Functionality expected from the bulk phase. More...

Collaboration diagram for Surface Problem Bulk Phase Mode:

Classes
class	solveSP
	Method to solve a pseudo steady state surface problem. More...

Functions
	solveSP (ImplicitSurfChem *surfChemPtr, int bulkFunc=BULK_ETCH)
	Constructor for the object. More...

	~solveSP ()
	Destructor. Deletes the integrator. More...

	solveSP (const solveSP &right)
	Unimplemented private copy constructor. More...

solveSP &	operator= (const solveSP &right)
	Unimplemented private assignment operator. More...

int	solveSurfProb (int ifunc, doublereal time_scale, doublereal TKelvin, doublereal PGas, doublereal reltol, doublereal abstol)
	Main routine that actually calculates the pseudo steady state of the surface problem. More...

void	print_header (int ioflag, int ifunc, doublereal time_scale, int damping, doublereal reltol, doublereal abstol)
	Printing routine that optionally gets called at the start of every invocation. More...

void	printIteration (int ioflag, doublereal damp, int label_d, int label_t, doublereal inv_t, doublereal t_real, size_t iter, doublereal update_norm, doublereal resid_norm, bool do_time, bool final=false)
	Printing routine that gets called after every iteration. More...

doublereal	calc_t (doublereal netProdRateSolnSP[], doublereal XMolSolnSP[], int label, int label_old, doublereal *label_factor, int ioflag)
	Calculate a conservative delta T to use in a pseudo-steady state algorithm. More...

void	calcWeights (doublereal wtSpecies[], doublereal wtResid[], const Array2D &Jac, const doublereal CSolnSP[], const doublereal abstol, const doublereal reltol)
	Calculate the solution and residual weights. More...

void	updateState (const doublereal *cSurfSpec)
	Update the surface states of the surface phases. More...

void	updateMFSolnSP (doublereal *XMolSolnSP)
	Update mole fraction vector consisting of unknowns in surface problem. More...

void	updateMFKinSpecies (doublereal *XMolKinSp, int isp)
	Update the mole fraction vector for a specific kinetic species vector corresponding to one InterfaceKinetics object. More...

void	evalSurfLarge (const doublereal *CSolnSP)
	Update the vector that keeps track of the largest species in each surface phase. More...

void	fun_eval (doublereal resid, const doublereal CSolnSP, const doublereal *CSolnOldSP, const bool do_time, const doublereal deltaT)
	Main Function evaluation. More...

void	resjac_eval (DenseMatrix &jac, doublereal resid, doublereal CSolnSP, const doublereal *CSolnSPOld, const bool do_time, const doublereal deltaT)
	Main routine that calculates the current residual and Jacobian. More...

Variables
const int	BULK_DEPOSITION = 1
	Deposition of a bulk phase is to be expected. More...

const int	BULK_ETCH = 2
	Etching of a bulk phase is to be expected. More...

ImplicitSurfChem *	m_SurfChemPtr
	Pointer to the manager of the implicit surface chemistry problem. More...

std::vector< InterfaceKinetics * > &	m_objects
	Vector of interface kinetics objects. More...

size_t	m_neq
	Total number of equations to solve in the implicit problem. More...

int	m_bulkFunc
	This variable determines how the bulk phases are to be handled. More...

size_t	m_numSurfPhases
	Number of surface phases in the surface problem. More...

size_t	m_numTotSurfSpecies
	Total number of surface species in all surface phases. More...

std::vector< size_t >	m_indexKinObjSurfPhase
	Mapping between the surface phases and the InterfaceKinetics objects. More...

std::vector< size_t >	m_nSpeciesSurfPhase
	Vector of length number of surface phases containing the number of surface species in each phase. More...

std::vector< SurfPhase * >	m_ptrsSurfPhase
	Vector of surface phase pointers. More...

std::vector< size_t >	m_eqnIndexStartSolnPhase
	Index of the start of the unknowns for each solution phase. More...

std::vector< size_t >	m_kinObjPhaseIDSurfPhase
	Phase ID in the InterfaceKinetics object of the surface phase. More...

