/[MITgcm]/manual/s_algorithm/text/time_stepping.tex

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-revision 1.15 by cnh,
Thu Feb 28 19:32:19 2002 UTC
+revision 1.23 by edhill,
Tue Jun 27 22:29:56 2006 UTC
 Line 10 
 describe the spatial discretization. The
  terms are described first, afterwards the schemes that apply to
  passive and dynamically active tracers are described.
+ \input{part2/notation}
  \section{Time-stepping}
+ \begin{rawhtml}
+ <!-- CMIREDIR:time-stepping: -->
+ \end{rawhtml}
  The equations of motion integrated by the model involve four
  prognostic equations for flow, $u$ and $v$, temperature, $\theta$, and
  salt/moisture, $S$, and three diagnostic equations for vertical flow,
-Line 61 
 treated more exactly, including non-line
+Line 66 
 treated more exactly, including non-line
  described in section \ref{sect:nonlinear-freesurface}.
- \section{Pressure method with rigid-lid} \label{sect:pressure-method-rigid-lid}
+ \section{Pressure method with rigid-lid}
+ \label{sect:pressure-method-rigid-lid}
+ \begin{rawhtml}
+ <!-- CMIREDIR:pressure_method_rigid_lid: -->
+ \end{rawhtml}
  \begin{figure}
  \begin{center}
-Line 81 
 temporary.}
+Line 90 
 temporary.}
  \begin{figure}
  \begin{center} \fbox{ \begin{minipage}{4.5in} \begin{tabbing}
  aaa \= aaa \= aaa \= aaa \= aaa \= aaa \kill
- \proclink{FORWARD\_STEP}{../code/._model_src_forward_step.F} \\
+ \filelink{FORWARD\_STEP}{model-src-forward_step.F} \\
  \> DYNAMICS \\
  \>\> TIMESTEP \` $u^*$,$v^*$ (\ref{eq:ustar-rigid-lid},\ref{eq:vstar-rigid-lid}) \\
  \> SOLVE\_FOR\_PRESSURE \\
  \>\> CALC\_DIV\_GHAT \` $H\widehat{u^*}$,$H\widehat{v^*}$ (\ref{eq:elliptic}) \\
  \>\> CG2D \` $\eta^{n+1}$ (\ref{eq:elliptic}) \\
- \> THE\_CORRECTION\_STEP  \\
+ \> MOMENTUM\_CORRECTION\_STEP  \\
  \>\> CALC\_GRAD\_PHI\_SURF \` $\nabla \eta^{n+1}$ \\
  \>\> CORRECTION\_STEP \` $u^{n+1}$,$v^{n+1}$ (\ref{eq:un+1-rigid-lid},\ref{eq:vn+1-rigid-lid})
  \end{tabbing} \end{minipage} } \end{center}
- \caption{Calling tree for the pressure method algorihtm}
+ \caption{Calling tree for the pressure method algorithm
+   (\filelink{FORWARD\_STEP}{model-src-forward_step.F})}
  \label{fig:call-tree-pressure-method}
  \end{figure}
-Line 173 
 The correspondence to the code is as fol
+Line 183 
 The correspondence to the code is as fol
  \item
  the prognostic phase, equations \ref{eq:ustar-rigid-lid} and \ref{eq:vstar-rigid-lid},
  stepping forward $u^n$ and $v^n$ to $u^{*}$ and $v^{*}$ is coded in
- \proclink{TIMESTEP}{../code/._model_src_timestep.F}
+ \filelink{TIMESTEP()}{model-src-timestep.F}
  \item
  the vertical integration, $H \widehat{u^*}$ and $H
  \widehat{v^*}$, divergence and inversion of the elliptic operator in
  equation \ref{eq:elliptic} is coded in
- \proclink{SOLVE\_FOR\_PRESSURE}{../code/._model_src_solve_for_pressure.F}
+ \filelink{SOLVE\_FOR\_PRESSURE()}{model-src-solve_for_pressure.F}
  \item
  finally, the new flow field at time level $n+1$ given by equations
  \ref{eq:un+1-rigid-lid} and \ref{eq:vn+1-rigid-lid} is calculated in
- \proclink{CORRECTION\_STEP}{../code/._model_src_correction_step.F}.
+ \filelink{CORRECTION\_STEP()}{model-src-correction_step.F}.
  \end{itemize}
  The calling tree for these routines is given in
  Fig.~\ref{fig:call-tree-pressure-method}.
