<p><b>mpetersen@lanl.gov</b> 2013-03-21 08:45:01 -0600 (Thu, 21 Mar 2013)</p><p>user's guide: update namelist sections<br>
</p><hr noshade><pre><font color="gray">Modified: trunk/documents/users_guide/ocean/mpas_ocean.bib
===================================================================
--- trunk/documents/users_guide/ocean/mpas_ocean.bib 2013-03-21 14:43:28 UTC (rev 2638)
+++ trunk/documents/users_guide/ocean/mpas_ocean.bib 2013-03-21 14:45:01 UTC (rev 2639)
@@ -124,6 +124,20 @@
number = {accepted}
}
+@ARTICLE{Vallis_Hua88jas,
+ author = {{Vallis}, G.~K. and {Hua}, B.-L.},
+ title = "{Eddy viscosity of the anticipated potential vorticity method}",
+ journal = {Journal of Atmospheric Sciences},
+ keywords = {COMPUTATIONAL FLUID DYNAMICS, EDDY VISCOSITY, VORTICITY EQUATIONS, BAROCLINIC WAVES, BAROTROPIC FLOW, COMPUTATIONAL GRIDS, CONSERVATION LAWS, OCEAN DYNAMICS, PRIMITIVE EQUATIONS},
+ year = 1988,
+ month = feb,
+ volume = 45,
+ pages = {617-627},
+ doi = {10.1175/1520-0469(1988)045<0617:EVOTAP>2.0.CO;2},
+ adsurl = {http://adsabs.harvard.edu/abs/1988JAtS...45..617V},
+ adsnote = {Provided by the SAO/NASA Astrophysics Data System}
+}
+
%%%%%%%% vertical mixing %%%%%%%%%
@article{Pacanowski_Philander81jpo,
Modified: trunk/documents/users_guide/ocean/namelist_section_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocean/namelist_section_documentation.tex 2013-03-21 14:43:28 UTC (rev 2638)
+++ trunk/documents/users_guide/ocean/namelist_section_documentation.tex 2013-03-21 14:45:01 UTC (rev 2639)
@@ -10,7 +10,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -26,7 +26,7 @@
\hline
Type: & character \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & '0000-01-01\_00:00:00' \\
\hline
@@ -42,7 +42,7 @@
\hline
Type: & character \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'none' \\
\hline
@@ -58,7 +58,7 @@
\hline
Type: & character \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & '0\_06:00:00' \\
\hline
@@ -74,7 +74,7 @@
\hline
Type: & character \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & '360day' \\
\hline
@@ -270,13 +270,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $s$ \\
\hline
Default Value: & 3000.0 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & Any real value, but limited by CFL condition. \\
\hline
- \caption{config\_dt: {\bf \color{red} MISSING}}
+ \caption{config\_dt: Length of model time-step.}
\end{longtable}
\end{center}
\subsection[config\_time\_integrator]{\hyperref[sec:nm_tab_time_integration]{config\_time\_integrator}}
@@ -286,13 +286,13 @@
\hline
Type: & character \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'split\_explicit' \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & 'split\_explicit', 'RK4', 'unsplit\_explicit' \\
\hline
- \caption{config\_time\_integrator: {\bf \color{red} MISSING}}
+ \caption{config\_time\_integrator: Time integration method.}
\end{longtable}
\end{center}
\section[grid]{\hyperref[sec:nm_tab_grid]{grid}}
@@ -304,7 +304,7 @@
\hline
Type: & integer \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & 3 \\
\hline
@@ -320,7 +320,7 @@
\hline
Type: & character \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'uniform\_stretching' \\
\hline
@@ -336,7 +336,7 @@
\hline
Type: & character \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'zlevel\_pbcs\_off' \\
\hline
@@ -352,7 +352,7 @@
\hline
Type: & real \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & 0.10 \\
\hline
@@ -386,7 +386,7 @@
\hline
Type: & character \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'graph.info.part.' \\
\hline
@@ -402,7 +402,7 @@
\hline
Type: & integer \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & 0 \\
\hline
@@ -418,7 +418,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -434,7 +434,7 @@
\hline
Type: & character \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'graph.info.part.' \\
\hline
@@ -452,11 +452,11 @@
\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\_hmix\_ScaleWithMesh: {\bf \color{red} MISSING}}
