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-revision 1.7 by cnh,
Wed Oct 24 23:14:44 2001 UTC
+revision 1.22 by jmc,
Wed Jun 28 17:01:34 2006 UTC
 Line 2
  % $Name$
  \section{Tracer equations}
- \label{sec:tracer_equations}
+ \label{sect:tracer_equations}
+ \begin{rawhtml}
+ <!-- CMIREDIR:tracer_equations: -->
+ \end{rawhtml}
  The basic discretization used for the tracer equations is the second
  order piece-wise constant finite volume form of the forced
- advection-diussion equations. There are many alternatives to second
+ advection-diffusion equations. There are many alternatives to second
  order method for advection and alternative parameterizations for the
  sub-grid scale processes. The Gent-McWilliams eddy parameterization,
  KPP mixing scheme and PV flux parameterization are all dealt with in
-Line 15 
 part of the tracer equations and the var
+Line 18 
 part of the tracer equations and the var
  described here.
  \subsection{Time-stepping of tracers: ABII}
- \label{sec:tracer_equations_abII}
+ \label{sect:tracer_equations_abII}
+ \begin{rawhtml}
+ <!-- CMIREDIR:tracer_equations_abII: -->
+ \end{rawhtml}
  The default advection scheme is the centered second order method which
  requires a second order or quasi-second order time-stepping scheme to
-Line 43 
 only affects the surface layer since the
+Line 49 
 only affects the surface layer since the
  everywhere else. This term is therefore referred to as the surface
  correction term. Global conservation is not possible using the
  flux-form (as here) and a linearized free-surface
- (\cite{Griffies00,Campin02}).
+ (\cite{griffies:00,campin:02}).
  The continuity equation can be recovered by setting
  $G_{diff}=G_{forc}=0$ and $\tau=1$.
- The driver routine that calls the routines to calculate tendancies are
+ The driver routine that calls the routines to calculate tendencies are
  {\em S/R CALC\_GT} and {\em S/R CALC\_GS} for temperature and salt
  (moisture), respectively. These in turn call a generic advection
  diffusion routine {\em S/R GAD\_CALC\_RHS} that is called with the
- flow field and relevent tracer as arguments and returns the collective
+ flow field and relevant tracer as arguments and returns the collective
- tendancy due to advection and diffusion. Forcing is add subsequently
+ tendency due to advection and diffusion. Forcing is add subsequently
- in {\em S/R CALC\_GT} or {\em S/R CALC\_GS} to the same tendancy
+ in {\em S/R CALC\_GT} or {\em S/R CALC\_GS} to the same tendency
  array.
  \fbox{ \begin{minipage}{4.75in}
-Line 68 
 $F_r$: {\bf fVerT} (argument)
+Line 74 
 $F_r$: {\bf fVerT} (argument)
  \end{minipage} }
- The space and time discretizations are treated seperately (method of
+ The space and time discretization are treated separately (method of
- lines). Tendancies are calculated at time levels $n$ and $n-1$ and
+ lines). Tendencies are calculated at time levels $n$ and $n-1$ and
  extrapolated to $n+1/2$ using the Adams-Bashforth method:
  \marginpar{$\epsilon$: {\bf AB\_eps}}
  \begin{equation}
-Line 77 
 G^{(n+1/2)} =
+Line 83 
 G^{(n+1/2)} =
  (\frac{3}{2} + \epsilon) G^{(n)} - (\frac{1}{2} + \epsilon) G^{(n-1)}
  \end{equation}
  where $G^{(n)} = G_{adv}^\tau + G_{diff}^\tau + G_{src}^\tau$ at time
- step $n$. The tendancy at $n-1$ is not re-calculated but rather the
+ step $n$. The tendency at $n-1$ is not re-calculated but rather the
- tendancy at $n$ is stored in a global array for later re-use.
+ tendency at $n$ is stored in a global array for later re-use.
