Material designed to form a std::vector of mass fractions of mineral concentrations from primary-species concentrations for an equilibrium precipitation-dissolution chemistry reaction system. More...

#include <PorousFlowAqueousPreDisChemistry.h>

Inheritance diagram for PorousFlowAqueousPreDisChemistry:

[legend]

Public Member Functions
	PorousFlowAqueousPreDisChemistry (const InputParameters &parameters)

Protected Member Functions
void	initQpStatefulProperties () override

void	computeQpProperties () override

Real	stoichiometry (unsigned reaction_num, unsigned primary_num) const
	The stoichiometric coefficient. More...

virtual void	computeQpReactionRates ()
	Compute the secondary-species concentration as defined by the chemistry Must be overridden by derived classes. More...

void	findZeroConcentration (unsigned &zero_conc_index, unsigned &zero_count) const
	Checks gamp[i] = _primary_activity_coefficients[i] * (*_primary[i])[qp]. More...

virtual void	dQpReactionRate_dprimary (unsigned reaction_num, std::vector< Real > &drr) const
	Computes derivative of the reaction rate with respect to the primary concentrations. More...

virtual Real	dQpReactionRate_dT (unsigned reaction_num) const
	Computes derivative of the reaction rate with respect to the temperature. More...

Real	rateConstantQp (unsigned reaction_num) const

Protected Attributes
const MaterialProperty< Real > &	_porosity_old
	Old values of the porosity. More...

const unsigned int	_aq_ph
	Aqueous phase number. More...

const MaterialProperty< std::vector< Real > > &	_saturation
	Saturation. More...

const MaterialProperty< Real > &	_temperature
	Temperature. More...

const MaterialProperty< std::vector< Real > > &	_dtemperature_dvar
	d(temperature)/(d porflow variable) More...

const unsigned int	_num_primary
	Number of primary species. More...

const unsigned int	_num_reactions
	Number of equations in the aqueous geochemistry system. More...

const bool	_equilibrium_constants_as_log10
	Whether the equilibium constants are written in their log10 form, or in absolute terms. More...

const unsigned	_num_equilibrium_constants
	Number of equilibrium_constants provided. More...

std::vector< const VariableValue * >	_equilibrium_constants
	Equilibrium constants (dimensionless) More...

const std::vector< Real >	_primary_activity_coefficients
	Activity coefficients for the primary species (dimensionless) More...

const std::vector< Real >	_reactions
	Stoichiometry defining the aqeuous geochemistry equilibrium reactions. More...

std::vector< unsigned int >	_primary_var_num
	The variable number of the primary variables. More...

std::vector< const VariableValue * >	_primary
	Values of the primary species' concentrations (dimensionless) More...

const MaterialProperty< std::vector< Real > > &	_sec_conc_old

std::vector< Real >	_mineral_sat
	Mineral saturation ratio - a useful temporary variable during computeQpProperties. More...

std::vector< bool >	_bounded_rate
	Whether the reaction rate has to be bounded in order that the precipitate stays inside [0, 1]. More...

MaterialProperty< std::vector< Real > > &	_reaction_rate
	Reaction rate of mineralisation. More...

MaterialProperty< std::vector< std::vector< Real > > > &	_dreaction_rate_dvar
	d(reaction rate of mineralisation)/d(porous flow var) More...

const std::vector< Real >	_r_area
	Reactive surface area (m^2/L) for each reaction. More...

const std::vector< Real >	_molar_volume
	Molar volume (L/mol) for each secondary species. More...

const std::vector< Real >	_ref_kconst
	Rate constant (mol/(m^2 s)) at reference temperature for each reaction. More...

const std::vector< Real >	_e_act
	Activation energy (J/mol) for each reaction. More...

const Real	_gas_const
	Gas constant (J/(mol K)) More...

const Real	_one_over_ref_temp
	1/reference_temperature (1/K) More...

const std::vector< Real >	_theta_exponent
	Theta exponent for the precipitation-dissolution for each reaction. More...

const std::vector< Real >	_eta_exponent
	Eta exponent for the precipitation-dissolution for each reaction. More...

std::vector< const VariableValue * >	_initial_conc
	Initial values of the secondary species concentrations. More...

const unsigned int	_num_phases
	Number of phases. More...

const unsigned int	_num_components
	Number of fluid components. More...

const unsigned int	_num_var
	Number of PorousFlow variables. More...