size_t	m_numBulkPhasesSS
	Total number of volumetric condensed phases included in the steady state problem handled by this routine. More...

std::vector< size_t >	m_numBulkSpecies
	Vector of number of species in the m_numBulkPhases phases. More...

size_t	m_numTotBulkSpeciesSS
	Total number of species in all bulk phases. More...

std::vector< ThermoPhase * >	m_bulkPhasePtrs
	Vector of bulk phase pointers, length is equal to m_numBulkPhases. More...

std::vector< size_t >	m_kinSpecIndex
	Index between the equation index and the position in the kinetic species array for the appropriate kinetics operator. More...

std::vector< size_t >	m_kinObjIndex
	Index between the equation index and the index of the InterfaceKinetics object. More...

std::vector< size_t >	m_spSurfLarge
	Vector containing the indices of the largest species in each surface phase. More...

doublereal	m_atol
	The absolute tolerance in real units. units are (kmol/m2) More...

doublereal	m_rtol
	The relative error tolerance. More...

doublereal	m_maxstep
	maximum value of the time step. units = seconds More...

size_t	m_maxTotSpecies
	Maximum number of species in any single kinetics operator -> also maxed wrt the total # of solution species. More...

vector_fp	m_netProductionRatesSave
	Temporary vector with length equal to max m_maxTotSpecies. More...

vector_fp	m_numEqn1
	Temporary vector with length equal to max m_maxTotSpecies. More...

vector_fp	m_numEqn2
	Temporary vector with length equal to max m_maxTotSpecies. More...

vector_fp	m_CSolnSave
	Temporary vector with length equal to max m_maxTotSpecies. More...

vector_fp	m_CSolnSP
	Solution vector. length MAX(1, m_neq) More...

vector_fp	m_CSolnSPInit
	Saved initial solution vector. length MAX(1, m_neq) More...

vector_fp	m_CSolnSPOld
	Saved solution vector at the old time step. length MAX(1, m_neq) More...

vector_fp	m_wtResid
	Weights for the residual norm calculation. length MAX(1, m_neq) More...

vector_fp	m_wtSpecies
	Weights for the species concentrations norm calculation. More...

vector_fp	m_resid
	Residual for the surface problem. More...

vector_fp	m_XMolKinSpecies
	Vector of mole fractions. length m_maxTotSpecies. More...

DenseMatrix	m_Jac
	Jacobian. More...

int	m_ioflag

Detailed Description

Functionality expected from the bulk phase.

This changes the equations that will be used to solve for the bulk mole fractions.

Function Documentation

◆ solveSP() [1/2]

solveSP	(	ImplicitSurfChem *	surfChemPtr,
		int	bulkFunc = `BULK_ETCH`
	)

Constructor for the object.

Parameters

surfChemPtr	Pointer to the ImplicitSurfChem object that defines the surface problem to be solved.
bulkFunc	Integer representing how the bulk phases should be handled. See Surface Problem Bulk Phase Mode. Currently, only the default value of BULK_ETCH is supported.

Definition at line 23 of file solveSP.cpp.

References BULK_DEPOSITION, Kinetics::kineticsSpeciesIndex(), solveSP::m_CSolnSave, solveSP::m_CSolnSP, solveSP::m_CSolnSPInit, solveSP::m_CSolnSPOld, solveSP::m_eqnIndexStartSolnPhase, solveSP::m_indexKinObjSurfPhase, solveSP::m_Jac, solveSP::m_kinObjIndex, solveSP::m_kinObjPhaseIDSurfPhase, solveSP::m_kinSpecIndex, solveSP::m_maxTotSpecies, solveSP::m_neq, solveSP::m_netProductionRatesSave, solveSP::m_nSpeciesSurfPhase, solveSP::m_numBulkPhasesSS, solveSP::m_numEqn1, solveSP::m_numEqn2, solveSP::m_numSurfPhases, solveSP::m_numTotBulkSpeciesSS, solveSP::m_numTotSurfSpecies, solveSP::m_objects, solveSP::m_ptrsSurfPhase, solveSP::m_resid, solveSP::m_spSurfLarge, solveSP::m_wtResid, solveSP::m_wtSpecies, solveSP::m_XMolKinSpecies, Cantera::npos, Phase::nSpecies(), DenseMatrix::resize(), Kinetics::surfacePhaseIndex(), and Kinetics::thermo().

