ESCOMP · samsrabin · Jul 17, 2024 · Jul 17, 2024 · Sep 7, 2024 · Sep 10, 2024
diff --git a/.gitmodules b/.gitmodules
@@ -27,8 +27,8 @@
 #
 [submodule "fates"]
 path = src/fates
-url = https://github.com/NGEET/fates
-fxtag = sci.1.87.0_api.41.0.0
+url = https://github.com/samsrabin/fates
+fxtag = 4d3b7d4fa09141c030fa28ab9687d916aaff6f0c  # edge-area-202410-ts20250909-2: Don't set nlevedgeforest=1 if hlm_use_edge_forest false.
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -807,7 +807,7 @@ sub setup_cmdl_fates_mode {
        my @list  = (  "fates_spitfire_mode", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                       "use_fates_cohort_age_tracking","use_fates_inventory_init","use_fates_fixed_biogeog",
                       "use_fates_nocomp","use_fates_sp","fates_inventory_ctrl_filename","fates_harvest_mode",
-                      "fates_parteh_mode","use_fates_tree_damage","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries",
+                      "fates_parteh_mode","use_fates_tree_damage","use_fates_edge_forest","fates_seeddisp_cadence","use_fates_luh","fluh_timeseries",
                       "flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel",
                       "use_fates_daylength_factor", "fates_photosynth_acclimation", "fates_stomatal_model",
                       "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
@@ -4764,7 +4764,7 @@ sub setup_logic_fates {
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
         my @list  = (  "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys",
                        "use_fates_inventory_init","fates_seeddisp_cadence","fates_history_dimlevel",
-                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage",
+                       "fates_harvest_mode","fates_parteh_mode", "use_fates_cohort_age_tracking","use_fates_tree_damage","use_fates_edge_forest",
                        "use_fates_daylength_factor", "fates_photosynth_acclimation", "fates_stomatal_model",
                        "fates_stomatal_assimilation", "fates_leafresp_model", "fates_cstarvation_model",
                        "fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model", "fates_electron_transport_model",

diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -555,7 +555,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- FATES default parameter file                                       -->
 <!-- ================================================================== -->
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params_api.41.0.0_14pft_c250813.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_default.a5f5a3b4d.nc</fates_paramfile>
 
 
 <!-- ================================================================== -->
@@ -2448,6 +2448,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <use_fates_managed_fire         use_fates=".true.">.false.</use_fates_managed_fire>
 <use_fates_planthydro           use_fates=".true.">.false.</use_fates_planthydro>
 <use_fates_tree_damage          use_fates=".true.">.false.</use_fates_tree_damage>
+<use_fates_edge_forest          use_fates=".true.">.false.</use_fates_edge_forest>
 <use_fates_cohort_age_tracking  use_fates=".true.">.false.</use_fates_cohort_age_tracking>
 <use_fates_daylength_factor     use_fates=".true.">.true.</use_fates_daylength_factor>
 <use_fates_ed_st3               use_fates=".true.">.false.</use_fates_ed_st3>

diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -736,6 +736,12 @@ Toggle to turn on the tree damage module in FATES
 (Only relevant if FATES is on)
 </entry>
 
+<entry id="use_fates_edge_forest" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on the edge forest module in FATES
+(Only relevant if FATES is on)
+</entry>
+
 <entry id="fates_spitfire_mode" type="integer" category="physics"
         group="clm_inparm" valid_values="0,1,2,3,4,5" value=".false.">
 Turn on spitfire module to simulate fire by setting fates_spitfire_mode > 0.

diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -13,6 +13,7 @@
         rxcropmaturity: Short tests to be run during development related to prescribed crop calendars
         matrixcn: Tests exercising the matrix-CN capability
         aux_clm_mpi_serial: aux_clm tests using mpi-serial. Useful for redoing tests that failed due to https://github.com/ESCOMP/CTSM/issues/2916, after having replaced libraries/mpi-serial with a fresh copy.
