Method to solve a pseudo steady state surface problem. More...

#include <solveSP.h>

Collaboration diagram for solveSP:

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

	~solveSP ()
	Destructor. Deletes the integrator.

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.

Public Attributes
int	m_ioflag

Private Member Functions
	solveSP (const solveSP &right)
	Unimplemented private copy constructor.

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

void	print_header (int ioflag, int ifunc, doublereal time_scale, int damping, doublereal reltol, doublereal abstol, doublereal TKelvin, doublereal PGas, doublereal netProdRate[], doublereal XMolKinSpecies[])
	Printing routine that gets called at the start of every invocation.

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, doublereal netProdRate[], doublereal CSolnSP[], doublereal resid[], doublereal XMolSolnSP[], doublereal wtSpecies[], size_t dim, bool do_time)
	Printing routine that gets called after every iteration.

void	printFinal (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, doublereal netProdRateKinSpecies[], const doublereal CSolnSP[], const doublereal resid[], doublereal XMolSolnSP[], const doublereal wtSpecies[], const doublereal wtRes[], size_t dim, bool do_time, doublereal TKelvin, doublereal PGas)
	Print a summary of the solution.

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.

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

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

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

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

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

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

void	resjac_eval (std::vector< doublereal * > &JacCol, doublereal resid, doublereal CSolnSP, const doublereal *CSolnSPOld, const bool do_time, const doublereal deltaT)
	Main routine that calculates the current residual and Jacobian.

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

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

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

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

size_t	m_numSurfPhases
	Number of surface phases in the surface problem.

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

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

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

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

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

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

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

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

size_t	m_numTotBulkSpeciesSS
	Total number of species in all bulk phases.

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

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

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

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

doublereal	m_atol
	m_atol is the absolute tolerance in real units.

doublereal	m_rtol
	m_rtol is the relative error tolerance.

doublereal	m_maxstep
	maximum value of the time step

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

vector_fp	m_netProductionRatesSave
	Temporary vector with length equal to max m_maxTotSpecies.

vector_fp	m_numEqn1
	Temporary vector with length equal to max m_maxTotSpecies.

vector_fp	m_numEqn2
	Temporary vector with length equal to max m_maxTotSpecies.

vector_fp	m_CSolnSave
	Temporary vector with length equal to max m_maxTotSpecies.

vector_fp	m_CSolnSP
	Solution vector.

vector_fp	m_CSolnSPInit
	Saved initial solution vector.

vector_fp	m_CSolnSPOld
	Saved solution vector at the old time step.

vector_fp	m_wtResid
	Weights for the residual norm calculation.

vector_fp	m_wtSpecies
	Weights for the species concentrations norm calculation.

vector_fp	m_resid
	Residual for the surface problem.

vector_fp	m_XMolKinSpecies
	Vector of mole fractions.

vector_int	m_ipiv
	pivots

std::vector< doublereal * >	m_JacCol
	Vector of pointers to the top of the columns of the jacobians.

Array2D	m_Jac
	Jacobian.

Detailed Description

Method to solve a pseudo steady state surface problem.

The following class handles solving the surface problem. The calculation uses Newton's method to obtain the surface fractions of the surface and bulk species by requiring that the surface species production rate = 0 and that the either the bulk fractions are proportional to their production rates or they are constants.

Currently, the bulk mole fractions are treated as constants. Implementation of their being added to the unknown solution vector is delayed.

Lets introduce the unknown vector for the "surface problem". The surface problem is defined as the evaluation of the surface site fractions for multiple surface phases. The unknown vector will consist of the vector of surface concentrations for each species in each surface vector. Species are grouped first by their surface phases

C_i_j = Concentration of the ith species in the jth surface phase Nj = number of surface species in the jth surface phase

The unknown solution vector is defined as follows:

         kindexSP

C_0_0 0 C_1_0 1 C_2_0 2 . . . ... C_N0-1_0 N0-1 C_0_1 N0 C_1_1 N0+1 C_2_1 N0+2 . . . ... C_N1-1_1 NO+N1-1

Note there are a couple of different types of species indices floating around in the formulation of this object.

kindexSP This is the species index in the contiguous vector of unknowns for the surface problem.

Note, in the future, BULK_DEPOSITION systems will be added, and the solveSP unknown vector will get more complicated. It will include the mole fraction and growth rates of specified bulk phases

Indices which relate to individual kinetics objects use the suffix KSI (kinetics species index).

Solution Method

This routine is typically used within a residual calculation in a large code. It's typically invoked millions of times for large calculations, and it must work every time. Therefore, requirements demand that it be robust but also efficient.

The solution methodology is largely determined by the ifunc<> parameter, that is input to the solution object. This parameter may have the following 4 values:

1: SFLUX_INITIALIZE = This assumes that the initial guess supplied to the routine is far from the correct one. Substantial work plus transient time-stepping is to be expected to find a solution.

