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 Types
typedef DerivativeMaterialPropertyNameInterface::SymbolName	SymbolName

Public Member Functions
	PorousFlowAqueousPreDisChemistry (const InputParameters &parameters)

const GenericMaterialProperty< U, is_ad > &	getDefaultMaterialProperty (const std::string &name)

const GenericMaterialProperty< U, is_ad > &	getDefaultMaterialPropertyByName (const std::string &name)

void	validateDerivativeMaterialPropertyBase (const std::string &base)

const MaterialPropertyName	derivativePropertyName (const MaterialPropertyName &base, const std::vector< SymbolName > &c) const

const MaterialPropertyName	derivativePropertyNameFirst (const MaterialPropertyName &base, const SymbolName &c1) const

const MaterialPropertyName	derivativePropertyNameSecond (const MaterialPropertyName &base, const SymbolName &c1, const SymbolName &c2) const

const MaterialPropertyName	derivativePropertyNameThird (const MaterialPropertyName &base, const SymbolName &c1, const SymbolName &c2, const SymbolName &c3) const

GenericMaterialProperty< U, is_ad > &	declarePropertyDerivative (const std::string &base, const std::vector< VariableName > &c)

GenericMaterialProperty< U, is_ad > &	declarePropertyDerivative (const std::string &base, const std::vector< SymbolName > &c)

GenericMaterialProperty< U, is_ad > &	declarePropertyDerivative (const std::string &base, const SymbolName &c1, const SymbolName &c2="", const SymbolName &c3="")

GenericMaterialProperty< U, is_ad > &	declarePropertyDerivative (const std::string &base, const std::vector< VariableName > &c)

GenericMaterialProperty< U, is_ad > &	declarePropertyDerivative (const std::string &base, const std::vector< SymbolName > &c)

GenericMaterialProperty< U, is_ad > &	declarePropertyDerivative (const std::string &base, const SymbolName &c1, const SymbolName &c2="", const SymbolName &c3="")

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, const std::vector< VariableName > &c)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, const std::vector< SymbolName > &c)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, const SymbolName &c1, const SymbolName &c2="", const SymbolName &c3="")

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, const SymbolName &c1, unsigned int v2, unsigned int v3=libMesh::invalid_uint)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, unsigned int v1, unsigned int v2=libMesh::invalid_uint, unsigned int v3=libMesh::invalid_uint)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, const std::vector< VariableName > &c)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, const std::vector< SymbolName > &c)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, const SymbolName &c1, const SymbolName &c2="", const SymbolName &c3="")

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, const SymbolName &c1, unsigned int v2, unsigned int v3=libMesh::invalid_uint)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivative (const std::string &base, unsigned int v1, unsigned int v2=libMesh::invalid_uint, unsigned int v3=libMesh::invalid_uint)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivativeByName (const MaterialPropertyName &base, const std::vector< VariableName > &c)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivativeByName (const MaterialPropertyName &base, const std::vector< SymbolName > &c)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivativeByName (const MaterialPropertyName &base, const SymbolName &c1, const SymbolName &c2="", const SymbolName &c3="")

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivativeByName (const MaterialPropertyName &base, const std::vector< VariableName > &c)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivativeByName (const MaterialPropertyName &base, const std::vector< SymbolName > &c)

const GenericMaterialProperty< U, is_ad > &	getMaterialPropertyDerivativeByName (const MaterialPropertyName &base, const SymbolName &c1, const SymbolName &c2="", const SymbolName &c3="")

void	validateCoupling (const MaterialPropertyName &base, const std::vector< VariableName > &c, bool validate_aux=true)

void	validateCoupling (const MaterialPropertyName &base, const VariableName &c1="", const VariableName &c2="", const VariableName &c3="")

void	validateCoupling (const MaterialPropertyName &base, const std::vector< VariableName > &c, bool validate_aux=true)

