diff --git a/include/cantera/kinetics/ImplicitSurfChem.h b/include/cantera/kinetics/ImplicitSurfChem.h
index f550d1d15..23dcbb49a 100644
--- a/include/cantera/kinetics/ImplicitSurfChem.h
+++ b/include/cantera/kinetics/ImplicitSurfChem.h
@@ -17,54 +17,46 @@
namespace Cantera
{
-
class solveSP;
-
//! Advances the surface coverages of the associated set of SurfacePhase
//! objects in time
/*!
- * This function advances a set of SurfacePhase objects, each
- * associated with one InterfaceKinetics object, in time.
- * The following equation is used for each surface phase, i.
+ * 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*.
*
* \f[
* \dot \theta_k = \dot s_k (\sigma_k / s_0)
* \f]
*
- * In this equation,
- * \f$ \theta_k \f$ is the site coverage for the kth species.
- * \f$ \dot s_k \f$ is the source term for the kth species
- * \f$ \sigma_k \f$ is the number of surface sites covered by
- * each species k.
- * \f$ s_0 \f$ is the total site density of the interfacial phase.
+ * In this equation,
+ * - \f$ \theta_k \f$ is the site coverage for the kth species.
+ * - \f$ \dot s_k \f$ is the source term for the kth species
+ * - \f$ \sigma_k \f$ is the number of surface sites covered by each species k.
+ * - \f$ s_0 \f$ 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
+ * Additionally, the 0'th equation in the set is discarded. Instead the
+ * alternate equation is solved for
*
- * \f[
- * \sum_{k=0}^{N-1} \dot \theta_k = 0
- * \f]
+ * \f[
+ * \sum_{k=0}^{N-1} \dot \theta_k = 0
+ * \f]
*
- * This last equation serves to ensure that sum of the \f$ \theta_k \f$
- * values stays constant.
+ * This last equation serves to ensure that sum of the \f$ \theta_k \f$ values
+ * stays constant.
*
- * The object uses the CVODE software to advance the surface equations.
+ * 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 \f$ N_s \f$ surface sites,
- * it consists of the surface coverages
- * \f$ \theta_k \f$ for \f$ k = 0, N_s - 1 \f$
+ * The solution vector used by this object is as follows: For each surface
+ * phase with \f$ N_s \f$ surface sites, it consists of the surface coverages
+ * \f$ \theta_k \f$ for \f$ k = 0, N_s - 1 \f$
*
* @ingroup kineticsmgr
- *
*/
class ImplicitSurfChem : public FuncEval
{
-
public:
-
-
//! Constructor for multiple surfaces.
/*!
* @param k Vector of pointers to InterfaceKinetics objects
@@ -79,13 +71,11 @@ public:
*/
virtual ~ImplicitSurfChem();
- /**
- * Overloads the virtual function
- * declared in FuncEval.
+ /*!
+ * Must be called before calling method 'advance'
*/
virtual void initialize(doublereal t0 = 0.0);
-
//! Integrate from t0 to t1. The integrator is reinitialized first.
/*!
* This routine does a time accurate solve from t = t0 to t = t1.
@@ -96,19 +86,16 @@ public:
*/
void integrate(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.
+ * Use when the coverages have not changed from their values on return
+ * from the last call to integrate or integrate0.
*
* @param t0 Initial Time -> this is an input
* @param t1 Final Time -> This is an input
*/
void integrate0(doublereal t0, doublereal t1);
-
//! Solve for the pseudo steady-state of the surface problem
/*!
* Solve for the steady state of the surface problem.
@@ -118,13 +105,13 @@ public:
* Note, a direct solve is carried out under the hood here,
* to reduce the computational time.
*
- * @param ifuncOverride 4 values are possible
- * 1 SFLUX_INITIALIZE
- * 2 SFLUX_RESIDUAL
- * 3 SFLUX_JACOBIAN
- * 4 SFLUX_TRANSIENT
- * The default is -1, which means that the program
- * will decide.
+ * @param ifuncOverride 4 values are possible. The default is -1, which
+ * means that the program will decide:
+ * - 1 SFLUX_INITIALIZE
+ * - 2 SFLUX_RESIDUAL
+ * - 3 SFLUX_JACOBIAN
+ * - 4 SFLUX_TRANSIENT
+ *
* @param timeScaleOverride When a pseudo transient is
* selected this value can be used to override
* the default time scale for integration which
@@ -138,7 +125,6 @@ public:
void solvePseudoSteadyStateProblem(int ifuncOverride = -1,
doublereal timeScaleOverride = 1.0);
-
// overloaded methods of class FuncEval
//! Return the number of equations
@@ -168,27 +154,24 @@ public:
virtual void getInitialConditions(doublereal t0,
size_t leny, doublereal* y);
- /*
+ /*!
* Get the specifications for the problem from the values
* in the ThermoPhase objects for all phases.
*
- * 1) concentrations of all species in all phases, m_concSpecies[]
- * 2) Temperature and pressure
+ * 1. concentrations of all species in all phases, #m_concSpecies
+ * 2. Temperature and pressure
*
- *
- * @param vecConcSpecies Vector of concentrations. The
- * phase concentration vectors are contiguous
- * within the object, in the same order as the
- * unknown vector.
+ * @param vecConcSpecies Vector of concentrations. The phase
+ * concentration vectors are contiguous within the
+ * object, in the same order as the unknown vector.
*/
void getConcSpecies(doublereal* const vecConcSpecies) const;
//! 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.
