<p><b>duda</b> 2013-03-20 12:09:30 -0600 (Wed, 20 Mar 2013)</p><p>BRANCH COMMIT<br>
<br>
Add comments to Registry.xml for init_nhyd_atmos core; also modify whitespace and order of some variables.<br>
<br>
<br>
M    src/core_init_nhyd_atmos/Registry.xml<br>
</p><hr noshade><pre><font color="gray">Modified: branches/xml_registry/src/core_init_nhyd_atmos/Registry.xml
===================================================================
--- branches/xml_registry/src/core_init_nhyd_atmos/Registry.xml        2013-03-20 17:21:27 UTC (rev 2634)
+++ branches/xml_registry/src/core_init_nhyd_atmos/Registry.xml        2013-03-20 18:09:30 UTC (rev 2635)
@@ -1,5 +1,10 @@
 <?xml version="1.0"?>
 <registry>
+
+<!-- **************************************************************************************** -->
+<!-- ************************************** Dimensions ************************************** -->
+<!-- **************************************************************************************** -->
+
         <dims>
                 <dim name="nCells"/>
                 <dim name="nEdges"/>
@@ -19,155 +24,195 @@
                 <dim name="nVertLevelsP1"      definition="nVertLevels+1"/>
                 <dim name="nMonths"            definition="namelist:config_months"/>
         </dims>
+
+
+<!-- **************************************************************************************** -->
+<!-- ************************************** Namelists *************************************** -->
+<!-- **************************************************************************************** -->
+
         <nml_record name="nhyd_model">
-                <nml_option name="config_test_case"                  type="integer"       default_value="7"/>
-                <nml_option name="config_calendar_type"              type="character"     default_value="gregorian"/>
-                <nml_option name="config_start_time"                 type="character"     default_value="none"/>
-                <nml_option name="config_stop_time"                  type="character"     default_value="none"/>
-                <nml_option name="config_theta_adv_order"            type="integer"       default_value="3"/>
-                <nml_option name="config_coef_3rd_order"             type="real"          default_value="0.25"/>
-                <nml_option name="config_num_halos"                  type="integer"       default_value="2"/>
+                <nml_option name="config_test_case"             type="integer"       default_value="7"/>
+                <nml_option name="config_calendar_type"         type="character"     default_value="gregorian"/>
+                <nml_option name="config_start_time"            type="character"     default_value="none"/>
+                <nml_option name="config_stop_time"             type="character"     default_value="none"/>
+                <nml_option name="config_theta_adv_order"       type="integer"       default_value="3"/>
+                <nml_option name="config_coef_3rd_order"        type="real"          default_value="0.25"/>
+                <nml_option name="config_num_halos"             type="integer"       default_value="2"/>
         </nml_record>
+
         <nml_record name="dcmip">
-                <nml_option name="config_dcmip_case"                 type="character"     default_value="2-0-0"/>
-                <nml_option name="config_planet_scale"               type="real"          default_value="1.0"/>
-                <nml_option name="config_rotation_rate_scale"        type="real"          default_value="1.0"/>
+                <nml_option name="config_dcmip_case"            type="character"     default_value="2-0-0"/>
+                <nml_option name="config_planet_scale"          type="real"          default_value="1.0"/>
+                <nml_option name="config_rotation_rate_scale"   type="real"          default_value="1.0"/>
         </nml_record>
+
         <nml_record name="dimensions">
-                <nml_option name="config_nvertlevels"                type="integer"       default_value="26"/>
-                <nml_option name="config_nsoillevels"                type="integer"       default_value="4"/>
-                <nml_option name="config_nfglevels"                  type="integer"       default_value="27"/>
-                <nml_option name="config_nfgsoillevels"              type="integer"       default_value="4"/>
-                <nml_option name="config_months"                     type="integer"       default_value="12"/>
+                <nml_option name="config_nvertlevels"           type="integer"       default_value="26"/>
+                <nml_option name="config_nsoillevels"           type="integer"       default_value="4"/>
+                <nml_option name="config_nfglevels"             type="integer"       default_value="27"/>
+                <nml_option name="config_nfgsoillevels"         type="integer"       default_value="4"/>
+                <nml_option name="config_months"                type="integer"       default_value="12"/>
         </nml_record>
