[Doc] Fix notation for natural log

Always write \log_{10} in the rare instances where that's what's
actually meant.

include/cantera/kinetics/ChebyshevRate.h

@@ -62,8 +62,8 @@ struct ChebyshevData : public ReactionData
 /*!
  * The rate constant can be written as:
  * @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})
+ *     \log_{10} 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$
  * is the Chebyshev polynomial of the first kind of degree *n* evaluated at
@@ -73,8 +73,8 @@ struct ChebyshevData : public ReactionData
  *                        {T_\mathrm{max}^{-1} - T_\mathrm{min}^{-1}}
  * @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}}
+ *  \tilde{P} \equiv \frac{2 \log_{10} P - \log_{10} P_\mathrm{min} - \log_{10} P_\mathrm{max}}
+ *                        {\log_{10} P_\mathrm{max} - \log_{10} P_\mathrm{min}}
  * @f]
  * are reduced temperature and reduced pressures which map the ranges
  * @f$ (T_\mathrm{min}, T_\mathrm{max}) @f$ and

include/cantera/kinetics/PlogRate.h

@@ -64,8 +64,8 @@ struct PlogData : public ReactionData
  *
  * The rate at an intermediate pressure @f$ P_1 < P < P_2 @f$ is computed as
  * @f[
- *  \log k(T,P) = \log k_1(T) + \bigl(\log k_2(T) - \log k_1(T)\bigr)
- *      \frac{\log P - \log P_1}{\log P_2 - \log P_1}
+ *  \ln k(T,P) = \ln k_1(T) + \bigl(\ln k_2(T) - \ln k_1(T)\bigr)
+ *      \frac{\ln P - \ln P_1}{\ln P_2 - \ln P_1}
  * @f]
  * Multiple rate expressions may be given at the same pressure, in which case
  * the rate used in the interpolation formula is the sum of all the rates given

include/cantera/numerics/Func1.h

@@ -405,7 +405,7 @@ class Exp1 : public Func1
 
 //! Implements the @c log() (natural logarithm) function.
 /*!
- * The functor class with type @c "log" returns @f$ f(x) = \log(a x) @f$.
+ * The functor class with type @c "log" returns @f$ f(x) = \ln(a x) @f$.
  * @param a  Factor (default=1.0)
  * @ingroup func1simple
  * @since New in %Cantera 3.0

include/cantera/thermo/DebyeHuckel.h

@@ -231,7 +231,7 @@ class PDSS_Water;
  *
  * @f[
  *    \ln(\gamma_k^\triangle) = -z_k^2 \frac{A_{Debye} \sqrt{I}}{ 1 + B_{Debye}  a_k \sqrt{I}}
- *                        + \log(10) B^{dot}_k  I
+ *                        + \ln(10) B^{dot}_k  I
  * @f]
  *
  * Note, this particular form where @f$ a_k @f$ can differ in multielectrolyte
@@ -245,7 +245,7 @@ class PDSS_Water;
  *       \ln(a_o) = \frac{X_o - 1.0}{X_o}
  *        + \frac{ 2 A_{Debye} \tilde{M}_o}{3} (I)^{1/2}
  *                        \left[ \sum_k{\frac{1}{2} m_k z_k^2 \sigma( B_{Debye} a_k \sqrt{I} ) } \right]
- *                        - \frac{\log(10)}{2} \tilde{M}_o I \sum_k{ B^{dot}_k m_k}
+ *                        - \frac{\ln 10}{2} \tilde{M}_o I \sum_k{ B^{dot}_k m_k}
  *  @f]
  *    where
  *  @f[
@@ -263,15 +263,15 @@ class PDSS_Water;
  *
  * @f[
  *    \ln(\gamma_k^\triangle) = -z_k^2 \frac{A_{Debye} \sqrt{I}}{ 1 + B_{Debye}  a \sqrt{I}}
- *                        + \log(10) B^{dot}_k  I
+ *                        + \ln(10) B^{dot}_k  I
  * @f]
  *
  * The value of a is determined at the beginning of the calculation, and not changed.
  *
  *  @f[
  *       \ln(a_o) = \frac{X_o - 1.0}{X_o}
  *        + \frac{ 2 A_{Debye} \tilde{M}_o}{3} (I)^{3/2} \sigma( B_{Debye} a \sqrt{I} )
- *                        - \frac{\log(10)}{2} \tilde{M}_o I \sum_k{ B^{dot}_k m_k}
+ *                        - \frac{\ln 10}{2} \tilde{M}_o I \sum_k{ B^{dot}_k m_k}
  *  @f]
  *
  * ### Beta_IJ formulation
@@ -475,7 +475,7 @@ class DebyeHuckel : public MolalityVPSSTP
     //! @name Activities, Standard States, and Activity Concentrations
     //!
     //! The activity @f$ a_k @f$ of a species in solution is related to the
-    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \log a_k. @f] The
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \ln a_k. @f] The
     //! quantity @f$ \mu_k^0(T,P) @f$ is the chemical potential at unit activity,
     //! which depends only on temperature and the pressure. Activity is assumed
     //! to be molality-based here.

