Numerical implementation of boundary conditions

We adopt a mixed approach for implementing boundary conditions that uses both halo regions and "direct" imposition of boundary conditions, depending on the condition prescribed.

We illustrate how boundary conditions are implemented by considering the tracer equation

\begin{align} \partial_t c = - \boldsymbol{v} \boldsymbol{\cdot} \boldsymbol{\nabla} c - \boldsymbol{\nabla} \boldsymbol{\cdot} \boldsymbol{q}_c + F_c \, , \label{eq:tracer} \end{align}

where $\boldsymbol{q}_c$ is the diffusive flux of $c$ and $F_c$ is an arbitrary source term.

See Model setup: boundary conditions for how to create and use these boundary conditions in Oceananigans.

Users impose gradient boundary conditions by prescribing the gradient $\gamma$ of a field $c$ across an external boundary $\partial \Omega_b$. The prescribed gradient $\gamma$ may be a constant, discrete array of values, or an arbitrary function. The gradient boundary condition is enforced setting the value of halo points located outside the domain interior such that

$$$$$\label{eq:gradient-bc} \hat{\boldsymbol{n}} \boldsymbol{\cdot} \boldsymbol{\nabla} c |_{\partial \Omega_b} = \gamma \, .$$$$$

where $\hat{\boldsymbol{n}}$ is the vector normal to $\partial \Omega_b$.

Across the bottom boundary in $z$, for example, this requires that

$$$$$\label{eq:linear-extrapolation} c_{i, j, 0} = c_{i, j, 1} + \gamma_{i, j, 1} \tfrac{1}{2} \left ( \Delta z_{i, j, 1} + \Delta z_{i, j, 0} \right ) \, ,$$$$$

where $\Delta z_{i, j, 1} = \Delta z_{i, j, 0}$ are the heights of the finite volume at $i, j$ and $k=1$ and $k=0$. This prescription implies that the $z$-derivative of $c$ across the boundary at $k=1$ is

$$$$$\partial_z c \, |_{i, j, 1} \equiv \frac{c_{i, j, 1} - c_{i, j, 0}}{\tfrac{1}{2} \left ( \Delta z_{i, j, 1} + \Delta z_{i, j, 0} \right )} = \gamma_{i, j, 1} \, ,$$$$$

as prescribed by the user.

Gradient boundary conditions are represented by the Gradient type.

Value boundary conditions

Users impose value boundary conditions by prescribing $c^b$, the value of $c$ on the external boundary $\partial \Omega_b$. The value $c^b$ may be a constant, array of discrete values, or an arbitrary function. To enforce a value boundary condition, the gradient associated with the difference between $c^b$ and $c$ at boundary-adjacent nodes is diagnosed and used to set the value of the $c$ halo point located outside the boundary.

At the bottom boundary in $z$, for example, this means that the gradient of $c$ is determined by

$$$$$\gamma = \frac{c_{i, j, 1} - c^b_{i, j, 1}}{\tfrac{1}{2} \Delta z_{i, j, 1}} \, ,$$$$$

which is then used to set the halo point $c_{i, j, 0}$ via linear extrapolation.

Value boundary conditions are represented by the Value type.

Flux boundary conditions

Users impose flux boundary conditions by prescribing the flux $q_c \, |_b$ of $c$ across the external boundary $\partial \Omega_b$. The flux $q_c \, |_b$ may be a constant, array of discrete values, or arbitrary function. To explain how flux boundary conditions are imposed in Oceananigans.jl, we note that the average of the tracer conservation equation over a finite volume yields

$$$$$\label{eq:dc/dt} \partial_t c_{i, j, k} = - \frac{1}{V_{i, j, k}} \oint_{\partial \Omega_{i, j, k}} (\boldsymbol{v} c + \boldsymbol{q}_c) \boldsymbol{\cdot} \hat{\boldsymbol{n}} \, \mathrm{d} S + \frac{1}{V_{i, j, k}} \int_{V_{i, j, k}} F_c \, \mathrm{d} V \, ,$$$$$

where the surface integral over $\partial \Omega_{i, j, k}$ averages the flux of $c$ across the six faces of the finite volume. The right-hand-side of \eqref{eq:dc/dt} above is denoted as $G_c |_{i, j, k}$.

An external boundary of a finite volume is associated with a no-penetration condition such that $\hat{\boldsymbol{n}} \boldsymbol{\cdot} \boldsymbol{v} \, |_{\partial \Omega_b} = 0$, where $\hat{\boldsymbol{n}}$ is the vector normal to $\partial \Omega_b$. Furthermore, the closures currently available in Oceananigans.jl have the property that $\boldsymbol{q}_c \propto \boldsymbol{\nabla} c$. Thus setting $\hat{\boldsymbol{n}} \boldsymbol{\cdot} \boldsymbol{\nabla} c \, |_{\partial \Omega_b} = 0$ on the external boundary implies that the total flux of $c$ across the external boundary is

$$$$$\hat{\boldsymbol{n}} \boldsymbol{\cdot} \left ( \boldsymbol{v} c + \boldsymbol{q}_c \right ) |_{\partial \Omega_b} = 0 \, .$$$$$

Oceananigans.jl exploits this fact to define algorithm that prescribe fluxes across external boundaries $\partial \Omega_b$:

1. Impose a constant gradient $\hat{\boldsymbol{n}} \boldsymbol{\cdot} \boldsymbol{\nabla} c \, |_{\partial \Omega_b} = 0$ across external boundaries via using halo points (similar to \eqref{eq:gradient-bc}), which ensures that the evaluation of $G_c$ in boundary-adjacent cells does not include fluxes across the external boundary, and;

2. Add the prescribed flux to the boundary-adjacent volumes prior to calculating $G_c$: $G_c \, |_b = G_c \, |_b - \frac{A_b}{V_b} q_c \, |_b \, \text{sign}(\hat{\boldsymbol{n}})$, where $G_c \, |_b$ denotes values of $G_c$ in boundary-adjacent volumes, $q_c \, |_b$ is the flux prescribed along the boundary, $V_b$ is the volume of the boundary-adjacent cell, and $A_b$ is the area of the external boundary of the boundary-adjacent cell.

The factor $\text{sign}(\hat{\boldsymbol{n}})$ is $-$1 and $+$1 on "left" and "right" boundaries, and accounts for the fact that a positive flux on a left boundary where $\text{sign}(\hat{\boldsymbol{n}}) = -1$ implies an "inward" flux of $c$ that increases interior values of $c$, whereas a positive flux on a right boundary where $\text{sign}(\hat{\boldsymbol{n}}) = 1$ implies an "outward" flux that decreases interior values of $c$.

Flux boundary conditions are represented by the Flux type.