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FatesRestartInterfaceMod.F90
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module FatesRestartInterfaceMod
use FatesConstantsMod, only : r8 => fates_r8
use FatesConstantsMod, only : fates_avg_flag_length
use FatesConstantsMod, only : fates_short_string_length
use FatesConstantsMod, only : fates_long_string_length
use FatesConstantsMod, only : itrue
use FatesConstantsMod, only : ifalse
use FatesConstantsMod, only : fates_unset_r8, fates_unset_int
use FatesConstantsMod, only : primaryforest
use FatesConstantsMod, only : nearzero
use FatesGlobals, only : fates_log
use FatesGlobals, only : endrun => fates_endrun
use FatesIODimensionsMod, only : fates_io_dimension_type
use FatesIOVariableKindMod, only : fates_io_variable_kind_type
use FatesRestartVariableMod, only : fates_restart_variable_type
use FatesInterfaceTypesMod, only : nlevcoage
use FatesInterfaceTypesMod, only : bc_in_type
use FatesInterfaceTypesMod, only : bc_out_type
use FatesInterfaceTypesMod, only : hlm_use_planthydro
use FatesInterfaceTypesMod, only : hlm_parteh_mode
use FatesInterfaceTypesMod, only : hlm_use_sp
use FatesInterfaceTypesMod, only : hlm_use_nocomp, hlm_use_fixed_biogeog
use FatesInterfaceTypesMod, only : fates_maxElementsPerSite
use FatesInterfaceTypesMod, only : hlm_use_tree_damage
use EDCohortDynamicsMod, only : UpdateCohortBioPhysRates
use FatesHydraulicsMemMod, only : nshell
use FatesHydraulicsMemMod, only : n_hypool_ag
use FatesHydraulicsMemMod, only : n_hypool_troot
use FatesHydraulicsMemMod, only : nlevsoi_hyd_max
use FatesPlantHydraulicsMod, only : UpdatePlantPsiFTCFromTheta
use PRTGenericMod, only : prt_global
use PRTGenericMod, only : prt_cnp_flex_allom_hyp
use EDCohortDynamicsMod, only : nan_cohort
use EDCohortDynamicsMod, only : zero_cohort
use EDCohortDynamicsMod, only : InitPRTObject
use EDCohortDynamicsMod, only : InitPRTBoundaryConditions
use FatesPlantHydraulicsMod, only : InitHydrCohort
use FatesInterfaceTypesMod, only : nlevsclass
use FatesInterfaceTypesMod, only : nlevdamage
use FatesLitterMod, only : litter_type
use FatesLitterMod, only : ncwd
use FatesLitterMod, only : ndcmpy
use EDTypesMod, only : nfsc, nlevleaf, area
use PRTGenericMod, only : prt_global
use PRTGenericMod, only : num_elements
use FatesRunningMeanMod, only : rmean_type
use FatesRunningMeanMod, only : ema_lpa
! CIME GLOBALS
use shr_log_mod , only : errMsg => shr_log_errMsg
implicit none
private ! Modules are private by default
! ------------------------------------------------------------
! A note on variable naming conventions.
! Many variables in this restart IO portion of the code will
! follow the conventions:
!
! <use_case>_<description>_<dimension>
!
! For instance we use an index for restart variable "ir_"
! to point the object that contains the number of patches per
! site "npatch" and this value is relevant to all sites "si"
! thus: ir_npatch_si
!
! We also use associations to the data arrays of restart IO
! variables "rio", for example the leaf litter "leaf_litter"
! is retrieved for every patch and every functional type "paft"
! thus: rio_leaf_litter_paft
!
