<p><b>mpetersen@lanl.gov</b> 2013-03-13 07:14:43 -0600 (Wed, 13 Mar 2013)</p><p>ocean user's guide: clean up references from renaming ocn directory as ocean.<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/documents/users_guide/mpas_ocean_users_guide.tex
===================================================================
--- trunk/documents/users_guide/mpas_ocean_users_guide.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/mpas_ocean_users_guide.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -47,7 +47,7 @@
 \maketitle
 \tableofcontents
 
-\input{ocn/quick_start.tex}
+\input{ocean/quick_start.tex}
 
 \part{The MPAS Framework}
 \input{shared/mpas_build_instructions.tex}
@@ -55,24 +55,24 @@
 \input{shared/mpas_visualization.tex}
 
 \part{MPAS-Ocean}
-\input{ocn/core_intro.tex}
-\input{ocn/dimension_table_documentation.tex}
-\input{ocn/namelist_table_documentation.tex}
-\input{ocn/variable_table_documentation.tex}
+\input{ocean/core_intro.tex}
+\input{ocean/dimension_table_documentation.tex}
+\input{ocean/namelist_table_documentation.tex}
+\input{ocean/variable_table_documentation.tex}
 
-\input{ocn/test_case_descriptions.tex}
-\input{ocn/cesm_coupling.tex}
-\input{ocn/troubleshooting.tex}
-\input{ocn/knownissues.tex}
+\input{ocean/test_case_descriptions.tex}
+\input{ocean/cesm_coupling.tex}
+\input{ocean/troubleshooting.tex}
+\input{ocean/knownissues.tex}
 
 \part{Bibliography}
 \bibliographystyle{shared/ametsoc}
-\bibliography{shared/mpas_shared,ocn/mpas_ocean}
+\bibliography{shared/mpas_shared,ocean/mpas_ocean}
 
 \part{Appendices}
 \appendix
-\input{ocn/namelist_section_documentation.tex}
-\input{ocn/variable_section_documentation.tex}
+\input{ocean/namelist_section_documentation.tex}
+\input{ocean/variable_section_documentation.tex}
 
 \end{document}
 

Modified: trunk/documents/users_guide/ocean/core_intro.tex
===================================================================
--- trunk/documents/users_guide/ocean/core_intro.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/core_intro.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -4,7 +4,7 @@
 The governing equations for MPAS-Ocean are\\ \\
 {\it momentum equation:}
 \begin{equation}
-\label{ocn:momentum continuous 1}
+\label{ocean:momentum continuous 1}
 \frac{\partial {\bf u}}{\partial t} 
 + \eta {\bf k} \times {\bf u}
 + w\frac{\partial {\bf u}}{\partial z}
@@ -13,7 +13,7 @@
 \end{equation}
 {\it thickness equation:}
 \begin{equation}
-\label{ocn:thickness continuous 1}
+\label{ocean:thickness continuous 1}
 \frac{\partial h}{\partial t}
 + </font>
<font color="gray">abla\cdot\left(h \overline{ {\bf u} }^z\right)
 + \left.  w \right|_{z=s^{top}} 
@@ -22,7 +22,7 @@
 \end{equation}
 {\it tracer equation:}
 \begin{equation}
-\label{ocn:tracer continuous 1}
+\label{ocean:tracer continuous 1}
 \frac{\partial}{\partial t} h \overline{\varphi}^z
 + </font>
<font color="gray">abla\cdot\left(h \overline{\varphi {\bf u} }^z\right)
 + \left. \varphi w \right|_{z=s^{top}} 
@@ -31,19 +31,19 @@
 \end{equation}
 {\it hydrostatic condition:}
 \begin{equation}
-\label{ocn:pressure continuous 1}
+\label{ocean:pressure continuous 1}
 p(x,y,z) = p^{s}(x,y) + \int_{z}^{z^s} \rho g dz'
 \end{equation}
 {\it equation of state:}
 \begin{equation}
-\label{ocn:eos continuous 1}
+\label{ocean:eos continuous 1}
 \rho = f_{eos}(\Theta,S,p)
 \end{equation}
 
