[Doc] Introduce some LaTeX macros in Sphinx and fix text subscripts

doc/sphinx/conf.py

@@ -225,6 +225,15 @@ def escape_splats(app, what, name, obj, options, lines):
 
 myst_enable_extensions = ["dollarmath", "amsmath", "deflist", "colon_fence"]
 
+mathjax3_config = {
+    'tex': {
+        'macros': {
+            't': ['\\mathrm{#1}', 1],
+            'pxpy': ['\\frac{\\partial #1}{\\partial #2}', 2]
+        }
+    }
+}
+
 # Ensure that the primary domain is the Python domain, since we've added the
 # MATLAB domain with sphinxcontrib.matlab
 primary_domain = 'py'

doc/sphinx/develop/reactor-integration.md

@@ -165,7 +165,7 @@ example, using the {py:class}`ExtensibleReactor` class, the governing equations
 reactor are written in the form:
 
 $$
-\mathrm{LHS}_i \frac{dy_i}{dt} = \mathrm{RHS}_i
+\t{LHS}_i \frac{dy_i}{dt} = \t{RHS}_i
 $$
 
 where the {ct}`Reactor::eval` method or the `eval()` method of any class derived from

doc/sphinx/reference/kinetics/rate-constants.md

@@ -25,22 +25,22 @@ field.
 ## Falloff Reactions
 
 A falloff reaction is one that has a rate that is first-order in the total concentration
-of third-body colliders $\def\MM{[\mathrm{M}]} \MM$ at low pressure, like a
-[three-body reaction](sec-three-body-reaction), but becomes zero-order in $\MM$ as $\MM$
-increases. Dissociation/association reactions of polyatomic molecules often exhibit this
-behavior.
+of third-body colliders $[\t{M}]$ at low pressure, like a
+[three-body reaction](sec-three-body-reaction), but becomes zero-order in $[\t{M}]$ as
+$[\t{M}]$ increases. Dissociation/association reactions of polyatomic molecules often
+exhibit this behavior.
 
 The simplest expression for the rate coefficient for a falloff reaction is the Lindemann
 form {cite:p}`lindemann1922`:
 
-$$  k_f(T, \MM) = \frac{k_0 \MM}{1 + \frac{k_0 \MM}{k_\infty}}  $$
+$$  k_f(T, [\t{M}]) = \frac{k_0 [\t{M}]}{1 + \frac{k_0 [\t{M}]}{k_\infty}}  $$
 
-In the low-pressure limit, this approaches $k_0 \MM$, and in the high-pressure limit it
-approaches $k_\infty$.
+In the low-pressure limit, this approaches $k_0 [\t{M}]$, and in the high-pressure limit
+it approaches $k_\infty$.
 
 Defining the non-dimensional reduced pressure:
 
-$$  P_r = \frac{k_0 \MM}{k_\infty}  $$
+$$  P_r = \frac{k_0 [\t{M}]}{k_\infty}  $$
 
 The rate constant may be written as
 
@@ -67,15 +67,15 @@ A falloff reaction may be defined in the YAML format using the
 A widely-used falloff function is the one proposed by {cite:t}`gilbert1983`:
 
 \begin{gather*}
-\log_{10} F(T, P_r) = \frac{\log_{10} F_{cent}(T)}{1 + f_1^2} \\
+\log_{10} F(T, P_r) = \frac{\log_{10} F_\t{cent}(T)}{1 + f_1^2} \\
 
-F_{cent}(T) = (1-A) \exp(-T/T_3) + A \exp (-T/T_1) + \exp(-T_2/T) \\
+F_\t{cent}(T) = (1-A) \exp(-T/T_3) + A \exp (-T/T_1) + \exp(-T_2/T) \\
 
 f_1 = (\log_{10} P_r + C) / (N - 0.14 (\log_{10} P_r + C)) \\
 
-C = -0.4 - 0.67\; \log_{10} F_{cent} \\
+C = -0.4 - 0.67\; \log_{10} F_\t{cent} \\
 
-N = 0.75 - 1.27\; \log_{10} F_{cent}
+N = 0.75 - 1.27\; \log_{10} F_\t{cent}
 \end{gather*}
 
 ```{admonition} YAML Usage
@@ -87,13 +87,13 @@ term of the falloff function is not used.
 ```
 
 (sec-tsang-falloff)=
-### Tsang's Approximation to $F_{cent}$
+### Tsang's Approximation to $F_\t{cent}$
 