! si: site dimension
! pa: patch dimension
! co: cohort dimension
! ft: functional type dimension
! cl: canopy layer dimension (upper, lower, etc)
! ls: layer sublayer dimension (fine discretization of upper,lower)
! wm: the number of memory slots for water (currently 10)
! -------------------------------------------------------------
! Indices to the restart variable object
integer :: ir_npatch_si
integer :: ir_cd_status_si
integer :: ir_dd_status_si
integer :: ir_nchill_days_si
integer :: ir_ncold_days_si
integer :: ir_cleafondate_si
integer :: ir_cleafoffdate_si
integer :: ir_dleafondate_si
integer :: ir_dleafoffdate_si
integer :: ir_phenmodeldate_si
integer :: ir_acc_ni_si
integer :: ir_gdd_si
integer :: ir_snow_depth_si
integer :: ir_trunk_product_si
integer :: ir_ncohort_pa
integer :: ir_canopy_layer_co
integer :: ir_canopy_layer_yesterday_co
integer :: ir_crowndamage_co
integer :: ir_canopy_trim_co
integer :: ir_l2fr_co
integer :: ir_cx_int_co
integer :: ir_emadcxdt_co
integer :: ir_cx0_co
integer :: ir_cnplimiter_co
integer :: ir_daily_nh4_uptake_co
integer :: ir_daily_no3_uptake_co
integer :: ir_daily_n_fixation_co
integer :: ir_daily_p_uptake_co
integer :: ir_daily_n_demand_co
integer :: ir_daily_p_demand_co
integer :: ir_size_class_lasttimestep_co
integer :: ir_dbh_co
integer :: ir_coage_co
integer :: ir_g_sb_laweight_co
integer :: ir_height_co
integer :: ir_nplant_co
integer :: ir_gpp_acc_co
integer :: ir_npp_acc_co
integer :: ir_resp_acc_co
integer :: ir_gpp_acc_hold_co
integer :: ir_npp_acc_hold_co
integer :: ir_resp_acc_hold_co
integer :: ir_resp_excess_co
integer :: ir_bmort_co
integer :: ir_hmort_co
integer :: ir_cmort_co
integer :: ir_frmort_co
integer :: ir_smort_co
integer :: ir_asmort_co
integer :: ir_dgmort_co
integer :: ir_c_area_co
integer :: ir_treelai_co
integer :: ir_treesai_co
integer :: ir_canopy_layer_tlai_pa
!Logging
integer :: ir_lmort_direct_co
integer :: ir_lmort_collateral_co
integer :: ir_lmort_infra_co
! Radiation
integer :: ir_fcansno_pa
integer :: ir_solar_zenith_flag_pa
integer :: ir_solar_zenith_angle_pa
integer :: ir_gnd_alb_dif_pasb
integer :: ir_gnd_alb_dir_pasb
! Running Means
integer :: ir_tveg24_pa
integer :: ir_tveglpa_pa
integer :: ir_tveglongterm_pa
! (Keeping as an example)
!!integer :: ir_tveglpa_co
integer :: ir_ddbhdt_co
integer :: ir_resp_tstep_co
integer :: ir_pft_co
integer :: ir_status_co
integer :: ir_isnew_co
! Litter
integer :: ir_agcwd_litt
integer :: ir_bgcwd_litt
integer :: ir_leaf_litt
integer :: ir_fnrt_litt
integer :: ir_seed_litt
integer :: ir_seedgerm_litt
integer :: ir_seed_decay_litt
integer :: ir_seedgerm_decay_litt
integer :: ir_seed_prod_co
integer :: ir_livegrass_pa
integer :: ir_age_pa
integer :: ir_area_pa
integer :: ir_agesinceanthrodist_pa
integer :: ir_patchdistturbcat_pa
integer :: ir_nocomp_pft_label_pa
! Litter Fluxes (needed to restart
! with nutrient dynamics on, restarting
! mid-day
integer :: ir_agcwd_frag_litt
integer :: ir_bgcwd_frag_litt
integer :: ir_lfines_frag_litt
integer :: ir_rfines_frag_litt
integer :: ir_scorch_ht_pa_pft
integer :: ir_litter_moisture_pa_nfsc
! Site level
integer :: ir_recl2fr_sipfcl
integer :: ir_watermem_siwm
integer :: ir_vegtempmem_sitm
integer :: ir_seed_bank_sift
integer :: ir_spread_si
integer :: ir_recrate_sift
integer :: ir_use_this_pft_sift
integer :: ir_area_pft_sift
integer :: ir_fmortrate_cano_siscpf
integer :: ir_fmortrate_usto_siscpf
integer :: ir_imortrate_siscpf
integer :: ir_fmortrate_crown_siscpf