void	validateCoupling (const MaterialPropertyName &base, const VariableName &c1="", const VariableName &c2="", const VariableName &c3="")

void	validateNonlinearCoupling (const MaterialPropertyName &base, const VariableName &c1="", const VariableName &c2="", const VariableName &c3="")

void	validateNonlinearCoupling (const MaterialPropertyName &base, const VariableName &c1="", const VariableName &c2="", const VariableName &c3="")

const MaterialPropertyName	propertyName (const MaterialPropertyName &base, const std::vector< SymbolName > &c) const

const MaterialPropertyName	propertyName (const MaterialPropertyName &base, const std::vector< SymbolName > &c) const

const MaterialPropertyName	propertyNameFirst (const MaterialPropertyName &base, const SymbolName &c1) const

const MaterialPropertyName	propertyNameFirst (const MaterialPropertyName &base, const SymbolName &c1) const

const MaterialPropertyName	propertyNameSecond (const MaterialPropertyName &base, const SymbolName &c1, const SymbolName &c2) const

const MaterialPropertyName	propertyNameSecond (const MaterialPropertyName &base, const SymbolName &c1, const SymbolName &c2) const

const MaterialPropertyName	propertyNameThird (const MaterialPropertyName &base, const SymbolName &c1, const SymbolName &c2, const SymbolName &c3) const

const MaterialPropertyName	propertyNameThird (const MaterialPropertyName &base, const SymbolName &c1, const SymbolName &c2, const SymbolName &c3) const

Static Public Member Functions
static InputParameters	validParams ()

Protected Member Functions
void	initQpStatefulProperties () override

void	computeQpProperties () override

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

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

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

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

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

Real	rateConstantQp (unsigned reaction_num) const

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

const unsigned int	_aq_ph
	Aqueous phase number.

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

const MaterialProperty< Real > &	_temperature
	Temperature.

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

const unsigned int	_num_primary
	Number of primary species.

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

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

const unsigned	_num_equilibrium_constants
	Number of equilibrium_constants provided.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

const Real	_one_over_ref_temp
	1/reference_temperature (1/K)

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

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

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

const unsigned int	_num_phases
	Number of phases.

const unsigned int	_num_components
	Number of fluid components.

const unsigned int	_num_var
	Number of PorousFlow variables.

Private Member Functions
bool	haveMaterialProperty (const std::string &prop_name)

std::vector< VariableName >	buildVariableVector (const VariableName &c1, const VariableName &c2, const VariableName &c3)

void	validateCouplingHelper (const MaterialPropertyName &base, const std::vector< VariableName > &c, const System &system, std::vector< VariableName > &missing)

bool	isNotObjectVariable (const VariableName &name)

Private Attributes
FEProblemBase &	_dmi_fe_problem

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 19 of file PorousFlowAqueousPreDisChemistry.h.

Constructor & Destructor Documentation

◆ PorousFlowAqueousPreDisChemistry()

PorousFlowAqueousPreDisChemistry::PorousFlowAqueousPreDisChemistry ( const InputParameters & parameters )

Definition at line 69 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);
    // A primary concentration need not be a PorousFlow variable (the derivative loop below skips
    // any that is not), and a prescribed one may be an elemental AuxVariable, which has no nodal
    // value to read.  This matches the treatment of the mass fractions, which are the same kind of
    // quantity, in PorousFlowMassFraction.
    _primary[i] = &nodalOrQpValue("primary_concentrations", i);
  }
 
  for (unsigned i = 0; i < _num_equilibrium_constants; ++i)
  {
    // If equilibrium_constants are elemental AuxVariables (or constants), we want to use
    // coupledGenericValue() rather than coupledGenericDofValue()
    const bool is_nodal = isCoupled("equilibrium_constants")
                              ? getFieldVar("equilibrium_constants", i)->isNodal()
                              : false;
 
    _equilibrium_constants[i] =
        (_nodal_material && is_nodal ? &coupledDofValues("equilibrium_constants", i)
                                     : &coupledValue("equilibrium_constants", i));
  }
}

Member Function Documentation

◆ computeQpProperties()

void PorousFlowAqueousPreDisChemistry::computeQpProperties ( )

overrideprotected

Definition at line 246 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 310 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 376 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 461 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 292 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 237 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 454 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 285 of file PorousFlowAqueousPreDisChemistry.C.

