Inheritance diagram for BMIPhreeqcRM:

[legend]

Collaboration diagram for BMIPhreeqcRM:

[legend]

Public Member Functions
	BMIPhreeqcRM ()

	BMIPhreeqcRM (int ngrid, int nthreads)

	~BMIPhreeqcRM () override

void	Initialize (std::string config_file="") override

void	Update () override

void	UpdateUntil (double end_time) override

void	Finalize () override

std::string	GetComponentName () override

int	GetInputItemCount () override

int	GetOutputItemCount () override

int	GetPointableItemCount ()

std::vector< std::string >	GetInputVarNames () override

std::vector< std::string >	GetOutputVarNames () override

std::vector< std::string >	GetPointableVarNames ()

std::vector< std::string >	GetReadOnlyVarNames ()

int	GetVarGrid (const std::string name) override

std::string	GetVarType (const std::string name) override

std::string	GetVarUnits (const std::string name) override

int	GetVarItemsize (const std::string name) override

int	GetVarNbytes (const std::string name) override

std::string	GetVarLocation (const std::string name) override

double	GetCurrentTime () override

double	GetStartTime () override

double	GetEndTime () override

std::string	GetTimeUnits () override

double	GetTimeStep () override

void	GetValue (const std::string name, void *dest) override

void	GetValue (const std::string name, bool &OUTPUT)

void	GetValue (const std::string name, bool *OUTPUT)

void	GetValue (const std::string name, double &OUTPUT)

void	GetValue (const std::string name, double *OUTPUT)

void	GetValue (const std::string name, int &OUTPUT)

void	GetValue (const std::string name, int *OUTPUT)

void	GetValue (const std::string name, std::string &OUTPUT)

void	GetValue (const std::string name, std::vector< double > &OUTPUT)

void	GetValue (const std::string name, std::vector< int > &OUTPUT)

void	GetValue (const std::string name, std::vector< std::string > &OUTPUT)

void *	GetValuePtr (std::string name) override

void	GetValueAtIndices (std::string name, void dest, int inds, int count) override

void	SetValue (const std::string name, void *src) override

void	SetValue (const std::string name, bool src)

void	SetValue (const std::string name, const char *src)

void	SetValue (const std::string name, double src)

void	SetValue (const std::string name, int src)

void	SetValue (const std::string name, const std::string src)

void	SetValue (const std::string name, std::vector< double > src)

void	SetValue (const std::string name, std::vector< int > src)

void	SetValue (const std::string name, std::vector< std::string > src)

void	SetValueAtIndices (std::string name, int inds, int count, void src) override

int	GetGridRank (const int grid) override

int	GetGridSize (const int grid) override

std::string	GetGridType (const int grid) override

void	GetGridShape (const int grid, int *shape) override

void	GetGridSpacing (const int grid, double *spacing) override

void	GetGridOrigin (const int grid, double *origin) override

void	GetGridX (const int grid, double *x) override

void	GetGridY (const int grid, double *y) override

void	GetGridZ (const int grid, double *z) override

int	GetGridNodeCount (const int grid) override

int	GetGridEdgeCount (const int grid) override

int	GetGridFaceCount (const int grid) override

void	GetGridEdgeNodes (const int grid, int *edge_nodes) override

void	GetGridFaceEdges (const int grid, int *face_edges) override

void	GetGridFaceNodes (const int grid, int *face_nodes) override

void	GetGridNodesPerFace (const int grid, int *nodes_per_face) override

void	AddOutputVars (std::string option, std::string def) override

IRM_RESULT	SetLanguage (const char *string)

Public Member Functions inherited from PhreeqcRM
	PhreeqcRM (int nxyz, int thread_count_or_communicator, PHRQ_io *io=NULL, bool delay_construct=false)

virtual	~PhreeqcRM (void)

IRM_RESULT	CloseFiles (void)

IPhreeqc *	Concentrations2Utility (const std::vector< double > &c, const std::vector< double > &tc, const std::vector< double > &p_atm)

IRM_RESULT	CreateMapping (const std::vector< int > &grid2chem)

void	DecodeError (int result)

IRM_RESULT	DumpModule (bool dump_on, bool append=false)

void	ErrorHandler (int result, const std::string &e_string)

void	ErrorMessage (const std::string &error_string, bool prepend=true)

int	FindComponents ()

const std::vector< std::vector< int > > &	GetBackwardMapping (void)

int	GetChemistryCellCount (void) const

int	GetComponentCount (void) const

const std::vector< std::string > &	GetComponents (void) const

IRM_RESULT	GetConcentrations (std::vector< double > &c_output)

int	GetCurrentSelectedOutputUserNumber (void)

std::string	GetDatabaseFileName (void)

IRM_RESULT	GetDensityCalculated (std::vector< double > &d_output)

IRM_RESULT	GetDensity (std::vector< double > &d_output)

const std::vector< int > &	GetEndCell (void)

const std::vector< std::string > &	GetEquilibriumPhases (void) const

int	GetEquilibriumPhasesCount (void) const

int	GetErrorHandlerMode (void)

std::string	GetErrorString (void)

const std::vector< std::string > &	GetExchangeNames (void) const

const std::vector< std::string > &	GetExchangeSpecies (void) const

int	GetExchangeSpeciesCount (void) const

std::string	GetFilePrefix (void)

const std::vector< int > &	GetForwardMapping (void)

const std::vector< std::string > &	GetGasComponents (void) const

int	GetGasComponentsCount (void) const

IRM_RESULT	GetGasCompMoles (std::vector< double > &gas_moles_output)

IRM_RESULT	GetGasCompPhi (std::vector< double > &gas_phi)

IRM_RESULT	GetGasCompPressures (std::vector< double > &gas_pressure)

IRM_RESULT	GetGasPhaseVolume (std::vector< double > &gas_volume_output)

const std::vector< double > &	GetGfw (void)

int	GetGridCellCount (void)

IPhreeqc *	GetIPhreeqcPointer (int i)

IRM_RESULT	GetIthConcentration (int i, std::vector< double > &c_output)

IRM_RESULT	GetIthSpeciesConcentration (int i, std::vector< double > &c_output)

const std::vector< std::string > &	GetKineticReactions (void) const

int	GetKineticReactionsCount (void) const

int	GetMpiMyself (void) const

int	GetMpiTasks (void) const

int	GetNthSelectedOutputUserNumber (int n)

bool	GetPartitionUZSolids (void) const

const std::vector< double > &	GetPorosity (void)

const std::vector< double > &	GetPressure (void)

const std::vector< int > &	GetPrintChemistryMask (void)

const std::vector< bool > &	GetPrintChemistryOn (void)

bool	GetRebalanceByCell (void) const

double	GetRebalanceFraction (void) const

IRM_RESULT	GetSaturationCalculated (std::vector< double > &sat_output)