-Line 202 
 G_u^{(n+1/2)}
+Line 212 
 G_u^{(n+1/2)}
  \section{Pressure method with implicit linear free-surface}
  \label{sect:pressure-method-linear-backward}
+ \begin{rawhtml}
+ <!-- CMIREDIR:pressure_method_linear_backward: -->
+ \end{rawhtml}
  The rigid-lid approximation filters out external gravity waves
  subsequently modifying the dispersion relation of barotropic Rossby
-Line 213 
 The rigid-lid approximation can be easil
+Line 226 
 The rigid-lid approximation can be easil
  of the free-surface equation which can be written:
  \begin{equation}
  \partial_t \eta + \partial_x H \widehat{u} + \partial_y H \widehat{v} = P-E+R
- \label{eq:linear-free-surface=P-E+R}
+ \label{eq:linear-free-surface=P-E}
  \end{equation}
  which differs from the depth integrated continuity equation with
  rigid-lid (\ref{eq:rigid-lid-continuity}) by the time-dependent term
-Line 221 
 and fresh-water source term.
+Line 234 
 and fresh-water source term.
  Equation \ref{eq:discrete-time-cont-rigid-lid} in the rigid-lid
  pressure method is then replaced by the time discretization of
- \ref{eq:linear-free-surface=P-E+R} which is:
+ \ref{eq:linear-free-surface=P-E} which is:
  \begin{equation}
  \eta^{n+1}
  + \Delta t \partial_x H \widehat{u^{n+1}}
  + \Delta t \partial_y H \widehat{v^{n+1}}
  =
  \eta^{n}
- + \Delta t ( P - E + R )
+ + \Delta t ( P - E )
  \label{eq:discrete-time-backward-free-surface}
  \end{equation}
  where the use of flow at time level $n+1$ makes the method implicit
-Line 243 
 As for the rigid-lid pressure method, eq
+Line 256 
 As for the rigid-lid pressure method, eq
  \begin{eqnarray}
  u^{*} & = & u^{n} + \Delta t G_u^{(n+1/2)} \label{eq:ustar-backward-free-surface} \\
  v^{*} & = & v^{n} + \Delta t G_v^{(n+1/2)} \label{eq:vstar-backward-free-surface} \\
- \eta^* & = & \epsilon_{fs} \left( \eta^{n} +P-E+R \right)- \Delta t
+ \eta^* & = & \epsilon_{fs} \left( \eta^{n} + \Delta t (P-E) \right)- \Delta t
    \partial_x H \widehat{u^{*}}
  + \partial_y H \widehat{v^{*}}
  \\
    \partial_x g H \partial_x \eta^{n+1}
- + \partial_y g H \partial_y \eta^{n+1}
+ & + & \partial_y g H \partial_y \eta^{n+1}
- - \frac{\epsilon_{fs} \eta^{n+1}}{\Delta t^2}
+  - \frac{\epsilon_{fs} \eta^{n+1}}{\Delta t^2}
- & = &
+  =
  - \frac{\eta^*}{\Delta t^2}
  \label{eq:elliptic-backward-free-surface}
  \\
-Line 278 
 pressure-method.
+Line 291 
 pressure-method.
  \section{Explicit time-stepping: Adams-Bashforth}
  \label{sect:adams-bashforth}
+ \begin{rawhtml}
+ <!-- CMIREDIR:adams_bashforth: -->
+ \end{rawhtml}
  In describing the the pressure method above we deferred describing the
  time discretization of the explicit terms. We have historically used
-Line 293 
 FORWARD\_STEP \\
+Line 309 
 FORWARD\_STEP \\
  \> THERMODYNAMICS \\
  \>\> CALC\_GT \\
  \>\>\> GAD\_CALC\_RHS \` $G_\theta^n = G_\theta( u, \theta^n )$ \\
- \>\>\> EXTERNAL\_FORCING \` $G_\theta^n = G_\theta^n + {\cal Q}$ \\
+ \>either\>\> EXTERNAL\_FORCING \` $G_\theta^n = G_\theta^n + {\cal Q}$ \\
  \>\>\> ADAMS\_BASHFORTH2 \` $G_\theta^{(n+1/2)}$ (\ref{eq:adams-bashforth2}) \\
+ \>or\>\> EXTERNAL\_FORCING \` $G_\theta^{(n+1/2)} = G_\theta^{(n+1/2)} + {\cal Q}$ \\
  \>\> TIMESTEP\_TRACER \` $\tau^*$ (\ref{eq:taustar}) \\
  \>\> IMPLDIFF \` $\tau^{(n+1)}$ (\ref{eq:tau-n+1-implicit})
  \end{tabbing} \end{minipage} } \end{center}
-Line 331 
 simpler to include these terms and this
+Line 348 
 simpler to include these terms and this
  and forcing evolves smoothly. Problems can, and do, arise when forcing
  or motions are high frequency and this corresponds to a reduced
  stability compared to a simple forward time-stepping of such terms.
+ The model offers the possibility to leave the forcing term outside the
+ Adams-Bashforth extrapolation, by turning off the logical flag
+ {\bf forcing\_In\_AB } (parameter file {\em data}, namelist {\em PARM01},
+ default value = True).
