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revised covdepthermo main code block
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reformatted covdep_test

revised constructors
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@jongyoonbae
jongyoonbae committed Apr 19, 2022
1 parent 9e2c621 commit 0140687
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222 changes: 58 additions & 164 deletions include/cantera/thermo/CoverageDependentSurfPhase.h
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Original file line number Diff line number Diff line change
Expand Up @@ -17,30 +17,29 @@

namespace Cantera
{

//! Set of parameters modifying SurfPhase enthalpy and entropy based on fractional surface coverages
//! using a polynomial model. Linear model is a subset of the polynomial model.
struct PolynomialDependency
{
//! Constructor
//! @param name_k_ name of a species whose thermodynamics are calculated
//! @param name_j_ name of a species whose coverage affects thermodynamics of the target species
//! @param k_ index of a species whose thermodynamics are calculated
//! @param j_ index of a species whose coverage affects thermodynamics of the target species
//! @param enthalpy_coeffs_ array of polynomial coefficients describing enthalpy change
//! containing 1st-order, 2nd-order, 3rd-order, and 4th-order
//! coefficients as a function of coverage [J/kmol]
//! @param entropy_coeffs_ array of polynomial coefficients describing entropy change
//! containing 1st-order, 2nd-order, 3rd-order, and 4th-order
//! coefficients as a function of coverage [J/kmol/K]
PolynomialDependency(std::string name_k_, std::string name_j_,
PolynomialDependency(size_t k_, size_t j_,
vector_fp enthalpy_coeffs_, vector_fp entropy_coeffs_):
name_k(name_k_), name_j(name_j_),
k(k_), j(j_),
enthalpy_coeffs(enthalpy_coeffs_),
entropy_coeffs(entropy_coeffs_) {}
PolynomialDependency() {}
//! name of a species whose thermodynamics are calculated
std::string name_k;
//! name of a species whose coverage affects thermodynamics of the target species
std::string name_j;
//! index of a species whose thermodynamics are calculated
size_t k;
//! index of a species whose coverage affects thermodynamics of the target species
size_t j;
//! array of polynomial coefficients describing enthalpy change containing 1st-order, 2nd-order,
//! 3rd-order, and 4th-order coefficients as a function of coverage [J/kmol]
vector_fp enthalpy_coeffs;
Expand All @@ -54,8 +53,8 @@ struct PolynomialDependency
struct PiecewiseDependency
{
//! Constructor
//! @param name_k_ name of a species whose thermodynamics are calculated
//! @param name_j_ name of a species whose coverage affects thermodynamics of the target species
//! @param k_ index of a species whose thermodynamics are calculated
//! @param j_ index of a species whose coverage affects thermodynamics of the target species
//! @param enthalpy_params_ array of three parameters to calculate coverage-dependent enthalpy:
//! slope of enthalpy change in the first region [J/kmol], slope of
//! enthalpy change in the second region [J/kmol], and coverage
Expand All @@ -64,16 +63,16 @@ struct PiecewiseDependency
//! slope of entropy change in the first region [J/kmol/K], slope of
//! entropy change in the second region [J/kmol/K], and coverage
//! dividing first and second region [dimensionless]
PiecewiseDependency(std::string name_k_, std::string name_j_,
PiecewiseDependency(size_t k_, size_t j_,
vector_fp enthalpy_params_, vector_fp entropy_params_):
name_k(name_k_), name_j(name_j_),
k(k_), j(j_),
enthalpy_params(enthalpy_params_),
entropy_params(entropy_params_) {}
PiecewiseDependency() {}
//! name of a species whose thermodynamics are calculated
std::string name_k;
//! name of a species whose coverage affects thermodynamics of the target species
std::string name_j;
//! index of a species whose thermodynamics are calculated
size_t k;
//! index of a species whose coverage affects thermodynamics of the target species
size_t j;
//! array of three parameters to calculate coverage-dependent enthalpy: slope of enthalpy change
//! in the first region [J/kmol], slope of enthalpy change in the second region [J/kmol],
//! and coverage dividing first and second region [dimensionless]
Expand All @@ -89,74 +88,64 @@ struct PiecewiseDependency
struct InterpolativeDependency
{
//! Constructor
//! @param name_k_ name of a species whose thermodynamics are calculated
//! @param name_j_ name of a species whose coverage affects thermodynamics of the target species
//! @param enthalpy_coverages_ array of coverages for coverage-dependent enthalpy interpolation
//! [dimensionless]
//! @param enthalpies_ array of enthalpies at corresponding coverages in enthalpy-coverages
//! [J/kmol]
//! @param entropy_coverages_ array of coverages for coverage-dependent entropy interpolation
//! [dimensionless]
//! @param entropies_ array of entropies at corresponding coverages in entropy-coverages
//! [J/kmol/K]
InterpolativeDependency(std::string name_k_, std::string name_j_,
vector_fp enthalpy_coverages_, vector_fp enthalpies_,
vector_fp entropy_coverages_, vector_fp entropies_):
name_k(name_k_), name_j(name_j_),
enthalpy_coverages(enthalpy_coverages_),
enthalpies(enthalpies_),
entropy_coverages(entropy_coverages_),
entropies(entropies_) {}
//! @param k_ index of a species whose thermodynamics are calculated
//! @param j_ index of a species whose coverage affects thermodynamics of the target species
//! @param enthalpy_map_ map of <coverage, enthalpy> as a key-value pair where coverage
//! is [dimensionless] and enthalpy has [J/kmol] unit
//! @param entropy_map_ map of <coverage, entropy> as a key-value pair where coverage
//! is [dimensionless] and entropy has [J/kmol/K] unit
InterpolativeDependency(size_t k_, size_t j_,
std::map<double, double> enthalpy_map_,
std::map<double, double> entropy_map_):
k(k_), j(j_),
enthalpy_map(enthalpy_map_),
entropy_map(entropy_map_){}
InterpolativeDependency() {}
//! name of a species whose thermodynamics are calculated
std::string name_k;
//! name of a species whose coverage affects thermodynamics of the target species
std::string name_j;
//! array of coverages for coverage-dependent enthalpy interpolation [dimensionless]
vector_fp enthalpy_coverages;
//! array of enthalpies at corresponding coverages in enthalpy-coverages [J/kmol]
vector_fp enthalpies;
//! array of coverages for coverage-dependent entropy interpolation [dimensionless]
vector_fp entropy_coverages;
//! array of entropies at corresponding coverages in entropy-coverages [J/kmol/K]
vector_fp entropies;
//! index of a species whose thermodynamics are calculated
size_t k;
//! index of a species whose coverage affects thermodynamics of the target species
size_t j;
//! map of coverage-enthalpy pairs for coverage-dependent enthalpy interpolation
std::map<double, double> enthalpy_map;
//! map of coverage-entropy pairs for coverage-dependent entropy interpolation
std::map<double, double> entropy_map;
};