IRM_RESULT	GetSaturation (std::vector< double > &sat_output)

IRM_RESULT	GetSelectedOutput (std::vector< double > &s_output)

int	GetSelectedOutputColumnCount (void)

int	GetSelectedOutputCount (void)

IRM_RESULT	GetSelectedOutputHeading (int icol, std::string &heading)

IRM_RESULT	GetSelectedOutputHeadings (std::vector< std::string > &headings)

bool	GetSelectedOutputOn (void)

int	GetSelectedOutputRowCount (void)

int	GetSICount (void) const

const std::vector< std::string > &	GetSINames (void) const

const std::vector< std::string > &	GetSolidSolutionComponents (void) const

int	GetSolidSolutionComponentsCount (void) const

const std::vector< std::string > &	GetSolidSolutionNames (void) const

const std::vector< double > &	GetSolutionVolume (void)

IRM_RESULT	GetSpeciesConcentrations (std::vector< double > &species_conc_output)

int	GetSpeciesCount (void)

const std::vector< double > &	GetSpeciesD25 (void)

IRM_RESULT	GetSpeciesLog10Gammas (std::vector< double > &species_log10gammas)

IRM_RESULT	GetSpeciesLog10Molalities (std::vector< double > &species_log10molalities)

const std::vector< std::string > &	GetSpeciesNames (void)

bool	GetSpeciesSaveOn (void)

const std::vector< cxxNameDouble > &	GetSpeciesStoichiometry (void)

const std::vector< double > &	GetSpeciesZ (void)

const std::vector< int > &	GetStartCell (void)

const std::vector< std::string > &	GetSurfaceNames (void) const

const std::vector< std::string > &	GetSurfaceSpecies (void) const

int	GetSurfaceSpeciesCount (void) const

const std::vector< std::string > &	GetSurfaceTypes (void) const

const std::vector< double > &	GetTemperature (void)

int	GetThreadCount ()

double	GetTime (void) const

double	GetTimeConversion (void)

double	GetTimeStep (void)

int	GetUnitsExchange (void)

int	GetUnitsGasPhase (void)

int	GetUnitsKinetics (void)

int	GetUnitsPPassemblage (void)

int	GetUnitsSolution (void)

int	GetUnitsSSassemblage (void)

int	GetUnitsSurface (void)

const std::vector< double > &	GetViscosity ()

const std::vector< IPhreeqcPhast * > &	GetWorkers ()

IRM_RESULT	InitializeYAML (std::string yamlfile)

IRM_RESULT	InitialPhreeqc2Concentrations (std::vector< double > &destination_c, const std::vector< int > &boundary_solution1)

IRM_RESULT	InitialPhreeqc2Concentrations (std::vector< double > &destination_c, const std::vector< int > &boundary_solution1, const std::vector< int > &boundary_solution2, const std::vector< double > &fraction1)

IRM_RESULT	InitialEquilibriumPhases2Module (const std::vector< int > &equilibrium_phases)

IRM_RESULT	InitialExchanges2Module (const std::vector< int > &exchanges)

IRM_RESULT	InitialGasPhases2Module (const std::vector< int > &gas_phases)

IRM_RESULT	InitialKinetics2Module (const std::vector< int > &kinetics)

IRM_RESULT	InitialPhreeqc2Module (const std::vector< int > &initial_conditions1)

IRM_RESULT	InitialPhreeqc2Module (const std::vector< int > &initial_conditions1, const std::vector< int > &initial_conditions2, const std::vector< double > &fraction1)

IRM_RESULT	InitialPhreeqc2SpeciesConcentrations (std::vector< double > &destination_c, const std::vector< int > &boundary_solution1)

IRM_RESULT	InitialPhreeqc2SpeciesConcentrations (std::vector< double > &destination_c, const std::vector< int > &boundary_solution1, const std::vector< int > &boundary_solution2, const std::vector< double > &fraction1)

IRM_RESULT	InitialPhreeqcCell2Module (int n, const std::vector< int > &cell_numbers)

IRM_RESULT	InitialSolidSolutions2Module (const std::vector< int > &solid_solutions)

IRM_RESULT	InitialSolutions2Module (const std::vector< int > &solutions)

IRM_RESULT	InitialSurfaces2Module (const std::vector< int > &surfaces)

IRM_RESULT	LoadDatabase (const std::string &database)

void	LogMessage (const std::string &str)

int	MpiAbort ()

IRM_RESULT	MpiWorker ()

IRM_RESULT	MpiWorkerBreak ()

IRM_RESULT	OpenFiles (void)

void	OutputMessage (const std::string &str)

IRM_RESULT	ReturnHandler (IRM_RESULT result, const std::string &e_string)

IRM_RESULT	RunCells (void)

IRM_RESULT	RunFile (bool workers, bool initial_phreeqc, bool utility, const std::string &chemistry_name)

IRM_RESULT	RunString (bool workers, bool initial_phreeqc, bool utility, const std::string &input_string)

void	ScreenMessage (const std::string &str)

IRM_RESULT	SetComponentH2O (bool tf)

IRM_RESULT	SetConcentrations (const std::vector< double > &c)

IRM_RESULT	SetCurrentSelectedOutputUserNumber (int n_user)

IRM_RESULT	SetDensityUser (const std::vector< double > &density)

IRM_RESULT	SetDensity (const std::vector< double > &density)

IRM_RESULT	SetDumpFileName (const std::string &dump_name)

IRM_RESULT	SetErrorHandlerMode (int mode)

IRM_RESULT	SetErrorOn (bool tf)

IRM_RESULT	SetFilePrefix (const std::string &prefix)

IRM_RESULT	SetGasCompMoles (const std::vector< double > &gas_moles)

IRM_RESULT	SetGasPhaseVolume (const std::vector< double > &gas_volume)

IRM_RESULT	SetIthConcentration (int i, std::vector< double > &c)

IRM_RESULT	SetIthSpeciesConcentration (int i, std::vector< double > &c)

IRM_RESULT	SetMpiWorkerCallbackC (int(fcn)(int method, void *cookie))

IRM_RESULT	SetMpiWorkerCallbackCookie (void *cookie)

