Solve nekRS wrapped as a MOOSE app. More...

#include <NekRSProblem.h>

Inheritance diagram for NekRSProblem:

Public Member Functions
	NekRSProblem (const InputParameters &params)

	~NekRSProblem ()
	Write nekRS's solution at the last output step. More...

virtual void	initialSetup () override
	Perform some sanity checks on the problem setup. More...

void	sendBoundaryHeatFluxToNek ()
	Send boundary heat flux to nekRS. More...

void	sendBoundaryDeformationToNek ()
	Send boundary deformation to nekRS. More...

void	sendVolumeDeformationToNek ()
	Send volume mesh deformation flux to nekRS. More...

void	sendVolumeHeatSourceToNek ()
	Send volume heat source to nekRS. More...

void	getBoundaryTemperatureFromNek ()
	Get boundary temperature from nekRS. More...

void	getVolumeTemperatureFromNek ()
	Get volume temperature from nekRS. More...

virtual void	adjustNekSolution () override

virtual void	syncSolutions (ExternalProblem::Direction direction) override

virtual void	addExternalVariables () override

virtual double	maxInterpolatedTemperature () const

virtual double	minInterpolatedTemperature () const

virtual const bool	hasMovingNekMesh () const override

bool	isDataTransferHappening (ExternalProblem::Direction direction)

unsigned int	minimumScratchSizeForCoupling () const

unsigned int	firstReservedUsrwrkSlot () const

void	sendScalarValuesToNek ()
	Send values from NekScalarValue userobjects to NekRS. More...

void	getNekScalarValueUserObjects ()
	Setup to fetch NekScalarValue user objects for sending scalar values into NekRS scratch space. More...

void	mapFaceDataToNekFace (const unsigned int &e, const unsigned int &var_num, const Real &multiplier, double **outgoing_data)

void	mapVolumeDataToNekVolume (const unsigned int &e, const unsigned int &var_num, const Real &multiplier, double **outgoing_data)

void	mapFaceDataToNekVolume (const unsigned int &e, const unsigned int &var_num, const Real &multiplier, double **outgoing_data)
	Map nodal points on a MOOSE face element to the GLL points on a Nek volume element. More...

void	writeFieldFile (const Real &time, const int &step) const

virtual bool	isOutputStep () const
	Whether nekRS should write an output file for the current time step. More...

virtual void	externalSolve () override

virtual bool	converged (unsigned int) override

virtual bool	nondimensional () const

virtual bool	synchronizeIn ()

virtual bool	synchronizeOut ()

double	L_ref () const

unsigned int	nUsrWrkSlots () const

template<typename T >
void	checkDuplicateEntries (const std::vector< T > &var, const std::string &name) const

void	checkDuplicateVariableName (const std::string &name) const

bool	stringHasEnding (std::string const &full, std::string const &ending) const

Static Public Member Functions
static InputParameters	validParams ()

Protected Member Functions
bool	normalizeHeatSource (const double moose_integral, const double nek_integral, double &normalized_nek_integral)

void	checkInitialFluxValues (const Real &nek_flux, const Real &moose_flux) const

virtual void	addTemperatureVariable () override

void	calculateMeshVelocity (int e, const field::NekWriteEnum &field)

void	copyScratchToDevice ()

void	interpolateBoundarySolutionToNek (double incoming_moose_value, double outgoing_nek_value)

void	interpolateVolumeSolutionToNek (const int elem_id, double incoming_moose_value, double outgoing_nek_value)

void	writeVolumeSolution (const int elem_id, const field::NekWriteEnum &field, double T, const std::vector< double > add=nullptr)

void	writeBoundarySolution (const int elem_id, const field::NekWriteEnum &field, double *T)

void	volumeSolution (const field::NekFieldEnum &f, double *T)

void	boundarySolution (const field::NekFieldEnum &f, double *T)

void	initializeInterpolationMatrices ()
	Initialize interpolation matrices for transfers in/out of nekRS. More...

virtual void	fillAuxVariable (const unsigned int var_number, const double *value)

virtual void	extractOutputs ()

virtual InputParameters	getExternalVariableParameters ()

std::string	fieldFilePrefix (const int &number) const

Protected Attributes
const bool &	_has_heat_source
	Whether a heat source will be applied to NekRS from MOOSE. More...

const bool &	_conserve_flux_by_sideset

const Real &	_abs_tol
	Absolute tolerance for checking flux/heat source normalizations. More...

const Real &	_rel_tol
	Relative tolerance for checking flux/heat source normalizations. More...

const PostprocessorValue *	_flux_integral = nullptr
	Total surface-integrated flux coming from the coupled MOOSE app. More...

const VectorPostprocessorValue *	_flux_integral_vpp = nullptr
	Sideset-wise surface-integrated flux coming from the coupled MOOSE app. More...

const PostprocessorValue *	_source_integral = nullptr
	Total volume-integrated heat source coming from the coupled MOOSE app. More...

const PostprocessorValue *	_min_T = nullptr
	Postprocessor to limit the minimum temperature. More...

const PostprocessorValue *	_max_T = nullptr
	Postprocessor to limit the maximum temperature. More...

double *	_T = nullptr
	nekRS temperature interpolated onto the data transfer mesh More...

double *	_flux_face = nullptr
	MOOSE flux interpolated onto the (boundary) data transfer mesh. More...

double *	_flux_elem = nullptr
	MOOSE flux interpolated onto the (volume) data transfer mesh. More...

double *	_source_elem = nullptr
	MOOSE heat source interpolated onto the data transfer mesh. More...

double *	_displacement_x = nullptr
	displacement in x for all nodes from MOOSE, for moving mesh problems More...

double *	_displacement_y = nullptr
	displacement in y for all nodes from MOOSE, for moving mesh problems More...

double *	_displacement_z = nullptr
	displacement in z for all nodes from MOOSE, for moving mesh problems More...

