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PRTAllometricCNPMod.F90
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PRTAllometricCNPMod.F90
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module PRTAllometricCNPMod
! ------------------------------------------------------------------------------------
!
! This module contains all of the specific functions and types for
! Plant Allocation and Reactive Transport Extensible Hypotheses (PARTEH)
!
! Carbon-Nitrogen-Phosphorus (CNP) Prioritized Allometric Allocations
!
! Ryan Knox Aug 2018
!
! ------------------------------------------------------------------------------------
use PRTGenericMod , only : prt_global_type
use PRTGenericMod , only : prt_global
use PRTGenericMod , only : prt_vartypes
use PRTGenericMod , only : carbon12_element
use PRTGenericMod , only : nitrogen_element
use PRTGenericMod , only : phosphorus_element
use PRTGenericMod , only : max_nleafage
use PRTGenericMod , only : l2fr_min
use PRTGenericMod , only : leaf_organ
use PRTGenericMod , only : fnrt_organ
use PRTGenericMod , only : sapw_organ
use PRTGenericMod , only : store_organ
use PRTGenericMod , only : repro_organ
use PRTGenericMod , only : struct_organ
use PRTGenericMod , only : num_organ_types
use PRTGenericMod , only : prt_cnp_flex_allom_hyp
use PRTGenericMod , only : StorageNutrientTarget
use FatesAllometryMod , only : bleaf
use FatesAllometryMod , only : bsap_allom
use FatesAllometryMod , only : bfineroot
use FatesAllometryMod , only : bstore_allom
use FatesAllometryMod , only : bdead_allom
use FatesAllometryMod , only : bbgw_allom
use FatesAllometryMod , only : bagw_allom
use FatesAllometryMod , only : h_allom
use FatesAllometryMod , only : CheckIntegratedAllometries
use FatesGlobals , only : endrun => fates_endrun
use FatesGlobals , only : fates_log
use shr_log_mod , only : errMsg => shr_log_errMsg
use FatesConstantsMod , only : r8 => fates_r8
use FatesConstantsMod , only : i4 => fates_int
use FatesConstantsMod , only : calloc_abs_error
use FatesConstantsMod , only : rsnbl_math_prec
use FatesConstantsMod , only : years_per_day
use FatesConstantsMod , only : mm_per_cm
use FatesIntegratorsMod , only : RKF45
use FatesIntegratorsMod , only : Euler
use FatesConstantsMod , only : calloc_abs_error
use FatesConstantsMod , only : nearzero
use FatesConstantsMod , only : itrue
use FatesConstantsMod , only : fates_unset_r8
use FatesConstantsMod , only : fates_unset_int
use FatesConstantsMod , only : sec_per_day
use FatesConstantsMod , only : TRS_regeneration
use FatesConstantsMod , only : default_regeneration
use FatesConstantsMod , only : TRS_no_seedling_dyn
use FatesConstantsMod , only : min_max_dbh_for_trees
use PRTParametersMod , only : prt_params
use FatesConstantsMod , only : leaves_on,leaves_off
use FatesConstantsMod , only : leaves_shedding
use EDParamsMod , only : p_uptake_mode
use EDParamsMod , only : n_uptake_mode
use FatesConstantsMod , only : prescribed_p_uptake
use FatesConstantsMod , only : prescribed_n_uptake
use EDPftvarcon, only : EDPftvarcon_inst
use EDParamsMod , only : regeneration_model
implicit none
private
! -------------------------------------------------------------------------------------
!
! Define the state variables for this specific hypothesis. Give them units and define
! the indices that correspond with the generic classifications of PRT variables
!
! -------------------------------------------------------------------------------------
integer, parameter :: leaf_c_id = 1 ! leaf carbon index
integer, parameter :: fnrt_c_id = 2 ! fine-root carbon index
integer, parameter :: sapw_c_id = 3 ! sapwood carbon index
integer, parameter :: store_c_id = 4 ! storage carbon index
integer, parameter :: repro_c_id = 5 ! reproductive carbon index
integer, parameter :: struct_c_id = 6 ! structural carbon index
integer, parameter :: leaf_n_id = 7
integer, parameter :: fnrt_n_id = 8
integer, parameter :: sapw_n_id = 9
integer, parameter :: store_n_id = 10
integer, parameter :: repro_n_id = 11
integer, parameter :: struct_n_id = 12
integer, parameter :: leaf_p_id = 13
integer, parameter :: fnrt_p_id = 14
integer, parameter :: sapw_p_id = 15
integer, parameter :: store_p_id = 16
integer, parameter :: repro_p_id = 17
integer, parameter :: struct_p_id = 18
! Total number of state variables
integer, parameter :: num_vars = 18
! Global identifiers for the two stoichiometry values
integer,public, parameter :: stoich_growth_min = 1 ! Flag for stoichiometry associated with
! minimum needed for growth
! This is deprecated until a reasonable hypothesis is in place (RGK)
integer,public, parameter :: stoich_max = 2 ! Flag for stoichiometry associated with
! maximum for that organ
! This is the ordered list of organs used in this module
! -------------------------------------------------------------------------------------
integer, parameter :: num_organs = 6
! Converting from local to global organ id
integer, parameter,dimension(num_organs) :: l2g_organ_list = &
[leaf_organ, fnrt_organ, sapw_organ, store_organ, repro_organ, struct_organ]
! These are local indices associated with organs and quantities
! that can be integrated (namely, growth respiration during stature growth
! and dbh)
integer, parameter :: leaf_id = 1
integer, parameter :: fnrt_id = 2
integer, parameter :: sapw_id = 3
integer, parameter :: store_id = 4
integer, parameter :: repro_id = 5
integer, parameter :: struct_id = 6
integer, parameter :: dbh_id = 7
integer, parameter :: num_intgr_vars = 7
! -------------------------------------------------------------------------------------
! Input/Output Boundary Indices (These are public, and therefore
! each boundary condition across all modules must
! have a unique name !!!!)
