[docs] Fix LaTeX log/ln/exp

doc/doxygen/thermoprops.dox

@@ -362,19 +362,19 @@
  * activity coefficients:
  *
  * @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})
+ *  \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]
  *
  * And, the solvent employs the following convention
  * @f[
- *    \mu_o = \mu^o_o(T,P) + RT ln(a_o)
+ *    \mu_o = \mu^o_o(T,P) + RT \ln(a_o)
  * @f]
  *
  * where @f$ a_o @f$ is often redefined in terms of the osmotic coefficient @f$ \phi @f$.
  *
  *   @f[
- *       \phi = \frac{- ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
+ *       \phi = \frac{- \ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
  *   @f]
  *
  *  %ThermoPhase classes which employ the molality based convention are all derived

include/cantera/equil/vcs_solve.h

@@ -820,7 +820,7 @@ class VCS_SOLVE
      * We are checking the equation:
      *
      *         sum_u = sum_j_comp [ sigma_i_j * u_j ]
-     *               = u_i_O + log((AC_i * W_i)/m_tPhaseMoles_old)
+     *               = u_i_O + \log((AC_i * W_i)/m_tPhaseMoles_old)
      *
      * by first evaluating:
      *

include/cantera/kinetics/Falloff.h

@@ -395,7 +395,7 @@ class TroeRate final : public FalloffRate
  *  where
  *  @f[ P_r = \frac{k_0 [M]}{k_{\infty}} @f]
  *
- *  @f[ F = {\left( a \; exp(\frac{-b}{T}) + exp(\frac{-T}{c})\right)}^n
+ *  @f[ F = {\left( a \; \exp(\frac{-b}{T}) + \exp(\frac{-T}{c})\right)}^n
  *              \;  d \; T^e @f]
  *      where
  *  @f[ n = \frac{1.0}{1.0 + (\log_{10} P_r)^2} @f]

include/cantera/kinetics/Kinetics.h

@@ -60,7 +60,7 @@ class AnyMap;
 //! quantities internally, and re-evaluate them only when the temperature has
 //! actually changed. Or a manager designed for use with reaction mechanisms
 //! with a few repeated activation energies might precompute the terms @f$
-//! exp(-E/RT) @f$, instead of evaluating the exponential repeatedly for each
+//! \exp(-E/RT) @f$, instead of evaluating the exponential repeatedly for each
 //! reaction. There are many other possible 'management styles', each of which
 //! might be better suited to some reaction mechanisms than others.
 //!
@@ -401,7 +401,7 @@ class Kinetics
      *  total number of reactions.
      *
      * @f[
-     *       Kc_i = exp [ \Delta G_{ss,i} ] prod(Cs_k) exp(\sum_k \nu_{k,i} F \phi_n) ]
+     *       Kc_i = \exp [ \Delta G_{ss,i} ] \prod(Cs_k) \exp(\sum_k \nu_{k,i} F \phi_n)
      * @f]
      *
      * @param kc   Output vector containing the equilibrium constants.

include/cantera/thermo/ConstCpPoly.h

@@ -30,7 +30,7 @@ namespace Cantera
  * \frac{h^0(T)}{RT} = \frac{1}{T} * (h0\_R + (T - T_0) * Cp0\_R)
  * @f]
  * @f[
- * \frac{s^0(T)}{R} =  (s0\_R + (log(T) - log(T_0)) * Cp0\_R)
+ * \frac{s^0(T)}{R} =  (s0\_R + (log(T) - \log(T_0)) * Cp0\_R)
  * @f]
  *
  * This parameterization takes 4 input values. These are:

