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FatesPlantHydraulicsMod.F90
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module FatesPlantHydraulicsMod
! ==============================================================================================
! This module contains the relevant code for plant hydraulics. Currently, one hydraulics module
! is available. Other methods of estimating plant hydraulics may become available in future
! releases. For now, please cite the following reference if this module is used to generate
! published research:
!
! Christoffersen, B.O., Gloor, M., Fauset, S., Fyllas, N. M., Galbraith, D. R., Baker,
! T. R., Kruijt, B., Rowland, L., Fisher, R. A., Binks, O. J., Sevanto, S., Xu, C., Jansen,
! S., Choat, B., Mencuccini, M., McDowell, N. G., Meir, P. Linking hydraulic traits to
! tropical forest function in a size-structured and trait-driven model (TFS~v.1-Hydro).
! Geoscientific Model Development, 9(11), 2016, pp: 4227-4255,
! https://www.geosci-model-dev.net/9/4227/2016/, DOI = 10.5194/gmd-9-4227-2016.
!
! WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING
!
! PLANT HYDRAULICS IS AN EXPERIMENTAL OPTION THAT IS STILL UNDERGOING TESTING.
!
! WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING WARNING
!
! ==============================================================================================
use FatesGlobals, only : endrun => fates_endrun
use FatesGlobals, only : fates_log
use FatesConstantsMod, only : r8 => fates_r8
use FatesConstantsMod, only : fates_huge
use FatesConstantsMod, only : denh2o => dens_fresh_liquid_water
use FatesConstantsMod, only : grav_earth
use FatesConstantsMod, only : ifalse, itrue
use FatesConstantsMod, only : pi_const
use FatesConstantsMod, only : cm2_per_m2
use FatesConstantsMod, only : g_per_kg
use FatesConstantsMod, only : nearzero
use FatesConstantsMod, only : mpa_per_pa
use FatesConstantsMod, only : m_per_mm
use FatesConstantsMod, only : mg_per_kg
use FatesConstantsMod, only : pa_per_mpa
use FatesConstantsMod, only : rsnbl_math_prec
use FatesConstantsMod, only : m3_per_mm3
use FatesConstantsMod, only : cm3_per_m3
use FatesConstantsMod, only : kg_per_g
use FatesConstantsMod, only : fates_unset_r8
use FatesConstantsMod, only : nocomp_bareground
use EDParamsMod , only : hydr_kmax_rsurf1
use EDParamsMod , only : hydr_kmax_rsurf2
use EDParamsMod , only : hydr_psi0
use EDParamsMod , only : hydr_psicap
use EDParamsMod , only : hydr_htftype_node
use EDTypesMod , only : ed_site_type
use FatesPatchMod , only : fates_patch_type
use FatesCohortMod , only : fates_cohort_type
use EDTypesMod , only : AREA_INV
use EDTypesMod , only : AREA
use FatesConstantsMod , only : leaves_on
use FatesInterfaceTypesMod , only : bc_in_type
use FatesInterfaceTypesMod , only : bc_out_type
use FatesInterfaceTypesMod , only : hlm_use_planthydro
use FatesInterfaceTypesMod , only : hlm_ipedof
use FatesInterfaceTypesMod , only : numpft
use FatesInterfaceTypesMod , only : nlevsclass
use FatesInterfaceTypesMod , only : hlm_hydr_solver
use FatesAllometryMod, only : bleaf
use FatesAllometryMod, only : bsap_allom
use FatesAllometryMod, only : CrownDepth
use FatesHydraulicsMemMod, only: hydr_solver_1DTaylor
use FatesHydraulicsMemMod, only: hydr_solver_2DNewton
use FatesHydraulicsMemMod, only: hydr_solver_2DPicard
use FatesHydraulicsMemMod, only: ed_site_hydr_type
use FatesHydraulicsMemMod, only: ed_cohort_hydr_type
use FatesHydraulicsMemMod, only: n_hypool_plant
use FatesHydraulicsMemMod, only: n_hypool_leaf
use FatesHydraulicsMemMod, only: n_hypool_tot
use FatesHydraulicsMemMod, only: n_hypool_stem
use FatesHydraulicsMemMod, only: n_hypool_troot
use FatesHydraulicsMemMod, only: n_hypool_aroot
use FatesHydraulicsMemMod, only: n_plant_media
use FatesHydraulicsMemMod, only: nshell
use FatesHydraulicsMemMod, only: n_hypool_ag
use FatesHydraulicsMemMod, only: stomata_p_media
use FatesHydraulicsMemMod, only: leaf_p_media
use FatesHydraulicsMemMod, only: stem_p_media
use FatesHydraulicsMemMod, only: troot_p_media
use FatesHydraulicsMemMod, only: aroot_p_media
use FatesHydraulicsMemMod, only: rhiz_p_media
use FatesHydraulicsMemMod, only: nlevsoi_hyd_max
use FatesHydraulicsMemMod, only: rwccap, rwcft
use PRTGenericMod, only : carbon12_element
use PRTGenericMod, only : leaf_organ, fnrt_organ, sapw_organ
use PRTGenericMod, only : store_organ, repro_organ, struct_organ
use PRTGenericMod, only : num_elements
use PRTGenericMod, only : element_list
use EDPftvarcon, only : EDPftvarcon_inst
use PRTParametersMod, only : prt_params
use FatesHydroWTFMod, only : wrf_arr_type
use FatesHydroWTFMod, only : wkf_arr_type
use FatesHydroWTFMod, only : wrf_type, wrf_type_vg, wrf_type_cch, wrf_type_tfs
use FatesHydroWTFMod, only : wkf_type, wkf_type_vg, wkf_type_cch, wkf_type_tfs
use FatesHydroWTFMod, only : wrf_type_smooth_cch, wkf_type_smooth_cch
! CIME Globals
use shr_log_mod , only : errMsg => shr_log_errMsg
use shr_infnan_mod , only : isnan => shr_infnan_isnan
implicit none
! 1=leaf, 2=stem, 3=troot, 4=aroot
! Several of these may be better transferred to the parameter file in due time (RGK)
integer, public :: use_ed_planthydraulics = 1 ! 0 => use vanilla btran
! 1 => use BC hydraulics;
! 2 => use CX hydraulics
! The following options are temporarily unavailable (RGK 09-06-19)
! ----------------------------------------------------------------------------------
! logical, public :: do_dqtopdth_leaf = .false. ! should a nonzero dqtopdth_leaf
! term be applied to the plant
! hydraulics numerical solution?
