fix the some math rendering in docs

this seems to be a sphinx 9 issue

Author: zingale

Docs/source/networks.rst

@@ -559,10 +559,8 @@ X_a / (A_a m_u)`, our rate equation is
 
 .. math::
 
-   \begin{align}
     \frac{dX_f}{dt} &= - \frac{r_0}{m_u} \rho X_f^2 \frac{1}{A_f} \left (\frac{T}{T_0}\right)^\nu \equiv \omegadot_f  \\
     \frac{dX_a}{dt} &= \frac{1}{2}\frac{r_0}{m_u} \rho X_f^2 \frac{A_a}{A_f^2} \left (\frac{T}{T_0}\right)^\nu = \frac{r_0}{m_u} \rho X_f^2 \frac{1}{A_f} \left (\frac{T}{T_0}\right)^\nu
-   \end{align}
 
 We define a new rate constant, :math:`\rt` with units of :math:`[\mathrm{s^{-1}}]` as
 

Docs/source/ode_integrators.rst

@@ -231,7 +231,7 @@ Some suggestions when setting tolerances:
 * The VODE integrator has additional logic meant to ensure that
   species don't change too much per timestep.  This is controlled by
   ``integrator.X_reject_buffer``.  If a species $k$, has a mass
-  fraction $X_k > \mbox{X_reject_buffer} \cdot \mbox{atol_spec}$ then
+  fraction $X_k > \mathrm{X_reject_buffer} \cdot \mathrm{atol_spec}$ then
   we reject a VODE timestep if the mass fraction changes by more than
   a factor of 4 in a single VODE timestep and we try again.  This is
   all done internally to VODE.  Making ``X_reject_buffer`` larger will

Docs/source/sdc.rst

@@ -58,12 +58,10 @@ $k+1$ appears as:
 
 .. math::
 
-   \begin{align*}
     \Uc^{m+1,(k+1)} = \Uc^{m,(k+1)}
      &+ \delta t_m\left[\Advs{\Uc^{m,(k+1)}} - \Advs{\Uc^{m,(k)}}\right] \\
      &+ \delta t_m\left[\Rbs{\Uc^{m+1,(k+1)}} - \Rbs{\Uc^{m+1,(k)}}\right]\\
      &+ \int_{t^m}^{t^{m+1}}\Advs{\Uc^{(k)}} + \Rbs{\Uc^{(k)}}d\tau.
-   \end{align*}
 
 Solving this requires a nonlinear solve of:
 
@@ -76,11 +74,9 @@ define ${\bf C}$ for convenience as:
 
 .. math::
 
-   \begin{align}
    {\bf C} &= \left [ {\Advs{\Uc}}^{m,(k+1)} - {\Advs{\Uc}}^{m,(k)} \right ]
                   -  {\Rbs{\Uc}}^{{m+1},(k)}  \nonumber \\
-               &+ \frac{1}{\delta t_m} \int_{t^m}^{t^{m+1}} \left  ( {\Advs{\Uc}}^{(k)} + {\Rbs{\Uc}}^{(k)}\right ) d\tau
-   \end{align}
+           &+ \frac{1}{\delta t_m} \int_{t^m}^{t^{m+1}} \left  ( {\Advs{\Uc}}^{(k)} + {\Rbs{\Uc}}^{(k)}\right ) d\tau
 
 This can be cast as an ODE system as: