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[docs] Add spaces between Doxygen and LaTeX commands
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ischoegl committed Jul 28, 2023
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6 changes: 3 additions & 3 deletions doc/doxygen/thermoprops.dox
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Expand Up @@ -48,7 +48,7 @@
*
* The first type are those whose underlying species have a reference state associated
* with them. The reference state describes the thermodynamic functions for a
* species at a single reference pressure, @f$p_0@f$. The thermodynamic functions
* species at a single reference pressure, @f$ p_0 @f$. The thermodynamic functions
* are specified via derived objects of the SpeciesThermoInterpType object class, and usually
* consist of polynomials in temperature such as the NASA polynomial or the SHOMATE
* polynomial. Calculators for these
Expand Down Expand Up @@ -346,14 +346,14 @@
* </H3>
*
*
* The activity @f$a_k@f$ and activity coefficient @f$ \gamma_k @f$ of a
* The activity @f$ a_k @f$ and activity coefficient @f$ \gamma_k @f$ of a
* species in solution is related to the chemical potential by
*
* @f[
* \mu_k = \mu_k^0(T,P) + \hat R T \log a_k.= \mu_k^0(T,P) + \hat R T \log x_k \gamma_k
* @f]
*
* The quantity @f$\mu_k^0(T,P)@f$ is
* The quantity @f$ \mu_k^0(T,P) @f$ is
* the standard chemical potential at unit activity,
* which depends on the temperature and pressure,
* but not on the composition. The
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2 changes: 1 addition & 1 deletion include/cantera/equil/MultiPhase.h
Original file line number Diff line number Diff line change
Expand Up @@ -550,7 +550,7 @@ class MultiPhase
//! MultiPhaseEquil solver.
/*!
* @param XY Integer flag specifying properties to hold fixed.
* @param err Error tolerance for @f$\Delta \mu/RT @f$ for all reactions.
* @param err Error tolerance for @f$ \Delta \mu/RT @f$ for all reactions.
* Also used as the relative error tolerance for the outer loop.
* @param maxsteps Maximum number of steps to take in solving the fixed TP
* problem.
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2 changes: 1 addition & 1 deletion include/cantera/kinetics/ChebyshevRate.h
Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,7 @@ struct ChebyshevData : public ReactionData
* \log k(T,P) = \sum_{t=1}^{N_T} \sum_{p=1}^{N_P} \alpha_{tp}
* \phi_t(\tilde{T}) \phi_p(\tilde{P})
* @f]
* where @f$\alpha_{tp}@f$ are the constants defining the rate, @f$\phi_n(x)@f$
* where @f$ \alpha_{tp} @f$ are the constants defining the rate, @f$ \phi_n(x) @f$
* is the Chebyshev polynomial of the first kind of degree *n* evaluated at
* *x*, and
* @f[
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36 changes: 18 additions & 18 deletions include/cantera/kinetics/Kinetics.h
Original file line number Diff line number Diff line change
Expand Up @@ -733,8 +733,8 @@ class Kinetics
* mole fractions at constant temperature, pressure and molar concentration.
*
* The method returns a matrix with nReactions rows and nTotalSpecies columns.
* For a derivative with respect to @f$X_i@f$, all other @f$X_j@f$ are held
* constant, rather than enforcing @f$\sum X_j = 1@f$.
* For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
* constant, rather than enforcing @f$ \sum X_j = 1 @f$.
*
* @warning This method is an experimental part of the %Cantera API and
* may be changed or removed without notice.
Expand All @@ -751,7 +751,7 @@ class Kinetics
* concentrations.
*
* The method returns a matrix with nReactions rows and nTotalSpecies columns.
* For a derivative with respect to @f$c_i@f$, all other @f$c_j@f$ are held
* For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
* constant.
*
* @warning This method is an experimental part of the %Cantera API and
Expand Down Expand Up @@ -806,8 +806,8 @@ class Kinetics
* mole fractions at constant temperature, pressure and molar concentration.
*
* The method returns a matrix with nReactions rows and nTotalSpecies columns.
* For a derivative with respect to @f$X_i@f$, all other @f$X_j@f$ are held
* constant, rather than enforcing @f$\sum X_j = 1@f$.