! logical, public :: do_dyn_xylemrefill = .false. ! should the dynamics of xylem refilling
! (i.e., non-instantaneous) be considered
! within plant hydraulics?
! logical, public :: do_kbound_upstream = .true. ! should the hydraulic conductance at the
! boundary between nodes be taken to be a
! function of the upstream loss of
! conductivity (flc)?
! DO NOT TURN THIS ON. LEAVING THIS ONLY IF THE HLMS START HAVING
! TROUBLE RESPONDING TO SUPERSATURATION
logical :: purge_supersaturation = .false. ! If for some reason the roots force water
! into a saturated soil layer, or push it slightly
! past saturation, should we attempt to help
! fix the situation by assigning some
! of the water to a runoff term?
logical, public :: do_growthrecruiteffects = .true. ! should size- or root length-dependent
! hydraulic properties and states be
! updated every day when trees grow or
! when recruitment happens?
! If this is set to true, then the conductance over a path between nodes, is defined
! by the side of the path with higher potential only.
logical, parameter :: do_upstream_k = .true.
logical :: do_parallel_stem = .true. ! If this mode is active, we treat the conduit through
! the plant (in 1D solves) as closed from root layer
! to the stomata. The effect of this, is that
! the conductances through stem and leaf surfaces
! are reduced by the fraction of active root
! conductance, and for each soil-layer, integration
! proceeds over the entire time-step.
! These switches are for developers who which to understand if there simulations
! are ever entering regimes where water contents go negative (yes physically impossible)
! or water pressures exceed that at saturation (maybe, maybe not likely)
! These situations are possible/likely due to the nature of the constant flux boundary condition
! of transpiration, due to the loosely-coupled nature of the hydro-land-energy-photosynthesis
! system
logical, parameter :: trap_neg_wc = .false.
logical, parameter :: trap_supersat_psi = .false.
real(r8), parameter :: error_thresh = 1.e-5_r8 ! site level conservation error threshold in CLM
! (mm = kg/m2)
real(r8), parameter :: thsat_buff = 0.001_r8 ! Ensure that this amount of buffer
! is left between soil moisture and saturation [m3/m3]
! (if we are going to help purge super-saturation)
logical,parameter :: debug = .false. ! flag to report warning in hydro
character(len=*), parameter, private :: sourcefile = &
__FILE__
! These index flags specify which pressure-volumen and pressure
! conductivity relationship are available.
! For plants: Users can option between useing tfs and van_genuchten
! by specifying their choice in the parameter file,
! with the model parameter hydr_htftype_node,
! the value should be 1 for TFS or 2 for VG (as shown below).
! Campbell, could technically be used, but the parameters for
! that hypothesis are not in the parameter file, so it not currently available.
! For soil: The soil hypothesis should follow the hypothesis for water transfer
! in the Host Land Model. At this time campbell is the default for both
! ELM and ALM. However, if alternatives arise (like VG), we still need to write
! interface routines to transfer over parameters. Right now we just hard-code
! the use of campbell_type for the soil (see a few lines below).
integer, public, parameter :: van_genuchten_type = 2
integer, public, parameter :: campbell_type = 3
integer, public, parameter :: smooth1_campbell_type = 31
integer, public, parameter :: smooth2_campbell_type = 32
integer, public, parameter :: tfs_type = 1
integer, parameter :: soil_wrf_type = campbell_type
integer, parameter :: soil_wkf_type = campbell_type
! Define the global object that holds the water retention functions
! for plants of each different porous media type, and plant functional type
class(wrf_arr_type),pointer :: wrf_plant(:,:)
! Define the global object that holds the water conductance functions
! for plants of each different porous media type, and plant functional type
class(wkf_arr_type), pointer :: wkf_plant(:,:)
! Testing parameters for Van Genuchten soil WRTs
! unused unless van_genuchten_type is selected, also
! it would be much better to use the native parameters passed in
! from the HLM's soil model
real(r8), parameter :: alpha_vg = 0.001_r8
real(r8), parameter :: th_sat_vg = 0.65_r8
real(r8), parameter :: th_res_vg = 0.15_r8
real(r8), parameter :: psd_vg = 2.7_r8
real(r8), parameter :: m_vg = 0.62963_r8
real(r8), parameter :: soil_tort_vg = 0.5_r8
real(r8), parameter :: plant_tort_vg = 0.0_r8
! The maximum allowable water balance error over a plant-soil continuum
! for a given step [kgs] (2 mg)
real(r8), parameter :: max_wb_step_err = 2.e-6_r8 ! original is 1.e-7_r8, Junyan changed to 2.e-6_r8
!