! They are used in the routine, and also changed in the routine before
! being passed back
! -------------------------------------------------------------------------------------
integer, public, parameter :: acnp_bc_inout_id_dbh = 1 ! Plant DBH
integer, public, parameter :: acnp_bc_inout_id_resp_excess = 2 ! Respiration of excess storage
integer, public, parameter :: acnp_bc_inout_id_l2fr = 3 ! leaf 2 fineroot scalar, this
! is dynamic with CNP
integer, public, parameter :: acnp_bc_inout_id_netdn = 4 ! Index for the net daily NH4 input BC
integer, public, parameter :: acnp_bc_inout_id_netdp = 5 ! Index for the net daily P input BC
integer, public, parameter :: acnp_bc_inout_id_cx_int = 6 ! Index for the EMA log storage ratio max(N,P)/C
integer, public, parameter :: acnp_bc_inout_id_cx0 = 7 ! Index for the previous step's log storage ratio max(N,P)/C
integer, public, parameter :: acnp_bc_inout_id_emadcxdt = 8 ! Index for the EMA log storage ratio derivative d max(NP)/C dt
integer, public, parameter :: num_bc_inout = 8
! -------------------------------------------------------------------------------------
! Input only Boundary Indices (These are public)
! -------------------------------------------------------------------------------------
integer, public, parameter :: acnp_bc_in_id_pft = 1 ! Index for the PFT input BC
integer, public, parameter :: acnp_bc_in_id_ctrim = 2 ! Index for the canopy trim function
integer, public, parameter :: acnp_bc_in_id_lstat = 3 ! phenology status logical
integer, public, parameter :: acnp_bc_in_id_netdc = 4 ! Index for the net daily C input BC
integer, public, parameter :: acnp_bc_in_id_nc_repro = 5
integer, public, parameter :: acnp_bc_in_id_pc_repro = 6
integer, public, parameter :: acnp_bc_in_id_cdamage = 7 ! Index for the crowndamage input BC
integer, public, parameter :: acnp_bc_in_id_efleaf = 8 ! Leaf elongation factor
integer, public, parameter :: acnp_bc_in_id_effnrt = 9 ! Fine-root "elongation factor"
integer, public, parameter :: acnp_bc_in_id_efstem = 10 ! Stem "elongation factor"
integer, parameter :: num_bc_in = 10
! -------------------------------------------------------------------------------------
! Output Boundary Indices (These are public)
! -------------------------------------------------------------------------------------
integer, public, parameter :: acnp_bc_out_id_cefflux = 1 ! Daily exudation of C [kg]
integer, public, parameter :: acnp_bc_out_id_nefflux = 2 ! Daily exudation of N [kg]
integer, public, parameter :: acnp_bc_out_id_pefflux = 3 ! Daily exudation of P [kg]
integer, public, parameter :: acnp_bc_out_id_limiter = 4 ! The minimum of the Nutrient ratio over c ratio
integer, parameter :: num_bc_out = 4 ! Total number of
! Indices for parameters passed to the integrator
integer,private, parameter :: intgr_parm_ctrim = 1
integer,private, parameter :: intgr_parm_pft = 2
integer,private, parameter :: intgr_parm_l2fr = 3
integer,private, parameter :: intgr_parm_cdamage = 4
integer,private, parameter :: intgr_parm_efleaf = 5
integer,private, parameter :: intgr_parm_effnrt = 6
integer,private, parameter :: intgr_parm_efstem = 7
integer,private, parameter :: num_intgr_parm = 7
! -------------------------------------------------------------------------------------
! Define the size of the coorindate vector. For this hypothesis, there is only
! one pool per each species x organ combination, except for leaves (WHICH HAVE AGE)
! icd refers to the first index in the leaf array, which is the youngest. Growth
! and allocation only happens in the youngest bin by definition
! -------------------------------------------------------------------------------------
integer, parameter :: icd = 1
! These constants define different methods of dealing with excess carbon at
! the end of the allocation process, assuming that N or P is limiting growth.
! You can either exude (send to soil), retain (grow storage without limit),
! or burn (as respiration to the atm).
integer, parameter :: exude_c_store_overflow = 1
integer, parameter :: retain_c_store_overflow = 2
integer, parameter :: burn_c_store_overflow = 3
integer, parameter :: store_c_overflow = burn_c_store_overflow
! These constants define if/how growth is limited by
! one of the 3 chemical species, 0 indicates there is some
! degree of co limitation
integer, parameter :: cnp_limited = 0
integer, parameter :: c_limited = 1
integer, parameter :: n_limited = 2
integer, parameter :: p_limited = 3
! Flags to select using the equivalent carbon method of co-limitation,
! or to just grow with available carbon and let it fix itself on the
! next step
integer, parameter :: grow_lim_conly = 1 ! Just use C to decide stature on this step
integer, parameter :: grow_lim_estNP = 2 ! Estimate equivalent C from N and P
integer, parameter :: grow_lim_type = grow_lim_estNP
! Following growth, if desired, you can prioritize that
! reproductive tissues get balanced CNP
logical, parameter :: prioritize_repro_nutr_growth = .true.
! If this parameter is true, then the fine-root l2fr optimization
! scheme will remove biomass from roots without restriction if the
! l2fr is getting smaller.
logical, parameter :: use_unrestricted_contraction = .true.
