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clmfates_interfaceMod.F90
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module CLMFatesInterfaceMod
! -------------------------------------------------------------------------------------
! This module contains various functions and definitions to aid in the
! coupling of the FATES library/API with the CLM/ALM/ATS/etc model driver.
! All connections between the two models should occur in this file alone.
!
! This is also the only location where CLM code is allowed to see FATES memory
! structures.
! The routines here, that call FATES library routines, will not pass any types defined
! by the driving land model (HLM).
!
! either native type arrays (int,real,log, etc) or packed into fates boundary condition
! structures.
!
! Note that CLM/ALM does use Shared Memory Parallelism (SMP), where processes such as
! the update of state variables are forked. However, IO is not assumed to be
! threadsafe and therefore memory spaces reserved for IO must be continuous vectors,
! and moreover they must be pushed/pulled from history IO for each individual
! bounds_proc memory space as a unit.
!
! Therefore, the state variables in the clm_fates communicator is vectorized by
! threadcount, and the IO communication arrays are not.
!
!
! Conventions:
! keep line widths within 90 spaces
! HLM acronym = Host Land Model
!
! -------------------------------------------------------------------------------------
! use ed_driver_interface, only:
! Used CLM Modules
use PatchType , only : patch
use shr_kind_mod , only : r8 => shr_kind_r8
use decompMod , only : bounds_type
use WaterStateType , only : waterstate_type
use WaterFluxType , only : waterflux_type
use CanopyStateType , only : canopystate_type
use TemperatureType , only : temperature_type
use EnergyFluxType , only : energyflux_type
use SoilStateType , only : soilstate_type
use clm_varctl , only : iulog
use clm_varctl , only : use_vertsoilc
use clm_varctl , only : fates_parteh_mode
use clm_varctl , only : use_fates
use clm_varctl , only : use_fates_spitfire
use clm_varctl , only : use_fates_planthydro
use clm_varctl , only : use_fates_cohort_age_tracking
use clm_varctl , only : use_fates_ed_st3
use clm_varctl , only : use_fates_ed_prescribed_phys
use clm_varctl , only : use_fates_logging
use clm_varctl , only : use_fates_inventory_init
use clm_varctl , only : fates_inventory_ctrl_filename
use clm_varcon , only : tfrz
use clm_varcon , only : spval
use clm_varcon , only : denice
use clm_varcon , only : ispval
use clm_varpar , only : natpft_size
use clm_varpar , only : numrad
use clm_varpar , only : ivis
use clm_varpar , only : inir
use clm_varpar , only : nlevgrnd
use clm_varpar , only : nlevdecomp
use clm_varpar , only : nlevdecomp_full
use PhotosynthesisMod , only : photosyns_type
use atm2lndType , only : atm2lnd_type
use SurfaceAlbedoType , only : surfalb_type
use SolarAbsorbedType , only : solarabs_type
use SoilBiogeochemCarbonFluxType, only : soilbiogeochem_carbonflux_type
use SoilBiogeochemCarbonStateType, only : soilbiogeochem_carbonstate_type
use FrictionVelocityMod , only : frictionvel_type
use clm_time_manager , only : is_restart
use ncdio_pio , only : file_desc_t, ncd_int, ncd_double
use restUtilMod, only : restartvar
use clm_time_manager , only : get_days_per_year, &
get_curr_date, &
get_ref_date, &
timemgr_datediff, &
is_beg_curr_day, &
get_step_size, &
get_nstep
use spmdMod , only : masterproc
use decompMod , only : get_proc_bounds, &
get_proc_clumps, &
get_clump_bounds
use GridCellType , only : grc
use ColumnType , only : col
use LandunitType , only : lun
use landunit_varcon , only : istsoil
use abortutils , only : endrun
use shr_log_mod , only : errMsg => shr_log_errMsg
use clm_varcon , only : dzsoi_decomp
use FuncPedotransferMod, only: get_ipedof
! use SoilWaterPlantSinkMod, only : Compute_EffecRootFrac_And_VertTranSink_Default
! Used FATES Modules
use FatesInterfaceTypesMod , only : fates_interface_type
use FatesInterfaceMod, only : FatesInterfaceInit, FatesReportParameters
use FatesInterfaceMod, only : SetFatesGlobalElements
use FatesInterfaceMod , only : allocate_bcin
use FatesInterfaceMod , only : allocate_bcout
use FatesInterfaceMod , only : zero_bcs