! !PUBLIC MEMBER FUNCTIONS:
public :: AccumulateMortalityWaterStorage
public :: RecruitWaterStorage
public :: hydraulics_drive
public :: InitHydrSites
public :: HydrSiteColdStart
public :: BTranForHLMDiagnosticsFromCohortHydr
public :: InitHydrCohort
public :: DeallocateHydrCohort
public :: UpdateH2OVeg
public :: FuseCohortHydraulics
public :: UpdateSizeDepPlantHydProps
public :: UpdateSizeDepPlantHydStates
public :: UpdatePlantPsiFTCFromTheta
public :: InitPlantHydStates
public :: UpdateSizeDepRhizHydProps
public :: RestartHydrStates
public :: SavePreviousCompartmentVolumes
public :: SavePreviousRhizVolumes
public :: UpdatePlantHydrNodes
public :: UpdatePlantHydrLenVol
public :: UpdatePlantKmax
public :: ConstrainRecruitNumber
public :: InitHydroGlobals
! RGK 12-2021: UpdateSizeDepRhizHydStates was removed
! this code can be found in tags prior to
! sci.1.52.0_api.20.0.0
!------------------------------------------------------------------------------
! 01/18/16: Created by Brad Christoffersen
! 02/xx/17: Refactoring by Ryan Knox and Brad Christoffersen
!------------------------------------------------------------------------------
contains
!------------------------------------------------------------------------------
subroutine hydraulics_drive( nsites, sites, bc_in,bc_out,dtime )
! ARGUMENTS:
! -----------------------------------------------------------------------------------
integer,intent(in) :: nsites
type(ed_site_type),intent(inout),target :: sites(nsites)
type(bc_in_type),intent(in) :: bc_in(nsites)
type(bc_out_type),intent(inout) :: bc_out(nsites)
real(r8),intent(in) :: dtime
select case (use_ed_planthydraulics)
case (1)
call FillDrainRhizShells(nsites, sites, bc_in, bc_out )
call hydraulics_BC(nsites, sites,bc_in,bc_out,dtime )
case (2)
!call Hydraulics_CX()
case DEFAULT
end select
end subroutine Hydraulics_Drive
! =====================================================================================
subroutine RestartHydrStates(sites,nsites,bc_in,bc_out)
! It is assumed that the following state variables have been read in by
! the restart machinery.
!
! co_hydr%th_ag
! co_hydr%th_troot
! co_hydr%th_aroot
! si_hydr%r_node_shell
! si_hydr%v_shell
! si_hydr%h2osoi_liqvol_shell
! si_hydr%l_aroot_layer
!
! The goal of this subroutine is to call
! the correct sequence of hydraulics initializations to repopulate
! information that relies on these key states, as well as other vegetation
! states such as carbon pools and plant geometry.
integer , intent(in) :: nsites
type(ed_site_type) , intent(inout), target :: sites(nsites)
type(bc_in_type) , intent(in) :: bc_in(nsites)
type(bc_out_type) , intent(inout) :: bc_out(nsites)
! locals
! ----------------------------------------------------------------------------------
! LL pointers
type(fates_patch_type),pointer :: cpatch ! current patch
type(fates_cohort_type),pointer :: ccohort ! current cohort
type(ed_cohort_hydr_type),pointer :: ccohort_hydr
type(ed_site_hydr_type),pointer :: csite_hydr
integer :: s ! site loop counter
integer :: j ! soil layer index
integer :: j_bc ! soil layer index of boundary condition
class(wrf_type_vg), pointer :: wrf_vg
class(wkf_type_vg), pointer :: wkf_vg
class(wrf_type_cch), pointer :: wrf_cch
class(wkf_type_cch), pointer :: wkf_cch
class(wrf_type_smooth_cch), pointer :: wrf_smooth_cch
class(wkf_type_smooth_cch), pointer :: wkf_smooth_cch
real(r8) :: watsat ! Mean wsat across soil layers contributing to current root layer
real(r8) :: sucsat ! Mean sucsat across soil layers contributing to current root layer
real(r8) :: bsw ! Mean bsw across soil layers contributing to current root layer
do s = 1,nsites
csite_hydr=>sites(s)%si_hydr
cpatch => sites(s)%oldest_patch
do while(associated(cpatch))
ccohort => cpatch%shortest
do while(associated(ccohort))
ccohort_hydr => ccohort%co_hydr
! This calculates node heights
call UpdatePlantHydrNodes(ccohort,ccohort%pft,ccohort%height, &
sites(s)%si_hydr)
! This calculates volumes and lengths
call UpdatePlantHydrLenVol(ccohort,csite_hydr)
! This updates the Kmax's of the plant's compartments
call UpdatePlantKmax(ccohort_hydr,ccohort,sites(s)%si_hydr)
! Since this is a newly initialized plant, we set the previous compartment-size
! equal to the ones we just calculated.
call SavePreviousCompartmentVolumes(ccohort_hydr)
ccohort => ccohort%taller
enddo
cpatch => cpatch%younger
end do
sites(s)%si_hydr%l_aroot_layer_init(:) = fates_unset_r8
sites(s)%si_hydr%r_node_shell_init(:,:) = fates_unset_r8
sites(s)%si_hydr%v_shell_init(:,:) = fates_unset_r8
! --------------------------------------------------------------------------------
! Initialize water transfer functions
! which include both water retention functions (WRFs)
! as well as the water conductance (K) functions (WKFs)
! But, this is only for soil!