+        fates_edgeforest: Tests exercising (or not) the FATES edge forest module
         subset_data: Tests exercising the subset_data tool and running CTSM with its output
         decomp_init: Initialization tests specifically for examining the PE layout decomposition initialization
         uhr_decomp_init: Initialization tests at Ultra High Resolution - specifically for examining the PE layout decomposition initialization
@@ -2935,6 +2936,38 @@
     </options>
   </test>
 
+  <test name="SMS_Lm49" grid="f10_f10_mg37" compset="I2000Clm60Fates" testmods="clm/FatesColdAllVarsMonthly">
+    <machines>
+      <machine name="derecho" compiler="intel"   category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">03:00:00</option>
+      <option name="comment"  >This is a long fates test with a lot of variables being written.</option>
+    </options>
+  </test>
+
+  <test name="SMS_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm60Fates" testmods="clm/FatesColdEdgeForest">
+    <machines>
+      <machine name="derecho" compiler="intel"   category="fates"/>
+      <machine name="derecho" compiler="intel"   category="fates_edgeforest"/>
+      <machine name="izumi"   compiler="nag"     category="fates"/>
+      <machine name="izumi"   compiler="nag"     category="fates_edgeforest"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
+
+  <test name="SMS_Lm49" grid="f10_f10_mg37" compset="I2000Clm60Fates" testmods="clm/FatesColdEdgeForestMonthly">
+    <machines>
+      <machine name="derecho" compiler="intel"   category="fates"/>
+      <machine name="derecho" compiler="intel"   category="fates_edgeforest"/>
+    </machines>
+    <options>
+      <option name="wallclock">03:00:00</option>
+    </options>
+  </test>
+
   <test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm60Fates" testmods="clm/FatesFireLightningPopDens--clm/NEON/FATES/NIWO">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>

diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm
@@ -59,4 +59,10 @@ hist_fincl1       = 'FATES_TLONGTERM',
 'FATES_LBLAYER_COND_AP','FATES_STOMATAL_COND_AP','FATES_TLONGTERM','FATES_PRIMARY_AREA_AP','FATES_NPP_LU','FATES_GPP_LU',
 'FATES_SEED_BANK_PF','FATES_UNGERM_SEED_BANK_PF','FATES_SEEDLING_POOL_PF','FATES_SEEDS_IN_PF','FATES_SEEDS_IN_LOCAL_PF',
 'FATES_SAPWOOD_AREA_SZPF','FATES_CANOPYAREA','FATES_NCL','FATES_PATCHAREA','FATES_PRIMARY_AREA','FATES_SCORCH_HEIGHT_PF',
-'FATES_SECONDARY_AREA_ANTHRO','FATES_SECONDARY_AREA','FATES_ZSTAR'
+'FATES_SECONDARY_AREA_ANTHRO','FATES_SECONDARY_AREA','FATES_ZSTAR','FATES_LAI_AP','FATES_FUEL_AMOUNT_AP','FATES_ZSTAR_AP',
+'FATES_BURNFRAC_AP','FATES_CANOPYAREA_AP','FATES_SCORCH_HEIGHT_APPF',
+'FATES_AREA_PLANTS_AP', 'FATES_AREA_TREES_AP', 'FATES_IS_FOREST', 'FATES_IS_FOREST_AP',
+'FATES_IS_FOREST_PCT10', 'FATES_IS_FOREST_PCT10_0GRASS', 'FATES_IS_FOREST_PCT25',
+'FATES_IS_FOREST_PCT25_0GRASS', 'FATES_IS_FOREST_PCT50', 'FATES_IS_FOREST_PCT50_0GRASS',
+'FATES_IS_FOREST_PCT75', 'FATES_IS_FOREST_PCT75_0GRASS', 'FATES_IS_FOREST_PCT90',
+'FATES_IS_FOREST_PCT90_0GRASS', 'FATES_FOREST_AREA_EB'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVarsMonthly/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVarsMonthly/include_user_mods
@@ -0,0 +1 @@
+../FatesColdAllVars
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVarsMonthly/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVarsMonthly/shell_commands
@@ -0,0 +1,3 @@
+./xmlchange CLM_BLDNML_OPTS="-no-megan" --append
+./xmlchange BFBFLAG="TRUE"
+./xmlchange CLM_FORCE_COLDSTART="on"
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVarsMonthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVarsMonthly/user_nl_clm
@@ -0,0 +1,3 @@
+
+hist_mfilt        = 12
+hist_nhtfrq       = 0
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForest/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForest/shell_commands
@@ -0,0 +1,3 @@
+./xmlchange CLM_BLDNML_OPTS="-no-megan" --append
+./xmlchange BFBFLAG="TRUE"
+./xmlchange CLM_FORCE_COLDSTART="on"
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForest/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForest/user_nl_clm
@@ -0,0 +1,33 @@
+
+fates_spitfire_mode = 5
+use_fates_edge_forest = .true.