Detailed Description

Material designed to form a std::vector of mass fractions of mineral concentrations from primary-species concentrations for an equilibrium precipitation-dissolution chemistry reaction system.

Definition at line 24 of file PorousFlowAqueousPreDisChemistry.h.

Constructor & Destructor Documentation

◆ PorousFlowAqueousPreDisChemistry()

PorousFlowAqueousPreDisChemistry::PorousFlowAqueousPreDisChemistry ( const InputParameters & parameters )

Definition at line 70 of file PorousFlowAqueousPreDisChemistry.C.

   : PorousFlowMaterialVectorBase(parameters),
     _porosity_old(_nodal_material ? getMaterialPropertyOld<Real>("PorousFlow_porosity_nodal")
                                   : getMaterialPropertyOld<Real>("PorousFlow_porosity_qp")),
     _aq_ph(_dictator.aqueousPhaseNumber()),
     _saturation(_nodal_material
                     ? getMaterialProperty<std::vector<Real>>("PorousFlow_saturation_nodal")
                     : getMaterialProperty<std::vector<Real>>("PorousFlow_saturation_qp")),
  
     _temperature(_nodal_material ? getMaterialProperty<Real>("PorousFlow_temperature_nodal")
                                  : getMaterialProperty<Real>("PorousFlow_temperature_qp")),
     _dtemperature_dvar(
         _nodal_material
             ? getMaterialProperty<std::vector<Real>>("dPorousFlow_temperature_nodal_dvar")
             : getMaterialProperty<std::vector<Real>>("dPorousFlow_temperature_qp_dvar")),
  
     _num_primary(coupledComponents("primary_concentrations")),
     _num_reactions(getParam<unsigned>("num_reactions")),
     _equilibrium_constants_as_log10(getParam<bool>("equilibrium_constants_as_log10")),
     _num_equilibrium_constants(coupledComponents("equilibrium_constants")),
     _equilibrium_constants(_num_equilibrium_constants),
     _primary_activity_coefficients(getParam<std::vector<Real>>("primary_activity_coefficients")),
     _reactions(getParam<std::vector<Real>>("reactions")),
  
     _sec_conc_old(
         _nodal_material
             ? getMaterialPropertyOld<std::vector<Real>>("PorousFlow_mineral_concentration_nodal")
             : getMaterialPropertyOld<std::vector<Real>>("PorousFlow_mineral_concentration_qp")),
  
     _mineral_sat(_num_reactions),
     _bounded_rate(_num_reactions),
     _reaction_rate(
         _nodal_material
             ? declareProperty<std::vector<Real>>("PorousFlow_mineral_reaction_rate_nodal")
             : declareProperty<std::vector<Real>>("PorousFlow_mineral_reaction_rate_qp")),
     _dreaction_rate_dvar(_nodal_material ? declareProperty<std::vector<std::vector<Real>>>(
                                                "dPorousFlow_mineral_reaction_rate_nodal_dvar")
                                          : declareProperty<std::vector<std::vector<Real>>>(
                                                "dPorousFlow_mineral_reaction_rate_qp_dvar")),
  
     _r_area(getParam<std::vector<Real>>("specific_reactive_surface_area")),
     _molar_volume(getParam<std::vector<Real>>("molar_volume")),
     _ref_kconst(getParam<std::vector<Real>>("kinetic_rate_constant")),
     _e_act(getParam<std::vector<Real>>("activation_energy")),
     _gas_const(getParam<Real>("gas_constant")),
     _one_over_ref_temp(1.0 / getParam<Real>("reference_temperature")),
     _theta_exponent(isParamValid("theta_exponent") ? getParam<std::vector<Real>>("theta_exponent")
                                                    : std::vector<Real>(_num_reactions, 1.0)),
     _eta_exponent(isParamValid("eta_exponent") ? getParam<std::vector<Real>>("eta_exponent")
                                                : std::vector<Real>(_num_reactions, 1.0))
 {
   if (_dictator.numPhases() < 1)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of fluid phases must not be zero");
  
   if (_num_primary != _num_components - 1)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of mass_fraction_vars is ",
                _num_components,
                " which must be one greater than the number of primary concentrations (which is ",
                _num_primary,
                ")");
  
   // correct number of equilibrium constants
   if (_num_equilibrium_constants != _num_reactions)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of equilibrium constants is ",
                _num_equilibrium_constants,
                " which must be equal to the number of reactions (",
                _num_reactions,
                ")");
  
