<p><b>mpetersen@lanl.gov</b> 2013-03-21 08:43:28 -0600 (Thu, 21 Mar 2013)</p><p>branch commit: add namelist and variables information.<br>
</p><hr noshade><pre><font color="gray">Modified: branches/xml_registry/src/core_ocean/Registry.xml
===================================================================
--- branches/xml_registry/src/core_ocean/Registry.xml        2013-03-20 21:31:24 UTC (rev 2637)
+++ branches/xml_registry/src/core_ocean/Registry.xml        2013-03-21 14:43:28 UTC (rev 2638)
@@ -113,13 +113,13 @@
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;time_integration&quot;&gt;
-                &lt;nml_option name=&quot;config_dt&quot; type=&quot;real&quot; default_value=&quot;3000.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_dt&quot; type=&quot;real&quot; default_value=&quot;3000.0&quot; units=&quot;s&quot;
+                            description=&quot;Length of model time-step.&quot;
+                            possible_values=&quot;Any positive real value, but limited by CFL condition.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_time_integrator&quot; type=&quot;character&quot; default_value=&quot;'split_explicit'&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_time_integrator&quot; type=&quot;character&quot; default_value=&quot;'split_explicit'&quot; units=&quot;unitless&quot;
+                            description=&quot;Time integration method.&quot;
+                            possible_values=&quot;'split_explicit', 'RK4', 'unsplit_explicit'&quot;
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;grid&quot;&gt;
@@ -163,60 +163,60 @@
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;hmix&quot;&gt;
-                &lt;nml_option name=&quot;config_hmix_ScaleWithMesh&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_hmix_ScaleWithMesh&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;unitless&quot;
+                            description=&quot;If false, del2 and del4 coefficients are constant throughout the mesh (equivalent to setting $\rho_m=1$ throughout the mesh).  If true, these coefficients scale as mesh density to the -3/4 power.&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_visc_vorticity_term&quot; type=&quot;logical&quot; default_value=&quot;.true.&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_visc_vorticity_term&quot; type=&quot;logical&quot; default_value=&quot;.true.&quot; units=&quot;unitless&quot;
+                            description=&quot;{\color{red} TO BE DELETED}&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_apvm_scale_factor&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_apvm_scale_factor&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;unitless&quot;
+                            description=&quot;Anticipated potential vorticity (APV) method scale factor, $c_{apv}$.  When zero, APV is off.&quot;
+                            possible_values=&quot;Any non-negative number, typically between zero and one.&quot;
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;hmix_del2&quot;&gt;
-                &lt;nml_option name=&quot;config_use_mom_del2&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_use_mom_del2&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;unitless&quot;
+                            description=&quot;If true, the Laplacian horizontal mixing is used on the momentum equation.&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_use_tracer_del2&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_use_tracer_del2&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;unitless&quot;
+                            description=&quot;If true, the Laplacian horizontal mixing is used on the tracer equation.&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_mom_del2&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_mom_del2&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;m^2 s^{-1}&quot;
+                            description=&quot;Horizonal viscosity, $</font>
<font color="gray">u_h$.&quot;
+                            possible_values=&quot;any positive real&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_tracer_del2&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_tracer_del2&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;m^2 s^{-1}&quot;
+                            description=&quot;Horizonal diffusion, $\kappa_h$.&quot;
+                            possible_values=&quot;any positive real&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_vorticity_del2_scale&quot; type=&quot;real&quot; default_value=&quot;1.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
+                &lt;nml_option name=&quot;config_vorticity_del2_scale&quot; type=&quot;real&quot; default_value=&quot;1.0&quot; units=&quot;unitless&quot;