+
         <nml_record name="data_sources">
-                <nml_option name="config_geog_data_path"             type="character"     default_value="/mmm/users/wrfhelp/WPS_GEOG/"/>
-                <nml_option name="config_met_prefix"                 type="character"     default_value="FILE"/>
-                <nml_option name="config_sfc_prefix"                 type="character"     default_value="FILE"/>
-                <nml_option name="config_fg_interval"                type="integer"       default_value="21600"/>
+                <nml_option name="config_geog_data_path"        type="character"     default_value="/mmm/users/wrfhelp/WPS_GEOG/"/>
+                <nml_option name="config_met_prefix"            type="character"     default_value="FILE"/>
+                <nml_option name="config_sfc_prefix"            type="character"     default_value="FILE"/>
+                <nml_option name="config_fg_interval"           type="integer"       default_value="21600"/>
         </nml_record>
+
         <nml_record name="vertical_grid">
-                <nml_option name="config_ztop"                       type="real"          default_value="28000.0"/>
-                <nml_option name="config_nsmterrain"                 type="integer"       default_value="2"/>
-                <nml_option name="config_smooth_surfaces"            type="logical"       default_value="false"/>
+                <nml_option name="config_ztop"                  type="real"          default_value="28000.0"/>
+                <nml_option name="config_nsmterrain"            type="integer"       default_value="2"/>
+                <nml_option name="config_smooth_surfaces"       type="logical"       default_value="false"/>
         </nml_record>
+
         <nml_record name="preproc_stages">
-                <nml_option name="config_static_interp"              type="logical"       default_value="true"/>
-                <nml_option name="config_vertical_grid"              type="logical"       default_value="true"/>
-                <nml_option name="config_met_interp"                 type="logical"       default_value="true"/>
-                <nml_option name="config_input_sst"                  type="logical"       default_value="false"/>
-                <nml_option name="config_frac_seaice"                type="logical"       default_value="false"/>
+                <nml_option name="config_static_interp"         type="logical"       default_value="true"/>
+                <nml_option name="config_vertical_grid"         type="logical"       default_value="true"/>
+                <nml_option name="config_met_interp"            type="logical"       default_value="true"/>
+                <nml_option name="config_input_sst"             type="logical"       default_value="false"/>
+                <nml_option name="config_frac_seaice"           type="logical"       default_value="false"/>
         </nml_record>
+
         <nml_record name="io">
-                <nml_option name="config_input_name"                 type="character"     default_value="grid.nc"/>
-                <nml_option name="config_sfc_update_name"            type="character"     default_value="sfc_update.nc"/>
-                <nml_option name="config_output_name"                type="character"     default_value="init.nc"/>
-                <nml_option name="config_restart_name"               type="character"     default_value="restart.nc"/>
-                <nml_option name="config_frames_per_outfile"         type="integer"       default_value="0"/>
-                <nml_option name="config_pio_num_iotasks"            type="integer"       default_value="0"/>
-                <nml_option name="config_pio_stride"                 type="integer"       default_value="1"/>
+                <nml_option name="config_input_name"            type="character"     default_value="grid.nc"/>
+                <nml_option name="config_sfc_update_name"       type="character"     default_value="sfc_update.nc"/>
+                <nml_option name="config_output_name"           type="character"     default_value="init.nc"/>
+                <nml_option name="config_restart_name"          type="character"     default_value="restart.nc"/>
+                <nml_option name="config_frames_per_outfile"    type="integer"       default_value="0"/>
+                <nml_option name="config_pio_num_iotasks"       type="integer"       default_value="0"/>
+                <nml_option name="config_pio_stride"            type="integer"       default_value="1"/>
         </nml_record>
+
         <nml_record name="decomposition">
                 <nml_option name="config_block_decomp_file_prefix"   type="character"     default_value="graph.info.part."/>
                 <nml_option name="config_number_of_blocks"           type="integer"       default_value="0"/>
                 <nml_option name="config_explicit_proc_decomp"       type="logical"       default_value=".false."/>
                 <nml_option name="config_proc_decomp_file_prefix"    type="character"     default_value="graph.info.part."/>
