<p><b>dwj07@fsu.edu</b> 2013-02-25 10:21:52 -0700 (Mon, 25 Feb 2013)</p><p><br>
-- DOCUMENTS COMMIT --<br>
<br>
Adding ocean specific documentation. <br>
Removing appendix line from visualization section.<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 2013-02-22 00:11:49 UTC (rev 2505)
+++ trunk/documents/users_guide/mpas_ocean_users_guide.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -32,5 +32,14 @@
\input{shared/mpas_grid_information.tex}
\input{shared/mpas_visualization.tex}
+\part{Ocean Model Specifics}
+\input{ocn/dimension_table_documentation.tex}
+\input{ocn/namelist_table_documentation.tex}
+\input{ocn/variable_table_documentation.tex}
+\input{ocn/namelist_section_documentation.tex}
+\input{ocn/variable_section_documentation.tex}
+
\end{document}
+
+
Added: trunk/documents/users_guide/ocn/dimension_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/dimension_table_documentation.tex (rev 0)
+++ trunk/documents/users_guide/ocn/dimension_table_documentation.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -0,0 +1,38 @@
+\chapter{Dimensions}
+{\small
+\begin{center}
+\begin{longtable}{| c | c |}
+ \hline
+ Name & Description \\
+ \hline
+ nCells & {\bf \color{red} MISSING} \\
+ \hline
+ nEdges & {\bf \color{red} MISSING} \\
+ \hline
+ maxEdges & {\bf \color{red} MISSING} \\
+ \hline
+ maxEdges2 & {\bf \color{red} MISSING} \\
+ \hline
+ nAdvectionCells & {\bf \color{red} MISSING} \\
+ \hline
+ nVertices & {\bf \color{red} MISSING} \\
+ \hline
+ TWO & {\bf \color{red} MISSING} \\
+ \hline
+ R3 & {\bf \color{red} MISSING} \\
+ \hline
+ FIFTEEN & {\bf \color{red} MISSING} \\
+ \hline
+ TWENTYONE & {\bf \color{red} MISSING} \\
+ \hline
+ vertexDegree & {\bf \color{red} MISSING} \\
+ \hline
+ nVertLevels & {\bf \color{red} MISSING} \\
+ \hline
+ nVertLevelsP1 & {\bf \color{red} MISSING} \\
+ \hline
+ nMonths & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
Added: trunk/documents/users_guide/ocn/namelist_section_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/namelist_section_documentation.tex (rev 0)
+++ trunk/documents/users_guide/ocn/namelist_section_documentation.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -0,0 +1,1122 @@
+\chapter{Namelist options}
+\section{time\_management}
+\label{sec:nm_sec_time_management}
+\subsection{config\_do\_restart}
+\label{subsec:nm_sec_config_do_restart}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls starting simulation from a restart, or inital conditions that are built into the input file.
+\end{itemize}
+\subsection{config\_start\_time}
+\label{subsec:nm_sec_config_start_time}
+\begin{itemize}
+ \item Type: string
+ \item Units: YYYY\_MM\_DD\_HH:MM:SS
+ \item Default Value: '0000-01-01\_00:00:00'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Time stamp that describes the initial time of the simulation.
+\end{itemize}
+\subsection{config\_stop\_time}
+\label{subsec:nm_sec_config_stop_time}
+\begin{itemize}
+ \item Type: string
+ \item Units: YYYY\_MM\_DD\_HH:MM:SS
+ \item Default Value: 'none'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Time stamp that describes the ending time of the simulation. If the value is 'none', config\_stop\_time is inferred using config\_run\_duration and config\_start\_time.
+\end{itemize}
+\subsection{config\_run\_duration}
+\label{subsec:nm_sec_config_run_duration}
+\begin{itemize}
+ \item Type: string
+ \item Units: DD\_HH:MM:SS
+ \item Default Value: '0\_06:00:00'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Time stamp that describes the amount of time in the simulation. If the value is 'none', config\_run\_duration is inferred using config\_start\_time and config\_stop\_time.
+\end{itemize}
+\subsection{config\_calendar\_type}
+\label{subsec:nm_sec_config_calendar_type}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: '360day'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Calendar type that defines the calendar used in the simualtion.
+\end{itemize}
+\section{io}
+\label{sec:nm_sec_io}
+\subsection{config\_input\_name}
+\label{subsec:nm_sec_config_input_name}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'grid.nc'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: String that defines the full or relative path to the input file.
+\end{itemize}
+\subsection{config\_output\_name}
+\label{subsec:nm_sec_config_output_name}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'output.nc'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: String that defines the full or relative path to where the output file(s) will be written.
+\end{itemize}
+\subsection{config\_restart\_name}
+\label{subsec:nm_sec_config_restart_name}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'restart.nc'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: String that defines the full or relative path to where the restart file(s) will be read and written.
+\end{itemize}
+\subsection{config\_restart\_interval}
+\label{subsec:nm_sec_config_restart_interval}
+\begin{itemize}
+ \item Type: string
+ \item Units: DD\_HH:MM:SS
+ \item Default Value: '0\_06:00:00'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Time stamp that defines how often restart files should be written.
+\end{itemize}
+\subsection{config\_output\_interval}
+\label{subsec:nm_sec_config_output_interval}
+\begin{itemize}
+ \item Type: string
+ \item Units: DD\_HH:MM:SS
+ \item Default Value: '0\_06:00:00'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Time stamp that defines how often output files should be written.
+\end{itemize}
+\subsection{config\_stats\_interval}
+\label{subsec:nm_sec_config_stats_interval}
+\begin{itemize}
+ \item Type: string
+ \item Units: DD\_HH:MM:SS
+ \item Default Value: '0\_01:00:00'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Time stamp that defines how often statistics output should be written.
+\end{itemize}
+\subsection{config\_write\_stats\_on\_startup}
+\label{subsec:nm_sec_config_write_stats_on_startup}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that defines if statistics should be computed using the initial conditions.
+\end{itemize}
+\subsection{config\_write\_output\_on\_startup}
+\label{subsec:nm_sec_config_write_output_on_startup}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that defines if output should be performed using the initial conditions.
+\end{itemize}
+\subsection{config\_frames\_per\_outfile}
+\label{subsec:nm_sec_config_frames_per_outfile}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 1000
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Number of time slices in an output file.
+\end{itemize}
+\subsection{config\_pio\_num\_iotasks}
+\label{subsec:nm_sec_config_pio_num_iotasks}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Number of iotasks used with PIO in the simulation.
+\end{itemize}
+\subsection{config\_pio\_stride}
+\label{subsec:nm_sec_config_pio_stride}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 1
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Stride of PIO iotasks in the simulation.
+\end{itemize}
+\section{time\_integration}
+\label{sec:nm_sec_time_integration}
+\subsection{config\_dt}
+\label{subsec:nm_sec_config_dt}
+\begin{itemize}
+ \item Type: real
+ \item Units: Seconds
+ \item Default Value: 3000.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Length of a single time step.
+\end{itemize}
+\subsection{config\_time\_integrator}
+\label{subsec:nm_sec_config_time_integrator}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'split\_explicit'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Time integration scheme to be used for the simulation.
+\end{itemize}
+\section{grid}
+\label{sec:nm_sec_grid}
+\subsection{config\_num\_halos}
+\label{subsec:nm_sec_config_num_halos}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 3
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Defines the number of halos extending outward from owned cells.
+\end{itemize}
+\subsection{config\_vert\_coord\_movement}
+\label{subsec:nm_sec_config_vert_coord_movement}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'uniform\_stretching'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Defines the movement of the vertical coordinate.
+\end{itemize}
+\subsection{config\_alter\_ICs\_for\_pbcs}
+\label{subsec:nm_sec_config_alter_ICs_for_pbcs}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'zlevel\_pbcs\_off'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls how or if partial bottom cells are used.
+\end{itemize}
+\subsection{config\_min\_pbc\_fraction}
+\label{subsec:nm_sec_config_min_pbc_fraction}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.10
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Defines the minimum allowed fraction for partial bottom cells.
+\end{itemize}
+\subsection{config\_check\_ssh\_consistency}
+\label{subsec:nm_sec_config_check_ssh_consistency}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that enables an initial consistency check for sea surface height.
+\end{itemize}
+\section{decomposition}
+\label{sec:nm_sec_decomposition}
+\subsection{config\_block\_decomp\_file\_prefix}
+\label{subsec:nm_sec_config_block_decomp_file_prefix}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'graph.info.part.'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: String that defines the full or relative path and prefix for the block decomposition files.
