[docs] Differentiate Doxygen from LaTeX commands

doc/doxygen/thermoprops.dox

@@ -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$. The thermodynamic functions
  *   are specified via derived objects of the SpeciesThermoInterpType object class, and usually
  *   consist of polynomials in temperature such as the NASA polynomial or the SHOMATE
  *   polynomial.  Calculators for these
@@ -68,7 +68,7 @@
  *   have any nontrivial examples of these types of phases.
  *   In general, the independent variables that completely describe the state of the
  *   system  for this class are temperature, the
- *   phase density, and \f$ N - 1 \f$ species mole or mass fractions.
+ *   phase density, and @f$ N - 1 @f$ species mole or mass fractions.
  *   Additionally, if the
  *   phase involves charged species, the phase electric potential is an added independent variable.
  *   Examples of the first class of %ThermoPhase functions, which includes the
@@ -291,18 +291,18 @@
  * Treatment of the %Phase Potential and the electrochemical potential of a species
  * </H3>
  *
- *  The electrochemical potential of species k in a phase p, \f$ \zeta_k \f$,
+ *  The electrochemical potential of species k in a phase p, @f$ \zeta_k @f$,
  *  is related to the chemical potential via
  *  the following equation,
  *
- *  \f[
+ *  @f[
  *      \zeta_{k}(T,P) = \mu_{k}(T,P) + z_k \phi_p
- *  \f]
+ *  @f]
  *
- *  where \f$ \nu_k \f$ is the charge of species k, and \f$ \phi_p \f$ is
+ *  where @f$ \nu_k @f$ is the charge of species k, and @f$ \phi_p @f$ is
  *  the electric potential of phase p.
  *
- *  The potential  \f$ \phi_p \f$ is tracked and internally stored within
+ *  The potential  @f$ \phi_p @f$ is tracked and internally stored within
  *  the base %ThermoPhase object. It constitutes a specification of the
  *  internal state of the phase; it's the third state variable, the first
  *  two being temperature and density (or, pressure, for incompressible
@@ -314,9 +314,9 @@
  *  changed by the potential because many phases enforce charge
  *  neutrality:
  *
- *  \f[
+ *  @f[
  *      0 = \sum_k z_k X_k
- *  \f]
+ *  @f]
  *
  *  Whether charge neutrality is necessary for a phase is also specified
  *  within the ThermoPhase object, by the function call
@@ -326,7 +326,7 @@
  *  Cantera::HMWSoln for the proper specification of the chemical potentials.
  *
  *
- *  This equation, when applied to the \f$ \zeta_k \f$ equation described
+ *  This equation, when applied to the @f$ \zeta_k @f$ equation described
  *  above, results in a zero net change in the effective Gibbs free
  *  energy of the phase. However, specific charged species in the phase
  *  may increase or decrease their electrochemical potentials, which will
@@ -346,36 +346,36 @@
  *  </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[
+ * @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]
+ * @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
  * activity is dimensionless. Within liquid electrolytes it's common to use a
  * molality convention, where solute species employ the molality-based
  * activity coefficients:
  *
- * \f[
+ * @f[
  *  \mu_k =  \mu_k^\triangle(T,P) + R T ln(a_k^{\triangle}) =
  *            \mu_k^\triangle(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
- * \f]
+ * @f]
  *
  * And, the solvent employs the following convention
- * \f[
+ * @f[
  *    \mu_o = \mu^o_o(T,P) + RT ln(a_o)
- * \f]
+ * @f]
  *
- * where \f$ a_o \f$ is often redefined in terms of the osmotic coefficient \f$ \phi \f$.
+ * where @f$ a_o @f$ is often redefined in terms of the osmotic coefficient @f$ \phi @f$.
  *
- *   \f[
+ *   @f[
  *       \phi = \frac{- ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
- *   \f]
+ *   @f]
  *
  *  %ThermoPhase classes which employ the molality based convention are all derived
  *  from the MolalityVPSSTP class. See the class description for further information
@@ -418,37 +418,37 @@
  *   however, kinetics is usually expressed in terms of unitless activities,
  *   which most often equate to solid phase mole fractions. In order to
  *   accommodate variability here, %Cantera has come up with the idea
- *   of activity concentrations, \f$ C^a_k \f$. Activity concentrations are the expressions
+ *   of activity concentrations, @f$ C^a_k @f$. Activity concentrations are the expressions
  *   used directly in kinetics expressions.
  *   These activity (or generalized) concentrations are used
  *   by kinetics manager classes to compute the forward and
  *   reverse rates of elementary reactions. Note that they may
  *   or may not have units of concentration --- they might be
  *   partial pressures, mole fractions, or surface coverages,
- *   The activity concentrations for species <I>k</I>, \f$ C^a_k \f$, are
- *   related to the activity for species, k, \f$ a_k \f$,
+ *   The activity concentrations for species <I>k</I>, @f$ C^a_k @f$, are
+ *   related to the activity for species, k, @f$ a_k @f$,
  *   via the following expression:
  *
- *   \f[
+ *   @f[
  *       a_k = C^a_k / C^0_k
- *   \f]
+ *   @f]
  *
- *  \f$ C^0_k \f$ are called standard concentrations. They serve as multiplicative factors
+ *  @f$ C^0_k @f$ are called standard concentrations. They serve as multiplicative factors
  *  between the activities and the generalized concentrations. Standard concentrations
  *  may be different for each species. They may depend on both the temperature
  *  and the pressure. However, they may not depend
  *  on the composition of the phase. For example, for the IdealGasPhase object
  *  the standard concentration is defined as
  *
- *  \f[
+ *  @f[
  *     C^0_k = P/ R T
- *  \f]
+ *  @f]
  *
  *  In many solid phase kinetics problems,
  *
- *   \f[
+ *   @f[
  *     C^0_k = 1.0 ,
- *  \f]
+ *   @f]
  *
  *  is employed making the units for activity concentrations in solids unitless.
  *

