Cantera
2.4.0
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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) | |
Constructor for multiple surfaces. More... | |
virtual void | initialize (doublereal t0=0.0) |
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... | |
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... | |
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 | ) |
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. |
Definition at line 20 of file ImplicitSurfChem.cpp.
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virtual |
Must be called before calling method 'advance'
Definition at line 107 of file ImplicitSurfChem.cpp.
References ImplicitSurfChem::m_integ.
Referenced by InterfaceKinetics::advanceCoverages(), and InterfaceKinetics::solvePseudoSteadyStateProblem().
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.
t0 | Initial Time -> this is an input |
t1 | Final Time -> This is an input |
Definition at line 113 of file ImplicitSurfChem.cpp.
References ImplicitSurfChem::m_integ, and ImplicitSurfChem::updateState().
Referenced by InterfaceKinetics::advanceCoverages().
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.
t0 | Initial Time -> this is an input |
t1 | Final Time -> This is an input |
Definition at line 121 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 155 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, ThermoPhase::pressure(), ImplicitSurfChem::setCommonState_TP(), ImplicitSurfChem::setConcSpecies(), SFLUX_INITIALIZE, SFLUX_RESIDUAL, and Phase::temperature().
Referenced by InterfaceKinetics::solvePseudoSteadyStateProblem().
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inlinevirtual |
Return the number of equations.
Implements FuncEval.
Definition at line 119 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 136 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 98 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 231 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 247 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 | ||
) |
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 263 of file ImplicitSurfChem.cpp.
References ImplicitSurfChem::m_bulkPhases, ImplicitSurfChem::m_surf, and ThermoPhase::setState_TP().
Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().
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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 180 of file ImplicitSurfChem.h.
References ImplicitSurfChem::m_vecKinPtrs.
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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.
y | Current value of the solution vector. The lenth is equal to the sum of the number of surface sites in all the surface phases. |
Definition at line 127 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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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 270 of file ImplicitSurfChem.h.
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vector of pointers to surface phases.
Definition at line 203 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 206 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 209 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 212 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 215 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::eval().
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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 223 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::getConcSpecies(), ImplicitSurfChem::neq(), ImplicitSurfChem::setConcSpecies(), and ImplicitSurfChem::solvePseudoSteadyStateProblem().
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Pointer to the CVODE integrator.
Definition at line 230 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::initialize(), ImplicitSurfChem::integrate(), and ImplicitSurfChem::integrate0().
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max step size
Definition at line 232 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 240 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().
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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 247 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 252 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 257 of file ImplicitSurfChem.h.
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Pointer to the helper method, Placid, which solves the surface problem.
Definition at line 261 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 265 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().
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private |
Controls the amount of printing from this routine and underlying routines.
Definition at line 275 of file ImplicitSurfChem.h.
Referenced by ImplicitSurfChem::solvePseudoSteadyStateProblem().