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Merge pull request #2009 from glemieux/fates-drdt-decid-updates
FATES parameter file and test definition updates
2 parents bb2a8d2 + 601f8b3 commit 4a868c1

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‎Externals_CLM.cfg‎

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@@ -2,7 +2,7 @@
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local_path = src/fates
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protocol = git
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repo_url = https://github.com/NGEET/fates
5-
tag = sci.1.65.3_api.25.4.0
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tag = sci.1.66.1_api.25.5.0
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required = True
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[externals_description]

‎bld/namelist_files/namelist_defaults_ctsm.xml‎

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@@ -493,7 +493,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
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<!-- FATES default parameter file -->
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<!-- ================================================================== -->
495495

496-
<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.4.0_12pft_c230327.nc</fates_paramfile>
496+
<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230628.nc</fates_paramfile>
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<!-- ======================================================================================== -->
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<!-- clm 5.0 BGC nitrogen model -->

‎cime_config/testdefs/testlist_clm.xml‎

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@@ -1569,7 +1569,7 @@
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<option name="comment">Want to keep a little single-point testing on cheyenne</option>
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</options>
15711571
</test>
1572-
<test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/default--clm/NEON/NIWO">
1572+
<test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/default--clm/NEON/NIWO">
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<machines>
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<machine name="izumi" compiler="nag" category="aux_clm"/>
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</machines>
@@ -1579,7 +1579,7 @@
15791579
<option name="comment" >Add at least one test of a NEON site</option>
15801580
</options>
15811581
</test>
1582-
<test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51SpRs" testmods="clm/default--clm/NEON/TOOL">
1582+
<test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51SpRs" testmods="clm/default--clm/NEON/TOOL">
15831583
<machines>
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<machine name="izumi" compiler="nag" category="aux_clm"/>
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</machines>
@@ -1589,7 +1589,7 @@
15891589
<option name="comment" >Add at least one test of a NEON site with SP</option>
15901590
</options>
15911591
</test>
1592-
<test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/NEON/MOAB--clm/PRISM">
1592+
<test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Bgc" testmods="clm/NEON/MOAB--clm/PRISM">
15931593
<machines>
15941594
<machine name="izumi" compiler="nag" category="aux_clm"/>
15951595
</machines>
@@ -1599,7 +1599,7 @@
15991599
<option name="comment" >Add at least one test of a NEON site with PRISM precipitation</option>
16001600
</options>
16011601
</test>
1602-
<test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesFireLightningPopDens--clm/NEON/FATES/NIWO">
1602+
<test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesFireLightningPopDens--clm/NEON/FATES/NIWO">
16031603
<machines>
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<machine name="izumi" compiler="nag" category="aux_clm"/>
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<machine name="izumi" compiler="nag" category="fates"/>
@@ -1610,7 +1610,7 @@
16101610
<option name="comment" >Add at least one test of a FATES NEON site that needs lightning data</option>
16111611
</options>
16121612
</test>
1613-
<test name="SMS_L10d_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesPRISM--clm/NEON/FATES/YELL">
1613+
<test name="SMS_Ld10_D_Mmpi-serial" grid="CLM_USRDAT" compset="I1PtClm51Fates" testmods="clm/FatesPRISM--clm/NEON/FATES/YELL">
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<machines>
16151615
<machine name="izumi" compiler="nag" category="aux_clm"/>
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<machine name="izumi" compiler="nag" category="fates"/>

‎cime_config/testdefs/testmods_dirs/clm/Fates/user_nl_clm‎

Lines changed: 2 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,10 +5,8 @@ hist_empty_htapes = .true.
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hist_ndens = 1
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fates_spitfire_mode = 1
77
hist_fincl1 = 'FATES_NCOHORTS', 'FATES_TRIMMING', 'FATES_AREA_PLANTS',
8-
'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD',
9-
'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF',
10-
'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF',
11-
'FATES_DAYSINCE_DROUGHTLEAFON', 'FATES_MEANLIQVOL_DROUGHTPHEN',
8+
'FATES_AREA_TREES', 'FATES_COLD_STATUS', 'FATES_GDD',
9+
'FATES_NCHILLDAYS', 'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF','FATES_DAYSINCE_COLDLEAFON',
1210
'FATES_CANOPY_SPREAD', 'FATES_NESTEROV_INDEX', 'FATES_IGNITIONS', 'FATES_FDI',
1311
'FATES_ROS','FATES_EFFECT_WSPEED', 'FATES_FUELCONSUMED', 'FATES_FIRE_INTENSITY',
1412
'FATES_FIRE_INTENSITY_BURNFRAC', 'FATES_BURNFRAC', 'FATES_FUEL_MEF',