◆ ~solveSP()

~solveSP ( )

inline

Destructor. Deletes the integrator.

Definition at line 152 of file solveSP.h.

◆ solveSP() [2/2]

solveSP ( const solveSP & right )

private

Unimplemented private copy constructor.

◆ operator=()

solveSP& operator= ( const solveSP & right )

private

Unimplemented private assignment operator.

◆ solveSurfProb()

int solveSurfProb	(	int	ifunc,
		doublereal	time_scale,
		doublereal	TKelvin,
		doublereal	PGas,
		doublereal	reltol,
		doublereal	abstol
	)

Main routine that actually calculates the pseudo steady state of the surface problem.

The actual converged solution is returned as part of the internal state of the InterfaceKinetics objects.

Uses Newton's method to get the surface fractions of the surface and bulk species by requiring that the surface species production rate = 0 and that the bulk fractions are proportional to their production rates.

Parameters

ifunc	Determines the type of solution algorithm to be used. See Surface Problem Solver Methods for possible values.
time_scale	Time over which to integrate the surface equations, where applicable
TKelvin	Temperature (kelvin)
PGas	Pressure (pascals)
reltol	Relative tolerance to use
abstol	absolute tolerance.

Returns: 1 if the surface problem is successfully solved. -1 if the surface problem wasn't solved successfully. Note the actual converged solution is returned as part of the internal state of the InterfaceKinetics objects.

Definition at line 113 of file solveSP.cpp.

References solveSP::calc_t(), solveSP::calcWeights(), solveSP::evalSurfLarge(), solveSP::fun_eval(), solveSP::m_CSolnSP, solveSP::m_CSolnSPInit, solveSP::m_CSolnSPOld, solveSP::m_Jac, solveSP::m_neq, solveSP::m_netProductionRatesSave, solveSP::m_nSpeciesSurfPhase, solveSP::m_numEqn1, solveSP::m_numSurfPhases, solveSP::m_ptrsSurfPhase, solveSP::m_resid, solveSP::m_wtResid, solveSP::m_wtSpecies, solveSP::m_XMolKinSpecies, solveSP::print_header(), solveSP::printIteration(), solveSP::resjac_eval(), SFLUX_INITIALIZE, SFLUX_JACOBIAN, SFLUX_TRANSIENT, Cantera::solve(), solveSP::updateState(), Cantera::writelog(), and Cantera::writelogf().

◆ print_header()

void print_header	(	int	ioflag,
		int	ifunc,
		doublereal	time_scale,
		int	damping,
		doublereal	reltol,
		doublereal	abstol
	)

private

Printing routine that optionally gets called at the start of every invocation.

Definition at line 637 of file solveSP.cpp.

References BULK_DEPOSITION, BULK_ETCH, solveSP::m_bulkFunc, SFLUX_INITIALIZE, SFLUX_JACOBIAN, SFLUX_RESIDUAL, SFLUX_TRANSIENT, Cantera::writelog(), and Cantera::writelogf().

Referenced by solveSP::solveSurfProb().

◆ printIteration()

void printIteration	(	int	ioflag,
		doublereal	damp,
		int	label_d,
		int	label_t,
		doublereal	inv_t,
		doublereal	t_real,
		size_t	iter,
		doublereal	update_norm,
		doublereal	resid_norm,
		bool	do_time,
		bool	final = `false`
	)

private

Printing routine that gets called after every iteration.

Definition at line 686 of file solveSP.cpp.

References solveSP::m_kinObjIndex, solveSP::m_kinSpecIndex, solveSP::m_objects, Cantera::writelog(), and Cantera::writelogf().

Referenced by solveSP::solveSurfProb().

