merge to cam6_3_139; move 1 test to prealpha

Externals.cfg

@@ -1,5 +1,5 @@
 [ccs_config]
-tag = ccs_config_cesm0.0.80
+tag = ccs_config_cesm0.0.82
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm
 local_path = ccs_config
@@ -28,7 +28,7 @@ local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.21
+tag = cdeps1.0.24
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps
@@ -64,7 +64,7 @@ local_path = libraries/parallelio
 required = True
 
 [cime]
-tag = cime6.0.156
+tag = cime6.0.175
 protocol = git
 repo_url = https://github.com/ESMCI/cime
 local_path = cime
@@ -79,7 +79,7 @@ externals = Externals_CISM.cfg
 required = True
 
 [clm]
-tag = ctsm5.1.dev139
+tag = ctsm5.1.dev142
 protocol = git
 repo_url = https://github.com/ESCOMP/CTSM
 local_path = components/clm

Externals_CAM.cfg

@@ -68,7 +68,7 @@ local_path = src/dynamics/mpas/dycore
 protocol = git
 repo_url = https://github.com/MPAS-Dev/MPAS-Model.git
 sparse = ../.mpas_sparse_checkout
-hash = ff76a231
+hash = b8c33daa
 required = True
 
 [hemco]

bld/build-namelist

@@ -2422,6 +2422,11 @@ if (($chem =~ /_mam4/ or $chem =~ /_mam5/) and ($phys =~ /cam6/ or $phys =~ /cam
                     'num_a4_ar_ext_file' => 'num_a4',
                     'no2_ar_ext_file'    => 'NO2',
                     'so2_ar_ext_file'    => 'SO2' );
+    } elsif ($chem =~ /ghg_mam/) {
+        %species = (%species,
+                    'bc_a4_ar_ext_file'  => 'bc_a4',
+                    'num_a4_ar_ext_file' => 'num_a4',
+                    'so2_ar_ext_file'    => 'SO2' );
     }
 
     # for transient cases include volcanic emissions
@@ -4091,6 +4096,7 @@ if ($dyn =~ /mpas/) {
     add_default($nl, 'mpas_zd');
     add_default($nl, 'mpas_xnutr');
     add_default($nl, 'mpas_cam_coef');
+    add_default($nl, 'mpas_cam_damping_levels');
     add_default($nl, 'mpas_print_detailed_minmax_vel');
     add_default($nl, 'mpas_rayleigh_damp_u');
     add_default($nl, 'mpas_rayleigh_damp_u_timescale_days');

bld/namelist_files/namelist_defaults_cam.xml

@@ -274,6 +274,8 @@
 
 <ncdata dyn="se" hgrid="ne0np4CONUS.ne30x8"       nlev="70" ic_ymd="101">atm/waccm/ic/FW2000_CONUS_30x8_L70_01-01-0001_c200602.nc</ncdata>
 
+<ncdata hgrid="mpasa120" nlev="70" waccm_phys="1">atm/waccm/ic/mpasa120km.waccm_fulltopo_c220818.nc</ncdata>
+
 <ncdata hgrid="mpasa120" nlev="32" >atm/cam/inic/mpas/cami_01-01-2000_00Z_mpasa120_L32_CFSR_c210426.nc</ncdata>
 <ncdata hgrid="mpasa480" nlev="32" >atm/cam/inic/mpas/cami_01-01-2000_00Z_mpasa480_L32_CFSR_c211013.nc</ncdata>
 
@@ -1395,6 +1397,11 @@
 <so4_a1_an_ext_file   hgrid="ne30np4" npg="3" ver="cam6">atm/cam/chem/emis/historical_ne30pg3/emissions-cmip6_so4_a1_anthro-ene_vertical_mol_175001-201412_ne30pg3_c20200103.nc</so4_a1_an_ext_file>
 <num_a1_an_ext_file   hgrid="ne30np4" npg="3" ver="cam6">atm/cam/chem/emis/historical_ne30pg3/emissions-cmip6_num_so4_a1_anthro-ene_vertical_mol_175001-201412_ne30pg3_c20200103.nc</num_a1_an_ext_file>
 