IRM_RESULT	SetMpiWorkerCallbackFortran (int(fcn)(int method))

IRM_RESULT	SetNthSelectedOutput (int n)

IRM_RESULT	SetPartitionUZSolids (bool tf)

IRM_RESULT	SetPorosity (const std::vector< double > &por)

IRM_RESULT	SetPressure (const std::vector< double > &p)

IRM_RESULT	SetPrintChemistryMask (const std::vector< int > &cell_mask)

IRM_RESULT	SetPrintChemistryOn (bool workers, bool initial_phreeqc, bool utility)

IRM_RESULT	SetRebalanceByCell (bool tf)

IRM_RESULT	SetRebalanceFraction (double f)

IRM_RESULT	SetRepresentativeVolume (const std::vector< double > &rv)

IRM_RESULT	SetSaturationUser (const std::vector< double > &sat)

IRM_RESULT	SetSaturation (const std::vector< double > &sat)

IRM_RESULT	SetScreenOn (bool tf)

IRM_RESULT	SetSelectedOutputOn (bool tf)

IRM_RESULT	SetSpeciesSaveOn (bool save_on)

IRM_RESULT	SetTemperature (const std::vector< double > &t)

IRM_RESULT	SetTime (double time)

IRM_RESULT	SetTimeConversion (double conv_factor)

IRM_RESULT	SetTimeStep (double time_step)

IRM_RESULT	SetUnitsExchange (int option)

IRM_RESULT	SetUnitsGasPhase (int option)

IRM_RESULT	SetUnitsKinetics (int option)

IRM_RESULT	SetUnitsPPassemblage (int option)

IRM_RESULT	SetUnitsSolution (int option)

IRM_RESULT	SetUnitsSSassemblage (int option)

IRM_RESULT	SetUnitsSurface (int option)

IRM_RESULT	SpeciesConcentrations2Module (const std::vector< double > &species_conc)

IRM_RESULT	StateSave (int istate)

IRM_RESULT	StateApply (int istate)

IRM_RESULT	StateDelete (int istate)

void	UseSolutionDensityVolume (bool tf)

void	WarningMessage (const std::string &warnstr)

Public Member Functions inherited from StaticIndexer< PhreeqcRM >
	StaticIndexer (PhreeqcRM *self)

	~StaticIndexer ()

int	GetIndex ()

Static Public Member Functions
static void	CleanupBMIModuleInstances (void)

static int	CreateBMIModule ()

static int	CreateBMIModule (int nxyz, int nthreads)

static IRM_RESULT	DestroyBMIModule (int n)

static BMIPhreeqcRM *	GetInstance (int n)

Static Public Member Functions inherited from PhreeqcRM
static void	CleanupReactionModuleInstances (void)

static int	CreateReactionModule (int nxyz, int nthreads)

static IRM_RESULT	DestroyReactionModule (int n)

static int	GetGridCellCountYAML (const char *YAML_file)

static std::string	Char2TrimString (const char *str, size_t l=0)

static bool	FileExists (const std::string &name)

static void	FileRename (const std::string &temp_name, const std::string &name, const std::string &backup_name)

static IRM_RESULT	Int2IrmResult (int r, bool positive_ok)

Static Public Member Functions inherited from StaticIndexer< PhreeqcRM >
static PhreeqcRM *	GetInstance (int id)

static Derived *	GetInstance (int id)

static IRM_RESULT	Destroy (int id)

static void	DestroyAll ()

Public Attributes
std::string	language

Protected Member Functions
void	Construct (Initializer initializer) override

Additional Inherited Members
Protected Attributes inherited from StaticIndexer< PhreeqcRM >
size_t	_Index

Static Protected Attributes inherited from StaticIndexer< PhreeqcRM >
static std::mutex	_InstancesLock

static std::map< size_t, PhreeqcRM * >	_Instances

static size_t	_InstancesIndex

Detailed Description

Basic Model Interface implementation of the geochemical reaction module PhreeqcRM.

Constructor & Destructor Documentation

◆ BMIPhreeqcRM() [1/2]

BMIPhreeqcRM::BMIPhreeqcRM ( )

Default constructor for the BMIPhreeqcRM subclass of PhreeqcRM. Definition of the number of cells and threads (or MPI communicator) is deferred. Initialize must be called to initialize the BMIPhreeqcRM instance.

◆ BMIPhreeqcRM() [2/2]

BMIPhreeqcRM::BMIPhreeqcRM	(	int	ngrid,
		int	nthreads
	)

Constructor for the BMIPhreeqcRM subclass of PhreeqcRM. A BMIPhreeqcRM instance has the BMI methods plus all of the PhreeqcRM methods. The constructor requires two arguments: the number of cells in the user's model, and either (a) the number of threads for OpenMP parallelization, or (b) an MPI communicator.

Parameters

ngrid	Number of cells in the user's model.
nthreads	Number of threads for parallelization with OpenMP or an MPI communicator if PhreeqcRM is compiled with MPI. With OpenMP, a value of zero causes the program to set nthreads to the number of logical processors of the computer.

C++ Example:


int nthreads = 0;
std::string yaml_file = "myfile.yaml";
int nxyz = GetGridCellCountYAML(yaml_file);
BMIPhreeqcRM brm(nxyz, nthreads);
brm.Initialize(yaml_file);

◆ ~BMIPhreeqcRM()

BMIPhreeqcRM::~BMIPhreeqcRM ( )

override

Member Function Documentation

◆ AddOutputVars()

void BMIPhreeqcRM::AddOutputVars	(	std::string	option,
		std::string	def
	)

overridevirtual

AddOutputVars allows selection of sets of variables that can be retieved by the GetValue method. Sets of variables can be included or excluded with multiple calls to this method. All calls must precede the final call to FindComponents. FindComponents generates SELECTED_OUTPUT 333 and USER_PUNCH 333 data blocks that make the variables accessible. Variables will only be accessible if the system includes the given reactant; for example, no gas variables will be created if there are no GAS_PHASEs in the model.

Parameters

option	A string value, among those listed below, that includes or excludes variables from GetOutputVarNames, GetValue, and other BMI methods.
def	A string value that can be "false", "true", or a list of items to be included as accessible variables. A value of "false", excludes all variables of the given type; a value of "true" includes all variables of the given type for the current system; a list specifies a subset of items of the given type.

Values for the the parameter option:

AddOutputVars: False excludes all variables; True causes the settings for each variable group to determine the variables that will be defined. Default True;

SolutionProperties: False excludes all solution property variables; True includes variables pH, pe, alkalinity, ionic strength, water mass, charge balance, percent error, and specific conductance. Default True.