◆ calc_t()

doublereal calc_t	(	doublereal	netProdRateSolnSP[],
		doublereal	XMolSolnSP[],
		int *	label,
		int *	label_old,
		doublereal *	label_factor,
		int	ioflag
	)

private

Calculate a conservative delta T to use in a pseudo-steady state algorithm.

This routine calculates a pretty conservative 1/del_t based on MAX_i(sdot_i/(X_i*SDen0)). This probably guarantees diagonal dominance.

Small surface fractions are allowed to intervene in the del_t determination, no matter how small. This may be changed. Now minimum changed to 1.0e-12,

Maximum time step set to time_scale.

Parameters

netProdRateSolnSP	Output variable. Net production rate of all of the species in the solution vector.
XMolSolnSP	output variable. Mole fraction of all of the species in the solution vector
label	Output variable. Pointer to the value of the species index (kindexSP) that is controlling the time step
label_old	Output variable. Pointer to the value of the species index (kindexSP) that controlled the time step at the previous iteration
label_factor	Output variable. Pointer to the current factor that is used to indicate the same species is controlling the time step.
ioflag	Level of the output requested.

Returns: the 1. / delta T to be used on the next step

Definition at line 591 of file solveSP.cpp.

References Kinetics::getNetProductionRates(), Kinetics::kineticsSpeciesIndex(), solveSP::m_nSpeciesSurfPhase, solveSP::m_numEqn1, solveSP::m_numSurfPhases, solveSP::m_objects, Phase::molarDensity(), Kinetics::surfacePhaseIndex(), Kinetics::thermo(), and solveSP::updateMFSolnSP().

Referenced by solveSP::solveSurfProb().

◆ calcWeights()

void calcWeights	(	doublereal	wtSpecies[],
		doublereal	wtResid[],
		const Array2D &	Jac,
		const doublereal	CSolnSP[],
		const doublereal	abstol,
		const doublereal	reltol
	)

private

Calculate the solution and residual weights.

Parameters

wtSpecies	Weights to use for the soln unknowns. These are in concentration units
wtResid	Weights to sue for the residual unknowns.
Jac	Jacobian. Row sum scaling is used for the Jacobian
CSolnSP	Solution vector for the surface problem
abstol	Absolute error tolerance
reltol	Relative error tolerance

Definition at line 558 of file solveSP.cpp.

References BULK_DEPOSITION, solveSP::m_bulkFunc, solveSP::m_bulkPhasePtrs, solveSP::m_neq, solveSP::m_nSpeciesSurfPhase, solveSP::m_numBulkPhasesSS, solveSP::m_numBulkSpecies, solveSP::m_numSurfPhases, and solveSP::m_ptrsSurfPhase.

Referenced by solveSP::solveSurfProb().

◆ updateState()

void updateState ( const doublereal * cSurfSpec )

private

Update the surface states of the surface phases.

Definition at line 296 of file solveSP.cpp.

References solveSP::m_nSpeciesSurfPhase, solveSP::m_numSurfPhases, and solveSP::m_ptrsSurfPhase.

Referenced by solveSP::fun_eval(), and solveSP::solveSurfProb().

◆ updateMFSolnSP()

void updateMFSolnSP ( doublereal * XMolSolnSP )

private

Update mole fraction vector consisting of unknowns in surface problem.

Parameters

XMolSolnSP Vector of mole fractions for the unknowns in the surface problem.

Definition at line 305 of file solveSP.cpp.

References solveSP::m_eqnIndexStartSolnPhase, solveSP::m_numSurfPhases, and solveSP::m_ptrsSurfPhase.

Referenced by solveSP::calc_t().

◆ updateMFKinSpecies()

void updateMFKinSpecies	(	doublereal *	XMolKinSp,
		int	isp
	)

private

Update the mole fraction vector for a specific kinetic species vector corresponding to one InterfaceKinetics object.

Parameters

XMolKinSp	Mole fraction vector corresponding to a particular kinetic species for a single InterfaceKinetics Object This is a vector over all the species in all of the phases in the InterfaceKinetics object
isp	ID of the InterfaceKinetics Object.

