Outputs information (to the console) from a GeochemistryReactorBase at a point. More...

#include <GeochemistryConsoleOutput.h>

Inheritance diagram for GeochemistryConsoleOutput:

Public Types
typedef DataFileName	DataFileParameterType

Public Member Functions
	GeochemistryConsoleOutput (const InputParameters &parameters)

virtual Real	time ()

virtual Real	timeOld ()

virtual Real	dt ()

virtual Real	dtOld ()

virtual int	timeStep ()

const unsigned int &	interval () const

const MultiMooseEnum &	executeOn () const

bool	isAdvanced ()

virtual const OutputOnWarehouse &	advancedExecuteOn () const

void	allowOutput (bool state)

virtual void	outputStep (const ExecFlagType &type)

const std::set< Real > &	getSyncTimes ()

virtual bool	supportsMaterialPropertyOutput () const

virtual bool	enabled () const

std::shared_ptr< MooseObject >	getSharedPtr ()

std::shared_ptr< const MooseObject >	getSharedPtr () const

bool	isKokkosObject () const

MooseApp &	getMooseApp () const

const std::string &	type () const

const std::string &	name () const

std::string	typeAndName () const

MooseObjectParameterName	uniqueParameterName (const std::string &parameter_name) const

MooseObjectName	uniqueName () const

const InputParameters &	parameters () const

const hit::Node *	getHitNode () const

bool	hasBase () const

const std::string &	getBase () const

const T &	getParam (const std::string &name) const

std::vector< std::pair< T1, T2 > >	getParam (const std::string &param1, const std::string &param2) const

const T *	queryParam (const std::string &name) const

const T &	getRenamedParam (const std::string &old_name, const std::string &new_name) const

T	getCheckedPointerParam (const std::string &name, const std::string &error_string="") const

bool	isParamValid (const std::string &name) const

bool	isParamSetByUser (const std::string &name) const

void	connectControllableParams (const std::string &parameter, const std::string &object_type, const std::string &object_name, const std::string &object_parameter) const

void	paramError (const std::string &param, Args... args) const

void	paramWarning (const std::string &param, Args... args) const

void	paramWarning (const std::string &param, Args... args) const

void	paramInfo (const std::string &param, Args... args) const

std::string	messagePrefix (const bool hit_prefix=true) const

std::string	errorPrefix (const std::string &) const

void	mooseError (Args &&... args) const

void	mooseDocumentedError (const std::string &repo_name, const unsigned int issue_num, Args &&... args) const

void	mooseErrorNonPrefixed (Args &&... args) const

void	mooseWarning (Args &&... args) const

void	mooseWarning (Args &&... args) const

void	mooseWarningNonPrefixed (Args &&... args) const

void	mooseWarningNonPrefixed (Args &&... args) const

void	mooseDeprecated (Args &&... args) const

void	mooseDeprecated (Args &&... args) const

void	mooseDeprecatedNoTrace (Args &&... args) const

void	mooseInfo (Args &&... args) const

void	callMooseError (std::string msg, const bool with_prefix, const hit::Node *node=nullptr, const bool show_trace=true) const

std::string	getDataFileName (const std::string &param) const

std::string	getDataFileNameByName (const std::string &relative_path) const

std::string	getDataFilePath (const std::string &relative_path) const

virtual void	meshChanged ()

virtual void	initialSetup ()

virtual void	timestepSetup ()

virtual void	jacobianSetup ()

virtual void	residualSetup ()

virtual void	subdomainSetup ()

virtual void	customSetup (const ExecFlagType &)

const ExecFlagEnum &	getExecuteOnEnum () const

const Function &	getFunction (const std::string &name) const

const Function &	getFunctionByName (const FunctionName &name) const

bool	hasFunction (const std::string &param_name) const

bool	hasFunctionByName (const FunctionName &name) const

Moose::Kokkos::Function	getKokkosFunction (const std::string &name) const

const T &	getKokkosFunction (const std::string &name) const

Moose::Kokkos::Function	getKokkosFunctionByName (const FunctionName &name) const

const T &	getKokkosFunctionByName (const FunctionName &name) const

bool	hasKokkosFunction (const std::string &param_name) const

bool	hasKokkosFunctionByName (const FunctionName &name) const

bool	isDefaultPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

bool	hasPostprocessor (const std::string &param_name, const unsigned int index=0) const

bool	hasPostprocessorByName (const PostprocessorName &name) const

std::size_t	coupledPostprocessors (const std::string &param_name) const

const PostprocessorName &	getPostprocessorName (const std::string &param_name, const unsigned int index=0) const