         </nml_record>
+
         <nml_record name="restart">
-                <nml_option name="config_restart_interval"           type="integer"       default_value="0"/>
-                <nml_option name="config_do_restart"                 type="logical"       default_value="false"/>
-                <nml_option name="config_restart_time"               type="real"          default_value="172800.0"/>
+                <nml_option name="config_restart_interval"      type="integer"       default_value="0"/>
+                <nml_option name="config_do_restart"            type="logical"       default_value="false"/>
+                <nml_option name="config_restart_time"          type="real"          default_value="172800.0"/>
         </nml_record>
+
+
+<!-- **************************************************************************************** -->
+<!-- ************************************** Variables *************************************** -->
+<!-- **************************************************************************************** -->
+
+        <var_struct name="mesh" time_levs="0">
+                <var name="latCell"                      type="real"     dimensions="nCells"                      streams="io"/>
+                <var name="lonCell"                      type="real"     dimensions="nCells"                      streams="io"/>
+                <var name="xCell"                        type="real"     dimensions="nCells"                      streams="io"/>
+                <var name="yCell"                        type="real"     dimensions="nCells"                      streams="io"/>
+                <var name="zCell"                        type="real"     dimensions="nCells"                      streams="io"/>
+                <var name="indexToCellID"                type="integer"  dimensions="nCells"                      streams="io"/>
+                <var name="latEdge"                      type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="lonEdge"                      type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="xEdge"                        type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="yEdge"                        type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="zEdge"                        type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="indexToEdgeID"                type="integer"  dimensions="nEdges"                      streams="io"/>
+                <var name="latVertex"                    type="real"     dimensions="nVertices"                   streams="io"/>
+                <var name="lonVertex"                    type="real"     dimensions="nVertices"                   streams="io"/>
+                <var name="xVertex"                      type="real"     dimensions="nVertices"                   streams="io"/>
+                <var name="yVertex"                      type="real"     dimensions="nVertices"                   streams="io"/>
+                <var name="zVertex"                      type="real"     dimensions="nVertices"                   streams="io"/>
+                <var name="indexToVertexID"              type="integer"  dimensions="nVertices"                   streams="io"/>
+                <var name="cellsOnEdge"                  type="integer"  dimensions="TWO nEdges"                  streams="io"/>
+                <var name="nEdgesOnCell"                 type="integer"  dimensions="nCells"                      streams="io"/>
+                <var name="nEdgesOnEdge"                 type="integer"  dimensions="nEdges"                      streams="io"/>
+                <var name="edgesOnCell"                  type="integer"  dimensions="maxEdges nCells"             streams="io"/>
+                <var name="edgesOnEdge"                  type="integer"  dimensions="maxEdges2 nEdges"            streams="io"/>
+                <var name="weightsOnEdge"                type="real"     dimensions="maxEdges2 nEdges"            streams="io"/>
+                <var name="dvEdge"                       type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="dcEdge"                       type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="angleEdge"                    type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="areaCell"                     type="real"     dimensions="nCells"                      streams="io"/>
+                <var name="areaTriangle"                 type="real"     dimensions="nVertices"                   streams="io"/>
+                <var name="edgeNormalVectors"            type="real"     dimensions="R3 nEdges"                   streams="io"/>
+                <var name="localVerticalUnitVectors"     type="real"     dimensions="R3 nCells"                   streams="io"/>
+                <var name="cellTangentPlane"             type="real"     dimensions="R3 TWO nCells"               streams="io"/>
+                <var name="cellsOnCell"                  type="integer"  dimensions="maxEdges nCells"             streams="io"/>