\end{longtable}
@@ -468,11 +468,11 @@
\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. or .false. \\
\hline
\caption{config\_visc\_vorticity\_term: {\bf \color{red} MISSING}}
\end{longtable}
@@ -484,7 +484,7 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 0.0 \\
\hline
@@ -502,11 +502,11 @@
\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\_mom\_del2: {\bf \color{red} MISSING}}
\end{longtable}
@@ -518,11 +518,11 @@
\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\_tracer\_del2: {\bf \color{red} MISSING}}
\end{longtable}
@@ -566,7 +566,7 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 1.0 \\
\hline
@@ -584,11 +584,11 @@
\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. or .false. \\
\hline
\caption{config\_use\_mom\_del4: {\bf \color{red} MISSING}}
\end{longtable}
@@ -600,11 +600,11 @@
\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\_tracer\_del4: {\bf \color{red} MISSING}}
\end{longtable}
@@ -766,13 +766,13 @@
\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\_Rayleigh\_friction: {\bf \color{red} MISSING}}
+ \caption{config\_Rayleigh\_friction: If true, Rayleigh friction is included in the momentum equation.}
\end{longtable}
\end{center}
\subsection[config\_Rayleigh\_damping\_coeff]{\hyperref[sec:nm_tab_Rayleigh_damping]{config\_Rayleigh\_damping\_coeff}}
@@ -782,13 +782,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $s^{-1}$ \\
\hline
Default Value: & 0.0 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & Any real value. \\
\hline
- \caption{config\_Rayleigh\_damping\_coeff: {\bf \color{red} MISSING}}
+ \caption{config\_Rayleigh\_damping\_coeff: Inverse-time coefficient for the Rayleigh damping term, $c\_R$ .}
\end{longtable}
\end{center}
\section[vmix]{\hyperref[sec:nm_tab_vmix]{vmix}}
@@ -1112,13 +1112,13 @@
\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\_monthly\_forcing: {\bf \color{red} MISSING}}
+ \caption{config\_use\_monthly\_forcing: Controls time frequency of forcing. If false, a constant forcing is used, provided by the input fields u\_src, temperatureRestore, and salinityRestore. If true, forcing is interpolated between monthly fields given by windStressMonthly, temperatureRestoreMonthly, and salinityRestoreMonthly.}
\end{longtable}
\end{center}
\subsection[config\_restoreTS]{\hyperref[sec:nm_tab_forcing]{config\_restoreTS}}
@@ -1128,13 +1128,13 @@
\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\_restoreTS: {\bf \color{red} MISSING}}
+ \caption{config\_restoreTS: If true, the restoring term is activated in the tracer equation for temperature and salinity.}
\end{longtable}
\end{center}
\subsection[config\_restoreT\_timescale]{\hyperref[sec:nm_tab_forcing]{config\_restoreT\_timescale}}
@@ -1144,13 +1144,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $days$ \\
\hline
Default Value: & 90.0 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any real value, but typically between 30 and 90 days. \\
\hline
- \caption{config\_restoreT\_timescale: {\bf \color{red} MISSING}}
+ \caption{config\_restoreT\_timescale: Restoring timescale for temperature, $\tau\_r.$ }
\end{longtable}
\end{center}
\subsection[config\_restoreS\_timescale]{\hyperref[sec:nm_tab_forcing]{config\_restoreS\_timescale}}
@@ -1160,13 +1160,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $days$ \\
\hline
Default Value: & 90.0 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any real value, but typically between 30 and 90 days. \\
\hline
- \caption{config\_restoreS\_timescale: {\bf \color{red} MISSING}}
+ \caption{config\_restoreS\_timescale: Restoring timescale for salinity, $\tau\_r$ .}
\end{longtable}
\end{center}
\section[advection]{\hyperref[sec:nm_tab_advection]{advection}}
@@ -1260,13 +1260,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 1.0e-3 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any real, typically 1.0e-3 \\
\hline
