Advances the surface coverages of the associated set of SurfacePhase objects in time. More...

#include <ImplicitSurfChem.h>

Inheritance diagram for ImplicitSurfChem:

Collaboration diagram for ImplicitSurfChem:

Public Member Functions
	ImplicitSurfChem (std::vector< InterfaceKinetics * > k, double rtol=1.e-7, double atol=1.e-14, double maxStepSize=0, size_t maxSteps=20000, size_t maxErrTestFails=7)
	Constructor for multiple surfaces. More...

virtual void	initialize (doublereal t0=0.0)

virtual void	setMaxStepSize (double maxstep=0.0)

virtual void	setTolerances (double rtol=1.e-7, double atol=1.e-14)

virtual void	setMaxSteps (size_t maxsteps=20000)

virtual void	setMaxErrTestFails (size_t maxErrTestFails=7)

void	integrate (doublereal t0, doublereal t1)
	Integrate from t0 to t1. The integrator is reinitialized first. More...

void	integrate0 (doublereal t0, doublereal t1)
	Integrate from t0 to t1 without reinitializing the integrator. More...

void	solvePseudoSteadyStateProblem (int ifuncOverride=-1, doublereal timeScaleOverride=1.0)
	Solve for the pseudo steady-state of the surface problem. More...

virtual size_t	neq ()
	Return the number of equations. More...

virtual void	eval (doublereal t, doublereal y, doublereal ydot, doublereal *p)
	Evaluate the value of ydot[k] at the current conditions. More...

virtual void	getState (doublereal *y)
	Get the current state of the solution vector. More...

void	getConcSpecies (doublereal *const vecConcSpecies) const

void	setConcSpecies (const doublereal *const vecConcSpecies)
	Sets the concentrations within phases that are unknowns in the surface problem. More...

void	setCommonState_TP (doublereal TKelvin, doublereal PresPa)
	Sets the state variable in all thermodynamic phases (surface and surrounding bulk phases) to the input temperature and pressure. More...

std::vector< InterfaceKinetics * > &	getObjects ()
	Returns a reference to the vector of pointers to the InterfaceKinetics objects. More...

int	checkMatch (std::vector< ThermoPhase * > m_vec, ThermoPhase *thPtr)

void	setIOFlag (int ioFlag)

Public Member Functions inherited from FuncEval
int	eval_nothrow (double t, double y, double ydot)
	Evaluate the right-hand side using return code to indicate status. More...

virtual size_t	nparams ()
	Number of sensitivity parameters. More...

void	suppressErrors (bool suppress)
	Enable or disable suppression of errors when calling eval() More...

bool	suppressErrors () const
	Get current state of error suppression. More...

std::string	getErrors () const
	Return a string containing the text of any suppressed errors. More...

void	clearErrors ()
	Clear any previously-stored suppressed errors. More...

Protected Member Functions
void	updateState (doublereal *y)
	Set the mixture to a state consistent with solution vector y. More...

Protected Attributes
std::vector< SurfPhase * >	m_surf
	vector of pointers to surface phases. More...

std::vector< ThermoPhase * >	m_bulkPhases
	Vector of pointers to bulk phases. More...

std::vector< InterfaceKinetics * >	m_vecKinPtrs
	vector of pointers to InterfaceKinetics objects More...

std::vector< size_t >	m_nsp
	Vector of number of species in each Surface Phase. More...

std::vector< size_t >	m_surfindex
	index of the surface phase in each InterfaceKinetics object More...

std::vector< size_t >	m_specStartIndex

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

size_t	m_numTotalBulkSpecies

size_t	m_numTotalSpecies

std::vector< vector_int >	pLocVec

std::unique_ptr< Integrator >	m_integ
	Pointer to the CVODE integrator. More...

doublereal	m_atol

doublereal	m_rtol

doublereal	m_maxstep
	max step size More...

size_t	m_nmax
	maximum number of steps allowed More...

size_t	m_maxErrTestFails
	maximum number of error test failures allowed More...

vector_fp	m_work

vector_fp	m_concSpecies
	Temporary vector - length num species in the Kinetics object. More...

vector_fp	m_concSpeciesSave

int	m_mediumSpeciesStart
	Index into the species vector of the kinetics manager, pointing to the first species from the surrounding medium. More...

int	m_bulkSpeciesStart
	Index into the species vector of the kinetics manager, pointing to the first species from the condensed phase of the particles. More...

int	m_surfSpeciesStart
	Index into the species vector of the kinetics manager, pointing to the first species from the surface of the particles. More...

std::unique_ptr< solveSP >	m_surfSolver
	Pointer to the helper method, Placid, which solves the surface problem. More...

bool	m_commonTempPressForPhases
	If true, a common temperature and pressure for all surface and bulk phases associated with the surface problem is imposed. More...