const VectorPostprocessorValue &	getVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name, bool needs_broadcast) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const VectorPostprocessorValue &	getVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name, bool needs_broadcast) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValue (const std::string &param_name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueOld (const std::string &param_name, const std::string &vector_name) const

const ScatterVectorPostprocessorValue &	getScatterVectorPostprocessorValueOldByName (const VectorPostprocessorName &name, const std::string &vector_name) const

bool	hasVectorPostprocessor (const std::string &param_name, const std::string &vector_name) const

bool	hasVectorPostprocessor (const std::string &param_name) const

bool	hasVectorPostprocessorByName (const VectorPostprocessorName &name, const std::string &vector_name) const

bool	hasVectorPostprocessorByName (const VectorPostprocessorName &name) const

const VectorPostprocessorName &	getVectorPostprocessorName (const std::string &param_name) const

PerfGraph &	perfGraph ()

const PostprocessorValue &	getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValue (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOld (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const

const PostprocessorValue &	getPostprocessorValueOlder (const std::string &param_name, const unsigned int index=0) const

virtual const PostprocessorValue &	getPostprocessorValueByName (const PostprocessorName &name) const

virtual const PostprocessorValue &	getPostprocessorValueByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOldByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOldByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOlderByName (const PostprocessorName &name) const

const PostprocessorValue &	getPostprocessorValueOlderByName (const PostprocessorName &name) const

bool	isVectorPostprocessorDistributed (const std::string &param_name) const

bool	isVectorPostprocessorDistributed (const std::string &param_name) const

bool	isVectorPostprocessorDistributedByName (const VectorPostprocessorName &name) const

bool	isVectorPostprocessorDistributedByName (const VectorPostprocessorName &name) const

const Parallel::Communicator &	comm () const

processor_id_type	n_processors () const

processor_id_type	processor_id () const

UserObjectName	getUserObjectName (const std::string &param_name) const

const T &	getUserObject (const std::string &param_name, bool is_dependency=true) const

const T &	getUserObjectByName (const UserObjectName &object_name, bool is_dependency=true) const

const UserObjectBase &	getUserObjectBase (const std::string &param_name, bool is_dependency=true) const

const UserObjectBase &	getUserObjectBaseByName (const UserObjectName &object_name, bool is_dependency=true) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObject (const std::string &param_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

bool	hasUserObjectByName (const UserObjectName &object_name) const

Static Public Member Functions
static InputParameters	sharedParams ()
	contains params that are shared with Actions that use this object

static InputParameters	validParams ()

static void	callMooseError (MooseApp const app, const InputParameters &params, std::string msg, const bool with_prefix, const hit::Node node, const bool show_trace=true)

static ExecFlagEnum	getDefaultExecFlagEnum ()

static void	addDeprecatedInputParameters (InputParameters &params)

Public Attributes
	usingCombinedWarningSolutionWarnings

const ConsoleStream	_console

Static Public Attributes
static const std::string	type_param

static const std::string	name_param

static const std::string	unique_name_param

static const std::string	app_param

static const std::string	moose_base_param

static const std::string	kokkos_object_param

Protected Member Functions
virtual void	output () override

virtual void	solveSetup ()

virtual bool	shouldOutput ()

virtual bool	onInterval ()

void	setWallTimeIntervalFromCommandLineParam ()

void	flagInvalidSolutionInternal (const InvalidSolutionID invalid_solution_id) const

InvalidSolutionID	registerInvalidSolutionInternal (const std::string &message, const bool warning) const

T &	declareRestartableData (const std::string &data_name, Args &&... args)

ManagedValue< T >	declareManagedRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)

const T &	getRestartableData (const std::string &data_name) const

T &	declareRestartableDataWithContext (const std::string &data_name, void *context, Args &&... args)

T &	declareRecoverableData (const std::string &data_name, Args &&... args)

T &	declareRestartableDataWithObjectName (const std::string &data_name, const std::string &object_name, Args &&... args)

T &	declareRestartableDataWithObjectNameWithContext (const std::string &data_name, const std::string &object_name, void *context, Args &&... args)

std::string	restartableName (const std::string &data_name) const

virtual void	addPostprocessorDependencyHelper (const PostprocessorName &) const

virtual void	addVectorPostprocessorDependencyHelper (const VectorPostprocessorName &) const

const ReporterContextBase &	getReporterContextBaseByName (const ReporterName &reporter_name) const

const ReporterName &	getReporterName (const std::string &param_name) const

virtual void	addReporterDependencyHelper (const ReporterName &)