include/cantera/thermo/GibbsExcessVPSSTP.h

@@ -122,7 +122,7 @@ class GibbsExcessVPSSTP : public VPStandardStateTP
     //! @name Activities, Standard States, and Activity Concentrations
     //!
     //! The activity @f$ a_k @f$ of a species in solution is related to the
-    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \log a_k. @f] The
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \ln a_k. @f] The
     //! quantity @f$ \mu_k^0(T,P) @f$ is the chemical potential at unit activity,
     //! which depends only on temperature and pressure.
     //! @{

include/cantera/thermo/HMWSoln.h

@@ -900,7 +900,7 @@ class HMWSoln : public MolalityVPSSTP
     //! @name Activities, Standard States, and Activity Concentrations
     //!
     //! The activity @f$ a_k @f$ of a species in solution is related to the
-    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \log a_k. @f] The
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \ln a_k. @f] The
     //! quantity @f$ \mu_k^0(T,P) @f$ is the chemical potential at unit activity,
     //! which depends only on temperature and the pressure. Activity is assumed
     //! to be molality-based here.

include/cantera/thermo/IdealGasPhase.h

@@ -109,19 +109,19 @@ namespace Cantera
  * for species *k* is equal to
  *
  * @f[
- *      \mu_k(T,P) = \mu^o_k(T, P) + R T \log(X_k)
+ *      \mu_k(T,P) = \mu^o_k(T, P) + R T \ln X_k
  * @f]
  *
  * In terms of the reference state, the above can be rewritten
  *
  * @f[
- *      \mu_k(T,P) = \mu^{ref}_k(T, P) + R T \log(\frac{P X_k}{P_{ref}})
+ *      \mu_k(T,P) = \mu^{ref}_k(T, P) + R T \ln \frac{P X_k}{P_{ref}}
  * @f]
  *
  * The partial molar entropy for species *k* is given by the following relation,
  *
  * @f[
- *      \tilde{s}_k(T,P) = s^o_k(T,P) - R \log(X_k) = s^{ref}_k(T) - R \log(\frac{P X_k}{P_{ref}})
+ *      \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln X_k = s^{ref}_k(T) - R \ln \frac{P X_k}{P_{ref}}
  * @f]
  *
  * The partial molar enthalpy for species *k* is
@@ -190,7 +190,7 @@ namespace Cantera
  * and their associated activities, @f$ a_l @f$, repeated here:
  *
  * @f[
- *      \mu_l(T,P) = \mu^o_l(T, P) + R T \log(a_l)
+ *      \mu_l(T,P) = \mu^o_l(T, P) + R T \ln a_l
  * @f]
  *
  * We can switch over to expressing the equilibrium constant in terms of the
@@ -299,7 +299,7 @@ class IdealGasPhase: public ThermoPhase
      * Molar entropy. Units: J/kmol/K.
      * For an ideal gas mixture,
      * @f[
-     * \hat s(T, P) = \sum_k X_k \hat s^0_k(T) - \hat R \log (P/P^0).
+     * \hat s(T, P) = \sum_k X_k \hat s^0_k(T) - \hat R \ln \frac{P}{P^0}.
      * @f]
      * The reference-state pure-species entropies @f$ \hat s^0_k(T) @f$ are
      * computed by the species thermodynamic property manager.
@@ -408,8 +408,7 @@ class IdealGasPhase: public ThermoPhase
     //! The activity @f$ a_k @f$ of a species in solution is
     //! related to the chemical potential by
     //! @f[
-    //!  \mu_k(T,P,X_k) = \mu_k^0(T,P)
-    //! + \hat R T \log a_k.
+    //!  \mu_k(T,P,X_k) = \mu_k^0(T,P) + \hat R T \ln a_k.
     //!  @f]
     //! The quantity @f$ \mu_k^0(T,P) @f$ is the standard state chemical potential
     //! at unit activity. It may depend on the pressure and the temperature.