-Wing Tsang presented approximations for the value of $F_{cent}$ for Troe falloff in
+Wing Tsang presented approximations for the value of $F_\t{cent}$ for Troe falloff in
 databases of reactions, for example, {cite:t}`tsang1991`. Tsang's approximations are
 linear in temperature:
 
-$$  F_{cent} = A + BT  $$
+$$  F_\t{cent} = A + BT  $$
 
 where $A$ and $B$ are constants. The remaining equations for $C$, $N$, $f_1$, and $F$
 from the [Troe](sec-troe-falloff) falloff function are not affected.
@@ -132,11 +132,11 @@ An SRI falloff function may be specified in the YAML format using the
 For these reactions, the rate falls off as the pressure increases, due to collisional
 stabilization of a reaction intermediate. Example:
 
-$$  \mathrm{Si + SiH_4 (+M) \leftrightarrow Si_2H_2 + H_2 (+M)}  $$
+$$  \t{Si + SiH_4 (+M) \leftrightarrow Si_2H_2 + H_2 (+M)}  $$
 
 which competes with:
 
-$$  \mathrm{Si + SiH_4 (+M) \leftrightarrow Si_2H_4 (+M)}  $$
+$$  \t{Si + SiH_4 (+M) \leftrightarrow Si_2H_4 (+M)}  $$
 
 Like falloff reactions, chemically-activated reactions are described by blending between
 a low-pressure and a high-pressure rate expression. The difference is that the forward
@@ -210,15 +210,15 @@ defining the rate, $\phi_n(x)$ is the Chebyshev polynomial of the first kind of
 $n$ evaluated at $x$, and
 
 $$
-\tilde{T} \equiv \frac{2T^{-1} - T_\mathrm{min}^{-1} - T_\mathrm{max}^{-1}}
-                       {T_\mathrm{max}^{-1} - T_\mathrm{min}^{-1}}
+\tilde{T} \equiv \frac{2T^{-1} - T_\t{min}^{-1} - T_\t{max}^{-1}}
+                       {T_\t{max}^{-1} - T_\t{min}^{-1}}
 
-\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 P - \log P_\t{min} - \log P_\t{max}}
+                       {\log P_\t{max} - \log P_\t{min}}
 $$
 
-are reduced temperatures and reduced pressures which map the ranges $(T_\mathrm{min},
-T_\mathrm{max})$ and $(P_\mathrm{min}, P_\mathrm{max})$ to $(-1, 1)$.
+are reduced temperatures and reduced pressures which map the ranges $(T_\t{min},
+T_\t{max})$ and $(P_\t{min}, P_\t{max})$ to $(-1, 1)$.
 
 A Chebyshev rate expression is specified in terms of the coefficient matrix $\alpha$ and
 the temperature and pressure ranges.
@@ -284,7 +284,7 @@ Blowers Masel reactions can be defined in the YAML format using the
 
 Heterogeneous reactions on surfaces are represented by an extended Arrhenius- like rate
 expression, which combines the modified Arrhenius rate expression with further
-corrections dependent on the fractional surface coverages $\theta_{k}$ of one or more
+corrections dependent on the fractional surface coverages $\theta_k$ of one or more
 surface species. The forward rate constant for a reaction of this type is:
 
 $$
@@ -329,9 +329,9 @@ for all temperatures.
 
 The sticking coefficient is related to the forward rate constant by the formula:
 
-$$  k_f = \frac{\gamma}{\Gamma_\mathrm{tot}^m} \sqrt{\frac{RT}{2 \pi W}}  $$
+$$  k_f = \frac{\gamma}{\Gamma_\t{tot}^m} \sqrt{\frac{RT}{2 \pi W}}  $$
 
-where $\Gamma_\mathrm{tot}$ is the total molar site density, $m$ is the sum of all the
+where $\Gamma_\t{tot}$ is the total molar site density, $m$ is the sum of all the
 surface reactant stoichiometric coefficients, and $W$ is the molecular weight of the gas
 phase species.
 

doc/sphinx/reference/kinetics/reaction-rates.md

@@ -9,11 +9,11 @@ types.
 The basic reaction type is a homogeneous reaction with a pressure-independent
 rate coefficient and mass action kinetics. For example:
 
-$$  \mathrm{A + B \rightleftharpoons C + D}  $$
+$$  \t{A + B \rightleftharpoons C + D}  $$
 
 The forward reaction rate is then calculated as:
 
-$$  R_f = [\mathrm{A}] [\mathrm{B}] k_f  $$
+$$  R_f = [\t{A}] [\t{B}] k_f  $$
 
 where $k_f$ is the forward rate constant, calculated using one of the available rate
 parameterizations such as the [modified Arrhenius](sec-arrhenius-rate) form.
@@ -32,30 +32,30 @@ reaction type is [`three-body`](sec-yaml-three-body).
 