PerfID	registerTimedSection (const std::string &section_name, const unsigned int level) const

PerfID	registerTimedSection (const std::string &section_name, const unsigned int level, const std::string &live_message, const bool print_dots=true) const

std::string	timedSectionName (const std::string &section_name) const

const T &	getReporterValue (const std::string &param_name, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, const std::size_t time_index=0)

const T &	getReporterValue (const std::string &param_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, const std::size_t time_index=0)

const T &	getReporterValueByName (const ReporterName &reporter_name, ReporterMode mode, const std::size_t time_index=0)

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValue (const std::string &param_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

bool	hasReporterValueByName (const ReporterName &reporter_name) const

virtual void	addUserObjectDependencyHelper (const UserObjectBase &) const

Protected Attributes
const GeochemistryReactorBase &	_reactor
	the Reactor from which to extract info

const NearestNodeNumberUO &	_nnn
	UserObject defining the node of interest.

const unsigned	_precision
	precision of output

const Real	_stoi_tol
	Tolerance on stoichiometric coefficients before they are deemed to be zero.

const bool	_solver_info
	Whether to print solver info.

const Real	_mol_cutoff
	Species with molalities less than mol_cutoff will not be outputted.

FEProblemBase *	_problem_ptr

bool	_transient

bool	_use_displaced

libMesh::EquationSystems *	_es_ptr

MooseMesh *	_mesh_ptr

bool	_sequence

ExecFlagEnum	_execute_on

ExecFlagType	_current_execute_flag

Real &	_time

Real &	_time_old

int &	_t_step

Real &	_dt

Real &	_dt_old

unsigned int	_num

const bool	_time_step_interval_set_by_addparam

unsigned int	_time_step_interval

const Real	_min_simulation_time_interval

Real	_wall_time_interval

std::set< Real >	_sync_times

const Times *const	_sync_times_object

Real	_start_time

Real	_end_time

int	_start_step

int	_end_step

Real	_t_tol

bool	_sync_only

bool	_allow_output

bool	_is_advanced

OutputOnWarehouse	_advanced_execute_on

Real &	_last_output_simulation_time

std::chrono::time_point< std::chrono::steady_clock >	_last_output_wall_time

Real	_wall_time_since_last_output

const bool &	_enabled

MooseApp &	_app

Factory &	_factory

ActionFactory &	_action_factory

const std::string &	_type

const std::string &	_name

const InputParameters &	_pars

MooseApp &	_restartable_app

const std::string	_restartable_system_name

const THREAD_ID	_restartable_tid

const bool	_restartable_read_only

FEProblemBase &	_mci_feproblem

const ExecFlagEnum &	_execute_enum

MooseApp &	_pg_moose_app

const std::string	_prefix

const Parallel::Communicator &	_communicator

Private Member Functions
void	outputNernstInfo (const GeochemicalSystem &egs_ref) const

RestartableDataValue &	registerRestartableDataOnApp (std::unique_ptr< RestartableDataValue > data, THREAD_ID tid) const

void	registerRestartableNameWithFilterOnApp (const std::string &name, Moose::RESTARTABLE_FILTER filter)

RestartableData< T > &	declareRestartableDataHelper (const std::string &data_name, void *context, Args &&... args) const

const Moose::FunctionBase *	getKokkosFunctionByNameHelper (const FunctionName &name) const

const PostprocessorName &	getPostprocessorNameInternal (const std::string &param_name, const unsigned int index, const bool allow_default_value=true) const

bool	isDefaultPostprocessorValueByName (const PostprocessorName &name) const

PostprocessorValue	getDefaultPostprocessorValueByName (const PostprocessorName &name) const

void	checkParam (const std::string &param_name, const unsigned int index=std::numeric_limits< unsigned int >::max()) const

bool	postprocessorsAdded () const

const VectorPostprocessorValue &	getVectorPostprocessorByNameHelper (const VectorPostprocessorName &name, const std::string &vector_name, bool broadcast, std::size_t t_index) const

const VectorPostprocessorContext< VectorPostprocessorValue > &	getVectorPostprocessorContextByNameHelper (const VectorPostprocessorName &name, const std::string &vector_name) const

bool	vectorPostprocessorsAdded () const

bool	reportersAdded () const

void	possiblyCheckHasReporter (const ReporterName &reporter_name, const std::string &param_name="") const

const PostprocessorValue &	getPostprocessorValueInternal (const std::string &param_name, unsigned int index, std::size_t t_index) const

const PostprocessorValue &	getPostprocessorValueInternal (const std::string &param_name, unsigned int index, std::size_t t_index) const