  A stability analysis for an oscillation equation should be given at this point.
  \marginpar{AJA needs to find his notes on this...}
-Line 340 
 A stability analysis for a relaxation eq
+Line 361 
 A stability analysis for a relaxation eq
  \section{Implicit time-stepping: backward method}
+ \begin{rawhtml}
+ <!-- CMIREDIR:implicit_time-stepping_backward: -->
+ \end{rawhtml}
  Vertical diffusion and viscosity can be treated implicitly in time
- using the backward method which is an intrinsic scheme. For tracers,
+ using the backward method which is an intrinsic scheme.
+ Recently, the option to treat the vertical advection
+ implicitly has been added, but not yet tested; therefore,
+ the description hereafter is limited to diffusion and viscosity.
+ For tracers,
  the time discretized equation is:
  \begin{equation}
  \tau^{n+1} - \Delta t \partial_r \kappa_v \partial_r \tau^{n+1} =
-Line 373 
 Fig.~\ref{fig:call-tree-adams-bashforth}
+Line 401 
 Fig.~\ref{fig:call-tree-adams-bashforth}
  stepping forward a tracer variable such as temperature.
  In order to fit within the pressure method, the implicit viscosity
- must not alter the barotropic flow. In other words, it can on ly
+ must not alter the barotropic flow. In other words, it can only
  redistribute momentum in the vertical. The upshot of this is that
  although vertical viscosity may be backward implicit and
  unconditionally stable, no-slip boundary conditions may not be made
-Line 381 
 implicit and are thus cast as a an expli
+Line 409 
 implicit and are thus cast as a an expli
  \section{Synchronous time-stepping: variables co-located in time}
  \label{sect:adams-bashforth-sync}
+ \begin{rawhtml}
+ <!-- CMIREDIR:adams_bashforth_sync: -->
+ \end{rawhtml}
  \begin{figure}
  \begin{center}
-Line 401 
 is solved to yield the state variables a
+Line 432 
 is solved to yield the state variables a
  \end{figure}
  \begin{figure}
- \begin{center} \fbox{ \begin{minipage}{4.5in} \begin{tabbing}
+ \begin{center} \fbox{ \begin{minipage}{4.7in} \begin{tabbing}
  aaa \= aaa \= aaa \= aaa \= aaa \= aaa \kill
  FORWARD\_STEP \\
+ \>\> EXTERNAL\_FIELDS\_LOAD\\
+ \>\> DO\_ATMOSPHERIC\_PHYS \\
+ \>\> DO\_OCEANIC\_PHYS \\
  \> THERMODYNAMICS \\
  \>\> CALC\_GT \\
  \>\>\> GAD\_CALC\_RHS \` $G_\theta^n = G_\theta( u, \theta^n )$ (\ref{eq:Gt-n-sync})\\
  \>\>\> EXTERNAL\_FORCING \` $G_\theta^n = G_\theta^n + {\cal Q}$ \\
  \>\>\> ADAMS\_BASHFORTH2 \` $G_\theta^{(n+1/2)}$ (\ref{eq:Gt-n+5-sync}) \\
- \>\> TIMESTEP\_TRACER \` $\tau^*$ (\ref{eq:tstar-sync}) \\
+ \>\> TIMESTEP\_TRACER \` $\theta^*$ (\ref{eq:tstar-sync}) \\
- \>\> IMPLDIFF \` $\tau^{(n+1)}$ (\ref{eq:t-n+1-sync}) \\
+ \>\> IMPLDIFF \` $\theta^{(n+1)}$ (\ref{eq:t-n+1-sync}) \\
  \> DYNAMICS \\
  \>\> CALC\_PHI\_HYD \` $\phi_{hyd}^n$ (\ref{eq:phi-hyd-sync}) \\
  \>\> MOM\_FLUXFORM or MOM\_VECINV \` $G_{\vec{\bf v}}^n$ (\ref{eq:Gv-n-sync})\\
  \>\> TIMESTEP \` $\vec{\bf v}^*$ (\ref{eq:Gv-n+5-sync}, \ref{eq:vstar-sync}) \\
  \>\> IMPLDIFF \` $\vec{\bf v}^{**}$ (\ref{eq:vstarstar-sync}) \\
+ \> UPDATE\_R\_STAR or UPDATE\_SURF\_DR \` (NonLin-FS only)\\
  \> SOLVE\_FOR\_PRESSURE \\
  \>\> CALC\_DIV\_GHAT \` $\eta^*$ (\ref{eq:nstar-sync}) \\
  \>\> CG2D \` $\eta^{n+1}$ (\ref{eq:elliptic-sync}) \\
- \> THE\_CORRECTION\_STEP  \\
+ \> MOMENTUM\_CORRECTION\_STEP  \\
  \>\> CALC\_GRAD\_PHI\_SURF \` $\nabla \eta^{n+1}$ \\
- \>\> CORRECTION\_STEP \` $u^{n+1}$,$v^{n+1}$ (\ref{eq:v-n+1-sync})
+ \>\> CORRECTION\_STEP \` $u^{n+1}$,$v^{n+1}$ (\ref{eq:v-n+1-sync})\\
+ \> TRACERS\_CORRECTION\_STEP  \\
+ \>\> CYCLE\_TRACER \` $\theta^{n+1}$ \\
+ \>\> FILTER \` Shapiro Filter, Zonal Filter (FFT) \\
+ \>\> CONVECTIVE\_ADJUSTMENT \` \\
  \end{tabbing} \end{minipage} } \end{center}
  \caption{
  Calling tree for the overall synchronous algorithm using
- Adams-Bashforth time-stepping.}
+ Adams-Bashforth time-stepping.