include/cantera/base/ct_defs.h

@@ -77,19 +77,19 @@ const double Sqrt2 = 1.41421356237309504880;
 //! [NIST Reference on Constants, Units, and Uncertainty](https://physics.nist.gov/cuu/Constants/index.html).
 //! @{
 
-//! Avogadro's Number \f$ N_{\mathrm{A}} \f$ [number/kmol]
+//! Avogadro's Number @f$ N_{\mathrm{A}} @f$ [number/kmol]
 const double Avogadro = 6.02214076e26;
 
-//! Boltzmann constant \f$ k \f$ [J/K]
+//! Boltzmann constant @f$ k @f$ [J/K]
 const double Boltzmann = 1.380649e-23;
 
-//! Planck constant \f$ h \f$ [J-s]
+//! Planck constant @f$ h @f$ [J-s]
 const double Planck = 6.62607015e-34;
 
-//! Elementary charge \f$ e \f$ [C]
+//! Elementary charge @f$ e @f$ [C]
 const double ElectronCharge = 1.602176634e-19;
 
-//! Speed of Light in a vacuum \f$ c \f$ [m/s]
+//! Speed of Light in a vacuum @f$ c @f$ [m/s]
 const double lightSpeed = 299792458.0;
 
 //! One atmosphere [Pa]
@@ -104,10 +104,10 @@ const double OneBar = 1.0E5;
 //! These constants are measured and reported by CODATA
 //! @{
 
-//! Fine structure constant \f$ \alpha \f$ []
+//! Fine structure constant @f$ \alpha @f$ []
 const double fineStructureConstant = 7.2973525693e-3;
 
-//! Electron Mass \f$ m_e \f$ [kg]
+//! Electron Mass @f$ m_e @f$ [kg]
 const double ElectronMass = 9.1093837015e-31;
 
