Merge remote-tracking branch 'thorntonpe/thorntonpe/lnd/IM4' (PR E3SM…

…-Project#6433)

Introduce a new optional format for PFT physiology files (paramfile) that
allows user to specify a flexible number of PFTs, including additional
natural vegetation types and different numbers of crops. Backwards compatible
(BFB) with older style files.

New variables added in new format file:

climatezone (options are: 0 {nonspecific}, 1 {tropical}, 2 {temperate}, 3 {boreal}, 4 {arctic})
needleleaf (options are: 0, 1)
nfixer (options are: 0, 1)
nonvascular (options are: 0 {vascular}, 1 {moss}, 2 {lichen})
graminoid (options are: 0 {non-grass}, 1 {grass})
iscft (options are: 0 {natural PFT}, 1 {prognostic crop functional type})
Variables with expanded options in new format file:

woody (options are: 0{non-woody}, 1 {tree}, 2 {shrub})
Add 2 new tests for the user pft.
ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_default_I1850CNPRDCTCBC
ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_codetest_I1850CNPRDCTCBC

Thanks-to: Fengming Yuan (yuanf@ornl.gov), Ben Sulman (sulmanbn@ornl.gov)
[BFB]

cime_config/tests.py

@@ -76,7 +76,6 @@
             )
         },
 
-
     "e3sm_land_developer" : {
         "share" : True,
         "time"  : "0:45:00",
@@ -95,6 +94,8 @@
             "SMS.r05_r05.IELM.elm-topounit",
             "ERS.ELM_USRDAT.I1850ELM.elm-usrdat",
             "ERS.r05_r05.IELM.elm-lnd_rof_2way",
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_default_I1850CNPRDCTCBC",
+            "ERS.ELM_USRDAT.I1850CNPRDCTCBC.elm-usrpft_codetest_I1850CNPRDCTCBC",
             "ERS.r05_r05.IELM.elm-V2_ELM_MOSART_features",
             "ERS.ELM_USRDAT.IELM.elm-surface_water_dynamics"
             )

components/elm/bld/ELMBuildNamelist.pm

@@ -1552,13 +1552,19 @@ sub setup_cmdl_maxpft {
   $nl_flags->{'maxpft'} = $val;
 
   if ( ($nl_flags->{'bgc_mode'} ne "sp") && ($nl_flags->{'maxpft'} != $maxpatchpft{$nl_flags->{'use_crop'}}) ) {
-    fatal_error("** For CN or BGC mode you MUST set max patch PFT's to $maxpatchpft{$nl_flags->{'use_crop'}}\n" .
-    "**\n" .
-    "** When the crop model is on then it must be set to $maxpatchpft{'crop'} otherwise to $maxpatchpft{'nocrop'}\n" .
-    "** Set the bgc mode, crop and maxpft by the following means from highest to lowest precedence:\n" .
-    "** * by the command-line options -bgc, -crop and -maxpft\n" .
-    "** * by a default configuration file, specified by -defaults\n" .
-    "**\n");
+    if ($opts->{$var} eq "default") {
+      fatal_error("** For CN or BGC mode you MUST set max patch PFT $val to $maxpatchpft{$nl_flags->{'use_crop'}}\n" .
+      "**\n" .
+      "** When the crop model is on then it must be set to $maxpatchpft{'crop'} otherwise to $maxpatchpft{'nocrop'}\n" .
+      "** Set the bgc mode, crop and maxpft by the following means from highest to lowest precedence:\n" .
+      "** * by the command-line options -bgc, -crop and -maxpft\n" .
+      "** * by a default configuration file, specified by -defaults\n" .
+      "**\n");
+    } else {
+         message("running with maxpft NOT equal to $maxpatchpft{$nl_flags->{'use_crop'}} is " .
+              "NOT validated / scientifically supported.\n");
+
+      }
   }
   if ( $nl_flags->{'maxpft'} > $maxpatchpft{$nl_flags->{'use_crop'}} ) {
     fatal_error("** Max patch PFT's can NOT exceed $maxpatchpft{$nl_flags->{'use_crop'}}\n" .

components/elm/cime_config/testdefs/testmods_dirs/elm/usrpft_arctic_I1850CNPRDCTCBC/shell_commands