//! Set of parameters modifying SurfPhase heat capacity based on fractional surface coverages
//! using a quadratic model.
struct HeatCapacityDependency
{
//! Constructor
//! @param name_k_ name of a species whose thermodynamics are calculated
//! @param name_j_ name of a species whose coverage affects thermodynamics of the target species
//! @param k_ index of a species whose thermodynamics are calculated
//! @param j_ index of a species whose coverage affects thermodynamics of the target species
//! @param cpcov_a_ log model coefficient a [J/kmol/K]
//! @param cpcov_b_ log model coefficient b [J/kmol/K]
HeatCapacityDependency(std::string name_k_, std::string name_j_,
HeatCapacityDependency(size_t k_, size_t j_,
double cpcov_a_, double cpcov_b_):
name_k(name_k_), name_j(name_j_),
k(k_), j(j_),
cpcov_a(cpcov_a_), cpcov_b(cpcov_b_) {}
HeatCapacityDependency() {}
//! name of a species whose thermodynamics are calculated
std::string name_k;
//! name of a species whose coverage affects thermodynamics of the target species
std::string name_j;
//! index of a species whose thermodynamics are calculated
size_t k;
//! index of a species whose coverage affects thermodynamics of the target species
size_t j;
double cpcov_a; //! log model coefficient a [J/kmol/K]
double cpcov_b; //! log model coefficient b [J/kmol/K]
};

class CoverageDependentSurfPhase : public SurfPhase
{
public:
//! Constructor.
//! @param n0 Site Density of the Surface Phase [kmol m^-2]
CoverageDependentSurfPhase(double n0 = 1.0);
//! Default constructor
CoverageDependentSurfPhase();