 A three-body reaction is a gas-phase reaction of the form:
 
-$$  \mathrm{A + B + M \rightleftharpoons AB + M}  $$
+$$  \t{A + B + M \rightleftharpoons AB + M}  $$
 
-Here $\mathrm{M}$ is an unspecified collision partner that carries away excess energy to
-stabilize the $\mathrm{AB}$ molecule (forward direction) or supplies energy to break the
-$\mathrm{AB}$ bond (reverse direction). In addition to the generic collision partner
-$\mathrm{M}$, it is also possible to explicitly specify a colliding species. In both
+Here $\t{M}$ is an unspecified collision partner that carries away excess energy to
+stabilize the $\t{AB}$ molecule (forward direction) or supplies energy to break the
+$\t{AB}$ bond (reverse direction). In addition to the generic collision partner
+$\t{M}$, it is also possible to explicitly specify a colliding species. In both
 cases, the reaction type can be automatically inferred by Cantera and does not need to
 be explicitly specified by the user.
 
 Different species may be more or less effective in acting as the collision partner. A
-species that is much lighter than $\mathrm{A}$ and $\mathrm{B}$ may not be able to
+species that is much lighter than $\t{A}$ and $\t{B}$ may not be able to
 transfer much of its kinetic energy, and so would be inefficient as a collision partner.
 On the other hand, a species with a transition from its ground state that is nearly
-resonant with one in the $\mathrm{AB^*}$ activated complex may be much more effective at
+resonant with one in the $\t{AB^*}$ activated complex may be much more effective at
 exchanging energy than would otherwise be expected.
 
 These effects can be accounted for by defining a collision efficiency $\epsilon$ for
 each species, defined such that the forward reaction rate is
 
-$$  R_f = [\mathrm{A}][\mathrm{B}][\mathrm{M}]k_f(T)  $$
+$$  R_f = [\t{A}][\t{B}][\t{M}] k_f(T)  $$
 
 where
 
-$$  [\mathrm{M}] = \sum_{k} \epsilon_k C_k  $$
+$$  [\t{M}] = \sum_{k} \epsilon_k C_k  $$
 
 where $C_k$ is the concentration of species $k$. Since any constant collision efficiency
 can be absorbed into the rate coefficient $k_f(T)$, the default collision efficiency is
@@ -70,9 +70,9 @@ Sometimes, accounting for a particular third body's collision efficiency may req
 alternate set of rate parameters entirely. In this case, two reactions are written:
 
 $$
-\mathrm{A + B + M \rightleftharpoons AB + M \quad (R1)}
+\t{A + B + M \rightleftharpoons AB + M \quad (R1)}
 
-\mathrm{A + B + C \rightleftharpoons AB + C \quad (R2)}
+\t{A + B + C \rightleftharpoons AB + C \quad (R2)}
 $$
 
 where the third-body efficiency for C in the first reaction should be explicitly set to
@@ -105,14 +105,14 @@ Explicit reaction orders different from the stoichiometric coefficients are some
 used for non-elementary reactions. For example, consider the global reaction:
 
 $$
-\mathrm{C_8H_{18} + 12.5 O_2 \rightarrow 8 CO_2 + 9 H_2O}
+\t{C_8H_{18} + 12.5 O_2 \rightarrow 8 CO_2 + 9 H_2O}
 $$
 
 the forward rate constant might be given as {cite:p}`westbrook1981`:
 
 $$
-k_f = 4.6 \times 10^{11} [\mathrm{C_8H_{18}}]^{0.25} [\mathrm{O_2}]^{1.5}
-       \exp\left(\frac{30.0\,\mathrm{kcal/mol}}{RT}\right)
+k_f = 4.6 \times 10^{11} [\t{C_8H_{18}}]^{0.25} [\t{O_2}]^{1.5}
+       \exp\left(\frac{30.0\,\t{kcal/mol}}{RT}\right)
 $$
 
 Special care is required in this case since the units of the pre-exponential factor