namelist cleanup:

1. no more full_zs_filter
2. &surf_map_nml entries that do not have the namelist default are variables
3. Reorganize and comment gnv1_nested

tests/parm/input_global_nest.nml.IN

@@ -93,7 +93,6 @@
   fast_tau_w_sec = @[FAST_TAU_W_SEC_NEST02]
   consv_am = .false.
   fill = .true.
-  full_zs_filter = @[FULL_ZS_FILTER]
   dwind_2d = .false.
   print_freq = 6
   warm_start = @[WARM_START]
@@ -120,11 +119,11 @@
   cd2 = -1
   cd4 = 0.15
   max_slope = 0.15
-  n_del2_strong = 0
-  n_del2_weak = 24
-  n_del4 = 2
-  peak_fac = 1.
-  zero_ocean = .false.
+  n_del2_strong = @[N_DEL2_STRONG]
+  n_del2_weak = @[N_DEL2_WEAK_NEST02]
+  n_del4 = @[N_DEL4]
+  peak_fac = @[PEAK_FAC]
+  zero_ocean = @[ZERO_OCEAN]
 /
 
 &gfs_physics_nml
@@ -200,6 +199,10 @@
   imfshalcnv   = @[IMFSHALCNV_NEST02]
   imfdeepcnv   = @[IMFDEEPCNV_NEST02]
   do_deep      = @[DO_DEEP_NEST02]
+  ! NOTE: progsigma should be .true. for the global_nest_v1 suite.
+  ! The code turns it off automatically at low resolutions (nominally, less than C768 resolution).
+  ! That means it would turn off for the regression tests (C96 globe, C384 resolution nest).
+  ! Hence, we turn it off manually, to avoid advecting a field of 0.
   progsigma    = @[PROGSIGMA_NEST02]
   betascu      = @[BETASCU_NEST02]
   betamcu      = @[BETAMCU_NEST02]

tests/parm/input_global_parent.nml.IN

@@ -92,7 +92,6 @@
   fast_tau_w_sec = @[FAST_TAU_W_SEC]
   consv_am = .false.
   fill = .true.
-  full_zs_filter = @[FULL_ZS_FILTER]
   dwind_2d = .false.
   print_freq = 6
   warm_start = @[WARM_START]
@@ -120,11 +119,11 @@
   cd2 = -1
   cd4 = 0.15
   max_slope = 0.15
-  n_del2_strong = 0
-  n_del2_weak = 15
-  n_del4 = 2
-  peak_fac = 1.
-  zero_ocean = .false.
+  n_del2_strong = @[N_DEL2_STRONG]
+  n_del2_weak = @[N_DEL2_WEAK]
+  n_del4 = @[N_DEL4]
+  peak_fac = @[PEAK_FAC]
+  zero_ocean = @[ZERO_OCEAN]
 /
 
 &gfs_physics_nml
@@ -202,6 +201,10 @@
   imfshalcnv   = @[IMFSHALCNV]
   imfdeepcnv   = @[IMFDEEPCNV]
   do_deep      = @[DO_DEEP]
+  ! NOTE: progsigma should be .true. for the global_nest_v1 suite.
+  ! The code turns it off automatically at low resolutions (nominally, less than C768 resolution).
+  ! That means it would turn off for the regression tests (C96 globe, C384 resolution nest).
+  ! Hence, we turn it off manually, to avoid advecting a field of 0.
   progsigma    = @[PROGSIGMA]
   betascu      = @[BETASCU]
   betamcu      = @[BETAMCU]

tests/tests/gnv1_nested

@@ -53,12 +53,21 @@ export LIST_FILES="atmf002.nc \
                    RESTART/fv_BC_ne.res.nest02.nc \
                    RESTART/fv_BC_sw.res.nest02.nc"
 
+# Get all default variables for FV3
+export_fv3 # Must come before all other exports
 
-export_fv3
-export_tiled
+# Request tiled inputs in &namsfc
+export_tiled # Must come second, after export_fv3, before all export statements
+export TILEDFIX=.true.
+
+# Select input directories in control_run.IN
+export ATMRES=C96-nested
 
+# Master flag to enable nesting in control_run.IN. Also sent to &fv_core_nml
 export NESTED=.true.
 
+# ----------------------------------------
+# model_configure
 export SYEAR=2023
 export SMONTH=02
 export SDAY=24
@@ -83,6 +92,11 @@ export KCHUNK3D=1
 export IMO=384
 export JMO=192
 export OUTPUT_FH='1 -1'
+
+# NOTE: This script uses NTILES=6 despite having 7 tiles in total.
+# This is to match the logic inside FV3, which is based on mosaics.
+# The globe has one mosiac with 6 tiles, and each nest has one mosaic with 1 tile each.
+# Our workflow scripts are not aware of that detail; they only know about the global mosaic.
 export NTILES=6
 
 export OUTPUT_GRID_2=regional_latlon
@@ -97,19 +111,38 @@ export LAT2_2=72.500000
 export DLON_2=0.25
 export DLAT_2=0.25
 
+# ----------------------------------------
+# &atmos_model_nml
 export BLOCKSIZE=32
 export CCPP_SUITE=FV3_global_nest_v1
+
+# ----------------------------------------
+# &diag_manager_nml
 export MAX_OUTPUT_FIELDS=300
+
+# ----------------------------------------
+# &fms_nml
 export DOMAINS_STACK_SIZE=16000000
 