Protected Attributes inherited from FuncEval
bool	m_suppress_errors

std::vector< std::string >	m_errors
	Errors occuring during function evaluations. More...

Private Attributes
int	m_ioFlag
	Controls the amount of printing from this routine and underlying routines. More...

Friends
class	solveSS
	We make the solveSS class a friend because we need to access all of the above information directly. More...

Additional Inherited Members
Public Attributes inherited from FuncEval
vector_fp	m_sens_params
	Values for the problem parameters for which sensitivities are computed This is the array which is perturbed and passed back as the fourth argument to eval(). More...

vector_fp	m_paramScales
	Scaling factors for each sensitivity parameter. More...

Detailed Description

Advances the surface coverages of the associated set of SurfacePhase objects in time.

This function advances a set of SurfPhase objects, each associated with one InterfaceKinetics object, in time. The following equation is used for each surface phase, i.

\[ \dot \theta_k = \dot s_k (\sigma_k / s_0) \]

In this equation,

\( \theta_k \) is the site coverage for the kth species.
\( \dot s_k \) is the source term for the kth species
\( \sigma_k \) is the number of surface sites covered by each species k.
\( s_0 \) is the total site density of the interfacial phase.

Additionally, the 0'th equation in the set is discarded. Instead the alternate equation is solved for

\[ \sum_{k=0}^{N-1} \dot \theta_k = 0 \]

This last equation serves to ensure that sum of the \( \theta_k \) values stays constant.

The object uses the CVODE software to advance the surface equations.

The solution vector used by this object is as follows: For each surface phase with \( N_s \) surface sites, it consists of the surface coverages \( \theta_k \) for \( k = 0, N_s - 1 \)

Definition at line 56 of file ImplicitSurfChem.h.

Constructor & Destructor Documentation

◆ ImplicitSurfChem()

ImplicitSurfChem	(	std::vector< InterfaceKinetics * >	k,
		double	rtol = `1.e-7`,
		double	atol = `1.e-14`,
		double	maxStepSize = `0`,
		size_t	maxSteps = `20000`,
		size_t	maxErrTestFails = `7`
	)

Constructor for multiple surfaces.

Parameters

k	Vector of pointers to InterfaceKinetics objects Each object consists of a surface or an edge containing internal degrees of freedom representing the concentration of surface adsorbates.
rtol	The relative tolerance for the integrator
atol	The absolute tolerance for the integrator
maxStepSize	The maximum step-size the integrator is allowed to take. If zero, this option is disabled.
maxSteps	The maximum number of time-steps the integrator can take. If not supplied, uses the default value in the CVodesIntegrator (20000).
maxErrTestFails	the maximum permissible number of error test failures If not supplied, uses the default value in CVODES (7).

Definition at line 20 of file ImplicitSurfChem.cpp.

Member Function Documentation

◆ initialize()

void initialize ( doublereal t0 = 0.0 )

virtual

Must be called before calling method 'advance'

Definition at line 138 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_integ, ImplicitSurfChem::m_maxErrTestFails, ImplicitSurfChem::m_maxstep, ImplicitSurfChem::m_nmax, ImplicitSurfChem::setMaxErrTestFails(), ImplicitSurfChem::setMaxSteps(), ImplicitSurfChem::setMaxStepSize(), and ImplicitSurfChem::setTolerances().

Referenced by ImplicitSurfChem::integrate(), and InterfaceKinetics::solvePseudoSteadyStateProblem().

◆ setMaxStepSize()

void setMaxStepSize ( double maxstep = 0.0 )

virtual

Set the maximum integration step-size. Note, setting this value to zero disables this option

Definition at line 111 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_integ, and ImplicitSurfChem::m_maxstep.

Referenced by InterfaceKinetics::advanceCoverages(), and ImplicitSurfChem::initialize().