+                <var name="verticesOnCell"               type="integer"  dimensions="maxEdges nCells"             streams="io"/>
+                <var name="verticesOnEdge"               type="integer"  dimensions="TWO nEdges"                  streams="io"/>
+                <var name="edgesOnVertex"                type="integer"  dimensions="vertexDegree nVertices"      streams="io"/>
+                <var name="cellsOnVertex"                type="integer"  dimensions="vertexDegree nVertices"      streams="io"/>
+                <var name="kiteAreasOnVertex"            type="real"     dimensions="vertexDegree nVertices"      streams="io"/>
+                <var name="fEdge"                        type="real"     dimensions="nEdges"                      streams="io"/>
+                <var name="fVertex"                      type="real"     dimensions="nVertices"                   streams="io"/>
+                <var name="meshDensity"                  type="real"     dimensions="nCells"                      streams="iro"/>
+
+                <!-- coefficients for vertical extrapolation to the surface -->
+                <var name="cf1"                          type="real"     dimensions=""                            streams="io"/>
+                <var name="cf2"                          type="real"     dimensions=""                            streams="io"/>
+                <var name="cf3"                          type="real"     dimensions=""                            streams="io"/>
+
+                <!-- static terrestrial fields -->
+                <var name="ter"                                  type="real"     dimensions="nCells"              streams="io"/>
+                <var name="landmask"                             type="integer"  dimensions="nCells"              streams="io"/>
+                <var name="ivgtyp"   name_in_code="lu_index"     type="integer"  dimensions="nCells"              streams="io"/>
+                <var name="isltyp"   name_in_code="soilcat_top"  type="integer"  dimensions="nCells"              streams="io"/>
+                <var name="soilcat_bot"                          type="integer"  dimensions="nCells"              streams="io"/>
+                <var name="snoalb"                               type="real"     dimensions="nCells"              streams="io"/>
+                <var name="soiltemp"                             type="real"     dimensions="nCells"              streams="io"/>
+                <var name="greenfrac"                            type="real"     dimensions="nMonths nCells"      streams="io"/>
+                <var name="shdmin"                               type="real"     dimensions="nCells"              streams="io"/>
+                <var name="shdmax"                               type="real"     dimensions="nCells"              streams="io"/>
+                <var name="albedo12m"                            type="real"     dimensions="nMonths nCells"      streams="io"/>
+
+                <!-- description of the vertical grid structure -->
+                <var name="hx"                         type="real"     dimensions="nVertLevelsP1 nCells"        streams="io"/>
+                <var name="zgrid"                      type="real"     dimensions="nVertLevelsP1 nCells"        streams="io"/>
+                <var name="rdzw"                       type="real"     dimensions="nVertLevels"                 streams="io"/>
+                <var name="dzu"                        type="real"     dimensions="nVertLevels"                 streams="io"/>
+                <var name="rdzu"                       type="real"     dimensions="nVertLevels"                 streams="io"/>
+                <var name="fzm"                        type="real"     dimensions="nVertLevels"                 streams="io"/>
+                <var name="fzp"                        type="real"     dimensions="nVertLevels"                 streams="io"/>
+                <var name="zx"                         type="real"     dimensions="nVertLevelsP1 nEdges"        streams="io"/>
+                <var name="zz"                         type="real"     dimensions="nVertLevelsP1 nCells"        streams="io"/>
+                <var name="zb"                         type="real"     dimensions="nVertLevelsP1 TWO nEdges"    streams="io"/>
+                <var name="zb3"                        type="real"     dimensions="nVertLevelsP1 TWO nEdges"    streams="io"/>
+
+                <!-- W-Rayleigh damping coefficient -->
+                <var name="dss"                        type="real"     dimensions="nVertLevels nCells"          streams="io"/>
+
+                <var name="u_init"                     type="real"     dimensions="nVertLevels"                 streams="io"/>
+                <var name="t_init"                     type="real"     dimensions="nVertLevels nCells"          streams="io"/>
+                <var name="qv_init"                    type="real"     dimensions="nVertLevels"                 streams="io"/>
+
