ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp} Namespace Reference

Classes
struct	overloaded

Functions
template<class... Ts>
	overloaded (Ts...) -> overloaded< Ts... >
template<typename DataBlock>
std::ostream &	operator<< (std::ostream &os, std::vector< DataBlock > const &data_blocks)
void	setAqueousSolution (std::vector< double > const &concentrations, GlobalIndexType const &chemical_system_id, AqueousSolution &aqueous_solution)
template<typename Reactant>
void	initializeReactantMolality (Reactant &reactant, GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Phase const &solid_phase, MaterialPropertyLib::Phase const &liquid_phase, MaterialPropertyLib::Medium const &medium, ParameterLib::SpatialPosition const &pos, double const t)
template<typename Reactant>
void	setReactantMolality (Reactant &reactant, GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Phase const &solid_phase, MaterialPropertyLib::Phase const &liquid_phase, MaterialPropertyLib::VariableArray const &vars, ParameterLib::SpatialPosition const &pos, double const t, double const dt)
template<typename Site>
void	initializeSiteMolality (Site &site, GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Phase const &solid_phase, ParameterLib::SpatialPosition const &pos, double const t)
template<typename Reactant>
void	updateReactantVolumeFraction (Reactant &reactant, GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Medium const &medium, ParameterLib::SpatialPosition const &pos, double const porosity, double const t, double const dt)
template<typename Reactant>
void	setPorosityPostReaction (Reactant &reactant, GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Medium const &medium, double &porosity)
template<typename Reactant>
static double	averageReactantMolality (Reactant const &reactant, std::vector< GlobalIndexType > const &chemical_system_indices)

Function Documentation

averageReactantMolality()

template<typename Reactant>

double ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::averageReactantMolality ( Reactant const & reactant, std::vector< GlobalIndexType > const & chemical_system_indices )

static

Definition at line 250 of file PhreeqcIO.cpp.

{
    double const sum = std::accumulate(
        chemical_system_indices.begin(), chemical_system_indices.end(), 0.0,
        [&](double const s, GlobalIndexType const id)
        { return s + (*reactant.molality)[id]; });
    return sum / chemical_system_indices.size();
}

References averageReactantMolality().

Referenced by averageReactantMolality().

initializeReactantMolality()

template<typename Reactant>

void ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::initializeReactantMolality	(	Reactant &	reactant,
		GlobalIndexType const &	chemical_system_id,
		MaterialPropertyLib::Phase const &	solid_phase,
		MaterialPropertyLib::Phase const &	liquid_phase,
		MaterialPropertyLib::Medium const &	medium,
		ParameterLib::SpatialPosition const &	pos,
		double const	t )

Definition at line 86 of file PhreeqcIO.cpp.

{
    auto const& solid_constituent = solid_phase.component(reactant.name);
 
    if (solid_constituent.hasProperty(
            MaterialPropertyLib::PropertyType::molality))
    {
        auto const molality =
            solid_constituent[MaterialPropertyLib::PropertyType::molality]
                .template initialValue<double>(pos, t);
 
        (*reactant.molality)[chemical_system_id] = molality;
        (*reactant.molality_prev)[chemical_system_id] = molality;
    }
    else
    {
        auto const volume_fraction =
            solid_constituent
                [MaterialPropertyLib::PropertyType::volume_fraction]
                    .template initialValue<double>(pos, t);
 
        (*reactant.volume_fraction)[chemical_system_id] = volume_fraction;
 
        (*reactant.volume_fraction_prev)[chemical_system_id] = volume_fraction;
 
        auto const fluid_density =
            liquid_phase[MaterialPropertyLib::PropertyType::density]
                .template initialValue<double>(pos, t);
 
        auto const porosity =
            medium[MaterialPropertyLib::PropertyType::porosity]
                .template initialValue<double>(pos, t);
 
        auto const molar_volume =
            solid_constituent[MaterialPropertyLib::PropertyType::molar_volume]
                .template initialValue<double>(pos, t);
 
        (*reactant.molality)[chemical_system_id] =
            volume_fraction / fluid_density / porosity / molar_volume;
 
        (*reactant.molality_prev)[chemical_system_id] =
            (*reactant.molality)[chemical_system_id];
    }
}

References MaterialPropertyLib::Phase::component(), MaterialPropertyLib::density, initializeReactantMolality(), MaterialPropertyLib::molality, MaterialPropertyLib::molar_volume, MaterialPropertyLib::porosity, and MaterialPropertyLib::volume_fraction.

Referenced by initializeReactantMolality().

initializeSiteMolality()

template<typename Site>

void ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::initializeSiteMolality	(	Site &	site,
		GlobalIndexType const &	chemical_system_id,
		MaterialPropertyLib::Phase const &	solid_phase,
		ParameterLib::SpatialPosition const &	pos,
		double const	t )

Definition at line 179 of file PhreeqcIO.cpp.

{
    auto const& solid_constituent = solid_phase.component(site.name);
 
    auto const molality =
        solid_constituent[MaterialPropertyLib::PropertyType::molality]
            .template initialValue<double>(pos, t);
 
    (*site.molality)[chemical_system_id] = molality;
}

References MaterialPropertyLib::Phase::component(), initializeSiteMolality(), and MaterialPropertyLib::molality.

Referenced by initializeSiteMolality().

operator<<()

template<typename DataBlock>

std::ostream & ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::operator<<	(	std::ostream &	os,
		std::vector< DataBlock > const &	data_blocks )

Definition at line 54 of file PhreeqcIO.cpp.

{
    std::copy(data_blocks.begin(), data_blocks.end(),
              std::ostream_iterator<DataBlock>(os));
    return os;
}

overloaded()

template<class... Ts>

ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::overloaded

(

Ts...