double *	_mesh_velocity_elem = nullptr
	mesh velocity for a given element, used internally for calculating mesh velocity over one element More...

unsigned int	_temp_var
	temperature transfer variable written to be nekRS More...

unsigned int	_avg_flux_var
	flux transfer variable read from by nekRS More...

unsigned int	_disp_x_var
	x-displacment transfer variable read for moving mesh problems More...

unsigned int	_disp_y_var
	y-displacment transfer variable read for moving mesh problems More...

unsigned int	_disp_z_var
	z-displacment transfer variable read for moving mesh problems More...

unsigned int	_heat_source_var
	volumetric heat source variable read from by nekRS More...

std::unique_ptr< NumericVector< Number > >	_serialized_solution

const std::string &	_casename
	NekRS casename. More...

const bool &	_nondimensional
	Whether the nekRS solution is performed in nondimensional scales. More...

const Real &	_U_ref
	Reference characteristic velocity. More...

const Real &	_T_ref
	Reference characteristic temperature. More...

const Real &	_dT_ref
	Reference characteristic temperature delta. More...

const Real &	_L_ref
	Reference characteristic length. More...

const Real &	_rho_0
	Reference density. More...

const Real &	_Cp_0
	Reference isobaric specific heat capacity. More...

const bool &	_write_fld_files

const bool &	_disable_fld_file_output
	Whether to turn off all field file writing. More...

unsigned int	_n_usrwrk_slots

const unsigned int &	_constant_interval
	For constant synchronization intervals, the desired frequency (in units of Nek time steps) More...

const bool &	_skip_final_field_file
	Whether to skip writing a field file on NekRS's last time steo. More...

const unsigned int &	_first_reserved_usrwrk_slot
	First slice in usrwrk for Cardinal to read/write data from. More...

int	_n_surface_elems
	Number of surface elements in the data transfer mesh, across all processes. More...

int	_n_vertices_per_surface
	Number of vertices per surface element of the transfer mesh. More...

int	_n_volume_elems
	Number of volume elements in the data transfer mesh, across all processes. More...

int	_n_vertices_per_volume
	Number of vertices per volume element of the transfer mesh. More...

int	_n_vertices_per_elem
	Number of vertices per element in the data transfer mesh, which depends on whether boundary/volume coupling. More...

const std::vector< int > *	_boundary = nullptr
	Boundary IDs through which to couple nekRS and MOOSE. More...

bool	_volume
	Whether the mesh contains volume-based coupling. More...

double	_start_time
	Start time of the simulation based on NekRS's .par file. More...

bool	_is_output_step
	Whether the most recent time step was an output file writing step. More...

NekRSMesh *	_nek_mesh

NekTimeStepper *	_timestepper = nullptr
	The time stepper used for selection of time step size. More...

Transient *	_transient_executioner = nullptr
	Underlying executioner. More...

bool	_needs_interpolation

const MultiMooseEnum *	_outputs = nullptr
	NekRS solution fields to output to the mesh mirror. More...

std::vector< std::string >	_var_names
	Names of external variables when extracting the NekRS solution. More...

std::vector< unsigned int >	_external_vars
	Numeric identifiers for the external variables. More...

std::string	_var_string
	Descriptive string for the variables extracted from NekRS. More...

double *	_external_data = nullptr
	Scratch space to place external NekRS fields before writing into auxiliary variables. More...

int	_n_points
	Number of points for interpolated fields on the MOOSE mesh. More...

const PostprocessorValue *	_transfer_in = nullptr
	Postprocessor containing the signal of when a synchronization has occurred. More...

double *	_interpolation_outgoing = nullptr
	Vandermonde interpolation matrix (for outgoing transfers) More...

double *	_interpolation_incoming = nullptr
	Vandermonde interpolation matrix (for incoming transfers) More...

unsigned int	_minimum_scratch_size_for_coupling
	Minimum allowable scratch space size, strictly what is needed by Cardinal for coupling. More...

int	_moose_Nq
	For the MOOSE mesh, the number of quadrature points in each coordinate direction. More...

const std::vector< unsigned int > *	_usrwrk_output = nullptr
	Slots in the nrs->o_usrwrk array to write to a field file. More...

const std::vector< std::string > *	_usrwrk_output_prefix = nullptr
	Filename prefix to use for naming the field files containing the nrs->o_usrwrk array slots. More...

double	_elapsedStepSum
	Sum of the elapsed time in NekRS solves. More...

double	_elapsedTime
	Sum of the total elapsed time in NekRS solves. More...

double	_tSolveStepMin
	Minimum step solve time. More...

double	_tSolveStepMax
	Maximum step solve time. More...

synchronization::SynchronizationEnum	_synchronization_interval
	When to synchronize the NekRS solution with the mesh mirror. More...

std::vector< std::string >	_usrwrk_indices
	quantities to write to nrs->usrwrk (and the order to write them) More...

std::vector< NekScalarValue * >	_nek_uos
	Userobjects containing stochastic input data. More...

unsigned int	_scratch_counter
	Counter for any potential NekScalarValue objects in the input file. More...

unsigned int	_n_uo_slots
	Number of scratch space slots used for NekScalarValue usage. More...

Static Protected Attributes
static bool	_first
	flag to indicate whether this is the first pass to serialize the solution More...

Detailed Description

Solve nekRS wrapped as a MOOSE app.

This object controls all of the execution of and data transfers to/from nekRS, fully abstracted from the Nek5000 backend.

