<p><b>dwj07@fsu.edu</b> 2013-03-11 12:10:43 -0600 (Mon, 11 Mar 2013)</p><p><br>
        -- DOCUMENT COMMIT --<br>
<br>
        Updating ocean users guide.<br>
        Changing link color to blue, that way red text stands out more. (For missing documentation)<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/documents/users_guide/mpas_ocean_users_guide.tex
===================================================================
--- trunk/documents/users_guide/mpas_ocean_users_guide.tex        2013-03-11 17:37:48 UTC (rev 2581)
+++ trunk/documents/users_guide/mpas_ocean_users_guide.tex        2013-03-11 18:10:43 UTC (rev 2582)
@@ -12,7 +12,7 @@
 \definecolor{black}{rgb}{0.0,0.0,0.0}
 \definecolor{darkblue}{rgb}{0.0,0.0,0.5}
 \hypersetup{colorlinks,breaklinks,
-            linkcolor=red,urlcolor=red,
+            linkcolor=blue,urlcolor=blue,
             anchorcolor=black,citecolor=black}
 
 \setlength{\topmargin}{0in}

Modified: trunk/documents/users_guide/ocn/dimension_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/dimension_table_documentation.tex        2013-03-11 17:37:48 UTC (rev 2581)
+++ trunk/documents/users_guide/ocn/dimension_table_documentation.tex        2013-03-11 18:10:43 UTC (rev 2582)
@@ -1,4 +1,5 @@
 \chapter{Dimensions}
+\label{chap:dimensions}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}

Modified: trunk/documents/users_guide/ocn/figures/baroclinic_channel_10000m_20levs_10days.pdf
===================================================================
(Binary files differ)

Added: trunk/documents/users_guide/ocn/figures/baroclinic_channel_1000m_20levs_10days.pdf
===================================================================
(Binary files differ)

Index: trunk/documents/users_guide/ocn/figures/baroclinic_channel_1000m_20levs_10days.pdf
===================================================================
--- trunk/documents/users_guide/ocn/figures/baroclinic_channel_1000m_20levs_10days.pdf        2013-03-11 17:37:48 UTC (rev 2581)
+++ trunk/documents/users_guide/ocn/figures/baroclinic_channel_1000m_20levs_10days.pdf        2013-03-11 18:10:43 UTC (rev 2582)

Property changes on: trunk/documents/users_guide/ocn/figures/baroclinic_channel_1000m_20levs_10days.pdf
___________________________________________________________________
Added: svn:mime-type
## -0,0 +1 ##
+application/octet-stream
\ No newline at end of property
Modified: trunk/documents/users_guide/ocn/figures/baroclinic_channel_4000m_20levs_10days.pdf
===================================================================
(Binary files differ)

Modified: trunk/documents/users_guide/ocn/namelist_section_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/namelist_section_documentation.tex        2013-03-11 17:37:48 UTC (rev 2581)
+++ trunk/documents/users_guide/ocn/namelist_section_documentation.tex        2013-03-11 18:10:43 UTC (rev 2582)
@@ -1,7 +1,9 @@
-\chapter{Namelist options}
-\section{\hyperref[sec:nm_tab_time_management]{time\_management}}
+\chapter[Namelist options]{\hyperref[chap:namelist_tables]{Namelist options}}
+\label{chap:namelist_sections}
+Embedded links point to information in chapter \ref{chap:namelist_tables}
+\section[time\_management]{\hyperref[sec:nm_tab_time_management]{time\_management}}
 \label{sec:nm_sec_time_management}
-\subsection{\hyperref[sec:nm_tab_time_management]{config\_do\_restart}}
+\subsection[config\_do\_restart]{\hyperref[sec:nm_tab_time_management]{config\_do\_restart}}
 \label{subsec:nm_sec_config_do_restart}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -17,7 +19,7 @@
     \caption{config\_do\_restart: Flag that controls starting simulation from a restart, or inital conditions that are built into the input file.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_time_management]{config\_start\_time}}
+\subsection[config\_start\_time]{\hyperref[sec:nm_tab_time_management]{config\_start\_time}}
 \label{subsec:nm_sec_config_start_time}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -33,7 +35,7 @@
     \caption{config\_start\_time: Time stamp that describes the initial time of the simulation.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_time_management]{config\_stop\_time}}
+\subsection[config\_stop\_time]{\hyperref[sec:nm_tab_time_management]{config\_stop\_time}}
 \label{subsec:nm_sec_config_stop_time}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -49,7 +51,7 @@
     \caption{config\_stop\_time: 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{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_time_management]{config\_run\_duration}}
+\subsection[config\_run\_duration]{\hyperref[sec:nm_tab_time_management]{config\_run\_duration}}
 \label{subsec:nm_sec_config_run_duration}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -65,7 +67,7 @@
     \caption{config\_run\_duration: 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{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_time_management]{config\_calendar\_type}}
+\subsection[config\_calendar\_type]{\hyperref[sec:nm_tab_time_management]{config\_calendar\_type}}
 \label{subsec:nm_sec_config_calendar_type}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -81,9 +83,9 @@
     \caption{config\_calendar\_type: Calendar type that defines the calendar used in the simualtion.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_io]{io}}
+\section[io]{\hyperref[sec:nm_tab_io]{io}}
 \label{sec:nm_sec_io}
-\subsection{\hyperref[sec:nm_tab_io]{config\_input\_name}}
+\subsection[config\_input\_name]{\hyperref[sec:nm_tab_io]{config\_input\_name}}
 \label{subsec:nm_sec_config_input_name}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -99,7 +101,7 @@
     \caption{config\_input\_name: String that defines the full or relative path to the input file.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_output\_name}}
+\subsection[config\_output\_name]{\hyperref[sec:nm_tab_io]{config\_output\_name}}
 \label{subsec:nm_sec_config_output_name}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -115,7 +117,7 @@
     \caption{config\_output\_name: String that defines the full or relative path to where the output file(s) will be written.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_restart\_name}}
+\subsection[config\_restart\_name]{\hyperref[sec:nm_tab_io]{config\_restart\_name}}
 \label{subsec:nm_sec_config_restart_name}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -131,7 +133,7 @@
     \caption{config\_restart\_name: String that defines the full or relative path to where the restart file(s) will be read and written.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_restart\_interval}}
+\subsection[config\_restart\_interval]{\hyperref[sec:nm_tab_io]{config\_restart\_interval}}
 \label{subsec:nm_sec_config_restart_interval}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -147,7 +149,7 @@
     \caption{config\_restart\_interval: Time stamp that defines how often restart files should be written.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_output\_interval}}
+\subsection[config\_output\_interval]{\hyperref[sec:nm_tab_io]{config\_output\_interval}}
 \label{subsec:nm_sec_config_output_interval}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -163,7 +165,7 @@
     \caption{config\_output\_interval: Time stamp that defines how often output files should be written.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_stats\_interval}}
+\subsection[config\_stats\_interval]{\hyperref[sec:nm_tab_io]{config\_stats\_interval}}
 \label{subsec:nm_sec_config_stats_interval}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -179,7 +181,7 @@
     \caption{config\_stats\_interval: Time stamp that defines how often statistics output should be written.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_write\_stats\_on\_startup}}
+\subsection[config\_write\_stats\_on\_startup]{\hyperref[sec:nm_tab_io]{config\_write\_stats\_on\_startup}}
 \label{subsec:nm_sec_config_write_stats_on_startup}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -195,7 +197,7 @@
     \caption{config\_write\_stats\_on\_startup: Flag that defines if statistics should be computed using the initial conditions.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_write\_output\_on\_startup}}
+\subsection[config\_write\_output\_on\_startup]{\hyperref[sec:nm_tab_io]{config\_write\_output\_on\_startup}}
 \label{subsec:nm_sec_config_write_output_on_startup}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -211,7 +213,7 @@
     \caption{config\_write\_output\_on\_startup: Flag that defines if output should be performed using the initial conditions.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_frames\_per\_outfile}}
+\subsection[config\_frames\_per\_outfile]{\hyperref[sec:nm_tab_io]{config\_frames\_per\_outfile}}
 \label{subsec:nm_sec_config_frames_per_outfile}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -227,7 +229,7 @@
     \caption{config\_frames\_per\_outfile: Number of time slices in an output file.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_pio\_num\_iotasks}}
+\subsection[config\_pio\_num\_iotasks]{\hyperref[sec:nm_tab_io]{config\_pio\_num\_iotasks}}
 \label{subsec:nm_sec_config_pio_num_iotasks}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -243,7 +245,7 @@
     \caption{config\_pio\_num\_iotasks: Number of iotasks used with PIO in the simulation.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_io]{config\_pio\_stride}}
+\subsection[config\_pio\_stride]{\hyperref[sec:nm_tab_io]{config\_pio\_stride}}
 \label{subsec:nm_sec_config_pio_stride}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -259,9 +261,9 @@
     \caption{config\_pio\_stride: Stride of PIO iotasks in the simulation.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_time_integration]{time\_integration}}
+\section[time\_integration]{\hyperref[sec:nm_tab_time_integration]{time\_integration}}
 \label{sec:nm_sec_time_integration}
-\subsection{\hyperref[sec:nm_tab_time_integration]{config\_dt}}
+\subsection[config\_dt]{\hyperref[sec:nm_tab_time_integration]{config\_dt}}
 \label{subsec:nm_sec_config_dt}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -277,7 +279,7 @@
     \caption{config\_dt: Length of a single time step.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_time_integration]{config\_time\_integrator}}
+\subsection[config\_time\_integrator]{\hyperref[sec:nm_tab_time_integration]{config\_time\_integrator}}
 \label{subsec:nm_sec_config_time_integrator}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -293,9 +295,9 @@
     \caption{config\_time\_integrator: Time integration scheme to be used for the simulation.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_grid]{grid}}
+\section[grid]{\hyperref[sec:nm_tab_grid]{grid}}
 \label{sec:nm_sec_grid}
-\subsection{\hyperref[sec:nm_tab_grid]{config\_num\_halos}}
+\subsection[config\_num\_halos]{\hyperref[sec:nm_tab_grid]{config\_num\_halos}}
 \label{subsec:nm_sec_config_num_halos}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -311,7 +313,7 @@
     \caption{config\_num\_halos: Defines the number of halos extending outward from owned cells.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_grid]{config\_vert\_coord\_movement}}
+\subsection[config\_vert\_coord\_movement]{\hyperref[sec:nm_tab_grid]{config\_vert\_coord\_movement}}
 \label{subsec:nm_sec_config_vert_coord_movement}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -327,7 +329,7 @@
     \caption{config\_vert\_coord\_movement: Defines the movement of the vertical coordinate.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_grid]{config\_alter\_ICs\_for\_pbcs}}
+\subsection[config\_alter\_ICs\_for\_pbcs]{\hyperref[sec:nm_tab_grid]{config\_alter\_ICs\_for\_pbcs}}
 \label{subsec:nm_sec_config_alter_ICs_for_pbcs}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -343,7 +345,7 @@
     \caption{config\_alter\_ICs\_for\_pbcs: Flag that controls how or if partial bottom cells are used.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_grid]{config\_min\_pbc\_fraction}}
+\subsection[config\_min\_pbc\_fraction]{\hyperref[sec:nm_tab_grid]{config\_min\_pbc\_fraction}}
 \label{subsec:nm_sec_config_min_pbc_fraction}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -359,7 +361,7 @@
     \caption{config\_min\_pbc\_fraction: Defines the minimum allowed fraction for partial bottom cells.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_grid]{config\_check\_ssh\_consistency}}
+\subsection[config\_check\_ssh\_consistency]{\hyperref[sec:nm_tab_grid]{config\_check\_ssh\_consistency}}
 \label{subsec:nm_sec_config_check_ssh_consistency}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -375,9 +377,9 @@
     \caption{config\_check\_ssh\_consistency: Flag that enables an initial consistency check for sea surface height.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_decomposition]{decomposition}}
+\section[decomposition]{\hyperref[sec:nm_tab_decomposition]{decomposition}}
 \label{sec:nm_sec_decomposition}
-\subsection{\hyperref[sec:nm_tab_decomposition]{config\_block\_decomp\_file\_prefix}}