use FatesInterfaceMod , only : SetFatesTime
use FatesInterfaceMod , only : set_fates_ctrlparms
use FatesHistoryInterfaceMod, only : fates_history_interface_type
use FatesRestartInterfaceMod, only : fates_restart_interface_type
use EDTypesMod , only : ed_patch_type
use EDTypesMod , only : num_elements
use FatesInterfaceTypesMod , only : hlm_numlevgrnd
use EDMainMod , only : ed_ecosystem_dynamics
use EDMainMod , only : ed_update_site
use EDInitMod , only : zero_site
use EDInitMod , only : init_site_vars
use EDInitMod , only : init_patches
use EDInitMod , only : set_site_properties
use EDPftVarcon , only : EDpftvarcon_inst
use EDSurfaceRadiationMod , only : ED_SunShadeFracs, ED_Norman_Radiation
use EDBtranMod , only : btran_ed, &
get_active_suction_layers
use EDCanopyStructureMod , only : canopy_summarization, update_hlm_dynamics
use FatesPlantRespPhotosynthMod, only : FatesPlantRespPhotosynthDrive
use EDAccumulateFluxesMod , only : AccumulateFluxes_ED
use EDPhysiologyMod , only : FluxIntoLitterPools
use FatesPlantHydraulicsMod, only : hydraulics_drive
use FatesPlantHydraulicsMod, only : HydrSiteColdStart
use FatesPlantHydraulicsMod, only : InitHydrSites
use FatesPlantHydraulicsMod, only : RestartHydrStates
implicit none
type, public :: f2hmap_type
! This is the associated column index of each FATES site
integer, allocatable :: fcolumn (:)
! This is the associated site index of any HLM columns
! This vector may be sparse, and non-sites have index 0
integer, allocatable :: hsites (:)
end type f2hmap_type
type, public :: hlm_fates_interface_type
! private
! See above for descriptions of the sub-types populated
! by thread. This type is somewhat self-explanatory, in that it simply
! breaks up memory and process by thread. Each thread will have its
! own list of sites, and boundary conditions for those sites
type(fates_interface_type), allocatable :: fates (:)
! This memory structure is used to map fates sites
! into the host model. Currently, the FATES site
! and its column number matching are its only members
type(f2hmap_type), allocatable :: f2hmap(:)
! fates_hist is the interface class for the history output
type(fates_history_interface_type) :: fates_hist
! fates_restart is the inteface calss for restarting the model
type(fates_restart_interface_type) :: fates_restart
contains
procedure, public :: init
procedure, public :: check_hlm_active
procedure, public :: restart
procedure, public :: init_coldstart
procedure, public :: dynamics_driv
procedure, public :: wrap_sunfrac
procedure, public :: wrap_btran
procedure, public :: wrap_photosynthesis
procedure, public :: wrap_accumulatefluxes
procedure, public :: prep_canopyfluxes
procedure, public :: wrap_canopy_radiation
procedure, public :: wrap_bgc_summary
procedure, public :: TransferZ0mDisp
procedure, private :: init_history_io
procedure, private :: wrap_update_hlmfates_dyn
procedure, private :: init_soil_depths
procedure, public :: ComputeRootSoilFlux
procedure, public :: wrap_hydraulics_drive
end type hlm_fates_interface_type
! hlm_bounds_to_fates_bounds is not currently called outside the interface.
! Although there may be good reasons to, I privatized it so that the next
! developer will at least question its usage (RGK)
private :: hlm_bounds_to_fates_bounds
logical :: debug = .false.
character(len=*), parameter, private :: sourcefile = &
__FILE__
public :: CLMFatesGlobals
contains
subroutine CLMFatesGlobals()
! --------------------------------------------------------------------------------
! This is one of the first calls to fates
! Used for setting dimensions. This MUST
! be called after NL variables are specified and
! after the FATES parameter file has been read in
! Aside from setting global dimension info, which
! is used in the history file, we also transfer
! over the NL variables to FATES global settings.
! --------------------------------------------------------------------------------
logical :: verbose_output
integer :: pass_masterproc
integer :: pass_vertsoilc
integer :: pass_spitfire
integer :: pass_ed_st3
integer :: pass_logging
integer :: pass_ed_prescribed_phys
integer :: pass_planthydro
integer :: pass_inventory_init
integer :: pass_is_restart
integer :: pass_cohort_age_tracking
if (use_fates) then
verbose_output = .false.