‎cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm‎

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@@ -71,4 +71,7 @@ hist_fincl1 = 'FATES_CROWNAREA_PF', 'FATES_CANOPYCROWNAREA_PF',
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'FATES_CROOTMAINTAR_USTORY_SZ', 'FATES_FROOTMAINTAR_USTORY_SZ',
7272
'FATES_GROWAR_USTORY_SZ', 'FATES_MAINTAR_USTORY_SZ', 'FATES_VEGC_SZPF',
7373
'FATES_LEAFC_SZPF', 'FATES_FROOTC_SZPF', 'FATES_SAPWOODC_SZPF',
74-
'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF'
74+
'FATES_STOREC_SZPF', 'FATES_REPROC_SZPF', 'FATES_DROUGHT_STATUS_PF',
75+
'FATES_DAYSINCE_DROUGHTLEAFOFF_PF', 'FATES_DAYSINCE_DROUGHTLEAFON_PF',
76+
'FATES_MEANLIQVOL_DROUGHTPHEN_PF', 'FATES_MEANSMP_DROUGHTPHEN_PF',
77+
'FATES_ELONG_FACTOR_PF'

‎cime_config/usermods_dirs/fates_sp/user_nl_clm‎

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@@ -8,9 +8,9 @@ use_fates_fixed_biogeog = .true.
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use_fates_nocomp = .true.
99
hist_ndens = 1
1010
! Turn off a list of fields that are not needed for FATES-SP mode
11-
hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_DROUGHT_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS',
12-
'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON', 'FATES_DAYSINCE_DROUGHTLEAFOFF',
13-
'FATES_DAYSINCE_DROUGHTLEAFON', 'FATES_MEANLIQVOL_DROUGHTPHEN', 'FATES_CANOPY_SPREAD', 'FATES_VEGC_PF',
11+
hist_fexcl1 = 'FATES_TRIMMING', 'FATES_COLD_STATUS', 'FATES_GDD', 'FATES_NCHILLDAYS',
12+
'FATES_NCOLDDAYS', 'FATES_DAYSINCE_COLDLEAFOFF', 'FATES_DAYSINCE_COLDLEAFON',
13+
'FATES_CANOPY_SPREAD', 'FATES_VEGC_PF',
1414
'FATES_STOREC_PF', 'FATES_RECRUITMENT_PF', 'FATES_MORTALITY_PF', 'FATES_PATCHAREA_AP', 'FATES_LAI_AP',
1515
'FATES_CANOPYAREA_AP', 'FATES_NESTEROV_INDEX', 'FATES_IGNITIONS', 'FATES_FDI', 'FATES_ROS', 'FATES_EFFECT_WSPEED',
1616
'FATES_FUELCONSUMED', 'FATES_FIRE_INTENSITY', 'FATES_FIRE_INTENSITY_BURNFRAC', 'FATES_BURNFRAC', 'FATES_FUEL_MEF',