Definition at line 313 of file solveSP.cpp.

References Phase::getMoleFractions(), Kinetics::kineticsSpeciesIndex(), solveSP::m_objects, Kinetics::nPhases(), and Kinetics::thermo().

◆ evalSurfLarge()

void evalSurfLarge ( const doublereal * CSolnSP )

private

Update the vector that keeps track of the largest species in each surface phase.

Parameters

CSolnSP Vector of the current values of the surface concentrations in all of the surface species.

Definition at line 322 of file solveSP.cpp.

References solveSP::m_nSpeciesSurfPhase, solveSP::m_numSurfPhases, and solveSP::m_spSurfLarge.

Referenced by solveSP::solveSurfProb().

◆ fun_eval()

void fun_eval	(	doublereal *	resid,
		const doublereal *	CSolnSP,
		const doublereal *	CSolnOldSP,
		const bool	do_time,
		const doublereal	deltaT
	)

private

Main Function evaluation.

Parameters

resid	output Vector of residuals, length = m_neq
CSolnSP	Vector of species concentrations, unknowns in the problem, length = m_neq
CSolnOldSP	Old Vector of species concentrations, unknowns in the problem, length = m_neq
do_time	Calculate a time dependent residual
deltaT	Delta time for time dependent problem.

Definition at line 338 of file solveSP.cpp.

References BULK_DEPOSITION, Kinetics::getNetProductionRates(), Kinetics::kineticsSpeciesIndex(), solveSP::m_bulkFunc, solveSP::m_bulkPhasePtrs, solveSP::m_indexKinObjSurfPhase, solveSP::m_netProductionRatesSave, solveSP::m_nSpeciesSurfPhase, solveSP::m_numBulkPhasesSS, solveSP::m_numEqn1, solveSP::m_numSurfPhases, solveSP::m_numTotSurfSpecies, solveSP::m_objects, solveSP::m_ptrsSurfPhase, solveSP::m_spSurfLarge, Kinetics::surfacePhaseIndex(), and solveSP::updateState().

Referenced by solveSP::resjac_eval(), and solveSP::solveSurfProb().

◆ resjac_eval()

void resjac_eval	(	DenseMatrix &	jac,
		doublereal *	resid,
		doublereal *	CSolnSP,
		const doublereal *	CSolnSPOld,
		const bool	do_time,
		const doublereal	deltaT
	)

private

Main routine that calculates the current residual and Jacobian.

Parameters

jac	Jacobian to be evaluated.
resid	output Vector of residuals, length = m_neq
CSolnSP	Vector of species concentrations, unknowns in the problem, length = m_neq. These are tweaked in order to derive the columns of the Jacobian.
CSolnSPOld	Old Vector of species concentrations, unknowns in the problem, length = m_neq
do_time	Calculate a time dependent residual
deltaT	Delta time for time dependent problem.

Definition at line 445 of file solveSP.cpp.

References BULK_DEPOSITION, solveSP::fun_eval(), solveSP::m_bulkFunc, solveSP::m_bulkPhasePtrs, solveSP::m_neq, solveSP::m_nSpeciesSurfPhase, solveSP::m_numBulkPhasesSS, solveSP::m_numBulkSpecies, solveSP::m_numEqn2, solveSP::m_numSurfPhases, and solveSP::m_ptrsSurfPhase.

Referenced by solveSP::solveSurfProb().

Variable Documentation

◆ BULK_DEPOSITION

const int BULK_DEPOSITION = 1

Deposition of a bulk phase is to be expected.

Bulk mole fractions are determined from ratios of growth rates of bulk species.

Definition at line 51 of file solveSP.h.

Referenced by solveSP::calcWeights(), solveSP::fun_eval(), solveSP::print_header(), solveSP::resjac_eval(), and solveSP::solveSP().

◆ BULK_ETCH

const int BULK_ETCH = 2

Etching of a bulk phase is to be expected.

Bulk mole fractions are assumed constant, and given by the initial conditions. This is also used whenever the condensed phase is part of the larger solution.

Definition at line 56 of file solveSP.h.

Referenced by solveSP::print_header(), and ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ m_SurfChemPtr

ImplicitSurfChem* m_SurfChemPtr

private

Pointer to the manager of the implicit surface chemistry problem.

This object actually calls the current object. Thus, we are providing a loop-back functionality here.

Definition at line 311 of file solveSP.h.

◆ m_objects

std::vector<InterfaceKinetics*>& m_objects

private

Vector of interface kinetics objects.

Each of these is associated with one and only one surface phase.

Definition at line 317 of file solveSP.h.

Referenced by solveSP::calc_t(), solveSP::fun_eval(), solveSP::printIteration(), solveSP::solveSP(), and solveSP::updateMFKinSpecies().

◆ m_neq

size_t m_neq

private

Total number of equations to solve in the implicit problem.

Note, this can be zero, and frequently is

Definition at line 323 of file solveSP.h.

Referenced by solveSP::calcWeights(), solveSP::resjac_eval(), solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_bulkFunc

int m_bulkFunc

private

This variable determines how the bulk phases are to be handled.

Possible values are given in Surface Problem Bulk Phase Mode.

Definition at line 329 of file solveSP.h.

Referenced by solveSP::calcWeights(), solveSP::fun_eval(), solveSP::print_header(), and solveSP::resjac_eval().

◆ m_numSurfPhases

size_t m_numSurfPhases

private

Number of surface phases in the surface problem.

This number is equal to the number of InterfaceKinetics objects in the problem. (until further noted)

Definition at line 336 of file solveSP.h.

Referenced by solveSP::calc_t(), solveSP::calcWeights(), solveSP::evalSurfLarge(), solveSP::fun_eval(), solveSP::resjac_eval(), solveSP::solveSP(), solveSP::solveSurfProb(), solveSP::updateMFSolnSP(), and solveSP::updateState().

◆ m_numTotSurfSpecies

size_t m_numTotSurfSpecies

private

Total number of surface species in all surface phases.

This is also the number of equations to solve for m_mode=0 system It's equal to the sum of the number of species in each of the m_numSurfPhases.

Definition at line 344 of file solveSP.h.

Referenced by solveSP::fun_eval(), and solveSP::solveSP().

◆ m_indexKinObjSurfPhase

std::vector<size_t> m_indexKinObjSurfPhase

private

Mapping between the surface phases and the InterfaceKinetics objects.

Currently this is defined to be a 1-1 mapping (and probably assumed in some places) m_surfKinObjID[i] = i

Definition at line 352 of file solveSP.h.

Referenced by solveSP::fun_eval(), and solveSP::solveSP().

◆ m_nSpeciesSurfPhase

std::vector<size_t> m_nSpeciesSurfPhase

private

Vector of length number of surface phases containing the number of surface species in each phase.

Length is equal to the number of surface phases, m_numSurfPhases

Definition at line 359 of file solveSP.h.

Referenced by solveSP::calc_t(), solveSP::calcWeights(), solveSP::evalSurfLarge(), solveSP::fun_eval(), solveSP::resjac_eval(), solveSP::solveSP(), solveSP::solveSurfProb(), and solveSP::updateState().

◆ m_ptrsSurfPhase

std::vector<SurfPhase*> m_ptrsSurfPhase

private

Vector of surface phase pointers.

This is created during the constructor Length is equal to the number of surface phases, m_numSurfPhases

Definition at line 366 of file solveSP.h.

Referenced by solveSP::calcWeights(), solveSP::fun_eval(), solveSP::resjac_eval(), solveSP::solveSP(), solveSP::solveSurfProb(), solveSP::updateMFSolnSP(), and solveSP::updateState().

◆ m_eqnIndexStartSolnPhase

std::vector<size_t> m_eqnIndexStartSolnPhase

private

Index of the start of the unknowns for each solution phase.

  i_eqn = m_eqnIndexStartPhase[isp]

isp is the phase id in the list of phases solved by the surface problem.

i_eqn is the equation number of the first unknown in the solution vector corresponding to isp'th phase.