call FatesInterfaceInit(iulog, verbose_output)
! Force FATES parameters that are recieve type, to the unset value
call set_fates_ctrlparms('flush_to_unset')
! Send parameters individually
call set_fates_ctrlparms('num_sw_bbands',ival=numrad)
call set_fates_ctrlparms('vis_sw_index',ival=ivis)
call set_fates_ctrlparms('nir_sw_index',ival=inir)
call set_fates_ctrlparms('num_lev_ground',ival=nlevgrnd)
call set_fates_ctrlparms('hlm_name',cval='CLM')
call set_fates_ctrlparms('hio_ignore_val',rval=spval)
call set_fates_ctrlparms('soilwater_ipedof',ival=get_ipedof(0))
call set_fates_ctrlparms('max_patch_per_site',ival=(natpft_size-1))
call set_fates_ctrlparms('parteh_mode',ival=fates_parteh_mode)
if(is_restart()) then
pass_is_restart = 1
else
pass_is_restart = 0
end if
call set_fates_ctrlparms('is_restart',ival=pass_is_restart)
if(use_vertsoilc) then
pass_vertsoilc = 1
else
pass_vertsoilc = 0
end if
call set_fates_ctrlparms('use_vertsoilc',ival=pass_vertsoilc)
if(use_fates_spitfire) then
pass_spitfire = 1
else
pass_spitfire = 0
end if
call set_fates_ctrlparms('use_spitfire',ival=pass_spitfire)
if(use_fates_ed_st3) then
pass_ed_st3 = 1
else
pass_ed_st3 = 0
end if
call set_fates_ctrlparms('use_ed_st3',ival=pass_ed_st3)
if(use_fates_logging) then
pass_logging = 1
else
pass_logging = 0
end if
call set_fates_ctrlparms('use_logging',ival=pass_logging)
if(use_fates_ed_prescribed_phys) then
pass_ed_prescribed_phys = 1
else
pass_ed_prescribed_phys = 0
end if
call set_fates_ctrlparms('use_ed_prescribed_phys',ival=pass_ed_prescribed_phys)
if(use_fates_planthydro) then
pass_planthydro = 1
else
pass_planthydro = 0
end if
call set_fates_ctrlparms('use_planthydro',ival=pass_planthydro)
if(use_fates_cohort_age_tracking) then
pass_cohort_age_tracking = 1
else
pass_cohort_age_tracking = 0
end if
call set_fates_ctrlparms('use_cohort_age_tracking',ival=pass_cohort_age_tracking)
if(use_fates_inventory_init) then
pass_inventory_init = 1
else
pass_inventory_init = 0
end if
call set_fates_ctrlparms('use_inventory_init',ival=pass_inventory_init)
call set_fates_ctrlparms('inventory_ctrl_file',cval=fates_inventory_ctrl_filename)
if(masterproc)then
pass_masterproc = 1
else
pass_masterproc = 0
end if
call set_fates_ctrlparms('masterproc',ival=pass_masterproc)
! Check through FATES parameters to see if all have been set
call set_fates_ctrlparms('check_allset')
end if
! This determines the total amount of space it requires in its largest
! dimension. We are currently calling that the "cohort" dimension, but
! it is really a utility dimension that captures the models largest
! size need.
! Sets:
! fates_maxElementsPerPatch
! num_elements
! fates_maxElementsPerSite (where a site is roughly equivalent to a column)
! (Note: this needs to be called when use_fates=.false. as well, becuase
! it will return some nominal dimension sizes of 1
call SetFatesGlobalElements(use_fates)
return
end subroutine CLMFatesGlobals
! ====================================================================================
subroutine init(this, bounds_proc )
! ---------------------------------------------------------------------------------
! This initializes the hlm_fates_interface_type
!
! sites is the root of the fates state hierarchy (instantaneous info on
! the state of the ecosystem). As such, it governs the connection points between
! the host (which also dictates its allocation) and its patch structures.
!
! sites may associate with different scales in different models. In
! CLM, it is being designed to relate to column scale.
!
! This global may become relegated to this module.
!