+# ----------------------------------------
+# &fv_nest_nml
 export TILE_COARSE="0,6"
 export NUM_TILE_TOP=6
 export NEST_REFINE="0,4"
 export NEST_IOFFSETS="0,4"
 export NEST_JOFFSETS="0,9"
 
+# ----------------------------------------
+# &fv_core_nml
+export INPES=4
+export JNPES=4
+export INPES_NEST02=12
+export JNPES_NEST02=10
+
 export NPX=97
 export NPY=97
+export NPX_NEST02=361
+export NPY_NEST02=241
 export NPZ=127
 export DNATS=0
 export DO_SAT_ADJ=.false.
@@ -118,9 +151,6 @@ export FV_CORE_TAU=0.
 export RF_CUTOFF=10.
 export FAST_TAU_W_SEC=0.2
 
-export LDIAG3D=.true.
-export LDIAG_UGWP=.true.
-
 export FV_CORE_TAU_NEST02=$FV_CORE_TAU
 export RF_CUTOFF_NEST02=$RF_CUTOFF
 export FAST_TAU_W_SEC_NEST02=$FAST_TAU_W_SEC
@@ -129,6 +159,13 @@ export TARGET_LON=-135.0
 export TARGET_LAT=32.5
 export TWOWAYNEST02=.true.
 
+export TWOWAYNEST=.true.
+
+# ----------------------------------------
+# &gfs_physics_nml
+export LDIAG3D=.true.
+export LDIAG_UGWP=.true.
+
 export H2O_PHYS=.true.
 export IMP_PHYSICS=8
 export IOVR=3
@@ -155,8 +192,6 @@ export LHEATSTRG=.false.
 export LSEASPRAY=.false.
 export IMFDEEPCNV=5
 export IMFDEEPCNV_NEST02=5
-export PROGSIGMA=.false.
-export PROGSIGMA_NEST02=.false.
 export IOPT_DIAG=1
 export NSTF_NAME=2,0,0,0,0
 export EFFR_IN=.true.
@@ -191,7 +226,6 @@ export D2_BG_K1_NEST02=0.20
 export D2_BG_K2_NEST02=0.15
 export D4_BG_NEST02=0.15
 export DZ_MIN=2.0
-export FULL_ZS_FILTER=.false. # Must be false to avoid model instability
 export FV_SG_ADJ=300
 export HORD_DP=6
 export HORD_MT=6
@@ -244,8 +278,24 @@ export KNOB_UGWP_VERSION=1
 export KNOB_UGWP_PALAUNCH=275.0e2
 export LIGHTNING_THREAT=.true.
 
-export ATMRES=C96-nested
+# NOTE: The global_nest_v1 uses prognostic sigma, so this should be
+# .true.  HOWEVER, the code turns it off automatically for this
+# resolution. Hence, we turn it off here so we're not advecting a grid
+# of 0. The field_table must match this setting (see below).
+export PROGSIGMA=.false.
+export PROGSIGMA_NEST02=.false.
+
+# ----------------------------------------
+# &surf_map_nml
+export N_DEL2_STRONG=0        # namelist default is -1
+export N_DEL2_WEAK=15         # namelist default is 12
+export N_DEL2_WEAK_NEST02=24  # namelist default is 12
+export N_DEL4=2               # namelist default is -1
+export PEAK_FAC=1.            # namelist default is 1.05
+export ZERO_OCEAN=.false.     # namelist default is .true.
 
+# ----------------------------------------
+# &namsfc
 export FNALBC="'${ATMRES}.snowfree_albedo.tileX.nc'"
 export FNALBC2="'${ATMRES}.facsf.tileX.nc'"
 export FNTG3C="'${ATMRES}.substrate_temperature.tileX.nc'"
@@ -265,22 +315,32 @@ export FNACNA="''"
 export FNSNOA="''"
 
 export LANDICE=.false.
-export NPX_NEST02=361
-export NPY_NEST02=241
-export INPES_NEST02=12
-export JNPES_NEST02=10
-export TWOWAYNEST=.true.
-
-export INPES=4
-export JNPES=4
 
-export GRID_PES="$(( INPES * JNPES * 6 )),$(( INPES_NEST02 * JNPES_NEST02 ))"
+# ----------------------------------------
+# Select input files and resources for the regression test system.
 
+# Select model_configure template:
 export MODEL_CONFIGURE=model_configure_gnv1.IN
+
+# Select input.nml template:
 export INPUT_NML=input_global_parent.nml.IN
+
+# Select input_nest02.nml template:
 export INPUT_NEST02_NML=input_global_nest.nml.IN
-export TILEDFIX=.true.
+
+# Select the field_table.
+
+# NOTE: The global_nest_v1 uses prognostic sigma, so this should be
+# the progsigma field table. HOWEVER, the code turns it off
+# automatically for this resolution. Hence, we turn it off here so
+# we're not advecting a grid of 0
+
 export FIELD_TABLE=field_table_thompson_aero_tke
+
+# Request additional contents in diag_table for gravity wave diagnostics:
 export DIAG_TABLE_ADDITIONAL=diag_additional_ldiag3d_ugwp
 
+# Override atmosphere compute task count to include the nest (tile 7).
+# Note that NTILES=6, which is the size of the global mosaic.
+export GRID_PES="$(( INPES * JNPES * 6 )),$(( INPES_NEST02 * JNPES_NEST02 ))"
 ATM_compute_tasks=$(( INPES*JNPES*NTILES + INPES_NEST02*JNPES_NEST02 ))