const PostprocessorValue &	getPostprocessorValueByNameInternal (const PostprocessorName &name, std::size_t t_index) const

const PostprocessorValue &	getPostprocessorValueByNameInternal (const PostprocessorName &name, std::size_t t_index) const

void	possiblyCheckHasVectorPostprocessor (const std::string &param_name, const std::string &vector_name) const

void	possiblyCheckHasVectorPostprocessor (const std::string &param_name, const std::string &vector_name) const

void	possiblyCheckHasVectorPostprocessorByName (const VectorPostprocessorName &name, const std::string &vector_name) const

void	possiblyCheckHasVectorPostprocessorByName (const VectorPostprocessorName &name, const std::string &vector_name) const

const UserObjectBase &	getUserObjectFromFEProblem (const UserObjectName &object_name, const THREAD_ID tid=0) const

const T &	castUserObject (const UserObjectBase &uo_base, const std::string &param_name="") const

void	mooseObjectError (const std::string &param_name, std::stringstream &oss) const

const std::string &	userObjectType (const UserObjectBase &uo) const

const std::string &	userObjectName (const UserObjectBase &uo) const

Static Private Member Functions
static const hit::Node *	getHitNode (const InputParameters &params)

static std::string	messagePrefix (const InputParameters &params, const bool hit_prefix)

Private Attributes
const ParallelParamObject &	_parent

const MooseBase &	_si_moose_base

const FEProblemBase *	_si_problem

const RestartableDataMapName	_metaname

std::string	_restartable_name

ExecFlagEnum	_empty_execute_enum

const MooseObject &	_fni_object

const InputParameters &	_fni_params

FEProblemBase &	_fni_feproblem

const THREAD_ID	_fni_tid

const MooseObject &	_ppi_moose_object

const InputParameters &	_ppi_params

const FEProblemBase &	_ppi_feproblem

std::map< PostprocessorName, std::unique_ptr< PostprocessorValue > >	_default_values

const bool	_broadcast_by_default

const MooseObject &	_vpi_moose_object

const FEProblemBase &	_vpi_feproblem

const THREAD_ID	_vpi_tid

const InputParameters &	_ri_params

FEProblemBase &	_ri_fe_problem_base

const ReporterData &	_ri_reporter_data

const MooseObject &	_ri_moose_object

const MooseObject &	_uoi_moose_object

const FEProblemBase &	_uoi_feproblem

const THREAD_ID	_uoi_tid

Detailed Description

Outputs information (to the console) from a GeochemistryReactorBase at a point.

Definition at line 20 of file GeochemistryConsoleOutput.h.

Constructor & Destructor Documentation

◆ GeochemistryConsoleOutput()

GeochemistryConsoleOutput::GeochemistryConsoleOutput ( const InputParameters & parameters )

Definition at line 53 of file GeochemistryConsoleOutput.C.

  : Output(parameters),
    UserObjectInterface(this),
    _reactor(getUserObject<GeochemistryReactorBase>("geochemistry_reactor")),
    _nnn(getUserObject<NearestNodeNumberUO>("nearest_node_number_UO")),
    _precision(getParam<unsigned int>("precision")),
    _stoi_tol(getParam<Real>("stoichiometry_tolerance")),
    _solver_info(getParam<bool>("solver_info")),
    _mol_cutoff(getParam<Real>("mol_cutoff"))
{
}

Member Function Documentation

◆ output()

void GeochemistryConsoleOutput::output ( )

overrideprotectedvirtual

Implements Output.

Definition at line 66 of file GeochemistryConsoleOutput.C.

{
  const Node * closest_node = _nnn.getClosestNode();
  if (!closest_node)
    return;
  const dof_id_type closest_id = closest_node->id();
 
  if (_solver_info)
    _console << _reactor.getSolverOutput(closest_id).str();
 
  // retrieve information
  const GeochemicalSystem & egs = _reactor.getGeochemicalSystem(closest_id);
  const unsigned num_basis = egs.getNumInBasis();
  const unsigned num_eqm = egs.getNumInEquilibrium();
  const unsigned num_kin = egs.getNumKinetic();
  const std::vector<Real> & basis_molality = egs.getSolventMassAndFreeMolalityAndMineralMoles();
  const std::vector<Real> & basis_activity = egs.getBasisActivity();
  const std::vector<Real> & basis_act_coef = egs.getBasisActivityCoefficient();
  const std::vector<Real> & bulk_moles = egs.getBulkMolesOld();
  const std::vector<Real> & eqm_molality = egs.getEquilibriumMolality();
  const std::vector<Real> & eqm_act_coef = egs.getEquilibriumActivityCoefficient();
  const std::vector<Real> & eqm_SI = egs.getSaturationIndices();
  const std::vector<Real> & kin_moles = egs.getKineticMoles();
  const ModelGeochemicalDatabase & mgd = egs.getModelGeochemicalDatabase();
 