! Note: CLM/ALM currently wants sites to be allocated even if ed
! is not turned on
! ---------------------------------------------------------------------------------
use FatesInterfaceTypesMod, only : numpft_fates => numpft
use FatesParameterDerivedMod, only : param_derived
implicit none
! Input Arguments
class(hlm_fates_interface_type), intent(inout) :: this
type(bounds_type),intent(in) :: bounds_proc
! local variables
integer :: nclumps ! Number of threads
integer :: pass_masterproc
integer :: pass_vertsoilc
integer :: pass_spitfire
integer :: pass_ed_st3
integer :: pass_ed_prescribed_phys
integer :: pass_logging
integer :: pass_planthydro
integer :: pass_cohort_age_tracking
integer :: pass_inventory_init
integer :: pass_is_restart
integer :: nc ! thread index
integer :: s ! FATES site index
integer :: c ! HLM column index
integer :: l ! HLM LU index
integer :: g ! HLM grid index
integer :: pi,pf
integer, allocatable :: collist (:)
type(bounds_type) :: bounds_clump
integer :: nmaxcol
integer :: ndecomp
! Initialize the FATES communicators with the HLM
! This involves to stages
! 1) allocate the vectors
! 2) add the history variables defined in clm_inst to the history machinery
! Parameter Routines
call param_derived%Init( numpft_fates )
nclumps = get_proc_clumps()
allocate(this%fates(nclumps))
allocate(this%f2hmap(nclumps))
if(debug)then
write(iulog,*) 'clm_fates%init(): allocating for ',nclumps,' threads'
end if
nclumps = get_proc_clumps()
!$OMP PARALLEL DO PRIVATE (nc,bounds_clump,nmaxcol,s,c,l,g,collist,pi,pf)
do nc = 1,nclumps
call get_clump_bounds(nc, bounds_clump)
nmaxcol = bounds_clump%endc - bounds_clump%begc + 1
allocate(collist(1:nmaxcol))
! Allocate the mapping that points columns to FATES sites, 0 is NA
allocate(this%f2hmap(nc)%hsites(bounds_clump%begc:bounds_clump%endc))
! Initialize all columns with a zero index, which indicates no FATES site
this%f2hmap(nc)%hsites(:) = 0
s = 0
do c = bounds_clump%begc,bounds_clump%endc
l = col%landunit(c)
! These are the key constraints that determine if this column
! will have a FATES site associated with it
! INTERF-TODO: WE HAVE NOT FILTERED OUT FATES SITES ON INACTIVE COLUMNS.. YET
! NEED A RUN-TIME ROUTINE THAT CLEARS AND REWRITES THE SITE LIST
if (lun%itype(l) == istsoil ) then
s = s + 1
collist(s) = c
this%f2hmap(nc)%hsites(c) = s
if(debug)then
write(iulog,*) 'clm_fates%init(): thread',nc,': found column',c,'with lu',l
write(iulog,*) 'LU type:', lun%itype(l)
end if
endif
enddo
if(debug)then
write(iulog,*) 'clm_fates%init(): thread',nc,': allocated ',s,' sites'
end if
! Allocate vectors that match FATES sites with HLM columns
! RGK: Sites and fcolumns are forced as args during clm_driv() as of 6/4/2016
! We may have to give these a dummy allocation of 1, which should
! not be a problem since we always iterate on nsites.
allocate(this%f2hmap(nc)%fcolumn(s))
! Assign the h2hmap indexing
this%f2hmap(nc)%fcolumn(1:s) = collist(1:s)
! Deallocate the temporary arrays
deallocate(collist)
! Set the number of FATES sites
this%fates(nc)%nsites = s
! Allocate the FATES sites
allocate (this%fates(nc)%sites(this%fates(nc)%nsites))
! Allocate the FATES boundary arrays (in)
allocate(this%fates(nc)%bc_in(this%fates(nc)%nsites))
! Allocate the FATES boundary arrays (out)
allocate(this%fates(nc)%bc_out(this%fates(nc)%nsites))
! Allocate and Initialize the Boundary Condition Arrays
! These are staticaly allocated at maximums, so
! No information about the patch or cohort structure is needed at this step
do s = 1, this%fates(nc)%nsites
c = this%f2hmap(nc)%fcolumn(s)
if (use_vertsoilc) then
ndecomp = col%nbedrock(c)
else
ndecomp = 1
end if
call allocate_bcin(this%fates(nc)%bc_in(s),col%nbedrock(c),ndecomp)
call allocate_bcout(this%fates(nc)%bc_out(s),col%nbedrock(c),ndecomp)
call zero_bcs(this%fates(nc),s)
! Pass any grid-cell derived attributes to the site
! ---------------------------------------------------------------------------
c = this%f2hmap(nc)%fcolumn(s)
g = col%gridcell(c)
this%fates(nc)%sites(s)%lat = grc%latdeg(g)
this%fates(nc)%sites(s)%lon = grc%londeg(g)
end do
! Initialize site-level static quantities dictated by the HLM
! currently ground layering depth
call this%init_soil_depths(nc)
if (use_fates_planthydro) then
call InitHydrSites(this%fates(nc)%sites,this%fates(nc)%bc_in)
end if
if( this%fates(nc)%nsites == 0 ) then
write(iulog,*) 'Clump ',nc,' had no valid FATES sites'
write(iulog,*) 'This will likely cause problems until code is improved'
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
! Set patch itypes on natural veg columns to nonsense
! This will force a crash if the model outside of FATES tries to think
! of the patch as a PFT.
do s = 1, this%fates(nc)%nsites
c = this%f2hmap(nc)%fcolumn(s)
pi = col%patchi(c)+1
pf = col%patchf(c)
! patch%itype(pi:pf) = ispval
patch%is_fates(pi:pf) = .true.