//! Construct and initialize a CoverageDependentSurfPhase ThermoPhase object directly
//! from an input file
//! @param infile name of the input file
//! @param id name of the phase id in the file. If this is blank, the first phase
//! in the file is used
explicit CoverageDependentSurfPhase(const std::string& infile, const std::string& id);
explicit CoverageDependentSurfPhase(const std::string& infile,
const std::string& id="");

//! Set the polynomial coverage dependece for species
/*!
Expand Down Expand Up @@ -245,25 +234,6 @@ class CoverageDependentSurfPhase : public SurfPhase
virtual void initThermo();
virtual bool addSpecies(shared_ptr<Species> spec);

//! @copydoc SurfPhase::setCoverages
//! After setting coverages, covstateNum is incremented by 1.
virtual void setCoverages(const double* theta);

//! @copydoc SurfPhase::setCoveragesNoNorm
//! After setting coverages, covstateNum is incremented by 1.
virtual void setCoveragesNoNorm(const double* theta);

//! Return the covstateNum
int statecovNumber() const {
return m_covstateNum;
}

//! Convert given eneregy to the quantity with its default unit of J/kmol.
double convertEnergy(double value, const std::string& src) const;

//! Convert given energy per temperature to the quantity with its default unit of J/kmol/K.
double convertEnergy_T(double value, const std::string& src) const;

// Functions calculating reference state thermodyanmic properties--------------

//! Return the nondimensionalized reference state enthalpy.
Expand Down Expand Up @@ -428,17 +398,8 @@ class CoverageDependentSurfPhase : public SurfPhase
virtual double cp_mole() const;

protected:
//! Temporary storage for the reference state enthalpies.
mutable vector_fp m_h_ref;

//! Temporary storage for the reference state entropies.
mutable vector_fp m_s_ref;

//! Temporary storage for the reference state heat capacities.
mutable vector_fp m_cp_ref;

//! Temporary storage for the reference state chemical potentials.
mutable vector_fp m_mu_ref;
//! Temporary storage for the coverages.
mutable vector_fp m_cov;

//! Temporary storage for the coverage-dependent enthalpies.
mutable vector_fp m_h_cov;
Expand Down Expand Up @@ -468,96 +429,29 @@ class CoverageDependentSurfPhase : public SurfPhase
//! and coverage-dependent chemical potentials.
mutable vector_fp m_chempot;

/*! Indicate the surface coverages have changed by incrementing the
* coverage state number by one. This function is called whenever
* the setCoverages() or setCoveragesNoNorm() was used to update the
* coverage array.
*/
void coverageChanged();

//! Array of enthalpy and entropy coverage dependency parameters used in
//! the linear and polynomial models.
mutable std::vector<PolynomialDependency> m_PolynomialDependency;
std::vector<PolynomialDependency> m_PolynomialDependency;

//! Array of enthalpy and entropy coverage dependency parameters used in
//! the piecewise linear model.
mutable std::vector<PiecewiseDependency> m_PiecewiseDependency;
std::vector<PiecewiseDependency> m_PiecewiseDependency;

//! Array of enthalpy and entropy coverage dependency parameters used in
//! the interpolative model.
mutable std::vector<InterpolativeDependency> m_InterpolativeDependency;
std::vector<InterpolativeDependency> m_InterpolativeDependency;

//! Array of heat capacity coverage dependency parameters.
mutable std::vector<HeatCapacityDependency> m_HeatCapacityDependency;