+
+hist_empty_htapes = .true.
+hist_mfilt        = 1
+hist_nhtfrq       = -24
+fates_spitfire_mode = 1
+fates_history_dimlevel = 2,2
+use_fates_tree_damage = .true.
+hist_ndens = 1
+
+hist_fincl1 += 'FATES_CANOPYAREA_AP','FATES_PATCHAREA_LU'
+hist_fincl1 += 'FATES_CROWNAREA_PF','FATES_CANOPYCROWNAREA_PF'
+hist_fincl1 += 'FATES_VEGC_ABOVEGROUND'
+hist_fincl1 += 'FATES_VEGC','FATES_VEGC_AP','FATES_VEGC_APPF','FATES_VEGC_PF'
+hist_fincl1 += 'FATES_AREA_PLANTS_AP','FATES_AREA_TREES_AP'
+hist_fincl1 += 'FATES_LAI', 'FATES_LAI_CANOPY_SZPF','FATES_LAI_USTORY_SZPF'
+hist_fincl1 += 'FATES_BURNFRAC','FATES_FIRE_INTENSITY','FATES_FIRE_INTENSITY_BURNFRAC'
+hist_fincl1 += 'FATES_FUEL_MOISTURE_FC','FATES_FUEL_AMOUNT_FC'
+hist_fincl1 += 'FATES_IGNITIONS','FATES_ROS'
+hist_fincl1 += 'FATES_CROWNAREA_PF'
+hist_fincl1 += 'FATES_IS_FOREST_PCT10'
+hist_fincl1 += 'FATES_IS_FOREST_PCT25'
+hist_fincl1 += 'FATES_IS_FOREST_PCT50'
+hist_fincl1 += 'FATES_IS_FOREST_PCT75'
+hist_fincl1 += 'FATES_IS_FOREST_PCT90'
+hist_fincl1 += 'FATES_IS_FOREST_PCT10_0GRASS'
+hist_fincl1 += 'FATES_IS_FOREST_PCT25_0GRASS'
+hist_fincl1 += 'FATES_IS_FOREST_PCT50_0GRASS'
+hist_fincl1 += 'FATES_IS_FOREST_PCT75_0GRASS'
+hist_fincl1 += 'FATES_IS_FOREST_PCT90_0GRASS'
+hist_fincl1 += 'FATES_FOREST_AREA_EB'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForestMonthly/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForestMonthly/include_user_mods
@@ -0,0 +1 @@
+../FatesColdEdgeForest
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForestMonthly/shell_commands b/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForestMonthly/shell_commands
@@ -0,0 +1,3 @@
+./xmlchange CLM_BLDNML_OPTS="-no-megan" --append
+./xmlchange BFBFLAG="TRUE"
+./xmlchange CLM_FORCE_COLDSTART="on"
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForestMonthly/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdEdgeForestMonthly/user_nl_clm
@@ -0,0 +1,3 @@
+
+hist_mfilt        = 12
+hist_nhtfrq       = 0
diff --git a/combine_jackie_my_params.py b/combine_jackie_my_params.py
@@ -0,0 +1,163 @@
+"""
+Replace values in default parameter set with values from Jackie's South America work
+"""
+import os
+import numpy as np
+import xarray as xr
+
+PARAM_FILES_DIR = "/glade/u/home/samrabin/ctsm_fates-isforest/src/fates/parameter_files"
+file_in = os.path.join(PARAM_FILES_DIR, "fates_params_shuman24.a8f9da07.nc")
+file_out = os.path.join(PARAM_FILES_DIR, "fates_params_shuman24.a8f9da07.withchanges.nc")
+
+ds_in = xr.open_dataset(file_in)
+ds_out = ds_in.copy()
+
+def replace_values(ds, var, vals_in, indices=None):
+    """
+    Replace values in DataArray
+    """
+    da_in = ds[var]
+    print(var + ": " + da_in.attrs["long_name"])
+    ndims = len(da_in.dims)
+    if indices is None:
+        vals_in = np.array(vals_in)
+        if vals_in.size != da_in.size:
+            raise RuntimeError(f"vals_in.size {vals_in.size} but da_in.size {da_in.size}")
+        vals_new = vals_in
+    else:
+        vals_new = da_in.copy().values
+
+        # Handle shortcut to replace all values
+        if indices == "all":
+            if isinstance(vals_in, (list, np.ndarray)):
+                raise RuntimeError("For indices 'all', you must provide a single scalar vals_in")