The nekRS temperature solution is interpolated onto the NekRSMesh by multiplying the nekRS temperature by an interpolation matrix. In the opposite direction, the flux from MOOSE is interpolated onto the nekRS mesh by a similar interpolation matrix. This interpolation matrix expresses the nekRS/MOOSE solutions in terms of interpolating Legendre polynomials, and is equal to \(V_{moose}V_{nek}^{-1}\), where \(V_{moose}\) is the Vandermonde matrix of the MOOSE mesh's node points and \(V_{nek}\) is the Vandermonde matrix of the nekRS mesh's 1-D quadrature points. If the interpolation matrix is unity, this means that the libMesh node points exactly coincide with the nekRS quadrature point locations, and hence no interpolation is actually needed.

Constructor & Destructor Documentation

◆ NekRSProblem()

NekRSProblem::NekRSProblem ( const InputParameters & params )

◆ ~NekRSProblem()

NekRSProblem::~NekRSProblem ( )

Write nekRS's solution at the last output step.

If Nek is not the master app, the number of time steps it takes is controlled by the master app. Depending on the settings in the .par file, it becomes possible that nekRS may not write an output file on the simulation's actual last time step, because Nek may not know when that last time step is. Therefore, here we can force nekRS to write its output.

Member Function Documentation

◆ addExternalVariables()

virtual void NekRSProblem::addExternalVariables ( )

overridevirtual

Reimplemented from NekRSProblemBase.

◆ addTemperatureVariable()

virtual void NekRSProblem::addTemperatureVariable ( )

inlineoverrideprotectedvirtual

Add a variable to represent the temperature of the NekRS solution. We allow this to be an entry point for derived classes because they might already be adding a temperature variable for coupling purposes.

Reimplemented from NekRSProblemBase.

◆ adjustNekSolution()

virtual void NekRSProblem::adjustNekSolution ( )

overridevirtual

Adjust the NekRS solution by introducing max/min temperature clipping to help with underresolved flow

Reimplemented from NekRSProblemBase.

◆ boundarySolution()

void NekRSProblemBase::boundarySolution	(	const field::NekFieldEnum &	f,
		double *	T
	)

protectedinherited

Interpolate the NekRS boundary solution onto the boundary MOOSE mesh mirror (re2 -> mirror)

Parameters

[in]	f	field to interpolate
[out]	T	interpolated boundary value

◆ calculateMeshVelocity()

void NekRSProblem::calculateMeshVelocity	(	int	e,
		const field::NekWriteEnum &	field
	)

protected

Calculate mesh velocity for NekRS's blending solver using current and previous displacement values and write it to nrs->usrwrk, from where it can be accessed in nekRS's .oudf file.

Parameters

[in]	e	Boundary element that the displacement values belong to
[in]	field	NekWriteEnum mesh_velocity_x/y/z field

◆ checkDuplicateEntries()

template<typename T >

void CardinalProblem::checkDuplicateEntries	(	const std::vector< T > &	var,
		const std::string &	name
	)		const

inlineinherited

Check for duplicate entries in a 1-d vector

Parameters

[in]	var	input vector
[in]	name	string to use for printing error message

◆ checkDuplicateVariableName()

void CardinalProblem::checkDuplicateVariableName ( const std::string & name ) const

inherited

Check whether the user has already created a variable using one of the protected names that the wrapping is using.

Parameters

[in] name variable name

◆ checkInitialFluxValues()

void NekRSProblem::checkInitialFluxValues	(	const Real &	nek_flux,
		const Real &	moose_flux
	)		const

protected

Print a warning to the user if the initial fluxes (before normalization) differ significantly, since this can indicate an error with model setup.

Parameters

[in]	nek_flux	flux to be received by Nek
[in]	moose_flux	flux sent by MOOSE

◆ converged()

virtual bool NekRSProblemBase::converged ( unsigned int )

inlineoverridevirtualinherited

◆ copyScratchToDevice()

void NekRSProblemBase::copyScratchToDevice ( )

protectedinherited

Copy the data sent from MOOSE->Nek from host to device.

◆ externalSolve()

virtual void NekRSProblemBase::externalSolve ( )

overridevirtualinherited

◆ extractOutputs()

virtual void NekRSProblemBase::extractOutputs ( )

protectedvirtualinherited

Extract user-specified parts of the NekRS CFD solution onto the mesh mirror

◆ fieldFilePrefix()

std::string NekRSProblemBase::fieldFilePrefix ( const int & number ) const

protectedinherited

Get a three-character prefix for use in writing output files for repeated Nek sibling apps.

Parameters

[in] number multi-app number

◆ fillAuxVariable()

virtual void NekRSProblemBase::fillAuxVariable	(	const unsigned int	var_number,
		const double *	value
	)

protectedvirtualinherited

Fill an outgoing auxiliary variable field with nekRS solution data

Parameters

[in]	var_number	auxiliary variable number
[in]	value	nekRS solution data to fill the variable with

◆ firstReservedUsrwrkSlot()

unsigned int NekRSProblemBase::firstReservedUsrwrkSlot ( ) const

inlineinherited

Get the index of the first slot in the usrwrk that Cardinal is managing

Returns: index of first slot

◆ getBoundaryTemperatureFromNek()

void NekRSProblem::getBoundaryTemperatureFromNek ( )

Get boundary temperature from nekRS.

◆ getExternalVariableParameters()

virtual InputParameters NekRSProblemBase::getExternalVariableParameters ( )

protectedvirtualinherited

Get the parameters for the external variables to be added

Returns: external variable parameters

◆ getNekScalarValueUserObjects()

void NekRSProblemBase::getNekScalarValueUserObjects ( )

inherited

Setup to fetch NekScalarValue user objects for sending scalar values into NekRS scratch space.

◆ getVolumeTemperatureFromNek()

void NekRSProblem::getVolumeTemperatureFromNek ( )

Get volume temperature from nekRS.

◆ hasMovingNekMesh()

virtual const bool NekRSProblem::hasMovingNekMesh ( ) const

inlineoverridevirtual

Whether the mesh is moving

Returns: whether the mesh is moving

Reimplemented from NekRSProblemBase.