+<bc_a4_ar_ext_file    hgrid="ne30np4" npg="3" ver="cam6">atm/cam/chem/emis/historical_ne30pg3/emissions-cmip6_bc_a4_aircraft_vertical_1750-2015_ne30pg3_c20231112.nc</bc_a4_ar_ext_file>
+<num_a4_ar_ext_file   hgrid="ne30np4" npg="3" ver="cam6">atm/cam/chem/emis/historical_ne30pg3/emissions-cmip6_num_bc_a4_aircraft_vertical_1750-2015_ne30pg3_c20231112.nc</num_a4_ar_ext_file>
+<no2_ar_ext_file      hgrid="ne30np4" npg="3" ver="cam6">atm/cam/chem/emis/historical_ne30pg3/emissions-cmip6_NO2_aircraft_vertical_1750-2015_ne30pg3_c20231112.nc</no2_ar_ext_file>
+<so2_ar_ext_file      hgrid="ne30np4" npg="3" ver="cam6">atm/cam/chem/emis/historical_ne30pg3/emissions-cmip6_SO2_aircraft_vertical_1750-2015_ne30pg3_c20231112.nc</so2_ar_ext_file>
+
 <!-- ne30 pg2 -->
 
 <dms_ot_srf_file     hgrid="ne30np4" npg="2" ver="cam6">atm/cam/chem/emis/historical_ne30pg2/emissions-cmip6_DMS_other_surface_1750_2015_ne30pg2_c20200630.nc</dms_ot_srf_file>
@@ -3220,12 +3227,14 @@
 <mpas_time_integration_order  > 2 </mpas_time_integration_order>
 <mpas_dt                      > 1800.0D0 </mpas_dt>
 <mpas_dt hgrid="mpasa120"     >  900.0D0 </mpas_dt>
+<mpas_dt hgrid="mpasa120" waccm_phys="1"> 600.D0 </mpas_dt>
 <mpas_dt hgrid="mpasa60"      >  450.0D0 </mpas_dt>
 <mpas_dt hgrid="mpasa30"      >  225.0D0 </mpas_dt>
 
 <mpas_split_dynamics_transport>.true.</mpas_split_dynamics_transport>
 <mpas_number_of_sub_steps     > 2 </mpas_number_of_sub_steps>
 <mpas_dynamics_split_steps    > 3 </mpas_dynamics_split_steps>
+<mpas_dynamics_split_steps hgrid="mpasa120" waccm_phys="1"> 4 </mpas_dynamics_split_steps>
 <mpas_h_mom_eddy_visc2        > 0.0D0 </mpas_h_mom_eddy_visc2>
 <mpas_h_mom_eddy_visc4        > 0.0D0 </mpas_h_mom_eddy_visc4>
 <mpas_v_mom_eddy_visc2        > 0.0D0 </mpas_v_mom_eddy_visc2>
@@ -3255,12 +3264,17 @@
 <mpas_smagorinsky_coef        > 0.125D0 </mpas_smagorinsky_coef>
 <mpas_mix_full                > .true. </mpas_mix_full>
 <mpas_epssm                   > 0.1D0 </mpas_epssm>
+<mpas_epssm hgrid="mpasa120" waccm_phys="1"> 0.5D0 </mpas_epssm>
 <mpas_smdiv                   > 0.1D0 </mpas_smdiv>
 <mpas_apvm_upwinding          > 0.5D0 </mpas_apvm_upwinding>
+<mpas_apvm_upwinding hgrid="mpasa120" waccm_phys="1"> 0.0D0 </mpas_apvm_upwinding>
 <mpas_h_ScaleWithMesh         > .true. </mpas_h_ScaleWithMesh>
 <mpas_zd                      > 22000.0D0 </mpas_zd>
+<mpas_zd hgrid="mpasa120" waccm_phys="1"> 80000.0D0 </mpas_zd>
 <mpas_xnutr                   > 0.2D0 </mpas_xnutr>
 <mpas_cam_coef                > 0.0D0 </mpas_cam_coef>
+<mpas_cam_coef hgrid="mpasa120" waccm_phys="1"> 0.2D0 </mpas_cam_coef>
+<mpas_cam_damping_levels      > 0     </mpas_cam_damping_levels>
 <mpas_rayleigh_damp_u         > .true. </mpas_rayleigh_damp_u>
 <mpas_rayleigh_damp_u_timescale_days> 5.0 </mpas_rayleigh_damp_u_timescale_days>
 <mpas_number_rayleigh_damp_u_levels> 5 </mpas_number_rayleigh_damp_u_levels>