  \fbox{ \begin{minipage}{4.75in}
  {\em S/R ADAMS\_BASHFORTH2} ({\em model/src/adams\_bashforth2.F})
-Line 93 
 $\epsilon$: {\bf ABeps} (PARAMS.h)
+Line 99 
 $\epsilon$: {\bf ABeps} (PARAMS.h)
  \end{minipage} }
- The tracers are stepped forward in time using the extrapolated tendancy:
+ The tracers are stepped forward in time using the extrapolated tendency:
  \begin{equation}
  \tau^{(n+1)} = \tau^{(n)} + \Delta t G^{(n+1/2)}
  \end{equation}
-Line 113 
 $\Delta t$: {\bf deltaTtracer} (PARAMS.h
+Line 119 
 $\Delta t$: {\bf deltaTtracer} (PARAMS.h
  \end{minipage} }
  Strictly speaking the ABII scheme should be applied only to the
- advection terms. However, this scheme is only used in conjuction with
+ advection terms. However, this scheme is only used in conjunction with
  the standard second, third and fourth order advection
  schemes. Selection of any other advection scheme disables
  Adams-Bashforth for tracers so that explicit diffusion and forcing use
-Line 123 
 the forward method.
+Line 129 
 the forward method.
  \section{Linear advection schemes}
+ \label{sect:tracer-advection}
+ \begin{rawhtml}
+ <!-- CMIREDIR:linear_advection_schemes: -->
+ \end{rawhtml}
  \begin{figure}
  \resizebox{5.5in}{!}{\includegraphics{part2/advect-1d-lo.eps}}
-Line 171 
 commonly used in the field and most fami
+Line 181 
 commonly used in the field and most fami
  \subsection{Centered second order advection-diffusion}
  The basic discretization, centered second order, is the default. It is
- designed to be consistant with the continuity equation to facilitate
+ designed to be consistent with the continuity equation to facilitate
  conservation properties analogous to the continuum. However, centered
- second order advection is notoriously noisey and must be used in
+ second order advection is notoriously noisy and must be used in
- conjuction with some finite amount of diffusion to produce a sensible
+ conjunction with some finite amount of diffusion to produce a sensible
  solution.
  The advection operator is discretized:
-Line 200 
 W & = & {\cal A}_c w
+Line 210 
 W & = & {\cal A}_c w
  For non-divergent flow, this discretization can be shown to conserve
  the tracer both locally and globally and to globally conserve tracer
- variance, $\tau^2$. The proof is given in \cite{Adcroft95,Adcroft97}.
+ variance, $\tau^2$. The proof is given in \cite{adcroft:95,adcroft:97}.
  \fbox{ \begin{minipage}{4.75in}
  {\em S/R GAD\_C2\_ADV\_X} ({\em gad\_c2\_adv\_x.F})
-Line 248 
 F_r & = & W \overline{\tau - \frac{1}{6}
+Line 258 
 F_r & = & W \overline{\tau - \frac{1}{6}
  \end{eqnarray}
  At boundaries, $\delta_{\hat{n}} \tau$ is set to zero allowing
- $\delta_{nn}$ to be evaluated. We are currently examing the accuracy
+ $\delta_{nn}$ to be evaluated. We are currently examine the accuracy
  of this boundary condition and the effect on the solution.
  \fbox{ \begin{minipage}{4.75in}
-Line 282 
 $\tau$: {\bf tracer} (argument)
+Line 292 
 $\tau$: {\bf tracer} (argument)
  Centered fourth order advection is formally the most accurate scheme
  we have implemented and can be used to great effect in high resolution
- simultation where dynamical scales are well resolved. However, the
+ simulation where dynamical scales are well resolved. However, the
- scheme is noisey like the centered second order method and so must be
+ scheme is noisy like the centered second order method and so must be
  used with some finite amount of diffusion. Bi-harmonic is recommended
  since it is more scale selective and less likely to diffuse away the
  well resolved gradient the fourth order scheme worked so hard to
-Line 297 
 F_r & = & W \overline{\tau - \frac{1}{6}
+Line 307 
 F_r & = & W \overline{\tau - \frac{1}{6}
  \end{eqnarray}
  As for the third order scheme, the best discretization near boundaries
- is under investigation but currenlty $\delta_i \tau=0$ on a boundary.
+ is under investigation but currently $\delta_i \tau=0$ on a boundary.