◆ initializeInterpolationMatrices()

void NekRSProblemBase::initializeInterpolationMatrices ( )

protectedinherited

Initialize interpolation matrices for transfers in/out of nekRS.

◆ initialSetup()

virtual void NekRSProblem::initialSetup ( )

overridevirtual

Perform some sanity checks on the problem setup.

This function performs checks like making sure that a transient executioner is used to wrap nekRS, that no time shift has been requested to the start of nekRS, that the correct NekTimeStepper is used, etc.

Reimplemented from NekRSProblemBase.

◆ interpolateBoundarySolutionToNek()

void NekRSProblemBase::interpolateBoundarySolutionToNek	(	double *	incoming_moose_value,
		double *	outgoing_nek_value
	)

protectedinherited

Interpolate the MOOSE mesh mirror solution onto the NekRS boundary mesh (mirror -> re2)

Parameters

[in]	incoming_moose_value	MOOSE face values
[out]	outgoing_nek_value	interpolated MOOSE face values onto the NekRS boundary mesh

◆ interpolateVolumeSolutionToNek()

void NekRSProblemBase::interpolateVolumeSolutionToNek	(	const int	elem_id,
		double *	incoming_moose_value,
		double *	outgoing_nek_value
	)

protectedinherited

Interpolate the MOOSE mesh mirror solution onto the NekRS volume mesh (mirror -> re2)

Parameters

[in]	elem_id	element ID
[in]	incoming_moose_value	MOOSE face values
[out]	outgoing_nek_value	interpolated MOOSE face values onto the NekRS volume mesh

◆ isDataTransferHappening()

bool NekRSProblemBase::isDataTransferHappening ( ExternalProblem::Direction direction )

inherited

Whether a data transfer to/from Nek is occurring

Parameters

[in] direction direction of data transfer

Returns: whether a data transfer to Nek is about to occur

◆ isOutputStep()

virtual bool NekRSProblemBase::isOutputStep ( ) const

virtualinherited

Whether nekRS should write an output file for the current time step.

A nekRS output file (suffix .f000xx) is written if the time step is an integer multiple of the output writing interval or if the time step is the last time step.

Returns: whether to write a nekRS output file

◆ L_ref()

double NekRSProblemBase::L_ref ( ) const

inlineinherited

Get the characteristic length

Returns: characteristic length

◆ mapFaceDataToNekFace()

void NekRSProblemBase::mapFaceDataToNekFace	(	const unsigned int &	e,
		const unsigned int &	var_num,
		const Real &	multiplier,
		double **	outgoing_data
	)

inherited

Map nodal points on a MOOSE face element to the GLL points on a Nek face element.

Parameters

[in]	e	MOOSE element ID
[in]	var_num	variable index to fetch MOOSE data from
[in]	multiplier	multiplier to apply to the MOOSE data before sending to Nek
[out]	outgoing_data	data represented on Nek's GLL points, ready to be applied in Nek

◆ mapFaceDataToNekVolume()

void NekRSProblemBase::mapFaceDataToNekVolume	(	const unsigned int &	e,
		const unsigned int &	var_num,
		const Real &	multiplier,
		double **	outgoing_data
	)

inherited

Map nodal points on a MOOSE face element to the GLL points on a Nek volume element.

This function is to be used when MOOSE variables are defined over the entire volume (maybe the MOOSE transfer only sent meaningful values to the coupling boundaries), so we need to do a volume interpolation of the incoming MOOSE data into nrs->usrwrk, rather than a face interpolation. This could be optimized in the future to truly only just write the boundary values into the nekRS scratch space rather than the volume values, but it looks right now that our biggest expense occurs in the MOOSE transfer system, not these transfers internally to nekRS.

Parameters

[in]	e	MOOSE element ID
[in]	var_num	variable index to fetch MOOSE data from
[in]	multiplier	multiplier to apply to the MOOSE data before sending to Nek
[out]	outgoing_data	data represented on Nek's GLL points, ready to be applied in Nek

◆ mapVolumeDataToNekVolume()

void NekRSProblemBase::mapVolumeDataToNekVolume	(	const unsigned int &	e,
		const unsigned int &	var_num,
		const Real &	multiplier,
		double **	outgoing_data
	)

inherited

Map nodal points on a MOOSE volume element to the GLL points on a Nek volume element.

Parameters

[in]	e	MOOSE element ID
[in]	var_num	variable index to fetch MOOSE data from
[in]	multiplier	multiplier to apply to the MOOSE data before sending to Nek
[out]	outgoing_data	data represented on Nek's GLL points, ready to be applied in Nek

◆ maxInterpolatedTemperature()

virtual double NekRSProblem::maxInterpolatedTemperature ( ) const

virtual

Determine the maximum interpolated temperature on the NekRSMesh for diagnostic info

Returns: maximum interpolated surface temperature

◆ minimumScratchSizeForCoupling()

unsigned int NekRSProblemBase::minimumScratchSizeForCoupling ( ) const

inlineinherited

Get the minimum scratch space required for coupling; this space is guaranteed to be filled with data incoming from MOOSE, like heat flux boundary conditions or mesh displacements

Returns: minimum scratch space reserved for coupling

◆ minInterpolatedTemperature()

virtual double NekRSProblem::minInterpolatedTemperature ( ) const

virtual

Determine the minimum interpolated temperature on the NekRSMesh for diagnostic info

Returns: minimum interpolated surface temperature

◆ nondimensional()

virtual bool NekRSProblemBase::nondimensional ( ) const

inlinevirtualinherited

Whether the solve is in nondimensional form

Returns: whether solve is in nondimensional form

◆ normalizeHeatSource()

bool NekRSProblem::normalizeHeatSource	(	const double	moose_integral,
		const double	nek_integral,
		double &	normalized_nek_integral
	)

protected

Normalize the volumetric heat source sent to NekRS

Parameters

[in]	moose_integral	total integrated value from MOOSE to conserve
[in]	nek_integral	total integrated value in nekRS to adjust
[out]	normalized_nek_integral	final normalized value

Returns: whether normalization was successful, i.e. normalized_nek_integral equals moose_integral

◆ nUsrWrkSlots()

unsigned int NekRSProblemBase::nUsrWrkSlots ( ) const

inlineinherited

Get the number of usrwrk slots allocated

Returns: number of allocated usrwrk slots

◆ sendBoundaryDeformationToNek()

void NekRSProblem::sendBoundaryDeformationToNek ( )

Send boundary deformation to nekRS.