 //! @}
@@ -116,24 +116,24 @@ const double ElectronMass = 9.1093837015e-31;
 //! These constants are found from the defined and measured constants
 //! @{
 
-//! Universal Gas Constant \f$ R_u \f$ [J/kmol/K]
+//! Universal Gas Constant @f$ R_u @f$ [J/kmol/K]
 const double GasConstant = Avogadro * Boltzmann;
 
 const double logGasConstant = std::log(GasConstant);
 
 //! Universal gas constant in cal/mol/K
 const double GasConst_cal_mol_K = GasConstant / 4184.0;
 
-//! Stefan-Boltzmann constant \f$ \sigma \f$ [W/m2/K4]
+//! Stefan-Boltzmann constant @f$ \sigma @f$ [W/m2/K4]
 const double StefanBoltz = 2.0 * std::pow(Pi, 5) * std::pow(Boltzmann, 4) / (15.0 * std::pow(Planck, 3) * lightSpeed * lightSpeed); // 5.670374419e-8
 
-//! Faraday constant \f$ F \f$ [C/kmol]
+//! Faraday constant @f$ F @f$ [C/kmol]
 const double Faraday = ElectronCharge * Avogadro;
 
-//! Permeability of free space \f$ \mu_0 \f$ [N/A2]
+//! Permeability of free space @f$ \mu_0 @f$ [N/A2]
 const double permeability_0 = 2 * fineStructureConstant * Planck / (ElectronCharge * ElectronCharge * lightSpeed);
 
-//! Permittivity of free space \f$ \varepsilon_0 \f$ [F/m]
+//! Permittivity of free space @f$ \varepsilon_0 @f$ [F/m]
 const double epsilon_0 = 1.0 / (lightSpeed * lightSpeed * permeability_0);
 
 //! @}

include/cantera/equil/ChemEquil.h

@@ -152,7 +152,7 @@ class ChemEquil
      *
      * @param s mixture to be updated
      * @param x vector of non-dimensional element potentials
-     * \f[ \lambda_m/RT \f].
+     * @f[ \lambda_m/RT @f].
      * @param t temperature in K.
      */
     void setToEquilState(ThermoPhase& s,

include/cantera/equil/MultiPhase.h

@@ -259,7 +259,7 @@ class MultiPhase
 
     //! Charge (Coulombs) of phase with index \a p.
     /*!
-     *  The net charge is computed as \f[ Q_p = N_p \sum_k F z_k X_k \f]
+     *  The net charge is computed as @f[ Q_p = N_p \sum_k F z_k X_k @f]
      *  where the sum runs only over species in phase \a p.
      *  @param p index of the phase for which the charge is desired.
      */
@@ -276,9 +276,9 @@ class MultiPhase
      * Write into array \a mu the chemical potentials of all species
      * [J/kmol]. The chemical potentials are related to the activities by
      *
-     * \f$
+     * @f$
      *          \mu_k = \mu_k^0(T, P) + RT \ln a_k.
-     * \f$.
+     * @f$.
      *
      * @param mu Chemical potential vector. Length = num global species. Units
      *           = J/kmol.
@@ -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.

include/cantera/equil/MultiPhaseEquil.h

@@ -109,7 +109,7 @@ class MultiPhaseEquil
     //! Estimate the initial mole numbers. This is done by running each
     //! reaction as far forward or backward as possible, subject to the
     //! constraint that all mole numbers remain non-negative. Reactions for
-    //! which \f$ \Delta \mu^0 \f$ are positive are run in reverse, and ones
+    //! which @f$ \Delta \mu^0 @f$ are positive are run in reverse, and ones
     //! for which it is negative are run in the forward direction. The end
     //! result is equivalent to solving the linear programming problem of
     //! minimizing the linear Gibbs function subject to the element and non-