- \caption{config\_bottom\_drag\_coeff: {\bf \color{red} MISSING}}
+ \caption{config\_bottom\_drag\_coeff: Dimensionless bottom drag coefficient, $c\_{drag}$ .}
\end{longtable}
\end{center}
\section[pressure\_gradient]{\hyperref[sec:nm_tab_pressure_gradient]{pressure\_gradient}}
@@ -1278,13 +1278,13 @@
\hline
Type: & character \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $unitless$ \\
\hline
Default Value: & 'pressure\_and\_zmid' \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & 'pressure\_and\_zmid' or 'MontgomeryPotential' \\
\hline
- \caption{config\_pressure\_gradient\_type: {\bf \color{red} MISSING}}
+ \caption{config\_pressure\_gradient\_type: Form of pressure gradient terms in momentum equation. For most applications, the gradient of pressure and layer mid-depth are appropriate. For isopycnal coordinates, one may use the gradient of the Montgomery potential.}
\end{longtable}
\end{center}
\subsection[config\_rho0]{\hyperref[sec:nm_tab_pressure_gradient]{config\_rho0}}
@@ -1294,13 +1294,13 @@
\hline
Type: & real \\
\hline
- Units: & {\bf \color{red} MISSING} \\
+ Units: & $kg m^{-3}$ \\
\hline
Default Value: & 1014.65 \\
\hline
- Possible Values: & {\bf \color{red} MISSING} \\
+ Possible Values: & any real, but typically 1000-1035 \\
\hline
- \caption{config\_rho0: {\bf \color{red} MISSING}}
+ \caption{config\_rho0: Density used as a coefficient of the pressure gradient terms, $\rho\_0$ . This is a constant due to the Boussinesq approximation.}
\end{longtable}
\end{center}
\section[eos]{\hyperref[sec:nm_tab_eos]{eos}}
@@ -1606,7 +1606,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1622,7 +1622,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1638,7 +1638,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1654,7 +1654,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1670,7 +1670,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1686,7 +1686,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1702,7 +1702,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1718,7 +1718,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1734,7 +1734,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1750,7 +1750,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1766,7 +1766,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1782,7 +1782,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1798,7 +1798,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1814,7 +1814,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1830,7 +1830,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1846,7 +1846,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1862,7 +1862,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1878,7 +1878,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1894,7 +1894,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
@@ -1910,7 +1910,7 @@
\hline
Type: & logical \\
\hline
- Units: & unitless \\
+ Units: & $unitless$ \\
\hline
Default Value: & .false. \\
\hline
Modified: trunk/documents/users_guide/ocean/namelist_table_documentation.tex
===================================================================
--- trunk/documents/users_guide/ocean/namelist_table_documentation.tex 2013-03-21 14:43:28 UTC (rev 2638)
+++ trunk/documents/users_guide/ocean/namelist_table_documentation.tex 2013-03-21 14:45:01 UTC (rev 2639)
@@ -68,9 +68,9 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_dt]{config\_dt} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_dt]{config\_dt} & Length of model time-step. \\
\hline
- \hyperref[subsec:nm_sec_config_time_integrator]{config\_time\_integrator} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_time_integrator]{config\_time\_integrator} & Time integration method. \\
\hline
\end{longtable}
\end{center}
@@ -231,9 +231,9 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_Rayleigh_friction]{config\_Rayleigh\_friction} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_Rayleigh_friction]{config\_Rayleigh\_friction} & If true, Rayleigh friction is included in the momentum equation. \\