! -------------------------------------------------------------------------------------
! This is the core type that holds this specific
! plant reactive transport (PRT) module
! -------------------------------------------------------------------------------------
type, public, extends(prt_vartypes) :: cnp_allom_prt_vartypes
contains
procedure :: DailyPRT => DailyPRTAllometricCNP
procedure :: FastPRT => FastPRTAllometricCNP
procedure :: GetNutrientTarget => GetNutrientTargetCNP
! Extended functions specific to Allometric CNP
procedure :: CNPPrioritizedReplacement
procedure :: CNPStatureGrowth
procedure :: EstimateGrowthNC
procedure :: CNPAdjustFRootTargets
procedure :: CNPAllocateRemainder
procedure :: GetDeficit
procedure :: TrimFineRoot
end type cnp_allom_prt_vartypes
! ------------------------------------------------------------------------------------
!
! This next class is an extention of the base instance that maps state variables
! to the outside model.
!
! This is the instance of the mapping table and variable definitions
! this is only allocated once per node
! ------------------------------------------------------------------------------------
class(prt_global_type), public, target, allocatable :: prt_global_acnp
character(len=*), parameter, private :: sourcefile = __FILE__
logical, parameter :: debug = .false.
public :: InitPRTGlobalAllometricCNP
contains
subroutine InitPRTGlobalAllometricCNP()
! ----------------------------------------------------------------------------------
! Initialize and populate the general mapping table that
! organizes the specific variables in this module to
! pre-ordained groups, so they can be used to inform
! the rest of the model
!
! This routine is not part of the sp_pool_vartypes class
! because it is the same for all plants and we need not
! waste memory on it.
! -----------------------------------------------------------------------------------
integer :: nleafage
integer :: istat
character(len=255) :: smsg
allocate(prt_global_acnp, stat=istat, errmsg=smsg)
if (istat/=0) call endrun(msg='allocate stat/=0:'//trim(smsg)//errMsg(sourcefile, __LINE__))
allocate(prt_global_acnp%state_descriptor(num_vars), stat=istat, errmsg=smsg)
if (istat/=0) call endrun(msg='allocate stat/=0:'//trim(smsg)//errMsg(sourcefile, __LINE__))
prt_global_acnp%hyp_name = 'Allometric Flexible C+N+P'
prt_global_acnp%hyp_id = prt_cnp_flex_allom_hyp
call prt_global_acnp%ZeroGlobal()
! The number of leaf age classes can be determined from the parameter file,
! notably the size of the leaf-longevity parameter's second dimension.
! This is the same value in FatesInterfaceMod.F90
nleafage = size(prt_params%leaf_long,dim=2)
if(nleafage>max_nleafage) then
write(fates_log(),*) 'The allometric carbon PARTEH hypothesis'
write(fates_log(),*) 'sets a maximum number of leaf age classes'
write(fates_log(),*) 'used for scratch space. The model wants'
write(fates_log(),*) 'exceed that. Simply increase max_nleafage'
write(fates_log(),*) 'found in parteh/PRTAllometricCarbonMod.F90'
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
call prt_global_acnp%RegisterVarInGlobal(leaf_c_id,'Leaf Carbon','leaf_c',leaf_organ,carbon12_element,nleafage)
call prt_global_acnp%RegisterVarInGlobal(fnrt_c_id,'Fine Root Carbon','fnrt_c',fnrt_organ,carbon12_element,icd)
call prt_global_acnp%RegisterVarInGlobal(sapw_c_id,'Sapwood Carbon','sapw_c',sapw_organ,carbon12_element,icd)
call prt_global_acnp%RegisterVarInGlobal(store_c_id,'Storage Carbon','store_c',store_organ,carbon12_element,icd)
call prt_global_acnp%RegisterVarInGlobal(struct_c_id,'Structural Carbon','struct_c',struct_organ,carbon12_element,icd)
call prt_global_acnp%RegisterVarInGlobal(repro_c_id,'Reproductive Carbon','repro_c',repro_organ,carbon12_element,icd)
call prt_global_acnp%RegisterVarInGlobal(leaf_n_id,'Leaf Nitrogen','leaf_n',leaf_organ,nitrogen_element,nleafage)
call prt_global_acnp%RegisterVarInGlobal(fnrt_n_id,'Fine Root Nitrogen','fnrt_n',fnrt_organ,nitrogen_element,icd)
call prt_global_acnp%RegisterVarInGlobal(sapw_n_id,'Sapwood Nitrogen','sapw_n',sapw_organ,nitrogen_element,icd)
call prt_global_acnp%RegisterVarInGlobal(store_n_id,'Storage Nitrogen','store_n',store_organ,nitrogen_element,icd)
call prt_global_acnp%RegisterVarInGlobal(struct_n_id,'Structural Nitrogen','struct_n',struct_organ,nitrogen_element,icd)
call prt_global_acnp%RegisterVarInGlobal(repro_n_id,'Reproductive Nitrogen','repro_n',repro_organ,nitrogen_element,icd)
call prt_global_acnp%RegisterVarInGlobal(leaf_p_id,'Leaf Phosphorus','leaf_p',leaf_organ,phosphorus_element,nleafage)
call prt_global_acnp%RegisterVarInGlobal(fnrt_p_id,'Fine Root Phosphorus','fnrt_p',fnrt_organ,phosphorus_element,icd)
call prt_global_acnp%RegisterVarInGlobal(sapw_p_id,'Sapwood Phosphorus','sapw_p',sapw_organ,phosphorus_element,icd)
call prt_global_acnp%RegisterVarInGlobal(store_p_id,'Storage Phosphorus','store_p',store_organ,phosphorus_element,icd)
call prt_global_acnp%RegisterVarInGlobal(struct_p_id,'Structural Phosphorus','struct_p',struct_organ,phosphorus_element,icd)
call prt_global_acnp%RegisterVarInGlobal(repro_p_id,'Reproductive Phosphorus','repro_p',repro_organ,phosphorus_element,icd)
! Set some of the array sizes for input and output boundary conditions
prt_global_acnp%num_bc_in = num_bc_in
prt_global_acnp%num_bc_out = num_bc_out
prt_global_acnp%num_bc_inout = num_bc_inout
prt_global_acnp%num_vars = num_vars
! Have the global generic pointer, point to this hypothesis' object
prt_global => prt_global_acnp
return