+                <!-- variables needed for advection -->
+                <var name="deriv_two"                  type="real"     dimensions="FIFTEEN TWO nEdges"          streams="io"/>
+                <var name="advCells"                   type="integer"  dimensions="TWENTYONE nCells"            streams="io"/>
+
+                <!-- deformation calculation weights -->
+                <var name="defc_a"                     type="real"     dimensions="maxEdges nCells"             streams="io"/>
+                <var name="defc_b"                     type="real"     dimensions="maxEdges nCells"             streams="io"/>
+
+                <!-- arrays required for reconstruction of velocity field -->
+                <var name="coeffs_reconstruct"         type="real"     dimensions="R3 maxEdges nCells"          streams="io"/>
+        </var_struct>
+
         <var_struct name="state" time_levs="2">
-                <var name="xtime"                             type="text"     dimensions="Time"                        streams="so"/>
-                <var name="u"                                 type="real"     dimensions="nVertLevels nEdges Time"     streams="o"/>
-                <var name="w"                                 type="real"     dimensions="nVertLevelsP1 nCells Time"   streams="o"/>
-                <var name="rho_zz"                            type="real"     dimensions="nVertLevels nCells Time"     streams="o"/>
-                <var name="theta_m"                           type="real"     dimensions="nVertLevels nCells Time"     streams="o"/>
+                <var name="xtime"                      type="text"     dimensions="Time"                        streams="so"/>
+                <var name="u"                          type="real"     dimensions="nVertLevels nEdges Time"     streams="o"/>
+                <var name="w"                          type="real"     dimensions="nVertLevelsP1 nCells Time"   streams="o"/>
+                <var name="rho_zz"                     type="real"     dimensions="nVertLevels nCells Time"     streams="o"/>
+                <var name="theta_m"                    type="real"     dimensions="nVertLevels nCells Time"     streams="o"/>
+
                 <var_array name="scalars" type="real" dimensions="nVertLevels nCells Time">
-                        <var name="qv"                 array_group="moist"       streams="o"/>
-                        <var name="qc"                 array_group="moist"       streams="o"/>
-                        <var name="qr"                 array_group="moist"       streams="o"/>
+                        <var name="qv"      array_group="moist"       streams="o"/>
+                        <var name="qc"      array_group="moist"       streams="o"/>
+                        <var name="qr"      array_group="moist"       streams="o"/>
                 </var_array>
         </var_struct>
-        <var_struct name="mesh" time_levs="0">
-                <var name="latCell"                           type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="lonCell"                           type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="xCell"                             type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="yCell"                             type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="zCell"                             type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="indexToCellID"                     type="integer"  dimensions="nCells"                      streams="io"/>
-                <var name="latEdge"                           type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="lonEdge"                           type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="xEdge"                             type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="yEdge"                             type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="zEdge"                             type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="indexToEdgeID"                     type="integer"  dimensions="nEdges"                      streams="io"/>
-                <var name="latVertex"                         type="real"     dimensions="nVertices"                   streams="io"/>
-                <var name="lonVertex"                         type="real"     dimensions="nVertices"                   streams="io"/>
-                <var name="xVertex"                           type="real"     dimensions="nVertices"                   streams="io"/>
-                <var name="yVertex"                           type="real"     dimensions="nVertices"                   streams="io"/>
-                <var name="zVertex"                           type="real"     dimensions="nVertices"                   streams="io"/>
-                <var name="indexToVertexID"                   type="integer"  dimensions="nVertices"                   streams="io"/>
-                <var name="cellsOnEdge"                       type="integer"  dimensions="TWO nEdges"                  streams="io"/>
