<p><b>dwj07@fsu.edu</b> 2013-04-02 09:54:37 -0600 (Tue, 02 Apr 2013)</p><p> <br>
-- DOCUMENT COMMIT --<br>
<br>
Updating users guide files.<br>
Moving label below caption in figure definitions for referencing.<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/documents/users_guide/ocean/namelist_section_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocean/namelist_section_documentation.tex 2013-04-02 15:51:32 UTC (rev 2696)
+++ trunk/documents/users_guide/ocean/namelist_section_documentation.tex 2013-04-02 15:54:37 UTC (rev 2697)
@@ -666,13 +666,13 @@
\hline
Type: & logical \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & .true. or .false. \\
\hline
- \caption{config\_use\_Leith\_del2: {\bf \color{red} MISSING}}
+ \caption{config\_use\_Leith\_del2: If true, the Leith enstrophy-cascade closure is turned on}
\end{longtable}
\end{center}
\subsection[config\_Leith\_parameter]{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_parameter}}
@@ -682,13 +682,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $non-dimensional$ \\
\hline
Default Value: & 1.0 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any positive real \\
\hline
- \caption{config\_Leith\_parameter: {\bf \color{red} MISSING}}
+ \caption{config\_Leith\_parameter: Non-dimensional Leith closure parameter}
\end{longtable}
\end{center}
\subsection[config\_Leith\_dx]{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_dx}}
@@ -698,13 +698,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $m$ \\
\hline
Default Value: & 15000.0 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any positive real \\
\hline
- \caption{config\_Leith\_dx: {\bf \color{red} MISSING}}
+ \caption{config\_Leith\_dx: Characteristic length scale, usually the smallest dx in the mesh}
\end{longtable}
\end{center}
\subsection[config\_Leith\_visc2\_max]{\hyperref[sec:nm_tab_hmix_Leith]{config\_Leith\_visc2\_max}}
@@ -714,13 +714,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $m^2$ $s^{-1}$ \\
\hline
Default Value: & 2.5e3 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any positive real \\
\hline
- \caption{config\_Leith\_visc2\_max: {\bf \color{red} MISSING}}
+ \caption{config\_Leith\_visc2\_max: Upper bound on the allowable value of Leith-computed viscosity}
\end{longtable}
\end{center}
\section[standard\_GM]{\hyperref[sec:nm_tab_standard_GM]{standard\_GM}}
@@ -1178,13 +1178,13 @@
\hline
Type: & character \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'stencil' \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & 'spline' and 'stencil' \\
\hline
- \caption{config\_vert\_tracer\_adv: {\bf \color{red} MISSING}}
+ \caption{config\_vert\_tracer\_adv: Method for interpolating tracer values from layer centers to layer edges}
\end{longtable}
\end{center}
\subsection[config\_vert\_tracer\_adv\_order]{\hyperref[sec:nm_tab_advection]{config\_vert\_tracer\_adv\_order}}
@@ -1194,13 +1194,13 @@
\hline
Type: & integer \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 3 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & 2, 3 and 4 \\
\hline
- \caption{config\_vert\_tracer\_adv\_order: {\bf \color{red} MISSING}}
+ \caption{config\_vert\_tracer\_adv\_order: Order of polynomial used for tracer reconstruction at layer edges}
\end{longtable}
\end{center}
\subsection[config\_horiz\_tracer\_adv\_order]{\hyperref[sec:nm_tab_advection]{config\_horiz\_tracer\_adv\_order}}
@@ -1210,13 +1210,13 @@
\hline
Type: & integer \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 3 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & 2, 3 and 4 \\
\hline
- \caption{config\_horiz\_tracer\_adv\_order: {\bf \color{red} MISSING}}
+ \caption{config\_horiz\_tracer\_adv\_order: Order of polynomial used for tracer reconstruction at cell edges}
\end{longtable}
\end{center}
\subsection[config\_coef\_3rd\_order]{\hyperref[sec:nm_tab_advection]{config\_coef\_3rd\_order}}
@@ -1226,13 +1226,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $non-dimensional$ \\
\hline
Default Value: & 0.25 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any real between 0 and 1 \\
\hline