end subroutine InitPRTGlobalAllometricCNP
! =====================================================================================
subroutine DailyPRTAllometricCNP(this,phase)
class(cnp_allom_prt_vartypes) :: this
integer,intent(in) :: phase ! the phase splits the routine into parts
! note that phasing is used primarily to
! accomodate the damage module. Damage
! and nutrient cycling are not yet compatable though
! hence, we simply return from any phase but phase 1
! Pointers to in-out bcs
real(r8),pointer :: dbh ! Diameter at breast height [cm]
real(r8),pointer :: resp_excess ! Respiration of any un-allocatable C
real(r8),pointer :: l2fr ! Leaf to fineroot ratio of target biomass
! Input only bcs
integer :: ipft ! Plant Functional Type index
real(r8) :: c_gain ! Daily carbon balance for this cohort [kgC]
real(r8),pointer :: n_gain ! Daily nitrogen uptake through fine-roots [kgN]
real(r8),pointer :: p_gain ! Daily phosphorus uptake through fine-roots [kgN]
real(r8) :: canopy_trim ! The canopy trimming function [0-1]
integer :: crown_damage ! which crown damage clas
real(r8) :: elongf_leaf ! Leaf elongation factor [0-1]
real(r8) :: elongf_fnrt ! Fine-root "elongation factor" [0-1]
real(r8) :: elongf_stem ! Stem "elongation factor" [0-1]
! Pointers to output bcs
real(r8),pointer :: c_efflux ! Total plant efflux of carbon (kgC)
real(r8),pointer :: n_efflux ! Total plant efflux of nitrogen (kgN)
real(r8),pointer :: p_efflux ! Total plant efflux of phosphorus (kgP)
! Allometry targets (kg/plant) and (kg/cm/plant)
real(r8), dimension(num_organ_types) :: target_c, target_dcdd
! Initial states (for accounting) (kg/plant)
real(r8), dimension(num_organ_types) :: state_c0, state_n0, state_p0
! Allometry partial targets
real(r8) :: agw_c_target,agw_dcdd_target
real(r8) :: bgw_c_target,bgw_dcdd_target
real(r8) :: sapw_area
real(r8) :: store_flux
integer :: i ! generic organ loop index
integer :: i_org ! organ index
integer :: i_var ! variable index
! These are daily mass gains, frozen in time, not drawn from, and thus
! these are only used for evaluating mass balancing at the end
real(r8) :: dbh0
real(r8) :: c_gain0
real(r8) :: n_gain0
real(r8) :: p_gain0
real(r8) :: resp_excess0
! Used for mass checking, total mass allocated based
! on change in the states, should match gain0's
real(r8) :: allocated_c
real(r8) :: allocated_n
real(r8) :: allocated_p
real(r8) :: sum_c ! error checking sum
! Phasing is only used to accomodate the
! damage module. Since this is incompatible with CNP
! Ignore all subsequent calls after the first
if (phase.ne.1) return
! In/out boundary conditions
resp_excess => this%bc_inout(acnp_bc_inout_id_resp_excess)%rval
dbh => this%bc_inout(acnp_bc_inout_id_dbh)%rval
dbh0 = dbh
l2fr => this%bc_inout(acnp_bc_inout_id_l2fr)%rval
n_gain => this%bc_inout(acnp_bc_inout_id_netdn)%rval
p_gain => this%bc_inout(acnp_bc_inout_id_netdp)%rval
! Assume that there is no other source of excess respiration
! so it is safe to zero it. In the third stage we will
! decide if this should be updated
resp_excess = 0._r8
resp_excess0 = resp_excess
! integrator variables
! Copy the input only boundary conditions into readable local variables
! We don't use pointers, because inputs should be intent in only
! Also, we save the initial values of many of these BC's
! for checking and resetting if needed
! -----------------------------------------------------------------------------------
c_gain = this%bc_in(acnp_bc_in_id_netdc)%rval
canopy_trim = this%bc_in(acnp_bc_in_id_ctrim)%rval
ipft = this%bc_in(acnp_bc_in_id_pft)%ival
crown_damage = this%bc_in(acnp_bc_in_id_cdamage)%ival
elongf_leaf = this%bc_in(acnp_bc_in_id_efleaf)%rval
elongf_fnrt = this%bc_in(acnp_bc_in_id_effnrt)%rval
elongf_stem = this%bc_in(acnp_bc_in_id_efstem)%rval
! If either n or p uptake is in prescribed mode
! set the gains to something massive. 1 kilo of pure
! nutrient should be wayyy more than enough
if(n_uptake_mode.eq.prescribed_n_uptake) then
n_gain = 1.e3_r8
end if
if(p_uptake_mode.eq.prescribed_p_uptake) then
p_gain = 1.e3_r8
end if
n_gain0 = n_gain
p_gain0 = p_gain
c_gain0 = c_gain
! Calculate Carbon allocation targets
! -----------------------------------------------------------------------------------
! Set carbon targets based on the plant's current stature
target_c(:) = fates_unset_r8
target_dcdd(:) = fates_unset_r8
call bsap_allom(dbh,ipft,crown_damage,canopy_trim,elongf_stem,sapw_area,target_c(sapw_organ),target_dcdd(sapw_organ))
call bagw_allom(dbh,ipft,crown_damage,elongf_stem,agw_c_target,agw_dcdd_target)
call bbgw_allom(dbh,ipft,elongf_stem,bgw_c_target,bgw_dcdd_target)
call bdead_allom(agw_c_target,bgw_c_target,target_c(sapw_organ),ipft,target_c(struct_organ), &
agw_dcdd_target,bgw_dcdd_target,target_dcdd(sapw_organ),target_dcdd(struct_organ))
call bleaf(dbh,ipft,crown_damage,canopy_trim, elongf_leaf, target_c(leaf_organ), target_dcdd(leaf_organ))
call bfineroot(dbh,ipft,canopy_trim, l2fr, elongf_fnrt, target_c(fnrt_organ), target_dcdd(fnrt_organ))
call bstore_allom(dbh,ipft,crown_damage, canopy_trim, target_c(store_organ), target_dcdd(store_organ))
target_c(repro_organ) = 0._r8
target_dcdd(repro_organ) = 0._r8
! ===================================================================================
! Step 1: Evaluate nutrient storage in the plant. Depending on how low
! these stores are, we will move proportionally more or less of the daily carbon
! gain to increase the target fine-root biomass, fill up to target
! and then attempt to get them up to stoichiometry targets.
