Merge branch 'new_rawpftlai' of github.com:slevis-lmwg/CTSM into new_…

…rawpftlai

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -551,7 +551,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm6_0" >/glade/work/samrabin/ctsm_fire-li2024-pr2_paramfiles/ctsm60_params.c240822.li2024crujra.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c240822.nc</paramfile>
 <paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c240814.nc</paramfile>
 <paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c240814.nc</paramfile>
 <paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c240814.nc</paramfile>
@@ -1382,13 +1382,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm5_1_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 <finidat hgrid="0.9x1.25" mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" sim_year="1850" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false."
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!--
@@ -1430,7 +1430,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_GSWP3v1" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 
@@ -1515,7 +1515,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- clm6_0 and cam7.0 -->
@@ -1524,7 +1524,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- clm5_0 and cam7.0 -->
@@ -1589,7 +1589,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1653,7 +1653,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam7.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1728,15 +1728,15 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- NB: This pSASU finidat is from an 1850 spin-up -->
 <finidat hgrid="0.9x1.25"    maxpft="79"  mask="gx1v7" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1801,7 +1801,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm5_1_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1866,7 +1866,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
          ic_ymd="20000101" sim_year="2000" do_transient_pfts=".false."
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
          lnd_tuning_mode="clm6_0_cam6.0" use_init_interp=".true."
->lnd/clm2/initdata_esmf/ctsm5.3/ctsm52018_f09_xsiceON_acON_pSASU.clm2.r.0201-01-01-00000.nc
+>lnd/clm2/initdata_esmf/ctsm5.3/ctsm52026_f09_pSASU.clm2.r.0421-01-01-00000.nc
 </finidat>
 
 <!-- 2003 -->
@@ -1902,10 +1902,6 @@ lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_4x5_hist_2000_16pfts_c240216.nc</fsurd
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa60_hist_2000_16pfts_c240216.nc</fsurdat>
 <fsurdat hgrid="mpasa15"   sim_year="2000" use_crop=".false.">
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa15_hist_2000_16pfts_c240216.nc</fsurdat>
-<!--
-<fsurdat hgrid="mpasa15-3" sim_year="2000" use_crop=".false.">
-lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa15-3_hist_2000_16pfts_c240216.nc</fsurdat>
--->
 <fsurdat hgrid="mpasa3p75" sim_year="2000" use_crop=".false.">
 lnd/clm2/surfdata_esmf/ctsm5.2.0/surfdata_mpasa3p75_hist_2000_16pfts_c240216.nc</fsurdat>
 

bld/namelist_files/namelist_defaults_fire_emis.xml

@@ -17,6 +17,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <fire_emis_specifier>'bc_a1 = BC','pom_a1 = 1.4*OC','SO2 = SO2'</fire_emis_specifier>
 
-<fire_emis_factors_file>lnd/clm2/firedata/fire_emis_factors_c140116.nc</fire_emis_factors_file>
+<fire_emis_factors_file>lnd/clm2/firedata/fire_emission_factors_78PFTs_c20240624.nc</fire_emis_factors_file>
 
 </namelist_defaults>

cime_config/testdefs/testlist_clm.xml

@@ -914,22 +914,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_D_Ld5" grid="f09_g17" compset="I2000Clm50Vic" testmods="clm/vrtlay">
-    <machines>
-      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
-  <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Vic" testmods="clm/vrtlay">
-    <machines>
-      <machine name="derecho" compiler="intel" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld5" grid="f10_f10_mg37" compset="IHistClm50SpCru" testmods="clm/drydepnomegan">
     <machines>
       <machine name="derecho" compiler="gnu" category="aux_clm"/>
@@ -1263,22 +1247,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="ERP_Ld5" grid="f09_g17" compset="I2000Clm50Vic" testmods="clm/vrtlay">
-    <machines>
-      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
-  <test name="ERP_Ld5" grid="f10_f10_mg37" compset="I2000Clm50Vic" testmods="clm/decStart">
-    <machines>
-      <machine name="derecho" compiler="gnu" category="aux_clm"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-    </options>
-  </test>
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I1850Clm50Bgc" testmods="clm/ciso">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>
@@ -2417,15 +2385,6 @@
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_Ld1" grid="f19_g17" compset="I2000Clm50Vic" testmods="clm/default">
-    <machines>
-      <machine name="derecho" compiler="intel" category="ctsm_sci"/>
-    </machines>
-    <options>
-      <option name="wallclock">00:20:00</option>
-      <option name="comment"  >include a production gnu test of VIC for clm5_0</option>
-    </options>
-  </test>
   <test name="SMS_D_Ld1_Mmpi-serial" grid="f45_f45_mg37" compset="I2000Clm50SpRs" testmods="clm/ptsROA">
     <machines>
       <machine name="izumi" compiler="gnu" category="aux_clm"/>

cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm

@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240814.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c240822.nc'

python/ctsm/subset_data.py

@@ -597,18 +597,13 @@ def setup_files(args, defaults, cesmroot):
             clmforcingindir,
             os.path.join(defaults.get("surfdat", "dir")),
         ),
-        "mesh_dir": os.path.join(
-            clmforcingindir,
-            os.path.join(defaults.get("surfdat", "mesh_dir")),
-        ),
         "fluse_dir": os.path.join(
             clmforcingindir,
             os.path.join(defaults.get("landuse", "dir")),
         ),
         "fsurf_in": fsurf_in,
         "fsurf_out": fsurf_out,
         "fluse_in": fluse_in,
-        "mesh_surf": defaults.get("surfdat", "mesh_surf"),
         "datm_tuple": DatmFiles(
             dir_input_datm,
             dir_output_datm,
@@ -736,9 +731,6 @@ def subset_region(args, file_dict: dict):
             specify_fsurf_out=file_dict["fsurf_out"],
         )
 