- \caption{config\_coef\_3rd\_order: {\bf \color{red} MISSING}}
+ \caption{config\_coef\_3rd\_order: Reconstruction of 3rd-order reconstruction to blend with 4th-order reconstuction}
\end{longtable}
\end{center}
\subsection[config\_monotonic]{\hyperref[sec:nm_tab_advection]{config\_monotonic}}
@@ -1242,13 +1242,13 @@
\hline
Type: & logical \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & .true. \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & .true. and .false. \\
\hline
- \caption{config\_monotonic: {\bf \color{red} MISSING}}
+ \caption{config\_monotonic: If .true. then fluxes are limited to produce a monotonic advection scheme}
\end{longtable}
\end{center}
\section[bottom\_drag]{\hyperref[sec:nm_tab_bottom_drag]{bottom\_drag}}
@@ -1312,13 +1312,13 @@
\hline
Type: & character \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'jm' \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & Jackett McDougall EOS = 'jm' and Linear EOS = 'linear' \\
\hline
- \caption{config\_eos\_type: {\bf \color{red} MISSING}}
+ \caption{config\_eos\_type: Character string to choose EOS formulation}
\end{longtable}
\end{center}
\section[eos\_linear]{\hyperref[sec:nm_tab_eos_linear]{eos\_linear}}
@@ -1330,13 +1330,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $kg$ $m^{-3}$ $C^{-1}$ \\
\hline
Default Value: & 2.55e-1 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any positive real \\
\hline
- \caption{config\_eos\_linear\_alpha: {\bf \color{red} MISSING}}
+ \caption{config\_eos\_linear\_alpha: Linear thermal expansion coefficient}
\end{longtable}
\end{center}
\subsection[config\_eos\_linear\_beta]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_beta}}
@@ -1346,13 +1346,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $kg$ $m^{-3}$ $PSU^{-1}$ \\
\hline
Default Value: & 7.64e-1 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any positive real \\
\hline
- \caption{config\_eos\_linear\_beta: {\bf \color{red} MISSING}}
+ \caption{config\_eos\_linear\_beta: Linear haline contraction coefficient}
\end{longtable}
\end{center}
\subsection[config\_eos\_linear\_Tref]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_Tref}}
@@ -1362,13 +1362,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $C$ \\
\hline
Default Value: & 19.0 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any real \\
\hline
- \caption{config\_eos\_linear\_Tref: {\bf \color{red} MISSING}}
+ \caption{config\_eos\_linear\_Tref: Reference temperature}
\end{longtable}
\end{center}
\subsection[config\_eos\_linear\_Sref]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_Sref}}
@@ -1378,13 +1378,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $PSU$ \\
\hline
Default Value: & 35.0 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any real \\
\hline
- \caption{config\_eos\_linear\_Sref: {\bf \color{red} MISSING}}
+ \caption{config\_eos\_linear\_Sref: Reference salinity}
\end{longtable}
\end{center}
\subsection[config\_eos\_linear\_rhoref]{\hyperref[sec:nm_tab_eos_linear]{config\_eos\_linear\_rhoref}}
@@ -1394,13 +1394,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $kg$ $m^{-3}$ \\
\hline
Default Value: & 1025.022 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any positive real \\
\hline
- \caption{config\_eos\_linear\_rhoref: {\bf \color{red} MISSING}}
+ \caption{config\_eos\_linear\_rhoref: Reference density, i.e. density when T=Tref and S=Sref}
\end{longtable}
\end{center}
\section[split\_explicit\_ts]{\hyperref[sec:nm_tab_split_explicit_ts]{split\_explicit\_ts}}
Modified: trunk/documents/users_guide/ocean/namelist_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocean/namelist_table_documentation.tex 2013-04-02 15:51:32 UTC (rev 2696)
+++ trunk/documents/users_guide/ocean/namelist_table_documentation.tex 2013-04-02 15:54:37 UTC (rev 2697)
@@ -194,13 +194,13 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_use_Leith_del2]{config\_use\_Leith\_del2} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_use_Leith_del2]{config\_use\_Leith\_del2} & If true, the Leith enstrophy-cascade closure is turned on \\
\hline