+ The place where the model geometry
+ ({\bf hFac} factors) is updated is added here but is only relevant
+ for the non-linear free-surface algorithm.
+ For completeness, the external forcing,
+ ocean and atmospheric physics have been added, although they are mainly
+ optional}
  \label{fig:call-tree-adams-bashforth-sync}
  \end{figure}
-Line 454 
 G_{\theta,S}^{(n+1/2)} & = & (3/2+\epsil
+Line 499 
 G_{\theta,S}^{(n+1/2)} & = & (3/2+\epsil
  \label{eq:vstar-sync} \\
  \vec{\bf v}^{**} & = & {\cal L}_{\vec{\bf v}}^{-1} ( \vec{\bf v}^* )
  \label{eq:vstarstar-sync} \\
- \eta^* & = & \epsilon_{fs} \left( \eta^{n} +P-E+R \right)- \Delta t
+ \eta^* & = & \epsilon_{fs} \left( \eta^{n} + \Delta t (P-E) \right)- \Delta t
    \nabla \cdot H \widehat{ \vec{\bf v}^{**} }
  \label{eq:nstar-sync} \\
- \nabla \cdot g H \nabla \eta^{n+1} - \frac{\epsilon_{fs} \eta^{n+1}}{\Delta t^2}
+ \nabla \cdot g H \nabla \eta^{n+1} & - & \frac{\epsilon_{fs} \eta^{n+1}}{\Delta t^2}
- & = & - \frac{\eta^*}{\Delta t^2}
+ ~ = ~ - \frac{\eta^*}{\Delta t^2}
  \label{eq:elliptic-sync} \\
  \vec{\bf v}^{n+1} & = & \vec{\bf v}^{*} - \Delta t g \nabla \eta^{n+1}
  \label{eq:v-n+1-sync}
-Line 477 
 accelerations, stepping forward and solv
+Line 522 
 accelerations, stepping forward and solv
  surface pressure gradient terms, corresponding to equations
  \ref{eq:Gv-n-sync} to \ref{eq:v-n+1-sync}.
  These operations are carried out in subroutines {\em DYNAMCIS}, {\em
- SOLVE\_FOR\_PRESSURE} and {\em THE\_CORRECTION\_STEP}. This, then,
+ SOLVE\_FOR\_PRESSURE} and {\em MOMENTUM\_CORRECTION\_STEP}. This, then,
  represents an entire algorithm for stepping forward the model one
  time-step. The corresponding calling tree is given in
  \ref{fig:call-tree-adams-bashforth-sync}.
  \section{Staggered baroclinic time-stepping}
  \label{sect:adams-bashforth-staggered}
+ \begin{rawhtml}
+ <!-- CMIREDIR:adams_bashforth_staggered: -->
+ \end{rawhtml}
  \begin{figure}
  \begin{center}
-Line 492 
 time-step. The corresponding calling tre
+Line 540 
 time-step. The corresponding calling tre
  \caption{
  A schematic of the explicit Adams-Bashforth and implicit time-stepping
  phases of the algorithm but with staggering in time of thermodynamic
- variables with the flow. Explicit thermodynamics tendencies are
+ variables with the flow.
- evaluated at time level $n-1/2$ as a function of the thermodynamics
+ Explicit momentum tendencies are evaluated at time level $n-1/2$ as a
- state at that time level $n$ and flow at time $n$ (dotted arrow). The
+ function of the flow field at that time level $n-1/2$.
- explicit tendency from the previous time level, $n-3/2$, is used to
+ The explicit tendency from the previous time level, $n-3/2$, is used to
- extrapolate tendencies to $n$ (dashed arrow). This extrapolated
+ extrapolate tendencies to $n$ (dashed arrow).
- tendency allows thermo-dynamics variables to be stably integrated
+ The hydrostatic pressure/geo-potential $\phi_{hyd}$ is evaluated directly
- forward-in-time to render an estimate ($*$-variables) at the $n+1/2$
+ at time level $n$ (vertical arrows) and used with the extrapolated tendencies
- time level (solid arc-arrow). The implicit-in-time operator ${\cal
+ to step forward the flow variables from $n-1/2$ to $n+1/2$ (solid arc-arrow).