! --------------------------------------------------------------------------------
! Initialize the Water Retention Functions
! -----------------------------------------------------------------------------------
select case(soil_wrf_type)
case(van_genuchten_type)
do j=1,sites(s)%si_hydr%nlevrhiz
watsat = csite_hydr%AggBCToRhiz(bc_in(s)%watsat_sisl,j,bc_in(s)%dz_sisl)
allocate(wrf_vg)
sites(s)%si_hydr%wrf_soil(j)%p => wrf_vg
call wrf_vg%set_wrf_param([alpha_vg, psd_vg, m_vg, watsat, th_res_vg])
end do
case(campbell_type)
do j=1,sites(s)%si_hydr%nlevrhiz
watsat = csite_hydr%AggBCToRhiz(bc_in(s)%watsat_sisl,j,bc_in(s)%dz_sisl)
sucsat = csite_hydr%AggBCToRhiz(bc_in(s)%sucsat_sisl,j,bc_in(s)%dz_sisl)
bsw = csite_hydr%AggBCToRhiz(bc_in(s)%bsw_sisl,j,bc_in(s)%dz_sisl)
allocate(wrf_cch)
sites(s)%si_hydr%wrf_soil(j)%p => wrf_cch
call wrf_cch%set_wrf_param([watsat, &
(-1.0_r8)*sucsat*denh2o*grav_earth*mpa_per_pa*m_per_mm , &
bsw])
end do
case(smooth1_campbell_type)
do j=1,sites(s)%si_hydr%nlevrhiz
watsat = csite_hydr%AggBCToRhiz(bc_in(s)%watsat_sisl,j,bc_in(s)%dz_sisl)
sucsat = csite_hydr%AggBCToRhiz(bc_in(s)%sucsat_sisl,j,bc_in(s)%dz_sisl)
bsw = csite_hydr%AggBCToRhiz(bc_in(s)%bsw_sisl,j,bc_in(s)%dz_sisl)
allocate(wrf_smooth_cch)
sites(s)%si_hydr%wrf_soil(j)%p => wrf_smooth_cch
call wrf_smooth_cch%set_wrf_param([watsat, &
(-1.0_r8)*sucsat*denh2o*grav_earth*mpa_per_pa*m_per_mm , &
bsw,1._r8])
end do
case(smooth2_campbell_type)
do j=1,sites(s)%si_hydr%nlevrhiz
watsat = csite_hydr%AggBCToRhiz(bc_in(s)%watsat_sisl,j,bc_in(s)%dz_sisl)
sucsat = csite_hydr%AggBCToRhiz(bc_in(s)%sucsat_sisl,j,bc_in(s)%dz_sisl)
bsw = csite_hydr%AggBCToRhiz(bc_in(s)%bsw_sisl,j,bc_in(s)%dz_sisl)
allocate(wrf_smooth_cch)
sites(s)%si_hydr%wrf_soil(j)%p => wrf_smooth_cch
call wrf_smooth_cch%set_wrf_param([watsat, &
(-1.0_r8)*sucsat*denh2o*grav_earth*mpa_per_pa*m_per_mm , &
bsw,2._r8])
end do
case(tfs_type)
write(fates_log(),*) 'TFS water retention curves not available for soil'
call endrun(msg=errMsg(sourcefile, __LINE__))
case default
write(fates_log(),*) 'undefined water retention type for soil:',soil_wrf_type
call endrun(msg=errMsg(sourcefile, __LINE__))
end select
! -----------------------------------------------------------------------------------
! Initialize the Water Conductance (K) Functions
! -----------------------------------------------------------------------------------
select case(soil_wkf_type)
case(van_genuchten_type)
do j=1,sites(s)%si_hydr%nlevrhiz
allocate(wkf_vg)
sites(s)%si_hydr%wkf_soil(j)%p => wkf_vg
call wkf_vg%set_wkf_param([alpha_vg, psd_vg, m_vg, th_sat_vg, th_res_vg, soil_tort_vg])
end do
case(campbell_type)
do j=1,sites(s)%si_hydr%nlevrhiz
watsat = csite_hydr%AggBCToRhiz(bc_in(s)%watsat_sisl,j,bc_in(s)%dz_sisl)
sucsat = csite_hydr%AggBCToRhiz(bc_in(s)%sucsat_sisl,j,bc_in(s)%dz_sisl)
bsw = csite_hydr%AggBCToRhiz(bc_in(s)%bsw_sisl,j,bc_in(s)%dz_sisl)
allocate(wkf_cch)
sites(s)%si_hydr%wkf_soil(j)%p => wkf_cch
call wkf_cch%set_wkf_param([watsat, &
(-1.0_r8)*sucsat*denh2o*grav_earth*mpa_per_pa*m_per_mm , &
bsw])
end do
case(smooth1_campbell_type)
do j=1,sites(s)%si_hydr%nlevrhiz
watsat = csite_hydr%AggBCToRhiz(bc_in(s)%watsat_sisl,j,bc_in(s)%dz_sisl)
sucsat = csite_hydr%AggBCToRhiz(bc_in(s)%sucsat_sisl,j,bc_in(s)%dz_sisl)
bsw = csite_hydr%AggBCToRhiz(bc_in(s)%bsw_sisl,j,bc_in(s)%dz_sisl)
allocate(wkf_smooth_cch)
sites(s)%si_hydr%wkf_soil(j)%p => wkf_smooth_cch