- \hyperref[subsec:nm_sec_config_Leith_parameter]{config\_Leith\_parameter} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_Leith_parameter]{config\_Leith\_parameter} & Non-dimensional Leith closure parameter \\
\hline
- \hyperref[subsec:nm_sec_config_Leith_dx]{config\_Leith\_dx} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_Leith_dx]{config\_Leith\_dx} & Characteristic length scale, usually the smallest dx in the mesh \\
\hline
- \hyperref[subsec:nm_sec_config_Leith_visc2_max]{config\_Leith\_visc2\_max} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_Leith_visc2_max]{config\_Leith\_visc2\_max} & Upper bound on the allowable value of Leith-computed viscosity \\
\hline
\end{longtable}
\end{center}
@@ -355,15 +355,15 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_vert_tracer_adv]{config\_vert\_tracer\_adv} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_vert_tracer_adv]{config\_vert\_tracer\_adv} & Method for interpolating tracer values from layer centers to layer edges \\
\hline
- \hyperref[subsec:nm_sec_config_vert_tracer_adv_order]{config\_vert\_tracer\_adv\_order} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_vert_tracer_adv_order]{config\_vert\_tracer\_adv\_order} & Order of polynomial used for tracer reconstruction at layer edges \\
\hline
- \hyperref[subsec:nm_sec_config_horiz_tracer_adv_order]{config\_horiz\_tracer\_adv\_order} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_horiz_tracer_adv_order]{config\_horiz\_tracer\_adv\_order} & Order of polynomial used for tracer reconstruction at cell edges \\
\hline
- \hyperref[subsec:nm_sec_config_coef_3rd_order]{config\_coef\_3rd\_order} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_coef_3rd_order]{config\_coef\_3rd\_order} & Reconstruction of 3rd-order reconstruction to blend with 4th-order reconstuction \\
\hline
- \hyperref[subsec:nm_sec_config_monotonic]{config\_monotonic} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_monotonic]{config\_monotonic} & If .true. then fluxes are limited to produce a monotonic advection scheme \\
\hline
\end{longtable}
\end{center}
@@ -410,7 +410,7 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_eos_type]{config\_eos\_type} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_eos_type]{config\_eos\_type} & Character string to choose EOS formulation \\
\hline
\end{longtable}
\end{center}
@@ -425,15 +425,15 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_eos_linear_alpha]{config\_eos\_linear\_alpha} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_eos_linear_alpha]{config\_eos\_linear\_alpha} & Linear thermal expansion coefficient \\
\hline
- \hyperref[subsec:nm_sec_config_eos_linear_beta]{config\_eos\_linear\_beta} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_eos_linear_beta]{config\_eos\_linear\_beta} & Linear haline contraction coefficient \\
\hline
- \hyperref[subsec:nm_sec_config_eos_linear_Tref]{config\_eos\_linear\_Tref} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_eos_linear_Tref]{config\_eos\_linear\_Tref} & Reference temperature \\
\hline
- \hyperref[subsec:nm_sec_config_eos_linear_Sref]{config\_eos\_linear\_Sref} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_eos_linear_Sref]{config\_eos\_linear\_Sref} & Reference salinity \\
\hline
- \hyperref[subsec:nm_sec_config_eos_linear_rhoref]{config\_eos\_linear\_rhoref} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_eos_linear_rhoref]{config\_eos\_linear\_rhoref} & Reference density, i.e. density when T=Tref and S=Sref \\
\hline
\end{longtable}
\end{center}
Modified: trunk/documents/users_guide/ocean/test_case_descriptions.tex
===================================================================
--- trunk/documents/users_guide/ocean/test_case_descriptions.tex 2013-04-02 15:51:32 UTC (rev 2696)
+++ trunk/documents/users_guide/ocean/test_case_descriptions.tex 2013-04-02 15:54:37 UTC (rev 2697)
@@ -1,6 +1,8 @@
\chapter{Test Cases}
\label{chap:ocean_test_cases}
+All test cases can be downloaded from \href{http://mpas.sourceforge.net/ocean/release_\version/release_\version.html}{the release website}.
