$$ \newcommand{\uex}{{u_{\small\mbox{e}}}} \newcommand{\half}{\frac{1}{2}} \newcommand{\halfi}{{1/2}} \newcommand{\xpoint}{\boldsymbol{x}} \newcommand{\normalvec}{\boldsymbol{n}} \newcommand{\Oof}[1]{\mathcal{O}(#1)} \newcommand{\Ix}{\mathcal{I}_x} \newcommand{\Iy}{\mathcal{I}_y} \newcommand{\It}{\mathcal{I}_t} \newcommand{\setb}[1]{#1^0} % set begin \newcommand{\sete}[1]{#1^{-1}} % set end \newcommand{\setl}[1]{#1^-} \newcommand{\setr}[1]{#1^+} \newcommand{\seti}[1]{#1^i} \newcommand{\Real}{\mathbb{R}} $$

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Scalar computations: primary stencil

def advance_scalar(u, u_1, u_2, f, x, y, t, n, Cx2, Cy2, dt2,
                   V=None, step1=False):
    Ix = range(0, u.shape[0]);  Iy = range(0, u.shape[1])
    if step1:
        dt = sqrt(dt2)  # save
        Cx2 = 0.5*Cx2;  Cy2 = 0.5*Cy2; dt2 = 0.5*dt2  # redefine
        D1 = 1;  D2 = 0
    else:
        D1 = 2;  D2 = 1
    for i in Ix[1:-1]:
        for j in Iy[1:-1]:
            u_xx = u_1[i-1,j] - 2*u_1[i,j] + u_1[i+1,j]
            u_yy = u_1[i,j-1] - 2*u_1[i,j] + u_1[i,j+1]
            u[i,j] = D1*u_1[i,j] - D2*u_2[i,j] + \ 
                     Cx2*u_xx + Cy2*u_yy + dt2*f(x[i], y[j], t[n])
            if step1:
                u[i,j] += dt*V(x[i], y[j])
    # Boundary condition u=0
    j = Iy[0]
    for i in Ix: u[i,j] = 0
    j = Iy[-1]
    for i in Ix: u[i,j] = 0
    i = Ix[0]
    for j in Iy: u[i,j] = 0
    i = Ix[-1]
    for j in Iy: u[i,j] = 0
    return u

D1 and D2: allow advance_scalar to be used also for \( u^1_{i,j} \):

u = advance_scalar(u, u_1, u_2, f, x, y, t,
                   n, 0.5*Cx2, 0.5*Cy2, 0.5*dt2, D1=1, D2=0)

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