integer :: ir_fmortrate_cambi_siscpf
integer :: ir_termnindiv_cano_siscpf
integer :: ir_termnindiv_usto_siscpf
integer :: ir_growflx_fusion_siscpf
integer :: ir_demorate_sisc
integer :: ir_promrate_sisc
integer :: ir_termcarea_cano_si
integer :: ir_termcarea_usto_si
integer :: ir_imortcarea_si
integer :: ir_fmortcarea_cano_si
integer :: ir_fmortcarea_usto_si
integer :: ir_termcflux_cano_sipft
integer :: ir_termcflux_usto_sipft
integer :: ir_democflux_si
integer :: ir_promcflux_si
integer :: ir_imortcflux_sipft
integer :: ir_fmortcflux_cano_sipft
integer :: ir_fmortcflux_usto_sipft
integer :: ir_abg_term_flux_siscpf
integer :: ir_abg_imort_flux_siscpf
integer :: ir_abg_fmort_flux_siscpf
integer :: ir_cwdagin_flxdg
integer :: ir_cwdbgin_flxdg
integer :: ir_leaflittin_flxdg
integer :: ir_rootlittin_flxdg
integer :: ir_oldstock_mbal
integer :: ir_errfates_mbal
integer :: ir_woodprod_mbal
integer :: ir_prt_base ! Base index for all PRT variables
! Damage x damage or damage x size
integer :: ir_imortrate_sicdpf
integer :: ir_termnindiv_cano_sicdpf
integer :: ir_termnindiv_usto_sicdpf
integer :: ir_fmortrate_cano_sicdpf
integer :: ir_fmortrate_usto_sicdpf
integer :: ir_imortcflux_sicdsc
integer :: ir_termcflux_cano_sicdsc
integer :: ir_termcflux_usto_sicdsc
integer :: ir_fmortcflux_cano_sicdsc
integer :: ir_fmortcflux_usto_sicdsc
integer :: ir_crownarea_cano_si
integer :: ir_crownarea_usto_si
! Hydraulic indices
integer :: ir_hydro_th_ag_covec
integer :: ir_hydro_th_troot
integer :: ir_hydro_th_aroot_covec
integer :: ir_hydro_liqvol_shell_si
integer :: ir_hydro_recruit_si
integer :: ir_hydro_dead_si
integer :: ir_hydro_growturn_err_si
integer :: ir_hydro_hydro_err_si
integer :: ir_hydro_errh2o
! The number of variable dim/kind types we have defined (static)
integer, parameter, public :: fates_restart_num_dimensions = 2 !(cohort,column)
integer, parameter, public :: fates_restart_num_dim_kinds = 4 !(cohort-int,cohort-r8,site-int,site-r8)
! integer constants for storing logical data
integer, parameter, public :: old_cohort = 0
integer, parameter, public :: new_cohort = 1
real(r8), parameter, public :: flushinvalid = -9999.0
real(r8), parameter, public :: flushzero = 0.0
real(r8), parameter, public :: flushone = 1.0
! Local debug flag
logical, parameter, public :: debug=.false.
character(len=*), parameter :: sourcefile = &
__FILE__
! This structure is allocated by thread, and must be calculated after the FATES
! sites are allocated, and their mapping to the HLM is identified. This structure
! is not combined with iovar_bounds, because that one is multi-instanced. This
! structure is used more during the update phase, wherease _bounds is used
! more for things like flushing
type, public :: restart_map_type
integer, allocatable :: site_index(:) ! maps site indexes to the HIO site position
integer, allocatable :: cohort1_index(:) ! maps site index to the HIO cohort 1st position
end type restart_map_type
type, public :: fates_restart_interface_type
type(fates_restart_variable_type),allocatable :: rvars(:)
integer,private :: num_restart_vars_
! Instanteate one registry of the different dimension/kinds (dk)
! All output variables will have a pointer to one of these dk's
type(fates_io_variable_kind_type) :: dim_kinds(fates_restart_num_dim_kinds)
! This is a structure that explains where FATES patch boundaries
! on each thread point to in the host IO array, this structure is
! allocated by number of threads. This could be dynamically
! allocated, but is unlikely to change...?