+\end{itemize}
+\subsection{config\_number\_of\_blocks}
+\label{subsec:nm_sec_config_number_of_blocks}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: The number of computational blocks in the simulation.
+\end{itemize}
+\subsection{config\_explicit\_proc\_decomp}
+\label{subsec:nm_sec_config_explicit_proc_decomp}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that enables/disables the use of a config\_proc\_decomp\_file to distribute computational blocks through processors.
+\end{itemize}
+\subsection{config\_proc\_decomp\_file\_prefix}
+\label{subsec:nm_sec_config_proc_decomp_file_prefix}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'graph.info.part.'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: String that defines the fille or relative path and prefix for the processor decomposition files.
+\end{itemize}
+\section{hmix}
+\label{sec:nm_sec_hmix}
+\input{ocn/section_descriptions/hmix.tex}
+\subsection{config\_hmix\_ScaleWithMesh}
+\label{subsec:nm_sec_config_hmix_ScaleWithMesh}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if horizontal mixing parameters scale with the mesh density.
+\end{itemize}
+\subsection{config\_visc\_vorticity\_term}
+\label{subsec:nm_sec_config_visc_vorticity_term}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_apvm\_scale\_factor}
+\label{subsec:nm_sec_config_apvm_scale_factor}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\section{hmix\_del2}
+\label{sec:nm_sec_hmix_del2}
+\input{ocn/section_descriptions/hmix_del2.tex}
+\subsection{config\_use\_mom\_del2}
+\label{subsec:nm_sec_config_use_mom_del2}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if del2 will be used for horizontal mixing of momentum.
+\end{itemize}
+\subsection{config\_use\_tracer\_del2}
+\label{subsec:nm_sec_config_use_tracer_del2}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if del2 will be used for horizontal mixing of tracers.
+\end{itemize}
+\subsection{config\_mom\_del2}
+\label{subsec:nm_sec_config_mom_del2}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of del2 coefficient for horizontal mixing of momentum.
+\end{itemize}
+\subsection{config\_tracer\_del2}
+\label{subsec:nm_sec_config_tracer_del2}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of del2 coefficient for horizontal mixing of tracers.
+\end{itemize}
+\subsection{config\_vorticity\_del2\_scale}
+\label{subsec:nm_sec_config_vorticity_del2_scale}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\section{hmix\_del4}
+\label{sec:nm_sec_hmix_del4}
+\subsection{config\_use\_mom\_del4}
+\label{subsec:nm_sec_config_use_mom_del4}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if del4 will be used for horizontal mixing of momentum.
+\end{itemize}
+\subsection{config\_use\_tracer\_del4}
+\label{subsec:nm_sec_config_use_tracer_del4}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if del4 will be used for horizontal mixing of tracers.
+\end{itemize}
+\subsection{config\_mom\_del4}
+\label{subsec:nm_sec_config_mom_del4}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 5.0e13
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of del4 coefficient for horizontal mixing of momentum.
+\end{itemize}
+\subsection{config\_tracer\_del4}
+\label{subsec:nm_sec_config_tracer_del4}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of del4 coefficient for horizontal mixing of tracers.
+\end{itemize}
+\subsection{config\_vorticity\_del4\_scale}
+\label{subsec:nm_sec_config_vorticity_del4_scale}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\section{hmix\_Leith}
+\label{sec:nm_sec_hmix_Leith}
+\subsection{config\_use\_Leith\_del2}
+\label{subsec:nm_sec_config_use_Leith_del2}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if the Leith closure will be used for horizontal mixing.
+\end{itemize}
+\subsection{config\_Leith\_parameter}
+\label{subsec:nm_sec_config_Leith_parameter}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_Leith\_dx}
+\label{subsec:nm_sec_config_Leith_dx}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 15000.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_Leith\_visc2\_max}
+\label{subsec:nm_sec_config_Leith_visc2_max}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 2.5e3
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\section{standard\_GM}
+\label{sec:nm_sec_standard_GM}
+\subsection{config\_h\_kappa}
+\label{subsec:nm_sec_config_h_kappa}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_h\_kappa\_q}
+\label{subsec:nm_sec_config_h_kappa_q}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\section{Rayleigh\_damping}
+\label{sec:nm_sec_Rayleigh_damping}
+\subsection{config\_Rayleigh\_friction}
+\label{subsec:nm_sec_config_Rayleigh_friction}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if Rayleigh friction will be used in the simulation.
+\end{itemize}
+\subsection{config\_Rayleigh\_damping\_coeff}
+\label{subsec:nm_sec_config_Rayleigh_damping_coeff}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of the Rayleigh friction coefficient.
+\end{itemize}
+\section{vmix}
+\label{sec:nm_sec_vmix}
+\subsection{config\_implicit\_vertical\_mix}
+\label{subsec:nm_sec_config_implicit_vertical_mix}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEPRECATED}
+\end{itemize}
+\subsection{config\_convective\_visc}
+\label{subsec:nm_sec_config_convective_visc}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of coefficient for convective vertical mixing of momentum.
+\end{itemize}
+\subsection{config\_convective\_diff}
+\label{subsec:nm_sec_config_convective_diff}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of coefficient for convective vertical mixing of tracers.
+\end{itemize}
+\section{vmix\_const}
+\label{sec:nm_sec_vmix_const}
+\subsection{config\_use\_const\_visc}
+\label{subsec:nm_sec_config_use_const_visc}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if constant vertical mixing of momentum is used.
+\end{itemize}
+\subsection{config\_use\_const\_diff}
+\label{subsec:nm_sec_config_use_const_diff}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if constant vertical mixing of tracers is used.
+\end{itemize}
+\subsection{config\_vert\_visc}
+\label{subsec:nm_sec_config_vert_visc}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 2.5e-4
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of coefficient for constant vertical mixing of momentum.
+\end{itemize}
+\subsection{config\_vert\_diff}
+\label{subsec:nm_sec_config_vert_diff}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 2.5e-5
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of coefficient for constant vertical mixing of tracers.
+\end{itemize}
+\section{vmix\_rich}
+\label{sec:nm_sec_vmix_rich}
+\subsection{config\_use\_rich\_visc}
+\label{subsec:nm_sec_config_use_rich_visc}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if Richarson number vertical mixing of momentum is used.
+\end{itemize}
+\subsection{config\_use\_rich\_diff}
+\label{subsec:nm_sec_config_use_rich_diff}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if Richarson number vertical mixing of tracers is used.
+\end{itemize}
+\subsection{config\_bkrd\_vert\_visc}
+\label{subsec:nm_sec_config_bkrd_vert_visc}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0e-4
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of coefficient for Richardson number vertical mixing of momentum.
+\end{itemize}
+\subsection{config\_bkrd\_vert\_diff}
+\label{subsec:nm_sec_config_bkrd_vert_diff}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0e-5
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of coefficient for Richardson number vertical mixing of tracers.
+\end{itemize}
+\subsection{config\_rich\_mix}
+\label{subsec:nm_sec_config_rich_mix}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.005
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\section{vmix\_tanh}
+\label{sec:nm_sec_vmix_tanh}
+\subsection{config\_use\_tanh\_visc}
+\label{subsec:nm_sec_config_use_tanh_visc}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if hyperbolic tangent vertical mixing of momentum is used.
+\end{itemize}
+\subsection{config\_use\_tanh\_diff}
+\label{subsec:nm_sec_config_use_tanh_diff}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if hyperbolic tangent vertical mixing of tracers is used.
+\end{itemize}
+\subsection{config\_max\_visc\_tanh}
+\label{subsec:nm_sec_config_max_visc_tanh}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 2.5e-1
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_min\_visc\_tanh}
+\label{subsec:nm_sec_config_min_visc_tanh}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0e-4
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_max\_diff\_tanh}
+\label{subsec:nm_sec_config_max_diff_tanh}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 2.5e-2
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_min\_diff\_tanh}
+\label{subsec:nm_sec_config_min_diff_tanh}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0e-5
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_zMid\_tanh}
+\label{subsec:nm_sec_config_zMid_tanh}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: -100
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_zWidth\_tanh}
+\label{subsec:nm_sec_config_zWidth_tanh}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 100
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\section{forcing}
+\label{sec:nm_sec_forcing}
+\subsection{config\_use\_monthly\_forcing}
+\label{subsec:nm_sec_config_use_monthly_forcing}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if monthly forcing is used in the simulation.
+\end{itemize}
+\subsection{config\_restoreTS}
+\label{subsec:nm_sec_config_restoreTS}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls is temperature and salinity restoring is used in the simulation.
+\end{itemize}
+\subsection{config\_restoreT\_timescale}
+\label{subsec:nm_sec_config_restoreT_timescale}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 90.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value in days of the restoring timescale for temperature.