end do
end do
!$OMP END PARALLEL DO
call this%init_history_io(bounds_proc)
! Report Fates Parameters (debug flag in lower level routines)
call FatesReportParameters(masterproc)
end subroutine init
! ===================================================================================
subroutine check_hlm_active(this, nc, bounds_clump)
! ---------------------------------------------------------------------------------
! This subroutine is not currently used. It is just a utility that may come
! in handy when we have dynamic sites in FATES
! ---------------------------------------------------------------------------------
implicit none
class(hlm_fates_interface_type), intent(inout) :: this
integer :: nc
type(bounds_type),intent(in) :: bounds_clump
! local variables
integer :: c
do c = bounds_clump%begc,bounds_clump%endc
! FATES ACTIVE BUT HLM IS NOT
if(this%f2hmap(nc)%hsites(c)>0 .and. .not.col%active(c)) then
write(iulog,*) 'INACTIVE COLUMN WITH ACTIVE FATES SITE'
write(iulog,*) 'c = ',c
call endrun(msg=errMsg(sourcefile, __LINE__))
elseif (this%f2hmap(nc)%hsites(c)==0 .and. col%active(c)) then
write(iulog,*) 'ACTIVE COLUMN WITH INACTIVE FATES SITE'
write(iulog,*) 'c = ',c
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
end do
end subroutine check_hlm_active
! ------------------------------------------------------------------------------------
subroutine dynamics_driv(this, nc, bounds_clump, &
atm2lnd_inst, soilstate_inst, temperature_inst, &
waterstate_inst, canopystate_inst, soilbiogeochem_carbonflux_inst, &
frictionvel_inst )
! This wrapper is called daily from clm_driver
! This wrapper calls ed_driver, which is the daily dynamics component of FATES
! ed_driver is not a hlm_fates_inst_type procedure because we need an extra step
! to process array bounding information
implicit none
class(hlm_fates_interface_type), intent(inout) :: this
type(bounds_type),intent(in) :: bounds_clump
type(atm2lnd_type) , intent(in) :: atm2lnd_inst
type(soilstate_type) , intent(in) :: soilstate_inst
type(temperature_type) , intent(in) :: temperature_inst
integer , intent(in) :: nc
type(waterstate_type) , intent(inout) :: waterstate_inst
type(canopystate_type) , intent(inout) :: canopystate_inst
type(soilbiogeochem_carbonflux_type), intent(inout) :: soilbiogeochem_carbonflux_inst
type(frictionvel_type) , intent(inout) :: frictionvel_inst
! !LOCAL VARIABLES:
integer :: s ! site index
integer :: c ! column index (HLM)
integer :: ifp ! patch index
integer :: p ! HLM patch index
integer :: yr ! year (0, ...)
integer :: mon ! month (1, ..., 12)
integer :: day ! day of month (1, ..., 31)
integer :: sec ! seconds of the day
integer :: nlevsoil ! number of soil layers at the site
integer :: nld_si ! site specific number of decomposition layers
integer :: current_year
integer :: current_month
integer :: current_day
integer :: current_tod
integer :: current_date
integer :: jan01_curr_year
integer :: reference_date
integer :: days_per_year
real(r8) :: model_day
real(r8) :: day_of_year
!-----------------------------------------------------------------------
! ---------------------------------------------------------------------------------
! Part I.
! Prepare input boundary conditions for FATES dynamics
! Note that timing information is the same across all sites, this may
! seem redundant, but it is possible that we may have asynchronous site simulations
! one day. The cost of holding site level boundary conditions is minimal
! and it keeps all the boundaries in one location
! ---------------------------------------------------------------------------------
days_per_year = get_days_per_year()
call get_curr_date(current_year,current_month,current_day,current_tod)