! Note: history io also instanteates fates_io_dimension_type
type(fates_io_dimension_type) :: dim_bounds(fates_restart_num_dimensions)
type(restart_map_type), pointer :: restart_map(:)
integer, private :: cohort_index_, column_index_
contains
! public functions
procedure :: Init
procedure :: SetThreadBoundsEach
procedure :: assemble_restart_output_types
procedure :: initialize_restart_vars
procedure :: num_restart_vars
procedure :: column_index
procedure :: cohort_index
procedure :: set_restart_vectors
procedure :: create_patchcohort_structure
procedure :: get_restart_vectors
procedure :: update_3dpatch_radiation
! private work functions
procedure, private :: init_dim_kinds_maps
procedure, private :: set_dim_indices
procedure, private :: set_cohort_index
procedure, private :: set_column_index
procedure, private :: flush_rvars
procedure, private :: define_restart_vars
procedure, private :: set_restart_var
procedure, private :: DefinePRTRestartVars
procedure, private :: GetCohortRealVector
procedure, private :: SetCohortRealVector
procedure, private :: RegisterCohortVector
procedure, private :: DefineRMeanRestartVar
procedure, private :: GetRMeanRestartVar
procedure, private :: SetRMeanRestartVar
end type fates_restart_interface_type
contains
! =====================================================================================
subroutine Init(this, num_threads, fates_bounds)
use FatesIODimensionsMod, only : fates_bounds_type, column, cohort
implicit none
class(fates_restart_interface_type), intent(inout) :: this
integer, intent(in) :: num_threads
type(fates_bounds_type), intent(in) :: fates_bounds
integer :: dim_count = 0
dim_count = dim_count + 1
call this%set_cohort_index(dim_count)
call this%dim_bounds(dim_count)%Init(cohort, num_threads, &
fates_bounds%cohort_begin, fates_bounds%cohort_end)
dim_count = dim_count + 1
call this%set_column_index(dim_count)
call this%dim_bounds(dim_count)%Init(column, num_threads, &
fates_bounds%column_begin, fates_bounds%column_end)
! FIXME(bja, 2016-10) assert(dim_count == FatesIOdimensionsmod::num_dimension_types)
! Allocate the mapping between FATES indices and the IO indices
allocate(this%restart_map(num_threads))
end subroutine Init
! ======================================================================
subroutine SetThreadBoundsEach(this, thread_index, thread_bounds)
use FatesIODimensionsMod, only : fates_bounds_type
implicit none
class(fates_restart_interface_type), intent(inout) :: this
integer, intent(in) :: thread_index
type(fates_bounds_type), intent(in) :: thread_bounds
integer :: index
index = this%cohort_index()
call this%dim_bounds(index)%SetThreadBounds(thread_index, &
thread_bounds%cohort_begin, thread_bounds%cohort_end)
index = this%column_index()
call this%dim_bounds(index)%SetThreadBounds(thread_index, &
thread_bounds%column_begin, thread_bounds%column_end)
end subroutine SetThreadBoundsEach
! ===================================================================================
subroutine assemble_restart_output_types(this)
use FatesIOVariableKindMod, only : site_r8, site_int, cohort_r8, cohort_int
implicit none
class(fates_restart_interface_type), intent(inout) :: this
call this%init_dim_kinds_maps()
call this%set_dim_indices(cohort_r8, 1, this%cohort_index())
call this%set_dim_indices(cohort_int, 1, this%cohort_index())
call this%set_dim_indices(site_r8, 1, this%column_index())
call this%set_dim_indices(site_int, 1, this%column_index())
end subroutine assemble_restart_output_types
! ===================================================================================
subroutine set_dim_indices(this, dk_name, idim, dim_index)
use FatesIOVariableKindMod , only : iotype_index
implicit none
! arguments
class(fates_restart_interface_type), intent(inout) :: this
character(len=*), intent(in) :: dk_name
integer, intent(in) :: idim ! dimension index
integer, intent(in) :: dim_index
! local
integer :: ityp
ityp = iotype_index(trim(dk_name), fates_restart_num_dim_kinds, this%dim_kinds)
! First check to see if the dimension is allocated
if (this%dim_kinds(ityp)%ndims < idim) then
write(fates_log(), *) 'Trying to define dimension size to a dim-type structure'
write(fates_log(), *) 'but the dimension index does not exist'
write(fates_log(), *) 'type: ',dk_name,' ndims: ',this%dim_kinds(ityp)%ndims,' input dim:',idim
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
if (idim == 1) then
this%dim_kinds(ityp)%dim1_index = dim_index
else if (idim == 2) then
this%dim_kinds(ityp)%dim2_index = dim_index
end if
! With the map, we can set the dimension size
this%dim_kinds(ityp)%dimsize(idim) = this%dim_bounds(dim_index)%upper_bound - &
this%dim_bounds(dim_index)%lower_bound + 1
end subroutine set_dim_indices
! =======================================================================
subroutine set_cohort_index(this, index)
implicit none
class(fates_restart_interface_type), intent(inout) :: this
integer, intent(in) :: index
this%cohort_index_ = index
end subroutine set_cohort_index
integer function cohort_index(this)
implicit none
class(fates_restart_interface_type), intent(in) :: this
cohort_index = this%cohort_index_
end function cohort_index
! =======================================================================
subroutine set_column_index(this, index)
implicit none
class(fates_restart_interface_type), intent(inout) :: this
integer, intent(in) :: index
this%column_index_ = index
end subroutine set_column_index
integer function column_index(this)
implicit none
class(fates_restart_interface_type), intent(in) :: this
column_index = this%column_index_
end function column_index
! =======================================================================
subroutine init_dim_kinds_maps(this)
! ----------------------------------------------------------------------------------
! This subroutine simply initializes the structures that define the different
! array and type formats for different IO variables
!