+\end{itemize}
+\subsection{config\_restoreS\_timescale}
+\label{subsec:nm_sec_config_restoreS_timescale}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 90.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value in days of the restoring timescale for salinity.
+\end{itemize}
+\section{advection}
+\label{sec:nm_sec_advection}
+\subsection{config\_vert\_tracer\_adv}
+\label{subsec:nm_sec_config_vert_tracer_adv}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'stencil'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEPRECATED}
+\end{itemize}
+\subsection{config\_vert\_tracer\_adv\_order}
+\label{subsec:nm_sec_config_vert_tracer_adv_order}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 3
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Order of vertical reconstruction of tracers used for vertical advection.
+\end{itemize}
+\subsection{config\_horiz\_tracer\_adv\_order}
+\label{subsec:nm_sec_config_horiz_tracer_adv_order}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 3
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Order of horizontal reconstruction of tracers used for horizontal advection.
+\end{itemize}
+\subsection{config\_coef\_3rd\_order}
+\label{subsec:nm_sec_config_coef_3rd_order}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.25
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Blending coefficient for 3rd and 4th order horizontal reconstruction of tracers.
+\end{itemize}
+\subsection{config\_monotonic}
+\label{subsec:nm_sec_config_monotonic}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that controls if monotonic advection is used in the simulation.
+\end{itemize}
+\section{bottom\_drag}
+\label{sec:nm_sec_bottom_drag}
+\subsection{config\_bottom\_drag\_coeff}
+\label{subsec:nm_sec_config_bottom_drag_coeff}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0e-3
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of the bottom drag coefficient.
+\end{itemize}
+\section{pressure\_gradient}
+\label{sec:nm_sec_pressure_gradient}
+\subsection{config\_pressure\_gradient\_type}
+\label{subsec:nm_sec_config_pressure_gradient_type}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'pressure\_and\_zmid'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: String that defines the type of pressure gradient used in the simulation.
+\end{itemize}
+\subsection{config\_rho0}
+\label{subsec:nm_sec_config_rho0}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1014.65
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of the reference density for the Boussineq approximation.
+\end{itemize}
+\section{eos}
+\label{sec:nm_sec_eos}
+\subsection{config\_eos\_type}
+\label{subsec:nm_sec_config_eos_type}
+\begin{itemize}
+ \item Type: string
+ \item Units: None
+ \item Default Value: 'jm'
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: String that defines the equation of state used in the simulation.
+\end{itemize}
+\section{eos\_linear}
+\label{sec:nm_sec_eos_linear}
+\subsection{config\_eos\_linear\_alpha}
+\label{subsec:nm_sec_config_eos_linear_alpha}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 2.55e-1
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of temperature expansion coefficient used in the linear equation of state.
+\end{itemize}
+\subsection{config\_eos\_linear\_beta}
+\label{subsec:nm_sec_config_eos_linear_beta}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 7.64e-1
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of salinity expansion coefficient used in the linear equation of state.
+\end{itemize}
+\subsection{config\_eos\_linear\_Tref}
+\label{subsec:nm_sec_config_eos_linear_Tref}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 19.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of the reference temperature used in the linear equation of state.
+\end{itemize}
+\subsection{config\_eos\_linear\_Sref}
+\label{subsec:nm_sec_config_eos_linear_Sref}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 35.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of the reference salinity used in the linear equation of state.
+\end{itemize}
+\subsection{config\_eos\_linear\_rhoref}
+\label{subsec:nm_sec_config_eos_linear_rhoref}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1025.022
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Value of the reference density used in the linear equation of state.
+\end{itemize}
+\section{split\_explicit\_ts}
+\label{sec:nm_sec_split_explicit_ts}
+\subsection{config\_n\_ts\_iter}
+\label{subsec:nm_sec_config_n_ts_iter}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 2
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_n\_bcl\_iter\_beg}
+\label{subsec:nm_sec_config_n_bcl_iter_beg}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 1
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_n\_bcl\_iter\_mid}
+\label{subsec:nm_sec_config_n_bcl_iter_mid}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 2
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_n\_bcl\_iter\_end}
+\label{subsec:nm_sec_config_n_bcl_iter_end}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 2
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_n\_btr\_subcycles}
+\label{subsec:nm_sec_config_n_btr_subcycles}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 20
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_n\_btr\_cor\_iter}
+\label{subsec:nm_sec_config_n_btr_cor_iter}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 2
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_u\_correction}
+\label{subsec:nm_sec_config_u_correction}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .true.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_btr\_subcycle\_loop\_factor}
+\label{subsec:nm_sec_config_btr_subcycle_loop_factor}
+\begin{itemize}
+ \item Type: integer
+ \item Units: None
+ \item Default Value: 2
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_btr\_gam1\_uWt1}
+\label{subsec:nm_sec_config_btr_gam1_uWt1}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 0.5
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_btr\_gam2\_SSHWt1}
+\label{subsec:nm_sec_config_btr_gam2_SSHWt1}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_btr\_gam3\_uWt2}
+\label{subsec:nm_sec_config_btr_gam3_uWt2}
+\begin{itemize}
+ \item Type: real
+ \item Units: None
+ \item Default Value: 1.0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_btr\_solve\_SSH2}
+\label{subsec:nm_sec_config_btr_solve_SSH2}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\section{sw\_model}
+\label{sec:nm_sec_sw_model}
+\subsection{config\_test\_case}
+\label{subsec:nm_sec_config_test_case}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Default Value: 0
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\section{debug}
+\label{sec:nm_sec_debug}
+\subsection{config\_check\_zlevel\_consistency}
+\label{subsec:nm_sec_config_check_zlevel_consistency}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that enables a zlevel consistency check on initialization.
+\end{itemize}
+\subsection{config\_filter\_btr\_mode}
+\label{subsec:nm_sec_config_filter_btr_mode}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that enables the filtering of the barotropic mode.
+\end{itemize}
+\subsection{config\_prescribe\_velocity}
+\label{subsec:nm_sec_config_prescribe_velocity}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that enables prescribed velocities, read from the input file, that remain constant throughout the simulation.
+\end{itemize}
+\subsection{config\_prescribe\_thickness}
+\label{subsec:nm_sec_config_prescribe_thickness}
+\begin{itemize}
+ \item Type: logical
+ \item Units: {\bf \color{red} MISSING}
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{config\_include\_KE\_vertex}
+\label{subsec:nm_sec_config_include_KE_vertex}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: {\bf \color{red} DEFINE}
+\end{itemize}
+\subsection{config\_check\_tracer\_monotonicity}
+\label{subsec:nm_sec_config_check_tracer_monotonicity}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that enables the check for monotonicity of tracers. Only available if config\_monotoic is true.
+\end{itemize}
+\subsection{config\_disable\_h\_all\_tend}
+\label{subsec:nm_sec_config_disable_h_all_tend}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables all thickness tendencies.
+\end{itemize}
+\subsection{config\_disable\_h\_hadv}
+\label{subsec:nm_sec_config_disable_h_hadv}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables horizontal advection of thickness.
+\end{itemize}
+\subsection{config\_disable\_h\_vadv}
+\label{subsec:nm_sec_config_disable_h_vadv}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables vertical advection of thickness.
+\end{itemize}
+\subsection{config\_disable\_u\_all\_tend}
+\label{subsec:nm_sec_config_disable_u_all_tend}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables all velocitiy tendencies.
+\end{itemize}
+\subsection{config\_disable\_u\_coriolis}
+\label{subsec:nm_sec_config_disable_u_coriolis}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables Coriolis tendencies of velocity.
+\end{itemize}
+\subsection{config\_disable\_u\_pgrad}
+\label{subsec:nm_sec_config_disable_u_pgrad}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables pressure gradient tendencies of velocity.
+\end{itemize}
+\subsection{config\_disable\_u\_hmix}
+\label{subsec:nm_sec_config_disable_u_hmix}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables horizontal mixing tendencies of velocity.
+\end{itemize}
+\subsection{config\_disable\_u\_windstress}
+\label{subsec:nm_sec_config_disable_u_windstress}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables windstress tendencies of velocity.
+\end{itemize}
+\subsection{config\_disable\_u\_vmix}
+\label{subsec:nm_sec_config_disable_u_vmix}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables vertical mixing of velocity.
+\end{itemize}
+\subsection{config\_disable\_u\_vadv}
+\label{subsec:nm_sec_config_disable_u_vadv}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables vertical advection tendencies of velocity.
+\end{itemize}
+\subsection{config\_disable\_tr\_all\_tend}
+\label{subsec:nm_sec_config_disable_tr_all_tend}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables all tracer tendencies.