  _console << std::setprecision(_precision);
 
  _console << "\nSummary:\n";
 
  _console << "Total number of iterations required = " << _reactor.getSolverIterations(closest_id)
           << "\n";
  _console << "Error in calculation = " << _reactor.getSolverResidual(closest_id) << "mol\n";
  _console << "Charge of solution = " << egs.getTotalChargeOld() << "mol";
  _console << " (charge-balance species = "
           << mgd.basis_species_name[egs.getChargeBalanceBasisIndex()] << ")\n";
 
  _console << "Mass of solvent water = " << basis_molality[0] << "kg\n";
 
  Real mass = bulk_moles[0] / GeochemistryConstants::MOLES_PER_KG_WATER;
  for (unsigned i = 1; i < num_basis; ++i) // do not loop over water
    mass += bulk_moles[i] * mgd.basis_species_molecular_weight[i] / 1000.0;
  _console << "Total mass = " << mass << "kg";
  if (num_kin == 0)
    _console << "\n";
  else
  {
    _console << " (including kinetic species and free minerals)\n";
    for (unsigned k = 0; k < num_kin; ++k)
      mass -= kin_moles[k] * mgd.kin_species_molecular_weight[k] / 1000.0;
    _console << "Mass without kinetic species but including free minerals = " << mass << "kg\n";
  }
  // remove the free minerals
  for (unsigned i = 1; i < num_basis; ++i) // do not loop over water
    if (mgd.basis_species_mineral[i])
      mass -= basis_molality[i] * mgd.basis_species_molecular_weight[i] / 1000.0;
  // remove surface complexes
  for (const auto & name_info :
       mgd.surface_complexation_info) // all minerals involved in surface complexation
    for (const auto & name_frac :
         name_info.second.sorption_sites) // all sorption sites on the given mineral
    {
      const unsigned i =
          mgd.basis_species_index.at(name_frac.first); // i = basis_index_of_sorption_site
      mass -= basis_molality[i] * mgd.basis_species_molecular_weight[i] / 1000.0;
    }
  _console << "Mass of aqueous solution = " << mass << "kg";
  if (num_kin == 0)
    _console << " (without free minerals)\n";
  else
    _console << " (without kinetic species and without free minerals)\n";
 
  // Output the aqueous solution pH, if relevant
  if (mgd.basis_species_index.count("H+"))
    _console << "pH = " << -std::log10(basis_activity[mgd.basis_species_index.at("H+")]) << "\n";
  if (mgd.eqm_species_index.count("H+"))
    _console << "pH = "
             << -std::log10(eqm_molality[mgd.eqm_species_index.at("H+")] *
                            eqm_act_coef[mgd.eqm_species_index.at("H+")])
             << "\n";
 
  // Output the aqueous solution pe, if relevant
  if (mgd.redox_stoichiometry.m() > 0)
    _console << "pe = " << egs.getRedoxLog10K(0) - egs.log10RedoxActivityProduct(0) << "\n";
 
  // Output ionic strengths
  _console << "Ionic strength = " << egs.getIonicStrength() << "mol/kg(solvent water)\n";
  _console << "Stoichiometric ionic strength = " << egs.getStoichiometricIonicStrength()
           << "mol/kg(solvent water)\n";
 
  // Output activity of water
  _console << "Activity of water = " << basis_activity[0] << "\n";
 
  // Output temperature
  _console << "Temperature = " << egs.getTemperature() << "\n";
 
