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ctsm5.3.027: Migrate FATES parameter file switches to the namelist #2904

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ctsm5.3.027: Migrate FATES parameter file switches to the namelist #2904

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922a317
add fates daylength factor switch
glemieux Dec 10, 2024
949c668
add FATES switch to enable photosynthetic temp acclimation
glemieux Dec 10, 2024
59fef8c
add FATES namelist switch for stomatal conductance
glemieux Dec 10, 2024
9edf742
add FATES namelist switch for stomatal assimilation
glemieux Dec 10, 2024
59eb9f4
add FATES namelist switch for leaf respiration model
glemieux Dec 10, 2024
11a1708
add FATES switch to select carbon starvation model
glemieux Dec 10, 2024
3f2ed72
add FATES seed regeneration model switch to namelist
glemieux Dec 10, 2024
adf7d56
add FATES hydro solver selection switch to namelist
glemieux Dec 10, 2024
47fd489
add FATES radiation model switch to the namelist
glemieux Dec 11, 2024
02bc32a
change fates photosynthethic acclimation switch from logical to named
glemieux Jan 15, 2025
660ed58
add year to model switch for fates_stomatal_model namelist option
glemieux Jan 15, 2025
f990b24
fix fates_hydro_solver option name check
glemieux Jan 15, 2025
13a16e5
Merge tag 'ctsm5.3.019' into fates-switch-migration
glemieux Jan 15, 2025
5a04385
Merge remote-tracking branch 'glemieux/fates-api37.1' into fates-swit…
glemieux Feb 20, 2025
fa63e28
update fates gitmodules tag
glemieux Feb 20, 2025
2d0a541
Merge tag 'ctsm5.3.025' into fates-switch-migration
glemieux Feb 22, 2025
877e986
update default fates parameter file
glemieux Feb 23, 2025
9af9f32
update fates twostream tests per switch migration
glemieux Feb 23, 2025
ef27e7d
fix namelist definition valid values
glemieux Feb 23, 2025
527a4e0
correct fates API check for radation model
glemieux Feb 23, 2025
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12 changes: 10 additions & 2 deletions bld/CLMBuildNamelist.pm
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Original file line number Diff line number Diff line change
Expand Up @@ -808,7 +808,11 @@ sub setup_cmdl_fates_mode {
"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",
"flandusepftdat","use_fates_potentialveg","use_fates_lupft","fates_history_dimlevel" );
"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",
"fates_regeneration_model", "fates_hydro_solver", "fates_radiation_model"
);

# dis-allow fates specific namelist items with non-fates runs
foreach my $var ( @list ) {
Expand Down Expand Up @@ -4703,7 +4707,11 @@ sub setup_logic_fates {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
my @list = ( "fates_spitfire_mode", "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_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"
);

foreach my $var ( @list ) {
add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'},
Expand Down
9 changes: 9 additions & 0 deletions bld/namelist_files/namelist_defaults_ctsm.xml
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Expand Up @@ -2387,11 +2387,20 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
<use_nitrif_denitrif >.true.</use_nitrif_denitrif>

<!-- ===== FATES DEFAULTS =========== -->
<fates_photosynth_acclimation use_fates=".true.">nonacclimating</fates_photosynth_acclimation>
<fates_spitfire_mode use_fates=".true.">0</fates_spitfire_mode>
<fates_harvest_mode use_fates=".true.">no_harvest</fates_harvest_mode>
<fates_stomatal_model use_fates=".true.">ballberry1987</fates_stomatal_model>
<fates_stomatal_assimilation use_fates=".true.">net</fates_stomatal_assimilation>
<fates_leafresp_model use_fates=".true.">ryan1991</fates_leafresp_model>
<fates_cstarvation_model use_fates=".true.">linear</fates_cstarvation_model>
<fates_regeneration_model use_fates=".true.">default</fates_regeneration_model>
<fates_radiation_model use_fates=".true.">norman</fates_radiation_model>
<fates_hydro_solver use_fates=".true.">1D_Taylor</fates_hydro_solver>
<use_fates_planthydro use_fates=".true.">.false.</use_fates_planthydro>
<use_fates_tree_damage use_fates=".true.">.false.</use_fates_tree_damage>
<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>
<use_fates_ed_prescribed_phys use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
<use_fates_inventory_init use_fates=".true.">.false.</use_fates_inventory_init>
Expand Down
51 changes: 51 additions & 0 deletions bld/namelist_files/namelist_definition_ctsm.xml
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Expand Up @@ -780,6 +780,57 @@ Allowed values are:
This option is older than the luhdata options and may be depricated at some point in the future.
</entry>

<entry id="fates_radiation_model" type="char*256" category="physics"
group="clm_inparm" valid_values="norman, twostream" value="norman">
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I like the use of strings for switches in this PR, it is much more intuitive than using integer switches. When we finish nutrient coupling with FATES, I'd like to change the prt mode switch to a string as well.