* For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
* constant, rather than enforcing @f$ \sum X_j = 1 @f$.
*
* @warning This method is an experimental part of the %Cantera API and
* may be changed or removed without notice.
Expand All @@ -824,7 +824,7 @@ class Kinetics
* concentrations.
*
* The method returns a matrix with nReactions rows and nTotalSpecies columns.
* For a derivative with respect to @f$c_i@f$, all other @f$c_j@f$ are held
* For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
* constant.
*
* @warning This method is an experimental part of the %Cantera API and
Expand Down Expand Up @@ -879,8 +879,8 @@ class Kinetics
* mole fractions at constant temperature, pressure and molar concentration.
*
* The method returns a matrix with nReactions rows and nTotalSpecies columns.
* For a derivative with respect to @f$X_i@f$, all other @f$X_j@f$ are held
* constant, rather than enforcing @f$\sum X_j = 1@f$.
* For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
* constant, rather than enforcing @f$ \sum X_j = 1 @f$.
*
* @warning This method is an experimental part of the %Cantera API and
* may be changed or removed without notice.
Expand All @@ -897,7 +897,7 @@ class Kinetics
* concentrations.
*
* The method returns a matrix with nReactions rows and nTotalSpecies columns.
* For a derivative with respect to @f$c_i@f$, all other @f$c_j@f$ are held
* For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
* constant.
*
* @warning This method is an experimental part of the %Cantera API and
Expand Down Expand Up @@ -940,8 +940,8 @@ class Kinetics
* mole fractions at constant temperature, pressure and molar concentration.
*
* The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
* For a derivative with respect to @f$X_i@f$, all other @f$X_j@f$ are held
* constant, rather than enforcing @f$\sum X_j = 1@f$.
* For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
* constant, rather than enforcing @f$ \sum X_j = 1 @f$.
*
* @warning This method is an experimental part of the %Cantera API and
* may be changed or removed without notice.
Expand All @@ -954,7 +954,7 @@ class Kinetics
* species.
*
* The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
* For a derivative with respect to @f$c_i@f$, all other @f$c_j@f$ are held
* For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
* constant.
*
* @warning This method is an experimental part of the %Cantera API and
Expand Down Expand Up @@ -993,8 +993,8 @@ class Kinetics
* mole fractions at constant temperature, pressure and molar concentration.
*
* The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
* For a derivative with respect to @f$X_i@f$, all other @f$X_j@f$ are held
* constant, rather than enforcing @f$\sum X_j = 1@f$.
* For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held
* constant, rather than enforcing @f$ \sum X_j = 1 @f$.
*
* @warning This method is an experimental part of the %Cantera API and
* may be changed or removed without notice.
Expand All @@ -1007,7 +1007,7 @@ class Kinetics
* species.
*
* The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
* For a derivative with respect to @f$c_i@f$, all other @f$c_j@f$ are held
* For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
* constant.
*
* @warning This method is an experimental part of the %Cantera API and
Expand Down Expand Up @@ -1046,8 +1046,8 @@ class Kinetics
* mole fractions at constant temperature, pressure and molar concentration.
*
* The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
* For a derivative with respect to @f$X_i@f$, all other @f$X_j@f$ are held constant,
* rather than enforcing @f$\sum X_j = 1@f$.
* For a derivative with respect to @f$ X_i @f$, all other @f$ X_j @f$ are held constant,
* rather than enforcing @f$ \sum X_j = 1 @f$.
*
* @warning This method is an experimental part of the %Cantera API and
* may be changed or removed without notice.
Expand All @@ -1060,7 +1060,7 @@ class Kinetics
* species.
*
* The method returns a matrix with nTotalSpecies rows and nTotalSpecies columns.
* For a derivative with respect to @f$c_i@f$, all other @f$c_j@f$ are held
* For a derivative with respect to @f$ c_i @f$, all other @f$ c_j @f$ are held
* constant.
