<p><b>mpetersen@lanl.gov</b> 2013-03-13 10:01:04 -0600 (Wed, 13 Mar 2013)</p><p>ocean user's guide: Added sections to namelist descriptions.<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/documents/users_guide/ocean/cesm_coupling.tex
===================================================================
--- trunk/documents/users_guide/ocean/cesm_coupling.tex        2013-03-13 15:48:02 UTC (rev 2598)
+++ trunk/documents/users_guide/ocean/cesm_coupling.tex        2013-03-13 16:01:04 UTC (rev 2599)
@@ -1,5 +1,5 @@
\chapter{Running MPAS-Ocean within the CESM}
-\label{chap:cesm_coupling}
+\label{chap:cesm_ocean_coupling}
Running MPAS-Ocean within the CESM is currently a work in progress, but this
chapter will be filled in later.
Modified: trunk/documents/users_guide/ocean/core_intro.tex
===================================================================
--- trunk/documents/users_guide/ocean/core_intro.tex        2013-03-13 15:48:02 UTC (rev 2598)
+++ trunk/documents/users_guide/ocean/core_intro.tex        2013-03-13 16:01:04 UTC (rev 2599)
@@ -8,8 +8,9 @@
\frac{\partial {\bf u}}{\partial t}
+ \eta {\bf k} \times {\bf u}
+ w\frac{\partial {\bf u}}{\partial z}
- = - \frac{1}{\rho_0}</font>
<font color="black">abla p - </font>
<font color="red">abla K
-+ {\bf D}^u_h + {\bf D}^u_v
+ = - \frac{1}{\rho_0}</font>
<font color="black">abla p - \frac{\rho g}{\rho_0}</font>
<font color="blue">abla z^{mid}
+ - </font>
<font color="gray">abla K
++ {\bf D}^u_h + {\bf D}^u_v + {\cal F}^u
\end{equation}
{\it thickness equation:}
\begin{equation}
@@ -28,6 +29,7 @@
+ \left. \varphi w \right|_{z=s^{top}}
- \left. \varphi w \right|_{z=s^{bot}}
= D^\varphi_h + D^\varphi_v
++ {\cal F}^\varphi
\end{equation}
{\it hydrostatic condition:}
\begin{equation}
@@ -52,6 +54,8 @@
$ D^\varphi_h$, $ D^\varphi_v$ & tracer diff. terms & cell & \\
$f$ & Coriolis parameter & vertex \\
$f_{eos}$ & equation of state & - \\
+$ {\cal F}^u$ & momentum forcing & edge & \\
+$ {\cal F}^\varphi$ & tracer forcing & cell & \\
$g$ & grav. acceleration & constant \\
$h$ & layer thickness & cell &\\
${\bf k}$ & vertical unit vector & \\
Modified: trunk/documents/users_guide/ocean/namelist_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocean/namelist_table_documentation.tex        2013-03-13 15:48:02 UTC (rev 2598)
+++ trunk/documents/users_guide/ocean/namelist_table_documentation.tex        2013-03-13 16:01:04 UTC (rev 2599)
@@ -326,6 +326,7 @@
}
\section[forcing]{\hyperref[sec:nm_sec_forcing]{forcing}}
\label{sec:nm_tab_forcing}
+\input{ocean/section_descriptions/forcing.tex}
{\small
\begin{center}
\begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -369,6 +370,7 @@
}
\section[bottom\_drag]{\hyperref[sec:nm_sec_bottom_drag]{bottom\_drag}}
\label{sec:nm_tab_bottom_drag}
+\input{ocean/section_descriptions/bottom_drag.tex}
{\small
\begin{center}
\begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -383,6 +385,7 @@
}
\section[pressure\_gradient]{\hyperref[sec:nm_sec_pressure_gradient]{pressure\_gradient}}
\label{sec:nm_tab_pressure_gradient}
+\input{ocean/section_descriptions/pressure_gradient.tex}
{\small
\begin{center}
\begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -437,6 +440,7 @@
}
\section[split\_explicit\_ts]{\hyperref[sec:nm_sec_split_explicit_ts]{split\_explicit\_ts}}
\label{sec:nm_tab_split_explicit_ts}
+\input{ocean/section_descriptions/split_explicit_ts.tex}
{\small
\begin{center}
\begin{longtable}{| p{2.0in} || p{4.0in} |}
Modified: trunk/documents/users_guide/ocean/section_descriptions/Rayleigh_damping.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/Rayleigh_damping.tex        2013-03-13 15:48:02 UTC (rev 2598)
+++ trunk/documents/users_guide/ocean/section_descriptions/Rayleigh_damping.tex        2013-03-13 16:01:04 UTC (rev 2599)
@@ -1,2 +1,5 @@
-A linear damping toward a state of rest is available with this namelist option. It is implemented with a term on the RHS of the momentum equation (\ref{ocean:momentum continuous 1}) of the form $-c_R {\bf u}$.