   // correct number of activity coefficients
   if (_primary_activity_coefficients.size() != _num_primary)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of primary activity "
                "coefficients is ",
                _primary_activity_coefficients.size(),
                " which must be equal to the number of primary species (",
                _num_primary,
                ")");
  
   // correct number of stoichiometry coefficients
   if (_reactions.size() != _num_reactions * _num_primary)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of stoichiometric "
                "coefficients specified in 'reactions' (",
                _reactions.size(),
                ") must be equal to the number of reactions (",
                _num_reactions,
                ") multiplied by the number of primary species (",
                _num_primary,
                ")");
  
   if (_r_area.size() != _num_reactions)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of specific reactive "
                "surface areas provided is ",
                _r_area.size(),
                " which must be equal to the number of reactions (",
                _num_reactions,
                ")");
  
   if (_ref_kconst.size() != _num_reactions)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of kinetic rate constants is ",
                _ref_kconst.size(),
                " which must be equal to the number of reactions (",
                _num_reactions,
                ")");
  
   if (_e_act.size() != _num_reactions)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of activation energies is ",
                _e_act.size(),
                " which must be equal to the number of reactions (",
                _num_reactions,
                ")");
  
   if (_molar_volume.size() != _num_reactions)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of molar volumes is ",
                _molar_volume.size(),
                " which must be equal to the number of reactions (",
                _num_reactions,
                ")");
  
   if (_theta_exponent.size() != _num_reactions)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of theta exponents is ",
                _theta_exponent.size(),
                " which must be equal to the number of reactions (",
                _num_reactions,
                ")");
  
   if (_eta_exponent.size() != _num_reactions)
     mooseError("PorousFlowAqueousPreDisChemistry: The number of eta exponents is ",
                _eta_exponent.size(),
                " which must be equal to the number of reactions (",
                _num_reactions,
                ")");
  
   if (_num_reactions != _dictator.numAqueousKinetic())
     mooseError("PorousFlowAqueousPreDisChemistry: You have specified the number of "
                "reactions to be ",
                _num_reactions,
                " but the Dictator knows that the number of aqueous kinetic "
                "(precipitation-dissolution) reactions is ",
                _dictator.numAqueousKinetic());
  
   _primary_var_num.resize(_num_primary);
   _primary.resize(_num_primary);
   for (unsigned i = 0; i < _num_primary; ++i)
   {
     _primary_var_num[i] = coupled("primary_concentrations", i);
     _primary[i] = (_nodal_material ? &coupledDofValues("primary_concentrations", i)
                                    : &coupledValue("primary_concentrations", i));
   }
  
   for (unsigned i = 0; i < _num_equilibrium_constants; ++i)
     _equilibrium_constants[i] = (_nodal_material ? &coupledDofValues("equilibrium_constants", i)
                                                  : &coupledValue("equilibrium_constants", i));
 }

Member Function Documentation

◆ computeQpProperties()

void PorousFlowAqueousPreDisChemistry::computeQpProperties ( )

overrideprotected

Definition at line 235 of file PorousFlowAqueousPreDisChemistry.C.

 {
   _reaction_rate[_qp].resize(_num_reactions);
   _dreaction_rate_dvar[_qp].resize(_num_reactions);
   for (unsigned r = 0; r < _num_reactions; ++r)
     _dreaction_rate_dvar[_qp][r].assign(_num_var, 0.0);
  
   // Compute the reaction rates
   computeQpReactionRates();
  
   // Compute the derivatives of the reaction rates
   std::vector<std::vector<Real>> drr(_num_reactions);
   std::vector<Real> drr_dT(_num_reactions);
   for (unsigned r = 0; r < _num_reactions; ++r)
   {
     dQpReactionRate_dprimary(r, drr[r]);
     drr_dT[r] = dQpReactionRate_dT(r);
   }
  
   // compute _dreaction_rate_dvar[_qp]
   for (unsigned wrt = 0; wrt < _num_primary; ++wrt)
   {
     // derivative with respect to the "wrt"^th primary species concentration
     if (!_dictator.isPorousFlowVariable(_primary_var_num[wrt]))
       continue;
     const unsigned pf_wrt = _dictator.porousFlowVariableNum(_primary_var_num[wrt]);
  
     // run through the reactions, using drr in the appropriate places
     for (unsigned r = 0; r < _num_reactions; ++r)
       _dreaction_rate_dvar[_qp][r][pf_wrt] = drr[r][wrt];
   }
  
   // use the derivative wrt temperature
   for (unsigned r = 0; r < _num_reactions; ++r)
     for (unsigned v = 0; v < _num_var; ++v)
       _dreaction_rate_dvar[_qp][r][v] += drr_dT[r] * _dtemperature_dvar[_qp][v];
 }

◆ computeQpReactionRates()

void PorousFlowAqueousPreDisChemistry::computeQpReactionRates ( )

protectedvirtual

Compute the secondary-species concentration as defined by the chemistry Must be overridden by derived classes.