)

-> overloaded< Ts... >

setAqueousSolution()

void ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::setAqueousSolution	(	std::vector< double > const &	concentrations,
		GlobalIndexType const &	chemical_system_id,
		AqueousSolution &	aqueous_solution )

Definition at line 62 of file PhreeqcIO.cpp.

{
    GlobalIndexType const offset = aqueous_solution.pH->getRangeBegin();
    GlobalIndexType const global_index = offset + chemical_system_id;
 
    // components
    auto& components = aqueous_solution.components;
    for (unsigned component_id = 0; component_id < components.size();
         ++component_id)
    {
        MathLib::LinAlg::setLocalAccessibleVector(
            *components[component_id].amount);
        components[component_id].amount->set(global_index,
                                             concentrations[component_id]);
    }
 
    // pH
    MathLib::LinAlg::setLocalAccessibleVector(*aqueous_solution.pH);
    aqueous_solution.pH->set(global_index, concentrations.back());
}

References ChemistryLib::PhreeqcIOData::AqueousSolution::components, ChemistryLib::PhreeqcIOData::AqueousSolution::pH, setAqueousSolution(), and MathLib::LinAlg::setLocalAccessibleVector().

Referenced by setAqueousSolution().

setPorosityPostReaction()

template<typename Reactant>

void ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::setPorosityPostReaction	(	Reactant &	reactant,
		GlobalIndexType const &	chemical_system_id,
		MaterialPropertyLib::Medium const &	medium,
		double &	porosity )

Definition at line 230 of file PhreeqcIO.cpp.

{
    auto const& solid_phase = medium.phase("Solid");
 
    auto const& solid_constituent = solid_phase.component(reactant.name);
 
    if (solid_constituent.hasProperty(
            MaterialPropertyLib::PropertyType::molality))
    {
        return;
    }
 
    porosity -= ((*reactant.volume_fraction)[chemical_system_id] -
                 (*reactant.volume_fraction_prev)[chemical_system_id]);
}

References MaterialPropertyLib::Phase::component(), MaterialPropertyLib::molality, MaterialPropertyLib::Medium::phase(), and setPorosityPostReaction().

Referenced by setPorosityPostReaction().

setReactantMolality()

template<typename Reactant>

void ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::setReactantMolality	(	Reactant &	reactant,
		GlobalIndexType const &	chemical_system_id,
		MaterialPropertyLib::Phase const &	solid_phase,
		MaterialPropertyLib::Phase const &	liquid_phase,
		MaterialPropertyLib::VariableArray const &	vars,
		ParameterLib::SpatialPosition const &	pos,
		double const	t,
		double const	dt )

Definition at line 138 of file PhreeqcIO.cpp.

{
    auto const& solid_constituent = solid_phase.component(reactant.name);
 
    if (solid_constituent.hasProperty(
            MaterialPropertyLib::PropertyType::molality))
    {
        (*reactant.molality_prev)[chemical_system_id] =
            (*reactant.molality)[chemical_system_id];
 
        return;
    }
 
    auto const volume_fraction =
        (*reactant.volume_fraction)[chemical_system_id];
 
    (*reactant.volume_fraction_prev)[chemical_system_id] =
        (*reactant.volume_fraction)[chemical_system_id];
 
    auto const fluid_density =
        liquid_phase[MaterialPropertyLib::PropertyType::density]
            .template value<double>(vars, pos, t, dt);
 
    auto const molar_volume =
        solid_constituent[MaterialPropertyLib::PropertyType::molar_volume]
            .template value<double>(vars, pos, t, dt);
 
    (*reactant.molality)[chemical_system_id] =
        volume_fraction / fluid_density / vars.porosity / molar_volume;
 
    (*reactant.molality_prev)[chemical_system_id] =
        (*reactant.molality)[chemical_system_id];
}

References MaterialPropertyLib::Phase::component(), MaterialPropertyLib::density, MaterialPropertyLib::molality, MaterialPropertyLib::molar_volume, MaterialPropertyLib::VariableArray::porosity, and setReactantMolality().

Referenced by setReactantMolality().

updateReactantVolumeFraction()

template<typename Reactant>

void ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::updateReactantVolumeFraction	(	Reactant &	reactant,
		GlobalIndexType const &	chemical_system_id,
		MaterialPropertyLib::Medium const &	medium,
		ParameterLib::SpatialPosition const &	pos,
		double const	porosity,
		double const	t,
		double const	dt )

Definition at line 195 of file PhreeqcIO.cpp.

{
    auto const& solid_phase = medium.phase("Solid");
    auto const& liquid_phase = medium.phase("AqueousLiquid");
 
    MaterialPropertyLib::VariableArray vars;
 
    auto const liquid_density =
        liquid_phase[MaterialPropertyLib::PropertyType::density]
            .template value<double>(vars, pos, t, dt);
 
    auto const& solid_constituent = solid_phase.component(reactant.name);
 
    if (solid_constituent.hasProperty(
            MaterialPropertyLib::PropertyType::molality))
    {
        return;
    }
 
    auto const molar_volume =
        solid_constituent[MaterialPropertyLib::PropertyType::molar_volume]
            .template value<double>(vars, pos, t, dt);
 
    (*reactant.volume_fraction)[chemical_system_id] +=
        ((*reactant.molality)[chemical_system_id] -
         (*reactant.molality_prev)[chemical_system_id]) *
        liquid_density * porosity * molar_volume;
}

References MaterialPropertyLib::density, MaterialPropertyLib::molality, MaterialPropertyLib::molar_volume, MaterialPropertyLib::Medium::phase(), and updateReactantVolumeFraction().

Referenced by updateReactantVolumeFraction().