-                <var name="nEdgesOnCell"                      type="integer"  dimensions="nCells"                      streams="io"/>
-                <var name="nEdgesOnEdge"                      type="integer"  dimensions="nEdges"                      streams="io"/>
-                <var name="edgesOnCell"                       type="integer"  dimensions="maxEdges nCells"             streams="io"/>
-                <var name="edgesOnEdge"                       type="integer"  dimensions="maxEdges2 nEdges"            streams="io"/>
-                <var name="weightsOnEdge"                     type="real"     dimensions="maxEdges2 nEdges"            streams="io"/>
-                <var name="dvEdge"                            type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="dcEdge"                            type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="angleEdge"                         type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="areaCell"                          type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="areaTriangle"                      type="real"     dimensions="nVertices"                   streams="io"/>
-                <var name="edgeNormalVectors"                 type="real"     dimensions="R3 nEdges"                   streams="io"/>
-                <var name="localVerticalUnitVectors"          type="real"     dimensions="R3 nCells"                   streams="io"/>
-                <var name="cellTangentPlane"                  type="real"     dimensions="R3 TWO nCells"               streams="io"/>
-                <var name="cellsOnCell"                       type="integer"  dimensions="maxEdges nCells"             streams="io"/>
-                <var name="verticesOnCell"                    type="integer"  dimensions="maxEdges nCells"             streams="io"/>
-                <var name="verticesOnEdge"                    type="integer"  dimensions="TWO nEdges"                  streams="io"/>
-                <var name="edgesOnVertex"                     type="integer"  dimensions="vertexDegree nVertices"      streams="io"/>
-                <var name="cellsOnVertex"                     type="integer"  dimensions="vertexDegree nVertices"      streams="io"/>
-                <var name="kiteAreasOnVertex"                 type="real"     dimensions="vertexDegree nVertices"      streams="io"/>
-                <var name="fEdge"                             type="real"     dimensions="nEdges"                      streams="io"/>
-                <var name="fVertex"                           type="real"     dimensions="nVertices"                   streams="io"/>
-                <var name="meshDensity"                       type="real"     dimensions="nCells"                      streams="iro"/>
-                <var name="cf1"                               type="real"     dimensions=""                            streams="io"/>
-                <var name="cf2"                               type="real"     dimensions=""                            streams="io"/>
-                <var name="cf3"                               type="real"     dimensions=""                            streams="io"/>
-                <var name="ter"                               type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="landmask"                          type="integer"  dimensions="nCells"                      streams="io"/>
-                <var name="ivgtyp"   name_in_code="lu_index"     type="integer"  dimensions="nCells"                      streams="io"/>
-                <var name="isltyp"   name_in_code="soilcat_top"  type="integer"  dimensions="nCells"                      streams="io"/>
-                <var name="soilcat_bot"                       type="integer"  dimensions="nCells"                      streams="io"/>
-                <var name="snoalb"                            type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="soiltemp"                          type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="greenfrac"                         type="real"     dimensions="nMonths nCells"              streams="io"/>
-                <var name="shdmin"                            type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="shdmax"                            type="real"     dimensions="nCells"                      streams="io"/>
-                <var name="albedo12m"                         type="real"     dimensions="nMonths nCells"              streams="io"/>
-                <var name="hx"                                type="real"     dimensions="nVertLevelsP1 nCells"        streams="io"/>
-                <var name="zgrid"                             type="real"     dimensions="nVertLevelsP1 nCells"        streams="io"/>
-                <var name="rdzw"                              type="real"     dimensions="nVertLevels"                 streams="io"/>
-                <var name="dzu"                               type="real"     dimensions="nVertLevels"                 streams="io"/>