+            indices = np.arange(da_in.size)
+            vals_in = np.full(shape=indices.shape, fill_value=vals_in)
+
+        # Check input lists
+        if not isinstance(vals_in, (list, np.ndarray)):
+            vals_in = [vals_in]
+        if not isinstance(indices, (list, np.ndarray)):
+            indices = [indices]
+        if max(indices) + 1 > da_in.size:
+            raise RuntimeError(f"max(indices) {max(indices)} but da_in.size {da_in.size}")
+        if len(vals_in) != len(indices):
+            raise RuntimeError(f"len(vals_in) {len(vals_in)} but len(indices) {len(indices)}")
+
+        # Convert to 1-d, if needed
+        did_reshape = ndims > 1
+        if did_reshape:
+            orig_dims = vals_new.shape
+            vals_new = vals_new.ravel()
+
+        # Assign new values
+        for i, val in enumerate(vals_in):
+            vals_new[indices[i]] = val
+
+        # Convert back from 1-d, if needed
+        if did_reshape:
+            vals_new = vals_new.reshape(orig_dims)
+
+    # Print results
+    vals_new_raveled = vals_new.ravel()
+    this_str = ""
+    any_diff = False
+    for i, val_orig in enumerate(da_in.values.ravel()):
+        val_new = vals_new_raveled[i]
+        if val_orig != val_new:
+            this_str += f"{val_orig} → {val_new}"
+            any_diff = True
+        elif indices is None or i in indices:
+            this_str += "✔️"
+        else:
+            this_str += "_"
+        this_str += ", "
+    this_str = this_str[:-2]
+    if not any_diff:
+        this_str += " (Jackie's change[s] already incorporated into default param file)"
+    else:
+        print(da_in.values)
+        print(vals_new)
+    print(this_str)
+
+    # Save to Dataset
+    new_da = xr.DataArray(
+        data=vals_new,
+        attrs=da_in.attrs,
+        dims=da_in.dims,
+        coords=da_in.coords,
+    )
+    ds[var] = new_da
+    print(" ")
+    return ds
+
+ds_out = replace_values(ds_out, "fates_fire_FBD", 0.95, 5)
+ds_out = replace_values(ds_out, "fates_alloc_storage_cushion", 2.25, 2)
+ds_out = replace_values(ds_out, "fates_allom_d2h1", [57.6, 57.6, 1])
+ds_out = replace_values(ds_out, "fates_allom_d2h2", [0.74, 0.74, 1])
+ds_out = replace_values(ds_out, "fates_allom_la_per_sa_int", 1000, 2)
+ds_out = replace_values(ds_out, "fates_allom_sai_scaler", 0.0012, 2)
+ds_out = replace_values(ds_out, "fates_fire_alpha_SH", [0.1487, 0.06, 1])
+ds_out = replace_values(ds_out, "fates_fire_bark_scaler", [0.0301, 0.1085], [0, 1])
+ds_out = replace_values(ds_out, "fates_fire_crown_kill", [1, 0.05, 1])
+ds_out = replace_values(ds_out, "fates_grperc", [0.3, 0.3], [0, 1])
+ds_out = replace_values(ds_out, "fates_leaf_vcmax25top", [41, 40], [0, 2])
+ds_out = replace_values(ds_out, "fates_mort_hf_sm_threshold", [0.025, 0.025], [0, 1])
+ds_out = replace_values(ds_out, "fates_wood_density", [0.6305, 0.695, 0.01])
+ds_out = replace_values(ds_out, "fates_turnover_branch", [75, 75, 0.3208])
+ds_out = replace_values(ds_out, "fates_allom_h2cd1", [0.33, 0.1], [0, 1])
+ds_out = replace_values(ds_out, "fates_turnover_leaf", [[1.4025, 1.4025, 0.3208]])
+ds_out = replace_values(ds_out, "fates_recruit_height_min", 0.5, 2)
+ds_out = replace_values(ds_out, "fates_recruit_init_density", 20, 2)