current_date = current_year*10000 + current_month*100 + current_day
jan01_curr_year = current_year*10000 + 100 + 1
call get_ref_date(yr, mon, day, sec)
reference_date = yr*10000 + mon*100 + day
call timemgr_datediff(reference_date, sec, current_date, current_tod, model_day)
call timemgr_datediff(jan01_curr_year,0,current_date,sec,day_of_year)
call SetFatesTime(current_year, current_month, &
current_day, current_tod, &
current_date, reference_date, &
model_day, floor(day_of_year), &
days_per_year, 1.0_r8/dble(days_per_year))
do s=1,this%fates(nc)%nsites
c = this%f2hmap(nc)%fcolumn(s)
nlevsoil = this%fates(nc)%bc_in(s)%nlevsoil
this%fates(nc)%bc_in(s)%h2o_liqvol_sl(1:nlevsoil) = &
waterstate_inst%h2osoi_vol_col(c,1:nlevsoil)
this%fates(nc)%bc_in(s)%max_rooting_depth_index_col = &
min(nlevsoil, canopystate_inst%altmax_lastyear_indx_col(c))
do ifp = 1, this%fates(nc)%sites(s)%youngest_patch%patchno
p = ifp+col%patchi(c)
this%fates(nc)%bc_in(s)%t_veg24_pa(ifp) = &
temperature_inst%t_veg24_patch(p)
this%fates(nc)%bc_in(s)%precip24_pa(ifp) = &
atm2lnd_inst%prec24_patch(p)
this%fates(nc)%bc_in(s)%relhumid24_pa(ifp) = &
atm2lnd_inst%rh24_patch(p)
this%fates(nc)%bc_in(s)%wind24_pa(ifp) = &
atm2lnd_inst%wind24_patch(p)
end do
if(use_fates_planthydro)then
this%fates(nc)%bc_in(s)%hksat_sisl(1:nlevsoil) = soilstate_inst%hksat_col(c,1:nlevsoil)
this%fates(nc)%bc_in(s)%watsat_sisl(1:nlevsoil) = soilstate_inst%watsat_col(c,1:nlevsoil)
this%fates(nc)%bc_in(s)%watres_sisl(1:nlevsoil) = soilstate_inst%watres_col(c,1:nlevsoil)
this%fates(nc)%bc_in(s)%sucsat_sisl(1:nlevsoil) = soilstate_inst%sucsat_col(c,1:nlevsoil)
this%fates(nc)%bc_in(s)%bsw_sisl(1:nlevsoil) = soilstate_inst%bsw_col(c,1:nlevsoil)
this%fates(nc)%bc_in(s)%h2o_liq_sisl(1:nlevsoil) = waterstate_inst%h2osoi_liq_col(c,1:nlevsoil)
end if
end do
! ---------------------------------------------------------------------------------
! Part II: Call the FATES model now that input boundary conditions have been
! provided.
! ---------------------------------------------------------------------------------
do s = 1,this%fates(nc)%nsites
call ed_ecosystem_dynamics(this%fates(nc)%sites(s), &
this%fates(nc)%bc_in(s))
call ed_update_site(this%fates(nc)%sites(s), &
this%fates(nc)%bc_in(s))
enddo
! call subroutine to aggregate fates litter output fluxes and
! package them for handing across interface
call FluxIntoLitterPools(this%fates(nc)%nsites, &
this%fates(nc)%sites, &
this%fates(nc)%bc_in, &
this%fates(nc)%bc_out)
! ---------------------------------------------------------------------------------
! Part III: Process FATES output into the dimensions and structures that are part
! of the HLMs API. (column, depth, and litter fractions)
! ---------------------------------------------------------------------------------
do s = 1, this%fates(nc)%nsites
c = this%f2hmap(nc)%fcolumn(s)
soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lab_c_col(c,1:nlevdecomp) = 0.0_r8
soilbiogeochem_carbonflux_inst%FATES_c_to_litr_cel_c_col(c,1:nlevdecomp) = 0.0_r8
soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lig_c_col(c,1:nlevdecomp) = 0.0_r8
nld_si = this%fates(nc)%bc_in(s)%nlevdecomp
soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lab_c_col(c,1:nld_si) = &
this%fates(nc)%bc_out(s)%litt_flux_lab_c_si(1:nld_si)
soilbiogeochem_carbonflux_inst%FATES_c_to_litr_cel_c_col(c,1:nld_si) = &
this%fates(nc)%bc_out(s)%litt_flux_cel_c_si(1:nld_si)
soilbiogeochem_carbonflux_inst%FATES_c_to_litr_lig_c_col(c,1:nld_si) = &
this%fates(nc)%bc_out(s)%litt_flux_lig_c_si(1:nld_si)
end do
! ---------------------------------------------------------------------------------
! Part III.2 (continued).
! Update diagnostics of the FATES ecosystem structure that are used in the HLM.