-                <var name="rdzu"                              type="real"     dimensions="nVertLevels"                 streams="io"/>
-                <var name="fzm"                               type="real"     dimensions="nVertLevels"                 streams="io"/>
-                <var name="fzp"                               type="real"     dimensions="nVertLevels"                 streams="io"/>
-                <var name="zx"                                type="real"     dimensions="nVertLevelsP1 nEdges"        streams="io"/>
-                <var name="zz"                                type="real"     dimensions="nVertLevelsP1 nCells"        streams="io"/>
-                <var name="zb"                                type="real"     dimensions="nVertLevelsP1 TWO nEdges"    streams="io"/>
-                <var name="zb3"                               type="real"     dimensions="nVertLevelsP1 TWO nEdges"    streams="io"/>
-                <var name="dss"                               type="real"     dimensions="nVertLevels nCells"          streams="io"/>
-                <var name="u_init"                            type="real"     dimensions="nVertLevels"                 streams="io"/>
-                <var name="t_init"                            type="real"     dimensions="nVertLevels nCells"          streams="io"/>
-                <var name="qv_init"                           type="real"     dimensions="nVertLevels"                 streams="io"/>
-                <var name="deriv_two"                         type="real"     dimensions="FIFTEEN TWO nEdges"          streams="io"/>
-                <var name="advCells"                          type="integer"  dimensions="TWENTYONE nCells"            streams="io"/>
-                <var name="defc_a"                            type="real"     dimensions="maxEdges nCells"             streams="io"/>
-                <var name="defc_b"                            type="real"     dimensions="maxEdges nCells"             streams="io"/>
-                <var name="coeffs_reconstruct"                type="real"     dimensions="R3 maxEdges nCells"          streams="io"/>
-        </var_struct>
+
         <var_struct name="fg" time_levs="1">
+                
+                <!-- horizontally interpolated from first-guess data -->
                 <var name="u_fg"       name_in_code="u"       type="real"     dimensions="nFGLevels nEdges Time"/>
                 <var name="v_fg"       name_in_code="v"       type="real"     dimensions="nFGLevels nEdges Time"/>
                 <var name="t_fg"       name_in_code="t"       type="real"     dimensions="nFGLevels nCells Time"/>
@@ -182,6 +227,8 @@
                 <var name="zs_fg"                             type="real"     dimensions="nFGSoilLevels nCells Time"   streams="io"/>
                 <var name="st_fg"                             type="real"     dimensions="nFGSoilLevels nCells Time"   streams="io"/>
                 <var name="sm_fg"                             type="real"     dimensions="nFGSoilLevels nCells Time"   streams="io"/>
+
+                <!-- horizontally interpolated from first-guess data, and should be read in by model -->
                 <var name="dz"                                type="real"     dimensions="nSoilLevels nCells Time"     streams="io"/>
                 <var name="dzs"                               type="real"     dimensions="nSoilLevels nCells Time"     streams="io"/>
                 <var name="zs"                                type="real"     dimensions="nSoilLevels nCells Time"     streams="io"/>
@@ -202,6 +249,7 @@
                 <var name="sfc_albbck"                        type="real"     dimensions="nCells Time"                 streams="io"/>
                 <var name="xland"                             type="real"     dimensions="nCells Time"                 streams="io"/>
         </var_struct>
+
         <var_struct name="diag" time_levs="1">
                 <var name="pressure_p"                        type="real"     dimensions="nVertLevels nCells Time"/>
                 <var name="rho"                               type="real"     dimensions="nVertLevels nCells Time"     streams="o"/>
@@ -221,6 +269,8 @@
                 <var name="theta_base"                        type="real"     dimensions="nVertLevels nCells Time"     streams="io"/>
                 <var name="cqw"                               type="real"     dimensions="nVertLevels nCells Time"/>
                 <var name="surface_pressure"                  type="real"     dimensions="nCells Time"                 streams="io"/>
+
+                <!-- coupled variables needed by the solver, but not output -->
                 <var name="ru"                                type="real"     dimensions="nVertLevels nEdges Time"/>
                 <var name="rw"                                type="real"     dimensions="nVertLevelsP1 nCells Time"/>
                 <var name="rtheta_p"                          type="real"     dimensions="nVertLevels nCells Time"/>
</font>
</pre>