@@ -0,0 +1,11 @@
+./xmlchange LND_DOMAIN_FILE=domain.lnd.6x1pt_kougarok-NGEE_TransA_navy.nc
+./xmlchange ATM_DOMAIN_FILE=domain.lnd.6x1pt_kougarok-NGEE_TransA_navy.nc
+./xmlchange LND_DOMAIN_PATH="$DIN_LOC_ROOT/share/domains/domain.clm"
+./xmlchange ATM_DOMAIN_PATH="$DIN_LOC_ROOT/share/domains/domain.clm"
+./xmlchange ELM_USRDAT_NAME=6x1pt_kougarok-NGEE_TransA
+./xmlchange ELM_BLDNML_OPTS=" -maxpft 12 -bgc bgc -nutrient cnp -nutrient_comp_pathway rd  -soil_decomp ctc -methane "
+./xmlchange DATM_MODE=CLMGSWP3v1
+./xmlchange DATM_CLMNCEP_YR_START=1901
+./xmlchange DATM_CLMNCEP_YR_END=1920
+./xmlchange NTASKS=1
+./xmlchange NTHRDS=1

components/elm/cime_config/testdefs/testmods_dirs/elm/usrpft_arctic_I1850CNPRDCTCBC/user_nl_elm

@@ -0,0 +1,7 @@
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_6x1pt_kougarok-NGEE_TransA_simyr1850_c20201008-sub12.nc'
+! below is user-pft file example, developed by B. Sulman et al. (2021)
+! 12(+2) arctic PFTs: not_vegetated, arctic_lichen, arctic_bryophyte, (arctic_needleleaf_tree, arctic_broadleaf_tree,)
+!                 arctic_evergreen_shrub_dwarf, arctic_evergreen_shrub_tall,
+!                 arctic_deciduous_shrub_dwarf, arctic_deciduous_shrub_low, arctic_deciduous_shrub_tall, arctic_decidous_shrub_alder,
+!                 arctic_forb, arctic_dry_graminoid, arctic_wet_graminoid
+ paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm_params_c180524-sub12_updated20240201.nc'

components/elm/cime_config/testdefs/testmods_dirs/elm/usrpft_codetest_I1850CNPRDCTCBC/shell_commands

@@ -0,0 +1,10 @@
+./xmlchange LND_DOMAIN_FILE=domain_42_FLUXNETSITES_simyr1850_c170912.nc
+./xmlchange ATM_DOMAIN_FILE=domain_42_FLUXNETSITES_simyr1850_c170912.nc
+./xmlchange LND_DOMAIN_PATH="\$DIN_LOC_ROOT/share/domains/domain.clm"
+./xmlchange ATM_DOMAIN_PATH="\$DIN_LOC_ROOT/share/domains/domain.clm"
+./xmlchange DATM_MODE=CLM1PT
+./xmlchange DATM_CLMNCEP_YR_START=2000
+./xmlchange DATM_CLMNCEP_YR_END=2000
+./xmlchange ELM_USRDAT_NAME=42_FLUXNETSITES
+./xmlchange NTASKS=1
+./xmlchange NTHRDS=1

components/elm/cime_config/testdefs/testmods_dirs/elm/usrpft_codetest_I1850CNPRDCTCBC/user_nl_elm

@@ -0,0 +1,10 @@
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_42_FLUXNETSITES_simyr1850_c170912.nc'
+! paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm_params_c211124.nc'
+!
+! When 'user-pft' codes ready, comment out the above line while let the following in.
+!
+! below is user-pft file example, by editing default one as following
+! woody=1 for tree, or =2 for shrub, and defined other pft flags:
+! climatezone(0-4), nonvascular(0/1), graminoid(0/1), generic_crop(0/1), nfixer(0/1), needleleaf(0/1)
+! for not going by default, changing one PFT name by appending '_unexpected'.
+ paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm_params_c211124vpft.nc'

components/elm/cime_config/testdefs/testmods_dirs/elm/usrpft_default_I1850CNPRDCTCBC/shell_commands

@@ -0,0 +1,11 @@
+./xmlchange LND_DOMAIN_FILE=domain_42_FLUXNETSITES_simyr1850_c170912.nc
+./xmlchange ATM_DOMAIN_FILE=domain_42_FLUXNETSITES_simyr1850_c170912.nc
+./xmlchange LND_DOMAIN_PATH="\$DIN_LOC_ROOT/share/domains/domain.clm"
+./xmlchange ATM_DOMAIN_PATH="\$DIN_LOC_ROOT/share/domains/domain.clm"
+./xmlchange DATM_MODE=CLM1PT
+./xmlchange DATM_CLMNCEP_YR_START=2000
+./xmlchange DATM_CLMNCEP_YR_END=2000
+./xmlchange ELM_USRDAT_NAME=42_FLUXNETSITES
+./xmlchange NTASKS=1
+./xmlchange NTHRDS=1
+

components/elm/cime_config/testdefs/testmods_dirs/elm/usrpft_default_I1850CNPRDCTCBC/user_nl_elm

@@ -0,0 +1,2 @@
+fsurdat = '$DIN_LOC_ROOT/lnd/clm2/surfdata_map/surfdata_42_FLUXNETSITES_simyr1850_c170912.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/clm_params_c211124.nc'