+
\FloatBarrier
\input{ocean/test_cases/baroclinic_channel.tex}
\FloatBarrier
Modified: trunk/documents/users_guide/ocean/test_cases/baroclinic_channel.tex
===================================================================
--- trunk/documents/users_guide/ocean/test_cases/baroclinic_channel.tex 2013-04-02 15:51:32 UTC (rev 2696)
+++ trunk/documents/users_guide/ocean/test_cases/baroclinic_channel.tex 2013-04-02 15:54:37 UTC (rev 2697)
@@ -51,9 +51,9 @@
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.}
+ \label{fig:baroclinicChannelTemperature}
\subfigure[10km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocean/figures/baroclinic_channel_10000m_20levs_10days.pdf}}
\subfigure[4km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocean/figures/baroclinic_channel_4000m_20levs_10days.pdf}}
\subfigure[1km horizontal resolution temperature field after 10 simulation days.]{\includegraphics[scale=0.3]{ocean/figures/baroclinic_channel_1000m_20levs_10days.pdf}}
Modified: trunk/documents/users_guide/ocean/test_cases/overflow.tex
===================================================================
--- trunk/documents/users_guide/ocean/test_cases/overflow.tex 2013-04-02 15:51:32 UTC (rev 2696)
+++ trunk/documents/users_guide/ocean/test_cases/overflow.tex 2013-04-02 15:54:37 UTC (rev 2697)
@@ -35,10 +35,10 @@
\begin{figure}[H!]
+ \centering
+ \includegraphics[scale=1.0]{ocean/figures/overflow_1km_0hr.pdf}\\
+ \includegraphics[scale=1.0]{ocean/figures/overflow_1km_3hr.pdf}\\
+ \includegraphics[scale=1.0]{ocean/figures/overflow_1km_9hr.pdf}
+ \caption{Overflow test case results, showing vertical cross-sections of temperature (left) and kinetic energy (right). Each horizontal axis is distance in km, and each vertical axis is layer index. Rows show initial condition (top), 6 hours (middle) and 9 hours (bottom). {\color{red}TBA: these images were made with matlab. Next version will use python.}}
\label{fig:overflow}
- \centering
-\includegraphics[scale=1.0]{ocean/figures/overflow_1km_0hr.pdf}\\
-\includegraphics[scale=1.0]{ocean/figures/overflow_1km_3hr.pdf}\\
-\includegraphics[scale=1.0]{ocean/figures/overflow_1km_9hr.pdf}
-\caption{Overflow test case results, showing vertical cross-sections of temperature (left) and kinetic energy (right). Each horizontal axis is distance in km, and each vertical axis is layer index. Rows show initial condition (top), 6 hours (middle) and 9 hours (bottom). {\color{red}TBA: these images were made with matlab. Next version will use python.}}
\end{figure}
Modified: trunk/documents/users_guide/ocean/variable_section_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocean/variable_section_documentation.tex 2013-04-02 15:51:32 UTC (rev 2696)
+++ trunk/documents/users_guide/ocean/variable_section_documentation.tex 2013-04-02 15:54:37 UTC (rev 2697)
@@ -108,7 +108,7 @@
\hline
Persistence: & persistent \\
\hline
- Default Streams: & Input Restart Output \\
+ Default Streams: & Input Restart \\
\hline
Location in code: & domain \% blocklist \% state \% time\_levs(:) \% state \% u \\
\hline
</font>
</pre>