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I am trying to solve the three coupled PDEs;

$\frac{\partial{Q}}{\partial{t}} = -RaPra^2\theta - Pra^2Q + Pr\frac{\partial^2{Q}}{\partial{z}^2}, \ \ \ \ \ \ \ \ \ (1)$

$\frac{\partial{\theta}}{\partial{t}} = w - a^2\theta + \frac{\partial^2{\theta}}{\partial{z}^2}, \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ (2)$

$ Q = -a^2w + \frac{\partial^2{w}}{\partial{z}^2}, \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ \ (3)$

where $Ra, Pr, a$ are constants. I want a method which is second order accurate in both time and space. I tried using the Crank-Nicolson scheme for the first two equations;

$\frac{Q^{n+1} - Q^n}{\Delta{t}} = \frac{1}{2}(F^{n+1} + F^n)$

$\frac{\theta^{n+1} - \theta^n}{\Delta{t}} = \frac{1}{2}(G^{n+1} + G^n)$,

and a centered space finite difference scheme for the third equaiton - $F$ and $G$ are the right hand sides of Eq.1 and Eq.2 respectively. My problem is that when using the Crank-Nicolson scheme I do not know $\theta^{n+1}$ or $Q^{n+1}$ and therefore $w^{n+1}$. So far, I have just used;

$\frac{Q^{n+1} - Q^n}{\Delta{t}}= -RaPra^2\theta^n + \frac{1}{2}(H^{n+1} + H^n),$

$\frac{\theta^{n+1} - \theta^n}{\Delta{t}} = w^n + \frac{1}{2}(K^{n+1} + K^n)$,

which isn't fully second order in time. I had an idea that was to solve these equations using the scheme above. Then use RK2 or a similar predictor-corrector method where the above scheme is my predictor. Does this make sense? What scheme can I use to solve these equations which will be accurate to second order in space and time?

I am similar with finite difference methods and Runge-Kutta methods so anything involving these would be the best.

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I think your problem arises from the fact that after space discretization, you obtain a differential-algebraic system of equations (DAEs) instead of a system of ordinary differential equations (ODEs).

In a standard method of lines approach we discretize in space first (using centered finite differences as you mentioned). We define new vector-valued time-dependent functions $\boldsymbol{Q}, \boldsymbol{\theta}, \boldsymbol{w}$ with $\boldsymbol{Q}(t) = (Q_1(t),Q_2(t),\dots,Q_n(t))^{\top}$, where $Q_i(t) \simeq Q(z_i,t)$, $i = 1,2,\dots,n$, and analogous for $\boldsymbol{\theta}, \boldsymbol{w}$.

For these new functions we now obtain the DAEs \begin{eqnarray} \boldsymbol{\dot{Q}} &=& -RaPra^2 \boldsymbol{\theta} - Pra^2 \boldsymbol{Q} + Pr (\boldsymbol{\underline{A}}_Q \boldsymbol{Q} + \boldsymbol{b}_Q),\\ \boldsymbol{\dot{\theta}} &=& \boldsymbol{w} - a^2 \boldsymbol{\theta} + \boldsymbol{\underline{A}}_{\theta} \boldsymbol{\theta} + \boldsymbol{b}_{\theta},\\ \boldsymbol{Q} &=& - a^2 \boldsymbol{w} + \boldsymbol{\underline{A}}_w \boldsymbol{w} + \boldsymbol{b}_w, \end{eqnarray} with tridiagonal matrices $\boldsymbol{\underline{A}}_Q, \boldsymbol{\underline{A}}_{\theta}, \boldsymbol{\underline{A}}_w$ and with vectors $\boldsymbol{b}_Q, \boldsymbol{b}_{\theta}, \boldsymbol{b}_w$ which arise from the centered finite differences and from the boundary conditions on $Q, \theta, w$.

These are not ODEs because the time derivative of $\boldsymbol{w}$ is missing. However, because the third equation is linear, I would suggest to eliminate $\boldsymbol{w} = (\boldsymbol{\underline{A}}_w - a^2 \boldsymbol{\underline{I}})^{-1}(\boldsymbol{Q} - \boldsymbol{b}_w)$ using the third equation ($\boldsymbol{\underline{I}}$ denoting the identity matrix) and plug into the second equation to obtain an actual (linear) system of ODEs for $\boldsymbol{Q}$ and $\boldsymbol{\theta}$ only: \begin{eqnarray} \boldsymbol{\dot{Q}} &=& -RaPra^2 \boldsymbol{\theta} - Pra^2 \boldsymbol{Q} + Pr (\boldsymbol{\underline{A}}_Q \boldsymbol{Q} + \boldsymbol{b}_Q),\\ \boldsymbol{\dot{\theta}} &=& (\boldsymbol{\underline{A}}_w - a^2 \boldsymbol{\underline{I}})^{-1}(\boldsymbol{Q} - \boldsymbol{b}_w) - a^2 \boldsymbol{\theta} + \boldsymbol{\underline{A}}_{\theta} \boldsymbol{\theta} + \boldsymbol{b}_{\theta}. \end{eqnarray} You can now use your favorite Runge-Kutta method to solve the system of ODEs for $\boldsymbol{Q}, \boldsymbol{\theta}$.

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