2: SFLUX_RESIDUAL = Need to solve the surface problem in order to calculate the surface fluxes of gas-phase species. (Can expect a moderate change in the solution vector -> try to solve the system by direct methods with no damping first -> then, try time-stepping if the first method fails) A "time_scale" supplied here is used in the algorithm to determine when to shut off time-stepping.

3: SFLUX_JACOBIAN = Calculation of the surface problem is due to the need for a numerical jacobian for the gas-problem. The solution is expected to be very close to the initial guess, and extra accuracy is needed because solution variables have been delta'd from nominal values to create jacobian entries.

4: SFLUX_TRANSIENT = The transient calculation is performed here for an amount of time specified by "time_scale". It is not guaranteed to be time-accurate - just stable and fairly fast. The solution after del_t time is returned, whether it's converged to a steady state or not. This is a poor man's time stepping algorithm.

Pseudo time stepping algorithm: The time step is determined from sdot[], so so that the time step doesn't ever change the value of a variable by more than 100%.

This algorithm does use a damped Newton's method to relax the equations. Damping is based on a "delta damping" technique. The solution unknowns are not allowed to vary too much between iterations.

EXTRA_ACCURACY:A constant that is the ratio of the required update norm in this Newton iteration compared to that in the nonlinear solver. A value of 0.1 is used so surface species are safely overconverged.


Functions called:

ct_dgetrf – First half of LAPACK direct solve of a full Matrix

ct_dgetrs – Second half of LAPACK direct solve of a full matrix. Returns solution vector in the right-hand-side vector, resid.

Definition at line 197 of file solveSP.h.

Constructor & Destructor Documentation

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. Currently, only the default value of BULK_ETCH is supported.

Definition at line 40 of file solveSP.cpp.

References Kinetics::kineticsSpeciesIndex(), solveSP::m_CSolnSave, solveSP::m_CSolnSP, solveSP::m_CSolnSPInit, solveSP::m_CSolnSPOld, solveSP::m_eqnIndexStartSolnPhase, solveSP::m_indexKinObjSurfPhase, solveSP::m_ipiv, solveSP::m_Jac, solveSP::m_JacCol, 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, ckr::max(), Cantera::npos, Phase::nSpecies(), Array2D::ptrColumn(), Array2D::resize(), Kinetics::surfacePhaseIndex(), and Kinetics::thermo().

~solveSP ( )

Destructor. Deletes the integrator.

Definition at line 147 of file solveSP.cpp.

solveSP ( const solveSP & right )

private

Unimplemented private copy constructor.

Member Function Documentation

solveSP& operator= ( const solveSP & right )

private

Unimplemented private assignment operator.

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.

Parameters

ifunc	Determines the type of solution algorithm to be used. Possible values are SFLUX_INITIALIZE , SFLUX_RESIDUAL SFLUX_JACOBIAN SFLUX_TRANSIENT .
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: Returns 1 if the surface problem is successfully solved. Returns -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 158 of file solveSP.cpp.

References solveSP::calc_t(), solveSP::calcWeights(), DATA_PTR, solveSP::evalSurfLarge(), solveSP::fun_eval(), Phase::getConcentrations(), Cantera::int2str(), solveSP::m_CSolnSP, solveSP::m_CSolnSPInit, solveSP::m_CSolnSPOld, solveSP::m_ipiv, solveSP::m_Jac, solveSP::m_JacCol, solveSP::m_kinSpecIndex, 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, ckr::max(), solveSP::print_header(), solveSP::printFinal(), solveSP::printIteration(), solveSP::resjac_eval(), SFLUX_INITIALIZE, and solveSP::updateState().

Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().

void print_header	(	int	ioflag,
		int	ifunc,
		doublereal	time_scale,
		int	damping,
		doublereal	reltol,
		doublereal	abstol,
		doublereal	TKelvin,
		doublereal	PGas,
		doublereal	netProdRate[],
		doublereal	XMolKinSpecies[]
	)

private

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

Definition at line 901 of file solveSP.cpp.

References solveSP::m_bulkFunc, and SFLUX_INITIALIZE.

Referenced by solveSP::solveSurfProb().

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,
		doublereal	netProdRate[],
		doublereal	CSolnSP[],
		doublereal	resid[],
		doublereal	XMolSolnSP[],
		doublereal	wtSpecies[],
		size_t	dim,
		bool	do_time
	)

private

Printing routine that gets called after every iteration.

Definition at line 953 of file solveSP.cpp.

References Cantera::int2str(), Kinetics::kineticsSpeciesName(), solveSP::m_kinObjIndex, solveSP::m_kinSpecIndex, and solveSP::m_objects.

Referenced by solveSP::solveSurfProb().

void printFinal	(	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,
		doublereal	netProdRateKinSpecies[],
		const doublereal	CSolnSP[],
		const doublereal	resid[],
		doublereal	XMolSolnSP[],
		const doublereal	wtSpecies[],
		const doublereal	wtRes[],
		size_t	dim,
		bool	do_time,
		doublereal	TKelvin,
		doublereal	PGas
	)

private

Print a summary of the solution.

