<p><b>ringler@lanl.gov</b> 2013-03-12 14:45:52 -0600 (Tue, 12 Mar 2013)</p><p>added many section descriptions and made tba notes throughout<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/documents/users_guide/ocn/core_intro.tex
===================================================================
--- trunk/documents/users_guide/ocn/core_intro.tex 2013-03-12 18:53:55 UTC (rev 2591)
+++ trunk/documents/users_guide/ocn/core_intro.tex 2013-03-12 20:45:52 UTC (rev 2592)
@@ -82,7 +82,8 @@
\hline
$\delta$ & horizontal divergence & cell & $\delta=</font>
<font color="red">abla\cdot{\bf u}$ \\
$\zeta$ & sea surface height & cell \\
-$\eta$ & absolute vorticity & vertex & $\eta={\bf k} \cdot </font>
<font color="blue">abla \times {\bf u}+f$ \\
+$\omega$ & relative vorticity & vertex & $\omega={\bf k} \cdot \left( </font>
<font color="blue">abla \times {\bf u} \right)$\\
+$\eta$ & absolute vorticity & vertex & $\eta=\omega+f$ \\
$\Theta$ & potential temperature & cell & a tracer $\varphi$ \\
$\kappa_h$, $\kappa_h$ & diffusion & cell \\
$</font>
<font color="black">u_h$, $</font>
<font color="gray">u_v$ & viscosity & edge \\
Modified: trunk/documents/users_guide/ocn/mpas_ocean.bib
===================================================================
--- trunk/documents/users_guide/ocn/mpas_ocean.bib 2013-03-12 18:53:55 UTC (rev 2591)
+++ trunk/documents/users_guide/ocn/mpas_ocean.bib 2013-03-12 20:45:52 UTC (rev 2592)
@@ -69,6 +69,16 @@
pages = {481--491}
}
+@article{Smagorinsky:1963wc,
+author = {Smagorinsky, J.},
+title = {{General circulation experiments with the primitive equations}},
+journal = {Monthly Weather Review},
+year = {1963},
+volume = {91},
+number = {3},
+pages = {99--164}
+}
+
@ARTICLE{Ringler_Gent11om,
author = {{Ringler}, T.~D. and {Gent}, D.~A.},
title = "{An eddy closure for potential vorticity}",
Modified: trunk/documents/users_guide/ocn/namelist_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/namelist_table_documentation.tex 2013-03-12 18:53:55 UTC (rev 2591)
+++ trunk/documents/users_guide/ocn/namelist_table_documentation.tex 2013-03-12 20:45:52 UTC (rev 2592)
@@ -222,6 +222,7 @@
}
\section[Rayleigh\_damping]{\hyperref[sec:nm_sec_Rayleigh_damping]{Rayleigh\_damping}}
\label{sec:nm_tab_Rayleigh_damping}
+\input{ocn/section_descriptions/Rayleigh_damping.tex}
{\small
\begin{center}
\begin{longtable}{| p{2.0in} || p{4.0in} |}
Added: trunk/documents/users_guide/ocn/section_descriptions/Rayleigh_damping.tex
===================================================================
--- trunk/documents/users_guide/ocn/section_descriptions/Rayleigh_damping.tex (rev 0)
+++ trunk/documents/users_guide/ocn/section_descriptions/Rayleigh_damping.tex 2013-03-12 20:45:52 UTC (rev 2592)
@@ -0,0 +1 @@
+A linear damping toward a state of rest is available with this namelist option.
Modified: trunk/documents/users_guide/ocn/section_descriptions/advection.tex
===================================================================
--- trunk/documents/users_guide/ocn/section_descriptions/advection.tex 2013-03-12 18:53:55 UTC (rev 2591)
+++ trunk/documents/users_guide/ocn/section_descriptions/advection.tex 2013-03-12 20:45:52 UTC (rev 2592)
@@ -1,5 +1 @@
-advection here
-
-\cite{Zalesak:1979wm}
-
-\cite{Skamarock:2011tc}
\ No newline at end of file
+Three-dimensional tracer advection can be computed using 2$^{nd}$, 3$^{rd}$ or 4$^{th}$ flux reconstructions in the horizontal and vertical. In the horizontal, the high-order (i.e. 3$^{rd}$ or 4$^{th}$) flux reconstruction is done following \cite{Skamarock:2011tc}. Typically, the scheme is implemented with an upwind-bias ($\beta$=0.25 in (11) from \cite{Skamarock:2011tc}) to produce a 3$^{rd}$-order accurate reconstruction of tracer flux divergence on uniform hexagonal meshes. In the vertical, high-order estimates of tracer values at layer edges are reconstructed using a cubic spline. Monotone transport is guaranteed by blending these high-order flux approximations with the 1$^{st}$-order, upstream flux using the \cite{Zalesak:1979wm} flux-corrected transport scheme.