  \fbox{ \begin{minipage}{4.75in}
  {\em S/R GAD\_C4\_ADV\_X} ({\em gad\_c4\_adv\_x.F})
-Line 349 
 if the limiter is set to zero.
+Line 359 
 if the limiter is set to zero.
  \section{Non-linear advection schemes}
+ \begin{rawhtml}
+ <!-- CMIREDIR:non-linear_advection_schemes: -->
+ \end{rawhtml}
  Non-linear advection schemes invoke non-linear interpolation and are
  widely used in computational fluid dynamics (non-linear does not refer
-Line 387 
 r = \frac{ \tau_{i-1} - \tau_{i-2} }{ \t
+Line 400 
 r = \frac{ \tau_{i-1} - \tau_{i-2} }{ \t
  r = \frac{ \tau_{i+1} - \tau_{i} }{ \tau_{i} - \tau_{i-1} } & \forall & u < 0
  \end{eqnarray}
  as it's argument. There are many choices of limiter function but we
- only provide the Superbee limiter \cite{Roe85}:
+ only provide the Superbee limiter \cite{roe:85}:
  \begin{equation}
  \psi(r) = \max[0,\min[1,2r],\min[2,r]]
  \end{equation}
-Line 423 
 $\tau$: {\bf tracer} (argument)
+Line 436 
 $\tau$: {\bf tracer} (argument)
  \subsection{Third order direct space time}
  The direct-space-time method deals with space and time discretization
- together (other methods that treat space and time seperately are known
+ together (other methods that treat space and time separately are known
  collectively as the ``Method of Lines''). The Lax-Wendroff scheme
  falls into this category; it adds sufficient diffusion to a second
  order flux that the forward-in-time method is stable. The upwind
-Line 441 
 where
+Line 454 
 where
  d_1 & = & \frac{1}{6} ( 2 - |c| ) ( 1 - |c| ) \\
  d_2 & = & \frac{1}{6} ( 1 - |c| ) ( 1 + |c| )
  \end{eqnarray}
- The coefficients $d_0$ and $d_1$ approach $1/3$ and $1/6$ repectively
+ The coefficients $d_0$ and $d_1$ approach $1/3$ and $1/6$ respectively
  as the Courant number, $c$, vanishes. In this limit, the conventional
  third order upwind method is recovered. For finite Courant number, the
  deviations from the linear method are analogous to the diffusion added
-Line 449 
 to centered second order advection in th
+Line 462 
 to centered second order advection in th
  The DST3 method described above must be used in a forward-in-time
  manner and is stable for $0 \le |c| \le 1$. Although the scheme
- appears to be forward-in-time, it is in fact second order in time and
+ appears to be forward-in-time, it is in fact third order in time and
  the accuracy increases with the Courant number! For low Courant
  number, DST3 produces very similar results (indistinguishable in
  Fig.~\ref{fig:advect-1d-lo}) to the linear third order method but for
-Line 539 
 $\tau$: {\bf tracer} (argument)
+Line 552 
 $\tau$: {\bf tracer} (argument)
  \resizebox{5.5in}{!}{\includegraphics{part2/advect-2d-lo-diag.eps}}
  \caption{
  Comparison of advection schemes in two dimensions; diagonal advection
- of a resolved Guassian feature. Courant number is 0.01 with
+ of a resolved Gaussian feature. Courant number is 0.01 with
 $\times$30 points and solutions are shown for T=1/2. White lines
  indicate zero crossing (ie. the presence of false minima).  The left
  column shows the second order schemes; top) centered second order with
-Line 550 
 space-time method and bottom) the same w
+Line 563 
 space-time method and bottom) the same w
  right panel shows the centered fourth order scheme with
  Adams-Bashforth and right middle panel shows a fourth order variant on
  the DST method. Bottom right panel shows the Superbee flux limiter
- (second order) applied independantly in each direction (method of
+ (second order) applied independently in each direction (method of
  lines).
  \label{fig:advect-2d-lo-diag}
  }
-Line 560 
 lines).
+Line 573 
 lines).