- L_{\theta,S}}$ is solved to yield the thermodynamic variables at time
+ The implicit-in-time operator ${\cal L}_{\bf u,v}$ (vertical arrows) is
- level $n+1/2$. These are then used to calculate the hydrostatic
+ then applied to the previous estimation of the the flow field ($*$-variables)
- pressure/geo-potential, $\phi_{hyd}$ (vertical arrows). The
+ and yields to the two velocity components $u,v$ at time level $n+1/2$.
- hydrostatic pressure gradient is evaluated directly an time level
+ These are then used to calculate the advection term (dashed arc-arrow)
- $n+1/2$ in stepping forward the flow variables from $n$ to $n+1$
+ of the thermo-dynamics tendencies at time step $n$.
- (solid arc-arrow). }
+ The extrapolated thermodynamics tendency, from time level $n-1$ and $n$
+ to $n+1/2$, allows thermodynamic variables to be stably integrated
+ forward-in-time (solid arc-arrow) up to time level $n+1$.
+ }
  \label{fig:adams-bashforth-staggered}
  \end{figure}
-Line 515 
 circumstance, it is more efficient to st
+Line 566 
 circumstance, it is more efficient to st
  thermodynamic variables with the flow
  variables. Fig.~\ref{fig:adams-bashforth-staggered} illustrates the
  staggering and algorithm. The key difference between this and
- Fig.~\ref{fig:adams-bashforth-sync} is that the new thermodynamics
+ Fig.~\ref{fig:adams-bashforth-sync} is that the thermodynamic variables
- fields are used to compute the hydrostatic pressure at time level
+ are solved after the dynamics, using the recently updated flow field.
- $n+1/2$. The essentially allows the gravity wave terms to leap-frog in
+ This essentially allows the gravity wave terms to leap-frog in
  time giving second order accuracy and more stability.
- The essential change in the staggered algorithm is the calculation of
+ The essential change in the staggered algorithm is that the
- hydrostatic pressure which, in the context of the synchronous
+ thermodynamics solver is delayed from half a time step,
- algorithm involves replacing equation \ref{eq:phi-hyd-sync} with
+ allowing the use of the most recent velocities to compute
- \begin{displaymath}
+ the advection terms. Once the thermodynamics fields are
- \phi_{hyd}^n = \int b(\theta^{n+1},S^{n+1}) dr
+ updated, the hydrostatic pressure is computed
- \end{displaymath}
+ to step forwrad the dynamics.
- but the pressure gradient must also be taken out of the
+ Note that the pressure gradient must also be taken out of the
  Adams-Bashforth extrapolation. Also, retaining the integer time-levels,
  $n$ and $n+1$, does not give a user the sense of where variables are
  located in time.  Instead, we re-write the entire algorithm,
  \ref{eq:Gt-n-sync} to \ref{eq:v-n+1-sync}, annotating the
  position in time of variables appropriately:
  \begin{eqnarray}
- G_{\theta,S}^{n-1/2} & = & G_{\theta,S} ( u^n, \theta^{n-1/2}, S^{n-1/2} )
+ \phi^{n}_{hyd} & = & \int b(\theta^{n},S^{n}) dr
- \label{eq:Gt-n-staggered} \\