Definition at line 299 of file PorousFlowAqueousPreDisChemistry.C.

 {
   for (unsigned r = 0; r < _num_reactions; ++r)
   {
     _mineral_sat[r] =
         (_equilibrium_constants_as_log10 ? std::pow(10.0, -(*_equilibrium_constants[r])[_qp])
                                          : 1.0 / (*_equilibrium_constants[r])[_qp]);
     for (unsigned j = 0; j < _num_primary; ++j)
     {
       const Real gamp = _primary_activity_coefficients[j] * (*_primary[j])[_qp];
       if (gamp <= 0.0)
       {
         if (stoichiometry(r, j) < 0.0)
           _mineral_sat[r] = std::numeric_limits<Real>::max();
         else if (stoichiometry(r, j) == 0.0)
           _mineral_sat[r] *= 1.0;
         else
         {
           _mineral_sat[r] = 0.0;
           break;
         }
       }
       else
         _mineral_sat[r] *= std::pow(gamp, stoichiometry(r, j));
     }
     const Real fac = 1.0 - std::pow(_mineral_sat[r], _theta_exponent[r]);
     // if fac > 0 then dissolution occurs; if fac < 0 then precipitation occurs.
     const Real sgn = (fac < 0 ? -1.0 : 1.0);
     const Real unbounded_rr = -sgn * rateConstantQp(r) * _r_area[r] * _molar_volume[r] *
                               std::pow(std::abs(fac), _eta_exponent[r]);
  
     /*
      *
      * Note the use of the OLD value of porosity here.
      * This strategy, which breaks the cyclic dependency between porosity
      * and mineral concentration, is used in
      * Kernel: PorousFlowPreDis
      * Material: PorousFlowPorosity
      * Material: PorousFlowAqueousPreDisChemistry
      * Material: PorousFlowAqueousPreDisMineral
      *
      */
  
     // bound the reaction so _sec_conc lies between zero and unity
     const Real por_times_rr_dt = _porosity_old[_qp] * _saturation[_qp][_aq_ph] * unbounded_rr * _dt;
     if (_sec_conc_old[_qp][r] + por_times_rr_dt > 1.0)
     {
       _bounded_rate[r] = true;
       _reaction_rate[_qp][r] =
           (1.0 - _sec_conc_old[_qp][r]) / _porosity_old[_qp] / _saturation[_qp][_aq_ph] / _dt;
     }
     else if (_sec_conc_old[_qp][r] + por_times_rr_dt < 0.0)
     {
       _bounded_rate[r] = true;
       _reaction_rate[_qp][r] =
           -_sec_conc_old[_qp][r] / _porosity_old[_qp] / _saturation[_qp][_aq_ph] / _dt;
     }
     else
     {
       _bounded_rate[r] = false;
       _reaction_rate[_qp][r] = unbounded_rr;
     }
   }
 }

Referenced by computeQpProperties().

◆ dQpReactionRate_dprimary()

void PorousFlowAqueousPreDisChemistry::dQpReactionRate_dprimary	(	unsigned	reaction_num,
		std::vector< Real > &	drr
	)		const

protectedvirtual

Computes derivative of the reaction rate with respect to the primary concentrations.

Parameters

reaction_num	The reaction number corresponding to the secondary-species concentration
drr	drr[i] = d(reactionRate[reaction_num])/d(primary_species[i])

Definition at line 365 of file PorousFlowAqueousPreDisChemistry.C.