+\end{itemize}
+\subsection{config\_disable\_tr\_adv}
+\label{subsec:nm_sec_config_disable_tr_adv}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables advection tendencites of tracers.
+\end{itemize}
+\subsection{config\_disable\_tr\_hmix}
+\label{subsec:nm_sec_config_disable_tr_hmix}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag that disables horizontal mixing tendencites of tracers.
+\end{itemize}
+\subsection{config\_disable\_tr\_vmix}
+\label{subsec:nm_sec_config_disable_tr_vmix}
+\begin{itemize}
+ \item Type: logical
+ \item Units: None
+ \item Default Value: .false.
+ \item Possible Values: {\bf \color{red} MISSING}
+ \item Description: Flag taht disables vertical mixing of tracers.
+\end{itemize}
Added: trunk/documents/users_guide/ocn/namelist_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/namelist_table_documentation.tex (rev 0)
+++ trunk/documents/users_guide/ocn/namelist_table_documentation.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -0,0 +1,505 @@
+\chapter{Namelist options}
+\section{time\_management}
+\label{sec:nm_tab_time_management}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_do_restart]{config\_do\_restart} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_start_time]{config\_start\_time} & '0000-01-01\_00:00:00' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_stop_time]{config\_stop\_time} & 'none' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_run_duration]{config\_run\_duration} & '0\_06:00:00' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_calendar_type]{config\_calendar\_type} & '360day' & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{io}
+\label{sec:nm_tab_io}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_input_name]{config\_input\_name} & 'grid.nc' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_output_name]{config\_output\_name} & 'output.nc' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_restart_name]{config\_restart\_name} & 'restart.nc' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_restart_interval]{config\_restart\_interval} & '0\_06:00:00' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_output_interval]{config\_output\_interval} & '0\_06:00:00' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_stats_interval]{config\_stats\_interval} & '0\_01:00:00' & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_write_stats_on_startup]{config\_write\_stats\_on\_startup} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_write_output_on_startup]{config\_write\_output\_on\_startup} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_frames_per_outfile]{config\_frames\_per\_outfile} & 1000 & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_pio_num_iotasks]{config\_pio\_num\_iotasks} & 0 & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_pio_stride]{config\_pio\_stride} & 1 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{time\_integration}
+\label{sec:nm_tab_time_integration}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_dt]{config\_dt} & 3000.0 & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_time_integrator]{config\_time\_integrator} & 'split\_explicit' & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{grid}
+\label{sec:nm_tab_grid}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_num_halos]{config\_num\_halos} & 3 & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_vert_coord_movement]{config\_vert\_coord\_movement} & 'uniform\_stretching' & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_alter_ICs_for_pbcs]{config\_alter\_ICs\_for\_pbcs} & 'zlevel\_pbcs\_off' & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_min_pbc_fraction]{config\_min\_pbc\_fraction} & 0.10 & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_check_ssh_consistency]{config\_check\_ssh\_consistency} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{decomposition}
+\label{sec:nm_tab_decomposition}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_block_decomp_file_prefix]{config\_block\_decomp\_file\_prefix} & 'graph.info.part.' & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_number_of_blocks]{config\_number\_of\_blocks} & 0 & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_explicit_proc_decomp]{config\_explicit\_proc\_decomp} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_proc_decomp_file_prefix]{config\_proc\_decomp\_file\_prefix} & 'graph.info.part.' & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{hmix}
+\label{sec:nm_tab_hmix}
+\input{ocn/section_descriptions/hmix.tex}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_hmix_ScaleWithMesh]{config\_hmix\_ScaleWithMesh} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_visc_vorticity_term]{config\_visc\_vorticity\_term} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_apvm_scale_factor]{config\_apvm\_scale\_factor} & 0.0 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{hmix\_del2}
+\label{sec:nm_tab_hmix_del2}
+\input{ocn/section_descriptions/hmix_del2.tex}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_mom_del2]{config\_use\_mom\_del2} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_tracer_del2]{config\_use\_tracer\_del2} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_mom_del2]{config\_mom\_del2} & 0.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_tracer_del2]{config\_tracer\_del2} & 0.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_vorticity_del2_scale]{config\_vorticity\_del2\_scale} & 1.0 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{hmix\_del4}
+\label{sec:nm_tab_hmix_del4}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_mom_del4]{config\_use\_mom\_del4} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_tracer_del4]{config\_use\_tracer\_del4} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_mom_del4]{config\_mom\_del4} & 5.0e13 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_tracer_del4]{config\_tracer\_del4} & 0.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_vorticity_del4_scale]{config\_vorticity\_del4\_scale} & 1.0 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{hmix\_Leith}
+\label{sec:nm_tab_hmix_Leith}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_Leith_del2]{config\_use\_Leith\_del2} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_Leith_parameter]{config\_Leith\_parameter} & 1.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_Leith_dx]{config\_Leith\_dx} & 15000.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_Leith_visc2_max]{config\_Leith\_visc2\_max} & 2.5e3 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{standard\_GM}
+\label{sec:nm_tab_standard_GM}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_h_kappa]{config\_h\_kappa} & 0.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_h_kappa_q]{config\_h\_kappa\_q} & 0.0 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{Rayleigh\_damping}
+\label{sec:nm_tab_Rayleigh_damping}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_Rayleigh_friction]{config\_Rayleigh\_friction} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_Rayleigh_damping_coeff]{config\_Rayleigh\_damping\_coeff} & 0.0 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{vmix}
+\label{sec:nm_tab_vmix}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_implicit_vertical_mix]{config\_implicit\_vertical\_mix} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_convective_visc]{config\_convective\_visc} & 1.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_convective_diff]{config\_convective\_diff} & 1.0 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{vmix\_const}
+\label{sec:nm_tab_vmix_const}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_const_visc]{config\_use\_const\_visc} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_const_diff]{config\_use\_const\_diff} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_vert_visc]{config\_vert\_visc} & 2.5e-4 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_vert_diff]{config\_vert\_diff} & 2.5e-5 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{vmix\_rich}
+\label{sec:nm_tab_vmix_rich}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_rich_visc]{config\_use\_rich\_visc} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_rich_diff]{config\_use\_rich\_diff} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_bkrd_vert_visc]{config\_bkrd\_vert\_visc} & 1.0e-4 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_bkrd_vert_diff]{config\_bkrd\_vert\_diff} & 1.0e-5 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_rich_mix]{config\_rich\_mix} & 0.005 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{vmix\_tanh}
+\label{sec:nm_tab_vmix_tanh}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_tanh_visc]{config\_use\_tanh\_visc} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_tanh_diff]{config\_use\_tanh\_diff} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_max_visc_tanh]{config\_max\_visc\_tanh} & 2.5e-1 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_min_visc_tanh]{config\_min\_visc\_tanh} & 1.0e-4 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_max_diff_tanh]{config\_max\_diff\_tanh} & 2.5e-2 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_min_diff_tanh]{config\_min\_diff\_tanh} & 1.0e-5 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_zMid_tanh]{config\_zMid\_tanh} & -100 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_zWidth_tanh]{config\_zWidth\_tanh} & 100 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{forcing}