include/cantera/equil/vcs_solve.h

@@ -707,7 +707,7 @@ class VCS_SOLVE
     /*!
      * This is done by running each reaction as far forward or backward as
      * possible, subject to the constraint that all mole numbers remain non-
-     * negative. Reactions for which \f$ \Delta \mu^0 \f$ are positive are run
+     * negative. Reactions for which @f$ \Delta \mu^0 @f$ are positive are run
      * in reverse, and ones for which it is negative are run in the forward
      * direction. The end result is equivalent to solving the linear
      * programming problem of minimizing the linear Gibbs function subject to

include/cantera/kinetics/Arrhenius.h

@@ -161,9 +161,9 @@ class ArrheniusBase : public ReactionRate
 /*!
  * A reaction rate coefficient of the following form.
  *
- *   \f[
+ *   @f[
  *        k_f =  A T^b \exp (-Ea/RT)
- *   \f]
+ *   @f]
  *
  * @ingroup arrheniusGroup
  */

include/cantera/kinetics/BlowersMaselRate.h

@@ -50,19 +50,19 @@ struct BlowersMaselData : public ReactionData
  *               \Delta H)^2}{(V_P^2 - 4w^2 + (\Delta H)^2)}\; \text{Otherwise}
  *   \f}
  * where
- *   \f[
+ *   @f[
  *        V_P = \frac{2w (w + E_0)}{w - E_0},
- *   \f]
- * \f$ w \f$ is the average bond dissociation energy of the bond breaking
+ *   @f]
+ * @f$ w @f$ is the average bond dissociation energy of the bond breaking
  * and that being formed in the reaction. Since the expression is
- * very insensitive to \f$ w \f$ for \f$ w >= 2 E_0 \f$, \f$ w \f$
+ * very insensitive to @f$ w @f$ for @f$ w >= 2 E_0 @f$, @f$ w @f$
  * can be approximated to an arbitrary high value like 1000 kJ/mol.
  *
  * After the activation energy is determined by Blowers-Masel approximation,
  * it can be plugged into Arrhenius function to calculate the rate constant.
- *   \f[
+ *   @f[
  *        k_f =  A T^b \exp (-E_a/RT)
- *   \f]
+ *   @f]
  *
  * @ingroup arrheniusGroup
  */

include/cantera/kinetics/ChebyshevRate.h

@@ -61,27 +61,27 @@ struct ChebyshevData : public ReactionData
 //! as a bivariate Chebyshev polynomial in temperature and pressure.
 /*!
  * The rate constant can be written as:
- * \f[
+ * @f[
  *     \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$\phi_n(x)\f$
+ * @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[
+ * @f[
  *  \tilde{T} \equiv \frac{2T^{-1} - T_\mathrm{min}^{-1} - T_\mathrm{max}^{-1}}
  *                        {T_\mathrm{max}^{-1} - T_\mathrm{min}^{-1}}
- * \f]
- * \f[
+ * @f]
+ * @f[
  *  \tilde{P} \equiv \frac{2 \log P - \log P_\mathrm{min} - \log P_\mathrm{max}}
  *                        {\log P_\mathrm{max} - \log P_\mathrm{min}}
- * \f]
+ * @f]
  * are reduced temperature and reduced pressures which map the ranges
- * \f$ (T_\mathrm{min}, T_\mathrm{max}) \f$ and
- * \f$ (P_\mathrm{min}, P_\mathrm{max}) \f$ to (-1, 1).
+ * @f$ (T_\mathrm{min}, T_\mathrm{max}) @f$ and
+ * @f$ (P_\mathrm{min}, P_\mathrm{max}) @f$ to (-1, 1).
  *
  * A ChebyshevRate rate expression is specified in terms of the coefficient matrix
- * \f$ \alpha \f$ and the temperature and pressure ranges. Note that the
+ * @f$ \alpha @f$ and the temperature and pressure ranges. Note that the
  * Chebyshev polynomials are not defined outside the interval (-1,1), and
  * therefore extrapolation of rates outside the range of temperatures and
  * pressures for which they are defined is strongly discouraged.