  \resizebox{5.5in}{!}{\includegraphics{part2/advect-2d-mid-diag.eps}}
  \caption{
  Comparison of advection schemes in two dimensions; diagonal advection
- of a resolved Guassian feature. Courant number is 0.27 with
+ of a resolved Gaussian feature. Courant number is 0.27 with
 $\times$30 points and solutions are shown for T=1/2. White lines
  indicate zero crossing (ie. the presence of false minima).  The left
  column shows the second order schemes; top) centered second order with
-Line 571 
 space-time method and bottom) the same w
+Line 584 
 space-time method and bottom) the same w
  right panel shows the centered fourth order scheme with
  Adams-Bashforth and right middle panel shows a fourth order variant on
  the DST method. Bottom right panel shows the Superbee flux limiter
- (second order) applied independantly in each direction (method of
+ (second order) applied independently in each direction (method of
  lines).
  \label{fig:advect-2d-mid-diag}
  }
-Line 581 
 lines).
+Line 594 
 lines).
  \resizebox{5.5in}{!}{\includegraphics{part2/advect-2d-hi-diag.eps}}
  \caption{
  Comparison of advection schemes in two dimensions; diagonal advection
- of a resolved Guassian feature. Courant number is 0.47 with
+ of a resolved Gaussian feature. Courant number is 0.47 with
 $\times$30 points and solutions are shown for T=1/2. White lines
  indicate zero crossings and initial maximum values (ie. the presence
  of false extrema).  The left column shows the second order schemes;
-Line 592 
 middle) third order direct space-time me
+Line 605 
 middle) third order direct space-time me
  flux limiting. The top right panel shows the centered fourth order
  scheme with Adams-Bashforth and right middle panel shows a fourth
  order variant on the DST method. Bottom right panel shows the Superbee
- flux limiter (second order) applied independantly in each direction
+ flux limiter (second order) applied independently in each direction
  (method of lines).
  \label{fig:advect-2d-hi-diag}
  }
-Line 600 
 flux limiter (second order) applied inde
+Line 613 
 flux limiter (second order) applied inde
- In many of the aforementioned advection schemes the behaviour in
+ In many of the aforementioned advection schemes the behavior in
  multiple dimensions is not necessarily as good as the one dimensional
- behaviour. For instance, a shape preserving monotonic scheme in one
+ behavior. For instance, a shape preserving monotonic scheme in one
  dimension can have severe shape distortion in two dimensions if the
  two components of horizontal fluxes are treated independently. There
  is a large body of literature on the subject dealing with this problem
-Line 614 
 as if in one dimension:
+Line 627 
 as if in one dimension:
  \tau^{n+1/3} & = & \tau^{n}
  - \Delta t \left( \frac{1}{\Delta x} \delta_i F^x(\tau^{n})
             + \tau^{n} \frac{1}{\Delta x} \delta_i u \right) \\
- \tau^{n+2/3} & = & \tau^{n}
+ \tau^{n+2/3} & = & \tau^{n+1/3}
  - \Delta t \left( \frac{1}{\Delta y} \delta_j F^y(\tau^{n+1/3})
             + \tau^{n} \frac{1}{\Delta y} \delta_i v \right) \\
- \tau^{n+3/3} & = & \tau^{n}
+ \tau^{n+3/3} & = & \tau^{n+2/3}
  - \Delta t \left( \frac{1}{\Delta r} \delta_k F^x(\tau^{n+2/3})
             + \tau^{n} \frac{1}{\Delta r} \delta_i w \right)
  \end{eqnarray}
  In order to incorporate this method into the general model algorithm,
- we compute the effective tendancy rather than update the tracer so
+ we compute the effective tendency rather than update the tracer so
  that other terms such as diffusion are using the $n$ time-level and
  not the updated $n+3/3$ quantities:
  \begin{equation}
-Line 653 
 $W$: {\bf rTrans} (local)
+Line 666 
 $W$: {\bf rTrans} (local)
  \section{Comparison of advection schemes}
+ \label{sect:tracer_advection_schemes}
+ \begin{rawhtml}
+ <!-- CMIREDIR:comparison_of_advection_schemes: -->
+ \end{rawhtml}
+ \begin{table}[htb]
+ \centering
+  \begin{tabular}[htb]{|l|c|c|c|c|l|}