+\label{sec:nm_tab_forcing}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_use_monthly_forcing]{config\_use\_monthly\_forcing} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_restoreTS]{config\_restoreTS} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_restoreT_timescale]{config\_restoreT\_timescale} & 90.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_restoreS_timescale]{config\_restoreS\_timescale} & 90.0 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{advection}
+\label{sec:nm_tab_advection}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_vert_tracer_adv]{config\_vert\_tracer\_adv} & 'stencil' & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_vert_tracer_adv_order]{config\_vert\_tracer\_adv\_order} & 3 & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_horiz_tracer_adv_order]{config\_horiz\_tracer\_adv\_order} & 3 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_coef_3rd_order]{config\_coef\_3rd\_order} & 0.25 & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_monotonic]{config\_monotonic} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{bottom\_drag}
+\label{sec:nm_tab_bottom_drag}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_bottom_drag_coeff]{config\_bottom\_drag\_coeff} & 1.0e-3 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{pressure\_gradient}
+\label{sec:nm_tab_pressure_gradient}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_pressure_gradient_type]{config\_pressure\_gradient\_type} & 'pressure\_and\_zmid' & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_rho0]{config\_rho0} & 1014.65 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{eos}
+\label{sec:nm_tab_eos}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ string \hyperref[subsec:nm_sec_config_eos_type]{config\_eos\_type} & 'jm' & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{eos\_linear}
+\label{sec:nm_tab_eos_linear}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_eos_linear_alpha]{config\_eos\_linear\_alpha} & 2.55e-1 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_eos_linear_beta]{config\_eos\_linear\_beta} & 7.64e-1 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_eos_linear_Tref]{config\_eos\_linear\_Tref} & 19.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_eos_linear_Sref]{config\_eos\_linear\_Sref} & 35.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_eos_linear_rhoref]{config\_eos\_linear\_rhoref} & 1025.022 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{split\_explicit\_ts}
+\label{sec:nm_tab_split_explicit_ts}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_n_ts_iter]{config\_n\_ts\_iter} & 2 & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_n_bcl_iter_beg]{config\_n\_bcl\_iter\_beg} & 1 & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_n_bcl_iter_mid]{config\_n\_bcl\_iter\_mid} & 2 & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_n_bcl_iter_end]{config\_n\_bcl\_iter\_end} & 2 & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_n_btr_subcycles]{config\_n\_btr\_subcycles} & 20 & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_n_btr_cor_iter]{config\_n\_btr\_cor\_iter} & 2 & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_u_correction]{config\_u\_correction} & .true. & {\bf \color{red} MISSING} \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_btr_subcycle_loop_factor]{config\_btr\_subcycle\_loop\_factor} & 2 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_btr_gam1_uWt1]{config\_btr\_gam1\_uWt1} & 0.5 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_btr_gam2_SSHWt1]{config\_btr\_gam2\_SSHWt1} & 1.0 & {\bf \color{red} MISSING} \\
+ \hline
+ real \hyperref[subsec:nm_sec_config_btr_gam3_uWt2]{config\_btr\_gam3\_uWt2} & 1.0 & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_btr_solve_SSH2]{config\_btr\_solve\_SSH2} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{sw\_model}
+\label{sec:nm_tab_sw_model}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ integer \hyperref[subsec:nm_sec_config_test_case]{config\_test\_case} & 0 & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{debug}
+\label{sec:nm_tab_debug}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c |}
+ \hline
+ Type Name & Default Value & Possible Values \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_check_zlevel_consistency]{config\_check\_zlevel\_consistency} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_filter_btr_mode]{config\_filter\_btr\_mode} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_prescribe_velocity]{config\_prescribe\_velocity} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_prescribe_thickness]{config\_prescribe\_thickness} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_include_KE_vertex]{config\_include\_KE\_vertex} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_check_tracer_monotonicity]{config\_check\_tracer\_monotonicity} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_h_all_tend]{config\_disable\_h\_all\_tend} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_h_hadv]{config\_disable\_h\_hadv} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_h_vadv]{config\_disable\_h\_vadv} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_u_all_tend]{config\_disable\_u\_all\_tend} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_u_coriolis]{config\_disable\_u\_coriolis} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_u_pgrad]{config\_disable\_u\_pgrad} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_u_hmix]{config\_disable\_u\_hmix} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_u_windstress]{config\_disable\_u\_windstress} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_u_vmix]{config\_disable\_u\_vmix} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_u_vadv]{config\_disable\_u\_vadv} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_tr_all_tend]{config\_disable\_tr\_all\_tend} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_tr_adv]{config\_disable\_tr\_adv} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_tr_hmix]{config\_disable\_tr\_hmix} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+ logical \hyperref[subsec:nm_sec_config_disable_tr_vmix]{config\_disable\_tr\_vmix} & .false. & {\bf \color{red} MISSING} \\
+ \hline
+\end{longtable}
+\end{center}
+}
Added: trunk/documents/users_guide/ocn/section_descriptions/hmix.tex
===================================================================
--- trunk/documents/users_guide/ocn/section_descriptions/hmix.tex (rev 0)
+++ trunk/documents/users_guide/ocn/section_descriptions/hmix.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -0,0 +1,13 @@
+\section{hmix}
+
+There are several choices of horizontal mixing schemes available for the
+momentum and tracer equations. Each of these is a turbulence closure,
+and attempts to account for subgrid-scale mixing and diffusion. These
+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.
Added: trunk/documents/users_guide/ocn/section_descriptions/hmix_del2.tex
===================================================================
--- trunk/documents/users_guide/ocn/section_descriptions/hmix_del2.tex (rev 0)
+++ trunk/documents/users_guide/ocn/section_descriptions/hmix_del2.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -0,0 +1,30 @@
+\section{hmix\_del2}
+
+The biharmonic, or Laplacian, turbulence closure is simply
+\begin{eqnarray}
+\label{h_mom_diff_cont}
+& {\bf D}^u_h=</font>
<font color="black">u_h </font>
<font color="black">abla^2 {\bf u} = </font>
<font color="black">u_h(</font>
<font color="blue">abla \delta + {\bf
+k}\times </font>
<font color="blue">abla \eta),\\
+\label{h_tr_diff_cont}
+& D^\varphi_h = </font>
<font color="black">abla\cdot\left(h \kappa_h </font>
<font color="blue">abla\varphi \right)
+\end{eqnarray}
+in continuous form and
+\begin{eqnarray}
+\label{h_mom_diff_discrete}
+& \left[{\bf D}^u_h\right]_{k,e}
+ =</font>
<font color="black">u_h([</font>
<font color="black">abla \delta_{k,:}]_{e} +[ {\bf k}\times </font>
<font color="blue">abla
+\widehat{\eta}_{k,:}]_{e}),\\
+\label{h_tr_diff_discrete}
+& \left[D^\varphi_h\right]_{k,i}
+ = [</font>
<font color="black">abla\cdot(\widehat{h}_{k,:} \kappa_h </font>
<font color="blue">abla\varphi_{k,:} )]_{i}
+\end{eqnarray}
+in discrete form. The biharmonic operator smooths the momentum and
+tracer fields, and smooths more stongly at small scales than at large
+scales. This operator is the two dimensional form of the heat equation,
+$u_t=</font>
<font color="blue">u u_{xx}$, described in introductory books on partial
+differential equations. The strength of mixing is controlled by the
+viscosity, $</font>
<font color="gray">u_h$, for the momentum equation, and the diffusion,
+$\kappa_h$, for the tracer equation.