+\subsection[config\_block\_decomp\_file\_prefix]{\hyperref[sec:nm_tab_decomposition]{config\_block\_decomp\_file\_prefix}}
 \label{subsec:nm_sec_config_block_decomp_file_prefix}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -393,7 +395,7 @@
     \caption{config\_block\_decomp\_file\_prefix: String that defines the full or relative path and prefix for the block decomposition files.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_decomposition]{config\_number\_of\_blocks}}
+\subsection[config\_number\_of\_blocks]{\hyperref[sec:nm_tab_decomposition]{config\_number\_of\_blocks}}
 \label{subsec:nm_sec_config_number_of_blocks}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -409,7 +411,7 @@
     \caption{config\_number\_of\_blocks: The number of computational blocks in the simulation.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_decomposition]{config\_explicit\_proc\_decomp}}
+\subsection[config\_explicit\_proc\_decomp]{\hyperref[sec:nm_tab_decomposition]{config\_explicit\_proc\_decomp}}
 \label{subsec:nm_sec_config_explicit_proc_decomp}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -425,7 +427,7 @@
     \caption{config\_explicit\_proc\_decomp: Flag that enables/disables the use of a config\_proc\_decomp\_file to distribute computational blocks through processors.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_decomposition]{config\_proc\_decomp\_file\_prefix}}
+\subsection[config\_proc\_decomp\_file\_prefix]{\hyperref[sec:nm_tab_decomposition]{config\_proc\_decomp\_file\_prefix}}
 \label{subsec:nm_sec_config_proc_decomp_file_prefix}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -441,9 +443,9 @@
     \caption{config\_proc\_decomp\_file\_prefix: String that defines the fille or relative path and prefix for the processor decomposition files.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_hmix]{hmix}}
+\section[hmix]{\hyperref[sec:nm_tab_hmix]{hmix}}
 \label{sec:nm_sec_hmix}
-\subsection{\hyperref[sec:nm_tab_hmix]{config\_hmix\_ScaleWithMesh}}
+\subsection[config\_hmix\_ScaleWithMesh]{\hyperref[sec:nm_tab_hmix]{config\_hmix\_ScaleWithMesh}}
 \label{subsec:nm_sec_config_hmix_ScaleWithMesh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -459,7 +461,7 @@
     \caption{config\_hmix\_ScaleWithMesh: Flag that controls if horizontal mixing parameters scale with the mesh density.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix]{config\_visc\_vorticity\_term}}
+\subsection[config\_visc\_vorticity\_term]{\hyperref[sec:nm_tab_hmix]{config\_visc\_vorticity\_term}}
 \label{subsec:nm_sec_config_visc_vorticity_term}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -475,7 +477,7 @@
     \caption{config\_visc\_vorticity\_term: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix]{config\_apvm\_scale\_factor}}
+\subsection[config\_apvm\_scale\_factor]{\hyperref[sec:nm_tab_hmix]{config\_apvm\_scale\_factor}}
 \label{subsec:nm_sec_config_apvm_scale_factor}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -491,9 +493,9 @@
     \caption{config\_apvm\_scale\_factor: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_hmix_del2]{hmix\_del2}}
+\section[hmix\_del2]{\hyperref[sec:nm_tab_hmix_del2]{hmix\_del2}}
 \label{sec:nm_sec_hmix_del2}
-\subsection{\hyperref[sec:nm_tab_hmix_del2]{config\_use\_mom\_del2}}
+\subsection[config\_use\_mom\_del2]{\hyperref[sec:nm_tab_hmix_del2]{config\_use\_mom\_del2}}
 \label{subsec:nm_sec_config_use_mom_del2}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -509,7 +511,7 @@
     \caption{config\_use\_mom\_del2: Flag that controls if del2 will be used for horizontal mixing of momentum.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_del2]{config\_use\_tracer\_del2}}
+\subsection[config\_use\_tracer\_del2]{\hyperref[sec:nm_tab_hmix_del2]{config\_use\_tracer\_del2}}
 \label{subsec:nm_sec_config_use_tracer_del2}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -525,7 +527,7 @@
     \caption{config\_use\_tracer\_del2: Flag that controls if del2 will be used for horizontal mixing of tracers.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_del2]{config\_mom\_del2}}
+\subsection[config\_mom\_del2]{\hyperref[sec:nm_tab_hmix_del2]{config\_mom\_del2}}
 \label{subsec:nm_sec_config_mom_del2}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -541,7 +543,7 @@
     \caption{config\_mom\_del2: Value of del2 coefficient for horizontal mixing of momentum.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_del2]{config\_tracer\_del2}}
+\subsection[config\_tracer\_del2]{\hyperref[sec:nm_tab_hmix_del2]{config\_tracer\_del2}}
 \label{subsec:nm_sec_config_tracer_del2}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -557,7 +559,7 @@
     \caption{config\_tracer\_del2: Value of del2 coefficient for horizontal mixing of tracers.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_del2]{config\_vorticity\_del2\_scale}}
+\subsection[config\_vorticity\_del2\_scale]{\hyperref[sec:nm_tab_hmix_del2]{config\_vorticity\_del2\_scale}}
 \label{subsec:nm_sec_config_vorticity_del2_scale}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -573,9 +575,9 @@
     \caption{config\_vorticity\_del2\_scale: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_hmix_del4]{hmix\_del4}}
+\section[hmix\_del4]{\hyperref[sec:nm_tab_hmix_del4]{hmix\_del4}}
 \label{sec:nm_sec_hmix_del4}
-\subsection{\hyperref[sec:nm_tab_hmix_del4]{config\_use\_mom\_del4}}
+\subsection[config\_use\_mom\_del4]{\hyperref[sec:nm_tab_hmix_del4]{config\_use\_mom\_del4}}
 \label{subsec:nm_sec_config_use_mom_del4}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -591,7 +593,7 @@
     \caption{config\_use\_mom\_del4: Flag that controls if del4 will be used for horizontal mixing of momentum.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_del4]{config\_use\_tracer\_del4}}
+\subsection[config\_use\_tracer\_del4]{\hyperref[sec:nm_tab_hmix_del4]{config\_use\_tracer\_del4}}
 \label{subsec:nm_sec_config_use_tracer_del4}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -607,7 +609,7 @@
     \caption{config\_use\_tracer\_del4: Flag that controls if del4 will be used for horizontal mixing of tracers.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_del4]{config\_mom\_del4}}
+\subsection[config\_mom\_del4]{\hyperref[sec:nm_tab_hmix_del4]{config\_mom\_del4}}
 \label{subsec:nm_sec_config_mom_del4}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -623,7 +625,7 @@
     \caption{config\_mom\_del4: Value of del4 coefficient for horizontal mixing of momentum.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_del4]{config\_tracer\_del4}}
+\subsection[config\_tracer\_del4]{\hyperref[sec:nm_tab_hmix_del4]{config\_tracer\_del4}}
 \label{subsec:nm_sec_config_tracer_del4}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -639,7 +641,7 @@
     \caption{config\_tracer\_del4: Value of del4 coefficient for horizontal mixing of tracers.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_del4]{config\_vorticity\_del4\_scale}}
+\subsection[config\_vorticity\_del4\_scale]{\hyperref[sec:nm_tab_hmix_del4]{config\_vorticity\_del4\_scale}}
 \label{subsec:nm_sec_config_vorticity_del4_scale}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -655,9 +657,9 @@
     \caption{config\_vorticity\_del4\_scale: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_hmix_Leith]{hmix\_Leith}}
+\section[hmix\_Leith]{\hyperref[sec:nm_tab_hmix_Leith]{hmix\_Leith}}
 \label{sec:nm_sec_hmix_Leith}
-\subsection{\hyperref[sec:nm_tab_hmix_Leith]{config\_use\_Leith\_del2}}
+\subsection[config\_use\_Leith\_del2]{\hyperref[sec:nm_tab_hmix_Leith]{config\_use\_Leith\_del2}}
 \label{subsec:nm_sec_config_use_Leith_del2}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -673,7 +675,7 @@
     \caption{config\_use\_Leith\_del2: Flag that controls if the Leith closure will be used for horizontal mixing.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_parameter}}
+\subsection[config\_Leith\_parameter]{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_parameter}}
 \label{subsec:nm_sec_config_Leith_parameter}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -689,7 +691,7 @@
     \caption{config\_Leith\_parameter: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_dx}}
+\subsection[config\_Leith\_dx]{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_dx}}
 \label{subsec:nm_sec_config_Leith_dx}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -705,7 +707,7 @@
     \caption{config\_Leith\_dx: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_visc2\_max}}
+\subsection[config\_Leith\_visc2\_max]{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_visc2\_max}}
 \label{subsec:nm_sec_config_Leith_visc2_max}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -721,9 +723,9 @@
     \caption{config\_Leith\_visc2\_max: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_standard_GM]{standard\_GM}}
+\section[standard\_GM]{\hyperref[sec:nm_tab_standard_GM]{standard\_GM}}
 \label{sec:nm_sec_standard_GM}
-\subsection{\hyperref[sec:nm_tab_standard_GM]{config\_h\_kappa}}
+\subsection[config\_h\_kappa]{\hyperref[sec:nm_tab_standard_GM]{config\_h\_kappa}}
 \label{subsec:nm_sec_config_h_kappa}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -739,7 +741,7 @@
     \caption{config\_h\_kappa: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_standard_GM]{config\_h\_kappa\_q}}
+\subsection[config\_h\_kappa\_q]{\hyperref[sec:nm_tab_standard_GM]{config\_h\_kappa\_q}}
 \label{subsec:nm_sec_config_h_kappa_q}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -755,9 +757,9 @@
     \caption{config\_h\_kappa\_q: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_Rayleigh_damping]{Rayleigh\_damping}}
+\section[Rayleigh\_damping]{\hyperref[sec:nm_tab_Rayleigh_damping]{Rayleigh\_damping}}
 \label{sec:nm_sec_Rayleigh_damping}
-\subsection{\hyperref[sec:nm_tab_Rayleigh_damping]{config\_Rayleigh\_friction}}
+\subsection[config\_Rayleigh\_friction]{\hyperref[sec:nm_tab_Rayleigh_damping]{config\_Rayleigh\_friction}}
 \label{subsec:nm_sec_config_Rayleigh_friction}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -773,7 +775,7 @@
     \caption{config\_Rayleigh\_friction: Flag that controls if Rayleigh friction will be used in the simulation.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_Rayleigh_damping]{config\_Rayleigh\_damping\_coeff}}
+\subsection[config\_Rayleigh\_damping\_coeff]{\hyperref[sec:nm_tab_Rayleigh_damping]{config\_Rayleigh\_damping\_coeff}}
 \label{subsec:nm_sec_config_Rayleigh_damping_coeff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -789,9 +791,9 @@
     \caption{config\_Rayleigh\_damping\_coeff: Value of the Rayleigh friction coefficient.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_vmix]{vmix}}
+\section[vmix]{\hyperref[sec:nm_tab_vmix]{vmix}}
 \label{sec:nm_sec_vmix}
-\subsection{\hyperref[sec:nm_tab_vmix]{config\_convective\_visc}}
+\subsection[config\_convective\_visc]{\hyperref[sec:nm_tab_vmix]{config\_convective\_visc}}
 \label{subsec:nm_sec_config_convective_visc}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -807,7 +809,7 @@
     \caption{config\_convective\_visc: Value of coefficient for convective vertical mixing of momentum.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix]{config\_convective\_diff}}
+\subsection[config\_convective\_diff]{\hyperref[sec:nm_tab_vmix]{config\_convective\_diff}}
 \label{subsec:nm_sec_config_convective_diff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -823,9 +825,9 @@
     \caption{config\_convective\_diff: Value of coefficient for convective vertical mixing of tracers.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_vmix_const]{vmix\_const}}
+\section[vmix\_const]{\hyperref[sec:nm_tab_vmix_const]{vmix\_const}}
 \label{sec:nm_sec_vmix_const}
-\subsection{\hyperref[sec:nm_tab_vmix_const]{config\_use\_const\_visc}}
+\subsection[config\_use\_const\_visc]{\hyperref[sec:nm_tab_vmix_const]{config\_use\_const\_visc}}
 \label{subsec:nm_sec_config_use_const_visc}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -841,7 +843,7 @@
     \caption{config\_use\_const\_visc: Flag that controls if constant vertical mixing of momentum is used.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_const]{config\_use\_const\_diff}}
+\subsection[config\_use\_const\_diff]{\hyperref[sec:nm_tab_vmix_const]{config\_use\_const\_diff}}
 \label{subsec:nm_sec_config_use_const_diff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -857,7 +859,7 @@
     \caption{config\_use\_const\_diff: Flag that controls if constant vertical mixing of tracers is used.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_const]{config\_vert\_visc}}
+\subsection[config\_vert\_visc]{\hyperref[sec:nm_tab_vmix_const]{config\_vert\_visc}}
 \label{subsec:nm_sec_config_vert_visc}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -873,7 +875,7 @@
     \caption{config\_vert\_visc: Value of coefficient for constant vertical mixing of momentum.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_const]{config\_vert\_diff}}
+\subsection[config\_vert\_diff]{\hyperref[sec:nm_tab_vmix_const]{config\_vert\_diff}}
