25 namespace PhreeqcIOData
27 struct ChemicalSystem;
38 std::string
const& project_file_name,
39 std::string&& database,
40 std::unique_ptr<ChemicalSystem>&& chemical_system,
41 std::vector<ReactionRate>&& reaction_rates,
42 std::vector<SurfaceSite>&& surface,
43 std::unique_ptr<UserPunch>&& user_punch,
44 std::unique_ptr<Output>&& output,
45 std::unique_ptr<Dump>&& dump,
51 std::vector<double>
const& concentrations,
55 double const t)
override;
58 std::vector<double>
const& concentrations,
63 double const dt)
override;
72 int const component_id,
75 friend std::ostream&
operator<<(std::ostream& os,
84 double const t,
double const dt)
override;
88 double& porosity)
override;
91 std::size_t
const ele_id,
92 std::vector<GlobalIndexType>
const& chemical_system_indices)
override;
119 double _dt = std::numeric_limits<double>::quiet_NaN();
GlobalMatrix::IndexType GlobalIndexType
GlobalLinearSolver & linear_solver
std::vector< SurfaceSite > const _surface
std::string const _phreeqc_input_file
PhreeqcIO(GlobalLinearSolver &linear_solver, std::string const &project_file_name, std::string &&database, std::unique_ptr< ChemicalSystem > &&chemical_system, std::vector< ReactionRate > &&reaction_rates, std::vector< SurfaceSite > &&surface, std::unique_ptr< UserPunch > &&user_punch, std::unique_ptr< Output > &&output, std::unique_ptr< Dump > &&dump, Knobs &&knobs)
double getConcentration(int const component_id, GlobalIndexType const chemical_system_id) const override
void setAqueousSolutionsPrevFromDumpFile() override
std::unique_ptr< ChemicalSystem > _chemical_system
std::vector< ReactionRate > const _reaction_rates
std::unique_ptr< UserPunch > _user_punch
const int phreeqc_instance_id
void writeInputsToFile(double const dt)
void setChemicalSystemConcrete(std::vector< double > const &concentrations, GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Medium const *medium, MaterialPropertyLib::VariableArray const &vars, ParameterLib::SpatialPosition const &pos, double const t, double const dt) override
std::unique_ptr< Dump > const _dump
void initialize() override
std::unique_ptr< Output > const _output
friend std::istream & operator>>(std::istream &in, PhreeqcIO &phreeqc_io)
void readOutputsFromFile()
std::vector< GlobalVector * > getIntPtProcessSolutions() const override
friend std::ostream & operator<<(std::ostream &os, PhreeqcIO const &phreeqc_io)
std::size_t _num_chemical_systems
void computeSecondaryVariable(std::size_t const ele_id, std::vector< GlobalIndexType > const &chemical_system_indices) override
void initializeChemicalSystemConcrete(std::vector< double > const &concentrations, GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Medium const &medium, ParameterLib::SpatialPosition const &pos, double const t) override
void updateVolumeFractionPostReaction(GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Medium const &medium, ParameterLib::SpatialPosition const &pos, double const porosity, double const t, double const dt) override
PhreeqcIO & operator<<(double const dt)
void executeSpeciationCalculation(double const dt) override
std::string const _database
std::vector< std::string > const getComponentList() const override
void updatePorosityPostReaction(GlobalIndexType const &chemical_system_id, MaterialPropertyLib::Medium const &medium, double &porosity) override
std::array< VariableType, static_cast< int >(Variable::number_of_variables)> VariableArray