bld/namelist_files/namelist_definition.xml

@@ -8430,15 +8430,26 @@ Default: 0.2
 
 <entry id="mpas_cam_coef" type="real" category="mpas"
        group="damping" valid_values="">
-Coefficient for scaling the 2nd-order horizontal diffusion in the mpas_cam absorbing layer.
-A value of 1.0 will result in layered diffusion similar to CAM-SE and gives damping
-coefficients of 0.2216E7, 0.6482E6, 0.1927E6 in the top-most three layers on the dynamics
-variables u, w, and theta. The top 3 damping coefficients scale linearly with
-mpas_cam_coef. 0.0 disables SE like 2nd-order diffusion in the absorbing layer and is the
-current default. Sponge layer absorption can also be provided by Rayleigh damping.
+Coefficient for scaling the 2nd-order horizontal diffusion in the mpas_cam absorbing
+layer. The absorbing layer depth is controlled with mpas_cam_damping_levels. The damping
+coefficients scale linearly with mpas_cam_coef. A value of 0.0 (or
+mpas_cam_damping_levels=0) disables the 2nd-order diffusion in the absorbing layer. Sponge
+layer absorption can also be provided by Rayleigh damping.
+
+E.g. a value of 1.0 with mpas_cam_damping_levels=3 will result in damping coefficients of
+2E6 m^2/s, 6E5, 2E5 in the top-most three layers on the dynamics variables u, w, and
+theta.
 Default: 0.0
 </entry>
 
+<entry id="mpas_cam_damping_levels" type="integer" category="mpas"
+       group="damping" valid_values="">
+Number mpas_cam absorbing layers in which to apply 2nd-order horizontal diffusion.
+Viscocity linearly ramps to zero by layer number from the top. mpas_cam_damping_levels and
+mpas_cam_coef must both be greater than 0 for the diffusion to be enabled.
+Default: 0
+</entry>
+
 <entry id="mpas_rayleigh_damp_u" type="logical" category="mpas"
        group="damping" valid_values="">
 Whether to apply Rayleigh damping on horizontal velocity in the top-most model levels.

bld/namelist_files/use_cases/sd_waccm_tsmlt_cam6.xml

@@ -84,7 +84,7 @@
    'DCOCHM', 'DF_ALKNIT', 'DF_ALKOOH', 'DF_BENZOOH', 'DF_BZOOH', 'DF_C2H5OH', 'DF_C2H5OOH', 'DF_C3H7OOH', 'DF_C6H5OOH', 'DF_CH2O',
    'DF_CH3CHO', 'DF_CH3CN', 'DF_CH3COCH3', 'DF_CH3COCHO', 'DF_CH3COOH', 'DF_CH3COOOH', 'DF_CH3OH', 'DF_CH3OOH', 'DF_CO', 'DF_EOOH',
    'DF_GLYALD', 'DF_H2O2', 'DF_H2SO4', 'DF_HCN', 'DF_HCOOH', 'DF_HNO3', 'DF_HO2NO2', 'DF_HONITR', 'DF_HPALD', 'DF_HYAC', 'DF_HYDRALD',
-   'DF_IEPOX', 'DF_ISOPNITA', 'DF_ISOPNITB', 'DF_ISOPNO3', 'DF_ISOPNOOH', 'DF_ISOPOOH', 'DF_IVOC', 'DF_MACROOH', 'DF_MEKOOH',
+   'DF_IEPOX', 'DF_ISOPNITA', 'DF_ISOPNITB', 'DF_ISOPNOOH', 'DF_ISOPOOH', 'DF_IVOC', 'DF_MACROOH', 'DF_MEKOOH',
    'DF_MPAN', 'DF_NC4CH2OH', 'DF_NC4CHO', 'DF_NH3', 'DF_NH4', 'DF_NO2', 'DF_NO', 'DF_NOA', 'DF_NTERPOOH', 'DF_O3',
    'DF_ONITR', 'DF_PAN', 'DF_PHENOOH', 'DF_POOH', 'DF_ROOH', 'DF_SO2', 'DF_SOAG0', 'DF_SOAG1', 'DF_SOAG2', 'DF_SOAG3',
    'DF_SOAG4', 'DF_SVOC', 'DF_TERP2OOH', 'DF_TERPNIT', 'DF_TERPOOH', 'DF_TERPROD1', 'DF_TERPROD2', 'DF_TOLOOH', 'DF_XOOH', 'DF_XYLENOOH',