◆ setTolerances()

void setTolerances	(	double	rtol = `1.e-7`,
		double	atol = `1.e-14`
	)

virtual

Set the relative and absolute integration tolerances.

Definition at line 119 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_integ.

Referenced by InterfaceKinetics::advanceCoverages(), and ImplicitSurfChem::initialize().

◆ setMaxSteps()

void setMaxSteps ( size_t maxsteps = 20000 )

virtual

Set the maximum number of CVODES integration steps.

Definition at line 126 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_integ, and ImplicitSurfChem::m_nmax.

Referenced by InterfaceKinetics::advanceCoverages(), and ImplicitSurfChem::initialize().

◆ setMaxErrTestFails()

void setMaxErrTestFails ( size_t maxErrTestFails = 7 )

virtual

Set the maximum number of CVODES error test failures

Definition at line 132 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_integ, and ImplicitSurfChem::m_maxErrTestFails.

Referenced by InterfaceKinetics::advanceCoverages(), and ImplicitSurfChem::initialize().

◆ integrate()

void integrate	(	doublereal	t0,
		doublereal	t1
	)

Integrate from t0 to t1. The integrator is reinitialized first.

This routine does a time accurate solve from t = t0 to t = t1. of the surface problem.

Parameters

t0	Initial Time -> this is an input
t1	Final Time -> This is an input

Definition at line 147 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::initialize(), ImplicitSurfChem::m_integ, ImplicitSurfChem::m_maxstep, and ImplicitSurfChem::updateState().

Referenced by InterfaceKinetics::advanceCoverages().

◆ integrate0()

void integrate0	(	doublereal	t0,
		doublereal	t1
	)

Integrate from t0 to t1 without reinitializing the integrator.

Use when the coverages have not changed from their values on return from the last call to integrate or integrate0.

Parameters

t0	Initial Time -> this is an input
t1	Final Time -> This is an input

Definition at line 158 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_integ, and ImplicitSurfChem::updateState().

◆ solvePseudoSteadyStateProblem()

void solvePseudoSteadyStateProblem	(	int	ifuncOverride = `-1`,
		doublereal	timeScaleOverride = `1.0`
	)

Solve for the pseudo steady-state of the surface problem.

Solve for the steady state of the surface problem. This is the same thing as the advanceCoverages() function, but at infinite times.

Note, a direct solve is carried out under the hood here, to reduce the computational time.

Parameters

ifuncOverride	One of the values defined in Surface Problem Solver Methods. The default is -1, which means that the program will decide.
timeScaleOverride	When a pseudo transient is selected this value can be used to override the default time scale for integration which is one. When SFLUX_TRANSIENT is used, this is equal to the time over which the equations are integrated. When SFLUX_INITIALIZE is used, this is equal to the time used in the initial transient algorithm, before the equation system is solved directly.

Definition at line 192 of file ImplicitSurfChem.cpp.

References BULK_ETCH, ImplicitSurfChem::getConcSpecies(), ImplicitSurfChem::m_commonTempPressForPhases, ImplicitSurfChem::m_concSpecies, ImplicitSurfChem::m_ioFlag, ImplicitSurfChem::m_nv, ImplicitSurfChem::m_surfSolver, ImplicitSurfChem::m_vecKinPtrs, Phase::pressure(), Kinetics::reactionPhaseIndex(), ImplicitSurfChem::setCommonState_TP(), ImplicitSurfChem::setConcSpecies(), SFLUX_INITIALIZE, SFLUX_RESIDUAL, Phase::temperature(), and Kinetics::thermo().

Referenced by InterfaceKinetics::solvePseudoSteadyStateProblem().

◆ neq()

virtual size_t neq ( )

inlinevirtual

Return the number of equations.

Implements FuncEval.

Definition at line 151 of file ImplicitSurfChem.h.

References ImplicitSurfChem::m_nv.

◆ eval()

void eval	(	doublereal	t,
		doublereal *	y,
		doublereal *	ydot,
		doublereal *	p
	)

virtual

Evaluate the value of ydot[k] at the current conditions.

Parameters

t	Time (seconds)
y	Vector containing the current solution vector
ydot	Output vector containing the value of the derivative of the surface coverages.
p	Unused parameter pass-through parameter vector

Implements FuncEval.