- G_{\theta,S}^{(n)} & = & (3/2+\epsilon_{AB}) G_{\theta,S}^{n-1/2}-(1/2+\epsilon_{AB}) G_{\theta,S}^{n-3/2}
- \label{eq:Gt-n+5-staggered} \\
- (\theta^*,S^*) & = & (\theta^{n},S^{n}) + \Delta t G_{\theta,S}^{(n)}
- \label{eq:tstar-staggered} \\
- (\theta^{n+1/2},S^{n+1/2}) & = & {\cal L}^{-1}_{\theta,S} (\theta^*,S^*)
- \label{eq:t-n+1-staggered} \\
- \phi^{n+1/2}_{hyd} & = & \int b(\theta^{n+1/2},S^{n+1/2}) dr
  \label{eq:phi-hyd-staggered} \\
- \vec{\bf G}_{\vec{\bf v}}^{n} & = & \vec{\bf G}_{\vec{\bf v}} ( \vec{\bf v}^n )
+ \vec{\bf G}_{\vec{\bf v}}^{n-1/2} & = & \vec{\bf G}_{\vec{\bf v}} ( \vec{\bf v}^{n-1/2} )
  \label{eq:Gv-n-staggered} \\
- \vec{\bf G}_{\vec{\bf v}}^{(n+1/2)} & = & (3/2 + \epsilon_{AB} ) \vec{\bf G}_{\vec{\bf v}}^{n} - (1/2 + \epsilon_{AB} ) \vec{\bf G}_{\vec{\bf v}}^{n-1}
+ \vec{\bf G}_{\vec{\bf v}}^{(n)} & = & (3/2 + \epsilon_{AB} ) \vec{\bf G}_{\vec{\bf v}}^{n-1/2} - (1/2 + \epsilon_{AB} ) \vec{\bf G}_{\vec{\bf v}}^{n-3/2}
  \label{eq:Gv-n+5-staggered} \\
- \vec{\bf v}^{*} & = & \vec{\bf v}^{n} + \Delta t \left( \vec{\bf G}_{\vec{\bf v}}^{(n+1/2)} - \nabla \phi_{hyd}^{n+1/2} \right)
+ \vec{\bf v}^{*} & = & \vec{\bf v}^{n-1/2} + \Delta t \left( \vec{\bf G}_{\vec{\bf v}}^{(n)} - \nabla \phi_{hyd}^{n} \right)
  \label{eq:vstar-staggered} \\
  \vec{\bf v}^{**} & = & {\cal L}_{\vec{\bf v}}^{-1} ( \vec{\bf v}^* )
  \label{eq:vstarstar-staggered} \\
- \eta^* & = & \epsilon_{fs} \left( \eta^{n} +P-E+R \right)- \Delta t
+ \eta^* & = & \epsilon_{fs} \left( \eta^{n-1/2} + \Delta t (P-E)^n \right)- \Delta t
    \nabla \cdot H \widehat{ \vec{\bf v}^{**} }
  \label{eq:nstar-staggered} \\
- \nabla \cdot g H \nabla \eta^{n+1} - \frac{\epsilon_{fs} \eta^{n+1}}{\Delta t^2}
+ \nabla \cdot g H \nabla \eta^{n+1/2} & - & \frac{\epsilon_{fs} \eta^{n+1/2}}{\Delta t^2}
- & = & - \frac{\eta^*}{\Delta t^2}
+ ~ = ~ - \frac{\eta^*}{\Delta t^2}
  \label{eq:elliptic-staggered} \\
- \vec{\bf v}^{n+1} & = & \vec{\bf v}^{*} - \Delta t g \nabla \eta^{n+1}
+ \vec{\bf v}^{n+1/2} & = & \vec{\bf v}^{*} - \Delta t g \nabla \eta^{n+1/2}
- \label{eq:v-n+1-staggered}
+ \label{eq:v-n+1-staggered} \\
+ G_{\theta,S}^{n} & = & G_{\theta,S} ( u^{n+1/2}, \theta^{n}, S^{n} )
+ \label{eq:Gt-n-staggered} \\
+ G_{\theta,S}^{(n+1/2)} & = & (3/2+\epsilon_{AB}) G_{\theta,S}^{n}-(1/2+\epsilon_{AB}) G_{\theta,S}^{n-1}
+ \label{eq:Gt-n+5-staggered} \\
+ (\theta^*,S^*) & = & (\theta^{n},S^{n}) + \Delta t G_{\theta,S}^{(n+1/2)}
+ \label{eq:tstar-staggered} \\
+ (\theta^{n+1},S^{n+1}) & = & {\cal L}^{-1}_{\theta,S} (\theta^*,S^*)
+ \label{eq:t-n+1-staggered}
  \end{eqnarray}
- The calling sequence is unchanged from
+ The corresponding calling tree is given in
- Fig.~\ref{fig:call-tree-adams-bashforth-sync}. The staggered algorithm
+ \ref{fig:call-tree-adams-bashforth-staggered}.
- is activated with the run-time flag {\bf staggerTimeStep=.TRUE.} in
+ The staggered algorithm is activated with the run-time flag
- {\em PARM01} of {\em data}.
+ {\bf staggerTimeStep}{\em=.TRUE.} in parameter file {\em data},
+ namelist {\em PARM01}.