Definition at line 378 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::updateMFSolnSP().

◆ m_kinObjPhaseIDSurfPhase

std::vector<size_t> m_kinObjPhaseIDSurfPhase

private

Phase ID in the InterfaceKinetics object of the surface phase.

For each surface phase, this lists the PhaseId of the surface phase in the corresponding InterfaceKinetics object

Length is equal to m_numSurfPhases

Definition at line 387 of file solveSP.h.

Referenced by solveSP::solveSP().

◆ m_numBulkPhasesSS

size_t m_numBulkPhasesSS

private

Total number of volumetric condensed phases included in the steady state problem handled by this routine.

This is equal to or less than the total number of volumetric phases in all of the InterfaceKinetics objects. We usually do not include bulk phases. Bulk phases are only included in the calculation when their domain isn't included in the underlying continuum model conservation equation system.

This is equal to 0, for the time being

Definition at line 400 of file solveSP.h.

Referenced by solveSP::calcWeights(), solveSP::fun_eval(), solveSP::resjac_eval(), and solveSP::solveSP().

◆ m_numBulkSpecies

std::vector<size_t> m_numBulkSpecies

private

Vector of number of species in the m_numBulkPhases phases.

Length is number of bulk phases

Definition at line 406 of file solveSP.h.

Referenced by solveSP::calcWeights(), and solveSP::resjac_eval().

◆ m_numTotBulkSpeciesSS

size_t m_numTotBulkSpeciesSS

private

Total number of species in all bulk phases.

This is also the number of bulk equations to solve when bulk equation solving is turned on.

Definition at line 413 of file solveSP.h.

Referenced by solveSP::solveSP().

◆ m_bulkPhasePtrs

std::vector<ThermoPhase*> m_bulkPhasePtrs

private

Vector of bulk phase pointers, length is equal to m_numBulkPhases.

Definition at line 416 of file solveSP.h.

Referenced by solveSP::calcWeights(), solveSP::fun_eval(), and solveSP::resjac_eval().

◆ m_kinSpecIndex

std::vector<size_t> m_kinSpecIndex

private

Index between the equation index and the position in the kinetic species array for the appropriate kinetics operator.

Length = m_neq.

ksp = m_kinSpecIndex[ieq] ksp is the kinetic species index for the ieq'th equation.

Definition at line 426 of file solveSP.h.

Referenced by solveSP::printIteration(), and solveSP::solveSP().

◆ m_kinObjIndex

std::vector<size_t> m_kinObjIndex

private

Index between the equation index and the index of the InterfaceKinetics object.

Length m_neq

Definition at line 433 of file solveSP.h.

Referenced by solveSP::printIteration(), and solveSP::solveSP().

◆ m_spSurfLarge

std::vector<size_t> m_spSurfLarge

private

Vector containing the indices of the largest species in each surface phase.

k = m_spSurfLarge[i] where k is the local species index, i.e., it varies from 0 to (num species in phase - 1) and i is the surface phase index in the problem. Length is equal to m_numSurfPhases.

Definition at line 442 of file solveSP.h.

Referenced by solveSP::evalSurfLarge(), solveSP::fun_eval(), and solveSP::solveSP().

◆ m_atol

doublereal m_atol

private

The absolute tolerance in real units. units are (kmol/m2)

Definition at line 445 of file solveSP.h.

◆ m_rtol

doublereal m_rtol

private

The relative error tolerance.

Definition at line 448 of file solveSP.h.

◆ m_maxstep

doublereal m_maxstep

private

maximum value of the time step. units = seconds

Definition at line 451 of file solveSP.h.

◆ m_maxTotSpecies

size_t m_maxTotSpecies

private

Maximum number of species in any single kinetics operator -> also maxed wrt the total # of solution species.

Definition at line 455 of file solveSP.h.

Referenced by solveSP::solveSP().

◆ m_netProductionRatesSave

vector_fp m_netProductionRatesSave

private

Temporary vector with length equal to max m_maxTotSpecies.

Definition at line 458 of file solveSP.h.