SolutionTotalMolalities: False excludes all total element and element redox state variables; True includes all elements and element redox state variables for the system defined for the calculation; list restricts variables to the specified elements and redox states. Default True.

ExchangeMolalities: False excludes all variables related to exchange; True includes all variables related to exchange; list includes variables for the specified exchange species. Default True.

SurfaceMolalities: False excludes all variables related to surfaces; True includes all variables related to surfaces; list includes variables for the specified surface species. Default True.

EquilibriumPhases: False excludes all variables related to equilibrium phases; True includes all variables related to equilibrium phases; list includes variables for the specified equilibiurm phases. Default True.

Gases: False excludes all variables related to gases; True includes all variables related to gases; list includes variables for the specified gas components. Default True.

KineticReactants: False excludes all variables related to kinetic reactants; True includes all variables related to kinetic reactants; list includes variables for the specified kinetic reactants. Default True.

SolidSolutions: False excludes all variables related to solid solutions; True includes all variables related to solid solutions; list includes variables for the specified solid solutions components. Default True.

CalculateValues: False excludes all calculate values; True includes all calculate values; list includes the specified calculate values. CALCLUATE_VALUES can be used to calculate geochemical quantities not available in the other sets of variables. Default True.

SolutionActivities: False excludes all aqueous species; True includes all aqueous species; list includes only the specified aqueous species. Default False.

SolutionMolalities: False excludes all aqueous species; True includes all aqueous species; list includes only the specified aqueous species. Default False.

SaturationIndices: False excludes all saturation indices; True includes all saturation indices; list includes only the specified saturation indices. Default False.

Reimplemented from PhreeqcRM.

◆ CleanupBMIModuleInstances()

static void BMIPhreeqcRM::CleanupBMIModuleInstances ( void )

static

◆ Construct()

void BMIPhreeqcRM::Construct ( Initializer initializer )

overrideprotected

◆ CreateBMIModule() [1/2]

static int BMIPhreeqcRM::CreateBMIModule ( )

static

◆ CreateBMIModule() [2/2]

static int BMIPhreeqcRM::CreateBMIModule	(	int	nxyz,
		int	nthreads
	)

static

◆ DestroyBMIModule()

static IRM_RESULT BMIPhreeqcRM::DestroyBMIModule ( int n )

static

◆ Finalize()

void BMIPhreeqcRM::Finalize ( )

override

Finalize closes any files open in the BMIPhreeqcRM instance.

C++ Example:


brm.Finalize();

MPI:: Called by root, workers must be in the loop of MpiWorker.

◆ GetComponentName()

std::string BMIPhreeqcRM::GetComponentName ( )

inlineoverride

GetComponentName returns the component name–"BMI PhreeqcRM". BMI PhreeqcRM is a partial interface to PhreeqcRM, and provides the methods to implement chemical reactions in a multicomponent transport model. All of the native PhreeqcRM methods (non BMI methods) are also available, which provides a complete interface to PhreeqcRM.

Return values

The	string "BMI PhreeqcRM".

C++ Example:


std::string comp_name = brm.GetComponentName();

MPI:: Called by root.

◆ GetCurrentTime()

double BMIPhreeqcRM::GetCurrentTime ( )

override

GetCurrentTime returns the current simulation time, in seconds. (Same as GetTime.)

Return values

The	current simulation time, in seconds.

See also: GetEndTime, GetTimeStep, SetValue, GetTime, GetTimeStep, SetTime, SetTimeStep.

C++ Example:


std::cout << "Current time: " << GetCurrentTime() << " seconds\n";

MPI:: Called by root.

◆ GetEndTime()

double BMIPhreeqcRM::GetEndTime ( )

override

GetEndTime returns GetCurrentTime plus GetTimeStep, in seconds.

Return values

The	end of the time step, in seconds.

See also: GetCurrentTime, GetTimeStep, SetValue, GetTime, GetTimeStep, SetTime, SetTimeStep.

C++ Example:


std::cout << "End of time step " << GetEndTime() << " seconds\n";

MPI:: Called by root.

◆ GetGridEdgeCount()

int BMIPhreeqcRM::GetGridEdgeCount ( const int grid )

inlineoverride

GetGridEdgeCount is not implemented.

◆ GetGridEdgeNodes()

void BMIPhreeqcRM::GetGridEdgeNodes	(	const int	grid,
		int *	edge_nodes
	)

inlineoverride

GetGridEdgeNodes is not implemented.

◆ GetGridFaceCount()

int BMIPhreeqcRM::GetGridFaceCount ( const int grid )

inlineoverride

GetGridFaceCount is not implemented.

◆ GetGridFaceEdges()

void BMIPhreeqcRM::GetGridFaceEdges	(	const int	grid,
		int *	face_edges
	)

inlineoverride

GetGridFaceEdges is not implemented.

◆ GetGridFaceNodes()

void BMIPhreeqcRM::GetGridFaceNodes	(	const int	grid,
		int *	face_nodes
	)

inlineoverride

GetGridFaceNodes is not implemented.

◆ GetGridNodeCount()

int BMIPhreeqcRM::GetGridNodeCount ( const int grid )

inlineoverride

GetGridNodeCount is not implemented.

◆ GetGridNodesPerFace()

void BMIPhreeqcRM::GetGridNodesPerFace	(	const int	grid,
		int *	nodes_per_face
	)

inlineoverride

GetGridNodesPerFace is not implemented.

◆ GetGridOrigin()

void BMIPhreeqcRM::GetGridOrigin	(	const int	grid,
		double *	origin
	)

inlineoverride

GetGridOrigin is not implemented.

◆ GetGridRank()

int BMIPhreeqcRM::GetGridRank ( const int grid )

override

GetGridRank returns a rank of 1 for grid 0. BMIPhreeqcRM only has a 1D series of cells; any grid or spatial information must be found in the user's model.

Parameters

grid	Grid number, only grid 0 is considered.

Return values

Rank	of 1 is returned for grid 0; 0 for all other values of grid.

◆ GetGridShape()

void BMIPhreeqcRM::GetGridShape	(	const int	grid,
		int *	shape
	)

inlineoverride

GetGridShape is not implemented.

◆ GetGridSize()

int BMIPhreeqcRM::GetGridSize ( const int grid )

override

GetGridSize returns the number of cells specified at creation of the BMIPhreeqcRM instance.

Parameters

grid	Grid number, only grid 0 is considered.