 \label{subsec:nm_sec_config_vert_diff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -889,9 +891,9 @@
     \caption{config\_vert\_diff: Value of coefficient for constant vertical mixing of tracers.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_vmix_rich]{vmix\_rich}}
+\section[vmix\_rich]{\hyperref[sec:nm_tab_vmix_rich]{vmix\_rich}}
 \label{sec:nm_sec_vmix_rich}
-\subsection{\hyperref[sec:nm_tab_vmix_rich]{config\_use\_rich\_visc}}
+\subsection[config\_use\_rich\_visc]{\hyperref[sec:nm_tab_vmix_rich]{config\_use\_rich\_visc}}
 \label{subsec:nm_sec_config_use_rich_visc}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -907,7 +909,7 @@
     \caption{config\_use\_rich\_visc: Flag that controls if Richarson number vertical mixing of momentum is used.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_rich]{config\_use\_rich\_diff}}
+\subsection[config\_use\_rich\_diff]{\hyperref[sec:nm_tab_vmix_rich]{config\_use\_rich\_diff}}
 \label{subsec:nm_sec_config_use_rich_diff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -923,7 +925,7 @@
     \caption{config\_use\_rich\_diff: Flag that controls if Richarson number vertical mixing of tracers is used.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_rich]{config\_bkrd\_vert\_visc}}
+\subsection[config\_bkrd\_vert\_visc]{\hyperref[sec:nm_tab_vmix_rich]{config\_bkrd\_vert\_visc}}
 \label{subsec:nm_sec_config_bkrd_vert_visc}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -939,7 +941,7 @@
     \caption{config\_bkrd\_vert\_visc: Value of coefficient for Richardson number vertical mixing of momentum.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_rich]{config\_bkrd\_vert\_diff}}
+\subsection[config\_bkrd\_vert\_diff]{\hyperref[sec:nm_tab_vmix_rich]{config\_bkrd\_vert\_diff}}
 \label{subsec:nm_sec_config_bkrd_vert_diff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -955,7 +957,7 @@
     \caption{config\_bkrd\_vert\_diff: Value of coefficient for Richardson number vertical mixing of tracers.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_rich]{config\_rich\_mix}}
+\subsection[config\_rich\_mix]{\hyperref[sec:nm_tab_vmix_rich]{config\_rich\_mix}}
 \label{subsec:nm_sec_config_rich_mix}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -971,9 +973,9 @@
     \caption{config\_rich\_mix: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_vmix_tanh]{vmix\_tanh}}
+\section[vmix\_tanh]{\hyperref[sec:nm_tab_vmix_tanh]{vmix\_tanh}}
 \label{sec:nm_sec_vmix_tanh}
-\subsection{\hyperref[sec:nm_tab_vmix_tanh]{config\_use\_tanh\_visc}}
+\subsection[config\_use\_tanh\_visc]{\hyperref[sec:nm_tab_vmix_tanh]{config\_use\_tanh\_visc}}
 \label{subsec:nm_sec_config_use_tanh_visc}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -989,7 +991,7 @@
     \caption{config\_use\_tanh\_visc: Flag that controls if hyperbolic tangent vertical mixing of momentum is used.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_tanh]{config\_use\_tanh\_diff}}
+\subsection[config\_use\_tanh\_diff]{\hyperref[sec:nm_tab_vmix_tanh]{config\_use\_tanh\_diff}}
 \label{subsec:nm_sec_config_use_tanh_diff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1005,7 +1007,7 @@
     \caption{config\_use\_tanh\_diff: Flag that controls if hyperbolic tangent vertical mixing of tracers is used.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_tanh]{config\_max\_visc\_tanh}}
+\subsection[config\_max\_visc\_tanh]{\hyperref[sec:nm_tab_vmix_tanh]{config\_max\_visc\_tanh}}
 \label{subsec:nm_sec_config_max_visc_tanh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1021,7 +1023,7 @@
     \caption{config\_max\_visc\_tanh: {\bf \color{red} DEFINE} }
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_tanh]{config\_min\_visc\_tanh}}
+\subsection[config\_min\_visc\_tanh]{\hyperref[sec:nm_tab_vmix_tanh]{config\_min\_visc\_tanh}}
 \label{subsec:nm_sec_config_min_visc_tanh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1037,7 +1039,7 @@
     \caption{config\_min\_visc\_tanh: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_tanh]{config\_max\_diff\_tanh}}
+\subsection[config\_max\_diff\_tanh]{\hyperref[sec:nm_tab_vmix_tanh]{config\_max\_diff\_tanh}}
 \label{subsec:nm_sec_config_max_diff_tanh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1053,7 +1055,7 @@
     \caption{config\_max\_diff\_tanh: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_tanh]{config\_min\_diff\_tanh}}
+\subsection[config\_min\_diff\_tanh]{\hyperref[sec:nm_tab_vmix_tanh]{config\_min\_diff\_tanh}}
 \label{subsec:nm_sec_config_min_diff_tanh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1069,7 +1071,7 @@
     \caption{config\_min\_diff\_tanh: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_tanh]{config\_zMid\_tanh}}
+\subsection[config\_zMid\_tanh]{\hyperref[sec:nm_tab_vmix_tanh]{config\_zMid\_tanh}}
 \label{subsec:nm_sec_config_zMid_tanh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1085,7 +1087,7 @@
     \caption{config\_zMid\_tanh: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_vmix_tanh]{config\_zWidth\_tanh}}
+\subsection[config\_zWidth\_tanh]{\hyperref[sec:nm_tab_vmix_tanh]{config\_zWidth\_tanh}}
 \label{subsec:nm_sec_config_zWidth_tanh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1101,9 +1103,9 @@
     \caption{config\_zWidth\_tanh: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_forcing]{forcing}}
+\section[forcing]{\hyperref[sec:nm_tab_forcing]{forcing}}
 \label{sec:nm_sec_forcing}
-\subsection{\hyperref[sec:nm_tab_forcing]{config\_use\_monthly\_forcing}}
+\subsection[config\_use\_monthly\_forcing]{\hyperref[sec:nm_tab_forcing]{config\_use\_monthly\_forcing}}
 \label{subsec:nm_sec_config_use_monthly_forcing}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1119,7 +1121,7 @@
     \caption{config\_use\_monthly\_forcing: Flag that controls if monthly forcing is used in the simulation.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_forcing]{config\_restoreTS}}
+\subsection[config\_restoreTS]{\hyperref[sec:nm_tab_forcing]{config\_restoreTS}}
 \label{subsec:nm_sec_config_restoreTS}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1135,7 +1137,7 @@
     \caption{config\_restoreTS: Flag that controls is temperature and salinity restoring is used in the simulation.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_forcing]{config\_restoreT\_timescale}}
+\subsection[config\_restoreT\_timescale]{\hyperref[sec:nm_tab_forcing]{config\_restoreT\_timescale}}
 \label{subsec:nm_sec_config_restoreT_timescale}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1151,7 +1153,7 @@
     \caption{config\_restoreT\_timescale: Value in days of the restoring timescale for temperature.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_forcing]{config\_restoreS\_timescale}}
+\subsection[config\_restoreS\_timescale]{\hyperref[sec:nm_tab_forcing]{config\_restoreS\_timescale}}
 \label{subsec:nm_sec_config_restoreS_timescale}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1167,9 +1169,9 @@
     \caption{config\_restoreS\_timescale: Value in days of the restoring timescale for salinity.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_advection]{advection}}
+\section[advection]{\hyperref[sec:nm_tab_advection]{advection}}
 \label{sec:nm_sec_advection}
-\subsection{\hyperref[sec:nm_tab_advection]{config\_vert\_tracer\_adv}}
+\subsection[config\_vert\_tracer\_adv]{\hyperref[sec:nm_tab_advection]{config\_vert\_tracer\_adv}}
 \label{subsec:nm_sec_config_vert_tracer_adv}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1185,7 +1187,7 @@
     \caption{config\_vert\_tracer\_adv: {\bf \color{red} DEPRECATED}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_advection]{config\_vert\_tracer\_adv\_order}}
+\subsection[config\_vert\_tracer\_adv\_order]{\hyperref[sec:nm_tab_advection]{config\_vert\_tracer\_adv\_order}}
 \label{subsec:nm_sec_config_vert_tracer_adv_order}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1201,7 +1203,7 @@
     \caption{config\_vert\_tracer\_adv\_order: Order of vertical reconstruction of tracers used for vertical advection.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_advection]{config\_horiz\_tracer\_adv\_order}}
+\subsection[config\_horiz\_tracer\_adv\_order]{\hyperref[sec:nm_tab_advection]{config\_horiz\_tracer\_adv\_order}}
 \label{subsec:nm_sec_config_horiz_tracer_adv_order}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1217,7 +1219,7 @@
     \caption{config\_horiz\_tracer\_adv\_order: Order of horizontal reconstruction of tracers used for horizontal advection.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_advection]{config\_coef\_3rd\_order}}
+\subsection[config\_coef\_3rd\_order]{\hyperref[sec:nm_tab_advection]{config\_coef\_3rd\_order}}
 \label{subsec:nm_sec_config_coef_3rd_order}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1233,7 +1235,7 @@
     \caption{config\_coef\_3rd\_order: Blending coefficient for 3rd and 4th order horizontal reconstruction of tracers.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_advection]{config\_monotonic}}
+\subsection[config\_monotonic]{\hyperref[sec:nm_tab_advection]{config\_monotonic}}
 \label{subsec:nm_sec_config_monotonic}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1249,9 +1251,9 @@
     \caption{config\_monotonic: Flag that controls if monotonic advection is used in the simulation.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_bottom_drag]{bottom\_drag}}
+\section[bottom\_drag]{\hyperref[sec:nm_tab_bottom_drag]{bottom\_drag}}
 \label{sec:nm_sec_bottom_drag}
-\subsection{\hyperref[sec:nm_tab_bottom_drag]{config\_bottom\_drag\_coeff}}
+\subsection[config\_bottom\_drag\_coeff]{\hyperref[sec:nm_tab_bottom_drag]{config\_bottom\_drag\_coeff}}
 \label{subsec:nm_sec_config_bottom_drag_coeff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1267,9 +1269,9 @@
     \caption{config\_bottom\_drag\_coeff: Value of the bottom drag coefficient.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_pressure_gradient]{pressure\_gradient}}
+\section[pressure\_gradient]{\hyperref[sec:nm_tab_pressure_gradient]{pressure\_gradient}}
 \label{sec:nm_sec_pressure_gradient}
-\subsection{\hyperref[sec:nm_tab_pressure_gradient]{config\_pressure\_gradient\_type}}
+\subsection[config\_pressure\_gradient\_type]{\hyperref[sec:nm_tab_pressure_gradient]{config\_pressure\_gradient\_type}}
 \label{subsec:nm_sec_config_pressure_gradient_type}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1285,7 +1287,7 @@
     \caption{config\_pressure\_gradient\_type: String that defines the type of pressure gradient used in the simulation.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_pressure_gradient]{config\_rho0}}
+\subsection[config\_rho0]{\hyperref[sec:nm_tab_pressure_gradient]{config\_rho0}}
 \label{subsec:nm_sec_config_rho0}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1301,9 +1303,9 @@
     \caption{config\_rho0: Value of the reference density for the Boussineq approximation.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_eos]{eos}}
+\section[eos]{\hyperref[sec:nm_tab_eos]{eos}}
 \label{sec:nm_sec_eos}
-\subsection{\hyperref[sec:nm_tab_eos]{config\_eos\_type}}
+\subsection[config\_eos\_type]{\hyperref[sec:nm_tab_eos]{config\_eos\_type}}
 \label{subsec:nm_sec_config_eos_type}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1319,9 +1321,9 @@
     \caption{config\_eos\_type: String that defines the equation of state used in the simulation.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_eos_linear]{eos\_linear}}
+\section[eos\_linear]{\hyperref[sec:nm_tab_eos_linear]{eos\_linear}}
 \label{sec:nm_sec_eos_linear}
-\subsection{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_alpha}}
+\subsection[config\_eos\_linear\_alpha]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_alpha}}
 \label{subsec:nm_sec_config_eos_linear_alpha}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1337,7 +1339,7 @@
     \caption{config\_eos\_linear\_alpha: Value of temperature expansion coefficient used in the linear equation of state.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_beta}}
+\subsection[config\_eos\_linear\_beta]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_beta}}
 \label{subsec:nm_sec_config_eos_linear_beta}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1353,7 +1355,7 @@
     \caption{config\_eos\_linear\_beta: Value of salinity expansion coefficient used in the linear equation of state.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_Tref}}
+\subsection[config\_eos\_linear\_Tref]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_Tref}}
 \label{subsec:nm_sec_config_eos_linear_Tref}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1369,7 +1371,7 @@
     \caption{config\_eos\_linear\_Tref: Value of the reference temperature used in the linear equation of state.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_Sref}}
+\subsection[config\_eos\_linear\_Sref]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_Sref}}
 \label{subsec:nm_sec_config_eos_linear_Sref}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1385,7 +1387,7 @@