! ===================================================================================
! Remember the original C,N,P states to help with final
! evaluation of how much was allocated
! -----------------------------------------------------------------------------------
do i = 1,num_organs
i_org = l2g_organ_list(i) ! global index from PRTGeneric
i_var = prt_global%sp_organ_map(i_org,carbon12_element)
state_c0(i_org) = this%variables(i_var)%val(1)
i_var = prt_global%sp_organ_map(i_org,nitrogen_element)
state_n0(i_org) = this%variables(i_var)%val(1)
i_var = prt_global%sp_organ_map(i_org,phosphorus_element)
state_p0(i_org) = this%variables(i_var)%val(1)
end do
! Output only boundary conditions
c_efflux => this%bc_out(acnp_bc_out_id_cefflux)%rval; c_efflux = 0._r8
n_efflux => this%bc_out(acnp_bc_out_id_nefflux)%rval; n_efflux = 0._r8
p_efflux => this%bc_out(acnp_bc_out_id_pefflux)%rval; p_efflux = 0._r8
! ===================================================================================
! Step 0. Transfer all stored nutrient into the daily uptake pool. Also
! transfer C storage that is above the target (ie transfer overflow)
! ===================================================================================
! Put overflow storage into the net daily pool
store_flux = max(0._r8, this%variables(store_c_id)%val(1) - target_c(store_organ))
c_gain = c_gain + store_flux
this%variables(store_c_id)%val(1) = this%variables(store_c_id)%val(1) - store_flux
n_gain = n_gain + sum(this%variables(store_n_id)%val(:))
this%variables(store_n_id)%val(:) = 0._r8
p_gain = p_gain + sum(this%variables(store_p_id)%val(:))
this%variables(store_p_id)%val(:) = 0._r8
! ===================================================================================
! Step 2. Prioritized allocation to replace tissues from turnover, and/or pay
! any un-paid maintenance respiration from storage.
! ===================================================================================
call this%CNPPrioritizedReplacement(c_gain, n_gain, p_gain, target_c)
sum_c = 0._r8
do i = 1,num_organs
i_org = l2g_organ_list(i)
i_var = prt_global%sp_organ_map(i_org,carbon12_element)
sum_c = sum_c+this%variables(i_var)%val(1)
end do
if( abs((c_gain0-c_gain) - &
(sum_c-sum(state_c0(:),dim=1))) >calloc_abs_error ) then
write(fates_log(),*) 'Carbon not balancing I'
do i = 1,num_organs
i_org = l2g_organ_list(i)
write(fates_log(),*) 'c: ',this%variables(prt_global%sp_organ_map(i_org,carbon12_element))%val(1)
end do
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
! ===================================================================================
! Step 3. Grow out the stature of the plant by allocating to tissues beyond
! current targets.
! Attempts have been made to get all pools and species closest to allometric
! targets based on prioritized relative demand and allometry functions.
! ===================================================================================
call this%CNPStatureGrowth(c_gain, n_gain, p_gain, target_c, target_dcdd)
sum_c = 0._r8
do i = 1,num_organs
i_org = l2g_organ_list(i)
i_var = prt_global%sp_organ_map(i_org,carbon12_element)
sum_c = sum_c+this%variables(i_var)%val(1)
end do
if( abs((c_gain0-c_gain) - &
(sum_c-sum(state_c0(:),dim=1))) >calloc_abs_error ) then
write(fates_log(),*) 'Carbon not balancing II'
do i = 1,num_organs
i_org = l2g_organ_list(i)
write(fates_log(),*) 'c: ',this%variables(prt_global%sp_organ_map(i_org,carbon12_element))%val(1)
end do
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
! ===================================================================================
! Step 3.
! At this point, at least 1 of the 3 resources have been used up.
! Allocate the remaining resources, or as a last resort, efflux them.