Return values

Number of cells in the user's modle (same value as GetGridCellCount) is returned for grid 0; 0 for all other values of grid.

◆ GetGridSpacing()

void BMIPhreeqcRM::GetGridSpacing	(	const int	grid,
		double *	spacing
	)

inlineoverride

GetGridSpacing is not implemented.

◆ GetGridType()

std::string BMIPhreeqcRM::GetGridType ( const int grid )

override

GetGridType is considered to be points. No grid information is available in BMIPhreeqcRM; all grid information must be found in the user's model.

Parameters

grid	Grid number, only grid 0 is considered.

Return values

Points is returned for grid 0; "Undefined grid identifier" is returned for all other values of grid.

◆ GetGridX()

void BMIPhreeqcRM::GetGridX	(	const int	grid,
		double *	x
	)

inlineoverride

GetGridX is not implemented.

◆ GetGridY()

void BMIPhreeqcRM::GetGridY	(	const int	grid,
		double *	y
	)

inlineoverride

GetGridY is not implemented.

◆ GetGridZ()

void BMIPhreeqcRM::GetGridZ	(	const int	grid,
		double *	z
	)

inlineoverride

GetGridZ is not implemented.

◆ GetInputItemCount()

int BMIPhreeqcRM::GetInputItemCount ( )

override

GetInputVarNames returns the count of input variables that can be set with SetValue.

Return values

Count of input variables that can be set with SetValue.

See also: GetInputVarNames, GetVarItemsize, GetVarNbytes, GetVarType, GetVarUnits, SetValue.

C++ Example:


int count = brm.GetInputItemCount();
std::vector< std::string > InputVarNames = brm.GetInputVarNames();
oss << "SetValue variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << InputVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(InputVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(InputVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(InputVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(InputVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(InputVarNames[i]) /
           brm.GetVarItemsize(InputVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ GetInputVarNames()

std::vector< std::string > BMIPhreeqcRM::GetInputVarNames ( )

override

GetInputVarNames returns a list of the variable names that can be set with SetValue.

Return values

A	std::vector of the names of variables that can be set with SetValue.

See also: GetInputItemCount, GetVarItemsize, GetVarNbytes, GetVarType, GetVarUnits, SetValue.

C++ Example:


std::vector< std::string > InputVarNames = brm.GetInputVarNames();
int count = brm.GetInputItemCount();
oss << "SetValue variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << InputVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(InputVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(InputVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(InputVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(InputVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(InputVarNames[i]) /
           brm.GetVarItemsize(InputVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ GetInstance()

static BMIPhreeqcRM * BMIPhreeqcRM::GetInstance ( int n )

static

◆ GetOutputItemCount()

int BMIPhreeqcRM::GetOutputItemCount ( )

override

GetOutputItemCount returns the count of output variables that can be retrieved with GetValue.

Return values

Count of output variables that can be retrieved with GetValue.

See also: GetOutputVarNames, GetValue, GetVarItemsize, GetVarNbytes, GetVarType, GetVarUnits.

C++ Example:


int count = brm.GetOutputItemCount();
std::vector< std::string > OutputVarNames = brm.GetOutputVarNames();
oss << "GetValue variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << OutputVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(OutputVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(OutputVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(OutputVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(OutputVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(OutputVarNames[i]) /
           brm.GetVarItemsize(OutputVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ GetOutputVarNames()

std::vector< std::string > BMIPhreeqcRM::GetOutputVarNames ( )

override

GetOutputVarNames returns a list of the variable names that can be retrieved with GetValue.

Return values

A	list of the names of variable that can be retrieved with GetValue.

See also: GetOutputItemCount, GetValue, GetVarItemsize, GetVarNbytes, GetVarType, GetVarUnits.

C++ Example:


std::vector< std::string > OutputVarNames = brm.GetOutputVarNames();
int count = brm.GetOutputItemCount();
oss << "GetValue variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << OutputVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(OutputVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(OutputVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(OutputVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(OutputVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(OutputVarNames[i]) /
           brm.GetVarItemsize(OutputVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ GetPointableItemCount()

int BMIPhreeqcRM::GetPointableItemCount ( )

GetPointableItemCount returns the count of variables for which pointers can be obtained with GetValuePtr. The pointers point to current copies of the variables. Setting a value with one of the pointers will have no effect on the simulation, but will corrupt the copy of the variable.

Return values

Count of pointers to variables that can be accessed with GetValuePtr.

See also: GetPointableVarNames, GetValue, GetVarItemsize, GetVarNbytes, GetVarType, GetVarUnits.

C++ Example:


int count = brm.GetPointableItemCount();
std::vector< std::string > PointableVarNames = brm.GetPointableVarNames();
oss << "GetValuePtr variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << PointableVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(PointableVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(PointableVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(PointableVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(PointableVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(PointableVarNames[i]) /
           brm.GetVarItemsize(PointableVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ GetPointableVarNames()

std::vector< std::string > BMIPhreeqcRM::GetPointableVarNames ( )

GetPointableVarNames returns a list of the names of variables for which pointers can be retrieved with GetValuePtr.

Return values

A	list of the names of variables for which pointers can be retieved with GetValuePtr.

See also: GetPointableItemCount, GetValue, GetVarItemsize, GetVarNbytes, GetVarType, GetVarUnits.

C++ Example:


std::vector< std::string > PointableVarNames = brm.GetPointableVarNames();
int count = brm.GetPointableItemCount();
oss << "GetValuePtr variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << PointableVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(PointableVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(PointableVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(PointableVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(PointableVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(PointableVarNames[i]) /
           brm.GetVarItemsize(PointableVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ GetReadOnlyVarNames()

std::vector< std::string > BMIPhreeqcRM::GetReadOnlyVarNames ( )

Todo:

◆ GetStartTime()

double BMIPhreeqcRM::GetStartTime ( )

override

GetStartTime returns the current simulation time, in seconds. (Same as GetCurrentTime or GetTime.)

Return values

The	current simulation time, in seconds.

◆ GetTimeStep()

double BMIPhreeqcRM::GetTimeStep ( void )

inlineoverride

◆ GetTimeUnits()

std::string BMIPhreeqcRM::GetTimeUnits ( )

inlineoverride

GetTimeUnits returns the time units of PhreeqcRM. All time units are seconds.

Return values

Returns the string "seconds".

See also: GetCurrentTime, GetEndTime, GetTimeStep, SetValue, GetTime, GetTimeStep, SetTime, SetTimeStep.