+                            description=&quot;{\color{red} TO BE DELETED}&quot;
                             possible_values=&quot;&quot;
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;hmix_del4&quot;&gt;
-                &lt;nml_option name=&quot;config_use_mom_del4&quot; type=&quot;logical&quot; default_value=&quot;.true.&quot; units=&quot;&quot;
+                &lt;nml_option name=&quot;config_use_mom_del4&quot; type=&quot;logical&quot; default_value=&quot;.true.&quot; units=&quot;unitless&quot;
                             description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_use_tracer_del4&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;&quot;
+                &lt;nml_option name=&quot;config_use_tracer_del4&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;unitless&quot;
                             description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_mom_del4&quot; type=&quot;real&quot; default_value=&quot;5.0e13&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_mom_del4&quot; type=&quot;real&quot; default_value=&quot;5.0e13&quot; units=&quot;m^4 s^{-1}&quot;
+                            description=&quot;Coefficient for horizontal biharmonic operator on momentum.&quot;
+                            possible_values=&quot;any positive real&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_tracer_del4&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_tracer_del4&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;&quot;m^4 s^{-1}&quot;
+                            description=&quot;Coefficient for horizontal biharmonic operator on momentum.&quot;
+                            possible_values=&quot;any positive real&quot;
                 /&gt;
                 &lt;nml_option name=&quot;config_vorticity_del4_scale&quot; type=&quot;real&quot; default_value=&quot;1.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
+                            description=&quot;{\color{red} TO BE DELETED}&quot;
                             possible_values=&quot;&quot;
                 /&gt;
         &lt;/nml_record&gt;
@@ -249,13 +249,13 @@
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;Rayleigh_damping&quot;&gt;
-                &lt;nml_option name=&quot;config_Rayleigh_friction&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_Rayleigh_friction&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;unitless&quot;
+                            description=&quot;If true, Rayleigh friction is included in the momentum equation.&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_Rayleigh_damping_coeff&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_Rayleigh_damping_coeff&quot; type=&quot;real&quot; default_value=&quot;0.0&quot; units=&quot;s^{-1}&quot;
+                            description=&quot;Inverse-time coefficient for the Rayleigh damping term, $c_R$.&quot;
+                            possible_values=&quot;Any positive real value.&quot;
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;vmix&quot;&gt;
@@ -343,21 +343,21 @@
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;forcing&quot;&gt;
-                &lt;nml_option name=&quot;config_use_monthly_forcing&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_use_monthly_forcing&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;unitless&quot;
+                            description=&quot;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.&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_restoreTS&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_restoreTS&quot; type=&quot;logical&quot; default_value=&quot;.false.&quot; units=&quot;unitless&quot;
+                            description=&quot;If true, the restoring term is activated in the tracer equation for temperature and salinity.&quot;
+                            possible_values=&quot;.true. or .false.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_restoreT_timescale&quot; type=&quot;real&quot; default_value=&quot;90.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_restoreT_timescale&quot; type=&quot;real&quot; default_value=&quot;90.0&quot; units=&quot;days&quot;
+                            description=&quot;Restoring timescale for temperature, $\tau_r.$&quot;
+                            possible_values=&quot;any positive real value, but typically between 30 and 90 days.&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_restoreS_timescale&quot; type=&quot;real&quot; default_value=&quot;90.0&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_restoreS_timescale&quot; type=&quot;real&quot; default_value=&quot;90.0&quot; units=&quot;days&quot;
