Classes
struct	overloaded
class	StringViewLineIterator

Functions
template<class... Ts>
	overloaded (Ts...) -> overloaded< Ts... >
std::vector< std::string >	extractItemsFromLine (std::string const &line)
std::vector< double >	parseAndFilterChemicalData (std::string const &line, std::vector< int > const &dropped_item_ids, std::size_t chemical_system_id)
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 349 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().

◆ extractItemsFromLine()

std::vector< std::string > ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::extractItemsFromLine ( std::string const & line )

Definition at line 99 of file PhreeqcIO.cpp.

{
    std::vector<std::string> items;
    std::string line_str(line);
    boost::trim_if(line_str, boost::is_any_of("\t "));
    boost::algorithm::split(items, line_str, boost::is_any_of("\t "),
                            boost::token_compress_on);
    return items;
}

References extractItemsFromLine().

Referenced by extractItemsFromLine(), and parseAndFilterChemicalData().

◆ 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 182 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 275 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 150 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... >

◆ parseAndFilterChemicalData()

std::vector< double > ChemistryLib::PhreeqcIOData::anonymous_namespace{PhreeqcIO.cpp}::parseAndFilterChemicalData	(	std::string const &	line,
		std::vector< int > const &	dropped_item_ids,
		std::size_t	chemical_system_id )

Definition at line 109 of file PhreeqcIO.cpp.

{
    std::vector<double> accepted_items;
    std::vector<std::string> const items = extractItemsFromLine(line);
    for (int item_id = 0; item_id < static_cast<int>(items.size()); ++item_id)
    {
        if (std::find(dropped_item_ids.begin(), dropped_item_ids.end(),
                      item_id) != dropped_item_ids.end())
        {
            continue;
        }
        double value;
        try
        {
            value = std::stod(items[item_id]);
        }
        catch (const std::invalid_argument& e)
        {
            OGS_FATAL(
                "Invalid argument. Could not convert string '{:s}' to "
                "double for chemical system {:d}, column {:d}. "
                "Exception '{:s}' was thrown.",
                items[item_id], chemical_system_id + 1, item_id, e.what());
        }
        catch (const std::out_of_range& e)
        {
            OGS_FATAL(
                "Out of range error. Could not convert string "
                "'{:s}' to double for chemical system {:d}, column "
                "{:d}. Exception '{:s}' was thrown.",
                items[item_id], chemical_system_id + 1, item_id, e.what());
        }
        accepted_items.push_back(value);
    }
    return accepted_items;
}

References extractItemsFromLine(), OGS_FATAL, and parseAndFilterChemicalData().

Referenced by parseAndFilterChemicalData().

◆ 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 158 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 328 of file PhreeqcIO.cpp.

{
    auto const& solid_phase =
        medium.phase(MaterialPropertyLib::PhaseName::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(), setPorosityPostReaction(), and MaterialPropertyLib::Solid.

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 234 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 291 of file PhreeqcIO.cpp.

{
    auto const& solid_phase =
        medium.phase(MaterialPropertyLib::PhaseName::Solid);
    auto const& liquid_phase =
        medium.phase(MaterialPropertyLib::PhaseName::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::AqueousLiquid, MaterialPropertyLib::density, MaterialPropertyLib::molality, MaterialPropertyLib::molar_volume, MaterialPropertyLib::Medium::phase(), MaterialPropertyLib::Solid, and updateReactantVolumeFraction().

Referenced by updateReactantVolumeFraction().

Classes

Functions

Function Documentation

◆ averageReactantMolality()

◆ extractItemsFromLine()

◆ initializeReactantMolality()

◆ initializeSiteMolality()

◆ operator<<()

◆ overloaded()

◆ parseAndFilterChemicalData()

◆ setAqueousSolution()

◆ setPorosityPostReaction()

◆ setReactantMolality()

◆ updateReactantVolumeFraction()