 {
   drr.assign(_num_primary, 0.0);
  
   // handle corner case
   if (_bounded_rate[reaction_num])
     return;
  
   /*
    * Form the derivative of _mineral_sat, and store it in drr for now.
    * The derivatives are straightforward if all primary > 0.
    *
    * If more than one primary = 0 then I set the derivatives to zero, even though it could be
    * argued that with certain stoichiometric coefficients you might have derivative = 0/0 and it
    * might be appropriate to set this to a non-zero finite value.
    *
    * If exactly one primary = 0 and its stoichiometry = 1 then the derivative wrt this one is
    * nonzero.
    * If exactly one primary = 0 and its stoichiometry > 1 then all derivatives are zero.
    * If exactly one primary = 0 and its stoichiometry < 1 then the derivative wrt this one is
    * infinity
    */
  
   unsigned zero_count = 0;
   unsigned zero_conc_index = 0;
   findZeroConcentration(zero_conc_index, zero_count);
   if (zero_count == 0)
   {
     for (unsigned i = 0; i < _num_primary; ++i)
       drr[i] = stoichiometry(reaction_num, i) * _mineral_sat[reaction_num] /
                std::max((*_primary[i])[_qp], 0.0);
   }
   else
   {
     if (_theta_exponent[reaction_num] < 1.0)
       // dfac = infinity (see below) so the derivative may be inf, inf * 0, or inf/inf.  I simply
       // return with drr = 0
       return;
  
     // count the number of primary <= 0, and record the one that's zero
     if (zero_count == 1 && stoichiometry(reaction_num, zero_conc_index) == 1.0)
     {
       Real conc_without_zero = (_equilibrium_constants_as_log10
                                     ? std::pow(10.0, -(*_equilibrium_constants[reaction_num])[_qp])
                                     : 1.0 / (*_equilibrium_constants[reaction_num])[_qp]);
       for (unsigned i = 0; i < _num_primary; ++i)
       {
         if (i == zero_conc_index)
           conc_without_zero *= _primary_activity_coefficients[i];
         else
           conc_without_zero *=
               std::pow(_primary_activity_coefficients[i] * std::max((*_primary[i])[_qp], 0.0),
                        stoichiometry(reaction_num, i));
       }
       drr[zero_conc_index] = conc_without_zero;
     }
     else if (zero_count == 0 and stoichiometry(reaction_num, zero_conc_index) < 1.0)
       drr[zero_conc_index] = std::numeric_limits<Real>::max();
     else
       // all other cases have drr = 0, so return without performing any other calculations
       return;
   }
  
   // At the moment _drr = d(mineral_sat)/d(primary)
   // Multiply by appropriate term to give _drr = d(reaction_rate)/d(primary)
   const Real fac = 1.0 - std::pow(_mineral_sat[reaction_num], _theta_exponent[reaction_num]);
   const Real dfac = -_theta_exponent[reaction_num] *
                     std::pow(_mineral_sat[reaction_num], _theta_exponent[reaction_num] - 1.0);
   const Real multiplier = -rateConstantQp(reaction_num) * _r_area[reaction_num] *
                           _molar_volume[reaction_num] *
                           std::pow(std::abs(fac), _eta_exponent[reaction_num] - 1.0) *
                           _eta_exponent[reaction_num] * dfac;
   for (unsigned i = 0; i < _num_primary; ++i)
     drr[i] *= multiplier;
 }

Referenced by computeQpProperties().

◆ dQpReactionRate_dT()

Real PorousFlowAqueousPreDisChemistry::dQpReactionRate_dT ( unsigned reaction_num ) const

protectedvirtual

Computes derivative of the reaction rate with respect to the temperature.

Parameters

reaction_num The reaction number corresponding to the secondary-species concentration

Definition at line 450 of file PorousFlowAqueousPreDisChemistry.C.

 {
   // handle corner case
   if (_bounded_rate[reaction_num])
     return 0.0;
  
   const Real drate_const = rateConstantQp(reaction_num) * _e_act[reaction_num] / _gas_const *
                            std::pow(_temperature[_qp], -2.0);
   const Real fac = 1.0 - std::pow(_mineral_sat[reaction_num], _theta_exponent[reaction_num]);
   const Real sgn = (fac < 0 ? -1.0 : 1.0);
   const Real dkinetic_rate = -sgn * drate_const * _r_area[reaction_num] *
                              _molar_volume[reaction_num] *
                              std::pow(std::abs(fac), _eta_exponent[reaction_num]);
  
   return dkinetic_rate;
 }

Referenced by computeQpProperties().

◆ findZeroConcentration()

void PorousFlowAqueousPreDisChemistry::findZeroConcentration	(	unsigned &	zero_conc_index,
		unsigned &	zero_count
	)		const

protected

Checks gamp[i] = _primary_activity_coefficients[i] * (*_primary[i])[qp].