! CO_R8 : 1D cohort scale 8-byte reals
! SI_R8 : 1D site scale 8-byte reals
! CO_INT : 1D cohort scale integers
! SI_INT : 1D site scale integers
!
! The allocation on the structures is not dynamic and should only add up to the
! number of entries listed here.
!
! ----------------------------------------------------------------------------------
use FatesIOVariableKindMod, only : site_r8, site_int, cohort_r8, cohort_int
implicit none
! Arguments
class(fates_restart_interface_type), intent(inout) :: this
integer :: index
! 1d cohort r8
index = 1
call this%dim_kinds(index)%Init(cohort_r8, 1)
! 1d Site r8
index = index + 1
call this%dim_kinds(index)%Init(site_r8, 1)
! cohort int
index = index + 1
call this%dim_kinds(index)%Init(cohort_int, 1)
! site int
index = index + 1
call this%dim_kinds(index)%Init(site_int, 1)
! FIXME(bja, 2016-10) assert(index == fates_num_dim_kinds)
end subroutine init_dim_kinds_maps
! ====================================================================================
integer function num_restart_vars(this)
implicit none
class(fates_restart_interface_type), intent(in) :: this
num_restart_vars = this%num_restart_vars_
end function num_restart_vars
! ====================================================================================
subroutine initialize_restart_vars(this)
implicit none
class(fates_restart_interface_type), intent(inout) :: this
! Determine how many of the restart IO variables registered in FATES
! are going to be allocated
call this%define_restart_vars(initialize_variables=.false.)
! Allocate the list of restart output variable objects
allocate(this%rvars(this%num_restart_vars()))
! construct the object that defines all of the IO variables
call this%define_restart_vars(initialize_variables=.true.)
end subroutine initialize_restart_vars
! ======================================================================================
subroutine flush_rvars(this,nc)
class(fates_restart_interface_type) :: this
integer,intent(in) :: nc
integer :: ivar
type(fates_restart_variable_type),pointer :: rvar
integer :: lb1,ub1,lb2,ub2
do ivar=1,ubound(this%rvars,1)
associate( rvar => this%rvars(ivar) )
call rvar%Flush(nc, this%dim_bounds, this%dim_kinds)
end associate
end do
end subroutine flush_rvars
! ====================================================================================
subroutine define_restart_vars(this, initialize_variables)
! ---------------------------------------------------------------------------------
!
! REGISTRY OF RESTART OUTPUT VARIABLES
!
! Please add any restart variables to this registry. This registry will handle
! all variables that can make use of 1D column dimensioned or 1D cohort dimensioned
! variables. Note that restarts are only using 1D vectors in ALM and CLM. If you
! have a multi-dimensional variable that is below the cohort scale, then pack
! that variable into a cohort-sized output array by giving it a vtype "cohort_r8"
! or "cohort_int".
!
! Unlike history variables, restarts flush to zero.
! ---------------------------------------------------------------------------------
use FatesIOVariableKindMod, only : site_r8, site_int, cohort_int, cohort_r8
implicit none
class(fates_restart_interface_type), intent(inout) :: this
logical, intent(in) :: initialize_variables ! are we 'count'ing or 'initializ'ing?