call wkf_smooth_cch%set_wkf_param([watsat, &
(-1.0_r8)*sucsat*denh2o*grav_earth*mpa_per_pa*m_per_mm , &
bsw,1._r8])
end do
case(smooth2_campbell_type)
do j=1,sites(s)%si_hydr%nlevrhiz
watsat = csite_hydr%AggBCToRhiz(bc_in(s)%watsat_sisl,j,bc_in(s)%dz_sisl)
sucsat = csite_hydr%AggBCToRhiz(bc_in(s)%sucsat_sisl,j,bc_in(s)%dz_sisl)
bsw = csite_hydr%AggBCToRhiz(bc_in(s)%bsw_sisl,j,bc_in(s)%dz_sisl)
allocate(wkf_smooth_cch)
sites(s)%si_hydr%wkf_soil(j)%p => wkf_smooth_cch
call wkf_smooth_cch%set_wkf_param([watsat, &
(-1.0_r8)*sucsat*denh2o*grav_earth*mpa_per_pa*m_per_mm , &
bsw,2._r8])
end do
case(tfs_type)
write(fates_log(),*) 'TFS conductance not used in soil'
call endrun(msg=errMsg(sourcefile, __LINE__))
case default
write(fates_log(),*) 'undefined water conductance type for soil:',soil_wkf_type
call endrun(msg=errMsg(sourcefile, __LINE__))
end select
! The fraction of total conductance functions need to know psi_min
! to handle very very low conductances, therefore we need to construct
! a pointer in conductance structure to the water retention structure
do j=1,sites(s)%si_hydr%nlevrhiz
sites(s)%si_hydr%wkf_soil(j)%p%wrf => sites(s)%si_hydr%wrf_soil(j)%p
end do
! Update static quantities related to the rhizosphere
call UpdateSizeDepRhizVolLenCon(sites(s), bc_in(s))
! We update the "initial" values of the rhizosphere after
! the previous call to make sure that the conductances are updated
! Now we set the prevous to the current so that the water states
! are not perturbed
call SavePreviousRhizVolumes(sites(s))
call UpdateH2OVeg(sites(s),bc_out(s))
end do
return
end subroutine RestartHydrStates
! ====================================================================================
subroutine InitPlantHydStates(site, cohort)
! REQUIRED INPUTS:
!
! ccohort_hydr%z_node_troot(:)
! ccohort_hydr%z_node_aroot
! ccohort_hydr%z_node_ag
!
! !DESCRIPTION:
!
! !USES:
! !ARGUMENTS:
type(ed_site_type), intent(inout), target :: site ! current site pointer
type(fates_cohort_type), intent(inout), target :: cohort ! current cohort pointer
!
! !LOCAL VARIABLES:
type(ed_site_hydr_type), pointer :: csite_hydr
type(ed_cohort_hydr_type), pointer :: cohort_hydr
integer :: j,k ! layer and node indices
integer :: ft ! functional type index
real(r8) :: psi_rhiz1 ! pressure in first rhizosphere shell [MPa]
real(r8) :: dz ! depth of the current layer [m]
real(r8) :: h_aroot_mean ! minimum total potential of absorbing roots
real(r8), parameter :: psi_aroot_init = -0.2_r8 ! Initialize aroots with -0.2 MPa
real(r8), parameter :: dh_dz = 0.02_r8 ! amount to decrease downstream
! compartment total potentials [MPa/meter]
! In init mode = 1, set absorbing roots to -0.2 MPa
! = 2, use soil as starting point, match total potentials
! and then reduce plant compartment total potential by 1KPa
! for transporting root node, match the lowest total potential
! in absorbing roots
integer, parameter :: init_mode = 2
class(wrf_arr_type),pointer :: wrfa,wrft
class(wkf_arr_type),pointer :: wkfa,wkft
csite_hydr => site%si_hydr
cohort_hydr => cohort%co_hydr
ft = cohort%pft
wrfa => wrf_plant(aroot_p_media,ft)
wkfa => wkf_plant(aroot_p_media,ft)
wrft => wrf_plant(troot_p_media,ft)
wkft => wkf_plant(troot_p_media,ft)
! Set abosrbing root
if(init_mode == 2) then
! h_aroot_mean = 0._r8
do j=1, csite_hydr%nlevrhiz
! Checking apperance of roots. Only proceed if there are roots in that layer
if(cohort_hydr%l_aroot_layer(j) > nearzero) then
