Update comments in documentation

doc/source/icepack_index.rst

@@ -474,11 +474,6 @@ either Celsius or Kelvin units).
    "tr_FY", ":math:`\bullet` if true, use first-year area tracer", ""
    "tr_iage", ":math:`\bullet` if true, use ice age tracer", ""
    "tr_lvl", ":math:`\bullet` if true, use level ice area and volume tracers", ""
-
-.. 
-   comment We are deprecating this feature.
-   "tr_pond_cesm", ":math:`\bullet` if true, use CESM melt pond scheme", ""
-
    "tr_pond_cesm", "DEPRECATED", ""
    "tr_pond_lvl", ":math:`\bullet` if true, use level-ice melt pond scheme", ""
    "tr_pond_topo", ":math:`\bullet` if true, use topo melt pond scheme", ""
@@ -529,3 +524,7 @@ either Celsius or Kelvin units).
    "zref", "reference height for stability", "10. m"
    "zTrf", "reference height for :math:`T_{ref}`, :math:`Q_{ref}`, :math:`U_{ref}`", "2. m"
    "zvir", "gas constant (water vapor)/gas constant (air) - 1", "0.606"
+
+.. 
+   comment tr_pond_cesm is being deprecated
+   "tr_pond_cesm", ":math:`\bullet` if true, use CESM melt pond scheme", ""

doc/source/science_guide/sg_thermo.rst

@@ -105,6 +105,8 @@ the :ref:`tracers` section.
 CESM formulation (``tr_pond_cesm`` = true)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
+*Note that the CESM pond option is being deprecated.*
+
 Melt pond area and thickness tracers are carried on each ice thickness
 category as in the :ref:`tracers` section. Defined simply as the product
 of pond area, :math:`a_p`, and depth, :math:`h_p`, the melt pond volume,
@@ -128,7 +130,7 @@ and thickness are computed according to the assumed pond shape, and the
 pond area is then reduced in the presence of snow for the radiation
 calculation. Ponds are allowed only on ice at least 1 cm thick. This
 formulation differs slightly from that documented in
-:cite:`Holland12`. *Note that the CESM pond option has been deprecated.*
+:cite:`Holland12`. 
 
 Topographic formulation (``tr_pond_topo`` = true)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

doc/source/science_guide/sg_tracers.rst

@@ -45,6 +45,8 @@ is discussed in :cite:`Armour11`.
 Tracers that depend on other tracers 
 ------------------------------------
 
+*Note that the cesm pond option is being deprecated.*
+
 Tracers may be defined that depend on other tracers. Melt pond tracers
 provide an example (these equations pertain to cesm and topo tracers;
 level-ice tracers are similar with an extra factor of :math:`a_{lvl}`,
@@ -78,7 +80,7 @@ the grid cell. These quantities are illustrated in Figure :ref:`fig-tracers`.
 The graphic on the right illustrates the *grid cell* fraction of ponds or 
 level ice as defined by the tracers. The chart on the left provides 
 corresponding ice thickness and pond depth averages over the grid cell, 
-sea ice and pond area fractions. *Note that the cesm pond option has been deprecated.*
+sea ice and pond area fractions. 
 
 .. _fig-tracers:
 

doc/source/user_guide/ug_case_settings.rst

@@ -183,16 +183,15 @@ tracer_nml
    "``tr_iage``", "logical", "ice age", "``.false.``"
    "``tr_iso``", "logical", "isotopes", "``.false.``"
    "``tr_lvl``", "logical", "level ice area and volume", "``.false.``"
-
-.. comment Note that this has been deprecated.
-   "``tr_pond_cesm``", "logical", "CESM melt ponds", "``.false.``"
-
    "``tr_pond_cesm``", "logical", "DEPRECATED", "``.false.``"
    "``tr_pond_lvl``", "logical", "level-ice melt ponds", "``.false.``"
    "``tr_pond_topo``", "logical", "topo melt ponds", "``.false.``"
    "``tr_snow``", "logical", "advanced snow physics", "``.false.``"
    "", "", "", ""
 
+.. comment tr_pond_cesm is being deprecated
+   "``tr_pond_cesm``", "logical", "CESM melt ponds", "``.false.``"
+
 thermo_nml
 ~~~~~~~~~~~~~~~~~~~~~~~~~