integer :: ivar
ivar=0
! -----------------------------------------------------------------------------------
! Site level variables
! -----------------------------------------------------------------------------------
call this%set_restart_var(vname='fates_PatchesPerSite', vtype=site_int, &
long_name='Total number of FATES patches per column', units='none', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_npatch_si )
call this%set_restart_var(vname='fates_cold_dec_status', vtype=site_int, &
long_name='status flag for cold deciduous plants', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_cd_status_si )
call this%set_restart_var(vname='fates_drought_dec_status', vtype=site_int, &
long_name='status flag for drought deciduous plants', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_dd_status_si )
call this%set_restart_var(vname='fates_chilling_days', vtype=site_int, &
long_name='chilling day counter', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_nchill_days_si )
call this%set_restart_var(vname='fates_cold_days', vtype=site_int, &
long_name='cold day counter', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_ncold_days_si )
call this%set_restart_var(vname='fates_cold_leafondate', vtype=site_int, &
long_name='the model day of last cold leaf on', units='absolute integer day', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_cleafondate_si )
call this%set_restart_var(vname='fates_cold_leafoffdate', vtype=site_int, &
long_name='the model day last cold leaf off', units='absolute integer day', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_cleafoffdate_si )
call this%set_restart_var(vname='fates_drought_leafondate', vtype=site_int, &
long_name='the model day of last drought based leaf-on', units='absolute integer day', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_dleafondate_si )
call this%set_restart_var(vname='fates_drought_leafoffdate', vtype=site_int, &
long_name='the model day of last drought based leaf-off', units='absolute integer day', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_dleafoffdate_si )
call this%set_restart_var(vname='fates_phen_model_date', vtype=site_int, &
long_name='integer model day used for phen timing', units='absolute integer day', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_phenmodeldate_si )
call this%set_restart_var(vname='fates_acc_nesterov_id', vtype=site_r8, &
long_name='a nesterov index accumulator', units='unitless', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_acc_ni_si )
call this%set_restart_var(vname='fates_gdd_site', vtype=site_r8, &
long_name='growing degree days at each site', units='degC days', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_gdd_si )
call this%set_restart_var(vname='fates_snow_depth_site', vtype=site_r8, &
long_name='average snow depth', units='m', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_snow_depth_si )
call this%set_restart_var(vname='fates_trunk_product_site', vtype=site_r8, &
long_name='Accumulate trunk product flux at site', &
units='kgC/m2', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_trunk_product_si )
! -----------------------------------------------------------------------------------
! Variables stored within cohort vectors
! Note: Some of these are multi-dimensional variables in the patch/site dimension
! that are collapsed into the cohort vectors for storage and transfer
! -----------------------------------------------------------------------------------
! This variable may be confusing, because it is a patch level variables
! but it is using the cohort IO vector to hold data
call this%set_restart_var(vname='fates_CohortsPerPatch', vtype=cohort_int, &
long_name='the number of cohorts per patch', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_ncohort_pa )
call this%set_restart_var(vname='fates_fcansno_pa', vtype=cohort_r8, &
long_name='Fraction of canopy covered in snow', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_fcansno_pa )
call this%set_restart_var(vname='fates_solar_zenith_flag_pa', vtype=cohort_int, &
long_name='switch specifying if zenith is positive', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_solar_zenith_flag_pa )
call this%set_restart_var(vname='fates_solar_zenith_angle_pa', vtype=cohort_r8, &
long_name='the angle of the solar zenith for each patch', units='radians', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_solar_zenith_angle_pa )
! 1D cohort Variables
! -----------------------------------------------------------------------------------
call this%set_restart_var(vname='fates_seed_prod', vtype=cohort_r8, &
long_name='fates cohort - seed production', units='kgC/plant', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_seed_prod_co )
call this%set_restart_var(vname='fates_canopy_layer', vtype=cohort_int, &
long_name='ed cohort - canopy_layer', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_canopy_layer_co )
call this%set_restart_var(vname='fates_canopy_layer_yesterday', vtype=cohort_r8, &
long_name='ed cohort - canopy_layer_yesterday', units='unitless', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_canopy_layer_yesterday_co )
call this%set_restart_var(vname='fates_crowndamage', vtype=cohort_int, &
long_name='ed cohort - crowndamage class', units='unitless', flushval = flushinvalid, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_crowndamage_co )
call this%set_restart_var(vname='fates_canopy_trim', vtype=cohort_r8, &
long_name='ed cohort - canopy_trim', units='fraction', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_canopy_trim_co )