\hline
- \hyperref[subsec:nm_sec_config_Rayleigh_damping_coeff]{config\_Rayleigh\_damping\_coeff} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_Rayleigh_damping_coeff]{config\_Rayleigh\_damping\_coeff} & Inverse-time coefficient for the Rayleigh damping term, $c\_R$ . \\
\hline
\end{longtable}
\end{center}
@@ -334,13 +334,13 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_use_monthly_forcing]{config\_use\_monthly\_forcing} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_use_monthly_forcing]{config\_use\_monthly\_forcing} & Controls time frequency of forcing. If false, a constant forcing is used, provided by the input fields u\_src, temperatureRestore, and salinityRestore. If true, forcing is interpolated between monthly fields given by windStressMonthly, temperatureRestoreMonthly, and salinityRestoreMonthly. \\
\hline
- \hyperref[subsec:nm_sec_config_restoreTS]{config\_restoreTS} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_restoreTS]{config\_restoreTS} & If true, the restoring term is activated in the tracer equation for temperature and salinity. \\
\hline
- \hyperref[subsec:nm_sec_config_restoreT_timescale]{config\_restoreT\_timescale} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_restoreT_timescale]{config\_restoreT\_timescale} & Restoring timescale for temperature, $\tau\_r.$ \\
\hline
- \hyperref[subsec:nm_sec_config_restoreS_timescale]{config\_restoreS\_timescale} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_restoreS_timescale]{config\_restoreS\_timescale} & Restoring timescale for salinity, $\tau\_r$ . \\
\hline
\end{longtable}
\end{center}
@@ -378,7 +378,7 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_bottom_drag_coeff]{config\_bottom\_drag\_coeff} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_bottom_drag_coeff]{config\_bottom\_drag\_coeff} & Dimensionless bottom drag coefficient, $c\_{drag}$ . \\
\hline
\end{longtable}
\end{center}
@@ -393,9 +393,9 @@
{\bf Name} & {\bf Description} \\
\hline
\hline
- \hyperref[subsec:nm_sec_config_pressure_gradient_type]{config\_pressure\_gradient\_type} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_pressure_gradient_type]{config\_pressure\_gradient\_type} & Form of pressure gradient terms in momentum equation. For most applications, the gradient of pressure and layer mid-depth are appropriate. For isopycnal coordinates, one may use the gradient of the Montgomery potential. \\
\hline
- \hyperref[subsec:nm_sec_config_rho0]{config\_rho0} & {\bf \color{red} MISSING} \\
+ \hyperref[subsec:nm_sec_config_rho0]{config\_rho0} & Density used as a coefficient of the pressure gradient terms, $\rho\_0$ . This is a constant due to the Boussinesq approximation. \\
\hline
\end{longtable}
\end{center}
Modified: trunk/documents/users_guide/ocean/section_descriptions/forcing.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/forcing.tex 2013-03-21 14:43:28 UTC (rev 2638)
+++ trunk/documents/users_guide/ocean/section_descriptions/forcing.tex 2013-03-21 14:45:01 UTC (rev 2639)
@@ -2,10 +2,10 @@
\begin{equation}
{\cal F}^u = \frac{1}{\rho_0 h}\tau
\end{equation}
-where $\tau$ is typically the wind stress in $N/m^2$ applied to the top layer. More generally, momentum forcing may be applied to any layer in the ocean. The momentum forcing may be given by the input variables \verb|u_src| or \verb|windStressMonthly|, depending on the configuration settings below. When running within the CESM, the wind stress is provided by the coupler (see Chapter \ref{chap:cesm_ocean_coupling}).
+where $\tau$ is typically the wind stress in $N/m^2$ applied to the top layer. More generally, momentum forcing may be applied to any layer in the ocean. The momentum forcing may be constant or monthly, as described in the configuration settings below. When running within the CESM, the wind stress is provided by the coupler (see Chapter \ref{chap:cesm_ocean_coupling}).