     \caption{config\_eos\_linear\_Sref: Value of the reference salinity used in the linear equation of state.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_rhoref}}
+\subsection[config\_eos\_linear\_rhoref]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_rhoref}}
 \label{subsec:nm_sec_config_eos_linear_rhoref}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1401,9 +1403,9 @@
     \caption{config\_eos\_linear\_rhoref: Value of the reference density used in the linear equation of state.}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_split_explicit_ts]{split\_explicit\_ts}}
+\section[split\_explicit\_ts]{\hyperref[sec:nm_tab_split_explicit_ts]{split\_explicit\_ts}}
 \label{sec:nm_sec_split_explicit_ts}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_ts\_iter}}
+\subsection[config\_n\_ts\_iter]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_ts\_iter}}
 \label{subsec:nm_sec_config_n_ts_iter}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1419,7 +1421,7 @@
     \caption{config\_n\_ts\_iter: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_bcl\_iter\_beg}}
+\subsection[config\_n\_bcl\_iter\_beg]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_bcl\_iter\_beg}}
 \label{subsec:nm_sec_config_n_bcl_iter_beg}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1435,7 +1437,7 @@
     \caption{config\_n\_bcl\_iter\_beg: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_bcl\_iter\_mid}}
+\subsection[config\_n\_bcl\_iter\_mid]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_bcl\_iter\_mid}}
 \label{subsec:nm_sec_config_n_bcl_iter_mid}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1451,7 +1453,7 @@
     \caption{config\_n\_bcl\_iter\_mid: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_bcl\_iter\_end}}
+\subsection[config\_n\_bcl\_iter\_end]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_bcl\_iter\_end}}
 \label{subsec:nm_sec_config_n_bcl_iter_end}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1467,7 +1469,7 @@
     \caption{config\_n\_bcl\_iter\_end: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_btr\_subcycles}}
+\subsection[config\_n\_btr\_subcycles]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_btr\_subcycles}}
 \label{subsec:nm_sec_config_n_btr_subcycles}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1483,7 +1485,7 @@
     \caption{config\_n\_btr\_subcycles: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_btr\_cor\_iter}}
+\subsection[config\_n\_btr\_cor\_iter]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_n\_btr\_cor\_iter}}
 \label{subsec:nm_sec_config_n_btr_cor_iter}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1499,7 +1501,7 @@
     \caption{config\_n\_btr\_cor\_iter: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_u\_correction}}
+\subsection[config\_u\_correction]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_u\_correction}}
 \label{subsec:nm_sec_config_u_correction}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1515,7 +1517,7 @@
     \caption{config\_u\_correction: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_subcycle\_loop\_factor}}
+\subsection[config\_btr\_subcycle\_loop\_factor]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_subcycle\_loop\_factor}}
 \label{subsec:nm_sec_config_btr_subcycle_loop_factor}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1531,7 +1533,7 @@
     \caption{config\_btr\_subcycle\_loop\_factor: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_gam1\_uWt1}}
+\subsection[config\_btr\_gam1\_uWt1]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_gam1\_uWt1}}
 \label{subsec:nm_sec_config_btr_gam1_uWt1}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1547,7 +1549,7 @@
     \caption{config\_btr\_gam1\_uWt1: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_gam2\_SSHWt1}}
+\subsection[config\_btr\_gam2\_SSHWt1]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_gam2\_SSHWt1}}
 \label{subsec:nm_sec_config_btr_gam2_SSHWt1}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1563,7 +1565,7 @@
     \caption{config\_btr\_gam2\_SSHWt1: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_gam3\_uWt2}}
+\subsection[config\_btr\_gam3\_uWt2]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_gam3\_uWt2}}
 \label{subsec:nm_sec_config_btr_gam3_uWt2}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1579,7 +1581,7 @@
     \caption{config\_btr\_gam3\_uWt2: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_solve\_SSH2}}
+\subsection[config\_btr\_solve\_SSH2]{\hyperref[sec:nm_tab_split_explicit_ts]{config\_btr\_solve\_SSH2}}
 \label{subsec:nm_sec_config_btr_solve_SSH2}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1595,9 +1597,9 @@
     \caption{config\_btr\_solve\_SSH2: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:nm_tab_debug]{debug}}
+\section[debug]{\hyperref[sec:nm_tab_debug]{debug}}
 \label{sec:nm_sec_debug}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_check\_zlevel\_consistency}}
+\subsection[config\_check\_zlevel\_consistency]{\hyperref[sec:nm_tab_debug]{config\_check\_zlevel\_consistency}}
 \label{subsec:nm_sec_config_check_zlevel_consistency}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1613,7 +1615,7 @@
     \caption{config\_check\_zlevel\_consistency: Flag that enables a zlevel consistency check on initialization.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_filter\_btr\_mode}}
+\subsection[config\_filter\_btr\_mode]{\hyperref[sec:nm_tab_debug]{config\_filter\_btr\_mode}}
 \label{subsec:nm_sec_config_filter_btr_mode}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1629,7 +1631,7 @@
     \caption{config\_filter\_btr\_mode: Flag that enables the filtering of the barotropic mode.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_prescribe\_velocity}}
+\subsection[config\_prescribe\_velocity]{\hyperref[sec:nm_tab_debug]{config\_prescribe\_velocity}}
 \label{subsec:nm_sec_config_prescribe_velocity}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1645,7 +1647,7 @@
     \caption{config\_prescribe\_velocity: Flag that enables prescribed velocities, read from the input file, that remain constant throughout the simulation.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_prescribe\_thickness}}
+\subsection[config\_prescribe\_thickness]{\hyperref[sec:nm_tab_debug]{config\_prescribe\_thickness}}
 \label{subsec:nm_sec_config_prescribe_thickness}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1661,7 +1663,7 @@
     \caption{config\_prescribe\_thickness: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_include\_KE\_vertex}}
+\subsection[config\_include\_KE\_vertex]{\hyperref[sec:nm_tab_debug]{config\_include\_KE\_vertex}}
 \label{subsec:nm_sec_config_include_KE_vertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1677,7 +1679,7 @@
     \caption{config\_include\_KE\_vertex: {\bf \color{red} DEFINE}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_check\_tracer\_monotonicity}}
+\subsection[config\_check\_tracer\_monotonicity]{\hyperref[sec:nm_tab_debug]{config\_check\_tracer\_monotonicity}}
 \label{subsec:nm_sec_config_check_tracer_monotonicity}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1693,7 +1695,7 @@
     \caption{config\_check\_tracer\_monotonicity: Flag that enables the check for monotonicity of tracers. Only available if config\_monotoic is true.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_h\_all\_tend}}
+\subsection[config\_disable\_h\_all\_tend]{\hyperref[sec:nm_tab_debug]{config\_disable\_h\_all\_tend}}
 \label{subsec:nm_sec_config_disable_h_all_tend}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1709,7 +1711,7 @@
     \caption{config\_disable\_h\_all\_tend: Flag that disables all thickness tendencies.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_h\_hadv}}
+\subsection[config\_disable\_h\_hadv]{\hyperref[sec:nm_tab_debug]{config\_disable\_h\_hadv}}
 \label{subsec:nm_sec_config_disable_h_hadv}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1725,7 +1727,7 @@
     \caption{config\_disable\_h\_hadv: Flag that disables horizontal advection of thickness.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_h\_vadv}}
+\subsection[config\_disable\_h\_vadv]{\hyperref[sec:nm_tab_debug]{config\_disable\_h\_vadv}}
 \label{subsec:nm_sec_config_disable_h_vadv}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1741,7 +1743,7 @@
     \caption{config\_disable\_h\_vadv: Flag that disables vertical advection of thickness.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_all\_tend}}
+\subsection[config\_disable\_u\_all\_tend]{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_all\_tend}}
 \label{subsec:nm_sec_config_disable_u_all_tend}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1757,7 +1759,7 @@
     \caption{config\_disable\_u\_all\_tend: Flag that disables all velocitiy tendencies.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_coriolis}}
+\subsection[config\_disable\_u\_coriolis]{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_coriolis}}
 \label{subsec:nm_sec_config_disable_u_coriolis}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1773,7 +1775,7 @@
     \caption{config\_disable\_u\_coriolis: Flag that disables Coriolis tendencies of velocity.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_pgrad}}
+\subsection[config\_disable\_u\_pgrad]{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_pgrad}}
 \label{subsec:nm_sec_config_disable_u_pgrad}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1789,7 +1791,7 @@
     \caption{config\_disable\_u\_pgrad: Flag that disables pressure gradient tendencies of velocity.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_hmix}}
+\subsection[config\_disable\_u\_hmix]{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_hmix}}
 \label{subsec:nm_sec_config_disable_u_hmix}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1805,7 +1807,7 @@
     \caption{config\_disable\_u\_hmix: Flag that disables horizontal mixing tendencies of velocity.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_windstress}}
+\subsection[config\_disable\_u\_windstress]{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_windstress}}
 \label{subsec:nm_sec_config_disable_u_windstress}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1821,7 +1823,7 @@
     \caption{config\_disable\_u\_windstress: Flag that disables windstress tendencies of velocity.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_vmix}}
+\subsection[config\_disable\_u\_vmix]{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_vmix}}
 \label{subsec:nm_sec_config_disable_u_vmix}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1837,7 +1839,7 @@
     \caption{config\_disable\_u\_vmix: Flag that disables vertical mixing of velocity.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_vadv}}
+\subsection[config\_disable\_u\_vadv]{\hyperref[sec:nm_tab_debug]{config\_disable\_u\_vadv}}
 \label{subsec:nm_sec_config_disable_u_vadv}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1853,7 +1855,7 @@
     \caption{config\_disable\_u\_vadv: Flag that disables vertical advection tendencies of velocity.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_tr\_all\_tend}}
+\subsection[config\_disable\_tr\_all\_tend]{\hyperref[sec:nm_tab_debug]{config\_disable\_tr\_all\_tend}}
 \label{subsec:nm_sec_config_disable_tr_all_tend}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1869,7 +1871,7 @@
     \caption{config\_disable\_tr\_all\_tend: Flag that disables all tracer tendencies.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_tr\_adv}}
+\subsection[config\_disable\_tr\_adv]{\hyperref[sec:nm_tab_debug]{config\_disable\_tr\_adv}}
 \label{subsec:nm_sec_config_disable_tr_adv}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1885,7 +1887,7 @@
     \caption{config\_disable\_tr\_adv: Flag that disables advection tendencites of tracers.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_tr\_hmix}}
+\subsection[config\_disable\_tr\_hmix]{\hyperref[sec:nm_tab_debug]{config\_disable\_tr\_hmix}}
 \label{subsec:nm_sec_config_disable_tr_hmix}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1901,7 +1903,7 @@
     \caption{config\_disable\_tr\_hmix: Flag that disables horizontal mixing tendencites of tracers.}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:nm_tab_debug]{config\_disable\_tr\_vmix}}
+\subsection[config\_disable\_tr\_vmix]{\hyperref[sec:nm_tab_debug]{config\_disable\_tr\_vmix}}
 \label{subsec:nm_sec_config_disable_tr_vmix}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}

Modified: trunk/documents/users_guide/ocn/namelist_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/namelist_table_documentation.tex        2013-03-11 17:37:48 UTC (rev 2581)
+++ trunk/documents/users_guide/ocn/namelist_table_documentation.tex        2013-03-11 18:10:43 UTC (rev 2582)
@@ -1,7 +1,9 @@
-\chapter{Namelist options}
-\section{time\_management}
+\chapter[Namelist options]{\hyperref[chap:namelist_sections]{Namelist options}}
+\label{chap:namelist_tables}
+Embedded links point to more detailed namelist information in the appendix.