! Match the potential of the absorbing root to the inner rhizosphere shell
cohort_hydr%psi_aroot(j) = csite_hydr%wrf_soil(j)%p%psi_from_th(csite_hydr%h2osoi_liqvol_shell(j,1))
! Calculate the mean total potential (include height) of absorbing roots
! h_aroot_mean = h_aroot_mean + cohort_hydr%psi_aroot(j) +
! mpa_per_pa*denh2o*grav_earth*(-csite_hydr%zi_rhiz(j))
cohort_hydr%th_aroot(j) = max(wrfa%p%th_from_psi(cohort_hydr%psi_aroot(j)),wrfa%p%get_thmin())
cohort_hydr%ftc_aroot(j) = wkfa%p%ftc_from_psi(cohort_hydr%psi_aroot(j))
else
cohort_hydr%psi_aroot(j) = psi_aroot_init
cohort_hydr%th_aroot(j) = 0
end if
end do
else
do j=1, csite_hydr%nlevrhiz
cohort_hydr%psi_aroot(j) = psi_aroot_init
! Calculate the mean total potential (include height) of absorbing roots
! h_aroot_mean = h_aroot_mean + cohort_hydr%psi_aroot(j) +
! mpa_per_pa*denh2o*grav_earth*(-csite_hydr%zi_rhiz(j))
cohort_hydr%th_aroot(j) = max(wrfa%p%th_from_psi(cohort_hydr%psi_aroot(j)), &
wrfa%p%get_thmin())
cohort_hydr%ftc_aroot(j) = wkfa%p%ftc_from_psi(cohort_hydr%psi_aroot(j))
end do
end if
!h_aroot_mean = h_aroot_mean/real(csite_hydr%nlevrhiz,r8)
h_aroot_mean = minval(cohort_hydr%psi_aroot(:) + mpa_per_pa*denh2o*grav_earth* &
( -csite_hydr%zi_rhiz(:)+0.5*csite_hydr%dz_rhiz(:) )) ! Get layer centers
! initialize plant water potentials with slight potential gradient (or zero) (dh/dz = C)
! the assumption is made here that initial conditions for soil water will
! be in (or at least close to) hydrostatic equilibrium as well, so that
! it doesn't matter which absorbing root layer the transporting root water
! Set the transporting root to be in equilibrium with mean potential
! of the absorbing roots, minus any gradient we add
cohort_hydr%psi_troot = h_aroot_mean - &
mpa_per_pa*denh2o*grav_earth*cohort_hydr%z_node_troot - dh_dz
cohort_hydr%th_troot = max(wrft%p%th_from_psi(cohort_hydr%psi_troot), &
wrft%p%get_thmin())
cohort_hydr%ftc_troot = wkft%p%ftc_from_psi(cohort_hydr%psi_troot)
! working our way up a tree, assigning water potentials that are in
! hydrostatic equilibrium (minus dh_dz offset) with the water potential immediately below
dz = cohort_hydr%z_node_ag(n_hypool_ag) - cohort_hydr%z_node_troot
cohort_hydr%psi_ag(n_hypool_ag) = cohort_hydr%psi_troot - &
mpa_per_pa*denh2o*grav_earth*dz - dh_dz
cohort_hydr%th_ag(n_hypool_ag) = max(wrf_plant(stem_p_media,ft)%p%get_thmin(), &
wrf_plant(stem_p_media,ft)%p%th_from_psi(cohort_hydr%psi_ag(n_hypool_ag)))
cohort_hydr%ftc_ag(n_hypool_ag) = wkf_plant(stem_p_media,ft)%p%ftc_from_psi(cohort_hydr%psi_ag(n_hypool_ag))
do k=n_hypool_ag-1, 1, -1
dz = cohort_hydr%z_node_ag(k) - cohort_hydr%z_node_ag(k+1)
cohort_hydr%psi_ag(k) = cohort_hydr%psi_ag(k+1) - &
mpa_per_pa*denh2o*grav_earth*dz - &
dh_dz
cohort_hydr%th_ag(k) = max(wrf_plant(csite_hydr%pm_node(k),ft)%p%th_from_psi(cohort_hydr%psi_ag(k)), &
wrf_plant(csite_hydr%pm_node(k),ft)%p%get_thmin())
cohort_hydr%ftc_ag(k) = wkf_plant(csite_hydr%pm_node(k),ft)%p%ftc_from_psi(cohort_hydr%psi_ag(k))
end do
!initialize cohort-level btran
cohort_hydr%btran = wkf_plant(stomata_p_media,ft)%p%ftc_from_psi(cohort_hydr%psi_ag(1))
! We do allow for positive pressures.
! But starting off with positive pressures is something we try to avoid
if ( (cohort_hydr%psi_troot>0.0_r8) .or. &
any(cohort_hydr%psi_ag(:)>0._r8) .or. &
any(cohort_hydr%psi_aroot(:)>0._r8) ) then
write(fates_log(),*) 'Initialized plant compartments with positive pressure?'