◆ sendBoundaryHeatFluxToNek()

void NekRSProblem::sendBoundaryHeatFluxToNek ( )

Send boundary heat flux to nekRS.

◆ sendScalarValuesToNek()

void NekRSProblemBase::sendScalarValuesToNek ( )

inherited

Send values from NekScalarValue userobjects to NekRS.

◆ sendVolumeDeformationToNek()

void NekRSProblem::sendVolumeDeformationToNek ( )

Send volume mesh deformation flux to nekRS.

◆ sendVolumeHeatSourceToNek()

void NekRSProblem::sendVolumeHeatSourceToNek ( )

Send volume heat source to nekRS.

◆ stringHasEnding()

bool CardinalProblem::stringHasEnding	(	std::string const &	full,
		std::string const &	ending
	)		const

inherited

Whether a string ends in a particular sub-string

Parameters

[in]	full	full string
[in]	ending	sub-string ending

Returns: whether full string has ending

◆ synchronizeIn()

virtual bool NekRSProblemBase::synchronizeIn ( )

virtualinherited

Whether data should be synchronized in to nekRS

Returns: whether inward data synchronization should occur

◆ synchronizeOut()

virtual bool NekRSProblemBase::synchronizeOut ( )

virtualinherited

Whether data should be synchronized out of nekRS

Returns: whether outward data synchronization should occur

◆ syncSolutions()

virtual void NekRSProblem::syncSolutions ( ExternalProblem::Direction direction )

overridevirtual

Reimplemented from NekRSProblemBase.

◆ validParams()

static InputParameters NekRSProblem::validParams ( )

static

◆ volumeSolution()

void NekRSProblemBase::volumeSolution	(	const field::NekFieldEnum &	f,
		double *	T
	)

protectedinherited

Interpolate the NekRS volume solution onto the volume MOOSE mesh mirror (re2 -> mirror)

Parameters

[in]	f	field to interpolate
[out]	T	interpolated volume value

◆ writeBoundarySolution()

void NekRSProblemBase::writeBoundarySolution	(	const int	elem_id,
		const field::NekWriteEnum &	field,
		double *	T
	)

protectedinherited

Write into the NekRS solution space for coupling boundaries; for setting a mesh position in terms of a displacement, we need to add the displacement to the initial mesh coordinates.

Parameters

[in]	elem_id	element ID
[in]	field	field to write
[in]	T	solution values to write for the field for the given element

◆ writeFieldFile()

void NekRSProblemBase::writeFieldFile	(	const Real &	time,
		const int &	step
	)		const

inherited

Write NekRS solution field file

Parameters

[in]	time	solution time in NekRS (if NekRS is non-dimensional, this will be non-dimensional)
[in]	step	time step index

◆ writeVolumeSolution()

void NekRSProblemBase::writeVolumeSolution	(	const int	elem_id,
		const field::NekWriteEnum &	field,
		double *	T,
		const std::vector< double > *	add = `nullptr`
	)

protectedinherited

Write into the NekRS solution space for coupling volumes; for setting a mesh position in terms of a displacement, we need to add the displacement to the initial mesh coordinates. For this, the 'add' parameter lets you pass in a vector of values (in NekRS's mesh order, i.e. the re2 order) to add.

Parameters

[in]	elem_id	element ID
[in]	field	field to write
[in]	T	solution values to write for the field for the given element
[in]	add	optional vector of values to add to each value set on the NekRS end

Member Data Documentation

◆ _abs_tol

const Real& NekRSProblem::_abs_tol

protected

Absolute tolerance for checking flux/heat source normalizations.

◆ _avg_flux_var

unsigned int NekRSProblem::_avg_flux_var

protected

flux transfer variable read from by nekRS

◆ _boundary

const std::vector<int>* NekRSProblemBase::_boundary = nullptr

protectedinherited

Boundary IDs through which to couple nekRS and MOOSE.

◆ _casename

const std::string& NekRSProblemBase::_casename

protectedinherited

NekRS casename.

◆ _conserve_flux_by_sideset

const bool& NekRSProblem::_conserve_flux_by_sideset

protected

Whether to conserve heat flux received in NekRS by individually re-normalizing with integrals over individual sideset. This approach is technically more accurate, but places limitations on how the sidesets are defined (they should NOT share any nodes with one another) and more effort with vector postprocessors, so it is not the default.

◆ _constant_interval

const unsigned int& NekRSProblemBase::_constant_interval

protectedinherited

For constant synchronization intervals, the desired frequency (in units of Nek time steps)

◆ _Cp_0

const Real& NekRSProblemBase::_Cp_0

protectedinherited

Reference isobaric specific heat capacity.

◆ _disable_fld_file_output

const bool& NekRSProblemBase::_disable_fld_file_output

protectedinherited

Whether to turn off all field file writing.