  // Output the basis species information, sorted by molality
  std::vector<unsigned> basis_order =
      GeochemistrySortedIndices::sortedIndices(basis_molality, false);
  _console << "\nBasis Species:\n";
  for (const auto & i : basis_order)
    if (i == 0 || mgd.basis_species_gas[i])
      continue;
    else
    {
      _console << mgd.basis_species_name[i] << ";  bulk_moles = " << bulk_moles[i]
               << "mol;  bulk_conc = "
               << bulk_moles[i] * mgd.basis_species_molecular_weight[i] * 1000.0 / mass
               << "mg/kg(soln);";
      if (!mgd.basis_species_mineral[i])
        _console << "  molality = " << basis_molality[i] << "mol/kg(solvent water);  free_conc = "
                 << basis_molality[i] * basis_molality[0] / mass *
                        mgd.basis_species_molecular_weight[i] * 1000.0
                 << "mg/kg(soln);  act_coeff = " << basis_act_coef[i]
                 << ";  log10(a) = " << std::log10(basis_activity[i]) << "\n";
      else if (mgd.basis_species_mineral[i])
        _console << "  free_moles = " << basis_molality[i] << "mol;  free_mass = "
                 << basis_molality[i] * mgd.basis_species_molecular_weight[i] * 1000.0 << "mg\n";
    }
  for (unsigned i = 0; i < num_basis; ++i)
    if (mgd.basis_species_gas[i])
      _console << mgd.basis_species_name[i] << ";  fugacity = " << basis_activity[i] << "\n";
 
  // Output the equilibrium species info, sorted by molality
  std::vector<unsigned> eqm_order = GeochemistrySortedIndices::sortedIndices(eqm_molality, false);
  _console << "\nEquilibrium Species:\n";
  for (const auto & i : eqm_order)
    if (eqm_molality[i] <= _mol_cutoff)
      break;
    else if (mgd.eqm_species_gas[i])
      continue;
    else
      _console << mgd.eqm_species_name[i] << ";  molality = " << eqm_molality[i]
               << "mol/kg(solvent water);  free_conc = "
               << eqm_molality[i] * basis_molality[0] / mass * mgd.eqm_species_molecular_weight[i] *
                      1000.0
               << "mg/kg(soln);  act_coeff = " << eqm_act_coef[i]
               << ";  log10(a) = " << std::log10(eqm_molality[i] * eqm_act_coef[i]) << ";  "
               << mgd.eqm_species_name[i] << " = "
               << GeochemistryFormattedOutput::reaction(
                      mgd.eqm_stoichiometry, i, mgd.basis_species_name, _stoi_tol, _precision)
               << ";  log10K = " << egs.getLog10K(i) << "\n";
  for (unsigned i = 0; i < num_eqm; ++i)
    if (mgd.eqm_species_gas[i])
    {
      Real log10f = 0;
      for (unsigned basis_i = 0; basis_i < num_basis; ++basis_i)
        log10f += mgd.eqm_stoichiometry(i, basis_i) * std::log10(basis_activity[basis_i]);
      log10f -= egs.getLog10K(i);
      _console << mgd.eqm_species_name[i]
               << ";  act_coeff = " << egs.getEquilibriumActivityCoefficient(i)
               << ";  fugacity = " << std::pow(10.0, log10f) << ";  " << mgd.eqm_species_name[i]
               << " = "
               << GeochemistryFormattedOutput::reaction(
                      mgd.eqm_stoichiometry, i, mgd.basis_species_name, _stoi_tol, _precision)
               << ";  log10K = " << egs.getLog10K(i) << "\n";
    }
 
  // Output the kinetic species information, sorted by mole number
  std::vector<unsigned> kin_order = GeochemistrySortedIndices::sortedIndices(kin_moles, false);
  _console << "\nKinetic Species:\n";
  for (const auto & k : kin_order)
  {
    _console << mgd.kin_species_name[k] << ";  moles = " << kin_moles[k]
             << ";  mass = " << kin_moles[k] * mgd.kin_species_molecular_weight[k] * 1000.0
             << "mg;  ";
    if (mgd.kin_species_mineral[k])
      _console << "volume = " << kin_moles[k] * mgd.kin_species_molecular_volume[k] << "cm^3;  ";
    _console << mgd.kin_species_name[k] << " = "
             << GeochemistryFormattedOutput::reaction(
                    mgd.kin_stoichiometry, k, mgd.basis_species_name, _stoi_tol, _precision)
             << ";  log10(Q) = " << egs.log10KineticActivityProduct(k)
             << ";  log10K = " << egs.getKineticLog10K(k)
             << ";  dissolution_rate*dt = " << -_reactor.getMoleAdditions(closest_id)(num_basis + k)
             << "\n";
  }
 
  // Output the mineral info, sorted by saturation indices
  std::vector<unsigned> mineral_order = GeochemistrySortedIndices::sortedIndices(eqm_SI, false);
  _console << "\nMinerals:\n";
  for (const auto & i : mineral_order)
    if (mgd.eqm_species_mineral[i])
      _console << mgd.eqm_species_name[i] << " = "
               << GeochemistryFormattedOutput::reaction(
                      mgd.eqm_stoichiometry, i, mgd.basis_species_name, _stoi_tol, _precision)
               << ";  log10K = " << egs.getLog10K(i) << ";  SI = " << eqm_SI[i] << "\n";
 
