<p><b>dwj07@fsu.edu</b> 2013-03-06 10:05:22 -0700 (Wed, 06 Mar 2013)</p><p><br>
-- DOCUMENT COMMIT --<br>
<br>
Adding quick start guide. And description of baroclinic channel test case (as a template).<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/documents/users_guide/mpas_ocean_users_guide.tex
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--- trunk/documents/users_guide/mpas_ocean_users_guide.tex 2013-03-06 03:14:35 UTC (rev 2549)
+++ trunk/documents/users_guide/mpas_ocean_users_guide.tex 2013-03-06 17:05:22 UTC (rev 2550)
@@ -6,6 +6,7 @@
\usepackage{hyperref}
\usepackage{color}
\usepackage{caption}
+\usepackage[hang]{subfigure}
\definecolor{black}{rgb}{0.0,0.0,0.0}
\definecolor{darkblue}{rgb}{0.0,0.0,0.5}
Added: trunk/documents/users_guide/ocn/figures/baroclinic_channel_10000m_20levs_10days.pdf
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--- trunk/documents/users_guide/ocn/figures/baroclinic_channel_10000m_20levs_10days.pdf 2013-03-06 03:14:35 UTC (rev 2549)
+++ trunk/documents/users_guide/ocn/figures/baroclinic_channel_10000m_20levs_10days.pdf 2013-03-06 17:05:22 UTC (rev 2550)
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--- trunk/documents/users_guide/ocn/figures/baroclinic_channel_4000m_20levs_10days.pdf 2013-03-06 03:14:35 UTC (rev 2549)
+++ trunk/documents/users_guide/ocn/figures/baroclinic_channel_4000m_20levs_10days.pdf 2013-03-06 17:05:22 UTC (rev 2550)
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Modified: trunk/documents/users_guide/ocn/quick_start.tex
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--- trunk/documents/users_guide/ocn/quick_start.tex 2013-03-06 03:14:35 UTC (rev 2549)
+++ trunk/documents/users_guide/ocn/quick_start.tex 2013-03-06 17:05:22 UTC (rev 2550)
@@ -1,2 +1,34 @@
\chapter{MPAS-Ocean Quick Start Guide}
\label{chap:quick_start}
+
+This chapter provides MPAS-Ocean users with a quick start description of how to
+build and run the model. It is meant merely as a brief overview of the process,
+while the more detailed descriptions of each step are provided in later
+sections.
+
+In general, the build process follows the following steps.
+
+\begin{enumerate}
+ \item Build MPI Layer (OpenMPI, MVAPICH2, etc.)
+ \item Build serial NetCDF library (v3.6.3, v4.1.3, etc.)
+ \item Build Parallel-NetCDF library (v1.2.1, v1.3.0, etc.)
+ \item Build Parallel I/O library (v1.4.1, v1.6.1, etc.)
+ \item (Optional) Build METIS library and executables (v4.0, v5.0.2, etc.)
+ \item Checkout MPAS-Ocean from repository
+ \item Build ocean core
+\end{enumerate}
+
+After step 5, an executable should be created called ocean\_model.exe. After which, one can begin running MPAS-Ocean. The run process is as follows:
+
+\begin{enumerate}
+ \item Create run directory.
+ \item Copy executable to run directory.
+ \item Copy namelist.input into run directory.
+ \item (Optional) Copy input and graph files into run directory.
+ \item Edit namelist.input to have the proper parameters. \\
+ If step 4 was skipped, ensure paths to input and graph files are appropriately set.
+ \item (Optional) Create graph files, using METIS executable (pmetis or gpmetis depending on version). \\
+ A graph file is required for each processor count you want to use.
+ \item Run MPAS-Ocean.
+ \item Visualize output file, and perform analysis.
+\end{enumerate}
Modified: trunk/documents/users_guide/ocn/test_case_descriptions.tex
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--- trunk/documents/users_guide/ocn/test_case_descriptions.tex 2013-03-06 03:14:35 UTC (rev 2549)
+++ trunk/documents/users_guide/ocn/test_case_descriptions.tex 2013-03-06 17:05:22 UTC (rev 2550)
@@ -1,3 +1,5 @@
\chapter{MPAS-Ocean Test Cases}
\label{chap:ocean_test_cases}
+\input{ocn/test_cases/baroclinic_channel.tex}
+
Added: trunk/documents/users_guide/ocn/test_cases/baroclinic_channel.tex
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--- trunk/documents/users_guide/ocn/test_cases/baroclinic_channel.tex (rev 0)
+++ trunk/documents/users_guide/ocn/test_cases/baroclinic_channel.tex 2013-03-06 17:05:22 UTC (rev 2550)
@@ -0,0 +1,58 @@
+\section{Baroclinic Channel}
+\label{sec:baroclinic_channel_description}
+This section describes a periodic channel, that is driven by a baroclinic
+instability and a temperature gradient. This test case comes from
+\cite{ref:ilicak2011}. The domain is a planar channel that is periodic in the
+longitudinal direction. It's longitudinal extent is 160km, while it's
+latitudinal extent is 500km. The vertical depth of the domain is 1000m with a
+flat bottom. The channel is on an {\it f}-plane, with the Coriolis parameter $f
+= 1.2 \times 10^-4 s^-1$, with relates to roughly 55$^\circ$ latitude.
+
+To begin, the temperature is decreasing in the vertical direction, with a
+temperature gradient in the latitudinal direction. A cosine shape with
+wavelength $x = 120km$ is used to determine the interface between north and
+south, where the gradient occurs. In addition, a baroclinic instability is
+added to the temperature gradient.
+
+\subsection{Provided Files}
+\label{subsec:baroclinic_channel_files}
+Three resolutions of the baroclinic channel are provided for exploration. First
+is a 10km horizontal resolution, second is a 4km horizontal resolution, and
+third is a 1km horizontal resolution. All three horizontal resolutions have 20
+vertical levels with a uniform distribution and a 50m vertical resolution.
+
+Each resolution is provided in it's own tar file, which when extracted creates
+a "run directory" that is only missing the ocean\_model.exe executable.
+Included in each tar file are the following files.
+
+\begin{itemize}
+ \item grid.nc: \\
+ This is the input grid file that includes initial conditions. \\
+ It can be visualized in the same way output files can to see the initial conditions.
+ \item graph.info: \\
+ This file is a graph of all of the cells in the mesh. \\
+ It is used to decompose the mesh into partition files.
+ \item graph.info.part.2: \\
+ This is a partition file for use with a 2 processor run. \\
+ The graph.info file has been decomposed into two blocks for this file.
+ \item graph.info.part.4: \\
+ This is a partition file for use with a 4 processor run. \\
+ The graph.info file has been decomposed into four blocks for this file.
+ \item graph.info.part.8: \\
+ This is a partition file for use with a 8 processor run. \\
+ The graph.info file has been decomposed into eight blocks for this file.
+ \item namelist.input: \\
+ This is the namelist file with all parameters for the run. \\
+ It has a default setup which when run provides the results in the next section.
+\end{itemize}
+
+\subsection{Results}
+\label{subsecc:baroclinic_channel_results}
+Simulation results provided in this section relate only to the temperature
+field, and are created using the default namelists in each of the tar files.
+
+\begin{figure}[H!]
+ \subfigure[10km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocn/figures/baroclinic_channel_10000m_20levs_10days.pdf}}
+ \subfigure[4km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocn/figures/baroclinic_channel_4000m_20levs_10days.pdf}}
+\end{figure}
+
</font>
</pre>