‎doc/ChangeLog‎

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@@ -1,4 +1,97 @@
11
===============================================================
2+
Tag name: ctsm5.1.dev130
3+
Originator(s): glemieux (Greg Lemieux,LBL/NGEET,510-486-5049)
4+
Date: Sun Jul 9 23:24:29 MDT 2023
5+
One-line Summary: FATES parameter file and test definition update
6+
7+
Purpose and description of changes
8+
----------------------------------
9+
10+
This tag incorporates updates to the FATES parameter file and test
11+
definitions to be consistent with updates to the drought deciduous
12+
phenology model in FATES. This also updates the external FATES
13+
pointer to the tag associated with the drought deciduous phenology
14+
update.
15+
16+
Significant changes to scientifically-supported configurations
17+
--------------------------------------------------------------
18+
19+
Does this tag change answers significantly for any of the following physics configurations?
20+
(Details of any changes will be given in the "Answer changes" section below.)
21+
22+
[Put an [X] in the box for any configuration with significant answer changes.]
23+
24+
[ ] clm5_1
25+
26+
[ ] clm5_0
27+
28+
[ ] ctsm5_0-nwp
29+
30+
[ ] clm4_5
31+
32+
Bugs fixed or introduced
33+
------------------------
34+
35+
CTSM issues fixed (include CTSM Issue #):
36+
Fixes #2043 -- Five izumi NEON tests fail (for me) because the testnames include L10d instead of Ld10
37+
38+
Known bugs found since the previous tag (include issue #):
39+
#2049 -- Use of 0.01_r8 as a magic number
40+
#2042 -- Issue running SystemTests due to "conda activate" error
41+
#2039 -- Conditional for NEON usermods is too broad
42+
43+
Notes of particular relevance for users
44+
---------------------------------------
45+
Changes made to namelist defaults (e.g., changed parameter values):
46+
47+
FATES parameter file default updated to fates_params_api.25.5.0_12pft_c230628.nc
48+
49+
Testing summary:
50+
----------------
51+
52+
[PASS means all tests PASS; OK means tests PASS other than expected fails.]
53+
54+
regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
55+
56+
cheyenne ---- OK
57+
izumi ------- OK
58+
59+
fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
60+
cheyenne ---- OK
61+
izumi ------- OK
62+
63+
Answer changes
64+
--------------
65+
66+
Changes answers relative to baseline: YES for FATES tests only
67+
68+
Summarize any changes to answers, i.e.,
69+
- what code configurations: FATES
70+
- what platforms/compilers: ALL
71+
- nature of change (roundoff; larger than roundoff/same climate; new climate): larger than roundoff
72+
73+
If this tag changes climate describe the run(s) done to evaluate the new
74+
climate (put details of the simulations in the experiment database)
75+
76+
See FATES #958 for discussion. The update increased the dimensions of
77+
some FATES history output from site-level to pft-level. As such, these
78+
have been removed from some test cases to keep the test light weight and
79+
added to the AllVars test to maintain coverage.
80+
81+
Note that this FATES update also incorporates a number of additional science updates
82+
since the previous tag.
83+
84+
Other details
85+
-------------
86+
List any externals directories updated (cime, rtm, mosart, cism, fates, etc.): fates
87+
fates: sci.1.65.3_api.25.4.0 -> fates-sci.1.66.0_api.25.5.0
88+
89+
Pull Requests that document the changes (include PR ids):
90+
https://github.com/ESCOMP/ctsm/pull/2009
91+
https://github.com/NGEET/fates/pull/958
92+
93+
===============================================================
94+
===============================================================
295
Tag name: ctsm5.1.dev129
396
Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
497
Date: Thu Jun 22 01:21:56 MDT 2023
@@ -329,7 +422,7 @@ https://github.com/ESCOMP/CTSM/pull/2005
329422
===============================================================
330423
Tag name: ctsm5.1.dev125
331424
Originator(s): jpalex (John Alex)
332-
Date: Wed May 17 08:56:41 MDT 2023
425+
Date: Sun Jul 9 21:04:13 MDT 2023
333426
One-line Summary: Added cache for clock step_size in clm_time_manager.F90
334427

335428
Purpose and description of changes

‎doc/ChangeSum‎

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@@ -1,5 +1,6 @@
11
Tag Who Date Summary
22
============================================================================================================================
3+
ctsm5.1.dev130 glemieux 07/09/2023 FATES parameter file and test definition update
34
ctsm5.1.dev129 erik 06/22/2023 NEON fixes for TOOL and user-mods, add SP for NEON, some history file updates, black refactor for buildlib/buildnml
45
ctsm5.1.dev128 glemieux 06/01/2023 Update FATES tests to double precision
56
ctsm5.1.dev127 sacks 05/19/2023 Fix nuopc cplhist test

‎src/main/clm_driver.F90‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1151,7 +1151,7 @@ subroutine clm_drv(doalb, nextsw_cday, declinp1, declin, rstwr, nlend, rdate, ro
11511151
atm2lnd_inst, soilstate_inst, temperature_inst, active_layer_inst, &
11521152
water_inst%waterstatebulk_inst, water_inst%waterdiagnosticbulk_inst, &
11531153
water_inst%wateratm2lndbulk_inst, canopystate_inst, soilbiogeochem_carbonflux_inst, &
1154-
frictionvel_inst)
1154+
frictionvel_inst, soil_water_retention_curve)
11551155

11561156
! TODO(wjs, 2016-04-01) I think this setFilters call should be replaced by a
11571157
! call to reweight_wrapup, if it's needed at all.