  // Output the Nernst potentials, if relevant
  _console << "\nNernst potentials:\n";
  if (mgd.redox_stoichiometry.m() > 0)
    outputNernstInfo(egs);
 
  const unsigned num_pot = egs.getNumSurfacePotentials();
  if (num_pot > 0)
  {
    _console << "\nSorbing surfaces:\n";
    const std::vector<Real> area = egs.getSorbingSurfaceArea();
    for (unsigned sp = 0; sp < num_pot; ++sp)
      _console << mgd.surface_sorption_name[sp] << "; area = " << area[sp]
               << "m^2; specific charge = " << egs.getSurfaceCharge(sp)
               << "C/m^2; surface potential = " << egs.getSurfacePotential(sp) << "V\n";
  }
 
  DenseVector<Real> bulk_in_original_basis = egs.getBulkOldInOriginalBasis();
  DenseVector<Real> transported_bulk_in_original_basis = egs.getTransportedBulkInOriginalBasis();
  std::vector<std::string> original_basis_names =
      _reactor.getPertinentGeochemicalSystem().originalBasisNames();
  _console << "\nIn original basis:\n";
  for (unsigned i = 0; i < num_basis; ++i)
    _console << original_basis_names[i] << ";  total_bulk_moles = " << bulk_in_original_basis(i)
             << ";  transported_bulk_moles = " << transported_bulk_in_original_basis(i) << "\n";
 
  _console << std::flush;
}

◆ outputNernstInfo()

void GeochemistryConsoleOutput::outputNernstInfo ( const GeochemicalSystem & egs_ref ) const

private

Definition at line 281 of file GeochemistryConsoleOutput.C.

{
  // Copy egs_ref so we can call non-const methods (viz, swaps).  This does not copy the data in
  // egs.getModelGeochemicalDatabase(), only the reference (both references refer to the same
  // block of memory) and unfortunately the swaps below manipulate that memory
  GeochemicalSystem egs = egs_ref;
  // Since we only want to do the swaps to print out some Nernst info, but don't want to impact
  // the rest of the simulation, copy the mgd, so that we can copy it back into the aforementioned
  // block of memory at the end of this method
  ModelGeochemicalDatabase mgd_without_nernst_swaps = egs.getModelGeochemicalDatabase();
 
  const ModelGeochemicalDatabase & mgd_ref = egs.getModelGeochemicalDatabase();
  // attempt to undo the swaps that have been done to mgd_ref.
  // NOTE FOR FUTURE: In the current code (2020, June 1) swapping the redox stuff in mgd seems
  // redundant.  While the current code does these swaps, here we just undo all the swaps again to
  // write the redox stuff in the original basis.  Since this is the only place that the redox
  // stuff is used, doing any swaps on the redox stuff is currently just a waste of time! take a
  // copy of the following because they get modified during the swaps
  const std::vector<unsigned> have_swapped_out_of_basis = mgd_ref.have_swapped_out_of_basis;
  const std::vector<unsigned> have_swapped_into_basis = mgd_ref.have_swapped_into_basis;
  for (int sw = have_swapped_out_of_basis.size() - 1; sw >= 0; --sw)
  {
    // Don't check for gases being swapped in or out of the basis (which usually can't happen in
    // the middle of a Newton process) because we're going to trash all the swaps at the end of
    // this method, and we don't have to worry about bulk moles, etc: we just want the
    // stoichiometries and the activities
    try
    {
      egs.performSwapNoCheck(have_swapped_out_of_basis[sw], have_swapped_into_basis[sw]);
    }
    catch (const MooseException & e)
    {
      const std::string to_swap_in = mgd_ref.eqm_species_name[have_swapped_into_basis[sw]];
      const std::string to_swap_out = mgd_ref.basis_species_name[have_swapped_out_of_basis[sw]];
      // Don't crash the entire simulation, just because Nernst-related swapping does not work
      mooseWarning("Swapping ", to_swap_out, " and ", to_swap_in, ": ", e.what());
    }
  }
 
  const Real prefactor = -GeochemistryConstants::LOGTEN * GeochemistryConstants::GAS_CONSTANT *
                         (egs.getTemperature() + GeochemistryConstants::CELSIUS_TO_KELVIN) /
                         GeochemistryConstants::FARADAY;
 