-Equations \ref{ocn:momentum continuous 1} through \ref{ocn:eos continuous 1} are a normal expression of the primitive equations; i.e. the incompressible Boussinesq equations in hydrostatic balance.  Variable definitions are in Tables \ref{ocnTable:variables} and \ref{ocnTable:variables_Greek}.  The momentum advection and Coriolis terms in (\ref{ocn:momentum continuous 1}) are presented in vorticity-kinetic energy form \citep[eqn 5]{Ringler_ea10jcp}.  The thickness and tracer equations describe a single layer in the vertical, where the operator $\overline{\left(\cdot\right)}^z$ is a vertical average over that layer (see derivation in Appedix A.2 of \citet{Ringler_ea13om}).  Otherwise, \ref{ocn:momentum continuous 1}--\ref{ocn:eos continuous 1} are the model equations in continuous form.  Details of the conversion to fully discretized equations are given in the appendices of \citet{Ringler_ea13om}.  
+Equations \ref{ocean:momentum continuous 1} through \ref{ocean:eos continuous 1} are a normal expression of the primitive equations; i.e. the incompressible Boussinesq equations in hydrostatic balance.  Variable definitions are in Tables \ref{oceanTable:variables} and \ref{oceanTable:variables_Greek}.  The momentum advection and Coriolis terms in (\ref{ocean:momentum continuous 1}) are presented in vorticity-kinetic energy form \citep[eqn 5]{Ringler_ea10jcp}.  The thickness and tracer equations describe a single layer in the vertical, where the operator $\overline{\left(\cdot\right)}^z$ is a vertical average over that layer (see derivation in Appedix A.2 of \citet{Ringler_ea13om}).  Otherwise, \ref{ocean:momentum continuous 1}--\ref{ocean:eos continuous 1} are the model equations in continuous form.  Details of the conversion to fully discretized equations are given in the appendices of \citet{Ringler_ea13om}.  
 
 \begin{table}[ht] 
-\caption{Latin variables used in prognostic equation set.  Column 3 shows the native horizontal grid location.  {\bf TBA. All variables are not at layer center as text states} All variables are located at the center of the layer in the vertical.} 
+\caption{Latin variables used in prognostic equation set.  Column 3 shows the native horizontal grid location.  All variables are located at the center of the layer in the vertical unless noted.} 
 \vspace{0.5cm} \centering 
 \begin{tabular}{c c c c } 
 \hline\hline symbol &amp;  name &amp; grid &amp;  notes  \\
@@ -66,11 +66,11 @@
 $u$ &amp; horizontal velocity &amp; edge  &amp; normal component to edge\\
 ${\bf u}$ &amp; horizontal velocity   &amp; - \\
 ${\bf v}$ &amp; 3D velocity   &amp; - \\
-$w$ &amp; vertical transport &amp; cell  &amp; determined by coord. type \\
+$w$ &amp; vertical transport &amp; cell  &amp; top of layer in vertical \\
 $z$ &amp; vertical coordinate &amp; - &amp; positive upward \\
 $z^{s}$ &amp; sea surface location &amp; cell \\
 \hline 
-\end{tabular} \label{ocnTable:variables} 
+\end{tabular} \label{oceanTable:variables} 
 \end{table}
 
 \begin{table}[ht] 
@@ -90,5 +90,5 @@
 $\rho_0$ &amp; reference density &amp; constant &amp; \\
 $\varphi$ &amp; generic tracer &amp; cell &amp; e.g. $\Theta$, $S$ \\
 \hline 
-\end{tabular} \label{ocnTable:variables_Greek} 
+\end{tabular} \label{oceanTable:variables_Greek} 
 \end{table}