*
* @warning This method is an experimental part of the %Cantera API and
Expand Down
6 changes: 3 additions & 3 deletions include/cantera/kinetics/StoichManager.h
Original file line number Diff line number Diff line change
Expand Up @@ -564,16 +564,16 @@ inline static void _scale(InputIter begin, InputIter end,
* @f[
* r_i = \sum_m^{M_i} s_{k_{m,i}}
* @f]
* To understand the operations performed by this class, let @f$ N_{k,i}@f$
* To understand the operations performed by this class, let @f$ N_{k,i} @f$
* denote the stoichiometric coefficient of species k on one side (reactant or
* product) in reaction i. Then \b N is a sparse K by I matrix of stoichiometric
* coefficients.
*
* The following matrix operations may be carried out with a vector S of length
* K, and a vector R of length I:
*
* - @f$ S = S + N R@f$ (incrementSpecies)
* - @f$ S = S - N R@f$ (decrementSpecies)
* - @f$ S = S + N R @f$ (incrementSpecies)
* - @f$ S = S - N R @f$ (decrementSpecies)
* - @f$ R = R + N^T S @f$ (incrementReaction)
* - @f$ R = R - N^T S @f$ (decrementReaction)
*
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4 changes: 2 additions & 2 deletions include/cantera/numerics/Func1.h
Original file line number Diff line number Diff line change
Expand Up @@ -498,7 +498,7 @@ class Tabulated1 : public Func1
Tabulated1(size_t n, const double* tvals, const double* fvals,
const string& method="linear");

//! Constructor uses @f$ 2 n@f$ parameters in the following order:
//! Constructor uses @f$ 2 n @f$ parameters in the following order:
//! @f$ [t_0, t_1, \dots, t_{n-1}, f_0, f_1, \dots, f_{n-1}] @f$
Tabulated1(const vector<double>& params);

Expand Down Expand Up @@ -1302,7 +1302,7 @@ class Arrhenius1 : public Func1
}
}

//! Constructor uses @f$ 3 n@f$ parameters in the following order:
//! Constructor uses @f$ 3 n @f$ parameters in the following order:
//! @f$ [A_1, b_1, E_1, A_2, b_2, E_2, \dots, A_n, b_n, E_n] @f$
Arrhenius1(const vector<double>& params);

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2 changes: 1 addition & 1 deletion include/cantera/numerics/FuncEval.h
Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ namespace Cantera
/**
* Virtual base class for ODE/DAE right-hand-side function evaluators.
* Classes derived from FuncEval evaluate the right-hand-side function
* @f$ \vec{F}(t,\vec{y})@f$ in
* @f$ \vec{F}(t,\vec{y}) @f$ in
* @f[
* \dot{\vec{y}} = \vec{F}(t,\vec{y}).
* @f]
Expand Down
2 changes: 1 addition & 1 deletion include/cantera/numerics/IdasIntegrator.h
Original file line number Diff line number Diff line change
Expand Up @@ -103,7 +103,7 @@ class IdasIntegrator : public Integrator
void* m_linsol_matrix = nullptr; //!< matrix used by Sundials
SundialsContext m_sundials_ctx; //!< SUNContext object for Sundials>=6.0

//! Object implementing the DAE residual function @f$ f(t, y, \dot{y}) = 0@f$
//! Object implementing the DAE residual function @f$ f(t, y, \dot{y}) = 0 @f$
FuncEval* m_func = nullptr;

double m_t0 = 0.0; //!< The start time for the integrator
Expand Down
2 changes: 1 addition & 1 deletion include/cantera/numerics/polyfit.h
Original file line number Diff line number Diff line change
Expand Up @@ -17,7 +17,7 @@ namespace Cantera
* evaluated at those points, this function computes the weighted least-squares
* polynomial fit of degree *deg*:
*
* @f[ f(x) = p[0] + p[1]*x + p[2]*x^2 + \cdots + p[deg]*x^deg @f]
* @f[ f(x) = p[0] + p[1] x + p[2] x^2 + \cdots + p[deg] x^deg @f]
*
* @param n The number of points at which the function is evaluated
* @param deg The degree of the polynomial fit to be computed. deg <= n - 1.