+A linear damping toward a state of rest is available with this namelist option. It is implemented with a term on the RHS of the momentum equation (\ref{ocean:momentum continuous 1}) of the form
+\begin{equation}
+{\cal F}^u = -c_R {\bf u}.
+\end{equation}
Added: trunk/documents/users_guide/ocean/section_descriptions/bottom_drag.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/bottom_drag.tex         (rev 0)
+++ trunk/documents/users_guide/ocean/section_descriptions/bottom_drag.tex        2013-03-13 16:01:04 UTC (rev 2599)
@@ -0,0 +1,5 @@
+The bottom drag is applied as a bottom boundary condition within the implicit solve of vertical mixing in the momentum equation (\ref{ocean:momentum continuous 1}), as
+\begin{equation}
+\lim_{z\rightarrow z_{bot}} </font>
<font color="gray">u_v \frac{\partial u}{\partial z} = c_{drag} \left|u\right| u,
+\end{equation}
+where $c_{drag}$ is the dimensionless bottom drag coefficient, and $z_{bot}$ is the $z$-location of the ocean bottom.
Added: trunk/documents/users_guide/ocean/section_descriptions/forcing.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/forcing.tex         (rev 0)
+++ trunk/documents/users_guide/ocean/section_descriptions/forcing.tex        2013-03-13 16:01:04 UTC (rev 2599)
@@ -0,0 +1,11 @@
+Forcing may be applied to the RHS of the momentum equation (\ref{ocean:momentum continuous 1}) through the term
+\begin{equation}
+{\cal F}^u = \frac{1}{\rho_0 h}\tau
+\end{equation}
+where $\tau$ is typically the wind stress in $N/m^2$ applied to the top layer. More generally, momentum forcing may be applied to any layer in the ocean. The momentum forcing may be given by the input variables \verb|u_src| or \verb|windStressMonthly|, depending on the configuration settings below. When running within the CESM, the wind stress is provided by the coupler (see Chapter \ref{chap:cesm_ocean_coupling}).
+
+Temperature and salinity restoring are applied to the tracer equation (\ref{ocean:tracer continuous 1}) through the term
+\begin{equation}
+{\cal F}^\varphi = -h\frac{\varphi-\varphi_{r}}{\tau_{r}}
+\end{equation}
+where $\varphi_{r}$ is the tracer restoring value and $\tau_{r}$ is the restoring timescale. This term is only applied at the top layer, and is supplied by the input variables \verb|temperatureRestore| and \verb|salinityRestore| for constant forcing and \verb|temperatureRestoreMonthly| and \verb|salinityRestoreMonthly| for monthly forcing fields. When running within the CESM, the coupler provides surface heat, salinity, and freshwater fluxes rather than a restoring in this form (see Chapter \ref{chap:cesm_ocean_coupling}).
Added: trunk/documents/users_guide/ocean/section_descriptions/pressure_gradient.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/pressure_gradient.tex         (rev 0)
+++ trunk/documents/users_guide/ocean/section_descriptions/pressure_gradient.tex        2013-03-13 16:01:04 UTC (rev 2599)
@@ -0,0 +1,13 @@
+For most choices of the vertical coordinate, the pressure gradient terms in the momentum equation will have the form
+\begin{equation}
+- \frac{1}{\rho_0}</font>
<font color="black">abla p - \frac{\rho g}{\rho_0}</font>
<font color="blue">abla z^{mid}.
+\end{equation}
+For isopycnal vertical coordinates, the user may choose to use the Montgomery potential,
+\begin{equation}
+M = \frac{1}{\rho}p+gz
+\end{equation}
+and replace the pressure terms above with
+\begin{equation}
+- </font>
<font color="gray">abla M.
+\end{equation}
+See \citet[section 2.1]{Higdon05jcp} for details on the derivation and computation of the Montgomery potential.
Added: trunk/documents/users_guide/ocean/section_descriptions/split_explicit_ts.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/split_explicit_ts.tex         (rev 0)
+++ trunk/documents/users_guide/ocean/section_descriptions/split_explicit_ts.tex        2013-03-13 16:01:04 UTC (rev 2599)
@@ -0,0 +1,9 @@
+The split explicit time-stepping method solves the barotropic (vertically-integrated) velocities separately from the remaining baroclinic velocities. The time step for the barotropic solve is limited by fast surface gravity waves, and so is subcycled within a large timestep of the baroclinic velocity solve. This provides a 10 to 12-times speed-up over fourth-order Runge-Kutta time stepping.
+
+A single large timestep in the split explicit algorithm may be summarized as
+\begin{itemize}
+\item Stage 1: solve for baroclinic velocity (3D)
+\item Stage 2: solve for barotropic velocity (2D) with explicit sub-cycling
+\item Stage 3: update thickness, tracers, density and pressure
+\end{itemize}
+The algorithm includes iterations within stage 1, within each subcycle of stage 2, and over the full three-stage process. Further details are provided in \citet[Appendix A.5]{Ringler_ea13om}
</font>
</pre>