Modified: trunk/documents/users_guide/ocean/namelist_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocean/namelist_table_documentation.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/namelist_table_documentation.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -3,7 +3,7 @@
 Embedded links point to more detailed namelist information in the appendix.
 \section[time\_management]{\hyperref[sec:nm_sec_time_management]{time\_management}}
 \label{sec:nm_tab_time_management}
-\input{ocn/section_descriptions/time_management.tex}
+\input{ocean/section_descriptions/time_management.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -60,7 +60,7 @@
 }
 \section[time\_integration]{\hyperref[sec:nm_sec_time_integration]{time\_integration}}
 \label{sec:nm_tab_time_integration}
-\input{ocn/section_descriptions/time_integration.tex}
+\input{ocean/section_descriptions/time_integration.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -77,7 +77,7 @@
 }
 \section[grid]{\hyperref[sec:nm_sec_grid]{grid}}
 \label{sec:nm_tab_grid}
-\input{ocn/section_descriptions/grid.tex}
+\input{ocean/section_descriptions/grid.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -100,7 +100,7 @@
 }
 \section[decomposition]{\hyperref[sec:nm_sec_decomposition]{decomposition}}
 \label{sec:nm_tab_decomposition}
-\input{ocn/section_descriptions/decomposition.tex}
+\input{ocean/section_descriptions/decomposition.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -121,7 +121,7 @@
 }
 \section[hmix]{\hyperref[sec:nm_sec_hmix]{hmix}}
 \label{sec:nm_tab_hmix}
-\input{ocn/section_descriptions/hmix.tex}
+\input{ocean/section_descriptions/hmix.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -140,7 +140,7 @@
 }
 \section[hmix\_del2]{\hyperref[sec:nm_sec_hmix_del2]{hmix\_del2}}
 \label{sec:nm_tab_hmix_del2}
-\input{ocn/section_descriptions/hmix_del2.tex}
+\input{ocean/section_descriptions/hmix_del2.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -163,7 +163,7 @@
 }
 \section[hmix\_del4]{\hyperref[sec:nm_sec_hmix_del4]{hmix\_del4}}
 \label{sec:nm_tab_hmix_del4}
-\input{ocn/section_descriptions/hmix_del4.tex}
+\input{ocean/section_descriptions/hmix_del4.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -186,7 +186,7 @@
 }
 \section[hmix\_Leith]{\hyperref[sec:nm_sec_hmix_Leith]{hmix\_Leith}}
 \label{sec:nm_tab_hmix_Leith}
-\input{ocn/section_descriptions/hmix_Leith.tex}
+\input{ocean/section_descriptions/hmix_Leith.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -223,7 +223,7 @@
 }
 \section[Rayleigh\_damping]{\hyperref[sec:nm_sec_Rayleigh_damping]{Rayleigh\_damping}}
 \label{sec:nm_tab_Rayleigh_damping}
-\input{ocn/section_descriptions/Rayleigh_damping.tex}
+\input{ocean/section_descriptions/Rayleigh_damping.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -346,7 +346,7 @@
 }
 \section[advection]{\hyperref[sec:nm_sec_advection]{advection}}
 \label{sec:nm_tab_advection}
-\input{ocn/section_descriptions/advection.tex}
+\input{ocean/section_descriptions/advection.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -399,7 +399,7 @@
 }
 \section[eos]{\hyperref[sec:nm_sec_eos]{eos}}
 \label{sec:nm_tab_eos}
-\input{ocn/section_descriptions/eos.tex}
+\input{ocean/section_descriptions/eos.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -414,7 +414,7 @@
 }
 \section[eos\_linear]{\hyperref[sec:nm_sec_eos_linear]{eos\_linear}}
 \label{sec:nm_tab_eos_linear}
-\input{ocn/section_descriptions/eos_linear.tex}
+\input{ocean/section_descriptions/eos_linear.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -473,7 +473,7 @@
 }
 \section[debug]{\hyperref[sec:nm_sec_debug]{debug}}
 \label{sec:nm_tab_debug}
-\input{ocn/section_descriptions/debug.tex}
+\input{ocean/section_descriptions/debug.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 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/section_descriptions/Rayleigh_damping.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -1,2 +1,2 @@
-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 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 $-c_R {\bf u}$.
 

Modified: trunk/documents/users_guide/ocean/section_descriptions/hmix.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/hmix.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/section_descriptions/hmix.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -4,8 +4,10 @@
 schemes have the practical effect of reducing grid-scale noise in the 
 velocity and tracer fields, and improving numerical stability.
 
-Each horizontal mixing scheme has its own namelist, and may be turned on 
-with the \verb|_use_| logical configuration flags.  Multiple schemes may 
-be run simultaneously.  The horizontal mixing term is ${\bf D}^u_h$ for 
-momentum and $D^\varphi_h$ for tracers.  No horizontal mixing is applied 
-to the thickness equation.
+Each horizontal mixing scheme has its own namelist, and may be turned
+on with the \verb|_use_| logical configuration flags.  Multiple
+schemes may be run simultaneously.  The horizontal mixing terms in the
+governing equations (\ref{ocean:momentum continuous 1},
+\ref{ocean:tracer continuous 1}) are ${\bf D}^u_h$ for momentum and
+$D^\varphi_h$ for tracers.  No horizontal mixing is applied to the
+thickness equation.