+ \begin{figure}
+ \begin{center} \fbox{ \begin{minipage}{4.7in} \begin{tabbing}
+ aaa \= aaa \= aaa \= aaa \= aaa \= aaa \kill
+ FORWARD\_STEP \\
+ \>\> EXTERNAL\_FIELDS\_LOAD\\
+ \>\> DO\_ATMOSPHERIC\_PHYS \\
+ \>\> DO\_OCEANIC\_PHYS \\
+ \> DYNAMICS \\
+ \>\> CALC\_PHI\_HYD \` $\phi_{hyd}^n$ (\ref{eq:phi-hyd-staggered}) \\
+ \>\> MOM\_FLUXFORM or MOM\_VECINV \` $G_{\vec{\bf v}}^{n-1/2}$
+     (\ref{eq:Gv-n-staggered})\\
+ \>\> TIMESTEP \` $\vec{\bf v}^*$ (\ref{eq:Gv-n+5-staggered},
+                                   \ref{eq:vstar-staggered}) \\
+ \>\> IMPLDIFF \` $\vec{\bf v}^{**}$ (\ref{eq:vstarstar-staggered}) \\
+ \> UPDATE\_R\_STAR or UPDATE\_SURF\_DR \` (NonLin-FS only)\\
+ \> SOLVE\_FOR\_PRESSURE \\
+ \>\> CALC\_DIV\_GHAT \` $\eta^*$ (\ref{eq:nstar-staggered}) \\
+ \>\> CG2D \` $\eta^{n+1/2}$ (\ref{eq:elliptic-staggered}) \\
+ \> MOMENTUM\_CORRECTION\_STEP  \\
+ \>\> CALC\_GRAD\_PHI\_SURF \` $\nabla \eta^{n+1/2}$ \\
+ \>\> CORRECTION\_STEP \` $u^{n+1/2}$,$v^{n+1/2}$ (\ref{eq:v-n+1-staggered})\\
+ \> THERMODYNAMICS \\
+ \>\> CALC\_GT \\
+ \>\>\> GAD\_CALC\_RHS \` $G_\theta^n = G_\theta( u, \theta^n )$
+      (\ref{eq:Gt-n-staggered})\\
+ \>\>\> EXTERNAL\_FORCING \` $G_\theta^n = G_\theta^n + {\cal Q}$ \\
+ \>\>\> ADAMS\_BASHFORTH2 \` $G_\theta^{(n+1/2)}$ (\ref{eq:Gt-n+5-staggered}) \\
+ \>\> TIMESTEP\_TRACER \` $\theta^*$ (\ref{eq:tstar-staggered}) \\
+ \>\> IMPLDIFF \` $\theta^{(n+1)}$ (\ref{eq:t-n+1-staggered}) \\
+ \> TRACERS\_CORRECTION\_STEP  \\
+ \>\> CYCLE\_TRACER \` $\theta^{n+1}$ \\
+ \>\> FILTER \` Shapiro Filter, Zonal Filter (FFT) \\
+ \>\> CONVECTIVE\_ADJUSTMENT \` \\
+ \end{tabbing} \end{minipage} } \end{center}
+ \caption{
+ Calling tree for the overall staggered algorithm using
+ Adams-Bashforth time-stepping.
+ The place where the model geometry
+ ({\bf hFac} factors) is updated is added here but is only relevant
+ for the non-linear free-surface algorithm.
+ }
+ \label{fig:call-tree-adams-bashforth-staggered}
+ \end{figure}
  The only difficulty with this approach is apparent in equation
  \ref{eq:Gt-n-staggered} and illustrated by the dotted arrow
- connecting $u,v^n$ with $G_\theta^{n-1/2}$. The flow used to advect
+ connecting $u,v^{n+1/2}$ with $G_\theta^{n}$. The flow used to advect
  tracers around is not naturally located in time. This could be avoided
  by applying the Adams-Bashforth extrapolation to the tracer field
  itself and advecting that around but this approach is not yet
-Line 578 
 time-level variables and terms correspon
+Line 674 
 time-level variables and terms correspon
  \section{Non-hydrostatic formulation}
  \label{sect:non-hydrostatic}
+ \begin{rawhtml}
+ <!-- CMIREDIR:non-hydrostatic_formulation: -->
+ \end{rawhtml}
  The non-hydrostatic formulation re-introduces the full vertical
  momentum equation and requires the solution of a 3-D elliptic
-Line 650 
 the following equations:
+Line 749 
 the following equations:
  u^{*} & = & u^{n} + \Delta t G_u^{(n+1/2)} \label{eq:ustar-nh} \\
  v^{*} & = & v^{n} + \Delta t G_v^{(n+1/2)} \label{eq:vstar-nh} \\
  w^{*} & = & w^{n} + \Delta t G_w^{(n+1/2)} \label{eq:wstar-nh} \\
- \eta^* & = & \epsilon_{fs} \left( \eta^{n} +P-E+R \right)- \Delta t
+ \eta^* ~ = ~ \epsilon_{fs} \left( \eta^{n} + \Delta t (P-E) \right)
+ & - & \Delta t
    \partial_x H \widehat{u^{*}}
  + \partial_y H \widehat{v^{*}}
  \\
    \partial_x g H \partial_x \eta^{n+1}
  + \partial_y g H \partial_y \eta^{n+1}
- - \frac{\epsilon_{fs} \eta^{n+1}}{\Delta t^2}
+ & - & \frac{\epsilon_{fs} \eta^{n+1}}{\Delta t^2}
- & = &
+ ~ = ~
  - \frac{\eta^*}{\Delta t^2}
  \label{eq:elliptic-nh}
  \\
-Line 676 
 $w^{n+1}$.