-    # if region.create_mesh:
-    #    region.create_mesh_at_reg (file_dict["mesh_dir"], file_dict["mesh_surf"])
-
     # --  Create CTSM transient landuse data file
     if region.create_landuse:
         region.create_landuse_at_reg(

python/ctsm/test/test_sys_gen_mksurfdata_namelist.py

@@ -62,7 +62,7 @@ def test_simple_namelist(self):
         main()
         self.assertTrue(os.path.exists(self.outfile), "Output surface dataset file should exist")
 
-    def test_vic_nocrop_inlandwet_glc_namelist(self):
+    def test_nocrop_inlandwet_glc_namelist(self):
         """
         Test a namelist with several options on
         """
@@ -75,7 +75,6 @@ def test_vic_nocrop_inlandwet_glc_namelist(self):
                 "1850",
                 "--res",
                 "1.9x2.5",
-                "--vic",
                 "--nocrop",
                 "--inlandwet",
                 "--glc",
@@ -99,7 +98,6 @@ def test_hires_namelist(self):
                 "mpasa15",
                 "--glc-nec",
                 "10",
-                "--hires_pft",
                 "--hires_soitex",
             ]
         )

python/ctsm/toolchain/gen_mksurfdata_jobscript_multi.py

@@ -42,6 +42,7 @@
     "crop-global-hist-low-res",
     "crop-global-hist-ne16",
     "crop-global-hist-ne30",
+    "crop-global-hist-f09",
     "crop-global-SSP1-1.9-f09",
     "crop-global-SSP1-2.6-f09",
     "crop-global-SSP2-4.5-f09",
@@ -198,6 +199,7 @@ def main():
         "low_res_no_crop": ["4x5", "10x15"],
         "ultra_hi_res_no_crop": ["mpasa15", "mpasa3p75"],
         "standard_res": ["360x720cru", "0.9x1.25", "1.9x2.5", "C96", "mpasa120"],
+        "standard_res_no_f09": ["360x720cru", "1.9x2.5", "C96", "mpasa120"],
         "low_res": ["4x5", "10x15", "ne3np4.pg3"],
         "mpasa480": ["mpasa480"],
         "nldas_res": ["0.125nldas2"],
@@ -209,11 +211,13 @@ def main():
             "ne0np4.ARCTICGRIS.ne30x8",
             "ne0np4.ARCTIC.ne30x4",
             "ne0np4CONUS.ne30x8",
+            "ne0np4.POLARCAP.ne30x4",
         ],
         "ne120": [
             "ne0np4.ARCTICGRIS.ne30x8",
             "ne0np4.ARCTIC.ne30x4",
             "ne0np4CONUS.ne30x8",
+            "ne0np4.POLARCAP.ne30x4",
             "ne120np4.pg3",
         ],
     }
@@ -243,11 +247,11 @@ def main():
             "5x5_amazon",
         ),
         "crop-global-present": (
-            "--start-year 2000 --end-year 2000 --vic                           --res",
+            "--start-year 2000 --end-year 2000                                 --res",
             "standard_res",
         ),
         "crop-global-present-low-res": (
-            "--start-year 2000 --end-year 2000 --vic                           --res",
+            "--start-year 2000 --end-year 2000                                 --res",
             "low_res",
         ),
         "crop-global-present-ne16": (
@@ -267,7 +271,6 @@ def main():
             "mpasa480",
         ),
         "crop-global-present-nldas": (
-            # TODO slevis: --hirespft uses old data for now, so keep out
             "--start-year 2000 --end-year 2000                                 --res",
             "nldas_res",
         ),
@@ -296,21 +299,25 @@ def main():
             "mpasa480",
         ),
         "crop-global-hist": (
-            "--start-year 1850 --end-year 2015 --nosurfdata                    --res",
-            "standard_res",
+            "--start-year 1850 --end-year 2023 --nosurfdata                    --res",
+            "standard_res_no_f09",
         ),
         "crop-global-hist-low-res": (
-            "--start-year 1850 --end-year 2015 --nosurfdata                    --res",
+            "--start-year 1850 --end-year 2023 --nosurfdata                    --res",
             "low_res",
         ),
         "crop-global-hist-ne16": (
-            "--start-year 1850 --end-year 2015 --nosurfdata                    --res",
+            "--start-year 1850 --end-year 2023 --nosurfdata                    --res",
             "ne16",
         ),
         "crop-global-hist-ne30": (
-            "--start-year 1850 --end-year 2015 --nosurfdata                    --res",
+            "--start-year 1850 --end-year 2023 --nosurfdata                    --res",
             "ne30",
         ),
+        "crop-global-hist-f09": (
+            "--start-year 1700 --end-year 2023                                 --res",
+            "f09",
+        ),
         "crop-global-SSP1-1.9-f09": (
             "--start-year 1850 --end-year 2100 --nosurfdata --ssp-rcp SSP1-1.9 --res",
             "f09",