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

Referenced by computeQpReactionRates(), and dQpReactionRate_dprimary().

◆ validParams()

InputParameters PorousFlowAqueousPreDisChemistry::validParams ( )

static

Definition at line 15 of file PorousFlowAqueousPreDisChemistry.C.

{
  InputParameters params = PorousFlowMaterialVectorBase::validParams();
  params.addRequiredCoupledVar(
      "primary_concentrations",
      "List of MOOSE Variables that represent the concentrations of the primary species");
  params.addRequiredParam<unsigned>("num_reactions",
                                    "Number of equations in the system of chemical reactions");
  params.addParam<bool>("equilibrium_constants_as_log10",
                        false,
                        "If true, the equilibrium constants are written in their log10 form, eg, "
                        "-2.  If false, the equilibrium constants are written in absolute terms, "
                        "eg, 0.01");
  params.addRequiredCoupledVar("equilibrium_constants",
                               "Equilibrium constant for each equation (dimensionless).  If these "
                               "are temperature dependent AuxVariables, the Jacobian will not be "
                               "exact");
  params.addRequiredParam<std::vector<Real>>(
      "primary_activity_coefficients",
      "Activity coefficients for the primary species (dimensionless) (one for each)");
  params.addRequiredParam<std::vector<Real>>(
      "reactions",
      "A matrix defining the aqueous reactions.  The matrix is entered as a long vector: the first "
      "row is "
      "entered first, followed by the second row, etc.  There should be num_reactions rows.  All "
      "primary species should appear only on the LHS of each reaction (and there should be just "
      "one secondary species on the RHS, by definition) so they may have negative coefficients.  "
      "Each row should have number of primary_concentrations entries, which are the stoichiometric "
      "coefficients.  The first coefficient must always correspond to the first primary species, "
      "etc");
  params.addRequiredParam<std::vector<Real>>("specific_reactive_surface_area",
                                             "Specific reactive surface area in m^2/(L solution).");
  params.addRequiredParam<std::vector<Real>>(
      "kinetic_rate_constant",
      "Kinetic rate constant in mol/(m^2 s), at the reference temperature (one for each reaction)");
  params.addRequiredParam<std::vector<Real>>("molar_volume",
                                             "Volume occupied by one mole of the secondary species "
                                             "(L(solution)/mol) (one for each reaction)");
  params.addRequiredParam<std::vector<Real>>("activation_energy",
                                             "Activation energy, J/mol (one for each reaction)");
  params.addParam<Real>("gas_constant", 8.31434, "Gas constant, in J/(mol K)");
  params.addParam<Real>("reference_temperature", 298.15, "Reference temperature, K");
  params.addParam<std::vector<Real>>("theta_exponent",
                                     "Theta exponent.  Defaults to 1.  (one for each reaction)");
  params.addParam<std::vector<Real>>("eta_exponent",
                                     "Eta exponent.  Defaults to 1.  (one for each reaction)");
  params.addPrivateParam<std::string>("pf_material_type", "chemistry");
  params.addClassDescription("This Material forms a std::vector of mineralisation reaction rates "
                             "(L(precipitate)/L(solution)/s) appropriate to the aqueous "
                             "precipitation-dissolution system provided.  Note: the "
                             "PorousFlowTemperature must be measured in Kelvin.");
  return params;
}

Member Data Documentation

◆ _aq_ph

const unsigned int PorousFlowAqueousPreDisChemistry::_aq_ph

protected

Aqueous phase number.