Expand Down
34 changes: 17 additions & 17 deletions include/cantera/thermo/BinarySolutionTabulatedThermo.h
Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ namespace Cantera
* \Delta g_{\rm rxn} = -\frac{E_eq}{nF}
* @f]
*
* where @f$ n@f$ is the charge number transferred to the phase, via the
* where @f$ n @f$ is the charge number transferred to the phase, via the
* reaction, and @f$ F @f$ is Faraday's constant. The gibbs energy of
* reaction, in turn, can be separated into enthalpy and entropy of reaction
* components:
Expand All @@ -65,37 +65,37 @@ namespace Cantera
* @f]
*
* Where the 'reference' species is automatically assigned standard state
* thermo variables @f$ h^{\rm o} = 0@f$ and @f$ s^{\rm o} = 0@f$, and standard
* thermo variables @f$ h^{\rm o} = 0 @f$ and @f$ s^{\rm o} = 0 @f$, and standard
* state thermo variables for species in any other phases are calculated
* according to the rules specified in that phase definition.
*
* The present model is intended for modeling non-ideal, tabulated
* thermodynamics for binary solutions where the tabulated species is
* incorporated via an electrochemical reaction, such that the open circuit
* voltage can be measured, relative to a counter electrode species with
* standard state thermo properties @f$ h^{\rm o} = 0@f$.
* standard state thermo properties @f$ h^{\rm o} = 0 @f$.
* It is possible that this can be generalized such that this assumption about
* the counter-electrode is not required. At present, this is left as future
* work.
*
* The user therefore provides a table of three equally-sized vectors of
* tabulated data:
*
* - @f$ x_{\rm tab}@f$ = array of mole fractions for the tabulated species
* - @f$ x_{\rm tab} @f$ = array of mole fractions for the tabulated species
* at which measurements were conducted and thermo
* data are provided.
* - @f$ h_{\rm tab}@f$ = @f$ F\left(-E_{\rm eq}\left(x,T^{\rm o} \right) + T^{\rm o} \frac{dE_{\rm eq}\left(x,T^{\rm o} \right)}{dT}\right) @f$
* - @f$ s_{\rm tab}@f$ = @f$ F \left(\frac{dE_{\rm eq}\left(x,T^{\rm o} \right)}{dT} + s_{\rm counter}^{\rm o} \right) @f$
* - @f$ h_{\rm tab} @f$ = @f$ F\left(-E_{\rm eq}\left(x,T^{\rm o} \right) + T^{\rm o} \frac{dE_{\rm eq}\left(x,T^{\rm o} \right)}{dT}\right) @f$
* - @f$ s_{\rm tab} @f$ = @f$ F \left(\frac{dE_{\rm eq}\left(x,T^{\rm o} \right)}{dT} + s_{\rm counter}^{\rm o} \right) @f$
*
* where @f$ E_{\rm eq}\left(x,T^{\rm o} \right) @f$ and @f$ \frac{dE_{\rm eq}\left(x,T^{\rm o} \right)}{dT} @f$
* are the experimentally-measured open circuit voltage and derivative in
* open circuit voltage with respect to temperature, respectively, both
* measured as a mole fraction of @f$ x @f$ for the tabulated species and at a
* temperature of @f$ T^{\rm o} @f$. The arrays @f$ h_{\rm tab}@f$ and
* @f$ s_{\rm tab}@f$ must be the same length as the @f$ x_{\rm tab}@f$ array.
* temperature of @f$ T^{\rm o} @f$. The arrays @f$ h_{\rm tab} @f$ and
* @f$ s_{\rm tab} @f$ must be the same length as the @f$ x_{\rm tab} @f$ array.
*
* From these tabulated inputs, the standard state thermodynamic properties
* for the tabulated species (subscript @f$ k@f$, tab) are calculated as:
* for the tabulated species (subscript @f$ k @f$, tab) are calculated as:
*
* @f[
* h^{\rm o}_{k,\,{\rm tab}} = h_{\rm tab}
Expand All @@ -109,7 +109,7 @@ namespace Cantera
* thermodynamic data for the tabulated species.