+Line 776 
 $w^{n+1}$.
  \section{Variants on the Free Surface}
+ \label{sect:free-surface}
  We now describe the various formulations of the free-surface that
  include non-linear forms, implicit in time using Crank-Nicholson,
-Line 714 
 $\eta^{n+1}$: {\bf etaN} (\em DYNVARS.h)
+Line 815 
 $\eta^{n+1}$: {\bf etaN} (\em DYNVARS.h)
  Once ${\eta}^{n+1}$ has been found, substituting into
- \ref{eq:discrete-time-u,eq:discrete-time-v} yields $\vec{\bf v}^{n+1}$ if the model is
+ \ref{eq:discrete-time-u}, \ref{eq:discrete-time-v} yields $\vec{\bf v}^{n+1}$
- hydrostatic ($\epsilon_{nh}=0$):
+ if the model is hydrostatic ($\epsilon_{nh}=0$):
  $$
  \vec{\bf v}^{n+1} = \vec{\bf v}^{*}
  - \Delta t {\bf \nabla}_h b_s {\eta}^{n+1}
-Line 788 
 at the same point in the code.
+Line 889 
 at the same point in the code.
  \subsection{Crank-Nickelson barotropic time stepping}
+ \label{sect:freesurf-CrankNick}
  The full implicit time stepping described previously is
  unconditionally stable but damps the fast gravity waves, resulting in
-Line 802 
 stable, Crank-Nickelson scheme; $(\beta,
+Line 904 
 stable, Crank-Nickelson scheme; $(\beta,
  corresponds to the forward - backward scheme that conserves energy but is
  only stable for small time steps.\\
  In the code, $\beta,\gamma$ are defined as parameters, respectively
- {\it implicSurfPress}, {\it implicDiv2DFlow}. They are read from
+ {\bf implicSurfPress}, {\bf implicDiv2DFlow}. They are read from
- the main data file "{\it data}" and are set by default to 1,1.
+ the main parameter file "{\em data}" and are set by default to 1,1.
  Equations \ref{eq:ustar-backward-free-surface} --
  \ref{eq:vn+1-backward-free-surface} are modified as follows:
- $$
+ \begin{eqnarray*}
  \frac{ \vec{\bf v}^{n+1} }{ \Delta t }
  + {\bf \nabla}_h b_s [ \beta {\eta}^{n+1} + (1-\beta) {\eta}^{n} ]
  + \epsilon_{nh} {\bf \nabla}_h {\phi'_{nh}}^{n+1}
   = \frac{ \vec{\bf v}^* }{ \Delta t }
- $$
+ \end{eqnarray*}
- $$
+ \begin{eqnarray}
  \epsilon_{fs} \frac{ {\eta}^{n+1} - {\eta}^{n} }{ \Delta t}
  + {\bf \nabla}_h \cdot \int_{R_{fixed}}^{R_o}
  [ \gamma \vec{\bf v}^{n+1} + (1-\gamma) \vec{\bf v}^{n}] dr
  = \epsilon_{fw} (P-E)
- $$
+ \label{eq:eta-n+1-CrankNick}
+ \end{eqnarray}
  where:
  \begin{eqnarray*}
  \vec{\bf v}^* & = &
-Line 840 
 $$
+Line 943 
 $$
  {\bf \nabla}_h {\eta}^{n+1}
  = {\eta}^*
  $$
- and then to compute (correction step):
+ and then to compute ({\em CORRECTION\_STEP}):
  $$
  \vec{\bf v}^{n+1} = \vec{\bf v}^{*}
  - \beta \Delta t {\bf \nabla}_h b_s {\eta}^{n+1}
  $$
- The non-hydrostatic part is solved as described previously.
+ %The non-hydrostatic part is solved as described previously.
- Note that:
+ \noindent
+ Notes:
  \begin{enumerate}
+ \item The RHS term of equation \ref{eq:eta-n+1-CrankNick}
+ corresponds the contribution of fresh water flux (P-E)
+ to the free-surface variations ($\epsilon_{fw}=1$,
+ {\bf useRealFreshWater}{\em=TRUE} in parameter file {\em data}).
+ In order to remain consistent with the tracer equation, specially in
+ the non-linear free-surface formulation, this term is also
+ affected by the Crank-Nickelson time stepping. The RHS reads:
+ $\epsilon_{fw} ( \gamma (P-E)^{n+1/2} + (1-\gamma) (P-E)^{n-1/2} )$
  \item The non-hydrostatic part of the code has not yet been
- updated, so that this option cannot be used with $(\beta,\gamma) \neq (1,1)$.
+ updated, and therefore cannot be used with $(\beta,\gamma) \neq (1,1)$.
  \item The stability criteria with Crank-Nickelson time stepping
  for the pure linear gravity wave problem in cartesian coordinates is:
  \begin{itemize}

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