◆ _disp_x_var

unsigned int NekRSProblem::_disp_x_var

protected

x-displacment transfer variable read for moving mesh problems

◆ _disp_y_var

unsigned int NekRSProblem::_disp_y_var

protected

y-displacment transfer variable read for moving mesh problems

◆ _disp_z_var

unsigned int NekRSProblem::_disp_z_var

protected

z-displacment transfer variable read for moving mesh problems

◆ _displacement_x

double* NekRSProblem::_displacement_x = nullptr

protected

displacement in x for all nodes from MOOSE, for moving mesh problems

◆ _displacement_y

double* NekRSProblem::_displacement_y = nullptr

protected

displacement in y for all nodes from MOOSE, for moving mesh problems

◆ _displacement_z

double* NekRSProblem::_displacement_z = nullptr

protected

displacement in z for all nodes from MOOSE, for moving mesh problems

◆ _dT_ref

const Real& NekRSProblemBase::_dT_ref

protectedinherited

Reference characteristic temperature delta.

◆ _elapsedStepSum

double NekRSProblemBase::_elapsedStepSum

protectedinherited

Sum of the elapsed time in NekRS solves.

◆ _elapsedTime

double NekRSProblemBase::_elapsedTime

protectedinherited

Sum of the total elapsed time in NekRS solves.

◆ _external_data

double* NekRSProblemBase::_external_data = nullptr

protectedinherited

Scratch space to place external NekRS fields before writing into auxiliary variables.

◆ _external_vars

std::vector<unsigned int> NekRSProblemBase::_external_vars

protectedinherited

Numeric identifiers for the external variables.

◆ _first

bool NekRSProblemBase::_first

staticprotectedinherited

flag to indicate whether this is the first pass to serialize the solution

◆ _first_reserved_usrwrk_slot

const unsigned int& NekRSProblemBase::_first_reserved_usrwrk_slot

protectedinherited

First slice in usrwrk for Cardinal to read/write data from.

◆ _flux_elem

double* NekRSProblem::_flux_elem = nullptr

protected

MOOSE flux interpolated onto the (volume) data transfer mesh.

◆ _flux_face

double* NekRSProblem::_flux_face = nullptr

protected

MOOSE flux interpolated onto the (boundary) data transfer mesh.

◆ _flux_integral

const PostprocessorValue* NekRSProblem::_flux_integral = nullptr

protected

Total surface-integrated flux coming from the coupled MOOSE app.

The mesh used for the MOOSE app may be very different from the mesh used by nekRS. Elements may be much finer/coarser, and one element on the MOOSE app may not be a clear subset/superset of the elements on the nekRS mesh. Therefore, to ensure conservation of energy, we send the total flux integral to nekRS for internal normalization of the heat flux applied on the nekRS mesh.

◆ _flux_integral_vpp

const VectorPostprocessorValue* NekRSProblem::_flux_integral_vpp = nullptr

protected

Sideset-wise surface-integrated flux coming from the coupled MOOSE app.

The mesh used for the MOOSE app may be very different from the mesh used by nekRS. Elements may be much finer/coarser, and one element on the MOOSE app may not be a clear subset/superset of the elements on the nekRS mesh. Therefore, to ensure conservation of energy, we send the flux integrals for each sideset to nekRS for internal normalization of the heat flux applied on the nekRS mesh.

◆ _has_heat_source

const bool& NekRSProblem::_has_heat_source

protected

Whether a heat source will be applied to NekRS from MOOSE.

◆ _heat_source_var

unsigned int NekRSProblem::_heat_source_var

protected

volumetric heat source variable read from by nekRS

◆ _interpolation_incoming

double* NekRSProblemBase::_interpolation_incoming = nullptr

protectedinherited

Vandermonde interpolation matrix (for incoming transfers)

◆ _interpolation_outgoing

double* NekRSProblemBase::_interpolation_outgoing = nullptr

protectedinherited

Vandermonde interpolation matrix (for outgoing transfers)

◆ _is_output_step

bool NekRSProblemBase::_is_output_step

protectedinherited

Whether the most recent time step was an output file writing step.

◆ _L_ref

const Real& NekRSProblemBase::_L_ref

protectedinherited

Reference characteristic length.

◆ _max_T

const PostprocessorValue* NekRSProblem::_max_T = nullptr

protected

Postprocessor to limit the maximum temperature.

◆ _mesh_velocity_elem

double* NekRSProblem::_mesh_velocity_elem = nullptr

protected

mesh velocity for a given element, used internally for calculating mesh velocity over one element

◆ _min_T

const PostprocessorValue* NekRSProblem::_min_T = nullptr

protected

Postprocessor to limit the minimum temperature.

◆ _minimum_scratch_size_for_coupling

unsigned int NekRSProblemBase::_minimum_scratch_size_for_coupling

protectedinherited

Minimum allowable scratch space size, strictly what is needed by Cardinal for coupling.

◆ _moose_Nq

int NekRSProblemBase::_moose_Nq

protectedinherited

For the MOOSE mesh, the number of quadrature points in each coordinate direction.

◆ _n_points

int NekRSProblemBase::_n_points

protectedinherited

Number of points for interpolated fields on the MOOSE mesh.

◆ _n_surface_elems

int NekRSProblemBase::_n_surface_elems

protectedinherited

Number of surface elements in the data transfer mesh, across all processes.

◆ _n_uo_slots

unsigned int NekRSProblemBase::_n_uo_slots

protectedinherited

Number of scratch space slots used for NekScalarValue usage.

◆ _n_usrwrk_slots

unsigned int NekRSProblemBase::_n_usrwrk_slots

protectedinherited

Number of slices/slots to allocate in nrs->usrwrk to hold fields for coupling (i.e. data going into NekRS, written by Cardinal), or used for custom user actions, but not for coupling. By default, we just allocate 7 slots (no inherent reason, just a fairly big amount). For memory-limited cases, you can reduce this number to just the bare minimum necessary for your use case.

◆ _n_vertices_per_elem

int NekRSProblemBase::_n_vertices_per_elem

protectedinherited

Number of vertices per element in the data transfer mesh, which depends on whether boundary/volume coupling.