+
+{\color{red} \bf to do: describe scaling with mesh, visc vorticity term, and apvm scale
+factor.}
Added: trunk/documents/users_guide/ocn/variable_section_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/variable_section_documentation.tex (rev 0)
+++ trunk/documents/users_guide/ocn/variable_section_documentation.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -0,0 +1,1659 @@
+\chapter{Variable definions}
+\section{state}
+\label{sec:var_sec_state}
+\subsection{xtime}
+\label{subsec:var_sec_state_xtime}
+\begin{itemize}
+ \item Type: string
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: Time
+ \item Persistence: persistent
+ \item IO: Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{u}
+\label{subsec:var_sec_state_u}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: Input/Restart
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{h}
+\label{subsec:var_sec_state_h}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{rho}
+\label{subsec:var_sec_state_rho}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{temperature}
+\label{subsec:var_sec_state_temperature}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{salinity}
+\label{subsec:var_sec_state_salinity}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{tracer1}
+\label{subsec:var_sec_state_tracer1}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBtr}
+\label{subsec:var_sec_state_uBtr}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges Time
+ \item Persistence: persistent
+ \item IO: Restart
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{ssh}
+\label{subsec:var_sec_state_ssh}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBtrSubcycle}
+\label{subsec:var_sec_state_uBtrSubcycle}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{sshSubcycle}
+\label{subsec:var_sec_state_sshSubcycle}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{FBtr}
+\label{subsec:var_sec_state_FBtr}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{GBtrForcing}
+\label{subsec:var_sec_state_GBtrForcing}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBcl}
+\label{subsec:var_sec_state_uBcl}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{zMid}
+\label{subsec:var_sec_state_zMid}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{v}
+\label{subsec:var_sec_state_v}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uTransport}
+\label{subsec:var_sec_state_uTransport}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBolusGM}
+\label{subsec:var_sec_state_uBolusGM}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBolusGMX}
+\label{subsec:var_sec_state_uBolusGMX}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBolusGMY}
+\label{subsec:var_sec_state_uBolusGMY}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBolusGMZ}
+\label{subsec:var_sec_state_uBolusGMZ}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBolusGMZonal}
+\label{subsec:var_sec_state_uBolusGMZonal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uBolusGMMeridional}
+\label{subsec:var_sec_state_uBolusGMMeridional}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{hEddyFlux}
+\label{subsec:var_sec_state_hEddyFlux}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{h\_kappa}
+\label{subsec:var_sec_state_h_kappa}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{h\_kappa\_q}
+\label{subsec:var_sec_state_h_kappa_q}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{divergence}
+\label{subsec:var_sec_state_divergence}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{vorticity}
+\label{subsec:var_sec_state_vorticity}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nVertices Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{Vor\_edge}
+\label{subsec:var_sec_state_Vor_edge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{h\_edge}
+\label{subsec:var_sec_state_h_edge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{h\_vertex}
+\label{subsec:var_sec_state_h_vertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nVertices Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{ke}
+\label{subsec:var_sec_state_ke}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{kev}
+\label{subsec:var_sec_state_kev}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nVertices Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{kevc}
+\label{subsec:var_sec_state_kevc}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{ke\_edge}
+\label{subsec:var_sec_state_ke_edge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{Vor\_vertex}
+\label{subsec:var_sec_state_Vor_vertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nVertices Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{Vor\_cell}
+\label{subsec:var_sec_state_Vor_cell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uReconstructX}
+\label{subsec:var_sec_state_uReconstructX}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uReconstructY}
+\label{subsec:var_sec_state_uReconstructY}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uReconstructZ}
+\label{subsec:var_sec_state_uReconstructZ}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uReconstructZonal}
+\label{subsec:var_sec_state_uReconstructZonal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uReconstructMeridional}
+\label{subsec:var_sec_state_uReconstructMeridional}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uSrcReconstructX}
+\label{subsec:var_sec_state_uSrcReconstructX}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uSrcReconstructY}
+\label{subsec:var_sec_state_uSrcReconstructY}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uSrcReconstructZ}
+\label{subsec:var_sec_state_uSrcReconstructZ}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uSrcReconstructZonal}
+\label{subsec:var_sec_state_uSrcReconstructZonal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{uSrcReconstructMeridional}
+\label{subsec:var_sec_state_uSrcReconstructMeridional}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{MontPot}
+\label{subsec:var_sec_state_MontPot}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{pressure}
+\label{subsec:var_sec_state_pressure}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{wTop}
+\label{subsec:var_sec_state_wTop}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevelsP1 nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{vertVelocityTop}
+\label{subsec:var_sec_state_vertVelocityTop}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevelsP1 nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{rhoDisplaced}
+\label{subsec:var_sec_state_rhoDisplaced}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{BruntVaisalaFreqTop}
+\label{subsec:var_sec_state_BruntVaisalaFreqTop}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{viscosity}
+\label{subsec:var_sec_state_viscosity}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{vh}
+\label{subsec:var_sec_state_vh}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{circulation}
+\label{subsec:var_sec_state_circulation}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nVertices Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{gradVor\_t}
+\label{subsec:var_sec_state_gradVor_t}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{gradVor\_n}
+\label{subsec:var_sec_state_gradVor_n}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{areaCellGlobal}
+\label{subsec:var_sec_state_areaCellGlobal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{areaEdgeGlobal}
+\label{subsec:var_sec_state_areaEdgeGlobal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{areaTriangleGlobal}
+\label{subsec:var_sec_state_areaTriangleGlobal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{volumeCellGlobal}
+\label{subsec:var_sec_state_volumeCellGlobal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{volumeEdgeGlobal}
+\label{subsec:var_sec_state_volumeEdgeGlobal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{CFLNumberGlobal}
+\label{subsec:var_sec_state_CFLNumberGlobal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{nAccumulate}
+\label{subsec:var_sec_state_nAccumulate}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_ssh}
+\label{subsec:var_sec_state_acc_ssh}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_sshVar}
+\label{subsec:var_sec_state_acc_sshVar}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_uReconstructZonal}
+\label{subsec:var_sec_state_acc_uReconstructZonal}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_uReconstructMeridional}
+\label{subsec:var_sec_state_acc_uReconstructMeridional}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_uReconstructZonalVar}
+\label{subsec:var_sec_state_acc_uReconstructZonalVar}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_uReconstructMeridionalVar}
+\label{subsec:var_sec_state_acc_uReconstructMeridionalVar}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_u}
+\label{subsec:var_sec_state_acc_u}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_uVar}
+\label{subsec:var_sec_state_acc_uVar}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{acc\_vertVelocityTop}
+\label{subsec:var_sec_state_acc_vertVelocityTop}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevelsP1 nCells Time
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\section{mesh}
+\label{sec:var_sec_mesh}
+\subsection{latCell}
+\label{subsec:var_sec_mesh_latCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{lonCell}
+\label{subsec:var_sec_mesh_lonCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{xCell}
+\label{subsec:var_sec_mesh_xCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{yCell}
+\label{subsec:var_sec_mesh_yCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{zCell}
+\label{subsec:var_sec_mesh_zCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{indexToCellID}
+\label{subsec:var_sec_mesh_indexToCellID}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{latEdge}
+\label{subsec:var_sec_mesh_latEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{lonEdge}
+\label{subsec:var_sec_mesh_lonEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{xEdge}
+\label{subsec:var_sec_mesh_xEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{yEdge}
+\label{subsec:var_sec_mesh_yEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{zEdge}
+\label{subsec:var_sec_mesh_zEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{indexToEdgeID}
+\label{subsec:var_sec_mesh_indexToEdgeID}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{latVertex}
+\label{subsec:var_sec_mesh_latVertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{lonVertex}
+\label{subsec:var_sec_mesh_lonVertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{xVertex}
+\label{subsec:var_sec_mesh_xVertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{yVertex}
+\label{subsec:var_sec_mesh_yVertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{zVertex}
+\label{subsec:var_sec_mesh_zVertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{indexToVertexID}
+\label{subsec:var_sec_mesh_indexToVertexID}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{meshDensity}
+\label{subsec:var_sec_mesh_meshDensity}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{meshScalingDel2}
+\label{subsec:var_sec_mesh_meshScalingDel2}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{meshScalingDel4}
+\label{subsec:var_sec_mesh_meshScalingDel4}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{meshScaling}
+\label{subsec:var_sec_mesh_meshScaling}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{cellsOnEdge}
+\label{subsec:var_sec_mesh_cellsOnEdge}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: TWO nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{nEdgesOnCell}
+\label{subsec:var_sec_mesh_nEdgesOnCell}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{nEdgesOnEdge}
+\label{subsec:var_sec_mesh_nEdgesOnEdge}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{edgesOnCell}
+\label{subsec:var_sec_mesh_edgesOnCell}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{edgesOnEdge}
+\label{subsec:var_sec_mesh_edgesOnEdge}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges2 nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{weightsOnEdge}
+\label{subsec:var_sec_mesh_weightsOnEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges2 nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{dvEdge}
+\label{subsec:var_sec_mesh_dvEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{dcEdge}
+\label{subsec:var_sec_mesh_dcEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{angleEdge}
+\label{subsec:var_sec_mesh_angleEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{areaCell}
+\label{subsec:var_sec_mesh_areaCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{areaTriangle}
+\label{subsec:var_sec_mesh_areaTriangle}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{edgeNormalVectors}
+\label{subsec:var_sec_mesh_edgeNormalVectors}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: R3 nEdges
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{localVerticalUnitVectors}