  if (mgd_ref.redox_lhs == egs_ref.getOriginalRedoxLHS())
  {
    std::vector<Real> eh(mgd_ref.redox_stoichiometry.m());
    for (unsigned red = 0; red < mgd_ref.redox_stoichiometry.m(); ++red)
      eh[red] = prefactor * (egs.log10RedoxActivityProduct(red) - egs.getRedoxLog10K(red));
    const std::vector<unsigned> eh_order = GeochemistrySortedIndices::sortedIndices(eh, false);
    for (const auto & red : eh_order)
      _console << mgd_ref.redox_lhs << " = "
               << GeochemistryFormattedOutput::reaction(mgd_ref.redox_stoichiometry,
                                                        red,
                                                        mgd_ref.basis_species_name,
                                                        _stoi_tol,
                                                        _precision)
               << ";  Eh = " << eh[red] << "V\n";
  }
 
  _console << std::flush;
 
  // restore the original mgd by copying the data in copy_of_mgd into the memory referenced by
  // egs.getModelGeochemicalDatabase()
  egs.setModelGeochemicalDatabase(mgd_without_nernst_swaps);
}

Referenced by output().

◆ sharedParams()

InputParameters GeochemistryConsoleOutput::sharedParams ( )

static

contains params that are shared with Actions that use this object

Definition at line 18 of file GeochemistryConsoleOutput.C.

{
  InputParameters params = emptyInputParameters();
  params.addParam<unsigned int>("precision", 4, "Precision for printing values");
  params.addParam<Real>(
      "mol_cutoff",
      1E-40,
      "Information regarding species with molalities less than this amount will not be outputted");
  params.addParam<bool>(
      "solver_info",
      false,
      "Print information (to the console) from the solver including residuals, swaps, etc");
  return params;
}

Referenced by AddGeochemistrySolverAction::validParams(), and validParams().

◆ validParams()

InputParameters GeochemistryConsoleOutput::validParams ( )

static

Definition at line 34 of file GeochemistryConsoleOutput.C.

{
  InputParameters params = Output::validParams();
  params += GeochemistryConsoleOutput::sharedParams();
  params.addRequiredParam<UserObjectName>("geochemistry_reactor",
                                          "The name of the GeochemistryReactor UserObject");
  params.addRangeCheckedParam<Real>("stoichiometry_tolerance",
                                    1E-6,
                                    "stoichiometry_tolerance >= 0.0",
                                    "if abs(any stoichiometric coefficient) < stoi_tol then it is "
                                    "set to zero, and so will not appear in the output");
  params.addRequiredParam<UserObjectName>(
      "nearest_node_number_UO",
      "The NearestNodeNumber UserObject that defines the physical point at which to query the "
      "GeochemistryReactor");
  params.addClassDescription("Outputs results from a GeochemistryReactor at a particular point");
  return params;
}

Member Data Documentation

◆ _mol_cutoff

const Real GeochemistryConsoleOutput::_mol_cutoff

protected

Species with molalities less than mol_cutoff will not be outputted.

Definition at line 44 of file GeochemistryConsoleOutput.h.

Referenced by output().

◆ _nnn

const NearestNodeNumberUO& GeochemistryConsoleOutput::_nnn

protected

UserObject defining the node of interest.

Definition at line 36 of file GeochemistryConsoleOutput.h.

Referenced by output().

◆ _precision

const unsigned GeochemistryConsoleOutput::_precision

protected

precision of output

Definition at line 38 of file GeochemistryConsoleOutput.h.

Referenced by output(), and outputNernstInfo().

◆ _reactor

const GeochemistryReactorBase& GeochemistryConsoleOutput::_reactor

protected

the Reactor from which to extract info

Definition at line 34 of file GeochemistryConsoleOutput.h.

Referenced by output().

◆ _solver_info

const bool GeochemistryConsoleOutput::_solver_info

protected

Whether to print solver info.

Definition at line 42 of file GeochemistryConsoleOutput.h.

Referenced by output().

◆ _stoi_tol

const Real GeochemistryConsoleOutput::_stoi_tol

protected

Tolerance on stoichiometric coefficients before they are deemed to be zero.

Definition at line 40 of file GeochemistryConsoleOutput.h.

Referenced by output(), and outputNernstInfo().

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

geochemistry/include/outputs/GeochemistryConsoleOutput.h
geochemistry/src/outputs/GeochemistryConsoleOutput.C

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Protected Member Functions

Protected Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ GeochemistryConsoleOutput()

Member Function Documentation

◆ output()

◆ outputNernstInfo()

◆ sharedParams()

◆ validParams()

Member Data Documentation

◆ _mol_cutoff

◆ _nnn

◆ _precision

◆ _reactor

◆ _solver_info

◆ _stoi_tol