bld/namelist_files/use_cases/waccm_ma_2000_cam6.xml

@@ -21,7 +21,6 @@
 <!--Species IC -->
 <ncdata dyn="fv"  hgrid="0.9x1.25">cesm2_init/f.e22.FWma2000climo.f09_f09_mg17.cam6_2_021.c20200421/0004-01-01/f.e22.FWma2000climo.f09_f09_mg17.cam6_2_021.c20200421.cam.i.0004-01-01-00000.nc</ncdata>
 <ncdata dyn="fv"  hgrid="1.9x2.5" >cesm2_init/f.e22.FWma2000climo.f19_f19_mg17.cam6_2_021.c20200421/0008-01-01/f.e22.FWma2000climo.f19_f19_mg17.cam6_2_021.c20200421.cam.i.0008-01-01-00000.nc</ncdata>
-<ncdata  hgrid="ne30np4"  npg="3" >cesm2_init/f.e22.FWma2000climo.ne30pg3_ne30pg3_mg17.cam6_2_021.c20200421/0004-01-01/f.e22.FWma2000climo.ne30pg3_ne30pg3_mg17.cam6_2_021.c20200421.cam.i.0004-01-01-00000.nc</ncdata>
 <ncdata dyn="fv"  hgrid="4x5"     >atm/waccm/ic/f2000.waccm-mam3_4x5_L70.cam2.i.0017-01-01.c121113.nc</ncdata>
 
 

cime_config/SystemTests/tmc.py

@@ -6,6 +6,7 @@
 from CIME.SystemTests.system_tests_common import SystemTestsCommon
 from CIME.test_status import *
 from CIME.utils import append_testlog
+from CIME.baselines.performance import get_latest_cpl_logs
 import glob, gzip
 
 
@@ -22,7 +23,7 @@ def run_phase(self):
         with self._test_status:
             self._test_status.set_status("COMPARE_MASS", TEST_PEND_STATUS)
         self.run_indv()
-        cpllog = ''.join(self._get_latest_cpl_logs())
+        cpllog = ''.join(get_latest_cpl_logs(self._case))
         atmlog  = cpllog.replace("cpl.log","atm.log")
         atmlog  = atmlog.replace("drv.log","atm.log")
         if '.gz' == atmlog[-3:]:
@@ -35,9 +36,9 @@ def run_phase(self):
         first_val = -9.0
         with self._test_status:
             self._test_status.set_status("COMPARE_MASS", TEST_PASS_STATUS)
-        use_this_tt_un = False 
+        use_this_tt_un = False
         for line in lines:
-            if re.search('vvvvv gmean_mass: before tphysbc DRY',line.decode('utf-8')): 
+            if re.search('vvvvv gmean_mass: before tphysbc DRY',line.decode('utf-8')):
                 use_this_tt_un = True
             if re.search('TT_UN ',line.decode('utf-8')) and use_this_tt_un:
                 tt_un_flt=re.findall("\d+\.\d+",line.decode('utf-8'))
@@ -49,7 +50,7 @@ def run_phase(self):
                             self._test_status.set_status("COMPARE_MASS", TEST_FAIL_STATUS, comments="Mass Not Conserved")
                         comments = "CAM mass conservation test FAILED."
                         append_testlog(comments, self._orig_caseroot)
-                use_this_tt_un = False 
+                use_this_tt_un = False
         if first_val == -9.0:
             with self._test_status:
                 self._test_status.set_status("COMPARE_MASS", TEST_FAIL_STATUS, comments="Failed to find TT_UN in atm.log")