Set the FATES radiation model
</entry>

<entry id="fates_hydro_solver" type="char*256" category="physics"
group="clm_inparm" valid_values="1D_Taylor, 2D_Picard, 2D_Newton" value="1D_Taylor">
Set the FATES hydro solver method
</entry>

<entry id="fates_regeneration_model" type="char*256" category="physics"
group="clm_inparm" valid_values="default, trs, trs_no_seed_dyn" value="default">
Set the FATES seed regeneration model
Valid values:
default: default scheme
trs: Tree Recruitment Scheme (Hanbury-Brown et al., 2022)
trs_no_seed_dyn: Tree Recruitment Scheme (Hanbury-Brown et al., 2022) without seed dynamics
</entry>

<entry id="fates_cstarvation_model" type="char*256" category="physics"
group="clm_inparm" valid_values="linear, exponential" value="linear">
Set the FATES carbon starvation model
</entry>

<entry id="fates_leafresp_model" type="char*256" category="physics"
group="clm_inparm" valid_values="ryan1991, atkin2017" value="ryan1991">
Set the FATES leaf maintenance respiration model
</entry>

<entry id="fates_stomatal_assimilation" type="char*256" category="physics"
group="clm_inparm" valid_values="net, gross" value="net">
Set net or gross asslimiation for the FATES stomatal model
</entry>

<entry id="fates_stomatal_model" type="char*256" category="physics"
group="clm_inparm" valid_values="ballberry1987, medlyn2011" value="ballberry1987">
Set the FATES stomatal conductance model
</entry>

<entry id="fates_photosynth_acclimation" type="char*256" category="physics"
group="clm_inparm" valid_values="nonacclimating, kumarathunge2019" value="nonacclimating">
Set the FATES photosynthesis temperature acclimation model.
(Only relevant if FATES is on)
</entry>

<entry id="use_fates_daylength_factor" type="logical" category="physics"
group="clm_inparm" valid_values="" value=".true.">
If TRUE, enable FATES to utilize the day length factor from the host land model.
(Only relevant if FATES is on)
</entry>

<entry id="use_fates_planthydro" type="logical" category="physics"
group="clm_inparm" valid_values="" value=".false.">
Toggle to turn on plant hydraulics
Expand Down
10 changes: 10 additions & 0 deletions src/main/clm_varctl.F90
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Expand Up @@ -331,13 +331,23 @@ module clm_varctl
! see bld/namelist_files/namelist_definition_clm4_5.xml for details
logical, public :: use_fates_tree_damage = .false. ! true => turn on tree damage 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
character(len=256), public :: fates_leafresp_model = '' ! Leaf maintenance respiration model, Ryan or Atkin
character(len=256), public :: fates_cstarvation_model = '' ! linear or exponential function
character(len=256), public :: fates_regeneration_model = '' ! default, TRS, or TRS without seed dynamics
character(len=256), public :: fates_radiation_model = '' ! Norman or two-stream radiation model
character(len=256), public :: fates_hydro_solver = '' ! 1D Taylor, 2D Picard, 2D Newton
character(len=256), public :: fates_photosynth_acclimation = '' ! nonacclimating, kumarathunge2019
logical, public :: use_fates_planthydro = .false. ! true => turn on fates hydro
logical, public :: use_fates_cohort_age_tracking = .false. ! true => turn on cohort age tracking
logical, public :: use_fates_ed_st3 = .false. ! true => static stand structure
logical, public :: use_fates_ed_prescribed_phys = .false. ! true => prescribed physiology
logical, public :: use_fates_inventory_init = .false. ! true => initialize fates from inventory
logical, public :: use_fates_fixed_biogeog = .false. ! true => use fixed biogeography mode
logical, public :: use_fates_nocomp = .false. ! true => use no comopetition mode
logical, public :: use_fates_daylength_factor = .false. ! true => enable fates to use host land model daylength factor