+ds_out = replace_values(ds_out, "fates_stoich_nitr", [0.02675, 0.02675, 0.16], [0, 1, 2])
+ds_out = replace_values(ds_out, "fates_allom_d2bl1", [0.12668, 0.12668, 0.000964])
+ds_out = replace_values(ds_out, "fates_allom_d2bl2", [1.2813, 1.2813, 1.9492])
+ds_out = replace_values(ds_out, "fates_allom_d2ca_coefficient_max", [0.76865, 0.76865, 0.03])
+ds_out = replace_values(ds_out, "fates_allom_d2ca_coefficient_min", [0.76865, 0.76865, 0.03])
+ds_out = replace_values(ds_out, "fates_allom_l2fr", [0.4863, 0.4863], [0, 1])
+ds_out = replace_values(ds_out, "fates_leaf_slamax", [0.03992, 0.03992, 0.0135])
+ds_out = replace_values(ds_out, "fates_leaf_slatop", [0.01996, 0.01996, 0.0135])
+ds_out = replace_values(ds_out, "fates_mort_scalar_cstarvation", [0.02956, 0.02956, 0.2])
+ds_out = replace_values(ds_out, "fates_recruit_seed_alloc", [0.046801, 0.046801], [0, 1])
+ds_out = replace_values(ds_out, "fates_fire_cg_strikes", 0.1)
+ds_out = replace_values(ds_out, "fates_fire_threshold", 25.0)
+ds_out = replace_values(ds_out, "fates_comp_excln", -1.0)
+ds_out = replace_values(ds_out, "fates_mort_disturb_frac", 0.5)
+ds_out = replace_values(ds_out, "fates_mort_understorey_death", 1.0)
+ds_out = replace_values(ds_out, "fates_allom_agb1", [0.0673, 0.0673, 0.000964])
+ds_out = replace_values(ds_out, "fates_allom_agb2", [0.976, 0.976, 1.9462])
+ds_out = replace_values(ds_out, "fates_allom_amode", [3, 3], [0, 1])
+ds_out = replace_values(ds_out, "fates_allom_agb3", [np.nan, np.nan, 0])
+ds_out = replace_values(ds_out, "fates_allom_agb4", [np.nan, np.nan, 0])
+ds_out = replace_values(ds_out, "fates_allom_fmode", 2.0, "all")
+ds_out = replace_values(ds_out, "fates_allom_agb_frac", 1, 2)
+ds_out = replace_values(ds_out, "fates_allom_dbh_maxheight", [200.0, 200.0, 1.0])
+ds_out = replace_values(ds_out, "fates_allom_hmode", [5.0, 5.0, 3.0])
+ds_out = replace_values(ds_out, "fates_allom_lmode", [3.0, 3.0, 1.0])
+ds_out = replace_values(ds_out, "fates_allom_fnrt_prof_a", [7, 7], [1, 2])
+ds_out = replace_values(ds_out, "fates_allom_fnrt_prof_b", [1, 1], [1, 2])
+ds_out = replace_values(ds_out, "fates_rad_leaf_clumping_index", 0.85, 2)
+ds_out = replace_values(ds_out, "fates_phen_evergreen", [1, 1], [1, 2])
+ds_out = replace_values(ds_out, "fates_phen_stress_decid", [0, 0], [1, 2])
+ds_out = replace_values(ds_out, "fates_leaf_stomatal_intercept", 10000, 2)
+ds_out = replace_values(ds_out, "fates_leaf_stomatal_slope_ballberry", 4, 2)
+ds_out = replace_values(ds_out, "fates_leaf_stomatal_slope_medlyn", [4.1, 4.1, 4.1])
+ds_out = replace_values(ds_out, "fates_mort_bmort", [0.01303514, 0.01303514, 0.01303514])
+ds_out = replace_values(ds_out, "fates_stoich_phos", [0.0033, 24], [1, 5])
+ds_out = replace_values(ds_out, "fates_allom_d2h3", [21.6, 21.6], [0, 1])
+ds_out = replace_values(ds_out, "fates_allom_d2bl3", [np.nan, np.nan, 0])
+ds_out = replace_values(ds_out, "fates_cnp_turnover_nitr_retrans", np.nan, "all")
+ds_out = replace_values(ds_out, "fates_cnp_turnover_phos_retrans", np.nan, "all")
+ds_out = replace_values(ds_out, "fates_rad_leaf_xl", 0.1, 1)
+ds_out = replace_values(ds_out, "fates_rad_leaf_rhonir", [0.46, 0.46, 0.28])
+ds_out = replace_values(ds_out, "fates_rad_leaf_rhovis", [0.11, 0.11, 0.05])