write(fates_log(),*) 'psi troot: ',cohort_hydr%psi_troot
write(fates_log(),*) 'psi ag(:): ',cohort_hydr%psi_ag(:)
write(fates_log(),*) 'psi_aroot(:): ',cohort_hydr%psi_aroot(:)
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
end subroutine InitPlantHydStates
! =====================================================================================
subroutine UpdatePlantPsiFTCFromTheta(ccohort,csite_hydr)
! This subroutine updates the potential and the fractional
! of total conductivity based on the relative water
! content
! Arguments
type(fates_cohort_type),intent(inout), target :: ccohort
type(ed_site_hydr_type),intent(in), target :: csite_hydr
! Locals
integer :: ft ! Plant functional type
integer :: k ! loop index for compartments
integer :: j ! Loop index for soil layers
type(ed_cohort_hydr_type), pointer :: ccohort_hydr
ccohort_hydr => ccohort%co_hydr
ft = ccohort%pft
! Update Psi and FTC in above-ground compartments
! -----------------------------------------------------------------------------------
do k = 1,n_hypool_leaf
ccohort_hydr%psi_ag(k) = wrf_plant(leaf_p_media,ft)%p%psi_from_th(ccohort_hydr%th_ag(k))
ccohort_hydr%ftc_ag(k) = wkf_plant(leaf_p_media,ft)%p%ftc_from_psi(ccohort_hydr%psi_ag(k))
end do
ccohort_hydr%btran = wkf_plant(stomata_p_media,ft)%p%ftc_from_psi(ccohort_hydr%psi_ag(1))
do k = n_hypool_leaf+1, n_hypool_ag
ccohort_hydr%psi_ag(k) = wrf_plant(stem_p_media,ft)%p%psi_from_th(ccohort_hydr%th_ag(k))
ccohort_hydr%ftc_ag(k) = wkf_plant(stem_p_media,ft)%p%ftc_from_psi(ccohort_hydr%psi_ag(k))
end do
! Update the Psi and FTC for the transporting root compartment
ccohort_hydr%psi_troot = wrf_plant(troot_p_media,ft)%p%psi_from_th(ccohort_hydr%th_troot)
ccohort_hydr%ftc_troot = wkf_plant(troot_p_media,ft)%p%ftc_from_psi(ccohort_hydr%psi_troot)
! Update the Psi and FTC for the absorbing roots
do j = 1, csite_hydr%nlevrhiz
ccohort_hydr%psi_aroot(j) = wrf_plant(aroot_p_media,ft)%p%psi_from_th(ccohort_hydr%th_aroot(j))
ccohort_hydr%ftc_aroot(j) = wkf_plant(aroot_p_media,ft)%p%ftc_from_psi(ccohort_hydr%psi_aroot(j))
end do
return
end subroutine UpdatePlantPsiFTCFromTheta
! =====================================================================================
subroutine UpdatePlantHydrNodes(ccohort,ft,plant_height,csite_hydr)
! --------------------------------------------------------------------------------
! This subroutine calculates the nodal heights critical to hydraulics in the plant
!
! Inputs: Plant height
! Plant functional type
! Number of soil hydraulic layers
!
! Outputs: cohort_hydr%z_node_ag(:)
! %z_lower_ag(:)
! %z_upper_ag(:)
! %z_node_troot
! %z_node_aroot(:)
! --------------------------------------------------------------------------------
! Arguments
type(fates_cohort_type), intent(inout) :: ccohort
integer,intent(in) :: ft ! plant functional type index
real(r8), intent(in) :: plant_height ! [m]
type(ed_site_hydr_type), intent(in) :: csite_hydr
! Locals
type(ed_cohort_hydr_type), pointer :: ccohort_hydr
integer :: nlevrhiz ! number of rhizosphere layers
real(r8) :: roota ! root profile parameter a zeng2001_crootfr
real(r8) :: rootb ! root profile parameter b zeng2001_crootfr
real(r8) :: crown_depth ! crown depth for the plant [m]
real(r8) :: dz_canopy ! discrete crown depth intervals [m]
real(r8) :: z_stem ! the height of the plants stem below crown [m]
real(r8) :: dz_stem ! vertical stem discretization [m]
real(r8) :: dcumul_rf ! cumulative root distribution discretization [-]
real(r8) :: cumul_rf ! cumulative root distribution where depth is determined [-]
real(r8) :: z_cumul_rf ! depth at which cumul_rf occurs [m]
integer :: k ! Loop counter for compartments
real(r8) :: z_fr ! Maximum rooting depth of the plant [m]
ccohort_hydr => ccohort%co_hydr
! Crown Nodes
! in special case where n_hypool_leaf = 1, the node height of the canopy
! water pool is 1/2 the distance from the bottom of the canopy to the top of the tree
roota = prt_params%fnrt_prof_a(ft)
rootb = prt_params%fnrt_prof_b(ft)
nlevrhiz = csite_hydr%nlevrhiz
!call CrownDepth(plant_height,ft,crown_depth)
crown_depth = min(plant_height,0.1_r8)
dz_canopy = crown_depth / real(n_hypool_leaf,r8)
do k=1,n_hypool_leaf
ccohort_hydr%z_lower_ag(k) = plant_height - dz_canopy*real(k,r8)
ccohort_hydr%z_node_ag(k) = ccohort_hydr%z_lower_ag(k) + 0.5_r8*dz_canopy
ccohort_hydr%z_upper_ag(k) = ccohort_hydr%z_lower_ag(k) + dz_canopy
enddo
! Stem Nodes
! in special case where n_hypool_stem = 1, the node height of the stem water pool is
! 1/2 the height from the ground to the bottom of the canopy
z_stem = plant_height - crown_depth
dz_stem = z_stem / real(n_hypool_stem,r8)
do k=n_hypool_leaf+1,n_hypool_ag
ccohort_hydr%z_upper_ag(k) = real(n_hypool_stem - (k - 1 - n_hypool_leaf),r8)*dz_stem
ccohort_hydr%z_node_ag(k) = ccohort_hydr%z_upper_ag(k) - 0.5_r8*dz_stem
ccohort_hydr%z_lower_ag(k) = ccohort_hydr%z_upper_ag(k) - dz_stem
enddo
call MaximumRootingDepth(ccohort%dbh,ft,csite_hydr%zi_rhiz(nlevrhiz),z_fr)
! Transporting Root Node depth [m] (negative from surface)