C++ Example:


std::cout << "BMIPhreeqcRM time units are " << GetTimeUnits() << ".\n";

MPI:: Called by root.

◆ GetValue() [1/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		bool &	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [2/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		bool *	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [3/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		double &	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [4/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		double *	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [5/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		int &	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [6/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		int *	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [7/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		std::string &	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [8/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		std::vector< double > &	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [9/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		std::vector< int > &	OUTPUT
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ GetValue() [10/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		std::vector< std::string > &	OUTPUT
	)

◆ GetValue() [11/11]

void BMIPhreeqcRM::GetValue	(	const std::string	name,
		void *	dest
	)

override

GetValue retrieves model variables. Only variables in the list provided by GetOutputVarNames can be retrieved.

Parameters

name	Name of the variable to retrieve.
dest	Variable in which to place results. The dest variable can be of different types depending on the variable retrieved. The following list gives the name in the first argument and the corresponding data type of the dest argument:

"ComponentCount", dest: int;
"Components", dest: std::vector< std::string >;
"Concentrations", dest: std::vector< double >;
"CurrentSelectedOutputUserNumber", dest: int;
"DensityCalculated", dest: std::vector< double >;
"ErrorString", dest: std::string;
"FilePrefix", dest: std::string;
"Gfw", dest: std::vector< double >;
"GridCellCount", dest: int;
"Porosity", dest: std::vector< double >;
"Pressure", dest: std::vector< double >;
"SaturationCalculated", dest: std::vector< double >;
"SelectedOutput", dest: std::vector< double >;
"SelectedOutputColumnCount", dest: int;
"SelectedOutputCount", dest: int;
"SelectedOutputHeadings", dest: std::vector< std::string >;
"SelectedOutputOn", dest: bool;
"SelectedOutputRowCount", dest: int;
"SolutionVolume", dest: std::vector< double >;
"Temperature", dest: std::vector< double >;
"Time", dest: double;
"TimeStep", dest: double,
"Viscosity", dest: std::vector< double >.

See also: GetOutputVarNames, GetOutputItemCount, GetValuePtr; GetVarItemsize, GetVarNbytes, GetVarType, GetVarUnits.

C++ Example:


    std::vector< double > density;
    phreeqc_rm.GetValue("DensityCalculated", density);
    std::vector< std::string > comps;
    phreeqc_rm.GetValue("Components", comps);

MPI:: Called by root, workers must be in the loop of MpiWorker.

◆ GetValueAtIndices()

void BMIPhreeqcRM::GetValueAtIndices	(	std::string	name,
		void *	dest,
		int *	inds,
		int	count
	)

inlineoverride

GetValueAtIndices is not implemented

◆ GetValuePtr()

void * BMIPhreeqcRM::GetValuePtr ( std::string name )

override

GetValuePtr takes a variable name and returns a pointer to a current copy of the variable values. Unlike the buffer returned from GetValue, the reference always points to the current values of the variable, even if the model's state has changed.

Parameters

name	Name of the variable to retrieve.

Return values

Void pointer to data. The following list gives the name in the argument and the data type the void pointer should be cast to:
"ComponentCount": int*;
"Concentrations": double*;
"DensityCalculated": double*;
"Gfw": double*;
"GridCellCount": int*;
"Porosity": double*;
"Pressure": double*;
"SaturationCalculated": double*;
"SelectedOutputOn": bool*;
"SolutionVolume": double*;
"Temperature": double*;
"Time": double*;
"TimeStep": double*;
"Viscosity": double*;

◆ GetVarGrid()

int BMIPhreeqcRM::GetVarGrid ( const std::string name )

inlineoverride

GetVarGrid returns a value of 1, indicating points. BMIPhreeqcRM does not have a grid of its own. The cells of BMIPhreeqcRM are associated with the user's model grid, and all spatial characterists are assigned by the user's model.

Parameters

name	Varaiable name. (Return value is the same regardless of name.)

Return values

1	BMIPhreeqcRM cells derive meaning from the user's model.

◆ GetVarItemsize()

int BMIPhreeqcRM::GetVarItemsize ( const std::string name )

override

GetVarItemsize retrieves size of an individual item that can be set or retrived. Sizes may be sizeof(int), sizeof(double), or a character length for string variables.

Parameters

name	Name of the variable to retrieve size.

Return values

Size	of one element of the variable.

See also: GetVarNbytes, GetVarType, GetVarUnits.

C++ Example:


std::vector< std::string > OutputVarNames = brm.GetOutputVarNames();
int count = brm.GetOutputItemCount();
oss << "GetValue variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << OutputVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(OutputVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(OutputVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(OutputVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(OutputVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(OutputVarNames[i]) /
           brm.GetVarItemsize(OutputVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ GetVarLocation()

std::string BMIPhreeqcRM::GetVarLocation ( const std::string name )

inlineoverride

GetVarLocation has no explicit meaning in BMIPhreeqcRM. All grid-related information derives from the user's model.

Parameters

name	Name of the variable, but not used.

Return values

The	string "Unknown" is returned.

◆ GetVarNbytes()

int BMIPhreeqcRM::GetVarNbytes ( const std::string name )

override

GetVarNbytes retrieves the total number of bytes that are set for a variable with SetValue, retrieved for a variable with GetValue, or pointed to by GetValuePtr.

Parameters

name	Name of the variable to retrieve total bytes.

Return values

Total number of bytes set, retrieved, or pointed to for variable.

See also: GetVarItemsize, GetVarType, GetVarUnits.

C++ Example:


    std::vector< std::string > OutputVarNames = brm.GetOutputVarNames();
int count = brm.GetOutputItemCount();
oss << "GetValue variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << OutputVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(OutputVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(OutputVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(OutputVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(OutputVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(OutputVarNames[i]) /
        brm.GetVarItemsize(OutputVarNames[i]) << "\n";
}

MPI :: Called by root.

◆ GetVarType()

std::string BMIPhreeqcRM::GetVarType ( const std::string name )

override

GetVarType retrieves the type of a variable that can be set with SetValue, retrieved with GetValue, or pointed to by GetValuePtr. Types are "int", "double", "std::string", or "std::vector<std::string>".

Parameters

name	Name of the variable to retrieve type.

Return values

Character string of variable type.

See also: GetVarNbytes, GetVarItemsize, GetVarUnits.