◆ _n_vertices_per_surface

int NekRSProblemBase::_n_vertices_per_surface

protectedinherited

Number of vertices per surface element of the transfer mesh.

◆ _n_vertices_per_volume

int NekRSProblemBase::_n_vertices_per_volume

protectedinherited

Number of vertices per volume element of the transfer mesh.

◆ _n_volume_elems

int NekRSProblemBase::_n_volume_elems

protectedinherited

Number of volume elements in the data transfer mesh, across all processes.

◆ _needs_interpolation

bool NekRSProblemBase::_needs_interpolation

protectedinherited

Whether an interpolation needs to be performed on the nekRS temperature solution, or if we can just grab the solution at specified points

◆ _nek_mesh

NekRSMesh* NekRSProblemBase::_nek_mesh

protectedinherited

Underlying mesh object on which NekRS exchanges fields with MOOSE or extracts NekRS's solution for I/O features

◆ _nek_uos

std::vector<NekScalarValue *> NekRSProblemBase::_nek_uos

protectedinherited

Userobjects containing stochastic input data.

◆ _nondimensional

const bool& NekRSProblemBase::_nondimensional

protectedinherited

Whether the nekRS solution is performed in nondimensional scales.

If nekRS is solving in non-dimensional form, this means that the nekRS solution is performed for:

nondimensional temperature \(T^\dagger\), defined as \(T^\dagger=\frac{T-T_{ref}}{\Delta T_{ref}}\). The 'T_ref' and 'dT_ref' variables here represent these scales.
nondimensional velocity \(U^\dagger=\frac{u}{U_{ref}}\). The 'U_ref' variable here represents this velocity scale.
nondimensional pressure \(P^dagger=\frac{P}{\rho_{0}U_{ref}^2}\). The 'rho_0' variable here represents this density parameter.

In terms of heat flux boundary conditions, the entire energy conservation equation in nekRS is multiplied by \(\frac{L_{ref}}{\rho_{0}C_{p,0}U_{ref}\Delta T_{ref}}\) in order to clear the coefficient on the convective. Therefore, the heat source in nekRS is expressed in nondimensional form as \(q^\dagger=\frac{q}{\rho_{0}C_{p,0}U_{ref}\Delta T_{ref}}\). Here, 'Cp_0' is the specific heat capacity scale.

Unfortunately, there is no systematic way to get these reference scales from nekRS, so we need to inform MOOSE of any possible scaling so that we can appropriately scale the nekRS temperature to the dimensional form that is usually expected in MOOSE. Therefore, these scales just need to match what is used in the nekRS input files used to specify boundary conditions. Conversion between dimensional MOOSE heat flux to dimensionless nekRS heat flux is performed automatically, and does not require any special treatment in the nekRS scalarNeumannBC kernel.

◆ _outputs

const MultiMooseEnum* NekRSProblemBase::_outputs = nullptr

protectedinherited

NekRS solution fields to output to the mesh mirror.

◆ _rel_tol

const Real& NekRSProblem::_rel_tol

protected

Relative tolerance for checking flux/heat source normalizations.

◆ _rho_0

const Real& NekRSProblemBase::_rho_0

protectedinherited

Reference density.

◆ _scratch_counter

unsigned int NekRSProblemBase::_scratch_counter

protectedinherited

Counter for any potential NekScalarValue objects in the input file.

◆ _serialized_solution

std::unique_ptr<NumericVector<Number> > NekRSProblemBase::_serialized_solution

protectedinherited

◆ _skip_final_field_file

const bool& NekRSProblemBase::_skip_final_field_file

protectedinherited

Whether to skip writing a field file on NekRS's last time steo.

◆ _source_elem

double* NekRSProblem::_source_elem = nullptr

protected

MOOSE heat source interpolated onto the data transfer mesh.

◆ _source_integral

const PostprocessorValue* NekRSProblem::_source_integral = nullptr

protected

Total volume-integrated heat source coming from the coupled MOOSE app.

The mesh used for the MOOSE app may be very different from the mesh used by nekRS. Elements may be much finer/coarser, and one element on the MOOSE app may not be a clear subset/superset of the elements on the nekRS mesh. Therefore, to ensure conservation of energy, we send the total source integral to nekRS for internal normalization of the heat source applied on the nekRS mesh.

◆ _start_time

double NekRSProblemBase::_start_time

protectedinherited

Start time of the simulation based on NekRS's .par file.

◆ _synchronization_interval

synchronization::SynchronizationEnum NekRSProblemBase::_synchronization_interval

protectedinherited

When to synchronize the NekRS solution with the mesh mirror.

This parameter determines when to synchronize the NekRS solution with the mesh mirror - this entails:

Mapping from the NekRS spectral element mesh to the finite element mesh mirror, to extract information from NekRS and make it available to MOOSE
Mapping from the finite element mesh mirror into the NekRS spectral element mesh, to send information from MOOSE into NekRS

Several options are available:

'constant' will simply keep the NekRS solution and the mesh mirror entirely consistent with one another on a given constant frequency of time steps. By default, the 'constant_interval' is 1, so that NekRS and MOOSE communicate with each other on every single time step
'parent_app' will only send data between NekRS and a parent application when (1) the main application has just sent "new" information to NekRS, and when (2) the main application is just about to run a new time step (with updated BCs/source terms from NekRS).

nekRS is often subcycled relative to the application controlling it - that is, nekRS may be run with a time step 10x smaller than a conduction MOOSE app. If 'interpolate_transfers = false' in the master application, then the data going into nekRS is fixed for each of the subcycled time steps it takes, so these extra data transfers are completely unnecssary. This flag indicates that the information sent from MOOSE to NekRS should only be updated if the data from MOOSE is "new", and likewise whether the NekRS solution should only be interpolated to the mesh mirror once MOOSE is actually "ready" to solve a time step using it.