call this%set_restart_var(vname='fates_l2fr', vtype=cohort_r8, &
long_name='ed cohort - l2fr', units='fraction', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_l2fr_co )
if(hlm_parteh_mode .eq. prt_cnp_flex_allom_hyp) then
call this%set_restart_var(vname='fates_cx_int', vtype=cohort_r8, &
long_name='ed cohort - emacx', units='fraction', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_cx_int_co )
call this%set_restart_var(vname='fates_emadcxdt', vtype=cohort_r8, &
long_name='ed cohort - emadcxdt', units='fraction', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_emadcxdt_co )
call this%set_restart_var(vname='fates_cx0', vtype=cohort_r8, &
long_name='ed cohort - cx0', units='fraction', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_cx0_co )
call this%set_restart_var(vname='fates_cnplimiter', vtype=cohort_r8, &
long_name='ed cohort - cnp limiter index', units='index', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_cnplimiter_co )
call this%set_restart_var(vname='fates_daily_nh4_uptake', vtype=cohort_r8, &
long_name='fates cohort- daily ammonium [NH4] uptake', &
units='kg/plant/day', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_daily_nh4_uptake_co )
call this%set_restart_var(vname='fates_daily_no3_uptake', vtype=cohort_r8, &
long_name='fates cohort- daily ammonium [NO3] uptake', &
units='kg/plant/day', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_daily_no3_uptake_co )
call this%set_restart_var(vname='fates_daily_n_fixation', vtype=cohort_r8, &
long_name='fates cohort- daily N symbiotic fixation', &
units='kg/plant/day', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_daily_n_fixation_co )
call this%set_restart_var(vname='fates_daily_p_uptake', vtype=cohort_r8, &
long_name='fates cohort- daily phosphorus uptake', &
units='kg/plant/day', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_daily_p_uptake_co )
call this%set_restart_var(vname='fates_daily_p_demand', vtype=cohort_r8, &
long_name='fates cohort- daily phosphorus demand', &
units='kgP/plant/day', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_daily_p_demand_co )
call this%set_restart_var(vname='fates_daily_n_demand', vtype=cohort_r8, &
long_name='fates cohort- daily nitrogen demand', &
units='kgN/plant/day', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_daily_n_demand_co )
end if
call this%set_restart_var(vname='fates_size_class_lasttimestep', vtype=cohort_int, &
long_name='ed cohort - size-class last timestep', units='index', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_size_class_lasttimestep_co )
call this%set_restart_var(vname='fates_dbh', vtype=cohort_r8, &
long_name='ed cohort - diameter at breast height', units='cm', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_dbh_co )
call this%set_restart_var(vname='fates_coage', vtype=cohort_r8, &
long_name='ed cohort - age in days', units='days', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_coage_co )
call this%set_restart_var(vname='fates_height', vtype=cohort_r8, &
long_name='ed cohort - plant height', units='m', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_height_co )
call this%set_restart_var(vname='fates_nplant', vtype=cohort_r8, &
long_name='ed cohort - number of plants in the cohort', &
units='/patch', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_nplant_co )
call this%set_restart_var(vname='fates_gpp_acc', vtype=cohort_r8, &
long_name='ed cohort - accumulated gpp over dynamics step', &
units='kgC/indiv', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_gpp_acc_co )
call this%set_restart_var(vname='fates_npp_acc', vtype=cohort_r8, &
long_name='ed cohort - accumulated npp over dynamics step', &
units='kgC/indiv', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_npp_acc_co )
call this%set_restart_var(vname='fates_resp_acc', vtype=cohort_r8, &
long_name='ed cohort - accumulated respiration over dynamics step', &
units='kgC/indiv', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_resp_acc_co )
call this%set_restart_var(vname='fates_gpp_acc_hold', vtype=cohort_r8, &
long_name='ed cohort - current step gpp', &
units='kgC/indiv/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_gpp_acc_hold_co )
call this%set_restart_var(vname='fates_npp_acc_hold', vtype=cohort_r8, &
long_name='ed cohort - current step npp', &
units='kgC/indiv/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_npp_acc_hold_co )
call this%set_restart_var(vname='fates_resp_acc_hold', vtype=cohort_r8, &
long_name='ed cohort - current step resp', &
units='kgC/indiv/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_resp_acc_hold_co )
call this%set_restart_var(vname='fates_resp_excess', vtype=cohort_r8, &
long_name='ed cohort - maintenance respiration deficit', &
units='kgC/indiv', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_resp_excess_co )
call this%set_restart_var(vname='fates_bmort', vtype=cohort_r8, &
long_name='ed cohort - background mortality rate', &
units='/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_bmort_co )
call this%set_restart_var(vname='fates_hmort', vtype=cohort_r8, &
long_name='ed cohort - hydraulic mortality rate', &
units='/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_hmort_co )
call this%set_restart_var(vname='fates_cmort', vtype=cohort_r8, &
long_name='ed cohort - carbon starvation mortality rate', &
units='/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_cmort_co )
call this%set_restart_var(vname='fates_frmort', vtype=cohort_r8, &
long_name='ed cohort - freezing mortality rate', &
units='/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_frmort_co )