*
* Furthermore, there is an optional feature to include non-ideal effects regarding
* partial molar volumes of the species, @f$ \bar V_k@f$. Being derived from
* partial molar volumes of the species, @f$ \bar V_k @f$. Being derived from
* IdealSolidSolnPhase, the default assumption in BinarySolutionTabulatedThermo
* is that the species comprising the binary solution have constant partial molar
* volumes equal to their pure species molar volumes. However, this assumption only
Expand All @@ -121,11 +121,11 @@ namespace Cantera
* (XRD) measurements of the unit cell volume. Therefore, the user can provide an optional fourth vector of
* tabulated molar volume data with the same size as the other tabulated data:
*
* - @f$ V_{\mathrm{m,tab}}@f$ = array of the molar volume of the binary solution phase at
* - @f$ V_{\mathrm{m,tab}} @f$ = array of the molar volume of the binary solution phase at
* the tabulated mole fractions.
*
* The partial molar volumes @f$ \bar V_1@f$ of the tabulated species and
* @f$ \bar V_2@f$ of the 'reference' species, respectively, can then be derived from
* The partial molar volumes @f$ \bar V_1 @f$ of the tabulated species and
* @f$ \bar V_2 @f$ of the 'reference' species, respectively, can then be derived from
* the provided molar volume:
*
* @f[
Expand All @@ -148,8 +148,8 @@ namespace Cantera
* \rho = \frac{\sum_k{x_k W_k}}{V_\mathrm{m}}
* @f]
*
* where @f$x_k@f$ are the mole fractions, @f$W_k@f$ are the molecular weights, and
* @f$V_\mathrm{m}@f$ is the molar volume interpolated from @f$V_{\mathrm{m,tab}}@f$.
* where @f$ x_k @f$ are the mole fractions, @f$ W_k @f$ are the molecular weights, and
* @f$ V_\mathrm{m} @f$ is the molar volume interpolated from @f$ V_{\mathrm{m,tab}} @f$.
*
* If the optional fourth input vector is not specified, the molar volume is calculated
* by using the pure species molar volumes, as in IdealSolidSolnPhase. Regardless if the
Expand Down Expand Up @@ -203,8 +203,8 @@ class BinarySolutionTabulatedThermo : public IdealSolidSolnPhase
* \rho = \frac{\sum_k{X_k W_k}}{V_\mathrm{m}}
* @f]
*
* where @f$X_k@f$ are the mole fractions, @f$W_k@f$ are the molecular weights, and
* @f$V_\mathrm{m}@f$ is the molar volume interpolated from @f$V_{\mathrm{m,tab}}@f$.
* where @f$ X_k @f$ are the mole fractions, @f$ W_k @f$ are the molecular weights, and
* @f$ V_\mathrm{m} @f$ is the molar volume interpolated from @f$ V_{\mathrm{m,tab}} @f$.
*/
virtual void calcDensity();

Expand Down
4 changes: 2 additions & 2 deletions include/cantera/thermo/ConstCpPoly.h
Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,7 @@ namespace Cantera
* @f]
*
* This parameterization takes 4 input values. These are:
* - c[0] = @f$ T_0 @f$(Kelvin)
* - c[0] = @f$ T_0 @f$ (Kelvin)
* - c[1] = @f$ H_k^o(T_0, p_{ref}) @f$ (J/kmol)
* - c[2] = @f$ S_k^o(T_0, p_{ref}) @f$ (J/kmol K)
* - c[3] = @f$ {Cp}_k^o(T_0, p_{ref}) @f$ (J(kmol K)
Expand All @@ -54,7 +54,7 @@ class ConstCpPoly: public SpeciesThermoInterpType
* @param coeffs Vector of coefficients used to set the parameters for
* the standard state for species n. There are 4
* coefficients for the ConstCpPoly parameterization.
* - c[0] = @f$ T_0 @f$(Kelvin)
* - c[0] = @f$ T_0 @f$ (Kelvin)
* - c[1] = @f$ H_k^o(T_0, p_{ref}) @f$ (J/kmol)
* - c[2] = @f$ S_k^o(T_0, p_{ref}) @f$ (J/kmol K)
* - c[3] = @f$ {Cp}_k^o(T_0, p_{ref}) @f$ (J(kmol K)
Expand Down
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