NOTE: if 'interpolate_transfers = true' in the master application, then the data coming into nekRS is unique on each subcycled time step, so setting this to true will in effect override interpolate_transfers to be false. For the best performance, you should set interpolate_transfers to false so that you don't even bother computing the interpolated data, since it's not used if this parameter is set to true.

◆ _T

double* NekRSProblem::_T = nullptr

protected

nekRS temperature interpolated onto the data transfer mesh

◆ _T_ref

const Real& NekRSProblemBase::_T_ref

protectedinherited

Reference characteristic temperature.

◆ _temp_var

unsigned int NekRSProblem::_temp_var

protected

temperature transfer variable written to be nekRS

◆ _timestepper

NekTimeStepper* NekRSProblemBase::_timestepper = nullptr

protectedinherited

The time stepper used for selection of time step size.

◆ _transfer_in

const PostprocessorValue* NekRSProblemBase::_transfer_in = nullptr

protectedinherited

Postprocessor containing the signal of when a synchronization has occurred.

◆ _transient_executioner

Transient* NekRSProblemBase::_transient_executioner = nullptr

protectedinherited

Underlying executioner.

◆ _tSolveStepMax

double NekRSProblemBase::_tSolveStepMax

protectedinherited

Maximum step solve time.

◆ _tSolveStepMin

double NekRSProblemBase::_tSolveStepMin

protectedinherited

Minimum step solve time.

◆ _U_ref

const Real& NekRSProblemBase::_U_ref

protectedinherited

Reference characteristic velocity.

◆ _usrwrk_indices

std::vector<std::string> NekRSProblemBase::_usrwrk_indices

protectedinherited

quantities to write to nrs->usrwrk (and the order to write them)

◆ _usrwrk_output

const std::vector<unsigned int>* NekRSProblemBase::_usrwrk_output = nullptr

protectedinherited

Slots in the nrs->o_usrwrk array to write to a field file.

◆ _usrwrk_output_prefix

const std::vector<std::string>* NekRSProblemBase::_usrwrk_output_prefix = nullptr

protectedinherited

Filename prefix to use for naming the field files containing the nrs->o_usrwrk array slots.

◆ _var_names

std::vector<std::string> NekRSProblemBase::_var_names

protectedinherited

Names of external variables when extracting the NekRS solution.

◆ _var_string

std::string NekRSProblemBase::_var_string

protectedinherited

Descriptive string for the variables extracted from NekRS.

◆ _volume

bool NekRSProblemBase::_volume

protectedinherited

Whether the mesh contains volume-based coupling.

◆ _write_fld_files

const bool& NekRSProblemBase::_write_fld_files

protectedinherited

Whether to disable output file writing by NekRS and replace it by output file writing in Cardinal. Suppose the case name is 'channel'. If this parameter is false, then NekRS will write output files as usual, with names like channel0.f00001 for write step 1, channel0.f00002 for write step 2, and so on. If true, then NekRS itself does not output any files like this, and instead output files are written with names a01channel0.f00001, a01channel0.f00002 (for first Nek app), a02channel0.f00001, a02channel0.f00002 (for second Nek app), and so on. This feature should only be used when running repeated Nek sub apps so that the output from each app is retained. Otherwise, if running N repeated Nek sub apps, only a single output file is obtained because each app overwrites the output files of the other apps in the order that the apps reach the nekrs::outfld function.

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

include/base/NekRSProblem.h

Public Member Functions

Static Public Member Functions

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ NekRSProblem()

◆ ~NekRSProblem()

Member Function Documentation

◆ addExternalVariables()

◆ addTemperatureVariable()

◆ adjustNekSolution()

◆ boundarySolution()

◆ calculateMeshVelocity()

◆ checkDuplicateEntries()

◆ checkDuplicateVariableName()

◆ checkInitialFluxValues()

◆ converged()

◆ copyScratchToDevice()

◆ externalSolve()

◆ extractOutputs()

◆ fieldFilePrefix()

◆ fillAuxVariable()

◆ firstReservedUsrwrkSlot()

◆ getBoundaryTemperatureFromNek()

◆ getExternalVariableParameters()

◆ getNekScalarValueUserObjects()

◆ getVolumeTemperatureFromNek()

◆ hasMovingNekMesh()

◆ initializeInterpolationMatrices()

◆ initialSetup()

◆ interpolateBoundarySolutionToNek()

◆ interpolateVolumeSolutionToNek()

◆ isDataTransferHappening()

◆ isOutputStep()

◆ L_ref()

◆ mapFaceDataToNekFace()

◆ mapFaceDataToNekVolume()

◆ mapVolumeDataToNekVolume()

◆ maxInterpolatedTemperature()

◆ minimumScratchSizeForCoupling()

◆ minInterpolatedTemperature()

◆ nondimensional()

◆ normalizeHeatSource()

◆ nUsrWrkSlots()

◆ sendBoundaryDeformationToNek()

◆ sendBoundaryHeatFluxToNek()

◆ sendScalarValuesToNek()

◆ sendVolumeDeformationToNek()

◆ sendVolumeHeatSourceToNek()

◆ stringHasEnding()

◆ synchronizeIn()

◆ synchronizeOut()

◆ syncSolutions()

◆ validParams()

◆ volumeSolution()

◆ writeBoundarySolution()

◆ writeFieldFile()

◆ writeVolumeSolution()

Member Data Documentation

◆ _abs_tol

◆ _avg_flux_var

◆ _boundary

◆ _casename

◆ _conserve_flux_by_sideset

◆ _constant_interval

◆ _Cp_0

◆ _disable_fld_file_output

◆ _disp_x_var

◆ _disp_y_var

◆ _disp_z_var

◆ _displacement_x

◆ _displacement_y

◆ _displacement_z

◆ _dT_ref

◆ _elapsedStepSum

◆ _elapsedTime

◆ _external_data

◆ _external_vars