include/cantera/thermo/IdealMolalSoln.h

@@ -216,7 +216,7 @@ class IdealMolalSoln : public MolalityVPSSTP
     //! @name Activities and Activity Concentrations
     //!
     //! The activity @f$ a_k @f$ of a species in solution is related to the
-    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \log a_k. @f] The
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \ln a_k. @f] The
     //! quantity @f$ \mu_k^0(T) @f$ is the chemical potential at unit activity,
     //! which depends only on temperature and the pressure.
     //! @{

include/cantera/thermo/IdealSolidSolnPhase.h

@@ -193,8 +193,7 @@ class IdealSolidSolnPhase : public ThermoPhase
     //! The activity @f$ a_k @f$ of a species in solution is related to the
     //! chemical potential by
     //! @f[
-    //!  \mu_k(T,P,X_k) = \mu_k^0(T,P)
-    //! + \hat R T \log a_k.
+    //!   \mu_k(T,P,X_k) = \mu_k^0(T,P) + \hat R T \ln a_k.
     //!  @f]
     //! The quantity @f$ \mu_k^0(T,P) @f$ is the standard state chemical potential
     //! at unit activity. It may depend on the pressure and the temperature.

include/cantera/thermo/IonsFromNeutralVPSSTP.h

@@ -109,7 +109,7 @@ class IonsFromNeutralVPSSTP : public GibbsExcessVPSSTP
     //!
     //! The activity @f$ a_k @f$ of a species in solution is
     //! related to the chemical potential by @f[ \mu_k = \mu_k^0(T)
-    //! + \hat R T \log a_k. @f] The quantity @f$ \mu_k^0(T,P) @f$ is
+    //! + \hat R T \ln a_k. @f] The quantity @f$ \mu_k^0(T,P) @f$ is
     //! the chemical potential at unit activity, which depends only
     //! on temperature and pressure.
     //! @{

include/cantera/thermo/LatticePhase.h

@@ -80,13 +80,13 @@ namespace Cantera
  * for species *k* is equal to
  *
  * @f[
- *      \mu_k(T,P) = \mu^o_k(T, P) + R T \log(X_k)
+ *      \mu_k(T,P) = \mu^o_k(T, P) + R T \ln X_k
  * @f]
  *
  * The partial molar entropy for species *k* is given by the following relation,
  *
  * @f[
- *      \tilde{s}_k(T,P) = s^o_k(T,P) - R \log(X_k) = s^{ref}_k(T) - R \log(X_k)
+ *      \tilde{s}_k(T,P) = s^o_k(T,P) - R \ln X_k = s^{ref}_k(T) - R \ln X_k
  * @f]
  *
  * The partial molar enthalpy for species *k* is
@@ -163,7 +163,7 @@ namespace Cantera
  * @f$ a_l @f$, repeated here:
  *
  * @f[
- *      \mu_l(T,P) = \mu^o_l(T, P) + R T \log(a_l)
+ *      \mu_l(T,P) = \mu^o_l(T, P) + R T \ln a_l
  * @f]
  *
  * The concentration equilibrium constant, @f$ K_c @f$, may be obtained by
@@ -321,7 +321,7 @@ class LatticePhase : public ThermoPhase
     //! @name Activities, Standard States, and Activity Concentrations
     //!
     //! The activity @f$ a_k @f$ of a species in solution is related to the
-    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \log a_k. @f] The
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \ln a_k. @f] The
     //! quantity @f$ \mu_k^0(T,P) @f$ is the chemical potential at unit activity,
     //! which depends only on temperature and the pressure. Activity is assumed
     //! to be molality-based here.