Referenced by solveSP::fun_eval(), solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_numEqn1

vector_fp m_numEqn1

private

Temporary vector with length equal to max m_maxTotSpecies.

Definition at line 461 of file solveSP.h.

Referenced by solveSP::calc_t(), solveSP::fun_eval(), solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_numEqn2

vector_fp m_numEqn2

private

Temporary vector with length equal to max m_maxTotSpecies.

Definition at line 464 of file solveSP.h.

Referenced by solveSP::resjac_eval(), and solveSP::solveSP().

◆ m_CSolnSave

vector_fp m_CSolnSave

private

Temporary vector with length equal to max m_maxTotSpecies.

Definition at line 467 of file solveSP.h.

Referenced by solveSP::solveSP().

◆ m_CSolnSP

vector_fp m_CSolnSP

private

Solution vector. length MAX(1, m_neq)

Definition at line 470 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_CSolnSPInit

vector_fp m_CSolnSPInit

private

Saved initial solution vector. length MAX(1, m_neq)

Definition at line 473 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_CSolnSPOld

vector_fp m_CSolnSPOld

private

Saved solution vector at the old time step. length MAX(1, m_neq)

Definition at line 476 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_wtResid

vector_fp m_wtResid

private

Weights for the residual norm calculation. length MAX(1, m_neq)

Definition at line 479 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_wtSpecies

vector_fp m_wtSpecies

private

Weights for the species concentrations norm calculation.

length MAX(1, m_neq)

Definition at line 485 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_resid

vector_fp m_resid

private

Residual for the surface problem.

The residual vector of length "dim" that, that has the value of "sdot" for surface species. The residuals for the bulk species are a function of the sdots for all species in the bulk phase. The last residual of each phase enforces {Sum(fractions) = 1}. After linear solve (dgetrf_ & dgetrs_), resid holds the update vector.

length MAX(1, m_neq)

Definition at line 497 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_XMolKinSpecies

vector_fp m_XMolKinSpecies

private

Vector of mole fractions. length m_maxTotSpecies.

Definition at line 500 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::solveSurfProb().

◆ m_Jac

DenseMatrix m_Jac

private

Jacobian.

m_neq by m_neq computed Jacobian matrix for the local Newton's method.

Definition at line 504 of file solveSP.h.

Referenced by solveSP::solveSP(), and solveSP::solveSurfProb().

Classes

Functions

Variables

Detailed Description

Function Documentation

◆ solveSP() [1/2]

◆ ~solveSP()

◆ solveSP() [2/2]

◆ operator=()

◆ solveSurfProb()

◆ print_header()

◆ printIteration()

◆ calc_t()

◆ calcWeights()

◆ updateState()

◆ updateMFSolnSP()

◆ updateMFKinSpecies()

◆ evalSurfLarge()

◆ fun_eval()

◆ resjac_eval()

Variable Documentation

◆ BULK_DEPOSITION

◆ BULK_ETCH

◆ m_SurfChemPtr

◆ m_objects

◆ m_neq

◆ m_bulkFunc

◆ m_numSurfPhases

◆ m_numTotSurfSpecies

◆ m_indexKinObjSurfPhase

◆ m_nSpeciesSurfPhase

◆ m_ptrsSurfPhase

◆ m_eqnIndexStartSolnPhase

◆ m_kinObjPhaseIDSurfPhase

◆ m_numBulkPhasesSS

◆ m_numBulkSpecies

◆ m_numTotBulkSpeciesSS

◆ m_bulkPhasePtrs

◆ m_kinSpecIndex

◆ m_kinObjIndex

◆ m_spSurfLarge

◆ m_atol

◆ m_rtol

◆ m_maxstep

◆ m_maxTotSpecies

◆ m_netProductionRatesSave

◆ m_numEqn1

◆ m_numEqn2

◆ m_CSolnSave

◆ m_CSolnSP

◆ m_CSolnSPInit

◆ m_CSolnSPOld

◆ m_wtResid

◆ m_wtSpecies

◆ m_resid

◆ m_XMolKinSpecies

◆ m_Jac