Definition at line 1002 of file solveSP.cpp.

References Cantera::int2str(), Kinetics::kineticsSpeciesName(), solveSP::m_kinObjIndex, solveSP::m_kinSpecIndex, and solveSP::m_objects.

Referenced by solveSP::solveSurfProb().

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

Definition at line 839 of file solveSP.cpp.

References DATA_PTR, InterfaceKinetics::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().

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 786 of file solveSP.cpp.

References 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().

void updateState ( const doublereal * cSurfSpec )

private

Update the surface states of the surface phases.

Definition at line 450 of file solveSP.cpp.

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

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

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 462 of file solveSP.cpp.

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

Referenced by solveSP::calc_t().

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 474 of file solveSP.cpp.

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

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 489 of file solveSP.cpp.

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

Referenced by solveSP::solveSurfProb().

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
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 516 of file solveSP.cpp.

References DATA_PTR, InterfaceKinetics::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().

void resjac_eval	(	std::vector< doublereal * > &	JacCol,
		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

JacCol	Vector of pointers to the tops of columns of the 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 637 of file solveSP.cpp.

References DATA_PTR, 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, solveSP::m_ptrsSurfPhase, and ckr::max().

Referenced by solveSP::solveSurfProb().

Member Data Documentation

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 405 of file solveSP.h.

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 411 of file solveSP.h.

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

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 417 of file solveSP.h.

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

int m_bulkFunc

private

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

= BULK_ETCH (default) The concentrations of the bulk phases are considered constant, just as the gas phase is. They are not part of the solution vector. = BULK_DEPOSITION = We solve here for the composition of the bulk phases by calculating a growth rate. The equations for the species in the bulk phases are unknowns in this calculation.

Definition at line 430 of file solveSP.h.

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

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 437 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().

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 445 of file solveSP.h.

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

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 453 of file solveSP.h.

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

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 460 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().

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 467 of file solveSP.h.

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

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 479 of file solveSP.h.

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

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 488 of file solveSP.h.

Referenced by solveSP::solveSP().

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 501 of file solveSP.h.

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

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 507 of file solveSP.h.

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

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 518 of file solveSP.h.

Referenced by solveSP::solveSP().

std::vector<ThermoPhase*> m_bulkPhasePtrs

private

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

Definition at line 524 of file solveSP.h.

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

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 535 of file solveSP.h.

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

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 542 of file solveSP.h.

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

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 num species in phase-1 i is the surface phase index in the problem

length is equal to m_numSurfPhases

Definition at line 555 of file solveSP.h.

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

doublereal m_atol

private

m_atol is the absolute tolerance in real units.

units are (kmol/m2)

Definition at line 561 of file solveSP.h.

doublereal m_rtol

private

m_rtol is the relative error tolerance.

Definition at line 564 of file solveSP.h.

doublereal m_maxstep

private

maximum value of the time step

units = seconds

Definition at line 570 of file solveSP.h.

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 574 of file solveSP.h.

Referenced by solveSP::solveSP().

vector_fp m_netProductionRatesSave

private

Temporary vector with length equal to max m_maxTotSpecies.

Definition at line 577 of file solveSP.h.

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

vector_fp m_numEqn1

private

Temporary vector with length equal to max m_maxTotSpecies.

Definition at line 580 of file solveSP.h.

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

vector_fp m_numEqn2

private

Temporary vector with length equal to max m_maxTotSpecies.

Definition at line 583 of file solveSP.h.

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

vector_fp m_CSolnSave

private

Temporary vector with length equal to max m_maxTotSpecies.

Definition at line 586 of file solveSP.h.

Referenced by solveSP::solveSP().

vector_fp m_CSolnSP

private

Solution vector.

length MAX(1, m_neq)

Definition at line 592 of file solveSP.h.

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

vector_fp m_CSolnSPInit

private

Saved initial solution vector.

length MAX(1, m_neq)

Definition at line 598 of file solveSP.h.

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

vector_fp m_CSolnSPOld

private

Saved solution vector at the old time step.

length MAX(1, m_neq)

Definition at line 604 of file solveSP.h.

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

vector_fp m_wtResid

private

Weights for the residual norm calculation.

length MAX(1, m_neq)

Definition at line 610 of file solveSP.h.

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

vector_fp m_wtSpecies

private

Weights for the species concentrations norm calculation.

length MAX(1, m_neq)

Definition at line 616 of file solveSP.h.

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

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 629 of file solveSP.h.

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

vector_fp m_XMolKinSpecies

private

Vector of mole fractions.

*length m_maxTotSpecies

Definition at line 635 of file solveSP.h.

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

vector_int m_ipiv

private

pivots