+                            description=&quot;Restoring timescale for salinity, $\tau_r$.&quot;
+                            possible_values=&quot;any positive real value, but typically between 30 and 90 days.&quot;
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;advection&quot;&gt;
@@ -383,19 +383,19 @@
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;bottom_drag&quot;&gt;
-                &lt;nml_option name=&quot;config_bottom_drag_coeff&quot; type=&quot;real&quot; default_value=&quot;1.0e-3&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_bottom_drag_coeff&quot; type=&quot;real&quot; default_value=&quot;1.0e-3&quot; units=&quot;unitless&quot;
+                            description=&quot;Dimensionless bottom drag coefficient, $c_{drag}$.&quot;
+                            possible_values=&quot;any positive real, typically 1.0e-3&quot;
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;pressure_gradient&quot;&gt;
-                &lt;nml_option name=&quot;config_pressure_gradient_type&quot; type=&quot;character&quot; default_value=&quot;'pressure_and_zmid'&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_pressure_gradient_type&quot; type=&quot;character&quot; default_value=&quot;'pressure_and_zmid'&quot; units=&quot;unitless&quot;
+                            description=&quot;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.&quot;
+                            possible_values=&quot;'pressure_and_zmid' or 'MontgomeryPotential'&quot;
                 /&gt;
-                &lt;nml_option name=&quot;config_rho0&quot; type=&quot;real&quot; default_value=&quot;1014.65&quot; units=&quot;&quot;
-                            description=&quot;&quot;
-                            possible_values=&quot;&quot;
+                &lt;nml_option name=&quot;config_rho0&quot; type=&quot;real&quot; default_value=&quot;1014.65&quot; units=&quot;kg m^{-3}&quot;
+                            description=&quot;Density used as a coefficient of the pressure gradient terms, $\rho_0$.  This is a constant due to the Boussinesq approximation.&quot;
+                            possible_values=&quot;any positive real, but typically 1000-1035&quot;
                 /&gt;
         &lt;/nml_record&gt;
         &lt;nml_record name=&quot;eos&quot;&gt;
@@ -560,54 +560,54 @@
         &lt;/nml_record&gt;
         &lt;var_struct name=&quot;state&quot; time_levs=&quot;2&quot;&gt;
                 &lt;var_array name=&quot;tracers&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nCells Time&quot;&gt;
-                        &lt;var name=&quot;temperature&quot; array_group=&quot;dynamics&quot; streams=&quot;iro&quot; units=&quot;&quot;
-                             description=&quot;&quot;
+                        &lt;var name=&quot;temperature&quot; array_group=&quot;dynamics&quot; streams=&quot;iro&quot; units=&quot;degrees Celsius&quot;
+                             description=&quot;potential temperature&quot;
                         /&gt;
-                        &lt;var name=&quot;salinity&quot; array_group=&quot;dynamics&quot; streams=&quot;iro&quot; units=&quot;&quot;
-                             description=&quot;&quot;
+                        &lt;var name=&quot;salinity&quot; array_group=&quot;dynamics&quot; streams=&quot;iro&quot; units=&quot;grams salt per kilogram seawater&quot;
+                             description=&quot;salinity&quot;
                         /&gt;
-                        &lt;var name=&quot;tracer1&quot; array_group=&quot;testing&quot; streams=&quot;iro&quot; units=&quot;&quot;
-                             description=&quot;&quot;
+                        &lt;var name=&quot;tracer1&quot; array_group=&quot;testing&quot; streams=&quot;iro&quot; units=&quot;unitless&quot;
+                             description=&quot;A tracer with value 1.0 to test conservation.  {\color{red} REMOVE THIS VARIABLE}&quot;
                         /&gt;
                 &lt;/var_array&gt;
-                &lt;var name=&quot;xtime&quot; type=&quot;text&quot; dimensions=&quot;Time&quot; streams=&quot;ro&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;xtime&quot; type=&quot;text&quot; dimensions=&quot;Time&quot; streams=&quot;ro&quot; units=&quot;unitless&quot;
+                     description=&quot;model time, with format 'YYYY-MM-DD_HH:MM:SS'&quot;
                 /&gt;
-                &lt;var name=&quot;u&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nEdges Time&quot; streams=&quot;ir&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;u&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nEdges Time&quot; streams=&quot;ir&quot; units=&quot;m s^{-1}&quot;
+                     description=&quot;horizonal velocity, normal component to an edge&quot;
