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