Holds a user-specified description of a kinetic rate. More...

#include <GeochemistryKineticRateCalculator.h>

Public Member Functions
	KineticRateUserDescription (const std::string &kinetic_species_name, Real intrinsic_rate_constant, Real area_quantity, bool multiply_by_mass, Real kinetic_molal_index, Real kinetic_monod_index, Real kinetic_half_saturation, const std::vector< std::string > &promoting_species, const std::vector< Real > &promoting_indices, const std::vector< Real > &promoting_monod_indices, const std::vector< Real > &promoting_half_saturation, Real theta, Real eta, Real activation_energy, Real one_over_T0, DirectionChoiceEnum direction, std::string progeny, Real progeny_efficiency, Real kinetic_bio_efficiency, Real energy_captured)

bool	operator== (const KineticRateUserDescription &rhs) const

Public Attributes
std::string	kinetic_species_name

Real	intrinsic_rate_constant

Real	area_quantity

bool	multiply_by_mass

Real	kinetic_molal_index

Real	kinetic_monod_index

Real	kinetic_half_saturation

std::vector< std::string >	promoting_species

std::vector< Real >	promoting_indices

std::vector< Real >	promoting_monod_indices

std::vector< Real >	promoting_half_saturation

Real	theta

Real	eta

Real	activation_energy

Real	one_over_T0

DirectionChoiceEnum	direction

std::string	progeny

Real	progeny_efficiency

Real	kinetic_bio_efficiency

Real	energy_captured

Detailed Description

Holds a user-specified description of a kinetic rate.

Parameters

kinetic_species	name of the kinetic species
intrinsic_rate_constant	Note that intrinsic_rate_constant * area_quantity * [kinetic_species mass] must have dimensions mol.s^-1
area_quantity	Either 1, or the fixed surface area of the kinetic species, or a specific surface area (m^2/g)
multiply_by_mass	whether the rate should be multiplied by the kinetic_species mass
kinetic_molal_index,rate	is multiplied by kinetic_species_molality^kinetic_molal_index
kinetic_monod_index,rate	is multiplied by 1.0 / (kinetic_species_molality^kinetic_molal_index + kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index
kinetic_half_saturation,rate	is multiplied by 1.0 / (kinetic_species_molality^kinetic_molal_index + kinetic_half_saturation^kinetic_molal_index)^kinetic_monod_index
promoting_species	names of species (which must be primary or secondary species in the system)
promoting_indices	indices of mass, fugacity, activity or mobility (as appropriate)
promoting_monod_indices	monod indices of mass, fugacity, activity or mobility (as appropriate)
promoting_half_saturation	half saturation values of all promoting species
theta	exponent of (Q/K)
eta	exponent of \|1-(Q/K)^theta\|
activation_energy	in J.mol^-1
one_over_T0	measured in 1/Kelvin
direction	whether this kinetic rate is designed for: "both" precipitation and dissolution; "precipitation" only; "dissolution" only; and "raw" or "death" mean the rate does not depend on the sign of 1-(Q/K)
progeny	A non-kinetic species that catalyses the reaction, and potentially gets produced or consumed by it
progeny_efficiency	When one mole of reaction is catalysed, progeny_efficiency moles of the progeny is created
kinetic_bio_efficiency	the efficiency of a biologically-catalysed reaction, that is, when one mole of reaction is catalysed, the biomass increases by kinetic_bio_efficiency moles
energy	captured: energy captured by a biologically-catalysed reaction, essentially this reduces the equilibrium constant of the reaction by exp(-energy_capture / R / Tk)

Definition at line 75 of file GeochemistryKineticRateCalculator.h.

Constructor & Destructor Documentation

◆ KineticRateUserDescription()

KineticRateUserDescription::KineticRateUserDescription	(	const std::string &	kinetic_species_name,
		Real	intrinsic_rate_constant,
		Real	area_quantity,
		bool	multiply_by_mass,
		Real	kinetic_molal_index,
		Real	kinetic_monod_index,
		Real	kinetic_half_saturation,
		const std::vector< std::string > &	promoting_species,
		const std::vector< Real > &	promoting_indices,
		const std::vector< Real > &	promoting_monod_indices,
		const std::vector< Real > &	promoting_half_saturation,
		Real	theta,
		Real	eta,
		Real	activation_energy,
		Real	one_over_T0,
		DirectionChoiceEnum	direction,
		std::string	progeny,
		Real	progeny_efficiency,
		Real	kinetic_bio_efficiency,
		Real	energy_captured
	)

inline

Definition at line 77 of file GeochemistryKineticRateCalculator.h.

     : kinetic_species_name(kinetic_species_name),
       intrinsic_rate_constant(intrinsic_rate_constant),
       area_quantity(area_quantity),
       multiply_by_mass(multiply_by_mass),
       kinetic_molal_index(kinetic_molal_index),
       kinetic_monod_index(kinetic_monod_index),
       kinetic_half_saturation(kinetic_half_saturation),
       promoting_species(promoting_species),
       promoting_indices(promoting_indices),
       promoting_monod_indices(promoting_monod_indices),
       promoting_half_saturation(promoting_half_saturation),
       theta(theta),
       eta(eta),
       activation_energy(activation_energy),
       one_over_T0(one_over_T0),
       direction(direction),
       progeny(progeny),
       progeny_efficiency(progeny_efficiency),
       kinetic_bio_efficiency(kinetic_bio_efficiency),
       energy_captured(energy_captured)
   {
     if (promoting_species.size() != promoting_indices.size())
       mooseError("The promoting_species and promoting_indices vectors must be the same size");
     if (promoting_species.size() != promoting_monod_indices.size())
       mooseError("The promoting_species and promoting_monod_indices vectors must be the same size");
     if (promoting_species.size() != promoting_half_saturation.size())
       mooseError(
           "The promoting_species and promoting_half_saturation vectors must be the same size");
     std::unordered_map<std::string, int> check_for_repeats;
     for (const std::string & name : promoting_species)
       if (check_for_repeats.count(name) == 1)
         mooseError("Promoting species ", name, " has already been provided with an exponent");
       else
         check_for_repeats[name] = 1;
   };

Member Function Documentation

◆ operator==()

bool KineticRateUserDescription::operator== ( const KineticRateUserDescription & rhs ) const

inline

Definition at line 133 of file GeochemistryKineticRateCalculator.h.

   {
     return (kinetic_species_name == rhs.kinetic_species_name) &&
            (intrinsic_rate_constant == rhs.intrinsic_rate_constant) &&
            (area_quantity == rhs.area_quantity) && (multiply_by_mass == rhs.multiply_by_mass) &&
            (kinetic_molal_index == rhs.kinetic_molal_index) &&
            (kinetic_monod_index == rhs.kinetic_monod_index) &&
            (kinetic_half_saturation == rhs.kinetic_half_saturation) &&
            (promoting_species == rhs.promoting_species) &&
            (promoting_indices == rhs.promoting_indices) &&
            (promoting_monod_indices == rhs.promoting_monod_indices) &&
            (promoting_half_saturation == rhs.promoting_half_saturation) && (theta == rhs.theta) &&
            (eta == rhs.eta) && (activation_energy == rhs.activation_energy) &&
            (one_over_T0 == rhs.one_over_T0) && (direction == rhs.direction) &&
            (progeny == rhs.progeny) && (progeny_efficiency == rhs.progeny_efficiency) &&
            (kinetic_bio_efficiency == rhs.kinetic_bio_efficiency) &&
            (energy_captured == rhs.energy_captured);
   };