! ===================================================================================
call this%CNPAllocateRemainder(c_gain, n_gain, p_gain, &
c_efflux, n_efflux, p_efflux,target_c,target_dcdd)
if(n_uptake_mode.ne.prescribed_n_uptake) then
if( abs(n_gain) > 0.1_r8*calloc_abs_error) then
write(fates_log(),*) 'Allocation scheme should had used up all mass gain pools'
write(fates_log(),*) 'Any mass that cannot be allocated should be effluxed'
write(fates_log(),*) 'n_gain: ',n_gain
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
end if
if(p_uptake_mode.ne.prescribed_p_uptake) then
if( abs(p_gain) > 0.01_r8*calloc_abs_error) then
write(fates_log(),*) 'Allocation scheme should had used up all mass gain pools'
write(fates_log(),*) 'Any mass that cannot be allocated should be effluxed'
write(fates_log(),*) 'p_gain: ',p_gain
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
end if
if( abs(c_gain) > calloc_abs_error) then
write(fates_log(),*) 'Allocation scheme should had used up all mass gain pools'
write(fates_log(),*) 'Any mass that cannot be allocated should be effluxed'
write(fates_log(),*) 'c_gain: ',c_gain
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
! Perform a final tally on what was used (allocated)
! Since this is also a check against what was available
! we include what is lost through respiration of excess storage
allocated_c = (resp_excess-resp_excess0) + c_efflux
allocated_n = n_efflux
allocated_p = p_efflux
! Update the allocation flux diagnostic arrays for each 3 elements
do i = 1,num_organs
i_org = l2g_organ_list(i)
i_var = prt_global%sp_organ_map(i_org,carbon12_element)
this%variables(i_var)%net_alloc(1) = &
this%variables(i_var)%net_alloc(1) + (this%variables(i_var)%val(1) - state_c0(i_org))
allocated_c = allocated_c + (this%variables(i_var)%val(1) - state_c0(i_org))
i_var = prt_global%sp_organ_map(i_org,nitrogen_element)
this%variables(i_var)%net_alloc(1) = &
this%variables(i_var)%net_alloc(1) + (this%variables(i_var)%val(1) - state_n0(i_org))
allocated_n = allocated_n + (this%variables(i_var)%val(1) - state_n0(i_org))
i_var = prt_global%sp_organ_map(i_org,phosphorus_element)
this%variables(i_var)%net_alloc(1) = &
this%variables(i_var)%net_alloc(1) + (this%variables(i_var)%val(1) - state_p0(i_org))
allocated_p = allocated_p + (this%variables(i_var)%val(1) - state_p0(i_org))
end do
if(debug) then
! Error Check: Do a final balance between how much mass
! we had to work with, and how much was allocated
if ( abs(allocated_c - (c_gain0-c_gain)) > calloc_abs_error .or. &
abs(allocated_n - (n_gain0-n_gain)) > calloc_abs_error .or. &
abs(allocated_p - (p_gain0-p_gain)) > calloc_abs_error ) then
write(fates_log(),*) 'CNP allocation scheme did not balance mass.'
write(fates_log(),*) 'c_gain0: ',c_gain0,' allocated_c: ',allocated_c,resp_excess,resp_excess0,c_efflux
write(fates_log(),*) 'n_gain0: ',n_gain0,' allocated_n: ',allocated_n
write(fates_log(),*) 'p_gain0: ',p_gain0,' allocated_p: ',allocated_p
do i = 1,num_organs
i_org = l2g_organ_list(i)
i_var = prt_global%sp_organ_map(i_org,carbon12_element)
write(fates_log(),*) i_org, this%variables(i_var)%val(1)-state_c0(i_org)
end do
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
end if
! IF this was prescribed, then we dictate the uptake
! and pass that back as an output, otherwise
! we set the gains to what we started with so that
! it can be used again for mass balance checking and diagnostics
if(n_uptake_mode.eq.prescribed_n_uptake) then
n_gain = n_gain0-n_gain
else
n_gain = n_gain0
end if
if(p_uptake_mode.eq.prescribed_p_uptake) then
p_gain = p_gain0-p_gain
else
p_gain = p_gain0
end if
! If fine-roots are allocated above their
! target (perhaps with some buffer, but perhaps not)
! then
call this%TrimFineRoot()
return
end subroutine DailyPRTAllometricCNP
function SafeLog(val) result(logval)
! The log functions used to transform storage ratios
! need not be large. Even a ratio of 10 is sending a strong signal to the
! root adaptation algorithm to change course pretty strongly. We set
! bounds of e3 here to prevent numerical overflows and underflows
real(r8) :: val
real(r8) :: logval
real(r8), parameter :: safelog_min = 0.001_r8 !Don't pass anything smaller to a log
real(r8), parameter :: safelog_max = 1000._r8
logval = log(max(safelog_min,min(safelog_max,val)))
end function SafeLog
! =====================================================================================
subroutine CNPAdjustFRootTargets(this, target_c, target_dcdd)
class(cnp_allom_prt_vartypes) :: this
real(r8) :: target_c(:)
real(r8) :: target_dcdd(:)
real(r8), pointer :: l2fr ! leaf to fineroot target biomass scaler
integer :: ipft ! PFT index
real(r8), pointer :: dbh
real(r8) :: canopy_trim
integer :: leaf_status
integer, pointer :: limiter
real(r8) :: elongf_fnrt
real(r8) :: store_c_max, store_c_act
real(r8) :: store_nut_max, store_nut_act
real(r8) :: l2fr_delta
real(r8) :: cn_ratio, cp_ratio ! ratio of relative C storage over relative N or P storage
real(r8) :: dcxdt_ratio ! log change (derivative) of the maximum of the N/C and P/C storage ratio
real(r8) :: cx_logratio ! log Maximum of the C/N and C/P storage ratio
real(r8), pointer :: cx_int ! Integration of the cx_logratio
real(r8), pointer :: cx0 ! The log of the cx ratio from previous time-step
real(r8), pointer :: ema_dcxdt ! the EMA of the change in log storage ratio
real(r8), parameter :: pid_drv_wgt = 1._r8/20._r8 ! n-day smoothing of the derivative
! of the process function in the PID controller
leaf_status = this%bc_in(acnp_bc_in_id_lstat)%ival
ipft = this%bc_in(acnp_bc_in_id_pft)%ival
elongf_fnrt = this%bc_in(acnp_bc_in_id_effnrt)%rval
l2fr => this%bc_inout(acnp_bc_inout_id_l2fr)%rval
dbh => this%bc_inout(acnp_bc_inout_id_dbh)%rval
canopy_trim = this%bc_in(acnp_bc_in_id_ctrim)%rval
cx_int => this%bc_inout(acnp_bc_inout_id_cx_int)%rval
cx0 => this%bc_inout(acnp_bc_inout_id_cx0)%rval
ema_dcxdt => this%bc_inout(acnp_bc_inout_id_emadcxdt)%rval
limiter => this%bc_out(acnp_bc_out_id_limiter)%ival
! Abort if leaves are off
if(leaf_status.eq.leaves_off) return
! Step 1: Determine the process function for the controller. Generally, this is
! some indicator about the relative health of the plant in terms of carbon versus
! nutrient. There are a few ways to cast this function, but right now we are using
! the relative amount of Carbon storage (actual/maximum) divided by the relative amount
! of nutrient (actual/maximum). We take the natural log of this ratio. And then we take
! maximum of the two quotients that use nitrogen and phosphorus.