+\label{subsec:var_sec_mesh_localVerticalUnitVectors}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: R3 nCells
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{cellTangentPlane}
+\label{subsec:var_sec_mesh_cellTangentPlane}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: R3 TWO nEdges
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{cellsOnCell}
+\label{subsec:var_sec_mesh_cellsOnCell}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{verticesOnCell}
+\label{subsec:var_sec_mesh_verticesOnCell}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{verticesOnEdge}
+\label{subsec:var_sec_mesh_verticesOnEdge}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: TWO nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{edgesOnVertex}
+\label{subsec:var_sec_mesh_edgesOnVertex}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: vertexDegree nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{cellsOnVertex}
+\label{subsec:var_sec_mesh_cellsOnVertex}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: vertexDegree nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{kiteAreasOnVertex}
+\label{subsec:var_sec_mesh_kiteAreasOnVertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: vertexDegree nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{fEdge}
+\label{subsec:var_sec_mesh_fEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{fVertex}
+\label{subsec:var_sec_mesh_fVertex}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{bottomDepth}
+\label{subsec:var_sec_mesh_bottomDepth}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{deriv\_two}
+\label{subsec:var_sec_mesh_deriv_two}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges2 TWO nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{adv\_coefs}
+\label{subsec:var_sec_mesh_adv_coefs}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nAdvectionCells nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{adv\_coefs\_2nd}
+\label{subsec:var_sec_mesh_adv_coefs_2nd}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nAdvectionCells nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{adv\_coefs\_3rd}
+\label{subsec:var_sec_mesh_adv_coefs_3rd}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nAdvectionCells nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{advCellsForEdge}
+\label{subsec:var_sec_mesh_advCellsForEdge}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nAdvectionCells nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{nAdvCellsForEdge}
+\label{subsec:var_sec_mesh_nAdvCellsForEdge}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{highOrderAdvectionMask}
+\label{subsec:var_sec_mesh_highOrderAdvectionMask}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{lowOrderAdvectionMask}
+\label{subsec:var_sec_mesh_lowOrderAdvectionMask}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{defc\_a}
+\label{subsec:var_sec_mesh_defc_a}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges nCells
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{defc\_b}
+\label{subsec:var_sec_mesh_defc_b}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges nCells
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{kdiff}
+\label{subsec:var_sec_mesh_kdiff}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{coeffs\_reconstruct}
+\label{subsec:var_sec_mesh_coeffs_reconstruct}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: R3 maxEdges nCells
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{maxLevelCell}
+\label{subsec:var_sec_mesh_maxLevelCell}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{maxLevelEdgeTop}
+\label{subsec:var_sec_mesh_maxLevelEdgeTop}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{maxLevelEdgeBot}
+\label{subsec:var_sec_mesh_maxLevelEdgeBot}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{maxLevelVertexTop}
+\label{subsec:var_sec_mesh_maxLevelVertexTop}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{maxLevelVertexBot}
+\label{subsec:var_sec_mesh_maxLevelVertexBot}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertices
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{refBottomDepth}
+\label{subsec:var_sec_mesh_refBottomDepth}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{refBottomDepthTopOfCell}
+\label{subsec:var_sec_mesh_refBottomDepthTopOfCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevelsP1
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{hZLevel}
+\label{subsec:var_sec_mesh_hZLevel}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{vertCoordMovementWeights}
+\label{subsec:var_sec_mesh_vertCoordMovementWeights}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels
+ \item Persistence: persistent
+ \item IO: Input/Restart/Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{boundaryEdge}
+\label{subsec:var_sec_mesh_boundaryEdge}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{boundaryVertex}
+\label{subsec:var_sec_mesh_boundaryVertex}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nVertices
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{boundaryCell}
+\label{subsec:var_sec_mesh_boundaryCell}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{edgeMask}
+\label{subsec:var_sec_mesh_edgeMask}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{vertexMask}
+\label{subsec:var_sec_mesh_vertexMask}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nVertices
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{cellMask}
+\label{subsec:var_sec_mesh_cellMask}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells
+ \item Persistence: persistent
+ \item IO: Output
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{u\_src}
+\label{subsec:var_sec_mesh_u_src}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{temperatureRestore}
+\label{subsec:var_sec_mesh_temperatureRestore}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{salinityRestore}
+\label{subsec:var_sec_mesh_salinityRestore}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{windStressMonthly}
+\label{subsec:var_sec_mesh_windStressMonthly}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nMonths nEdges
+ \item Persistence: persistent
+ \item IO: Input/Restart
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{temperatureRestoreMonthly}
+\label{subsec:var_sec_mesh_temperatureRestoreMonthly}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nMonths nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{salinityRestoreMonthly}
+\label{subsec:var_sec_mesh_salinityRestoreMonthly}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nMonths nCells
+ \item Persistence: persistent
+ \item IO: Input/Restart
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{edgeSignOnCell}
+\label{subsec:var_sec_mesh_edgeSignOnCell}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges nCells
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{edgeSignOnVertex}
+\label{subsec:var_sec_mesh_edgeSignOnVertex}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges nVertices
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{kiteIndexOnCell}
+\label{subsec:var_sec_mesh_kiteIndexOnCell}
+\begin{itemize}
+ \item Type: integer
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: maxEdges nCells
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\section{tend}
+\label{sec:var_sec_tend}
+\subsection{tend\_u}
+\label{subsec:var_sec_tend_tend_u}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{tend\_h}
+\label{subsec:var_sec_tend_tend_h}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{tend\_ssh}
+\label{subsec:var_sec_tend_tend_ssh}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{tend\_temperature}
+\label{subsec:var_sec_tend_tend_temperature}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{tend\_salinity}
+\label{subsec:var_sec_tend_tend_salinity}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{tend\_tracer1}
+\label{subsec:var_sec_tend_tend_tracer1}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevels nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\section{diagnostics}
+\label{sec:var_sec_diagnostics}
+\subsection{RiTopOfCell}
+\label{subsec:var_sec_diagnostics_RiTopOfCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevelsP1 nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{RiTopOfEdge}
+\label{subsec:var_sec_diagnostics_RiTopOfEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevelsP1 nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{vertViscTopOfEdge}
+\label{subsec:var_sec_diagnostics_vertViscTopOfEdge}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevelsP1 nEdges Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
+\subsection{vertDiffTopOfCell}
+\label{subsec:var_sec_diagnostics_vertDiffTopOfCell}
+\begin{itemize}
+ \item Type: real
+ \item Units: {\bf \color{red} MISSING}
+ \item Dimensions: nVertLevelsP1 nCells Time
+ \item Persistence: persistent
+ \item IO: None
+ \item Description: {\bf \color{red} MISSING}
+\end{itemize}
Added: trunk/documents/users_guide/ocn/variable_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/variable_table_documentation.tex (rev 0)
+++ trunk/documents/users_guide/ocn/variable_table_documentation.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -0,0 +1,375 @@
+\chapter{Variable definions}
+\section{state}
+\label{sec:var_tab_state}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c | c |}
+ \hline
+ Type Persistence Name ( Dimensions ) & I/O & Units & Super Array \\
+ \hline
+ string persistent \hyperref[subsec:var_sec_state_xtime]{xtime} ( Time ) & Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_u]{u} ( nVertLevels nEdges Time ) & Input/Restart & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_h]{h} ( nVertLevels nCells Time ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_rho]{rho} ( nVertLevels nCells Time ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_temperature]{temperature} ( nVertLevels nCells Time ) & Input/Restart/Output & {\bf \color{red} MISSING} & tracers \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_salinity]{salinity} ( nVertLevels nCells Time ) & Input/Restart/Output & {\bf \color{red} MISSING} & tracers \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_tracer1]{tracer1} ( nVertLevels nCells Time ) & Input/Restart/Output & {\bf \color{red} MISSING} & tracers \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBtr]{uBtr} ( nEdges Time ) & Restart & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_ssh]{ssh} ( nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBtrSubcycle]{uBtrSubcycle} ( nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_sshSubcycle]{sshSubcycle} ( nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_FBtr]{FBtr} ( nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_GBtrForcing]{GBtrForcing} ( nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBcl]{uBcl} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_zMid]{zMid} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_v]{v} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uTransport]{uTransport} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBolusGM]{uBolusGM} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBolusGMX]{uBolusGMX} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBolusGMY]{uBolusGMY} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBolusGMZ]{uBolusGMZ} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBolusGMZonal]{uBolusGMZonal} ( nVertLevels nEdges Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uBolusGMMeridional]{uBolusGMMeridional} ( nVertLevels nEdges Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_hEddyFlux]{hEddyFlux} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_h_kappa]{h\_kappa} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_h_kappa_q]{h\_kappa\_q} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_divergence]{divergence} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_vorticity]{vorticity} ( nVertLevels nVertices Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_Vor_edge]{Vor\_edge} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_h_edge]{h\_edge} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_h_vertex]{h\_vertex} ( nVertLevels nVertices Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_ke]{ke} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_kev]{kev} ( nVertLevels nVertices Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_kevc]{kevc} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_ke_edge]{ke\_edge} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_Vor_vertex]{Vor\_vertex} ( nVertLevels