Definition at line 71 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 116 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 122 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 80 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 134 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 95 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 89 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 146 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 137 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 149 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 113 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 128 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 30 of file PorousFlowMaterialVectorBase.h.

Referenced by PorousFlowMassFractionAqueousEquilibriumChemistry::computeQpProperties(), PorousFlowAqueousPreDisChemistry(), PorousFlowDiffusivityBaseTempl< is_ad >::PorousFlowDiffusivityBaseTempl(), and PorousFlowMassFractionTempl< is_ad >::PorousFlowMassFractionTempl().

◆ _num_equilibrium_constants

const unsigned PorousFlowAqueousPreDisChemistry::_num_equilibrium_constants

protected

Number of equilibrium_constants provided.

Definition at line 92 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by PorousFlowAqueousPreDisChemistry().

◆ _num_phases

const unsigned int PorousFlowMaterialVectorBase::_num_phases

protectedinherited

Number of phases.

Definition at line 27 of file PorousFlowMaterialVectorBase.h.

Referenced by PorousFlowDiffusivityBaseTempl< is_ad >::PorousFlowDiffusivityBaseTempl(), PorousFlowDiffusivityConstTempl< is_ad >::PorousFlowDiffusivityConstTempl(), PorousFlowJoinerTempl< is_ad >::PorousFlowJoinerTempl(), PorousFlowMassFractionTempl< is_ad >::PorousFlowMassFractionTempl(), PorousFlowThermalConductivityFromPorosityTempl< is_ad >::PorousFlowThermalConductivityFromPorosityTempl(), PorousFlowThermalConductivityIdealTempl< is_ad >::PorousFlowThermalConductivityIdealTempl(), and PorousFlowTotalGravitationalDensityFullySaturatedFromPorosity::PorousFlowTotalGravitationalDensityFullySaturatedFromPorosity().

◆ _num_primary

const unsigned int PorousFlowAqueousPreDisChemistry::_num_primary

protected

Number of primary species.

Definition at line 83 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 86 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 33 of file PorousFlowMaterialVectorBase.h.

Referenced by computeQpProperties(), PorousFlowMassFractionAqueousEquilibriumChemistry::computeQpProperties(), PorousFlowPorosityExponentialBase::computeQpProperties(), PorousFlowPorosityHMBiotModulus::computeQpProperties(), PorousFlowPorosityLinear::computeQpProperties(), PorousFlowTotalGravitationalDensityFullySaturatedFromPorosity::computeQpProperties(), PorousFlowVolumetricStrain::computeQpProperties(), initQpStatefulProperties(), and PorousFlowPorosityLinear::initQpStatefulProperties().

◆ _one_over_ref_temp

const Real PorousFlowAqueousPreDisChemistry::_one_over_ref_temp

protected

1/reference_temperature (1/K)

Definition at line 140 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by rateConstantQp().

◆ _porosity_old

const MaterialProperty<Real>& PorousFlowAqueousPreDisChemistry::_porosity_old

protected

Old values of the porosity.

Definition at line 68 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 107 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 98 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 104 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 125 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 119 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 101 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 131 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by PorousFlowAqueousPreDisChemistry(), and rateConstantQp().

◆ _saturation

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

protected

Saturation.

Definition at line 74 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates().

◆ _sec_conc_old

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

protected

Definition at line 110 of file PorousFlowAqueousPreDisChemistry.h.

Referenced by computeQpReactionRates().

◆ _temperature

const MaterialProperty<Real>& PorousFlowAqueousPreDisChemistry::_temperature

protected

Temperature.

Definition at line 77 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 143 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 Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ PorousFlowAqueousPreDisChemistry()

Member Function Documentation

◆ computeQpProperties()

◆ computeQpReactionRates()

◆ dQpReactionRate_dprimary()

◆ dQpReactionRate_dT()

◆ findZeroConcentration()

◆ initQpStatefulProperties()

◆ rateConstantQp()

◆ stoichiometry()

◆ validParams()

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