! -----------------------------------------------------------------------------------
store_c_max = target_c(store_organ)
store_c_act = max(0.001_r8*store_c_max,this%GetState(store_organ, carbon12_element) + &
this%bc_in(acnp_bc_in_id_netdc)%rval)
if(n_uptake_mode.eq.prescribed_n_uptake)then
cn_ratio = -1._r8
else
! Calculate the relative nitrogen storage fraction,
! over the relative carbon storage fraction.
store_nut_max = this%GetNutrientTarget(nitrogen_element,store_organ,stoich_growth_min)
store_nut_act = max(0.001_r8*store_nut_max, &
this%GetState(store_organ, nitrogen_element) + &
this%bc_inout(acnp_bc_inout_id_netdn)%rval)
cn_ratio = (store_c_act/store_c_max)/(store_nut_act/store_nut_max)
end if
if(p_uptake_mode.eq.prescribed_p_uptake)then
cp_ratio = -1._r8
else
! Calculate the relative phosphorus storage fraction,
! over the relative carbon storage fraction.
store_nut_max = this%GetNutrientTarget(phosphorus_element,store_organ,stoich_growth_min)
store_nut_act = max(0.001_r8*store_nut_max, &
this%GetState(store_organ, phosphorus_element) + &
this%bc_inout(acnp_bc_inout_id_netdp)%rval)
cp_ratio = (store_c_act/store_c_max)/(store_nut_act/store_nut_max)
end if
! Use the limiting nutrient species
if( (n_uptake_mode.eq.prescribed_n_uptake) .and. &
(p_uptake_mode.eq.prescribed_p_uptake) )then
cx_int = 0._r8
ema_dcxdt = 0._r8
cx0 = 0.0_r8
return
else
if (n_uptake_mode.eq.prescribed_n_uptake) then
cx_logratio = SafeLog(cp_ratio)
elseif (p_uptake_mode.eq.prescribed_p_uptake) then
cx_logratio = SafeLog(cn_ratio)
else
cx_logratio = SafeLog(max(cp_ratio,cn_ratio))
end if
! If cx_logratio has just crossed zero, then
! reset the integrator. This will be true if
! the sign of the current ratio is different than
! the sign of the previous
cx_int = cx_int + cx_logratio
! Reset the integrator if its sign changes
if( abs(cx_logratio)>nearzero .and. abs(cx0)>nearzero) then
if( abs(cx_logratio/abs(cx_logratio) - cx0/abs(cx0)) > nearzero ) then
cx_int = cx_logratio
end if
end if
dcxdt_ratio = cx_logratio-cx0
ema_dcxdt = pid_drv_wgt*dcxdt_ratio + (1._r8-pid_drv_wgt)*ema_dcxdt
cx0 = cx_logratio
end if
l2fr_delta = prt_params%pid_kp(ipft)*cx_logratio + &
prt_params%pid_ki(ipft)*cx_int + &
prt_params%pid_kd(ipft)*ema_dcxdt
! Apply the delta, also, avoid generating incredibly small l2fr's,
! super small l2frs will occur in plants that perpetually get almost
! now carbon gain, such as newly recruited plants in a dark understory
l2fr = max(l2fr_min, l2fr + l2fr_delta)
! Find the updated target fineroot biomass
call bfineroot(dbh,ipft,canopy_trim, l2fr, elongf_fnrt, target_c(fnrt_organ),target_dcdd(fnrt_organ))
return
end subroutine CNPAdjustFRootTargets
! =====================================================================================
subroutine TrimFineRoot(this)
! The following section allows forceful turnover of fine-roots if a new L2FR is generated
! that is lower than the previous l2fr. The maintenance turnover (background) rate
! will automatically accomodate a lower l2fr, but if the change is large it will
! not keep pace. Note 1: however, that the algorithm for calculating l2fr will prevent
! large drops in l2fr (unless that safegaurd is removed). Note 2: this section may also
! generate mass check errors in the main CNPAllocation routine, this is because the "val" is
! changing but the net_allocated is not reciprocating, which is expected.
! Keep a buffer above the L2FR in the hopes that natural turnover will catch
! up.