C++ Example:


std::vector< std::string > OutputVarNames = brm.GetOutputVarNames();
int count = brm.GetOutputItemCount();
oss << "GetValue variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << OutputVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(OutputVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(OutputVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(OutputVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(OutputVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(OutputVarNames[i]) /
           brm.GetVarItemsize(OutputVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ GetVarUnits()

std::string BMIPhreeqcRM::GetVarUnits ( const std::string name )

override

GetVarUnits retrieves the units of a variable that can be set with SetValue, retrieved with GetValue, or pointed to by GetValuePtr.

Parameters

name	Name of the variable to retrieve units.

Return values

Character string of units for variable.

See also: GetVarNbytes, GetVarItemsize, GetVarType.

C++ Example:


std::vector< std::string > OutputVarNames = brm.GetOutputVarNames();
int count = brm.GetOutputItemCount();
oss << "GetValue variables:\n";
for (size_t i = 0; i < count; i++)
{
    oss << "  " << i << "  " << OutputVarNames[i] << "\n";
    oss << "     Type:        " << brm.GetVarType(OutputVarNames[i]) << "\n";
    oss << "     Units:       " << brm.GetVarUnits(OutputVarNames[i]) << "\n";
    oss << "     Total bytes: " << brm.GetVarNbytes(OutputVarNames[i]) << "\n";
    oss << "     Item bytes:  " << brm.GetVarItemsize(OutputVarNames[i]) << "\n";
    oss << "     Dim:         " << brm.GetVarNbytes(OutputVarNames[i]) /
           brm.GetVarItemsize(OutputVarNames[i]) << "\n";
}

MPI:: Called by root.

◆ Initialize()

void BMIPhreeqcRM::Initialize ( std::string config_file = "" )

override

Initialize must be called to initialize a BMIPhreeqcRM instance. A YAML file is normally used for initialization; however, an empty string can be used for the file name when initializing without use of a YAML file.

The YAML file contains a YAML map of PhreeqcRM methods and data corresponding to each PhreeqcRM method. For example,

    - key: LoadDatabase
      database: phreeqc.dat
    - key: RunFile
      workers: true
      initial_phreeqc: true
      utility: true
      chemistry_name: advect.pqi

Initialize will read the YAML file and execute the specified methods with the specified arguments. Using YAML terminology, the argument(s) for a method may be a scalar, a sequence, or a map, depending if the argument is a single item, a single vector, or there are multiple arguments. In the case of a map, the name associated with each argument (for example "chemistry_name" above) is arbitrary. The names of the map keys for map arguments are not used in parsing the YAML file; only the order of the arguments is important.

The PhreeqcRM methods that can be specified in a YAML file include:

CloseFiles();
CreateMapping(std::vector< int >& grid2chem);
DumpModule();
FindComponents();
InitialEquilibriumPhases2Module(std::vector< int > equilibrium_phases);
InitialExchanges2Module(std::vector< int > exchanges);
InitialGasPhases2Module(std::vector< int > gas_phases);
InitialKineticss2Module(std::vector< int > kinetics);
InitialSolidSolutions2Module(std::vector< int > solid_solutions);
InitialSolutions2Module(std::vector< int > solutions);
InitialSurfaces2Module(std::vector< int > surfaces);
InitialPhreeqc2Module(std::vector< int > initial_conditions1);
InitialPhreeqc2Module(std::vector< int > initial_conditions1,
    std::vector< int > initial_conditions2, std::vector< double > fraction1);
InitialPhreeqcCell2Module(int n, std::vector< int > cell_numbers);
LoadDatabase(std::string database);
OpenFiles();
OutputMessage(std::string str);
RunCells();
RunFile(bool workers, bool initial_phreeqc,
     bool utility, std::string chemistry_name);
RunString(bool workers, bool initial_phreeqc, bool utility, std::string input_string);
ScreenMessage(std::string str);
SetComponentH2O(bool tf);
SetConcentrations(std::vector< double > c);
SetCurrentSelectedOutputUserNumber(int n_user);
SetDensityUser(std::vector< double > density);
SetDumpFileName(std::string dump_name);
SetErrorHandlerMode(int mode);
SetErrorOn(bool tf);
SetFilePrefix(std::string prefix);
SetGasCompMoles(std::vector< double > gas_moles);
SetGasPhaseVolume(std::vector< double > gas_volume);
SetPartitionUZSolids(bool tf);
SetPorosity(std::vector< double > por);
SetPressure(std::vector< double > p);
SetPrintChemistryMask(std::vector< int > cell_mask);
SetPrintChemistryOn(bool workers, bool initial_phreeqc, bool utility);
SetRebalanceByCell(bool tf);
SetRebalanceFraction(double f);
SetRepresentativeVolume(std::vector< double > rv);
SetSaturationUser(std::vector< double > sat);
SetScreenOn(bool tf);
SetSelectedOutputOn(bool tf);
SetSpeciesSaveOn(bool save_on);
SetTemperature(std::vector< double > t);
SetTime(double time);
SetTimeConversion(double conv_factor);
SetTimeStep(double time_step);
SetUnitsExchange(int option);
SetUnitsGasPhase(int option);
SetUnitsKinetics(int option);
SetUnitsPPassemblage(int option);
SetUnitsSolution(int option);
SetUnitsSSassemblage(int option);
SetUnitsSurface(int option);
SpeciesConcentrations2Module(std::vector< double > species_conc);
StateSave(int istate);
StateApply(int istate);
StateDelete(int istate);
UseSolutionDensityVolume(bool tf);
WarningMessage(std::string warnstr);

See also: Update.

C++ Example:


int nthreads = 0;
std::string yaml_file = "myfile.yaml";
int nxyz = GetGridCellCountYAML(yaml_file);
BMIPhreeqcRM brm(nxyz, nthreads);
brm.Initialize(yaml_file);
int ncomps;
brm.GetValue("ComponentCount", &ncomps);
int ngrid;
brm.GetValue("GridCellCount", &ngrid);
std::vector< double > c;
brm.GetValue("Concentrations", c);
brm.SetValue("TimeStep", 86400);
for(double time = 0; time < 864000; time+=86400)
{
    // Take a transport time step here and update the vector c.
    brm.SetValue("Time", time);
    brm.SetValue("Concentrations", c);
    brm.Update();
    brm.GetValue("Concentrations", c);
}

MPI:: Called by root, workers must be in the loop of MpiWorker.