+\section[time\_management]{\hyperref[sec:nm_sec_time_management]{time\_management}}
 \label{sec:nm_tab_time_management}
-\input{ocn/section_descriptions//time_management.tex}
+\input{ocn/section_descriptions/time_management.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -22,7 +24,7 @@
 \end{longtable}
 \end{center}
 }
-\section{io}
+\section[io]{\hyperref[sec:nm_sec_io]{io}}
 \label{sec:nm_tab_io}
 {\small
 \begin{center}
@@ -56,7 +58,7 @@
 \end{longtable}
 \end{center}
 }
-\section{time\_integration}
+\section[time\_integration]{\hyperref[sec:nm_sec_time_integration]{time\_integration}}
 \label{sec:nm_tab_time_integration}
 {\small
 \begin{center}
@@ -72,9 +74,9 @@
 \end{longtable}
 \end{center}
 }
-\section{grid}
+\section[grid]{\hyperref[sec:nm_sec_grid]{grid}}
 \label{sec:nm_tab_grid}
-\input{ocn/section_descriptions//grid.tex}
+\input{ocn/section_descriptions/grid.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -95,9 +97,9 @@
 \end{longtable}
 \end{center}
 }
-\section{decomposition}
+\section[decomposition]{\hyperref[sec:nm_sec_decomposition]{decomposition}}
 \label{sec:nm_tab_decomposition}
-\input{ocn/section_descriptions//decomposition.tex}
+\input{ocn/section_descriptions/decomposition.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -116,9 +118,9 @@
 \end{longtable}
 \end{center}
 }
-\section{hmix}
+\section[hmix]{\hyperref[sec:nm_sec_hmix]{hmix}}
 \label{sec:nm_tab_hmix}
-\input{ocn/section_descriptions//hmix.tex}
+\input{ocn/section_descriptions/hmix.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -135,9 +137,9 @@
 \end{longtable}
 \end{center}
 }
-\section{hmix\_del2}
+\section[hmix\_del2]{\hyperref[sec:nm_sec_hmix_del2]{hmix\_del2}}
 \label{sec:nm_tab_hmix_del2}
-\input{ocn/section_descriptions//hmix_del2.tex}
+\input{ocn/section_descriptions/hmix_del2.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}
@@ -158,7 +160,7 @@
 \end{longtable}
 \end{center}
 }
-\section{hmix\_del4}
+\section[hmix\_del4]{\hyperref[sec:nm_sec_hmix_del4]{hmix\_del4}}
 \label{sec:nm_tab_hmix_del4}
 {\small
 \begin{center}
@@ -180,7 +182,7 @@
 \end{longtable}
 \end{center}
 }
-\section{hmix\_Leith}
+\section[hmix\_Leith]{\hyperref[sec:nm_sec_hmix_Leith]{hmix\_Leith}}
 \label{sec:nm_tab_hmix_Leith}
 \input{ocn/section_descriptions/hmix_Leith.tex}
 {\small
@@ -201,7 +203,7 @@
 \end{longtable}
 \end{center}
 }
-\section{standard\_GM}
+\section[standard\_GM]{\hyperref[sec:nm_sec_standard_GM]{standard\_GM}}
 \label{sec:nm_tab_standard_GM}
 {\small
 \begin{center}
@@ -217,7 +219,7 @@
 \end{longtable}
 \end{center}
 }
-\section{Rayleigh\_damping}
+\section[Rayleigh\_damping]{\hyperref[sec:nm_sec_Rayleigh_damping]{Rayleigh\_damping}}
 \label{sec:nm_tab_Rayleigh_damping}
 {\small
 \begin{center}
@@ -233,7 +235,7 @@
 \end{longtable}
 \end{center}
 }
-\section{vmix}
+\section[vmix]{\hyperref[sec:nm_sec_vmix]{vmix}}
 \label{sec:nm_tab_vmix}
 {\small
 \begin{center}
@@ -249,7 +251,7 @@
 \end{longtable}
 \end{center}
 }
-\section{vmix\_const}
+\section[vmix\_const]{\hyperref[sec:nm_sec_vmix_const]{vmix\_const}}
 \label{sec:nm_tab_vmix_const}
 {\small
 \begin{center}
@@ -269,7 +271,7 @@
 \end{longtable}
 \end{center}
 }
-\section{vmix\_rich}
+\section[vmix\_rich]{\hyperref[sec:nm_sec_vmix_rich]{vmix\_rich}}
 \label{sec:nm_tab_vmix_rich}
 {\small
 \begin{center}
@@ -291,7 +293,7 @@
 \end{longtable}
 \end{center}
 }
-\section{vmix\_tanh}
+\section[vmix\_tanh]{\hyperref[sec:nm_sec_vmix_tanh]{vmix\_tanh}}
 \label{sec:nm_tab_vmix_tanh}
 {\small
 \begin{center}
@@ -319,7 +321,7 @@
 \end{longtable}
 \end{center}
 }
-\section{forcing}
+\section[forcing]{\hyperref[sec:nm_sec_forcing]{forcing}}
 \label{sec:nm_tab_forcing}
 {\small
 \begin{center}
@@ -339,7 +341,7 @@
 \end{longtable}
 \end{center}
 }
-\section{advection}
+\section[advection]{\hyperref[sec:nm_sec_advection]{advection}}
 \label{sec:nm_tab_advection}
 \input{ocn/section_descriptions/advection.tex}
 {\small
@@ -362,7 +364,7 @@
 \end{longtable}
 \end{center}
 }
-\section{bottom\_drag}
+\section[bottom\_drag]{\hyperref[sec:nm_sec_bottom_drag]{bottom\_drag}}
 \label{sec:nm_tab_bottom_drag}
 {\small
 \begin{center}
@@ -376,7 +378,7 @@
 \end{longtable}
 \end{center}
 }
-\section{pressure\_gradient}
+\section[pressure\_gradient]{\hyperref[sec:nm_sec_pressure_gradient]{pressure\_gradient}}
 \label{sec:nm_tab_pressure_gradient}
 {\small
 \begin{center}
@@ -392,7 +394,7 @@
 \end{longtable}
 \end{center}
 }
-\section{eos}
+\section[eos]{\hyperref[sec:nm_sec_eos]{eos}}
 \label{sec:nm_tab_eos}
 \input{ocn/section_descriptions/eos.tex}
 {\small
@@ -407,7 +409,7 @@
 \end{longtable}
 \end{center}
 }
-\section{eos\_linear}
+\section[eos\_linear]{\hyperref[sec:nm_sec_eos_linear]{eos\_linear}}
 \label{sec:nm_tab_eos_linear}
 \input{ocn/section_descriptions/eos_linear.tex}
 {\small
@@ -430,7 +432,7 @@
 \end{longtable}
 \end{center}
 }
-\section{split\_explicit\_ts}
+\section[split\_explicit\_ts]{\hyperref[sec:nm_sec_split_explicit_ts]{split\_explicit\_ts}}
 \label{sec:nm_tab_split_explicit_ts}
 {\small
 \begin{center}
@@ -466,9 +468,9 @@
 \end{longtable}
 \end{center}
 }
-\section{debug}
+\section[debug]{\hyperref[sec:nm_sec_debug]{debug}}
 \label{sec:nm_tab_debug}
-\input{ocn/section_descriptions//debug.tex}
+\input{ocn/section_descriptions/debug.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} || p{4.0in} |}

Modified: trunk/documents/users_guide/ocn/test_cases/baroclinic_channel.tex
===================================================================
--- trunk/documents/users_guide/ocn/test_cases/baroclinic_channel.tex        2013-03-11 17:37:48 UTC (rev 2581)
+++ trunk/documents/users_guide/ocn/test_cases/baroclinic_channel.tex        2013-03-11 18:10:43 UTC (rev 2582)
@@ -47,12 +47,15 @@
 
 \subsection{Results}
 \label{subsecc:baroclinic_channel_results}
-The surface temperature fields at day 10 from the 4 km and 1 km simulations are shown in Figure \ref{fig:baroclinicChannelTemperature}.
-This results should be reproduced using the default ``run\_directory'' for the 4 km and 1 km resolutions. Regarding the plotting of the results, please see Chapter \ref{chap:knownissues}.
+The surface temperature fields at day 10 from the 10km, 4 km, and 1 km simulations are shown in Figure \ref{fig:baroclinicChannelTemperature}.
+This results should be reproduced using the default ``run\_directory'' for the 10 km, 4 km, and 1 km resolutions. Regarding plotting atrifacts of the results, please see Chapter \ref{chap:knownissues}.
 
 \begin{figure}[H!]
         \label{fig:baroclinicChannelTemperature}
+        \centering
+        \caption{Baroclinic channel test case results. Surface temperature field after 10 simulation days using default included namelists.}
         \subfigure[10km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocn/figures/baroclinic_channel_10000m_20levs_10days.pdf}}
         \subfigure[4km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocn/figures/baroclinic_channel_4000m_20levs_10days.pdf}}
+        \subfigure[1km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocn/figures/baroclinic_channel_1000m_20levs_10days.pdf}}
 \end{figure}
 

Modified: trunk/documents/users_guide/ocn/variable_section_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/variable_section_documentation.tex        2013-03-11 17:37:48 UTC (rev 2581)
+++ trunk/documents/users_guide/ocn/variable_section_documentation.tex        2013-03-11 18:10:43 UTC (rev 2582)
@@ -1,7 +1,9 @@
-\chapter{Variable definions}
-\section{\hyperref[sec:var_tab_state]{state}}
+\chapter[Variable definitions]{\hyperref[chap:variable_tables]{Variable definitions}}
+\label{chap:variable_sections}
+Embedded links point to information in chapter \ref{chap:variable_tables}
+\section[state]{\hyperref[sec:var_tab_state]{state}}
 \label{sec:var_sec_state}
-\subsection{\hyperref[sec:var_tab_state]{xtime}}
+\subsection[xtime]{\hyperref[sec:var_tab_state]{xtime}}
 \label{subsec:var_sec_state_xtime}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -17,7 +19,7 @@
     \caption{xtime: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{u}}
+\subsection[u]{\hyperref[sec:var_tab_state]{u}}
 \label{subsec:var_sec_state_u}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -33,7 +35,7 @@
     \caption{u: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{h}}
+\subsection[h]{\hyperref[sec:var_tab_state]{h}}
 \label{subsec:var_sec_state_h}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -49,7 +51,7 @@
     \caption{h: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{rho}}
+\subsection[rho]{\hyperref[sec:var_tab_state]{rho}}
 \label{subsec:var_sec_state_rho}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -65,7 +67,7 @@
     \caption{rho: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{temperature}}
+\subsection[temperature]{\hyperref[sec:var_tab_state]{temperature}}
 \label{subsec:var_sec_state_temperature}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -81,7 +83,7 @@
     \caption{temperature: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{salinity}}
+\subsection[salinity]{\hyperref[sec:var_tab_state]{salinity}}
 \label{subsec:var_sec_state_salinity}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -97,7 +99,7 @@
     \caption{salinity: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{tracer1}}
+\subsection[tracer1]{\hyperref[sec:var_tab_state]{tracer1}}
 \label{subsec:var_sec_state_tracer1}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -113,7 +115,7 @@
     \caption{tracer1: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBtr}}
+\subsection[uBtr]{\hyperref[sec:var_tab_state]{uBtr}}
 \label{subsec:var_sec_state_uBtr}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -129,7 +131,7 @@
     \caption{uBtr: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{ssh}}
+\subsection[ssh]{\hyperref[sec:var_tab_state]{ssh}}
 \label{subsec:var_sec_state_ssh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -145,7 +147,7 @@
     \caption{ssh: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBtrSubcycle}}
+\subsection[uBtrSubcycle]{\hyperref[sec:var_tab_state]{uBtrSubcycle}}
 \label{subsec:var_sec_state_uBtrSubcycle}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -161,7 +163,7 @@
     \caption{uBtrSubcycle: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{sshSubcycle}}
+\subsection[sshSubcycle]{\hyperref[sec:var_tab_state]{sshSubcycle}}
 \label{subsec:var_sec_state_sshSubcycle}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -177,7 +179,7 @@
     \caption{sshSubcycle: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{FBtr}}
+\subsection[FBtr]{\hyperref[sec:var_tab_state]{FBtr}}
 \label{subsec:var_sec_state_FBtr}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -193,7 +195,7 @@
     \caption{FBtr: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{GBtrForcing}}
+\subsection[GBtrForcing]{\hyperref[sec:var_tab_state]{GBtrForcing}}
 \label{subsec:var_sec_state_GBtrForcing}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -209,7 +211,7 @@
     \caption{GBtrForcing: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBcl}}
+\subsection[uBcl]{\hyperref[sec:var_tab_state]{uBcl}}
 \label{subsec:var_sec_state_uBcl}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -225,7 +227,7 @@
     \caption{uBcl: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{zMid}}
+\subsection[zMid]{\hyperref[sec:var_tab_state]{zMid}}
 \label{subsec:var_sec_state_zMid}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -241,7 +243,7 @@
     \caption{zMid: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{v}}
+\subsection[v]{\hyperref[sec:var_tab_state]{v}}
 \label{subsec:var_sec_state_v}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -257,7 +259,7 @@
     \caption{v: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uTransport}}
+\subsection[uTransport]{\hyperref[sec:var_tab_state]{uTransport}}
 \label{subsec:var_sec_state_uTransport}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -273,7 +275,7 @@
     \caption{uTransport: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBolusGM}}
+\subsection[uBolusGM]{\hyperref[sec:var_tab_state]{uBolusGM}}
 \label{subsec:var_sec_state_uBolusGM}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -289,7 +291,7 @@
     \caption{uBolusGM: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBolusGMX}}
+\subsection[uBolusGMX]{\hyperref[sec:var_tab_state]{uBolusGMX}}
 \label{subsec:var_sec_state_uBolusGMX}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -305,7 +307,7 @@
     \caption{uBolusGMX: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBolusGMY}}
+\subsection[uBolusGMY]{\hyperref[sec:var_tab_state]{uBolusGMY}}
 \label{subsec:var_sec_state_uBolusGMY}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -321,7 +323,7 @@
     \caption{uBolusGMY: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBolusGMZ}}
+\subsection[uBolusGMZ]{\hyperref[sec:var_tab_state]{uBolusGMZ}}
 \label{subsec:var_sec_state_uBolusGMZ}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -337,7 +339,7 @@
     \caption{uBolusGMZ: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBolusGMZonal}}
+\subsection[uBolusGMZonal]{\hyperref[sec:var_tab_state]{uBolusGMZonal}}
 \label{subsec:var_sec_state_uBolusGMZonal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -353,7 +355,7 @@
     \caption{uBolusGMZonal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uBolusGMMeridional}}
+\subsection[uBolusGMMeridional]{\hyperref[sec:var_tab_state]{uBolusGMMeridional}}
 \label{subsec:var_sec_state_uBolusGMMeridional}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -369,7 +371,7 @@
     \caption{uBolusGMMeridional: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{hEddyFlux}}
+\subsection[hEddyFlux]{\hyperref[sec:var_tab_state]{hEddyFlux}}
 \label{subsec:var_sec_state_hEddyFlux}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -385,7 +387,7 @@
