Cantera
3.1.0a1
|
Advances the surface coverages of the associated set of SurfacePhase objects in time. More...
#include <ImplicitSurfChem.h>
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 58 of file ImplicitSurfChem.h.
Public Member Functions | |
ImplicitSurfChem (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... | |
void | initialize (double t0=0.0) |
Must be called before calling method 'advance'. More... | |
void | setMaxStepSize (double maxstep=0.0) |
Set the maximum integration step-size. More... | |
void | setTolerances (double rtol=1.e-7, double atol=1.e-14) |
Set the relative and absolute integration tolerances. More... | |
void | setMaxSteps (size_t maxsteps=20000) |
Set the maximum number of CVODES integration steps. More... | |
void | setMaxErrTestFails (size_t maxErrTestFails=7) |
Set the maximum number of CVODES error test failures. More... | |
void | integrate (double t0, double t1) |
Integrate from t0 to t1. The integrator is reinitialized first. More... | |
void | integrate0 (double t0, double t1) |
Integrate from t0 to t1 without reinitializing the integrator. More... | |
void | solvePseudoSteadyStateProblem (int ifuncOverride=-1, double timeScaleOverride=1.0) |
Solve for the pseudo steady-state of the surface problem. More... | |
size_t | neq () const override |
Return the number of equations. More... | |
void | eval (double t, double *y, double *ydot, double *p) override |
Evaluate the value of ydot[k] at the current conditions. More... | |
void | getState (double *y) override |
Get the current state of the solution vector. More... | |
void | getConcSpecies (double *const vecConcSpecies) const |
Get the specifications for the problem from the values in the ThermoPhase objects for all phases. More... | |
void | setConcSpecies (const double *const vecConcSpecies) |
Sets the concentrations within phases that are unknowns in the surface problem. More... | |
void | setCommonState_TP (double TKelvin, double PresPa) |
Sets the state variable in all thermodynamic phases (surface and surrounding bulk phases) to the input temperature and pressure. More... | |
vector< InterfaceKinetics * > & | getObjects () |
Returns a reference to the vector of pointers to the InterfaceKinetics objects. More... | |
int | checkMatch (vector< ThermoPhase * > m_vec, ThermoPhase *thPtr) |
void | setIOFlag (int ioFlag) |
Public Member Functions inherited from FuncEval | |
virtual void | evalDae (double t, double *y, double *ydot, double *p, double *residual) |
Evaluate the right-hand-side DAE function. More... | |
virtual void | getConstraints (double *constraints) |
Given a vector of length neq(), mark which variables should be considered algebraic constraints. More... | |
int | evalNoThrow (double t, double *y, double *ydot) |
Evaluate the right-hand side using return code to indicate status. More... | |
int | evalDaeNoThrow (double t, double *y, double *ydot, double *residual) |
Evaluate the right-hand side using return code to indicate status. More... | |
virtual void | preconditionerSetup (double t, double *y, double gamma) |
Evaluate the setup processes for the Jacobian preconditioner. More... | |
virtual void | preconditionerSolve (double *rhs, double *output) |
Evaluate the linear system Ax=b where A is the preconditioner. More... | |
virtual void | updatePreconditioner (double gamma) |
Update the preconditioner based on already computed jacobian values. More... | |
int | preconditioner_setup_nothrow (double t, double *y, double gamma) |
Preconditioner setup that doesn't throw an error but returns a CVODES flag. More... | |
int | preconditioner_solve_nothrow (double *rhs, double *output) |
Preconditioner solve that doesn't throw an error but returns a CVODES flag. More... | |
virtual void | getStateDae (double *y, double *ydot) |
Fill in the vectors y and ydot with the current state of the system. More... | |
virtual size_t | nparams () const |
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... | |
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 (double *y) |
Set the mixture to a state consistent with solution vector y. More... | |
Protected Attributes | |
vector< SurfPhase * > | m_surf |
vector of pointers to surface phases. More... | |
vector< ThermoPhase * > | m_bulkPhases |
Vector of pointers to bulk phases. More... | |
vector< InterfaceKinetics * > | m_vecKinPtrs |
vector of pointers to InterfaceKinetics objects More... | |
vector< size_t > | m_nsp |
Vector of number of species in each Surface Phase. More... | |
vector< size_t > | m_specStartIndex |
size_t | m_nv = 0 |
Total number of surface species in all surface phases. More... | |
size_t | m_numTotalBulkSpecies = 0 |
size_t | m_numTotalSpecies = 0 |
vector< vector< int > > | pLocVec |
unique_ptr< Integrator > | m_integ |
Pointer to the CVODE integrator. More... | |
double | m_atol |
double | m_rtol |
double | 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< double > | m_work |
vector< double > | m_concSpecies |
Temporary vector - length num species in the Kinetics object. More... | |
vector< double > | m_concSpeciesSave |
int | m_mediumSpeciesStart = -1 |
Index into the species vector of the kinetics manager, pointing to the first species from the surrounding medium. More... | |
int | m_bulkSpeciesStart = -1 |
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 = -1 |
Index into the species vector of the kinetics manager, pointing to the first species from the surface of the particles. More... | |
unique_ptr< solveSP > | m_surfSolver |
Pointer to the helper method, Placid, which solves the surface problem. More... | |
bool | m_commonTempPressForPhases = true |
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 = false |
vector< string > | m_errors |
Errors occurring during function evaluations. More... | |
Private Attributes | |
int | m_ioFlag = 0 |
Controls the amount of printing from this routine and underlying routines. More... | |
Additional Inherited Members | |
Public Attributes inherited from FuncEval | |
vector< double > | 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< double > | m_paramScales |
Scaling factors for each sensitivity parameter. More... | |
ImplicitSurfChem | ( | 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.
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 18 of file ImplicitSurfChem.cpp.
void initialize | ( | double | t0 = 0.0 | ) |
Must be called before calling method 'advance'.
Definition at line 124 of file ImplicitSurfChem.cpp.
void setMaxStepSize | ( | double | maxstep = 0.0 | ) |
Set the maximum integration step-size.
Note, setting this value to zero disables this option
Definition at line 97 of file ImplicitSurfChem.cpp.
void setTolerances | ( | double | rtol = 1.e-7 , |
double | atol = 1.e-14 |
||
) |
Set the relative and absolute integration tolerances.
Definition at line 105 of file ImplicitSurfChem.cpp.
void setMaxSteps | ( | size_t | maxsteps = 20000 | ) |
Set the maximum number of CVODES integration steps.
Definition at line 112 of file ImplicitSurfChem.cpp.
void setMaxErrTestFails | ( | size_t | maxErrTestFails = 7 | ) |
Set the maximum number of CVODES error test failures.
Definition at line 118 of file ImplicitSurfChem.cpp.
void integrate | ( | double | t0, |
double | 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 133 of file ImplicitSurfChem.cpp.
void integrate0 | ( | double | t0, |
double | 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 144 of file ImplicitSurfChem.cpp.
void solvePseudoSteadyStateProblem | ( | int | ifuncOverride = -1 , |
double | 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.
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 176 of file ImplicitSurfChem.cpp.
|
inlineoverridevirtual |
Return the number of equations.
Implements FuncEval.
Definition at line 151 of file ImplicitSurfChem.h.
|
overridevirtual |
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 |
Reimplemented from FuncEval.
Definition at line 159 of file ImplicitSurfChem.cpp.
|
overridevirtual |
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 88 of file ImplicitSurfChem.cpp.
void getConcSpecies | ( | double *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 252 of file ImplicitSurfChem.cpp.
void setConcSpecies | ( | const double *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 268 of file ImplicitSurfChem.cpp.
void setCommonState_TP | ( | double | TKelvin, |
double | 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 284 of file ImplicitSurfChem.cpp.
|
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 211 of file ImplicitSurfChem.h.
|
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 length is equal to the sum of the number of surface sites in all the surface phases. |
Definition at line 150 of file ImplicitSurfChem.cpp.
|
protected |
vector of pointers to surface phases.
Definition at line 234 of file ImplicitSurfChem.h.
|
protected |
Vector of pointers to bulk phases.
Definition at line 237 of file ImplicitSurfChem.h.
|
protected |
vector of pointers to InterfaceKinetics objects
Definition at line 240 of file ImplicitSurfChem.h.
|
protected |
Vector of number of species in each Surface Phase.
Definition at line 243 of file ImplicitSurfChem.h.
|
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 251 of file ImplicitSurfChem.h.
|
protected |
Pointer to the CVODE integrator.
Definition at line 258 of file ImplicitSurfChem.h.
|
protected |
max step size
Definition at line 260 of file ImplicitSurfChem.h.
|
protected |
maximum number of steps allowed
Definition at line 261 of file ImplicitSurfChem.h.
|
protected |
maximum number of error test failures allowed
Definition at line 262 of file ImplicitSurfChem.h.
|
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 270 of file ImplicitSurfChem.h.
|
protected |
Index into the species vector of the kinetics manager, pointing to the first species from the surrounding medium.
Definition at line 277 of file ImplicitSurfChem.h.
|
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 282 of file ImplicitSurfChem.h.
|
protected |
Index into the species vector of the kinetics manager, pointing to the first species from the surface of the particles.
Definition at line 287 of file ImplicitSurfChem.h.
|
protected |
Pointer to the helper method, Placid, which solves the surface problem.
Definition at line 291 of file ImplicitSurfChem.h.
|
protected |
If true, a common temperature and pressure for all surface and bulk phases associated with the surface problem is imposed.
Definition at line 295 of file ImplicitSurfChem.h.
|
private |
Controls the amount of printing from this routine and underlying routines.
Definition at line 300 of file ImplicitSurfChem.h.