include/cantera/thermo/DebyeHuckel.h

@@ -103,10 +103,10 @@ class PDSS_Water;
  * @f$, which are based on the molality form, have the following general format:
  *
  * @f[
- *    \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
+ *    \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
  * @f]
  * @f[
- *    \mu_o = \mu^o_o(T,P) + RT ln(a_o)
+ *    \mu_o = \mu^o_o(T,P) + RT \ln(a_o)
  * @f]
  *
  * where @f$ \gamma_k^{\triangle} @f$ is the molality based activity coefficient
@@ -443,7 +443,7 @@ class DebyeHuckel : public MolalityVPSSTP
      * pure species phases which exhibit zero volume expansivity:
      * @f[
      * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T)
-     *      - \hat R  \sum_k X_k log(X_k)
+     *      - \hat R  \sum_k X_k \log(X_k)
      * @f]
      * The reference-state pure-species entropies
      * @f$ \hat s^0_k(T,p_{ref}) @f$ are computed by the
@@ -532,7 +532,7 @@ class DebyeHuckel : public MolalityVPSSTP
      * solution.
      *
      * @f[
-     *    \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} m_k)
+     *    \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} m_k)
      * @f]
      *
      * @param mu  Output vector of species chemical
@@ -575,7 +575,7 @@ class DebyeHuckel : public MolalityVPSSTP
      * For this phase, the partial molar entropies are equal to the SS species
      * entropies plus the ideal solution contribution:
      * @f[
-     *     \bar s_k(T,P) =  \hat s^0_k(T) - R log(M0 * molality[k])
+     *     \bar s_k(T,P) =  \hat s^0_k(T) - R \log(M0 * molality[k])
      * @f]
      * @f[
      *     \bar s_{solvent}(T,P) =  \hat s^0_{solvent}(T)

include/cantera/thermo/GibbsExcessVPSSTP.h

@@ -47,7 +47,7 @@ namespace Cantera
  * format:
  *
  * @f[
- *    \mu_k = \mu^o_k(T,P) + R T ln( \gamma_k X_k )
+ *    \mu_k = \mu^o_k(T,P) + R T \ln( \gamma_k X_k )
  * @f]
  *
  * where @f$ \gamma_k^{\triangle} @f$ is a molar based activity coefficient for

include/cantera/thermo/HMWSoln.h

@@ -129,10 +129,10 @@ class WaterProps;
  * @f$, which are based on the molality form, have the following general format:
  *
  * @f[
- *    \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
+ *    \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
  * @f]
  * @f[
- *    \mu_o = \mu^o_o(T,P) + RT ln(a_o)
+ *    \mu_o = \mu^o_o(T,P) + RT \ln(a_o)
  * @f]
  *
  * where @f$ \gamma_k^{\triangle} @f$ is the molality based activity coefficient
@@ -835,7 +835,7 @@ class HMWSoln : public MolalityVPSSTP
      * exhibit zero volume expansivity:
      * @f[
      * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T)
-     *      - \hat R  \sum_k X_k log(X_k)
+     *      - \hat R  \sum_k X_k \log(X_k)
      * @f]
      * The reference-state pure-species entropies @f$ \hat s^0_k(T,p_{ref}) @f$
      * are computed by the species thermodynamic property manager. The pure
@@ -1038,7 +1038,7 @@ class HMWSoln : public MolalityVPSSTP
      * species in solution.
      *
      * @f[
-     *    \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} m_k)
+     *    \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} m_k)
      * @f]
      *
      * @param mu  Output vector of species chemical

