Cantera 2.6.0
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Advances the surface coverages of the associated set of SurfacePhase objects in time. More...
#include <ImplicitSurfChem.h>
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 occurring 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... | |
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,
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.
ImplicitSurfChem | ( | std::vector< InterfaceKinetics * > | k, |
double | rtol = 1.e-7 , |
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double | atol = 1.e-14 , |
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double | maxStepSize = 0 , |
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size_t | maxSteps = 20000 , |
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size_t | maxErrTestFails = 7 |
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Constructor for multiple surfaces.
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.
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Definition at line 78 of file ImplicitSurfChem.h.
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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().
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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().
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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().
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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().
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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().
void integrate | ( | doublereal | t0, |
doublereal | t1 | ||
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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.
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().
void integrate0 | ( | doublereal | t0, |
doublereal | t1 | ||
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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.
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().
void solvePseudoSteadyStateProblem | ( | int | ifuncOverride = -1 , |
doublereal | timeScaleOverride = 1.0 |
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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.
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().
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Return the number of equations.
Implements FuncEval.
Definition at line 151 of file ImplicitSurfChem.h.
References ImplicitSurfChem::m_nv.
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Evaluate the value of ydot[k] at the current conditions.
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().
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Get the current state of the solution vector.
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.
void getConcSpecies | ( | doublereal *const | vecConcSpecies | ) | const |
Get the specifications for the problem from the values in the ThermoPhase objects for all phases.
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().
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.
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().
void setCommonState_TP | ( | doublereal | TKelvin, |
doublereal | PresPa | ||
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Sets the state variable in all thermodynamic phases (surface and surrounding bulk phases) to the input temperature and pressure.
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().
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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.
int checkMatch | ( | std::vector< ThermoPhase * > | m_vec, |
ThermoPhase * | thPtr | ||
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Definition at line 90 of file ImplicitSurfChem.cpp.
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Definition at line 218 of file ImplicitSurfChem.h.
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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.
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().
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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.
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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().
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Vector of pointers to bulk phases.
Definition at line 238 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::getConcSpecies(), ImplicitSurfChem::setCommonState_TP(), and ImplicitSurfChem::setConcSpecies().
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vector of pointers to InterfaceKinetics objects
Definition at line 241 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::eval(), ImplicitSurfChem::getObjects(), and ImplicitSurfChem::solvePseudoSteadyStateProblem().
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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().
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index of the surface phase in each InterfaceKinetics object
Definition at line 247 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::eval().
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Definition at line 249 of file ImplicitSurfChem.h.
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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().
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Definition at line 257 of file ImplicitSurfChem.h.
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Definition at line 258 of file ImplicitSurfChem.h.
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Definition at line 260 of file ImplicitSurfChem.h.
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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().
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Definition at line 263 of file ImplicitSurfChem.h.
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Definition at line 263 of file ImplicitSurfChem.h.
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max step size
Definition at line 264 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::initialize(), ImplicitSurfChem::integrate(), and ImplicitSurfChem::setMaxStepSize().
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maximum number of steps allowed
Definition at line 265 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::initialize(), and ImplicitSurfChem::setMaxSteps().
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maximum number of error test failures allowed
Definition at line 266 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::initialize(), and ImplicitSurfChem::setMaxErrTestFails().
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Definition at line 267 of file ImplicitSurfChem.h.
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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().
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Definition at line 275 of file ImplicitSurfChem.h.
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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.
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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.
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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.
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Pointer to the helper method, Placid, which solves the surface problem.
Definition at line 295 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().
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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().
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Controls the amount of printing from this routine and underlying routines.
Definition at line 309 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().