‎src/utils/clmfates_interfaceMod.F90‎

Lines changed: 24 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -97,6 +97,7 @@ module CLMFatesInterfaceMod
9797
get_clump_bounds
9898
use SoilBiogeochemDecompCascadeConType , only : mimics_decomp, decomp_method
9999
use SoilBiogeochemDecompCascadeConType , only : no_soil_decomp, century_decomp
100+
use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type
100101
use GridCellType , only : grc
101102
use ColumnType , only : col
102103
use LandunitType , only : lun
@@ -808,7 +809,8 @@ end subroutine check_hlm_active
808809
subroutine dynamics_driv(this, nc, bounds_clump, &
809810
atm2lnd_inst, soilstate_inst, temperature_inst, active_layer_inst, &
810811
waterstatebulk_inst, waterdiagnosticbulk_inst, wateratm2lndbulk_inst, &
811-
canopystate_inst, soilbiogeochem_carbonflux_inst, frictionvel_inst)
812+
canopystate_inst, soilbiogeochem_carbonflux_inst, frictionvel_inst, &
813+
soil_water_retention_curve)
812814

813815
! This wrapper is called daily from clm_driver
814816
! This wrapper calls ed_driver, which is the daily dynamics component of FATES
@@ -834,11 +836,13 @@ subroutine dynamics_driv(this, nc, bounds_clump, &
834836
type(canopystate_type) , intent(inout) :: canopystate_inst
835837
type(soilbiogeochem_carbonflux_type), intent(inout) :: soilbiogeochem_carbonflux_inst
836838
type(frictionvel_type) , intent(inout) :: frictionvel_inst
839+
class(soil_water_retention_curve_type), intent(in) :: soil_water_retention_curve
837840

838841
! !LOCAL VARIABLES:
839842
integer :: s ! site index
840843
integer :: g ! grid-cell index (HLM)
841844
integer :: c ! column index (HLM)
845+
integer :: j ! Soil layer index
842846
integer :: ifp ! patch index ft
843847
integer :: p ! HLM patch index
844848
integer :: nlevsoil ! number of soil layers at the site
@@ -849,6 +853,7 @@ subroutine dynamics_driv(this, nc, bounds_clump, &
849853
integer :: ier
850854
integer :: begg,endg
851855
real(r8) :: harvest_rates(bounds_clump%begg:bounds_clump%endg,num_harvest_inst)
856+
real(r8) :: s_node, smp_node ! local for relative water content and potential
852857
logical :: after_start_of_harvest_ts
853858
integer :: iharv
854859
!-----------------------------------------------------------------------
@@ -933,6 +938,24 @@ subroutine dynamics_driv(this, nc, bounds_clump, &
933938
this%fates(nc)%bc_in(s)%max_rooting_depth_index_col = &
934939
min(nlevsoil, active_layer_inst%altmax_lastyear_indx_col(c))
935940

941+
nlevsoil = this%fates(nc)%bc_in(s)%nlevsoil
942+
do j = 1,nlevsoil
943+
this%fates(nc)%bc_in(s)%tempk_sl(j) = temperature_inst%t_soisno_col(c,j)
944+
end do
945+
946+
call get_active_suction_layers(this%fates(nc)%nsites, &
947+
this%fates(nc)%sites, &
948+
this%fates(nc)%bc_in, &
949+
this%fates(nc)%bc_out)
950+
951+
do j = 1,nlevsoil
952+
if(this%fates(nc)%bc_out(s)%active_suction_sl(j)) then
953+
s_node = max(waterstatebulk_inst%h2osoi_vol_col(c,j)/soilstate_inst%eff_porosity_col(c,j) ,0.01_r8)
954+
call soil_water_retention_curve%soil_suction(c,j,s_node, soilstate_inst, smp_node)
955+
this%fates(nc)%bc_in(s)%smp_sl(j) = smp_node
956+
end if
957+
end do
958+
936959

937960
do ifp = 1, this%fates(nc)%sites(s)%youngest_patch%patchno !for vegetated patches
938961
! Mapping between IFP space (1,2,3) and HLM P space (looping by IFP)
@@ -1998,8 +2021,6 @@ subroutine wrap_btran(this,nc,fn,filterc,soilstate_inst, &
19982021
!
19992022
! ---------------------------------------------------------------------------------
20002023

2001-
use SoilWaterRetentionCurveMod, only : soil_water_retention_curve_type
2002-
20032024
implicit none
20042025

20052026
! Arguments

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