include/cantera/thermo/MargulesVPSSTP.h

@@ -161,7 +161,7 @@ namespace Cantera
  * and their associated activities, @f$ a_l @f$, repeated here:
  *
  * @f[
- *      \mu_l(T,P) = \mu^o_l(T, P) + R T \log(a_l)
+ *      \mu_l(T,P) = \mu^o_l(T, P) + R T \ln a_l
  * @f]
  *
  * We can switch over to expressing the equilibrium constant in terms of the
@@ -239,7 +239,7 @@ class MargulesVPSSTP : public GibbsExcessVPSSTP
     //! @name Activities, Standard States, and Activity Concentrations
     //!
     //! The activity @f$ a_k @f$ of a species in solution is related to the
-    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \log a_k. @f] The
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \ln a_k. @f] The
     //! quantity @f$ \mu_k^0(T,P) @f$ is the chemical potential at unit activity,
     //! which depends only on temperature and pressure.
     //! @{

include/cantera/thermo/MolalityVPSSTP.h

@@ -376,7 +376,7 @@ class MolalityVPSSTP : public VPStandardStateTP
     //! @name Activities, Standard States, and Activity Concentrations
     //!
     //! The activity @f$ a_k @f$ of a species in solution is related to the
-    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \log a_k. @f] The
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \ln a_k. @f] The
     //! quantity @f$ \mu_k^0(T,P) @f$ is the chemical potential at unit activity,
     //! which depends only on temperature and pressure.
     //! @{

include/cantera/thermo/Phase.h

@@ -773,7 +773,7 @@ class Phase
         return m_mmw;
     }
 
-    //! Evaluate @f$ \sum_k X_k \log X_k @f$.
+    //! Evaluate @f$ \sum_k X_k \ln X_k @f$.
     //! @return The indicated sum. Dimensionless.
     double sum_xlogx() const;
 

include/cantera/thermo/RedlichKisterVPSSTP.h

@@ -179,7 +179,7 @@ namespace Cantera
  * and their associated activities, @f$ a_l @f$, repeated here:
  *
  * @f[
- *      \mu_l(T,P) = \mu^o_l(T, P) + R T \log(a_l)
+ *      \mu_l(T,P) = \mu^o_l(T, P) + R T \ln a_l
  * @f]
  *
  * We can switch over to expressing the equilibrium constant in terms of the
@@ -258,7 +258,7 @@ class RedlichKisterVPSSTP : public GibbsExcessVPSSTP
     //!
     //! The activity @f$ a_k @f$ of a species in solution is
     //! related to the chemical potential by @f[ \mu_k = \mu_k^0(T)
-    //! + \hat R T \log a_k. @f] The quantity @f$ \mu_k^0(T,P) @f$ is
+    //! + \hat R T \ln a_k. @f] The quantity @f$ \mu_k^0(T,P) @f$ is
     //! the chemical potential at unit activity, which depends only
     //! on temperature and pressure.
     //! @{

include/cantera/thermo/SingleSpeciesTP.h

@@ -85,7 +85,7 @@ class SingleSpeciesTP : public ThermoPhase
     //! @name Activities, Standard State, and Activity Concentrations
     //!
     //! The activity @f$ a_k @f$ of a species in solution is related to the
-    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \log a_k. @f]
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T) + \hat R T \ln a_k. @f]
     //! The quantity @f$ \mu_k^0(T) @f$ is the chemical potential at unit activity,
     //! which depends only on temperature.
     //! @{