//! Storage for the linear and polynomial model coverage dependency
//! parameters for enthalpy.
mutable vector_fp m_polynomial_h;

//! Storage for the linear and polynomial model coverage dependency
//! parameters for entropy.
mutable vector_fp m_polynomial_s;

//! Storage for the piecewise linear model coverage dependency parameters
//! for enthalpy.
mutable vector_fp m_piecewise_h;

//! Storage for the piecewise linear model coverage dependency parameters
//! for entropy.
mutable vector_fp m_piecewise_s;

//! Storage for the interpolative model coverage array for enthalpy.
mutable vector_fp m_interpolative_hcov;

//! Storage for the interpolative model enthalpy array.
mutable vector_fp m_interpolative_h;

//! Storage for the interpolative model coverage array for entropy.
mutable vector_fp m_interpolative_scov;

//! Storage for the interpolative model entropy array.
mutable vector_fp m_interpolative_s;

//! Storage for the coverage-dependent heat capacity log model coefficients.
mutable double m_cpcov_a, m_cpcov_b;
std::vector<HeatCapacityDependency> m_HeatCapacityDependency;

private:
//! Coverage state change variable. Whenever the coverage array changes,
//! this number is incremented.
int m_covstateNum;

//! Last value of the coverage state number processed.
mutable int m_covstateNumlast;

//! Flag indicating polynomial coverage-dependent model is being used.
mutable bool m_has_polynomial_dependency;

//! Flag indicating piecewise linear coverage-dependent model is being used.
mutable bool m_has_piecewise_dependency;

//! Flag indicating interpolative coverage-dependent model is being used.
mutable bool m_has_interpolative_dependency;

//! Flag indicating coverage-dependent heat capacity is being calculated.
mutable bool m_has_heatcapacity_dependency;

//! Flag indicating user has defined the reference coverage.
mutable bool m_has_ref_coverage;
//! Last value of the state number processed.
mutable int m_stateNumlast;

//! Storage for the user-defined reference state coverage which has to be
//! greater than 0.0 and less than or equal to 1.0.
//! greater than 0.0 and less than or equal to 1.0. default = 1.0.
mutable double m_theta_ref;

//! Update the species ideal reference state thermodynamic functions
/*!
* The polynomials for the ideal surface reference functions are only
* reevaluated if the temperature has changed.
*
* @param force Boolean, which if true, forces a reevaluation of the thermo
* polynomials. default = false.
*/
void _updateReferenceThermo(bool force=false) const;

//! Update the species coverage-dependent thermodynamic functions
/*!
* The coverage-dependent enthalpy and entropy are only reevaluated
Expand All @@ -578,7 +472,7 @@ class CoverageDependentSurfPhase : public SurfPhase
* reference state as well as coverage-dependent functions.
* default = false.
*/
void _updateThermo(bool force=false) const;
void _updateTotalThermo(bool force=false) const;

};

Expand Down
5 changes: 2 additions & 3 deletions include/cantera/thermo/SurfPhase.h
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Original file line number Diff line number Diff line change
Expand Up @@ -358,7 +358,7 @@ class SurfPhase : public ThermoPhase
*
* This routine normalizes the theta's to 1, before application
*/
virtual void setCoverages(const doublereal* theta);
void setCoverages(const doublereal* theta);

//! Set the surface site fractions to a specified state.
/*!
Expand All @@ -370,7 +370,7 @@ class SurfPhase : public ThermoPhase
* @param theta This is the surface site fraction for the kth species in
* the surface phase. This is a dimensionless quantity.
*/
virtual void setCoveragesNoNorm(const doublereal* theta);
void setCoveragesNoNorm(const doublereal* theta);

//! Set the coverages from a string of colon-separated name:value pairs.
/*!
Expand Down Expand Up @@ -431,7 +431,6 @@ class SurfPhase : public ThermoPhase
*/
mutable vector_fp m_logsize;

private:
//! Update the species reference state thermodynamic functions
/*!
* The polynomials for the standard state functions are only reevaluated if
Expand Down
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