include/cantera/thermo/IdealSolidSolnPhase.h

@@ -89,7 +89,7 @@ class IdealSolidSolnPhase : public ThermoPhase
      * partial molar volume solution mixture with pure species phases which
      * exhibit zero volume expansivity:
      * @f[
-     * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T)  - \hat R \sum_k X_k log(X_k)
+     * \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T)  - \hat R \sum_k X_k \log(X_k)
      * @f]
      * The reference-state pure-species entropies
      * @f$ \hat s^0_k(T,p_{ref}) @f$ are computed by the species thermodynamic
@@ -104,7 +104,7 @@ class IdealSolidSolnPhase : public ThermoPhase
      * constant partial molar volume solution mixture with pure species phases
      * which exhibit zero volume expansivity:
      * @f[
-     * \hat g(T, P) = \sum_k X_k \hat g^0_k(T,P) + \hat R T \sum_k X_k log(X_k)
+     * \hat g(T, P) = \sum_k X_k \hat g^0_k(T,P) + \hat R T \sum_k X_k \log(X_k)
      * @f]
      * The reference-state pure-species Gibbs free energies
      * @f$ \hat g^0_k(T) @f$ are computed by the species thermodynamic
@@ -280,11 +280,11 @@ class IdealSolidSolnPhase : public ThermoPhase
      * This function returns a vector of chemical potentials of the
      * species in solution.
      * @f[
-     *    \mu_k = \mu^{ref}_k(T) + V_k * (p - p_o) + R T ln(X_k)
+     *    \mu_k = \mu^{ref}_k(T) + V_k * (p - p_o) + R T \ln(X_k)
      * @f]
      *  or another way to phrase this is
      * @f[
-     *    \mu_k = \mu^o_k(T,p) + R T ln(X_k)
+     *    \mu_k = \mu^o_k(T,p) + R T \ln(X_k)
      * @f]
      *  where @f$ \mu^o_k(T,p) = \mu^{ref}_k(T) + V_k * (p - p_o) @f$
      *
@@ -297,7 +297,7 @@ class IdealSolidSolnPhase : public ThermoPhase
      * chemical potentials at the current T and P
      * @f$ \mu_k / \hat R T @f$.
      * @f[
-     *  \mu^0_k(T,P) = \mu^{ref}_k(T) + (P - P_{ref}) * V_k + RT ln(X_k)
+     *  \mu^0_k(T,P) = \mu^{ref}_k(T) + (P - P_{ref}) * V_k + RT \ln(X_k)
      * @f]
      * where @f$ V_k @f$ is the molar volume of pure species *k*.
      * @f$ \mu^{ref}_k(T) @f$ is the chemical potential of pure
@@ -337,8 +337,8 @@ class IdealSolidSolnPhase : public ThermoPhase
      * solution. Units: J/kmol/K. For this phase, the partial molar entropies
      * are equal to the pure species entropies plus the ideal solution
      * contribution.
-     *  @f[
-     * \bar s_k(T,P) =  \hat s^0_k(T) - R log(X_k)
+     * @f[
+     *  \bar s_k(T,P) =  \hat s^0_k(T) - R \log(X_k)
      * @f]
      * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at
      * the reference pressure, @f$ P_{ref} @f$, are computed by the species

include/cantera/thermo/LatticePhase.h

@@ -227,7 +227,7 @@ class LatticePhase : public ThermoPhase
      * For an ideal, constant partial molar volume solution mixture with
      * pure species phases which exhibit zero volume expansivity:
      *   @f[
-     *       \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T)  - \hat R  \sum_k X_k log(X_k)
+     *      \hat s(T, P, X_k) = \sum_k X_k \hat s^0_k(T)  - \hat R  \sum_k X_k \log(X_k)
      *   @f]
      * The reference-state pure-species entropies @f$ \hat s^0_k(T,p_{ref}) @f$
      * are computed by the species thermodynamic property manager. The pure
@@ -395,7 +395,7 @@ class LatticePhase : public ThermoPhase
      * are equal to the pure species entropies plus the ideal solution
      * contribution.
      * @f[
-     * \bar s_k(T,P) =  \hat s^0_k(T) - R log(X_k)
+     * \bar s_k(T,P) =  \hat s^0_k(T) - R \log(X_k)
      * @f]
      * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at
      * the reference pressure, @f$ P_{ref} @f$, are computed by the species

include/cantera/thermo/LatticeSolidPhase.h

@@ -364,7 +364,7 @@ class LatticeSolidPhase : public ThermoPhase
      * are equal to the pure species entropies plus the ideal solution
      * contribution.
      *  @f[
-     * \bar s_k(T,P) =  \hat s^0_k(T) - R log(X_k)
+     * \bar s_k(T,P) =  \hat s^0_k(T) - R \log(X_k)
      * @f]
      * The reference-state pure-species entropies,@f$ \hat s^{ref}_k(T) @f$, at
      * the reference pressure, @f$ P_{ref} @f$, are computed by the species

