Given a partial differential equation
$\partial_t u(t,x) = F(t,x,u,u')$
Suppose I know the functions $u(t_0,x)$ and $u'(t_0,x)$ at some point $t_0$ for all $x$. In order to obtain the function $u$ at the next time step $t_0 + \Delta t$, I may use the Runge Kutta method. However, within Runge Kutta method, expressions of the form $F(t_0 + \Delta t, x, u + \Delta t \cdot g, ...)$ must be calculated. My question now is, if this "shift" of the function $u$ is carried out before differentiating with respect to $x$ or after.
In detail, does the expression look like this
$F\Big( t_0 + \Delta t, x, u + \Delta t \cdot g, \partial_x u + \Delta t \cdot g \Big)$
or like this
$F\Big( t_0 + \Delta t, x, u + \Delta t \cdot g, \partial_x (u + \Delta t \cdot g) \Big) = F\Big(t_0 + \Delta t, x, u + \Delta t \cdot g, \partial_x u \Big)$
RK is really an ODE time stepping method, so to use it to solve a dynamic PDE, you should first convert to an ODE by spatial discretization. So for example in 1 space dimension you might do finite differences as $u(t,x) = u^j_i$ with $t=j\Delta t,x=i\Delta x$ and $u_x(t,x) \approx (\partial_x u)^j_i := \frac{u^j_{i+1}-u^j_{i-1}}{2\Delta x}$ (centered space differences). Then far enough away from the boundary you can take $F(t,x,u,u') \approx F^j_i:=F(j\Delta t,i\Delta x,u^j_i,(\partial_x u)^j_i)$. Then when you adjust $u$ you must also adjust the spatial derivative accordingly.