include/cantera/thermo/SurfPhase.h

@@ -57,7 +57,7 @@ namespace Cantera
  *
  * The chemical potential for species *k* is equal to
  * @f[
- *      \mu_k(T,P) = \mu^o_k(T) + R T \log(\theta_k)
+ *      \mu_k(T,P) = \mu^o_k(T) + R T \ln \theta_k
  * @f]
  *
  * Pressure is defined as an independent variable in this phase. However, it has
@@ -72,7 +72,7 @@ namespace Cantera
  * independent of the pressure:
  *
  * @f[
- *      s_k(T,P) = s^o_k(T) - R \log(\theta_k)
+ *      s_k(T,P) = s^o_k(T) - R \ln \theta_k
  * @f]
  *
  * ## Application within Kinetics Managers
@@ -138,7 +138,7 @@ class SurfPhase : public ThermoPhase
     //! Return the Molar Entropy. Units: J/kmol-K
     /**
      * @f[
-     *  \hat s(T,P) = \sum_k X_k (\hat s^0_k(T) - R \log(\theta_k))
+     *  \hat s(T,P) = \sum_k X_k (\hat s^0_k(T) - R \ln \theta_k)
      * @f]
      */
     virtual double entropy_mole() const;

include/cantera/thermo/ThermoPhase.h

@@ -627,7 +627,7 @@ class ThermoPhase : public Phase
     //! @name Activities, Standard States, and Activity Concentrations
     //!
     //! The activity @f$ a_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. @f]
+    //! chemical potential by @f[ \mu_k = \mu_k^0(T,P) + \hat R T \ln a_k. @f]
     //! The quantity @f$ \mu_k^0(T,P) @f$ is the standard chemical potential at
     //! unit activity, which depends on temperature and pressure, but not on
     //! composition. The activity is dimensionless.

include/cantera/transport/GasTransport.h

@@ -233,19 +233,19 @@ class GasTransport : public Transport
     /*!
      * If CK_mode, then the fits are of the form
      * @f[
-     *      \log(\eta(i)) = \sum_{n=0}^3 a_n(i) \, (\log T)^n
+     *      \ln \eta(i) = \sum_{n=0}^3 a_n(i) \, (\ln T)^n
      * @f]
      * and
      * @f[
-     *      \log(\lambda(i)) = \sum_{n=0}^3 b_n(i) \, (\log T)^n
+     *      \ln \lambda(i) = \sum_{n=0}^3 b_n(i) \, (\ln T)^n
      * @f]
      * Otherwise the fits are of the form
      * @f[
-     *      \left(\eta(i)\right)^{1/2} = T^{1/4} \sum_{n=0}^4 a_n(i) \, (\log T)^n
+     *      \left(\eta(i)\right)^{1/2} = T^{1/4} \sum_{n=0}^4 a_n(i) \, (\ln T)^n
      * @f]
      * and
      * @f[
-     *      \lambda(i) = T^{1/2} \sum_{n=0}^4 b_n(i) \, (\log T)^n
+     *      \lambda(i) = T^{1/2} \sum_{n=0}^4 b_n(i) \, (\ln T)^n
      * @f]
      *
      * @param integrals interpolator for the collision integrals
@@ -256,11 +256,11 @@ class GasTransport : public Transport
     /*!
      * If CK_mode, then the fits are of the form
      * @f[
-     *      \log(D(i,j)) = \sum_{n=0}^3 c_n(i,j) \, (\log T)^n
+     *      \ln D(i,j) = \sum_{n=0}^3 c_n(i,j) \, (\ln T)^n
      * @f]
      * Otherwise the fits are of the form
      * @f[
-     *      D(i,j) = T^{3/2} \sum_{n=0}^4 c_n(i,j) \, (\log T)^n
+     *      D(i,j) = T^{3/2} \sum_{n=0}^4 c_n(i,j) \, (\ln T)^n
      * @f]
      *
      * @param integrals interpolator for the collision integrals