+ * Fills the local concentration vector for all of the species in all of
+ * the phases that are unknowns in the surface problem.
*
* @param vecConcSpecies Vector of concentrations. The
* phase concentration vectors are contiguous
@@ -205,12 +188,10 @@ public:
*/
void setCommonState_TP(doublereal TKelvin, doublereal PresPa);
-
//! 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.
+ * This should probably go away in the future, as it opens up the class.
*/
std::vector & getObjects() {
return m_vecKinPtrs;
@@ -223,18 +204,14 @@ public:
}
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.
+ * This function will set the surface site factions in the underlying
+ * SurfPhase objects to the current value of the solution vector.
*
- * @param 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
+ * @param 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.
*/
void updateState(doublereal* y);
@@ -278,15 +255,13 @@ protected:
//! Pointer to the cvode integrator
Integrator* m_integ;
doublereal m_atol, m_rtol; // tolerances
- doublereal m_maxstep; // max step size
+ doublereal m_maxstep; //!< max step size
vector_fp m_work;
-
-
/**
- * 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.
+ * 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.
*/
vector_fp m_concSpecies;
vector_fp m_concSpeciesSave;
@@ -327,7 +302,6 @@ protected:
friend class solveSS;
private:
-
//! Controls the amount of printing from this routine
//! and underlying routines.
int m_ioFlag;
@@ -335,4 +309,3 @@ private:
}
#endif
-
diff --git a/src/kinetics/ImplicitSurfChem.cpp b/src/kinetics/ImplicitSurfChem.cpp
index f73473256..e06c2048f 100644
--- a/src/kinetics/ImplicitSurfChem.cpp
+++ b/src/kinetics/ImplicitSurfChem.cpp
@@ -15,7 +15,6 @@ using namespace std;
namespace Cantera
{
-// Constructor
ImplicitSurfChem::ImplicitSurfChem(vector k) :
FuncEval(),
m_nsurf(0),
@@ -109,17 +108,12 @@ int ImplicitSurfChem::checkMatch(std::vector m_vec, ThermoPhase* t
return retn;
}
-/*
- * Destructor. Deletes the integrator.
- */
ImplicitSurfChem::~ImplicitSurfChem()
{
delete m_integ;
delete m_surfSolver;
}
-// overloaded method of FuncEval. Called by the integrator to
-// get the initial conditions.
void ImplicitSurfChem::getInitialConditions(doublereal t0, size_t lenc,
doublereal* c)
{
@@ -130,24 +124,12 @@ void ImplicitSurfChem::getInitialConditions(doublereal t0, size_t lenc,
}
}
-
-/*
- * Must be called before calling method 'advance'
- */
void ImplicitSurfChem::initialize(doublereal t0)
{
m_integ->setTolerances(m_rtol, m_atol);
m_integ->initialize(t0, *this);
}
-// 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.
- *
- * @param t0 Initial Time -> this is an input
- * @param t1 Final Time -> This is an input
- */
void ImplicitSurfChem::integrate(doublereal t0, doublereal t1)
{
m_integ->initialize(t0, *this);
@@ -156,15 +138,6 @@ void ImplicitSurfChem::integrate(doublereal t0, doublereal t1)
updateState(m_integ->solution());
}
-// 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.
- *
- * @param t0 Initial Time -> this is an input
- * @param t1 Final Time -> This is an input
- */
void ImplicitSurfChem::integrate0(doublereal t0, doublereal t1)
{
m_integ->integrate(t1);
@@ -180,9 +153,6 @@ void ImplicitSurfChem::updateState(doublereal* c)
}
}
-/*
- * Called by the integrator to evaluate ydot given y at time 'time'.
- */
void ImplicitSurfChem::eval(doublereal time, doublereal* y,
doublereal* ydot, doublereal* p)
{
@@ -204,19 +174,9 @@ void ImplicitSurfChem::eval(doublereal time, doublereal* y,
}
}
-// 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.
- */
void ImplicitSurfChem::solvePseudoSteadyStateProblem(int ifuncOverride,
doublereal timeScaleOverride)
{
-
int ifunc;
/*
* set bulkFunc
@@ -306,17 +266,6 @@ void ImplicitSurfChem::solvePseudoSteadyStateProblem(int ifuncOverride,
}
}
-
-
-/*
- * getConcSpecies():
- *
- * Fills the local concentration vector, m_concSpecies for all of the
- * species in all of the phases that are unknowns in the surface
- * problem.
- *
- * m_concSpecies[]
- */
void ImplicitSurfChem::getConcSpecies(doublereal* const vecConcSpecies) const
{
size_t kstart;
@@ -333,15 +282,6 @@ void ImplicitSurfChem::getConcSpecies(doublereal* const vecConcSpecies) const
}
}
-/*
- * setConcSpecies():
- *
- * Fills the local concentration vector, m_concSpecies for all of the
- * species in all of the phases that are unknowns in the surface
- * problem.
- *
- * m_concSpecies[]
- */
void ImplicitSurfChem::setConcSpecies(const doublereal* const vecConcSpecies)
{
size_t kstart;
@@ -358,15 +298,6 @@ void ImplicitSurfChem::setConcSpecies(const doublereal* const vecConcSpecies)
}
}
-/*
- * setCommonState_TP():
- *
- * Sets a common temperature and pressure amongst the
- * thermodynamic objects in the interfacial kinetics object.
- *
- * Units Temperature = Kelvin
- * Pressure = Pascal
- */
void ImplicitSurfChem::
setCommonState_TP(doublereal TKelvin, doublereal PresPa)
{