+ds_out = replace_values(ds_out, "fates_rad_stem_rhonir", [0.49, 0.49, 0.39])
+ds_out = replace_values(ds_out, "fates_rad_stem_rhovis", [0.21, 0.21, 0.16])
+ds_out = replace_values(ds_out, "fates_rad_leaf_taunir", [0.33, 0.33, 0.4])
+ds_out = replace_values(ds_out, "fates_rad_leaf_tauvis", [0.06, 0.06], [0, 1])
+ds_out = replace_values(ds_out, "fates_rad_stem_taunir", 0.001, 2)
+ds_out = replace_values(ds_out, "fates_rad_stem_tauvis", 0.001, 2)
+ds_out = replace_values(ds_out, "fates_recruit_seed_dbh_repro_threshold", [150, 0.5], [1, 2])
+ds_out = replace_values(ds_out, "fates_phen_flush_fraction", np.nan, "all")
+
+ds_out.to_netcdf(file_out)
diff --git a/src/fates b/src/fates
diff --git a/src/main/clm_varctl.F90 b/src/main/clm_varctl.F90
@@ -333,6 +333,7 @@ module clm_varctl
                                                                         ! see bld/namelist_files/namelist_definition_clm4_5.xml for details
   logical, public            :: use_fates_managed_fire = .false.        ! true => turn on managed fire
   logical, public            :: use_fates_tree_damage = .false.         ! true => turn on tree damage module
+  logical, public            :: use_fates_edge_forest = .false.         ! true => turn on edge forest module
   character(len=256), public :: fates_harvest_mode = ''                 ! five different harvest modes; see namelist definition
   character(len=256), public :: fates_stomatal_model = ''               ! stomatal conductance model, Ball-berry or Medlyn
   character(len=256), public :: fates_stomatal_assimilation = ''        ! net or gross assimilation modes
+10 −0		biogeochem/EDCanopyStructureMod.F90
+14 −0		biogeochem/FatesPatchMod.F90
+1 −1		fire/SFMainMod.F90
+8 −1		main/CMakeLists.txt
+1 −0		main/EDInitMod.F90
+11 −1		main/EDParamsMod.F90
+0 −34		main/EDTypesMod.F90
+81 −0		main/FatesEcotypesMod.F90
+653 −0		main/FatesEdgeForestMod.F90
+224 −0		main/FatesEdgeForestParamsMod.F90
+211 −30		main/FatesHistoryInterfaceMod.F90
+7 −0		main/FatesHistoryVariableType.F90
+6 −0		main/FatesIODimensionsMod.F90
+1 −0		main/FatesIOVariableKindMod.F90
+36 −7		main/FatesInterfaceMod.F90
+5 −0		main/FatesInterfaceTypesMod.F90
+1 −0		main/FatesParametersInterface.F90
+22 −0		main/FatesUtilsMod.F90
+1 −0		main/test/CMakeLists.txt
+56 −0		parameter_files/fates_params_default.cdl
+3 −0		testing/CMakeLists.txt
+24 −0		testing/functional_testing/edge_forest/CMakeLists.txt
+253 −0		testing/functional_testing/edge_forest/FatesTestEdgeForest.F90
+173 −0		testing/functional_testing/edge_forest/edge_forest_test.py
+1 −1		testing/functional_testing/fire/mortality/fire_mortality_test.py
+7 −0		testing/functional_tests.cfg
+1 −0		testing/load_functional_tests.py
+2 −59		testing/run_functional_tests.py
+38 −3		testing/run_unit_tests.py
+4 −0		testing/testing_shr/FatesFactoryMod.F90
+3 −0		testing/testing_shr/FatesUnitTestParamReaderMod.F90
+96 −38		testing/testing_shr/SyntheticPatchTypes.F90
+5 −0		testing/unit_testing/ecotypes_test/CMakeLists.txt
+172 −0		testing/unit_testing/ecotypes_test/test_Ecotypes.pf
+5 −0		testing/unit_testing/edge_forest_test/CMakeLists.txt
+637 −0		testing/unit_testing/edge_forest_test/test_EdgeForest.pf
+16 −1		testing/unit_tests.cfg
+73 −0		testing/utils.py
+9 −0		testing/utils_plotting.py