     \caption{hEddyFlux: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{h\_kappa}}
+\subsection[h\_kappa]{\hyperref[sec:var_tab_state]{h\_kappa}}
 \label{subsec:var_sec_state_h_kappa}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -401,7 +403,7 @@
     \caption{h\_kappa: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{h\_kappa\_q}}
+\subsection[h\_kappa\_q]{\hyperref[sec:var_tab_state]{h\_kappa\_q}}
 \label{subsec:var_sec_state_h_kappa_q}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -417,7 +419,7 @@
     \caption{h\_kappa\_q: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{divergence}}
+\subsection[divergence]{\hyperref[sec:var_tab_state]{divergence}}
 \label{subsec:var_sec_state_divergence}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -433,7 +435,7 @@
     \caption{divergence: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{vorticity}}
+\subsection[vorticity]{\hyperref[sec:var_tab_state]{vorticity}}
 \label{subsec:var_sec_state_vorticity}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -449,7 +451,7 @@
     \caption{vorticity: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{Vor\_edge}}
+\subsection[Vor\_edge]{\hyperref[sec:var_tab_state]{Vor\_edge}}
 \label{subsec:var_sec_state_Vor_edge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -465,7 +467,7 @@
     \caption{Vor\_edge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{h\_edge}}
+\subsection[h\_edge]{\hyperref[sec:var_tab_state]{h\_edge}}
 \label{subsec:var_sec_state_h_edge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -481,7 +483,7 @@
     \caption{h\_edge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{h\_vertex}}
+\subsection[h\_vertex]{\hyperref[sec:var_tab_state]{h\_vertex}}
 \label{subsec:var_sec_state_h_vertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -497,7 +499,7 @@
     \caption{h\_vertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{ke}}
+\subsection[ke]{\hyperref[sec:var_tab_state]{ke}}
 \label{subsec:var_sec_state_ke}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -513,7 +515,7 @@
     \caption{ke: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{kev}}
+\subsection[kev]{\hyperref[sec:var_tab_state]{kev}}
 \label{subsec:var_sec_state_kev}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -529,7 +531,7 @@
     \caption{kev: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{kevc}}
+\subsection[kevc]{\hyperref[sec:var_tab_state]{kevc}}
 \label{subsec:var_sec_state_kevc}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -545,7 +547,7 @@
     \caption{kevc: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{ke\_edge}}
+\subsection[ke\_edge]{\hyperref[sec:var_tab_state]{ke\_edge}}
 \label{subsec:var_sec_state_ke_edge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -561,7 +563,7 @@
     \caption{ke\_edge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{Vor\_vertex}}
+\subsection[Vor\_vertex]{\hyperref[sec:var_tab_state]{Vor\_vertex}}
 \label{subsec:var_sec_state_Vor_vertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -577,7 +579,7 @@
     \caption{Vor\_vertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{Vor\_cell}}
+\subsection[Vor\_cell]{\hyperref[sec:var_tab_state]{Vor\_cell}}
 \label{subsec:var_sec_state_Vor_cell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -593,7 +595,7 @@
     \caption{Vor\_cell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uReconstructX}}
+\subsection[uReconstructX]{\hyperref[sec:var_tab_state]{uReconstructX}}
 \label{subsec:var_sec_state_uReconstructX}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -609,7 +611,7 @@
     \caption{uReconstructX: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uReconstructY}}
+\subsection[uReconstructY]{\hyperref[sec:var_tab_state]{uReconstructY}}
 \label{subsec:var_sec_state_uReconstructY}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -625,7 +627,7 @@
     \caption{uReconstructY: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uReconstructZ}}
+\subsection[uReconstructZ]{\hyperref[sec:var_tab_state]{uReconstructZ}}
 \label{subsec:var_sec_state_uReconstructZ}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -641,7 +643,7 @@
     \caption{uReconstructZ: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uReconstructZonal}}
+\subsection[uReconstructZonal]{\hyperref[sec:var_tab_state]{uReconstructZonal}}
 \label{subsec:var_sec_state_uReconstructZonal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -657,7 +659,7 @@
     \caption{uReconstructZonal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uReconstructMeridional}}
+\subsection[uReconstructMeridional]{\hyperref[sec:var_tab_state]{uReconstructMeridional}}
 \label{subsec:var_sec_state_uReconstructMeridional}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -673,7 +675,7 @@
     \caption{uReconstructMeridional: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uSrcReconstructX}}
+\subsection[uSrcReconstructX]{\hyperref[sec:var_tab_state]{uSrcReconstructX}}
 \label{subsec:var_sec_state_uSrcReconstructX}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -689,7 +691,7 @@
     \caption{uSrcReconstructX: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uSrcReconstructY}}
+\subsection[uSrcReconstructY]{\hyperref[sec:var_tab_state]{uSrcReconstructY}}
 \label{subsec:var_sec_state_uSrcReconstructY}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -705,7 +707,7 @@
     \caption{uSrcReconstructY: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uSrcReconstructZ}}
+\subsection[uSrcReconstructZ]{\hyperref[sec:var_tab_state]{uSrcReconstructZ}}
 \label{subsec:var_sec_state_uSrcReconstructZ}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -721,7 +723,7 @@
     \caption{uSrcReconstructZ: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uSrcReconstructZonal}}
+\subsection[uSrcReconstructZonal]{\hyperref[sec:var_tab_state]{uSrcReconstructZonal}}
 \label{subsec:var_sec_state_uSrcReconstructZonal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -737,7 +739,7 @@
     \caption{uSrcReconstructZonal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{uSrcReconstructMeridional}}
+\subsection[uSrcReconstructMeridional]{\hyperref[sec:var_tab_state]{uSrcReconstructMeridional}}
 \label{subsec:var_sec_state_uSrcReconstructMeridional}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -753,7 +755,7 @@
     \caption{uSrcReconstructMeridional: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{MontPot}}
+\subsection[MontPot]{\hyperref[sec:var_tab_state]{MontPot}}
 \label{subsec:var_sec_state_MontPot}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -769,7 +771,7 @@
     \caption{MontPot: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{pressure}}
+\subsection[pressure]{\hyperref[sec:var_tab_state]{pressure}}
 \label{subsec:var_sec_state_pressure}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -785,7 +787,7 @@
     \caption{pressure: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{wTop}}
+\subsection[wTop]{\hyperref[sec:var_tab_state]{wTop}}
 \label{subsec:var_sec_state_wTop}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -801,7 +803,7 @@
     \caption{wTop: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{vertVelocityTop}}
+\subsection[vertVelocityTop]{\hyperref[sec:var_tab_state]{vertVelocityTop}}
 \label{subsec:var_sec_state_vertVelocityTop}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -817,7 +819,7 @@
     \caption{vertVelocityTop: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{rhoDisplaced}}
+\subsection[rhoDisplaced]{\hyperref[sec:var_tab_state]{rhoDisplaced}}
 \label{subsec:var_sec_state_rhoDisplaced}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -833,7 +835,7 @@
     \caption{rhoDisplaced: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{BruntVaisalaFreqTop}}
+\subsection[BruntVaisalaFreqTop]{\hyperref[sec:var_tab_state]{BruntVaisalaFreqTop}}
 \label{subsec:var_sec_state_BruntVaisalaFreqTop}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -849,7 +851,7 @@
     \caption{BruntVaisalaFreqTop: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{viscosity}}
+\subsection[viscosity]{\hyperref[sec:var_tab_state]{viscosity}}
 \label{subsec:var_sec_state_viscosity}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -865,7 +867,7 @@
     \caption{viscosity: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{vh}}
+\subsection[vh]{\hyperref[sec:var_tab_state]{vh}}
 \label{subsec:var_sec_state_vh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -881,7 +883,7 @@
     \caption{vh: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{circulation}}
+\subsection[circulation]{\hyperref[sec:var_tab_state]{circulation}}
 \label{subsec:var_sec_state_circulation}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -897,7 +899,7 @@
     \caption{circulation: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{gradVor\_t}}
+\subsection[gradVor\_t]{\hyperref[sec:var_tab_state]{gradVor\_t}}
 \label{subsec:var_sec_state_gradVor_t}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -913,7 +915,7 @@
     \caption{gradVor\_t: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{gradVor\_n}}
+\subsection[gradVor\_n]{\hyperref[sec:var_tab_state]{gradVor\_n}}
 \label{subsec:var_sec_state_gradVor_n}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -929,7 +931,7 @@
     \caption{gradVor\_n: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{areaCellGlobal}}
+\subsection[areaCellGlobal]{\hyperref[sec:var_tab_state]{areaCellGlobal}}
 \label{subsec:var_sec_state_areaCellGlobal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -945,7 +947,7 @@
     \caption{areaCellGlobal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{areaEdgeGlobal}}
+\subsection[areaEdgeGlobal]{\hyperref[sec:var_tab_state]{areaEdgeGlobal}}
 \label{subsec:var_sec_state_areaEdgeGlobal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -961,7 +963,7 @@
     \caption{areaEdgeGlobal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{areaTriangleGlobal}}
+\subsection[areaTriangleGlobal]{\hyperref[sec:var_tab_state]{areaTriangleGlobal}}
 \label{subsec:var_sec_state_areaTriangleGlobal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -977,7 +979,7 @@
     \caption{areaTriangleGlobal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{volumeCellGlobal}}
+\subsection[volumeCellGlobal]{\hyperref[sec:var_tab_state]{volumeCellGlobal}}
 \label{subsec:var_sec_state_volumeCellGlobal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -993,7 +995,7 @@
     \caption{volumeCellGlobal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{volumeEdgeGlobal}}
+\subsection[volumeEdgeGlobal]{\hyperref[sec:var_tab_state]{volumeEdgeGlobal}}
 \label{subsec:var_sec_state_volumeEdgeGlobal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1009,7 +1011,7 @@
     \caption{volumeEdgeGlobal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{CFLNumberGlobal}}
+\subsection[CFLNumberGlobal]{\hyperref[sec:var_tab_state]{CFLNumberGlobal}}
 \label{subsec:var_sec_state_CFLNumberGlobal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1025,7 +1027,7 @@
     \caption{CFLNumberGlobal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{nAccumulate}}
+\subsection[nAccumulate]{\hyperref[sec:var_tab_state]{nAccumulate}}
 \label{subsec:var_sec_state_nAccumulate}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1041,7 +1043,7 @@
     \caption{nAccumulate: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_ssh}}
+\subsection[acc\_ssh]{\hyperref[sec:var_tab_state]{acc\_ssh}}
 \label{subsec:var_sec_state_acc_ssh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1057,7 +1059,7 @@
     \caption{acc\_ssh: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_sshVar}}
+\subsection[acc\_sshVar]{\hyperref[sec:var_tab_state]{acc\_sshVar}}
 \label{subsec:var_sec_state_acc_sshVar}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1073,7 +1075,7 @@
     \caption{acc\_sshVar: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_uReconstructZonal}}
+\subsection[acc\_uReconstructZonal]{\hyperref[sec:var_tab_state]{acc\_uReconstructZonal}}
 \label{subsec:var_sec_state_acc_uReconstructZonal}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1089,7 +1091,7 @@
     \caption{acc\_uReconstructZonal: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_uReconstructMeridional}}
+\subsection[acc\_uReconstructMeridional]{\hyperref[sec:var_tab_state]{acc\_uReconstructMeridional}}
 \label{subsec:var_sec_state_acc_uReconstructMeridional}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1105,7 +1107,7 @@
     \caption{acc\_uReconstructMeridional: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_uReconstructZonalVar}}
+\subsection[acc\_uReconstructZonalVar]{\hyperref[sec:var_tab_state]{acc\_uReconstructZonalVar}}
 \label{subsec:var_sec_state_acc_uReconstructZonalVar}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1121,7 +1123,7 @@
     \caption{acc\_uReconstructZonalVar: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_uReconstructMeridionalVar}}
+\subsection[acc\_uReconstructMeridionalVar]{\hyperref[sec:var_tab_state]{acc\_uReconstructMeridionalVar}}
 \label{subsec:var_sec_state_acc_uReconstructMeridionalVar}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1137,7 +1139,7 @@
     \caption{acc\_uReconstructMeridionalVar: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_u}}
+\subsection[acc\_u]{\hyperref[sec:var_tab_state]{acc\_u}}
 \label{subsec:var_sec_state_acc_u}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1153,7 +1155,7 @@
     \caption{acc\_u: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_uVar}}
+\subsection[acc\_uVar]{\hyperref[sec:var_tab_state]{acc\_uVar}}
 \label{subsec:var_sec_state_acc_uVar}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1169,7 +1171,7 @@
     \caption{acc\_uVar: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_state]{acc\_vertVelocityTop}}
+\subsection[acc\_vertVelocityTop]{\hyperref[sec:var_tab_state]{acc\_vertVelocityTop}}