class(cnp_allom_prt_vartypes) :: this
real(r8) :: fnrt_flux_c
real(r8) :: turn_flux_c
real(r8) :: store_flux_c
real(r8) :: nc_fnrt
real(r8) :: pc_fnrt
real(r8) :: target_fnrt_c
real(r8),parameter :: nday_buffer = 0._r8
real(r8),parameter :: fnrt_opt_eff = 0._r8 ! If we want to transfer resources to storage
if(.not.use_unrestricted_contraction)return
associate( ipft => this%bc_in(acnp_bc_in_id_pft)%ival, &
l2fr => this%bc_inout(acnp_bc_inout_id_l2fr)%rval, &
dbh => this%bc_inout(acnp_bc_inout_id_dbh)%rval, &
elongf_fnrt => this%bc_in(acnp_bc_in_id_effnrt)%rval, &
canopy_trim => this%bc_in(acnp_bc_in_id_ctrim)%rval)
! Find the updated target fineroot biomass
call bfineroot(dbh,ipft,canopy_trim, l2fr, elongf_fnrt, target_fnrt_c)
fnrt_flux_c = max(0._r8,this%variables(fnrt_c_id)%val(1)*(1._r8-nday_buffer*(years_per_day / prt_params%root_long(ipft))) - target_fnrt_c )
if(fnrt_flux_c>nearzero) then
turn_flux_c = (1._r8 - fnrt_opt_eff)*fnrt_flux_c
store_flux_c = fnrt_opt_eff*fnrt_flux_c
nc_fnrt = this%variables(fnrt_n_id)%val(1)/this%variables(fnrt_c_id)%val(1)
pc_fnrt = this%variables(fnrt_p_id)%val(1)/this%variables(fnrt_c_id)%val(1)
this%variables(fnrt_c_id)%val(1) = this%variables(fnrt_c_id)%val(1) - fnrt_flux_c
this%variables(fnrt_c_id)%turnover(1) = this%variables(fnrt_c_id)%turnover(1) + turn_flux_c
this%variables(fnrt_c_id)%net_alloc(1) = this%variables(fnrt_c_id)%net_alloc(1) - store_flux_c
this%variables(store_c_id)%val(1) = this%variables(store_c_id)%val(1) + store_flux_c
this%variables(store_c_id)%net_alloc(1) = this%variables(store_c_id)%net_alloc(1) + store_flux_c
this%variables(fnrt_n_id)%val(1) = this%variables(fnrt_n_id)%val(1) - fnrt_flux_c * nc_fnrt
this%variables(fnrt_n_id)%turnover(1) = this%variables(fnrt_n_id)%turnover(1) + turn_flux_c * nc_fnrt
this%variables(fnrt_n_id)%net_alloc(1) = this%variables(fnrt_n_id)%net_alloc(1) - store_flux_c * nc_fnrt
this%variables(store_n_id)%val(1) = this%variables(store_n_id)%val(1) + store_flux_c * nc_fnrt
this%variables(store_n_id)%net_alloc(1) = this%variables(store_n_id)%net_alloc(1) + store_flux_c * nc_fnrt
this%variables(fnrt_p_id)%val(1) = this%variables(fnrt_p_id)%val(1) - fnrt_flux_c * pc_fnrt
this%variables(fnrt_p_id)%turnover(1) = this%variables(fnrt_p_id)%turnover(1) + turn_flux_c * pc_fnrt
this%variables(fnrt_p_id)%net_alloc(1) = this%variables(fnrt_p_id)%net_alloc(1) - store_flux_c * pc_fnrt
this%variables(store_p_id)%val(1) = this%variables(store_p_id)%val(1) + store_flux_c * pc_fnrt
this%variables(store_p_id)%net_alloc(1) = this%variables(store_p_id)%net_alloc(1) + store_flux_c * pc_fnrt
end if
end associate
return
end subroutine TrimFineRoot
! =====================================================================================
subroutine CNPPrioritizedReplacement(this,c_gain, n_gain, p_gain, target_c)
! -----------------------------------------------------------------------------------
! Alternative allocation hypothesis for the prioritized replacement phase.
! This is more similar to the current (04/2020) carbon only hypothesis.
! -----------------------------------------------------------------------------------
class(cnp_allom_prt_vartypes) :: this
real(r8), intent(inout) :: c_gain
real(r8), intent(inout) :: n_gain
real(r8), intent(inout) :: p_gain
real(r8), intent(in) :: target_c(:) ! Indexed by global organ (from PRTGenericMod)
integer :: n_curpri_org
integer, dimension(num_organs) :: curpri_org ! organ ID's of the current priority level
real(r8), dimension(num_organs) :: deficit_c ! Deficit to get to target from current [kg]
real(r8), dimension(num_organs) :: deficit_n ! Deficit to get to target from current [kg]
real(r8), dimension(num_organs) :: deficit_p ! Deficit to get to target from current [kg]
integer :: i, ii, i_org ! Loop indices (mostly for organs)
integer :: i_var ! variable index
integer :: i_pri ! loop index for priority
integer :: ipft ! Plant functional type index of this plant
integer :: leaf_status ! Is this plant in a leaf on or off status?
real(r8) :: canopy_trim ! trim factor for maximum leaf biomass
real(r8) :: target_n ! Target mass of N for a given organ [kg]
real(r8) :: target_p ! Target mass of P for a given organ [kg]
real(r8) :: elongf_leaf ! Leaf elongation factor
real(r8) :: elongf_fnrt ! Fine-root "elongation factor"
real(r8) :: elongf_stem ! Stem "elongation factor"
integer :: priority_code ! Index for priority level of each organ
real(r8) :: sum_c_demand ! Carbon demanded to bring tissues up to allometry (kg)
real(r8) :: store_below_target ! The amount of storage that is less than the target (kg)
real(r8) :: store_target_fraction ! The fraction of actual storage carbon over the target (kg)
real(r8) :: store_demand ! Based on the target fraction, an exponential function defining
! how much carbon we should try to put back into storage
real(r8) :: store_c_flux ! The amount of C we draw from gains to give back to storage (kg)
real(r8) :: sum_c_flux ! The flux to bring tissues up to allometry (kg)
real(r8) :: c_flux ! carbon flux into an arbitrary pool (kg)
integer :: n_max_priority ! Maximum possible number of priority levels is
! the total number organs plus 1, which allows
! each organ to have its own level, and ignore
! the specialized priority 1
leaf_status = this%bc_in(acnp_bc_in_id_lstat)%ival
elongf_leaf = this%bc_in(acnp_bc_in_id_efleaf)%rval
elongf_fnrt = this%bc_in(acnp_bc_in_id_effnrt)%rval
elongf_stem = this%bc_in(acnp_bc_in_id_efstem)%rval
ipft = this%bc_in(acnp_bc_in_id_pft)%ival
canopy_trim = this%bc_in(acnp_bc_in_id_ctrim)%rval
n_max_priority = maxval(prt_params%organ_param_id(:))
if(n_max_priority>10 .or. n_max_priority<0)then
write(fates_log(),*) 'was unable to interpret prt_params%organ_param_id'
write(fates_log(),*) 'for cnp allocation, there should be non-zero values <10'