! ---------------------------------------------------------------------------------
call this%wrap_update_hlmfates_dyn(nc, &
bounds_clump, &
waterstate_inst, &
canopystate_inst, &
frictionvel_inst)
! ---------------------------------------------------------------------------------
! Part IV:
! Update history IO fields that depend on ecosystem dynamics
! ---------------------------------------------------------------------------------
call this%fates_hist%update_history_dyn( nc, &
this%fates(nc)%nsites, &
this%fates(nc)%sites)
if (masterproc) then
write(iulog, *) 'clm: leaving fates model', bounds_clump%begg, &
bounds_clump%endg
end if
return
end subroutine dynamics_driv
! ------------------------------------------------------------------------------------
subroutine wrap_update_hlmfates_dyn(this, nc, bounds_clump, &
waterstate_inst, canopystate_inst, frictionvel_inst )
! ---------------------------------------------------------------------------------
! This routine handles the updating of vegetation canopy diagnostics, (such as lai)
! that either requires HLM boundary conditions (like snow accumulation) or
! provides boundary conditions (such as vegetation fractional coverage)
! ---------------------------------------------------------------------------------
implicit none
class(hlm_fates_interface_type), intent(inout) :: this
type(bounds_type),intent(in) :: bounds_clump
integer , intent(in) :: nc
type(waterstate_type) , intent(inout) :: waterstate_inst
type(canopystate_type) , intent(inout) :: canopystate_inst
type(frictionvel_type) , intent(inout) :: frictionvel_inst
integer :: npatch ! number of patches in each site
integer :: ifp ! index FATES patch
integer :: p ! HLM patch index
integer :: s ! site index
integer :: c ! column index
associate( &
tlai => canopystate_inst%tlai_patch , &
elai => canopystate_inst%elai_patch , &
tsai => canopystate_inst%tsai_patch , &
esai => canopystate_inst%esai_patch , &
htop => canopystate_inst%htop_patch , &
hbot => canopystate_inst%hbot_patch , &
z0m => frictionvel_inst%z0m_patch , & ! Output: [real(r8) (:) ] momentum roughness length (m)
displa => canopystate_inst%displa_patch, &
dleaf_patch => canopystate_inst%dleaf_patch, &
snow_depth => waterstate_inst%snow_depth_col, &
frac_sno_eff => waterstate_inst%frac_sno_eff_col, &
frac_veg_nosno_alb => canopystate_inst%frac_veg_nosno_alb_patch)
! Process input boundary conditions to FATES
! --------------------------------------------------------------------------------
do s=1,this%fates(nc)%nsites
c = this%f2hmap(nc)%fcolumn(s)
this%fates(nc)%bc_in(s)%snow_depth_si = snow_depth(c)
this%fates(nc)%bc_in(s)%frac_sno_eff_si = frac_sno_eff(c)
end do
! Canopy diagnostics for FATES
call canopy_summarization(this%fates(nc)%nsites, &
this%fates(nc)%sites, &
this%fates(nc)%bc_in)
! Canopy diagnostic outputs for HLM
call update_hlm_dynamics(this%fates(nc)%nsites, &
this%fates(nc)%sites, &
this%f2hmap(nc)%fcolumn, &
this%fates(nc)%bc_out )
!---------------------------------------------------------------------------------
! CHANGING STORED WATER DURING PLANT DYNAMICS IS NOT FULLY IMPLEMENTED
! LEAVING AS A PLACE-HOLDER FOR NOW.
! ! Diagnose water storage in canopy if hydraulics is on
! ! This updates the internal value and the bc_out value.
! ! If hydraulics is off, it returns 0 storage
if ( use_fates_planthydro ) then
do s = 1, this%fates(nc)%nsites
c = this%f2hmap(nc)%fcolumn(s)
waterstate_inst%total_plant_stored_h2o_col(c) = &
this%fates(nc)%bc_out(s)%plant_stored_h2o_si
end do
end if
!---------------------------------------------------------------------------------
! Convert FATES dynamics into HLM usable information
! Initialize weighting variables (note FATES is the only HLM module
! that uses "is_veg" and "is_bareground". The entire purpose of these
! variables is to inform patch%wtcol(p). wt_ed is imposed on wtcol,
! but only for FATES columns.
patch%is_veg(bounds_clump%begp:bounds_clump%endp) = .false.
patch%is_bareground(bounds_clump%begp:bounds_clump%endp) = .false.
patch%wt_ed(bounds_clump%begp:bounds_clump%endp) = 0.0_r8
do s = 1,this%fates(nc)%nsites
c = this%f2hmap(nc)%fcolumn(s)
! Other modules may have AI's we only flush values
! that are on the naturally vegetated columns
elai(col%patchi(c):col%patchf(c)) = 0.0_r8
tlai(col%patchi(c):col%patchf(c)) = 0.0_r8
esai(col%patchi(c):col%patchf(c)) = 0.0_r8
tsai(col%patchi(c):col%patchf(c)) = 0.0_r8
htop(col%patchi(c):col%patchf(c)) = 0.0_r8
hbot(col%patchi(c):col%patchf(c)) = 0.0_r8
! FATES does not dictate bare-ground so turbulent
! variables are not over-written.
z0m(col%patchi(c)+1:col%patchf(c)) = 0.0_r8
displa(col%patchi(c)+1:col%patchf(c)) = 0.0_r8
dleaf_patch(col%patchi(c)+1:col%patchf(c)) = 0.0_r8
frac_veg_nosno_alb(col%patchi(c):col%patchf(c)) = 0.0_r8
! Set the bareground patch indicator
patch%is_bareground(col%patchi(c)) = .true.