 \label{subsec:var_sec_state_acc_vertVelocityTop}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1185,9 +1187,9 @@
     \caption{acc\_vertVelocityTop: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:var_tab_mesh]{mesh}}
+\section[mesh]{\hyperref[sec:var_tab_mesh]{mesh}}
 \label{sec:var_sec_mesh}
-\subsection{\hyperref[sec:var_tab_mesh]{latCell}}
+\subsection[latCell]{\hyperref[sec:var_tab_mesh]{latCell}}
 \label{subsec:var_sec_mesh_latCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1203,7 +1205,7 @@
     \caption{latCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{lonCell}}
+\subsection[lonCell]{\hyperref[sec:var_tab_mesh]{lonCell}}
 \label{subsec:var_sec_mesh_lonCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1219,7 +1221,7 @@
     \caption{lonCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{xCell}}
+\subsection[xCell]{\hyperref[sec:var_tab_mesh]{xCell}}
 \label{subsec:var_sec_mesh_xCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1235,7 +1237,7 @@
     \caption{xCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{yCell}}
+\subsection[yCell]{\hyperref[sec:var_tab_mesh]{yCell}}
 \label{subsec:var_sec_mesh_yCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1251,7 +1253,7 @@
     \caption{yCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{zCell}}
+\subsection[zCell]{\hyperref[sec:var_tab_mesh]{zCell}}
 \label{subsec:var_sec_mesh_zCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1267,7 +1269,7 @@
     \caption{zCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{indexToCellID}}
+\subsection[indexToCellID]{\hyperref[sec:var_tab_mesh]{indexToCellID}}
 \label{subsec:var_sec_mesh_indexToCellID}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1283,7 +1285,7 @@
     \caption{indexToCellID: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{latEdge}}
+\subsection[latEdge]{\hyperref[sec:var_tab_mesh]{latEdge}}
 \label{subsec:var_sec_mesh_latEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1299,7 +1301,7 @@
     \caption{latEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{lonEdge}}
+\subsection[lonEdge]{\hyperref[sec:var_tab_mesh]{lonEdge}}
 \label{subsec:var_sec_mesh_lonEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1315,7 +1317,7 @@
     \caption{lonEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{xEdge}}
+\subsection[xEdge]{\hyperref[sec:var_tab_mesh]{xEdge}}
 \label{subsec:var_sec_mesh_xEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1331,7 +1333,7 @@
     \caption{xEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{yEdge}}
+\subsection[yEdge]{\hyperref[sec:var_tab_mesh]{yEdge}}
 \label{subsec:var_sec_mesh_yEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1347,7 +1349,7 @@
     \caption{yEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{zEdge}}
+\subsection[zEdge]{\hyperref[sec:var_tab_mesh]{zEdge}}
 \label{subsec:var_sec_mesh_zEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1363,7 +1365,7 @@
     \caption{zEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{indexToEdgeID}}
+\subsection[indexToEdgeID]{\hyperref[sec:var_tab_mesh]{indexToEdgeID}}
 \label{subsec:var_sec_mesh_indexToEdgeID}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1379,7 +1381,7 @@
     \caption{indexToEdgeID: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{latVertex}}
+\subsection[latVertex]{\hyperref[sec:var_tab_mesh]{latVertex}}
 \label{subsec:var_sec_mesh_latVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1395,7 +1397,7 @@
     \caption{latVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{lonVertex}}
+\subsection[lonVertex]{\hyperref[sec:var_tab_mesh]{lonVertex}}
 \label{subsec:var_sec_mesh_lonVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1411,7 +1413,7 @@
     \caption{lonVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{xVertex}}
+\subsection[xVertex]{\hyperref[sec:var_tab_mesh]{xVertex}}
 \label{subsec:var_sec_mesh_xVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1427,7 +1429,7 @@
     \caption{xVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{yVertex}}
+\subsection[yVertex]{\hyperref[sec:var_tab_mesh]{yVertex}}
 \label{subsec:var_sec_mesh_yVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1443,7 +1445,7 @@
     \caption{yVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{zVertex}}
+\subsection[zVertex]{\hyperref[sec:var_tab_mesh]{zVertex}}
 \label{subsec:var_sec_mesh_zVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1459,7 +1461,7 @@
     \caption{zVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{indexToVertexID}}
+\subsection[indexToVertexID]{\hyperref[sec:var_tab_mesh]{indexToVertexID}}
 \label{subsec:var_sec_mesh_indexToVertexID}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1475,7 +1477,7 @@
     \caption{indexToVertexID: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{meshDensity}}
+\subsection[meshDensity]{\hyperref[sec:var_tab_mesh]{meshDensity}}
 \label{subsec:var_sec_mesh_meshDensity}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1491,7 +1493,7 @@
     \caption{meshDensity: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{meshScalingDel2}}
+\subsection[meshScalingDel2]{\hyperref[sec:var_tab_mesh]{meshScalingDel2}}
 \label{subsec:var_sec_mesh_meshScalingDel2}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1507,7 +1509,7 @@
     \caption{meshScalingDel2: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{meshScalingDel4}}
+\subsection[meshScalingDel4]{\hyperref[sec:var_tab_mesh]{meshScalingDel4}}
 \label{subsec:var_sec_mesh_meshScalingDel4}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1523,7 +1525,7 @@
     \caption{meshScalingDel4: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{meshScaling}}
+\subsection[meshScaling]{\hyperref[sec:var_tab_mesh]{meshScaling}}
 \label{subsec:var_sec_mesh_meshScaling}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1539,7 +1541,7 @@
     \caption{meshScaling: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{cellsOnEdge}}
+\subsection[cellsOnEdge]{\hyperref[sec:var_tab_mesh]{cellsOnEdge}}
 \label{subsec:var_sec_mesh_cellsOnEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1555,7 +1557,7 @@
     \caption{cellsOnEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{nEdgesOnCell}}
+\subsection[nEdgesOnCell]{\hyperref[sec:var_tab_mesh]{nEdgesOnCell}}
 \label{subsec:var_sec_mesh_nEdgesOnCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1571,7 +1573,7 @@
     \caption{nEdgesOnCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{nEdgesOnEdge}}
+\subsection[nEdgesOnEdge]{\hyperref[sec:var_tab_mesh]{nEdgesOnEdge}}
 \label{subsec:var_sec_mesh_nEdgesOnEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1587,7 +1589,7 @@
     \caption{nEdgesOnEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{edgesOnCell}}
+\subsection[edgesOnCell]{\hyperref[sec:var_tab_mesh]{edgesOnCell}}
 \label{subsec:var_sec_mesh_edgesOnCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1603,7 +1605,7 @@
     \caption{edgesOnCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{edgesOnEdge}}
+\subsection[edgesOnEdge]{\hyperref[sec:var_tab_mesh]{edgesOnEdge}}
 \label{subsec:var_sec_mesh_edgesOnEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1619,7 +1621,7 @@
     \caption{edgesOnEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{weightsOnEdge}}
+\subsection[weightsOnEdge]{\hyperref[sec:var_tab_mesh]{weightsOnEdge}}
 \label{subsec:var_sec_mesh_weightsOnEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1635,7 +1637,7 @@
     \caption{weightsOnEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{dvEdge}}
+\subsection[dvEdge]{\hyperref[sec:var_tab_mesh]{dvEdge}}
 \label{subsec:var_sec_mesh_dvEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1651,7 +1653,7 @@
     \caption{dvEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{dcEdge}}
+\subsection[dcEdge]{\hyperref[sec:var_tab_mesh]{dcEdge}}
 \label{subsec:var_sec_mesh_dcEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1667,7 +1669,7 @@
     \caption{dcEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{angleEdge}}
+\subsection[angleEdge]{\hyperref[sec:var_tab_mesh]{angleEdge}}
 \label{subsec:var_sec_mesh_angleEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1683,7 +1685,7 @@
     \caption{angleEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{areaCell}}
+\subsection[areaCell]{\hyperref[sec:var_tab_mesh]{areaCell}}
 \label{subsec:var_sec_mesh_areaCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1699,7 +1701,7 @@
     \caption{areaCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{areaTriangle}}
+\subsection[areaTriangle]{\hyperref[sec:var_tab_mesh]{areaTriangle}}
 \label{subsec:var_sec_mesh_areaTriangle}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1715,7 +1717,7 @@
     \caption{areaTriangle: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{edgeNormalVectors}}
+\subsection[edgeNormalVectors]{\hyperref[sec:var_tab_mesh]{edgeNormalVectors}}
 \label{subsec:var_sec_mesh_edgeNormalVectors}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1731,7 +1733,7 @@
     \caption{edgeNormalVectors: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{localVerticalUnitVectors}}
+\subsection[localVerticalUnitVectors]{\hyperref[sec:var_tab_mesh]{localVerticalUnitVectors}}
 \label{subsec:var_sec_mesh_localVerticalUnitVectors}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1747,7 +1749,7 @@
     \caption{localVerticalUnitVectors: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{cellTangentPlane}}
+\subsection[cellTangentPlane]{\hyperref[sec:var_tab_mesh]{cellTangentPlane}}
 \label{subsec:var_sec_mesh_cellTangentPlane}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1763,7 +1765,7 @@
     \caption{cellTangentPlane: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{cellsOnCell}}
+\subsection[cellsOnCell]{\hyperref[sec:var_tab_mesh]{cellsOnCell}}
 \label{subsec:var_sec_mesh_cellsOnCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1779,7 +1781,7 @@
     \caption{cellsOnCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{verticesOnCell}}
+\subsection[verticesOnCell]{\hyperref[sec:var_tab_mesh]{verticesOnCell}}
 \label{subsec:var_sec_mesh_verticesOnCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1795,7 +1797,7 @@
     \caption{verticesOnCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{verticesOnEdge}}
+\subsection[verticesOnEdge]{\hyperref[sec:var_tab_mesh]{verticesOnEdge}}
 \label{subsec:var_sec_mesh_verticesOnEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1811,7 +1813,7 @@
     \caption{verticesOnEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{edgesOnVertex}}
+\subsection[edgesOnVertex]{\hyperref[sec:var_tab_mesh]{edgesOnVertex}}
 \label{subsec:var_sec_mesh_edgesOnVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1827,7 +1829,7 @@
     \caption{edgesOnVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{cellsOnVertex}}
+\subsection[cellsOnVertex]{\hyperref[sec:var_tab_mesh]{cellsOnVertex}}
 \label{subsec:var_sec_mesh_cellsOnVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1843,7 +1845,7 @@
     \caption{cellsOnVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{kiteAreasOnVertex}}
+\subsection[kiteAreasOnVertex]{\hyperref[sec:var_tab_mesh]{kiteAreasOnVertex}}
 \label{subsec:var_sec_mesh_kiteAreasOnVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1859,7 +1861,7 @@
     \caption{kiteAreasOnVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{fEdge}}
+\subsection[fEdge]{\hyperref[sec:var_tab_mesh]{fEdge}}
 \label{subsec:var_sec_mesh_fEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1875,7 +1877,7 @@
     \caption{fEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{fVertex}}
+\subsection[fVertex]{\hyperref[sec:var_tab_mesh]{fVertex}}
 \label{subsec:var_sec_mesh_fVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1891,7 +1893,7 @@
     \caption{fVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{bottomDepth}}
+\subsection[bottomDepth]{\hyperref[sec:var_tab_mesh]{bottomDepth}}
 \label{subsec:var_sec_mesh_bottomDepth}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1907,7 +1909,7 @@
     \caption{bottomDepth: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{deriv\_two}}
+\subsection[deriv\_two]{\hyperref[sec:var_tab_mesh]{deriv\_two}}
 \label{subsec:var_sec_mesh_deriv_two}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1923,7 +1925,7 @@
     \caption{deriv\_two: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{adv\_coefs}}
+\subsection[adv\_coefs]{\hyperref[sec:var_tab_mesh]{adv\_coefs}}
 \label{subsec:var_sec_mesh_adv_coefs}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1939,7 +1941,7 @@
     \caption{adv\_coefs: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{adv\_coefs\_2nd}}
+\subsection[adv\_coefs\_2nd]{\hyperref[sec:var_tab_mesh]{adv\_coefs\_2nd}}
 \label{subsec:var_sec_mesh_adv_coefs_2nd}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1955,7 +1957,7 @@
     \caption{adv\_coefs\_2nd: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{adv\_coefs\_3rd}}
+\subsection[adv\_coefs\_3rd]{\hyperref[sec:var_tab_mesh]{adv\_coefs\_3rd}}
 \label{subsec:var_sec_mesh_adv_coefs_3rd}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1971,7 +1973,7 @@
     \caption{adv\_coefs\_3rd: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{advCellsForEdge}}
+\subsection[advCellsForEdge]{\hyperref[sec:var_tab_mesh]{advCellsForEdge}}
 \label{subsec:var_sec_mesh_advCellsForEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -1987,7 +1989,7 @@
     \caption{advCellsForEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{nAdvCellsForEdge}}
+\subsection[nAdvCellsForEdge]{\hyperref[sec:var_tab_mesh]{nAdvCellsForEdge}}
 \label{subsec:var_sec_mesh_nAdvCellsForEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2003,7 +2005,7 @@
     \caption{nAdvCellsForEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{highOrderAdvectionMask}}