call this%set_restart_var(vname='fates_smort', vtype=cohort_r8, &
long_name='ed cohort - senescence mortality rate', &
units='/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_smort_co )
call this%set_restart_var(vname='fates_asmort', vtype=cohort_r8, &
long_name='ed cohort - age senescence mortality rate', &
units = '/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_asmort_co )
call this%set_restart_var(vname='fates_dgmort', vtype=cohort_r8, &
long_name='ed cohort - damage mortality rate', &
units = '/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_dgmort_co )
call this%set_restart_var(vname='fates_lmort_direct', vtype=cohort_r8, &
long_name='ed cohort - directly logging mortality rate', &
units='%/event', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_lmort_direct_co )
call this%set_restart_var(vname='fates_lmort_collateral', vtype=cohort_r8, &
long_name='ed cohort - collateral mortality rate', &
units='%/event', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_lmort_collateral_co )
call this%set_restart_var(vname='fates_lmort_in', vtype=cohort_r8, &
long_name='ed cohort - mechanical mortality rate', &
units='%/event', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_lmort_infra_co )
call this%set_restart_var(vname='fates_ddbhdt', vtype=cohort_r8, &
long_name='ed cohort - differential: ddbh/dt', &
units='cm/year', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_ddbhdt_co )
call this%set_restart_var(vname='fates_resp_tstep', vtype=cohort_r8, &
long_name='ed cohort - autotrophic respiration over timestep', &
units='kgC/indiv/timestep', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_resp_tstep_co )
call this%set_restart_var(vname='fates_pft', vtype=cohort_int, &
long_name='ed cohort - plant functional type', units='index', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_pft_co )
call this%set_restart_var(vname='fates_status_coh', vtype=cohort_int, &
long_name='ed cohort - plant phenology status', units='unitless', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_status_co )
call this%set_restart_var(vname='fates_isnew', vtype=cohort_int, &
long_name='ed cohort - binary flag specifying if a plant has experienced a full day cycle', &
units='0/1', flushval = flushone, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_isnew_co )
call this%set_restart_var(vname='fates_gsblaweight',vtype=cohort_r8, &
long_name='ed cohort - leaf-area weighted total stomatal+blayer conductance', &
units='[m/s]*[m2]', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_g_sb_laweight_co)
! Mixed dimension variables using the cohort vector
! -----------------------------------------------------------------------------------
call this%set_restart_var(vname='fates_gnd_alb_dif', vtype=cohort_r8, &
long_name='ground albedo of diffuse radiation vis and ir', &
units='fraction', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_gnd_alb_dif_pasb )
call this%set_restart_var(vname='fates_gnd_alb_dir', vtype=cohort_r8, &
long_name='ground albedo of direct radiation vis and ir', &
units='fraction', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_gnd_alb_dir_pasb )
call this%set_restart_var(vname='fates_spread', vtype=site_r8, &
long_name='dynamic ratio of dbh to canopy area, by patch x canopy-layer', &
units='cm/m2', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_spread_si )
call this%set_restart_var(vname='fates_livegrass', vtype=cohort_r8, &
long_name='total AGB from grass, by patch', &
units='kgC/m2', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_livegrass_pa )
call this%set_restart_var(vname='fates_age', vtype=cohort_r8, &
long_name='age of the ED patch', units='yr', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_age_pa )
call this%set_restart_var(vname='fates_age_since_anthro_dist', vtype=cohort_r8, &
long_name='age of the ED patch since last anthropogenic disturbance', &
units='yr', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, &
index = ir_agesinceanthrodist_pa )
call this%set_restart_var(vname='fates_patchdistturbcat', vtype=cohort_int, &
long_name='Disturbance label of patch', units='yr', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_patchdistturbcat_pa )
call this%set_restart_var(vname='fates_nocomp_pft_label', vtype=cohort_int, &
long_name='PFT label of patch in nocomp mode', units='none', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_nocomp_pft_label_pa )
call this%set_restart_var(vname='fates_area', vtype=cohort_r8, &
long_name='are of the ED patch', units='m2', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_area_pa )
if(hlm_use_sp.eq.ifalse)then
call this%set_restart_var(vname='fates_scorch_ht_pa_pft', vtype=cohort_r8, &
long_name='scorch height', units='m', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_scorch_ht_pa_pft)
call this%set_restart_var(vname='fates_litter_moisture_pa_nfsc', vtype=cohort_r8, &
long_name='scorch height', units='m', flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_litter_moisture_pa_nfsc)
end if
! Site Level Diagnostics over multiple nutrients
! Patch Level Litter Pools are potentially multi-element
if(hlm_use_sp.eq.ifalse)then
call this%RegisterCohortVector(symbol_base='fates_ag_cwd', vtype=cohort_r8, &
long_name_base='above ground CWD', &
units='kg/m2', veclength=num_elements, flushval = flushzero, &
hlms='CLM:ALM', initialize=initialize_variables, ivar=ivar, index = ir_agcwd_litt)
call this%RegisterCohortVector(symbol_base='fates_bg_cwd', vtype=cohort_r8, &
long_name_base='below ground CWD', &
units='kg/m2', veclength=num_elements, flushval = flushzero, &