\ No newline at end of file
Modified: trunk/documents/users_guide/ocn/section_descriptions/eos.tex
===================================================================
--- trunk/documents/users_guide/ocn/section_descriptions/eos.tex 2013-03-12 18:53:55 UTC (rev 2591)
+++ trunk/documents/users_guide/ocn/section_descriptions/eos.tex 2013-03-12 20:45:52 UTC (rev 2592)
@@ -1,3 +1 @@
-eos here
-
-\cite{Jackett_McDougall95jaot}
+Two forms of EOS are supported. The full EOS from \cite{Jackett_McDougall95jaot} and a linear EOS.
Modified: trunk/documents/users_guide/ocn/section_descriptions/eos_linear.tex
===================================================================
--- trunk/documents/users_guide/ocn/section_descriptions/eos_linear.tex 2013-03-12 18:53:55 UTC (rev 2591)
+++ trunk/documents/users_guide/ocn/section_descriptions/eos_linear.tex 2013-03-12 20:45:52 UTC (rev 2592)
@@ -1 +1,4 @@
-linear EOS here
+The linear equation of state (leos) is specified as follows:
+\begin{equation}
+\rho = \rho_{ref} - \alpha_{leos}(T-T_{ref})+\beta_{leos}(S-S_{ref})
+\end{equation}
\ No newline at end of file
Modified: trunk/documents/users_guide/ocn/section_descriptions/hmix_Leith.tex
===================================================================
--- trunk/documents/users_guide/ocn/section_descriptions/hmix_Leith.tex 2013-03-12 18:53:55 UTC (rev 2591)
+++ trunk/documents/users_guide/ocn/section_descriptions/hmix_Leith.tex 2013-03-12 20:45:52 UTC (rev 2592)
@@ -1,3 +1,12 @@
-Leith here
+The \cite{Leith:1996wu} closure is the enstrophy-cascade analogy to the \cite{Smagorinsky:1963wc} energy-cascade closure, i.e. the Leith closure assumes an inertial range of enstrophy flux moving toward the grid scale. The assumption of an enstrophy cascade and dimensional analysis produces right-hand-side dissipation, $\bf{D}$, of velocity of the form
-\cite{Leith:1996wu}
+\begin{equation}
+\label{eq:Leith}
+{\bf D} = </font>
<font color="black">abla \cdot \left( \Gamma \left| </font>
<font color="black">abla \omega \right| \left( \Delta x \right)^3 </font>
<font color="black">abla \bf{u} \right)=</font>
<font color="black">abla \cdot \left( </font>
<font color="black">u_\ast </font>
<font color="blue">abla {\bf u} \right)
+\end{equation}
+where $\omega$ is the relative vorticity, ${\bf u}$ is the horizontal velocity, $\Delta x$ is the local grid spacing and $\Gamma$ is a non-dimensional, $O(1)$ parameter. This beta release approximates the RHS of the \ref{eq:Leith} as
+
+\begin{equation}
+\bf{D^u}=</font>
<font color="black">u_\ast </font>
<font color="blue">abla^2 {\bf u}
+\end{equation}
+where the $</font>
<font color="black">abla^2 {\bf u}$ is computed using the form shown in \ref{h_mom_diff_cont}. Future releases will remove this approximation by computing the rate-of-strain, i.e. $</font>
<font color="gray">abla {\bf u}$, directly.
\ No newline at end of file
Modified: trunk/documents/users_guide/ocn/section_descriptions/time_management.tex
===================================================================
--- trunk/documents/users_guide/ocn/section_descriptions/time_management.tex 2013-03-12 18:53:55 UTC (rev 2591)
+++ trunk/documents/users_guide/ocn/section_descriptions/time_management.tex 2013-03-12 20:45:52 UTC (rev 2592)
@@ -1,8 +1,9 @@
General time management is handled by the time\_management namelist record.
-Included options handle time related parts of MPAS such as the calendar that is
-used throughout a simulation, and if the simulation is a restart or not.
+Included options handle time-related parts of MPAS, such as the calendar and if the simulation is a restart or not.
Users should use this record to specify the beginning time of the simulation,
and either the duration or the end of the simulation. Only the end or the
duration need to be specified as the other is derived within MPAS from the
beginning time and other specified one.
+
+{\bf TBA: If both duration and stop are specified, then what happens?)}
</font>
</pre>