◆ SetLanguage()

IRM_RESULT BMIPhreeqcRM::SetLanguage ( const char * string )

inline

◆ SetValue() [1/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		bool	src
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ SetValue() [2/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		const char *	src
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ SetValue() [3/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		const std::string	src
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ SetValue() [4/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		double	src
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ SetValue() [5/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		int	src
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ SetValue() [6/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		std::vector< double >	src
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ SetValue() [7/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		std::vector< int >	src
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ SetValue() [8/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		std::vector< std::string >	src
	)

This is an overloaded member function, provided for convenience. It differs from the above function only in what argument(s) it accepts.

◆ SetValue() [9/9]

void BMIPhreeqcRM::SetValue	(	const std::string	name,
		void *	src
	)

override

SetValue sets model variables. Only variables in the list provided by GetInputVarNames can be set.

Parameters

name	Name of the variable to retrieve.
src	Data used to set the variable. The src data type can vary depending on the variable retrieved. The following list gives the name in the first argument and the corresponding data type and size of the src argument:

"Concentrations", std::vector, [GridCellCount*ComponentCount];
"DensityUser", std::vector, [GridCellCount];
"FilePrefix", std::string;
"NthSelectedOutput", int;
"Porosity", std::vector, [GridCellCount];
"Pressure", std::vector, [GridCellCount];
"SaturationUser", std::vector, [GridCellCount];
"SelectedOutputOn", bool;
"Temperature", std::vector, [GridCellCount];
"Time", double;
"TimeStep", double;

See also: GetInputVarNames, GetInputItemCount, GetValue, GetVarItemsize, GetVarNbytes, GetVarType, GetVarUnits.

C++ Example:


std::vector< double > temperature(ngrid, 28.0);
phreeqc_rm.SetValue("Temperature", temperature);

MPI:: Called by root, workers must be in the loop of MpiWorker.

◆ SetValueAtIndices()

void BMIPhreeqcRM::SetValueAtIndices	(	std::string	name,
		int *	inds,
		int	count,
		void *	src
	)

inlineoverride

SetValueAtIndices is not implemented.

◆ Update()

void BMIPhreeqcRM::Update ( )

override

Update runs PhreeqcRM for one time step. PhreeqcRM will equilibrate the solutions with all equilibrium reactants (EQUILIBRIUM_PHASES, EXCHANGE, GAS_PHASE, SOLID_SOLUTIONS, and SURFACE) and integrate KINETICS reactions for the specified time step (TimeStep or SetTimeStep).

See also: Initialize, UpdateUntil.

C++ Example:


BMIPhreeqcRM brm(nxyz, nthreads);
brm.Initialize("myfile.yaml");
int ncomps;
brm.GetValue("ComponentCount", &ncomps);
int ngrid;
brm.GetValue("GridCellCount", &ngrid);
std::vector< double > c;
brm.GetValue("Concentrations", c);
brm.SetValue("TimeStep", 86400);
for(double time = 0; time < 864000; time+=86400)
{
    // Take a transport time step here and update the vector c.
    brm.SetValue("Time", time);
    brm.SetValue("Concentrations", c);
    brm.Update();
    brm.GetValue("Concentrations", c);
}

MPI:: Called by root, workers must be in the loop of MpiWorker.

◆ UpdateUntil()

void BMIPhreeqcRM::UpdateUntil ( double end_time )

override

UpdateUntil is the same as Update, except the time step is calculated from the argument end_time. The time step is calculated to be end_time minus the current time (GetCurrentTime).

Parameters

end_time Time at the end of the time step.

See also: Initialize, Update.

C++ Example:


BMIPhreeqcRM brm(nxyz, nthreads);
brm.Initialize("myfile.yaml");
int ncomps;
brm.GetValue("ComponentCount", &ncomps);
int ngrid;
brm.GetValue("GridCellCount", &ngrid);
std::vector< double > c;
brm.GetValue("Concentrations", c);
for(double time = 0; time < 864000; time+=86400)
{
    // Take a transport time step here and update the vector c.
    brm.SetValue("Time", time);
    brm.SetValue("Concentrations", c);
    brm.UpdateUntil(time + 86400.0);
    brm.GetValue("Concentrations", c);
}

MPI:: Called by root, workers must be in the loop of MpiWorker.

Member Data Documentation

◆ language

std::string BMIPhreeqcRM::language

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

BMIPhreeqcRM.h

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BMIPhreeqcRM() [1/2]

◆ BMIPhreeqcRM() [2/2]

◆ ~BMIPhreeqcRM()

Member Function Documentation

◆ AddOutputVars()

◆ CleanupBMIModuleInstances()

◆ Construct()

◆ CreateBMIModule() [1/2]

◆ CreateBMIModule() [2/2]

◆ DestroyBMIModule()

◆ Finalize()

◆ GetComponentName()

◆ GetCurrentTime()

◆ GetEndTime()

◆ GetGridEdgeCount()

◆ GetGridEdgeNodes()

◆ GetGridFaceCount()

◆ GetGridFaceEdges()

◆ GetGridFaceNodes()

◆ GetGridNodeCount()

◆ GetGridNodesPerFace()

◆ GetGridOrigin()

◆ GetGridRank()

◆ GetGridShape()

◆ GetGridSize()

◆ GetGridSpacing()

◆ GetGridType()

◆ GetGridX()

◆ GetGridY()

◆ GetGridZ()

◆ GetInputItemCount()

◆ GetInputVarNames()

◆ GetInstance()

◆ GetOutputItemCount()

◆ GetOutputVarNames()

◆ GetPointableItemCount()

◆ GetPointableVarNames()

◆ GetReadOnlyVarNames()

◆ GetStartTime()

◆ GetTimeStep()

◆ GetTimeUnits()

◆ GetValue() [1/11]

◆ GetValue() [2/11]

◆ GetValue() [3/11]

◆ GetValue() [4/11]

◆ GetValue() [5/11]

◆ GetValue() [6/11]

◆ GetValue() [7/11]

◆ GetValue() [8/11]

◆ GetValue() [9/11]

◆ GetValue() [10/11]

◆ GetValue() [11/11]

◆ GetValueAtIndices()

◆ GetValuePtr()

◆ GetVarGrid()

◆ GetVarItemsize()

◆ GetVarLocation()

◆ GetVarNbytes()

◆ GetVarType()

◆ GetVarUnits()

◆ Initialize()

◆ SetLanguage()

◆ SetValue() [1/9]

◆ SetValue() [2/9]

◆ SetValue() [3/9]

◆ SetValue() [4/9]

◆ SetValue() [5/9]

◆ SetValue() [6/9]

◆ SetValue() [7/9]

◆ SetValue() [8/9]

◆ SetValue() [9/9]

◆ SetValueAtIndices()

◆ Update()