npatch = this%fates(nc)%sites(s)%youngest_patch%patchno
! Precision errors on the canopy_fraction_pa sum, even small (e-12)
! do exist, and can create potentially negetive bare-soil fractions
! (ie -1e-12 or smaller). Even though this is effectively zero,
! it can generate weird logic scenarios in the ctsm/elm code, so we
! protext it here with a lower bound of 0.0_r8.
patch%wt_ed(col%patchi(c)) = max(0.0_r8, &
1.0_r8-sum(this%fates(nc)%bc_out(s)%canopy_fraction_pa(1:npatch)))
if(sum(this%fates(nc)%bc_out(s)%canopy_fraction_pa(1:npatch))>1.0_r8)then
write(iulog,*)'Projected Canopy Area of all FATES patches'
write(iulog,*)'cannot exceed 1.0'
!end_run()
end if
do ifp = 1, npatch
p = ifp+col%patchi(c)
! bc_out(s)%canopy_fraction_pa(ifp) is the area fraction
! the site's total ground area that is occupied by the
! area footprint of the current patch's vegetation canopy
patch%is_veg(p) = .true.
patch%wt_ed(p) = this%fates(nc)%bc_out(s)%canopy_fraction_pa(ifp)
elai(p) = this%fates(nc)%bc_out(s)%elai_pa(ifp)
tlai(p) = this%fates(nc)%bc_out(s)%tlai_pa(ifp)
esai(p) = this%fates(nc)%bc_out(s)%esai_pa(ifp)
tsai(p) = this%fates(nc)%bc_out(s)%tsai_pa(ifp)
hbot(p) = this%fates(nc)%bc_out(s)%hbot_pa(ifp)
htop(p) = this%fates(nc)%bc_out(s)%htop_pa(ifp)
frac_veg_nosno_alb(p) = this%fates(nc)%bc_out(s)%frac_veg_nosno_alb_pa(ifp)
! Note that while we pass the following values at this point
! we have to send the same values after each time-step because
! the HLM keeps changing the value and re-setting, so we
! re-send instead of re-set. See clm_fates%TransferZ0mDisp()
z0m(p) = this%fates(nc)%bc_out(s)%z0m_pa(ifp)
displa(p) = this%fates(nc)%bc_out(s)%displa_pa(ifp)
dleaf_patch(p) = this%fates(nc)%bc_out(s)%dleaf_pa(ifp)
end do
end do
end associate
end subroutine wrap_update_hlmfates_dyn
! ====================================================================================
subroutine restart( this, bounds_proc, ncid, flag, waterstate_inst, &
canopystate_inst, frictionvel_inst, soilstate_inst)
! ---------------------------------------------------------------------------------
! The ability to restart the model is handled through three different types of calls
! "Define" the variables in the restart file, we "read" those variables into memory
! or "write" data into the file from memory. This subroutine accomodates all three
! of those modes through the "flag" argument. FATES as an external model also
! requires an initialization step, where we set-up the dimensions, allocate and
! flush the memory space that is used to transfer data in and out of the file. This
! Only occurs once, where as the define step occurs every time a file is opened.
!
! Note: waterstate_inst and canopystate_inst are arguments only because following
! the reading of variables, it is necessary to update diagnostics of the canopy
! throug the interface call clm_fates%wrap_update_hlmfates_dyn() which requires
! this information from the HLM.
! ---------------------------------------------------------------------------------
use FatesConstantsMod, only : fates_long_string_length
use FatesIODimensionsMod, only: fates_bounds_type
use FatesIOVariableKindMod, only : site_r8, site_int, cohort_r8, cohort_int
use EDMainMod, only : ed_update_site
use FatesInterfaceTypesMod, only: fates_maxElementsPerSite
implicit none
! Arguments
class(hlm_fates_interface_type), intent(inout) :: this
type(bounds_type) , intent(in) :: bounds_proc
type(file_desc_t) , intent(inout) :: ncid ! netcdf id
character(len=*) , intent(in) :: flag
type(waterstate_type) , intent(inout) :: waterstate_inst
type(canopystate_type) , intent(inout) :: canopystate_inst
type(frictionvel_type) , intent(inout) :: frictionvel_inst
type(soilstate_type) , intent(inout) :: soilstate_inst
! Locals
type(bounds_type) :: bounds_clump
integer :: nc
integer :: nclumps
type(fates_bounds_type) :: fates_bounds
type(fates_bounds_type) :: fates_clump
integer :: c ! HLM column index
integer :: s ! Fates site index
integer :: g ! grid-cell index
integer :: dk_index
integer :: nlevsoil
character(len=fates_long_string_length) :: ioname
integer :: nvar
integer :: ivar
logical :: readvar
logical, save :: initialized = .false.