Temperature and salinity restoring are applied to the tracer equation (\ref{ocean:tracer}) through the term
\begin{equation}
{\cal F}^\varphi = -h\frac{\varphi-\varphi_{r}}{\tau_{r}}
\end{equation}
-where $\varphi_{r}$ is the tracer restoring value and $\tau_{r}$ is the restoring timescale. This term is only applied at the top layer, and is supplied by the input variables \verb|temperatureRestore| and \verb|salinityRestore| for constant forcing and \verb|temperatureRestoreMonthly| and \verb|salinityRestoreMonthly| for monthly forcing fields. When running within the CESM, the coupler provides surface heat, salinity, and freshwater fluxes rather than a restoring in this form (see Chapter \ref{chap:cesm_ocean_coupling}).
+where $\varphi_{r}$ is the tracer restoring value and $\tau_{r}$ is the restoring timescale. This term is only applied at the top layer, and may be constant or monthly, as described in the configuration settings below. When running within the CESM, the coupler provides surface heat, salinity, and freshwater fluxes rather than a restoring in this form (see Chapter \ref{chap:cesm_ocean_coupling}).
Modified: trunk/documents/users_guide/ocean/section_descriptions/hmix.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/hmix.tex 2013-03-21 14:43:28 UTC (rev 2638)
+++ trunk/documents/users_guide/ocean/section_descriptions/hmix.tex 2013-03-21 14:45:01 UTC (rev 2639)
@@ -11,3 +11,11 @@
\ref{ocean:tracer}) are ${\bf D}^u_h$ for momentum and
$D^\varphi_h$ for tracers. No horizontal mixing is applied to the
thickness equation.
+
+All horizontal mixing coefficients can be set to scale with the mesh as $\rho_m^{-3/4}$ in equations (\ref{ocean:h_mom_del2}, \ref{ocean:h_tr_del2}, \ref{ocean:h_mom_del4}, \ref{ocean:h_tr_del4}). The mesh density, $\rho_m$, is a variable in the input and restart file. It can vary between zero and one, and is one in the highest resolution region. Scaling with the mesh can be turned off, as described in the options below.
+
+The anticipated potential Vorticity (APV) method is a parameterization of the effects of subgrid or unresolved scales on those explicitly resolved \citep{Vallis_Hua88jas}. It contributes an upstream bias to the vorticity in the del2 and del4 momentum terms as follows,
+\begin{equation}
+\eta_{apv} = \eta - c_{apv} dt \left({\bf u}\cdot </font>
<font color="gray">abla \eta\right),
+\end{equation}
+where the altered vorticity $\eta_{apv}$ is used in equations (\ref{ocean:h_mom_del2}, \ref{ocean:h_mom_del4a}, \ref{ocean:h_mom_del4b}).
Modified: trunk/documents/users_guide/ocean/section_descriptions/hmix_del2.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/hmix_del2.tex 2013-03-21 14:43:28 UTC (rev 2638)
+++ trunk/documents/users_guide/ocean/section_descriptions/hmix_del2.tex 2013-03-21 14:45:01 UTC (rev 2639)
@@ -1,14 +1,15 @@
The ``del2'', or Laplacian, turbulence closures are
\begin{eqnarray}
-\label{h_mom_diff_cont}
-& {\bf D}^u_h=</font>
<font color="black">u_h </font>
<font color="black">abla^2 {\bf u} = </font>
<font color="black">u_h(</font>
<font color="blue">abla \delta + {\bf
+\label{ocean:h_mom_del2}
+& {\bf D}^u_h=\displaystyle\frac{</font>
<font color="black">u_h}{\rho_m^{3/4}} </font>
<font color="blue">abla^2 {\bf u}
+= \displaystyle\frac{</font>
<font color="black">u_h}{\rho_m^{3/4}}(</font>
<font color="black">abla \delta + {\bf
k}\times </font>
<font color="red">abla \eta),\\
-\label{h_tr_diff_cont}
-& D^\varphi_h = </font>
<font color="black">abla\cdot\left(h \kappa_h </font>
<font color="blue">abla\varphi \right)
+\label{ocean:h_tr_del2}
+& D^\varphi_h = </font>
<font color="blue">abla\cdot\left(h
+ \displaystyle\frac{\kappa_h}{\rho_m^{3/4}} </font>
<font color="gray">abla\varphi \right)
\end{eqnarray}
-for momentum and tracers, respectively. Variable definitions appear in Tables \ref{oceanTable:variables} and \ref{oceanTable:variables_Greek}. The momentum diffusion is in divergence-vorticity form because it is a natural discretization of the vector Laplacian operator with a C-grid staggering.