Returns: if all of these are positive, then zero_count = 0, zero_conc_index = 0 if one of these is zero, then zero_count = 1, zero_conc_index = the index of the zero gamp if more than one is zero, then zero_count = 2, and zero_conc_index is the index of the 2nd zero

Definition at line 281 of file PorousFlowAqueousPreDisChemistry.C.

 {
   zero_count = 0;
   for (unsigned i = 0; i < _num_primary; ++i)
   {
     if (_primary_activity_coefficients[i] * (*_primary[i])[_qp] <= 0.0)
     {
       zero_count += 1;
       zero_conc_index = i;
       if (zero_count > 1)
         return;
     }
   }
   return;
 }

Referenced by dQpReactionRate_dprimary().

◆ initQpStatefulProperties()

void PorousFlowAqueousPreDisChemistry::initQpStatefulProperties ( )

overrideprotected

Definition at line 226 of file PorousFlowAqueousPreDisChemistry.C.

 {
   _reaction_rate[_qp].resize(_num_reactions);
   _dreaction_rate_dvar[_qp].resize(_num_reactions);
   for (unsigned r = 0; r < _num_reactions; ++r)
     _dreaction_rate_dvar[_qp][r].assign(_num_var, 0.0);
 }

◆ rateConstantQp()

Real PorousFlowAqueousPreDisChemistry::rateConstantQp ( unsigned reaction_num ) const

protected

Definition at line 443 of file PorousFlowAqueousPreDisChemistry.C.

 {
   return _ref_kconst[reaction_num] * std::exp(_e_act[reaction_num] / _gas_const *
                                               (_one_over_ref_temp - 1.0 / _temperature[_qp]));
 }

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), and dQpReactionRate_dT().

◆ stoichiometry()

Real PorousFlowAqueousPreDisChemistry::stoichiometry	(	unsigned	reaction_num,
		unsigned	primary_num
	)		const

protected

The stoichiometric coefficient.

Parameters

reaction_num	Reaction number (0, ..., _num_reactions - 1)
primary_num	The number of the primary species (0, ..., _num_primary - 1)

Definition at line 274 of file PorousFlowAqueousPreDisChemistry.C.

 {
   const unsigned index = reaction_num * _num_primary + primary_num;
   return _reactions[index];
 }

Referenced by computeQpReactionRates(), and dQpReactionRate_dprimary().

Member Data Documentation

◆ _aq_ph

const unsigned int PorousFlowAqueousPreDisChemistry::_aq_ph

protected

Aqueous phase number.

Definition at line 74 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates().

◆ _bounded_rate

std::vector<bool> PorousFlowAqueousPreDisChemistry::_bounded_rate

protected

Whether the reaction rate has to be bounded in order that the precipitate stays inside [0, 1].

Definition at line 119 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), and dQpReactionRate_dT().

◆ _dreaction_rate_dvar

MaterialProperty<std::vector<std::vector<Real> > >& PorousFlowAqueousPreDisChemistry::_dreaction_rate_dvar

protected

d(reaction rate of mineralisation)/d(porous flow var)

Definition at line 125 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpProperties(), and initQpStatefulProperties().

◆ _dtemperature_dvar

const MaterialProperty<std::vector<Real> >& PorousFlowAqueousPreDisChemistry::_dtemperature_dvar

protected

d(temperature)/(d porflow variable)

Definition at line 83 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpProperties().

◆ _e_act

const std::vector<Real> PorousFlowAqueousPreDisChemistry::_e_act

protected

Activation energy (J/mol) for each reaction.

Definition at line 137 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by dQpReactionRate_dT(), PorousFlowAqueousPreDisChemistry(), and rateConstantQp().

◆ _equilibrium_constants

std::vector<const VariableValue *> PorousFlowAqueousPreDisChemistry::_equilibrium_constants

protected

Equilibrium constants (dimensionless)

Definition at line 98 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), and PorousFlowAqueousPreDisChemistry().

◆ _equilibrium_constants_as_log10

const bool PorousFlowAqueousPreDisChemistry::_equilibrium_constants_as_log10

protected

Whether the equilibium constants are written in their log10 form, or in absolute terms.

Definition at line 92 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), and dQpReactionRate_dprimary().

◆ _eta_exponent

const std::vector<Real> PorousFlowAqueousPreDisChemistry::_eta_exponent

protected

Eta exponent for the precipitation-dissolution for each reaction.