Modified: trunk/documents/users_guide/ocean/section_descriptions/hmix_del2.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/hmix_del2.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/section_descriptions/hmix_del2.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -6,7 +6,7 @@
 \label{h_tr_diff_cont}
 &amp; D^\varphi_h = </font>
<font color="black">abla\cdot\left(h \kappa_h </font>
<font color="gray">abla\varphi \right)
 \end{eqnarray}
-for momentum and tracers, respectively.  Variable definitions appear in Tables \ref{ocnTable:variables} and \ref{ocnTable:variables_Greek}.  The momentum diffusion is in divergence-vorticity form because it is a natural discretization of the vector Laplacian operator with a C-grid staggering.
+for momentum and tracers, respectively.  Variable definitions appear in Tables \ref{oceanTable:variables} and \ref{oceanTable:variables_Greek}.  The momentum diffusion is in divergence-vorticity form because it is a natural discretization of the vector Laplacian operator with a C-grid staggering.
 
 
 The Laplacian operator smooths the momentum and 

Modified: trunk/documents/users_guide/ocean/section_descriptions/hmix_del4.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/hmix_del4.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/section_descriptions/hmix_del4.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -1,4 +1,3 @@
-{\color{red} TBA: check negative sign}
 The ``del4'', or biharmonic, turbulence closures are
 \begin{eqnarray}
 \label{h_mom_del4_cont}
@@ -14,7 +13,6 @@
 &amp;\delta_2=</font>
<font color="black">abla\cdot(</font>
<font color="black">abla^2{\bf u})\\
 &amp;\eta_2={\bf k} \cdot \left( </font>
<font color="black">abla \times (</font>
<font color="black">abla^2{\bf u}) \right)+f\\
 &amp; {\bf D}^u_h= </font>
<font color="black">u_h (</font>
<font color="black">abla \delta_2 + {\bf k}\times </font>
<font color="gray">abla \eta_2)
-\label{h_tr_del4_cont}
 \end{eqnarray}
 
 The biharmonic operator is similar to the Laplacian operator, but smooths more strongly at high wavenumbers.

Modified: trunk/documents/users_guide/ocean/test_case_descriptions.tex
===================================================================
--- trunk/documents/users_guide/ocean/test_case_descriptions.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/test_case_descriptions.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -1,5 +1,5 @@
 \chapter{Test Cases}
 \label{chap:ocean_test_cases}
 
-\input{ocn/test_cases/baroclinic_channel.tex}
+\input{ocean/test_cases/baroclinic_channel.tex}
 

Modified: trunk/documents/users_guide/ocean/test_cases/baroclinic_channel.tex
===================================================================
--- trunk/documents/users_guide/ocean/test_cases/baroclinic_channel.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/test_cases/baroclinic_channel.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -54,8 +54,8 @@
         \label{fig:baroclinicChannelTemperature}
         \centering
         \caption{Baroclinic channel test case results. Surface temperature field after 10 simulation days using default included namelists.}
-        \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}}
-        \subfigure[1km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocn/figures/baroclinic_channel_1000m_20levs_10days.pdf}}
+        \subfigure[10km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocean/figures/baroclinic_channel_10000m_20levs_10days.pdf}}
+        \subfigure[4km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocean/figures/baroclinic_channel_4000m_20levs_10days.pdf}}
+        \subfigure[1km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocean/figures/baroclinic_channel_1000m_20levs_10days.pdf}}
 \end{figure}
 

Modified: trunk/documents/users_guide/ocean/variable_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocean/variable_table_documentation.tex        2013-03-13 12:48:50 UTC (rev 2596)
+++ trunk/documents/users_guide/ocean/variable_table_documentation.tex        2013-03-13 13:14:43 UTC (rev 2597)
@@ -3,7 +3,7 @@
 Embedded links point to more detailed variable information in the appendix.
 \section[state]{\hyperref[sec:var_sec_state]{state}}
 \label{sec:var_tab_state}
-\input{ocn/section_descriptions/state.tex}
+\input{ocean/section_descriptions/state.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -163,7 +163,7 @@
 }
 \section[mesh]{\hyperref[sec:var_sec_mesh]{mesh}}
 \label{sec:var_tab_mesh}
-\input{ocn/section_descriptions/mesh.tex}
+\input{ocean/section_descriptions/mesh.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -339,7 +339,7 @@
 }
 \section[tend]{\hyperref[sec:var_sec_tend]{tend}}
 \label{sec:var_tab_tend}
-\input{ocn/section_descriptions/tend.tex}
+\input{ocean/section_descriptions/tend.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -363,7 +363,7 @@
 }
 \section[diagnostics]{\hyperref[sec:var_sec_diagnostics]{diagnostics}}
 \label{sec:var_tab_diagnostics}
-\input{ocn/section_descriptions/diagnostics.tex}
+\input{ocean/section_descriptions/diagnostics.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}

</font>
</pre>