! FATES history dimension level
! fates can produce history at either the daily timescale (dynamics)
Expand Down
27 changes: 27 additions & 0 deletions src/main/controlMod.F90
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Expand Up @@ -243,9 +243,18 @@ subroutine control_init(dtime)
fluh_timeseries, &
flandusepftdat, &
fates_inventory_ctrl_filename, &
fates_stomatal_model, &
fates_stomatal_assimilation, &
fates_leafresp_model, &
fates_cstarvation_model, &
fates_regeneration_model, &
fates_radiation_model, &
fates_hydro_solver, &
fates_parteh_mode, &
fates_seeddisp_cadence, &
use_fates_tree_damage, &
use_fates_daylength_factor, &
fates_photosynth_acclimation, &
fates_history_dimlevel

! Ozone vegetation stress method
Expand Down Expand Up @@ -801,6 +810,13 @@ subroutine control_spmd()

call mpi_bcast (fates_spitfire_mode, 1, MPI_INTEGER, 0, mpicom, ier)
call mpi_bcast (fates_harvest_mode, len(fates_harvest_mode) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_stomatal_model, len(fates_stomatal_model) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_stomatal_assimilation, len(fates_stomatal_assimilation) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_leafresp_model, len(fates_leafresp_model) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_cstarvation_model, len(fates_cstarvation_model) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_regeneration_model, len(fates_regeneration_model) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_radiation_model, len(fates_radiation_model) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_hydro_solver, len(fates_hydro_solver) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (use_fates_planthydro, 1, MPI_LOGICAL, 0, mpicom, ier)
call mpi_bcast (use_fates_tree_damage, 1, MPI_LOGICAL, 0, mpicom, ier)
call mpi_bcast (use_fates_cohort_age_tracking, 1, MPI_LOGICAL, 0, mpicom, ier)
Expand All @@ -814,6 +830,8 @@ subroutine control_spmd()
call mpi_bcast (use_fates_lupft, 1, MPI_LOGICAL, 0, mpicom, ier)
call mpi_bcast (use_fates_potentialveg, 1, MPI_LOGICAL, 0, mpicom, ier)
call mpi_bcast (use_fates_bgc, 1, MPI_LOGICAL, 0, mpicom, ier)
call mpi_bcast (use_fates_daylength_factor, 1, MPI_LOGICAL, 0, mpicom, ier)
call mpi_bcast (fates_photosynth_acclimation, len(fates_photosynth_acclimation), MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_inventory_ctrl_filename, len(fates_inventory_ctrl_filename), MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fates_paramfile, len(fates_paramfile) , MPI_CHARACTER, 0, mpicom, ier)
call mpi_bcast (fluh_timeseries, len(fluh_timeseries) , MPI_CHARACTER, 0, mpicom, ier)
Expand Down Expand Up @@ -1202,11 +1220,20 @@ subroutine control_print ()
if (use_fates) then
write(iulog, *) ' fates_spitfire_mode = ', fates_spitfire_mode
write(iulog, *) ' fates_harvest_mode = ', fates_harvest_mode
write(iulog, *) ' fates_stomatal_model = ', fates_stomatal_model
write(iulog, *) ' fates_stomatal_assimilation = ', fates_stomatal_assimilation
write(iulog, *) ' fates_leafresp_model = ', fates_leafresp_model
write(iulog, *) ' fates_cstarvation_model = ', fates_cstarvation_model
write(iulog, *) ' fates_regeneration_model = ', fates_regeneration_model
write(iulog, *) ' fates_radiation_model = ', fates_radiation_model
write(iulog, *) ' fates_hydro_solver = ', fates_hydro_solver
write(iulog, *) ' fates_paramfile = ', fates_paramfile
write(iulog, *) ' fates_parteh_mode = ', fates_parteh_mode
write(iulog, *) ' fates_photosynth_acclimation = ', trim(fates_photosynth_acclimation)
write(iulog, *) ' use_fates_planthydro = ', use_fates_planthydro
write(iulog, *) ' use_fates_tree_damage = ', use_fates_tree_damage
write(iulog, *) ' use_fates_cohort_age_tracking = ', use_fates_cohort_age_tracking
write(iulog, *) ' use_fates_daylength_factor = ', use_fates_daylength_factor
write(iulog, *) ' use_fates_ed_st3 = ',use_fates_ed_st3
write(iulog, *) ' use_fates_ed_prescribed_phys = ',use_fates_ed_prescribed_phys
write(iulog, *) ' use_fates_inventory_init = ',use_fates_inventory_init
Expand Down
85 changes: 85 additions & 0 deletions src/utils/clmfates_interfaceMod.F90
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Expand Up @@ -52,9 +52,18 @@ module CLMFatesInterfaceMod
use clm_varctl , only : use_fates_tree_damage
use clm_varctl , only : use_fates_planthydro
use clm_varctl , only : use_fates_cohort_age_tracking
use clm_varctl , only : use_fates_daylength_factor
use clm_varctl , only : fates_photosynth_acclimation
use clm_varctl , only : use_fates_ed_st3
use clm_varctl , only : use_fates_ed_prescribed_phys
use clm_varctl , only : fates_harvest_mode
use clm_varctl , only : fates_stomatal_model
use clm_varctl , only : fates_stomatal_assimilation
use clm_varctl , only : fates_leafresp_model
use clm_varctl , only : fates_cstarvation_model
use clm_varctl , only : fates_regeneration_model
use clm_varctl , only : fates_hydro_solver
use clm_varctl , only : fates_radiation_model
use clm_varctl , only : use_fates_inventory_init
use clm_varctl , only : use_fates_fixed_biogeog
use clm_varctl , only : use_fates_nocomp
Expand Down Expand Up @@ -399,6 +408,15 @@ subroutine CLMFatesGlobals2()
integer :: pass_use_potentialveg
integer :: pass_num_luh_states
integer :: pass_num_luh_transitions
integer :: pass_photosynth_acclimation_switch
integer :: pass_daylength_factor_switch
integer :: pass_stomatal_model
integer :: pass_stomatal_assimilation
integer :: pass_leafresp_model
integer :: pass_cstarvation_model
integer :: pass_regeneration_model
integer :: pass_hydro_solver
integer :: pass_radiation_model