+\subsection[highOrderAdvectionMask]{\hyperref[sec:var_tab_mesh]{highOrderAdvectionMask}}
 \label{subsec:var_sec_mesh_highOrderAdvectionMask}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2019,7 +2021,7 @@
     \caption{highOrderAdvectionMask: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{lowOrderAdvectionMask}}
+\subsection[lowOrderAdvectionMask]{\hyperref[sec:var_tab_mesh]{lowOrderAdvectionMask}}
 \label{subsec:var_sec_mesh_lowOrderAdvectionMask}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2035,7 +2037,7 @@
     \caption{lowOrderAdvectionMask: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{defc\_a}}
+\subsection[defc\_a]{\hyperref[sec:var_tab_mesh]{defc\_a}}
 \label{subsec:var_sec_mesh_defc_a}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2051,7 +2053,7 @@
     \caption{defc\_a: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{defc\_b}}
+\subsection[defc\_b]{\hyperref[sec:var_tab_mesh]{defc\_b}}
 \label{subsec:var_sec_mesh_defc_b}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2067,7 +2069,7 @@
     \caption{defc\_b: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{kdiff}}
+\subsection[kdiff]{\hyperref[sec:var_tab_mesh]{kdiff}}
 \label{subsec:var_sec_mesh_kdiff}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2083,7 +2085,7 @@
     \caption{kdiff: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{coeffs\_reconstruct}}
+\subsection[coeffs\_reconstruct]{\hyperref[sec:var_tab_mesh]{coeffs\_reconstruct}}
 \label{subsec:var_sec_mesh_coeffs_reconstruct}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2099,7 +2101,7 @@
     \caption{coeffs\_reconstruct: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{maxLevelCell}}
+\subsection[maxLevelCell]{\hyperref[sec:var_tab_mesh]{maxLevelCell}}
 \label{subsec:var_sec_mesh_maxLevelCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2115,7 +2117,7 @@
     \caption{maxLevelCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{maxLevelEdgeTop}}
+\subsection[maxLevelEdgeTop]{\hyperref[sec:var_tab_mesh]{maxLevelEdgeTop}}
 \label{subsec:var_sec_mesh_maxLevelEdgeTop}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2131,7 +2133,7 @@
     \caption{maxLevelEdgeTop: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{maxLevelEdgeBot}}
+\subsection[maxLevelEdgeBot]{\hyperref[sec:var_tab_mesh]{maxLevelEdgeBot}}
 \label{subsec:var_sec_mesh_maxLevelEdgeBot}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2147,7 +2149,7 @@
     \caption{maxLevelEdgeBot: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{maxLevelVertexTop}}
+\subsection[maxLevelVertexTop]{\hyperref[sec:var_tab_mesh]{maxLevelVertexTop}}
 \label{subsec:var_sec_mesh_maxLevelVertexTop}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2163,7 +2165,7 @@
     \caption{maxLevelVertexTop: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{maxLevelVertexBot}}
+\subsection[maxLevelVertexBot]{\hyperref[sec:var_tab_mesh]{maxLevelVertexBot}}
 \label{subsec:var_sec_mesh_maxLevelVertexBot}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2179,7 +2181,7 @@
     \caption{maxLevelVertexBot: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{refBottomDepth}}
+\subsection[refBottomDepth]{\hyperref[sec:var_tab_mesh]{refBottomDepth}}
 \label{subsec:var_sec_mesh_refBottomDepth}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2195,7 +2197,7 @@
     \caption{refBottomDepth: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{refBottomDepthTopOfCell}}
+\subsection[refBottomDepthTopOfCell]{\hyperref[sec:var_tab_mesh]{refBottomDepthTopOfCell}}
 \label{subsec:var_sec_mesh_refBottomDepthTopOfCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2211,7 +2213,7 @@
     \caption{refBottomDepthTopOfCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{hZLevel}}
+\subsection[hZLevel]{\hyperref[sec:var_tab_mesh]{hZLevel}}
 \label{subsec:var_sec_mesh_hZLevel}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2227,7 +2229,7 @@
     \caption{hZLevel: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{vertCoordMovementWeights}}
+\subsection[vertCoordMovementWeights]{\hyperref[sec:var_tab_mesh]{vertCoordMovementWeights}}
 \label{subsec:var_sec_mesh_vertCoordMovementWeights}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2243,7 +2245,7 @@
     \caption{vertCoordMovementWeights: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{boundaryEdge}}
+\subsection[boundaryEdge]{\hyperref[sec:var_tab_mesh]{boundaryEdge}}
 \label{subsec:var_sec_mesh_boundaryEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2259,7 +2261,7 @@
     \caption{boundaryEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{boundaryVertex}}
+\subsection[boundaryVertex]{\hyperref[sec:var_tab_mesh]{boundaryVertex}}
 \label{subsec:var_sec_mesh_boundaryVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2275,7 +2277,7 @@
     \caption{boundaryVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{boundaryCell}}
+\subsection[boundaryCell]{\hyperref[sec:var_tab_mesh]{boundaryCell}}
 \label{subsec:var_sec_mesh_boundaryCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2291,7 +2293,7 @@
     \caption{boundaryCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{edgeMask}}
+\subsection[edgeMask]{\hyperref[sec:var_tab_mesh]{edgeMask}}
 \label{subsec:var_sec_mesh_edgeMask}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2307,7 +2309,7 @@
     \caption{edgeMask: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{vertexMask}}
+\subsection[vertexMask]{\hyperref[sec:var_tab_mesh]{vertexMask}}
 \label{subsec:var_sec_mesh_vertexMask}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2323,7 +2325,7 @@
     \caption{vertexMask: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{cellMask}}
+\subsection[cellMask]{\hyperref[sec:var_tab_mesh]{cellMask}}
 \label{subsec:var_sec_mesh_cellMask}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2339,7 +2341,7 @@
     \caption{cellMask: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{u\_src}}
+\subsection[u\_src]{\hyperref[sec:var_tab_mesh]{u\_src}}
 \label{subsec:var_sec_mesh_u_src}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2355,7 +2357,7 @@
     \caption{u\_src: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{temperatureRestore}}
+\subsection[temperatureRestore]{\hyperref[sec:var_tab_mesh]{temperatureRestore}}
 \label{subsec:var_sec_mesh_temperatureRestore}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2371,7 +2373,7 @@
     \caption{temperatureRestore: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{salinityRestore}}
+\subsection[salinityRestore]{\hyperref[sec:var_tab_mesh]{salinityRestore}}
 \label{subsec:var_sec_mesh_salinityRestore}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2387,7 +2389,7 @@
     \caption{salinityRestore: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{windStressMonthly}}
+\subsection[windStressMonthly]{\hyperref[sec:var_tab_mesh]{windStressMonthly}}
 \label{subsec:var_sec_mesh_windStressMonthly}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2403,7 +2405,7 @@
     \caption{windStressMonthly: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{temperatureRestoreMonthly}}
+\subsection[temperatureRestoreMonthly]{\hyperref[sec:var_tab_mesh]{temperatureRestoreMonthly}}
 \label{subsec:var_sec_mesh_temperatureRestoreMonthly}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2419,7 +2421,7 @@
     \caption{temperatureRestoreMonthly: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{salinityRestoreMonthly}}
+\subsection[salinityRestoreMonthly]{\hyperref[sec:var_tab_mesh]{salinityRestoreMonthly}}
 \label{subsec:var_sec_mesh_salinityRestoreMonthly}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2435,7 +2437,7 @@
     \caption{salinityRestoreMonthly: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{edgeSignOnCell}}
+\subsection[edgeSignOnCell]{\hyperref[sec:var_tab_mesh]{edgeSignOnCell}}
 \label{subsec:var_sec_mesh_edgeSignOnCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2451,7 +2453,7 @@
     \caption{edgeSignOnCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{edgeSignOnVertex}}
+\subsection[edgeSignOnVertex]{\hyperref[sec:var_tab_mesh]{edgeSignOnVertex}}
 \label{subsec:var_sec_mesh_edgeSignOnVertex}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2467,7 +2469,7 @@
     \caption{edgeSignOnVertex: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{kiteIndexOnCell}}
+\subsection[kiteIndexOnCell]{\hyperref[sec:var_tab_mesh]{kiteIndexOnCell}}
 \label{subsec:var_sec_mesh_kiteIndexOnCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2483,7 +2485,7 @@
     \caption{kiteIndexOnCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_mesh]{seaSurfacePressure}}
+\subsection[seaSurfacePressure]{\hyperref[sec:var_tab_mesh]{seaSurfacePressure}}
 \label{subsec:var_sec_mesh_seaSurfacePressure}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2499,9 +2501,9 @@
     \caption{seaSurfacePressure: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:var_tab_tend]{tend}}
+\section[tend]{\hyperref[sec:var_tab_tend]{tend}}
 \label{sec:var_sec_tend}
-\subsection{\hyperref[sec:var_tab_tend]{tend\_u}}
+\subsection[tend\_u]{\hyperref[sec:var_tab_tend]{tend\_u}}
 \label{subsec:var_sec_tend_tend_u}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2517,7 +2519,7 @@
     \caption{tend\_u: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_tend]{tend\_h}}
+\subsection[tend\_h]{\hyperref[sec:var_tab_tend]{tend\_h}}
 \label{subsec:var_sec_tend_tend_h}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2533,7 +2535,7 @@
     \caption{tend\_h: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_tend]{tend\_ssh}}
+\subsection[tend\_ssh]{\hyperref[sec:var_tab_tend]{tend\_ssh}}
 \label{subsec:var_sec_tend_tend_ssh}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2549,7 +2551,7 @@
     \caption{tend\_ssh: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_tend]{tend\_temperature}}
+\subsection[tend\_temperature]{\hyperref[sec:var_tab_tend]{tend\_temperature}}
 \label{subsec:var_sec_tend_tend_temperature}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2565,7 +2567,7 @@
     \caption{tend\_temperature: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_tend]{tend\_salinity}}
+\subsection[tend\_salinity]{\hyperref[sec:var_tab_tend]{tend\_salinity}}
 \label{subsec:var_sec_tend_tend_salinity}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2581,7 +2583,7 @@
     \caption{tend\_salinity: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_tend]{tend\_tracer1}}
+\subsection[tend\_tracer1]{\hyperref[sec:var_tab_tend]{tend\_tracer1}}
 \label{subsec:var_sec_tend_tend_tracer1}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2597,9 +2599,9 @@
     \caption{tend\_tracer1: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\section{\hyperref[sec:var_tab_diagnostics]{diagnostics}}
+\section[diagnostics]{\hyperref[sec:var_tab_diagnostics]{diagnostics}}
 \label{sec:var_sec_diagnostics}
-\subsection{\hyperref[sec:var_tab_diagnostics]{RiTopOfCell}}
+\subsection[RiTopOfCell]{\hyperref[sec:var_tab_diagnostics]{RiTopOfCell}}
 \label{subsec:var_sec_diagnostics_RiTopOfCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2615,7 +2617,7 @@
     \caption{RiTopOfCell: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_diagnostics]{RiTopOfEdge}}
+\subsection[RiTopOfEdge]{\hyperref[sec:var_tab_diagnostics]{RiTopOfEdge}}
 \label{subsec:var_sec_diagnostics_RiTopOfEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2631,7 +2633,7 @@
     \caption{RiTopOfEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_diagnostics]{vertViscTopOfEdge}}
+\subsection[vertViscTopOfEdge]{\hyperref[sec:var_tab_diagnostics]{vertViscTopOfEdge}}
 \label{subsec:var_sec_diagnostics_vertViscTopOfEdge}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -2647,7 +2649,7 @@
     \caption{vertViscTopOfEdge: {\bf \color{red} MISSING}}
 \end{longtable}
 \end{center}
-\subsection{\hyperref[sec:var_tab_diagnostics]{vertDiffTopOfCell}}
+\subsection[vertDiffTopOfCell]{\hyperref[sec:var_tab_diagnostics]{vertDiffTopOfCell}}
 \label{subsec:var_sec_diagnostics_vertDiffTopOfCell}
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}

Modified: trunk/documents/users_guide/ocn/variable_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocn/variable_table_documentation.tex        2013-03-11 17:37:48 UTC (rev 2581)
+++ trunk/documents/users_guide/ocn/variable_table_documentation.tex        2013-03-11 18:10:43 UTC (rev 2582)
@@ -1,7 +1,9 @@
-\chapter{Variable definions}
-\section{state}
+\chapter[Variable definitions]{\hyperref[chap:variable_sections]{Variable definitions}}
+\label{chap:variable_tables}
+Embedded links point to more detailed variable information in the appendix.
+\section[state]{\hyperref[sec:var_sec_state]{state}}
 \label{sec:var_tab_state}
-\input{ocn/section_descriptions//state.tex}
+\input{ocn/section_descriptions/state.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -159,9 +161,9 @@
 \end{longtable}
 \end{center}
 }
-\section{mesh}
+\section[mesh]{\hyperref[sec:var_sec_mesh]{mesh}}
 \label{sec:var_tab_mesh}
-\input{ocn/section_descriptions//mesh.tex}
+\input{ocn/section_descriptions/mesh.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -335,9 +337,9 @@
 \end{longtable}
 \end{center}
 }
-\section{tend}
+\section[tend]{\hyperref[sec:var_sec_tend]{tend}}
 \label{sec:var_tab_tend}
-\input{ocn/section_descriptions//tend.tex}
+\input{ocn/section_descriptions/tend.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}
@@ -359,9 +361,9 @@
 \end{longtable}
 \end{center}
 }
-\section{diagnostics}
+\section[diagnostics]{\hyperref[sec:var_sec_diagnostics]{diagnostics}}
 \label{sec:var_tab_diagnostics}
-\input{ocn/section_descriptions//diagnostics.tex}
+\input{ocn/section_descriptions/diagnostics.tex}
 {\small
 \begin{center}
 \begin{longtable}{| p{2.0in} | p{4.0in} |}

</font>
</pre>