Definition at line 149 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), dQpReactionRate_dT(), and PorousFlowAqueousPreDisChemistry().

◆ _gas_const

const Real PorousFlowAqueousPreDisChemistry::_gas_const

protected

Gas constant (J/(mol K))

Definition at line 140 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by dQpReactionRate_dT(), and rateConstantQp().

◆ _initial_conc

std::vector<const VariableValue *> PorousFlowAqueousPreDisChemistry::_initial_conc

protected

Initial values of the secondary species concentrations.

Definition at line 152 of file PorousFlowAqueousPreDisChemistry.h.

◆ _mineral_sat

std::vector<Real> PorousFlowAqueousPreDisChemistry::_mineral_sat

protected

Mineral saturation ratio - a useful temporary variable during computeQpProperties.

Definition at line 116 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), and dQpReactionRate_dT().

◆ _molar_volume

const std::vector<Real> PorousFlowAqueousPreDisChemistry::_molar_volume

protected

Molar volume (L/mol) for each secondary species.

Definition at line 131 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), dQpReactionRate_dT(), and PorousFlowAqueousPreDisChemistry().

◆ _num_components

const unsigned int PorousFlowMaterialVectorBase::_num_components

protectedinherited

Number of fluid components.

Definition at line 33 of file PorousFlowMaterialVectorBase.h.

Referenced by PorousFlowDiffusivityBase::computeQpProperties(), PorousFlowMassFractionAqueousEquilibriumChemistry::computeQpProperties(), PorousFlowMassFraction::computeQpProperties(), PorousFlowAqueousPreDisChemistry(), PorousFlowDiffusivityBase::PorousFlowDiffusivityBase(), and PorousFlowMassFraction::PorousFlowMassFraction().

◆ _num_equilibrium_constants

const unsigned PorousFlowAqueousPreDisChemistry::_num_equilibrium_constants

protected

Number of equilibrium_constants provided.

Definition at line 95 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by PorousFlowAqueousPreDisChemistry().

◆ _num_phases

const unsigned int PorousFlowMaterialVectorBase::_num_phases

protectedinherited

Number of phases.

Definition at line 30 of file PorousFlowMaterialVectorBase.h.

Referenced by PorousFlowDiffusivityBase::computeQpProperties(), PorousFlowDiffusivityMillingtonQuirk::computeQpProperties(), PorousFlowEffectiveFluidPressure::computeQpProperties(), PorousFlowMassFraction::computeQpProperties(), PorousFlowJoiner::computeQpProperties(), PorousFlowEffectiveFluidPressure::initQpStatefulProperties(), PorousFlowJoiner::initQpStatefulProperties(), PorousFlowDiffusivityBase::PorousFlowDiffusivityBase(), PorousFlowDiffusivityConst::PorousFlowDiffusivityConst(), PorousFlowJoiner::PorousFlowJoiner(), PorousFlowMassFraction::PorousFlowMassFraction(), PorousFlowThermalConductivityFromPorosity::PorousFlowThermalConductivityFromPorosity(), PorousFlowThermalConductivityIdeal::PorousFlowThermalConductivityIdeal(), and PorousFlowTotalGravitationalDensityFullySaturatedFromPorosity::PorousFlowTotalGravitationalDensityFullySaturatedFromPorosity().

◆ _num_primary

const unsigned int PorousFlowAqueousPreDisChemistry::_num_primary

protected

Number of primary species.

Definition at line 86 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpProperties(), computeQpReactionRates(), dQpReactionRate_dprimary(), findZeroConcentration(), PorousFlowAqueousPreDisChemistry(), and stoichiometry().

◆ _num_reactions

const unsigned int PorousFlowAqueousPreDisChemistry::_num_reactions

protected

Number of equations in the aqueous geochemistry system.

Definition at line 89 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpProperties(), computeQpReactionRates(), initQpStatefulProperties(), and PorousFlowAqueousPreDisChemistry().

◆ _num_var

const unsigned int PorousFlowMaterialVectorBase::_num_var

protectedinherited

Number of PorousFlow variables.

Definition at line 36 of file PorousFlowMaterialVectorBase.h.

◆ _one_over_ref_temp

const Real PorousFlowAqueousPreDisChemistry::_one_over_ref_temp

protected

1/reference_temperature (1/K)

Definition at line 143 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by rateConstantQp().

◆ _porosity_old

const MaterialProperty<Real>& PorousFlowAqueousPreDisChemistry::_porosity_old

protected

Old values of the porosity.

