
    fpReactant2 = pReactant2;
}

SetReactionID()

void G4DNAMolecularReactionData::SetReactionID

(

int

ID

)

Definition at line 142 of file G4DNAMolecularReactionTable.cc.

{
    fReactionID = ID;
}

Referenced by G4DNAMolecularReactionTable::SetReaction().

SetReactionRadius()

void G4DNAMolecularReactionData::SetReactionRadius

(

G4double

radius

)

Definition at line 239 of file G4DNAMolecularReactionTable.cc.

{
    fReactionRadius = radius;
    fEffectiveReactionRadius = -fOnsagerRadius / (1-exp(fOnsagerRadius / fReactionRadius));
}

SetReactionType()

void G4DNAMolecularReactionData::SetReactionType

(

G4int

type

)

Definition at line 275 of file G4DNAMolecularReactionTable.cc.

{
    G4double sumDiffCoeff = 0.;
 
    if(type == 1)
    {
 
        sumDiffCoeff = fpReactant1->GetDiffusionCoefficient() + 
                       fpReactant2->GetDiffusionCoefficient();
 
        fReactionRadius = fpReactant1->GetVanDerVaalsRadius() +
                          fpReactant2->GetVanDerVaalsRadius();
 
        G4double Rs = 0.29 * nm;
        if(fOnsagerRadius == 0) // Type II
        {
            fEffectiveReactionRadius = fReactionRadius;
            fDiffusionRate = 4 * pi * sumDiffCoeff * fReactionRadius * Avogadro;
            if (fpReactant1 == fpReactant2) fDiffusionRate/=2;
            fActivationRate = fDiffusionRate * fObservedReactionRate / (fDiffusionRate - fObservedReactionRate);
            fProbability =  Rs / (Rs + (fDiffusionRate / fActivationRate) * (fReactionRadius + Rs));
 
        }else{ // Type IV
            fEffectiveReactionRadius = -fOnsagerRadius/(1-exp(fOnsagerRadius/fReactionRadius));
            fDiffusionRate = 4 * pi * sumDiffCoeff * fEffectiveReactionRadius * Avogadro;
            if (fpReactant1 == fpReactant2) fDiffusionRate/=2;
 
            fActivationRate = fDiffusionRate * fObservedReactionRate / (fDiffusionRate - fObservedReactionRate);
            fProbability = Rs / (Rs + (fDiffusionRate / fActivationRate) * (fEffectiveReactionRadius + Rs));
        }
    }
 
    fType = type;
}

Referenced by G4EmDNAChemistry_option3::ConstructReactionTable().

SetScaledParameterization()

void G4DNAMolecularReactionData::SetScaledParameterization	(	double	temperature_K,
		double	rateCste )

Definition at line 788 of file G4DNAMolecularReactionTable.cc.

{
    fRateParam = std::bind(ScaledParameterization,
                           std::placeholders::_1,
                           temperature_K,
                           rateCste);
}

Member Data Documentation

fActivationRate

G4double G4DNAMolecularReactionData::fActivationRate

protected

Definition at line 154 of file G4DNAMolecularReactionTable.hh.

Referenced by GetActivationRateConstant(), and SetReactionType().

fDiffusionRate

G4double G4DNAMolecularReactionData::fDiffusionRate

protected

Definition at line 155 of file G4DNAMolecularReactionTable.hh.

Referenced by GetDiffusionRateConstant(), and SetReactionType().

fEffectiveReactionRadius

G4double G4DNAMolecularReactionData::fEffectiveReactionRadius

protected

Definition at line 160 of file G4DNAMolecularReactionTable.hh.

Referenced by ComputeEffectiveRadius(), GetEffectiveReactionRadius(), SetEffectiveReactionRadius(), SetReactionRadius(), and SetReactionType().

fObservedReactionRate

G4double G4DNAMolecularReactionData::fObservedReactionRate

protected

Definition at line 153 of file G4DNAMolecularReactionTable.hh.

Referenced by ComputeEffectiveRadius(), GetObservedReactionRateConstant(), SetObservedReactionRateConstant(), and SetReactionType().

fOnsagerRadius

G4double G4DNAMolecularReactionData::fOnsagerRadius

protected

Definition at line 157 of file G4DNAMolecularReactionTable.hh.

Referenced by ComputeEffectiveRadius(), GetOnsagerRadius(), SetReactionRadius(), and SetReactionType().

fpReactant1

Reactant* G4DNAMolecularReactionData::fpReactant1

protected

Definition at line 150 of file G4DNAMolecularReactionTable.hh.

Referenced by ComputeEffectiveRadius(), GetReactant1(), GetReactants(), SetReactant1(), SetReactant1(), SetReactants(), SetReactants(), and SetReactionType().

fpReactant2

Reactant* G4DNAMolecularReactionData::fpReactant2

protected

Definition at line 151 of file G4DNAMolecularReactionTable.hh.

Referenced by ComputeEffectiveRadius(), GetReactant2(), GetReactants(), SetReactant2(), SetReactant2(), SetReactants(), SetReactants(), and SetReactionType().

fProbability

G4double G4DNAMolecularReactionData::fProbability

protected

Definition at line 162 of file G4DNAMolecularReactionTable.hh.

Referenced by ComputeEffectiveRadius(), GetProbability(), SetProbability(), and SetReactionType().

fProducts

ReactionProducts G4DNAMolecularReactionData::fProducts

protected

Definition at line 165 of file G4DNAMolecularReactionTable.hh.

Referenced by AddProduct(), AddProduct(), GetNbProducts(), GetProduct(), GetProducts(), RemoveProducts(), and ~G4DNAMolecularReactionData().

fRateParam

RateParam G4DNAMolecularReactionData::fRateParam

protected

Definition at line 166 of file G4DNAMolecularReactionTable.hh.

Referenced by ScaleForNewTemperature(), SetArrehniusParameterization(), SetPolynomialParameterization(), and SetScaledParameterization().

fReactionID

int G4DNAMolecularReactionData::fReactionID

protected

Definition at line 167 of file G4DNAMolecularReactionTable.hh.

Referenced by ComputeEffectiveRadius(), GetReactionID(), and SetReactionID().

fReactionRadius

G4double G4DNAMolecularReactionData::fReactionRadius

protected

Definition at line 159 of file G4DNAMolecularReactionTable.hh.

Referenced by ComputeEffectiveRadius(), GetReactionRadius(), SetReactionRadius(), and SetReactionType().

fType

G4int G4DNAMolecularReactionData::fType

protected

Definition at line 163 of file G4DNAMolecularReactionTable.hh.

Referenced by GetReactionType(), and SetReactionType().

---

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

• G4DNAMolecularReactionTable.hh
• G4DNAMolecularReactionTable.cc