                 /&gt;
-                &lt;var name=&quot;h&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nCells Time&quot; streams=&quot;iro&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;h&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nCells Time&quot; streams=&quot;iro&quot; units=&quot;m&quot;
+                     description=&quot;layer thickness&quot;
                 /&gt;
-                &lt;var name=&quot;rho&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nCells Time&quot; streams=&quot;iro&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;rho&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nCells Time&quot; streams=&quot;iro&quot; units=&quot;kg m^{-3}&quot;
+                     description=&quot;density&quot;
                 /&gt;
-                &lt;var name=&quot;uBtr&quot; type=&quot;real&quot; dimensions=&quot;nEdges Time&quot; streams=&quot;r&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;uBtr&quot; type=&quot;real&quot; dimensions=&quot;nEdges Time&quot; streams=&quot;r&quot; units=&quot;m s^{-1}&quot;
+                     description=&quot;barotropic velocity, used in split-explicit time-stepping&quot;
                 /&gt;
-                &lt;var name=&quot;ssh&quot; type=&quot;real&quot; dimensions=&quot;nCells Time&quot; streams=&quot;o&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;ssh&quot; type=&quot;real&quot; dimensions=&quot;nCells Time&quot; streams=&quot;o&quot; units=&quot;m&quot;
+                     description=&quot;sea surface height&quot;
                 /&gt;
-                &lt;var name=&quot;uBtrSubcycle&quot; type=&quot;real&quot; dimensions=&quot;nEdges Time&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;uBtrSubcycle&quot; type=&quot;real&quot; dimensions=&quot;nEdges Time&quot; units=&quot;m s^{-1}&quot;
+                     description=&quot;barotropic velocity, used in subcycling in stage 2 of split-explicit time-stepping&quot;
                 /&gt;
-                &lt;var name=&quot;sshSubcycle&quot; type=&quot;real&quot; dimensions=&quot;nCells Time&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;sshSubcycle&quot; type=&quot;real&quot; dimensions=&quot;nCells Time&quot; units=&quot;m&quot;
+                     description=&quot;sea surface height, used in subcycling in stage 2 of split-explicit time-stepping&quot;
                 /&gt;
-                &lt;var name=&quot;FBtr&quot; type=&quot;real&quot; dimensions=&quot;nEdges Time&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;FBtr&quot; type=&quot;real&quot; dimensions=&quot;nEdges Time&quot; units=&quot;m^2 s^{-1}&quot;
+                     description=&quot;Barotropic thickness flux at each edge, used to advance sea surface height in each subcycle of stage 2 of the split-explicit algorithm.&quot;
                 /&gt;
-                &lt;var name=&quot;GBtrForcing&quot; type=&quot;real&quot; dimensions=&quot;nEdges Time&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;GBtrForcing&quot; type=&quot;real&quot; dimensions=&quot;nEdges Time&quot; units=&quot;m s^{-2}&quot;
+                     description=&quot;Barotropic tendency computed from the baroclinic equations in stage 1 of the split-explicit algorithm.&quot;
                 /&gt;
-                &lt;var name=&quot;uBcl&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nEdges Time&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;uBcl&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nEdges Time&quot; units=&quot;m s^{-1}&quot;
+                     description=&quot;baroclinic velocity, used in split-explicit time-stepping&quot;
                 /&gt;
-                &lt;var name=&quot;zMid&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nCells Time&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;zMid&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nCells Time&quot; units=&quot;m&quot;
+                     description=&quot;z-coordinate of the mid-depth of the layer&quot;
                 /&gt;
-                &lt;var name=&quot;v&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nEdges Time&quot; units=&quot;&quot;
-                     description=&quot;&quot;
+                &lt;var name=&quot;v&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nEdges Time&quot; units=&quot;m s^{-1}&quot;
+                     description=&quot;horizontal velocity, tangential to an edge&quot;
                 /&gt;
                 &lt;var name=&quot;uTransport&quot; type=&quot;real&quot; dimensions=&quot;nVertLevels nEdges Time&quot; units=&quot;m s^{-1}&quot;
                      description=&quot;horizontal velocity used to transport mass and tracers&quot;

</font>
</pre>