call t_startf('fates_globals2')

Expand Down Expand Up @@ -515,6 +533,73 @@ subroutine CLMFatesGlobals2()
end if
call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking)

if(trim(fates_photosynth_acclimation) == 'kumarathunge2019') then
pass_photosynth_acclimation_switch = 1
else if(trim(fates_photosynth_acclimation) == 'nonacclimating') then
pass_photosynth_acclimation_switch = 0
end if
call set_fates_ctrlparms('photosynth_acclimation',ival=pass_photosynth_acclimation_switch)

if(use_fates_daylength_factor) then
pass_daylength_factor_switch = 1
else
pass_daylength_factor_switch = 0
end if
call set_fates_ctrlparms('use_daylength_factor_switch',ival=pass_daylength_factor_switch)

if (trim(fates_stomatal_model) == 'ballberry1987') then
pass_stomatal_model = 1
else if (trim(fates_stomatal_model) == 'medlyn2011') then
pass_stomatal_model = 2
end if
call set_fates_ctrlparms('stomatal_model',ival=pass_stomatal_model)

if (trim(fates_stomatal_assimilation) == 'net') then
pass_stomatal_assimilation = 1
else if (trim(fates_stomatal_assimilation) == 'gross') then
pass_stomatal_assimilation = 2
end if
call set_fates_ctrlparms('stomatal_assim_model',ival=pass_stomatal_assimilation)

if (trim(fates_leafresp_model) == 'ryan1991') then
pass_leafresp_model = 1
else if (trim(fates_leafresp_model) == 'atkin2017') then
pass_leafresp_model = 2
end if
call set_fates_ctrlparms('maintresp_leaf_model',ival=pass_leafresp_model)

if (trim(fates_cstarvation_model) == 'linear') then
pass_cstarvation_model = 1
else if (trim(fates_cstarvation_model) == 'expontential') then
pass_cstarvation_model = 2
end if
call set_fates_ctrlparms('mort_cstarvation_model',ival=pass_cstarvation_model)

if (trim(fates_regeneration_model) == 'default') then
pass_regeneration_model = 1
else if (trim(fates_regeneration_model) == 'trs') then
pass_regeneration_model = 2
else if (trim(fates_regeneration_model) == 'trs_no_seed_dyn') then
pass_regeneration_model = 3
end if
call set_fates_ctrlparms('regeneration_model',ival=pass_regeneration_model)

if (trim(fates_hydro_solver) == '1D_Taylor') then
pass_hydro_solver = 1
else if (trim(fates_hydro_solver) == '2D_Picard') then
pass_hydro_solver = 2
else if (trim(fates_hydro_solver) == '2D_Newton') then
pass_hydro_solver = 3
end if
call set_fates_ctrlparms('hydr_solver',ival=pass_hydro_solver)

if (trim(fates_radiation_model) == 'norman') then
pass_radiation_model = 1
else if (trim(fates_hydro_solver) == 'twostream') then
pass_radiation_model = 2
end if
call set_fates_ctrlparms('radiation_model',ival=pass_radiation_model)

! FATES logging and harvest modes
pass_logging = 0
pass_lu_harvest = 0
Expand Down
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