+    \hline
+    Advection Scheme & code & use  & use Multi- & Stencil & comments \\
+                     &      & A.B. & dimension & (1 dim) & \\
+    \hline \hline
+    $1^{rst}$order upwind  & 1 &  No & Yes & 3 pts & linear/$\tau$, non-linear/v\\
+    \hline
+    centered $2^{nd}$order & 2 &  Yes & No & 3 pts & linear \\
+    \hline
+    $3^{rd}$order upwind   & 3 &  Yes & No & 5 pts & linear/$\tau$\\
+    \hline
+    centered $4^{th}$order & 4 &  Yes & No & 5 pts & linear \\
+    \hline \hline
+    $2^{nd}$order DST (Lax-Wendroff)  & 20 &
+                          No & Yes & 3 pts & linear/$\tau$, non-linear/v\\
+    \hline
+    $3^{rd}$order DST & 30 &  No & Yes & 5 pts & linear/$\tau$, non-linear/v\\
+    \hline \hline
+    $2^{nd}$order Flux Limiters & 77 &  No & Yes & 5 pts & non-linear \\
+    \hline
+    $3^{nd}$order DST Flux limiter & 33 &  No & Yes & 5 pts & non-linear \\
+    \hline
+  \end{tabular}
+  \caption{Summary of the different advection schemes available in MITgcm.
+           ``A.B.'' stands for Adams-Bashforth and ``DST'' for direct space time.
+           The code corresponds to the number used to select the corresponding
+           advection scheme in the parameter file (e.g., {\bf tempAdvScheme}=3 in
+           file {\em data} selects the $3^{rd}$ order upwind advection scheme
+           for temperature).
+    }
+  \label{tab:advectionShemes_summary}
+ \end{table}
  Figs.~\ref{fig:advect-2d-lo-diag}, \ref{fig:advect-2d-mid-diag} and
  \ref{fig:advect-2d-hi-diag} show solutions to a simple diagonal
-Line 669 
 stable at high Courant number where the
+Line 722 
 stable at high Courant number where the
  bottom row (left and middle) shows the limited schemes and most
  obvious is the absence of false extrema. The accuracy and stability of
  the unlimited non-linear schemes is retained at high Courant number
- but at low Courant number the tendancy is to loose amplitude in sharp
+ but at low Courant number the tendency is to loose amplitude in sharp
  peaks due to diffusion. The one dimensional tests shown in
  Figs.~\ref{fig:advect-1d-lo} and \ref{fig:advect-1d-hi} showed this
- phenomenum.
+ phenomenon.
  Finally, the bottom left and right panels use the same advection
- scheme but the right does not use the mutli-dimensional method. At low
+ scheme but the right does not use the multi-dimensional method. At low
  Courant number this appears to not matter but for moderate Courant
- number severe distortion of the feature is apparent. Moreoever, the
+ number severe distortion of the feature is apparent. Moreover, the
  stability of the multi-dimensional scheme is determined by the maximum
  Courant number applied of each dimension while the stability of the
  method of lines is determined by the sum. Hence, in the high Courant
-Line 698 
 introduce more noise. In this case, simp
+Line 751 
 introduce more noise. In this case, simp
  scheme will give a more accurate solution but scale-selective
  diffusion might need to be employed. The flux limited methods
  offer similar accuracy in this regime.
- \item If your solution has shocks or propagatin fronts then a
+ \item If your solution has shocks or propagating fronts then a
  flux limited scheme is almost essential.
  \item If your time-step is limited by advection, the multi-dimensional
- non-linear schemes have the most stablility (upto Courant number 1).
+ non-linear schemes have the most stability (up to Courant number 1).
- \item If you need to know how much diffusion/dissipation has occured you
+ \item If you need to know how much diffusion/dissipation has occurred you
  will have a lot of trouble figuring it out with a non-linear method.
- \item The presence of false extrema is unphysical and this alone is the
+ \item The presence of false extrema is non-physical and this alone is the
  strongest argument for using a positive scheme.
  \end{itemize}

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