nVertices Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_Vor_cell]{Vor\_cell} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uReconstructX]{uReconstructX} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uReconstructY]{uReconstructY} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uReconstructZ]{uReconstructZ} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uReconstructZonal]{uReconstructZonal} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uReconstructMeridional]{uReconstructMeridional} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uSrcReconstructX]{uSrcReconstructX} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uSrcReconstructY]{uSrcReconstructY} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uSrcReconstructZ]{uSrcReconstructZ} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uSrcReconstructZonal]{uSrcReconstructZonal} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_uSrcReconstructMeridional]{uSrcReconstructMeridional} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_MontPot]{MontPot} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_pressure]{pressure} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_wTop]{wTop} ( nVertLevelsP1 nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_vertVelocityTop]{vertVelocityTop} ( nVertLevelsP1 nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_rhoDisplaced]{rhoDisplaced} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_BruntVaisalaFreqTop]{BruntVaisalaFreqTop} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_viscosity]{viscosity} ( nVertLevels nEdges Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_vh]{vh} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_circulation]{circulation} ( nVertLevels nVertices Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_gradVor_t]{gradVor\_t} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_gradVor_n]{gradVor\_n} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_areaCellGlobal]{areaCellGlobal} ( Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_areaEdgeGlobal]{areaEdgeGlobal} ( Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_areaTriangleGlobal]{areaTriangleGlobal} ( Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_volumeCellGlobal]{volumeCellGlobal} ( Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_volumeEdgeGlobal]{volumeEdgeGlobal} ( Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_CFLNumberGlobal]{CFLNumberGlobal} ( Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_nAccumulate]{nAccumulate} ( Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_ssh]{acc\_ssh} ( nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_sshVar]{acc\_sshVar} ( nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_uReconstructZonal]{acc\_uReconstructZonal} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_uReconstructMeridional]{acc\_uReconstructMeridional} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_uReconstructZonalVar]{acc\_uReconstructZonalVar} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_uReconstructMeridionalVar]{acc\_uReconstructMeridionalVar} ( nVertLevels nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_u]{acc\_u} ( nVertLevels nEdges Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_uVar]{acc\_uVar} ( nVertLevels nEdges Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_state_acc_vertVelocityTop]{acc\_vertVelocityTop} ( nVertLevelsP1 nCells Time ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{mesh}
+\label{sec:var_tab_mesh}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c | c |}
+ \hline
+ Type Persistence Name ( Dimensions ) & I/O & Units & Super Array \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_latCell]{latCell} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_lonCell]{lonCell} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_xCell]{xCell} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_yCell]{yCell} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_zCell]{zCell} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_indexToCellID]{indexToCellID} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_latEdge]{latEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_lonEdge]{lonEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_xEdge]{xEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_yEdge]{yEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_zEdge]{zEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_indexToEdgeID]{indexToEdgeID} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_latVertex]{latVertex} ( nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_lonVertex]{lonVertex} ( nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_xVertex]{xVertex} ( nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_yVertex]{yVertex} ( nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_zVertex]{zVertex} ( nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_indexToVertexID]{indexToVertexID} ( nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_meshDensity]{meshDensity} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_meshScalingDel2]{meshScalingDel2} ( nEdges ) & Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_meshScalingDel4]{meshScalingDel4} ( nEdges ) & Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_meshScaling]{meshScaling} ( nEdges ) & Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_cellsOnEdge]{cellsOnEdge} ( TWO nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_nEdgesOnCell]{nEdgesOnCell} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_nEdgesOnEdge]{nEdgesOnEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_edgesOnCell]{edgesOnCell} ( maxEdges nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_edgesOnEdge]{edgesOnEdge} ( maxEdges2 nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_weightsOnEdge]{weightsOnEdge} ( maxEdges2 nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_dvEdge]{dvEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_dcEdge]{dcEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_angleEdge]{angleEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_areaCell]{areaCell} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_areaTriangle]{areaTriangle} ( nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_edgeNormalVectors]{edgeNormalVectors} ( R3 nEdges ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_localVerticalUnitVectors]{localVerticalUnitVectors} ( R3 nCells ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_cellTangentPlane]{cellTangentPlane} ( R3 TWO nEdges ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_cellsOnCell]{cellsOnCell} ( maxEdges nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_verticesOnCell]{verticesOnCell} ( maxEdges nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_verticesOnEdge]{verticesOnEdge} ( TWO nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_edgesOnVertex]{edgesOnVertex} ( vertexDegree nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_cellsOnVertex]{cellsOnVertex} ( vertexDegree nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_kiteAreasOnVertex]{kiteAreasOnVertex} ( vertexDegree nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_fEdge]{fEdge} ( nEdges ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_fVertex]{fVertex} ( nVertices ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_bottomDepth]{bottomDepth} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_deriv_two]{deriv\_two} ( maxEdges2 TWO nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_adv_coefs]{adv\_coefs} ( nAdvectionCells nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_adv_coefs_2nd]{adv\_coefs\_2nd} ( nAdvectionCells nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_adv_coefs_3rd]{adv\_coefs\_3rd} ( nAdvectionCells nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_advCellsForEdge]{advCellsForEdge} ( nAdvectionCells nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_nAdvCellsForEdge]{nAdvCellsForEdge} ( nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_highOrderAdvectionMask]{highOrderAdvectionMask} ( nVertLevels nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_lowOrderAdvectionMask]{lowOrderAdvectionMask} ( nVertLevels nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_defc_a]{defc\_a} ( maxEdges nCells ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_defc_b]{defc\_b} ( maxEdges nCells ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_kdiff]{kdiff} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_coeffs_reconstruct]{coeffs\_reconstruct} ( R3 maxEdges nCells ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_maxLevelCell]{maxLevelCell} ( nCells ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_maxLevelEdgeTop]{maxLevelEdgeTop} ( nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_maxLevelEdgeBot]{maxLevelEdgeBot} ( nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_maxLevelVertexTop]{maxLevelVertexTop} ( nVertices ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_maxLevelVertexBot]{maxLevelVertexBot} ( nVertices ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_refBottomDepth]{refBottomDepth} ( nVertLevels ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_refBottomDepthTopOfCell]{refBottomDepthTopOfCell} ( nVertLevelsP1 ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_hZLevel]{hZLevel} ( nVertLevels ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_vertCoordMovementWeights]{vertCoordMovementWeights} ( nVertLevels ) & Input/Restart/Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_boundaryEdge]{boundaryEdge} ( nVertLevels nEdges ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_boundaryVertex]{boundaryVertex} ( nVertLevels nVertices ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_boundaryCell]{boundaryCell} ( nVertLevels nCells ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_edgeMask]{edgeMask} ( nVertLevels nEdges ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_vertexMask]{vertexMask} ( nVertLevels nVertices ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_cellMask]{cellMask} ( nVertLevels nCells ) & Output & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_u_src]{u\_src} ( nVertLevels nEdges ) & Input/Restart & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_temperatureRestore]{temperatureRestore} ( nCells ) & Input/Restart & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_salinityRestore]{salinityRestore} ( nCells ) & Input/Restart & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_windStressMonthly]{windStressMonthly} ( nMonths nEdges ) & Input/Restart & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_temperatureRestoreMonthly]{temperatureRestoreMonthly} ( nMonths nCells ) & Input/Restart & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_mesh_salinityRestoreMonthly]{salinityRestoreMonthly} ( nMonths nCells ) & Input/Restart & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_edgeSignOnCell]{edgeSignOnCell} ( maxEdges nCells ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_edgeSignOnVertex]{edgeSignOnVertex} ( maxEdges nVertices ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ integer persistent \hyperref[subsec:var_sec_mesh_kiteIndexOnCell]{kiteIndexOnCell} ( maxEdges nCells ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{tend}
+\label{sec:var_tab_tend}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c | c |}
+ \hline
+ Type Persistence Name ( Dimensions ) & I/O & Units & Super Array \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_tend_tend_u]{tend\_u} ( nVertLevels nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_tend_tend_h]{tend\_h} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_tend_tend_ssh]{tend\_ssh} ( nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_tend_tend_temperature]{tend\_temperature} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & tracers \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_tend_tend_salinity]{tend\_salinity} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & tracers \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_tend_tend_tracer1]{tend\_tracer1} ( nVertLevels nCells Time ) & None & {\bf \color{red} MISSING} & tracers \\
+ \hline
+\end{longtable}
+\end{center}
+}
+\section{diagnostics}
+\label{sec:var_tab_diagnostics}
+{\small
+\begin{center}
+\begin{longtable}{| c | c | c | c |}
+ \hline
+ Type Persistence Name ( Dimensions ) & I/O & Units & Super Array \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_diagnostics_RiTopOfCell]{RiTopOfCell} ( nVertLevelsP1 nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_diagnostics_RiTopOfEdge]{RiTopOfEdge} ( nVertLevelsP1 nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_diagnostics_vertViscTopOfEdge]{vertViscTopOfEdge} ( nVertLevelsP1 nEdges Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+ real persistent \hyperref[subsec:var_sec_diagnostics_vertDiffTopOfCell]{vertDiffTopOfCell} ( nVertLevelsP1 nCells Time ) & None & {\bf \color{red} MISSING} & None \\
+ \hline
+\end{longtable}
+\end{center}
+}
Modified: trunk/documents/users_guide/shared/mpas_visualization.tex
===================================================================
--- trunk/documents/users_guide/shared/mpas_visualization.tex 2013-02-22 00:11:49 UTC (rev 2505)
+++ trunk/documents/users_guide/shared/mpas_visualization.tex 2013-02-25 17:21:52 UTC (rev 2506)
@@ -69,8 +69,3 @@
-\appendix %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
-\setlength\LTleft{0.0in}
-
-
</font>
</pre>