include/cantera/thermo/MolalityVPSSTP.h

@@ -35,8 +35,8 @@ namespace Cantera
  * using the following formula
  *
  * @f[
- *     ln(\gamma_k^{s2}) = ln(\gamma_k^{s1})
- *        + \frac{z_k}{z_j} \left(  ln(\gamma_j^{s2}) - ln(\gamma_j^{s1}) \right)
+ *     \ln(\gamma_k^{s2}) = \ln(\gamma_k^{s1})
+ *        + \frac{z_k}{z_j} \left( \ln(\gamma_j^{s2}) - \ln(\gamma_j^{s1}) \right)
  * @f]
  *
  * where j is any one species.
@@ -52,15 +52,15 @@ const int PHSCALE_PITZER = 0;
  * using the following formula
  *
  * @f[
- *     ln(\gamma_k^{s2}) = ln(\gamma_k^{s1})
- *        + \frac{z_k}{z_j} \left(  ln(\gamma_j^{s2}) - ln(\gamma_j^{s1}) \right)
+ *     \ln(\gamma_k^{s2}) = \ln(\gamma_k^{s1})
+ *        + \frac{z_k}{z_j} \left( \ln(\gamma_j^{s2}) - \ln(\gamma_j^{s1}) \right)
  * @f]
  *
  * where j is any one species. For the NBS scale, j is equal to the Cl- species
  * and
  *
  * @f[
- *     ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}}
+ *     \ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}}
  * @f]
  *
  * This is the NBS pH scale, which is used in all conventional pH measurements.
@@ -123,10 +123,10 @@ const int PHSCALE_NBS = 1;
  * have the following general format:
  *
  * @f[
- *    \mu_k = \mu^{\triangle}_k(T,P) + R T ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
+ *    \mu_k = \mu^{\triangle}_k(T,P) + R T \ln(\gamma_k^{\triangle} \frac{m_k}{m^\triangle})
  * @f]
  * @f[
- *    \mu_o = \mu^o_o(T,P) + RT ln(a_o)
+ *    \mu_o = \mu^o_o(T,P) + RT \ln(a_o)
  * @f]
  *
  * where @f$ \gamma_k^{\triangle} @f$ is the molality based activity coefficient
@@ -137,7 +137,7 @@ const int PHSCALE_NBS = 1;
  * solvent, @f$ a_o @f$, is further reexpressed in terms of an osmotic
  * coefficient, @f$ \phi @f$.
  * @f[
- *     \phi = \frac{- ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
+ *     \phi = \frac{- \ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
  * @f]
  *
  * MolalityVPSSTP::osmoticCoefficient() returns the value of @f$ \phi @f$. Note
@@ -195,15 +195,15 @@ const int PHSCALE_NBS = 1;
  * using the following formula
  *
  * @f[
- *     ln(\gamma_k^{s2}) = ln(\gamma_k^{s1})
- *        + \frac{z_k}{z_j} \left(  ln(\gamma_j^{s2}) - ln(\gamma_j^{s1}) \right)
+ *     \ln(\gamma_k^{s2}) = \ln(\gamma_k^{s1})
+ *        + \frac{z_k}{z_j} \left( \ln(\gamma_j^{s2}) - \ln(\gamma_j^{s1}) \right)
  * @f]
  *
  * where j is any one species. For the NBS scale, j is equal to the Cl- species
  * and
  *
  * @f[
- *     ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}}
+ *     \ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}}
  * @f]
  *
  * The Pitzer scale doesn't actually change anything. The pitzer scale is
@@ -453,15 +453,15 @@ class MolalityVPSSTP : public VPStandardStateTP
      * s2 using the following formula
      *
      * @f[
-     *     ln(\gamma_k^{s2}) = ln(\gamma_k^{s1})
-     *        + \frac{z_k}{z_j} \left(  ln(\gamma_j^{s2}) - ln(\gamma_j^{s1}) \right)
+     *     \ln(\gamma_k^{s2}) = \ln(\gamma_k^{s1})
+     *        + \frac{z_k}{z_j} \left( \ln(\gamma_j^{s2}) - \ln(\gamma_j^{s1}) \right)
      * @f]
      *
      * where j is any one species. For the NBS scale, j is equal to the Cl-
      * species and
      *
      * @f[
-     *     ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}}
+     *     \ln(\gamma_{Cl-}^{s2}) = \frac{-A_{\phi} \sqrt{I}}{1.0 + 1.5 \sqrt{I}}
      * @f]
      *
      * @param acMolality Output vector containing the molality based activity
@@ -472,7 +472,7 @@ class MolalityVPSSTP : public VPStandardStateTP
     //! Calculate the osmotic coefficient
     /*!
      * @f[
-     *     \phi = \frac{- ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
+     *     \phi = \frac{- \ln(a_o)}{\tilde{M}_o \sum_{i \ne o} m_i}
      * @f]
      *
      * Note there are a few of definitions of the osmotic coefficient floating