Definition at line 173 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_nsp, ImplicitSurfChem::m_surf, ImplicitSurfChem::m_surfindex, ImplicitSurfChem::m_vecKinPtrs, and ImplicitSurfChem::updateState().

◆ getState()

void getState ( doublereal * y )

virtual

Get the current state of the solution vector.

Parameters

y	Value of the solution vector to be used. On output, this contains the initial value of the solution.

Reimplemented from FuncEval.

Definition at line 102 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_nsp, and ImplicitSurfChem::m_surf.

◆ getConcSpecies()

void getConcSpecies ( doublereal *const vecConcSpecies ) const

Get the specifications for the problem from the values in the ThermoPhase objects for all phases.

concentrations of all species in all phases, m_concSpecies
Temperature and pressure

Parameters

vecConcSpecies Vector of concentrations. The phase concentration vectors are contiguous within the object, in the same order as the unknown vector.

Definition at line 268 of file ImplicitSurfChem.cpp.

References Phase::getConcentrations(), ImplicitSurfChem::m_bulkPhases, ImplicitSurfChem::m_nv, ImplicitSurfChem::m_surf, and Phase::nSpecies().

Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ setConcSpecies()

void setConcSpecies ( const doublereal *const vecConcSpecies )

Sets the concentrations within phases that are unknowns in the surface problem.

Fills the local concentration vector for all of the species in all of the phases that are unknowns in the surface problem.

Parameters

vecConcSpecies Vector of concentrations. The phase concentration vectors are contiguous within the object, in the same order as the unknown vector.

Definition at line 284 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_bulkPhases, ImplicitSurfChem::m_nv, ImplicitSurfChem::m_surf, Phase::nSpecies(), and Phase::setConcentrations().

Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ setCommonState_TP()

void setCommonState_TP	(	doublereal	TKelvin,
		doublereal	PresPa
	)

Sets the state variable in all thermodynamic phases (surface and surrounding bulk phases) to the input temperature and pressure.

Parameters

TKelvin	input temperature (kelvin)
PresPa	input pressure in pascal.

Definition at line 300 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_bulkPhases, ImplicitSurfChem::m_surf, and ThermoPhase::setState_TP().

Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ getObjects()

std::vector<InterfaceKinetics*>& getObjects ( )

inline

Returns a reference to the vector of pointers to the InterfaceKinetics objects.

This should probably go away in the future, as it opens up the class.

Definition at line 212 of file ImplicitSurfChem.h.

References ImplicitSurfChem::m_vecKinPtrs.

◆ updateState()

void updateState ( doublereal * y )

protected

Set the mixture to a state consistent with solution vector y.

This function will set the surface site factions in the underlying SurfPhase objects to the current value of the solution vector.

Parameters

y	Current value of the solution vector. The length is equal to the sum of the number of surface sites in all the surface phases.

Definition at line 164 of file ImplicitSurfChem.cpp.

References ImplicitSurfChem::m_nsp, and ImplicitSurfChem::m_surf.

Referenced by ImplicitSurfChem::eval(), ImplicitSurfChem::integrate(), and ImplicitSurfChem::integrate0().

Friends And Related Function Documentation

◆ solveSS

friend class solveSS

friend

We make the solveSS class a friend because we need to access all of the above information directly.

Adding the members into the class is also a possibility.

Definition at line 304 of file ImplicitSurfChem.h.

Member Data Documentation

◆ m_surf

std::vector<SurfPhase*> m_surf

protected

vector of pointers to surface phases.

Definition at line 235 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::eval(), ImplicitSurfChem::getConcSpecies(), ImplicitSurfChem::getState(), ImplicitSurfChem::setCommonState_TP(), ImplicitSurfChem::setConcSpecies(), and ImplicitSurfChem::updateState().

◆ m_bulkPhases

std::vector<ThermoPhase*> m_bulkPhases

protected

Vector of pointers to bulk phases.

Definition at line 238 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::getConcSpecies(), ImplicitSurfChem::setCommonState_TP(), and ImplicitSurfChem::setConcSpecies().

◆ m_vecKinPtrs

std::vector<InterfaceKinetics*> m_vecKinPtrs

protected

vector of pointers to InterfaceKinetics objects

Definition at line 241 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::eval(), ImplicitSurfChem::getObjects(), and ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ m_nsp

std::vector<size_t> m_nsp

protected

Vector of number of species in each Surface Phase.