+for momentum and tracers, respectively. Variable definitions appear in Tables \ref{oceanTable:variables} and \ref{oceanTable:variables_Greek}. The momentum diffusion is in divergence-vorticity form because it is a natural discretization of the vector Laplacian operator with a C-grid staggering.
-
The Laplacian operator smooths the momentum and
tracer fields, and smooths more strongly at small scales than at large
scales. This operator is the two dimensional form of the heat equation,
Modified: trunk/documents/users_guide/ocean/section_descriptions/hmix_del4.tex
===================================================================
--- trunk/documents/users_guide/ocean/section_descriptions/hmix_del4.tex 2013-03-21 14:43:28 UTC (rev 2638)
+++ trunk/documents/users_guide/ocean/section_descriptions/hmix_del4.tex 2013-03-21 14:45:01 UTC (rev 2639)
@@ -1,18 +1,19 @@
The ``del4'', or biharmonic, turbulence closures are
\begin{eqnarray}
-\label{h_mom_del4_cont}
-& {\bf D}^u_h=-</font>
<font color="black">u_h </font>
<font color="red">abla^4 {\bf u} \\
-\label{h_tr_del4_cont}
-& D^\varphi_h = -</font>
<font color="black">abla\cdot\left(h \kappa_h </font>
<font color="black">abla \left[</font>
<font color="black">abla\cdot\left(h </font>
<font color="blue">abla\varphi \right) \right] \right)
+\label{ocean:h_mom_del4}
+& {\bf D}^u_h=-\displaystyle\frac{</font>
<font color="black">u_h}{\rho_m^{3/4}} </font>
<font color="blue">abla^4 {\bf u} \\
+\label{ocean:h_tr_del4}
+& D^\varphi_h = -</font>
<font color="black">abla\cdot\left(h \displaystyle\frac{\kappa_h}{\rho_m^{3/4}} </font>
<font color="black">abla \left[</font>
<font color="black">abla\cdot\left(h </font>
<font color="red">abla\varphi \right) \right] \right)
\end{eqnarray}
-for momentum and tracers, respectively. These are both computed by applying the Laplacian operator twice. For momentum, this can be written in terms of divergence and vorticity as
+for momentum and tracers These are both computed by applying the Laplacian operator twice. For momentum, this can be written in terms of divergence and vorticity as
\begin{eqnarray}
&\delta=</font>
<font color="black">abla\cdot{\bf u}\\
&\eta={\bf k} \cdot \left( </font>
<font color="blue">abla \times {\bf u} \right)+f\\
+\label{ocean:h_mom_del4a}
&</font>
<font color="black">abla^2{\bf u}=(</font>
<font color="black">abla \delta + {\bf k}\times </font>
<font color="black">abla \eta) \\
&\delta_2=</font>
<font color="black">abla\cdot(</font>
<font color="black">abla^2{\bf u})\\
&\eta_2={\bf k} \cdot \left( </font>
<font color="black">abla \times (</font>
<font color="red">abla^2{\bf u}) \right)+f\\
-& {\bf D}^u_h= </font>
<font color="black">u_h (</font>
<font color="black">abla \delta_2 + {\bf k}\times </font>
<font color="blue">abla \eta_2)
+\label{ocean:h_mom_del4b}
+& {\bf D}^u_h= \displaystyle\frac{</font>
<font color="black">u_h}{\rho_m^{3/4}} (</font>
<font color="black">abla \delta_2 + {\bf k}\times </font>
<font color="red">abla \eta_2).
\end{eqnarray}
-
-The biharmonic operator is similar to the Laplacian operator, but smooths more strongly at high wavenumbers.
+The biharmonic operator is similar to the Laplacian operator, but smooths more strongly at high wavenumbers.
</font>
</pre>