Definition at line 71 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates().

◆ _primary

std::vector<const VariableValue *> PorousFlowAqueousPreDisChemistry::_primary

protected

Values of the primary species' concentrations (dimensionless)

Definition at line 110 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), findZeroConcentration(), and PorousFlowAqueousPreDisChemistry().

◆ _primary_activity_coefficients

const std::vector<Real> PorousFlowAqueousPreDisChemistry::_primary_activity_coefficients

protected

Activity coefficients for the primary species (dimensionless)

Definition at line 101 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), findZeroConcentration(), and PorousFlowAqueousPreDisChemistry().

◆ _primary_var_num

std::vector<unsigned int> PorousFlowAqueousPreDisChemistry::_primary_var_num

protected

The variable number of the primary variables.

Definition at line 107 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpProperties(), and PorousFlowAqueousPreDisChemistry().

◆ _r_area

const std::vector<Real> PorousFlowAqueousPreDisChemistry::_r_area

protected

Reactive surface area (m^2/L) for each reaction.

Definition at line 128 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), dQpReactionRate_dT(), and PorousFlowAqueousPreDisChemistry().

◆ _reaction_rate

MaterialProperty<std::vector<Real> >& PorousFlowAqueousPreDisChemistry::_reaction_rate

protected

Reaction rate of mineralisation.

Definition at line 122 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpProperties(), computeQpReactionRates(), and initQpStatefulProperties().

◆ _reactions

const std::vector<Real> PorousFlowAqueousPreDisChemistry::_reactions

protected

Stoichiometry defining the aqeuous geochemistry equilibrium reactions.

Definition at line 104 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by PorousFlowAqueousPreDisChemistry(), and stoichiometry().

◆ _ref_kconst

const std::vector<Real> PorousFlowAqueousPreDisChemistry::_ref_kconst

protected

Rate constant (mol/(m^2 s)) at reference temperature for each reaction.

Definition at line 134 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by PorousFlowAqueousPreDisChemistry(), and rateConstantQp().

◆ _saturation

const MaterialProperty<std::vector<Real> >& PorousFlowAqueousPreDisChemistry::_saturation

protected

Saturation.

Definition at line 77 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates().

◆ _sec_conc_old

const MaterialProperty<std::vector<Real> >& PorousFlowAqueousPreDisChemistry::_sec_conc_old

protected

Definition at line 113 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates().

◆ _temperature

const MaterialProperty<Real>& PorousFlowAqueousPreDisChemistry::_temperature

protected

Temperature.

Definition at line 80 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by dQpReactionRate_dT(), and rateConstantQp().

◆ _theta_exponent

const std::vector<Real> PorousFlowAqueousPreDisChemistry::_theta_exponent

protected

Theta exponent for the precipitation-dissolution for each reaction.

Definition at line 146 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates(), dQpReactionRate_dprimary(), dQpReactionRate_dT(), and PorousFlowAqueousPreDisChemistry().

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

porous_flow/include/materials/PorousFlowAqueousPreDisChemistry.h
porous_flow/src/materials/PorousFlowAqueousPreDisChemistry.C

Public Member Functions

Protected Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PorousFlowAqueousPreDisChemistry()

Member Function Documentation

◆ computeQpProperties()

◆ computeQpReactionRates()

◆ dQpReactionRate_dprimary()

◆ dQpReactionRate_dT()

◆ findZeroConcentration()

◆ initQpStatefulProperties()

◆ rateConstantQp()

◆ stoichiometry()

Member Data Documentation

◆ _aq_ph

◆ _bounded_rate

◆ _dreaction_rate_dvar

◆ _dtemperature_dvar

◆ _e_act

◆ _equilibrium_constants

◆ _equilibrium_constants_as_log10

◆ _eta_exponent

◆ _gas_const

◆ _initial_conc

◆ _mineral_sat

◆ _molar_volume

◆ _num_components

◆ _num_equilibrium_constants

◆ _num_phases

◆ _num_primary

◆ _num_reactions

◆ _num_var

◆ _one_over_ref_temp

◆ _porosity_old

◆ _primary

◆ _primary_activity_coefficients

◆ _primary_var_num

◆ _r_area

◆ _reaction_rate

◆ _reactions

◆ _ref_kconst

◆ _saturation

◆ _sec_conc_old

◆ _temperature

◆ _theta_exponent