Definition at line 244 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::eval(), ImplicitSurfChem::getState(), and ImplicitSurfChem::updateState().

◆ m_surfindex

std::vector<size_t> m_surfindex

protected

index of the surface phase in each InterfaceKinetics object

Definition at line 247 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::eval().

◆ m_nv

size_t m_nv

protected

Total number of surface species in all surface phases.

This is the total number of unknowns in m_mode 0 problem

Definition at line 255 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::getConcSpecies(), ImplicitSurfChem::neq(), ImplicitSurfChem::setConcSpecies(), and ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ m_integ

std::unique_ptr<Integrator> m_integ

protected

Pointer to the CVODE integrator.

Definition at line 262 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::initialize(), ImplicitSurfChem::integrate(), ImplicitSurfChem::integrate0(), ImplicitSurfChem::setMaxErrTestFails(), ImplicitSurfChem::setMaxSteps(), ImplicitSurfChem::setMaxStepSize(), and ImplicitSurfChem::setTolerances().

◆ m_maxstep

doublereal m_maxstep

protected

max step size

Definition at line 264 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::initialize(), ImplicitSurfChem::integrate(), and ImplicitSurfChem::setMaxStepSize().

◆ m_nmax

size_t m_nmax

protected

maximum number of steps allowed

Definition at line 265 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::initialize(), and ImplicitSurfChem::setMaxSteps().

◆ m_maxErrTestFails

size_t m_maxErrTestFails

protected

maximum number of error test failures allowed

Definition at line 266 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::initialize(), and ImplicitSurfChem::setMaxErrTestFails().

◆ m_concSpecies

vector_fp m_concSpecies

protected

Temporary vector - length num species in the Kinetics object.

This is the sum of the number of species in each phase included in the kinetics object.

Definition at line 274 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ m_mediumSpeciesStart

int m_mediumSpeciesStart

protected

Index into the species vector of the kinetics manager, pointing to the first species from the surrounding medium.

Definition at line 281 of file ImplicitSurfChem.h.

◆ m_bulkSpeciesStart

int m_bulkSpeciesStart

protected

Index into the species vector of the kinetics manager, pointing to the first species from the condensed phase of the particles.

Definition at line 286 of file ImplicitSurfChem.h.

◆ m_surfSpeciesStart

int m_surfSpeciesStart

protected

Index into the species vector of the kinetics manager, pointing to the first species from the surface of the particles.

Definition at line 291 of file ImplicitSurfChem.h.

◆ m_surfSolver

std::unique_ptr<solveSP> m_surfSolver

protected

Pointer to the helper method, Placid, which solves the surface problem.

Definition at line 295 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ m_commonTempPressForPhases

bool m_commonTempPressForPhases

protected

If true, a common temperature and pressure for all surface and bulk phases associated with the surface problem is imposed.

Definition at line 299 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().

◆ m_ioFlag

int m_ioFlag

private

Controls the amount of printing from this routine and underlying routines.

Definition at line 309 of file ImplicitSurfChem.h.

Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().

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

Public Member Functions

Protected Member Functions

Protected Attributes

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ ImplicitSurfChem()

Member Function Documentation

◆ initialize()

◆ setMaxStepSize()

◆ setTolerances()

◆ setMaxSteps()

◆ setMaxErrTestFails()

◆ integrate()

◆ integrate0()

◆ solvePseudoSteadyStateProblem()

◆ neq()

◆ eval()

◆ getState()

◆ getConcSpecies()

◆ setConcSpecies()

◆ setCommonState_TP()

◆ getObjects()

◆ updateState()

Friends And Related Function Documentation

◆ solveSS

Member Data Documentation

◆ m_surf

◆ m_bulkPhases

◆ m_vecKinPtrs

◆ m_nsp

◆ m_surfindex

◆ m_nv

◆ m_integ

◆ m_maxstep

◆ m_nmax

◆ m_maxErrTestFails

◆ m_concSpecies

◆ m_mediumSpeciesStart

◆ m_bulkSpeciesStart

◆ m_surfSpeciesStart

◆ m_surfSolver

◆ m_commonTempPressForPhases

◆ m_ioFlag