call bisect_rootfr(roota, rootb, z_fr, 0._r8, 1.E10_r8, &
0.001_r8, 0.001_r8, 0.5_r8, z_cumul_rf)
if(z_cumul_rf > csite_hydr%zi_rhiz(nlevrhiz) ) then
write(fates_log(),*) 'z_cumul_rf > zi_rhiz(nlevrhiz)?',z_cumul_rf,csite_hydr%zi_rhiz(nlevrhiz)
call endrun(msg=errMsg(sourcefile, __LINE__))
end if
z_cumul_rf = min(z_cumul_rf, abs(csite_hydr%zi_rhiz(nlevrhiz)))
ccohort_hydr%z_node_troot = -z_cumul_rf
return
end subroutine UpdatePlantHydrNodes
! =====================================================================================
subroutine SavePreviousCompartmentVolumes(ccohort_hydr)
type(ed_cohort_hydr_type),intent(inout) :: ccohort_hydr
! Saving the current compartment volumes into an "initial" save-space
! allows us to see how the compartments change size when plants
! change size and effect water contents
ccohort_hydr%v_ag_init(:) = ccohort_hydr%v_ag(:)
ccohort_hydr%v_troot_init = ccohort_hydr%v_troot
ccohort_hydr%v_aroot_layer_init(:) = ccohort_hydr%v_aroot_layer(:)
return
end subroutine SavePreviousCompartmentVolumes
! =====================================================================================
subroutine UpdateSizeDepPlantHydProps(currentSite,ccohort,bc_in)
! DESCRIPTION: Updates absorbing root length (total and its vertical distribution)
! as well as the consequential change in the size of the 'representative' rhizosphere
! shell radii, volumes, and compartment volumes of plant tissues
! !USES:
use shr_sys_mod , only : shr_sys_abort
! ARGUMENTS:
type(ed_site_type) , intent(in) :: currentSite ! Site stuff
type(fates_cohort_type) , intent(inout) :: ccohort ! current cohort pointer
type(bc_in_type) , intent(in) :: bc_in ! Boundary Conditions
! Locals
integer :: nlevrhiz ! Number of total soil layers
type(ed_cohort_hydr_type), pointer :: ccohort_hydr
integer :: ft
nlevrhiz = currentSite%si_hydr%nlevrhiz
ccohort_hydr => ccohort%co_hydr
ft = ccohort%pft
! Save the current vegetation compartment volumes into
! a save space so that it can be compared with the updated quantity.
call SavePreviousCompartmentVolumes(ccohort_hydr)
! This updates all of the z_node positions
call UpdatePlantHydrNodes(ccohort,ft,ccohort%height,currentSite%si_hydr)
! This updates plant compartment volumes, lengths and
! maximum conductances. Make sure for already
! initialized vegetation, that SavePreviousCompartment
! volumes, and UpdatePlantHydrNodes is called prior to this.
call UpdatePlantHydrLenVol(ccohort,currentSite%si_hydr)
! This updates the Kmax's of the plant's compartments
call UpdatePlantKmax(ccohort_hydr,ccohort,currentsite%si_hydr)
end subroutine UpdateSizeDepPlantHydProps
! =====================================================================================
subroutine UpdatePlantHydrLenVol(ccohort,csite_hydr)
! -----------------------------------------------------------------------------------
! This subroutine calculates two attributes of a plant:
! 1) the volumes of storage compartments in the plants
! 2) the lenghts of the organs
! These are not dependent on the hydraulic state of the
! plant, it is more about the structural characteristics and how much biomass
! is present in the different tissues.
!
! Inputs, plant geometries, plant carbon pools, z_node values
!
! -----------------------------------------------------------------------------------
! Arguments
type(fates_cohort_type),intent(inout) :: ccohort
type(ed_site_hydr_type),intent(in) :: csite_hydr
type(ed_cohort_hydr_type),pointer :: ccohort_hydr ! Plant hydraulics structure
integer :: j,k
integer :: ft ! Plant functional type index
real(r8) :: roota ! root profile parameter a zeng2001_crootfr
real(r8) :: rootb ! root profile parameter b zeng2001_crootfr
real(r8) :: leaf_c ! Current amount of leaf carbon in the plant [kg]
real(r8) :: leaf_c_target ! Target leaf carbon (with some conditions) [kgC]
real(r8) :: fnrt_c ! Current amount of fine-root carbon in the plant [kg]
real(r8) :: sapw_c ! Current amount of sapwood carbon in the plant [kg]
real(r8) :: struct_c ! Current amount of structural carbon in the plant [kg]
real(r8) :: woody_bg_c ! belowground woody biomass in carbon units [kgC/indiv]
real(r8) :: z_stem ! the height of the plants stem below crown [m]
real(r8) :: sla ! specific leaf area [cm2/g]
real(r8) :: v_aroot_tot ! total compartment volume of all absorbing roots for cohort [m3]
real(r8) :: l_aroot_tot ! total length of absorbing roots for cohrot [m]
real(r8) :: denleaf ! leaf dry mass per unit fresh leaf volume [kg/m3]
real(r8) :: a_sapwood ! sapwood area [m2]
real(r8) :: a_sapwood_target ! sapwood cross-section area at reference height, at target biomass [m2]
real(r8) :: sapw_c_target ! sapwood carbon, at target [kgC]
real(r8) :: v_sapwood ! sapwood volume [m3]
real(r8) :: v_troot ! transporting root volume [m3/indiv]
real(r8) :: rootfr ! mass fraction of roots in each layer [kg/kg]
real(r8) :: crown_depth ! Depth of the plant's crown [m]
real(r8) :: norm ! total root fraction used <1
integer :: nlevrhiz ! number of rhizosphere levels
real(r8) :: dbh ! the dbh of current cohort [cm]
real(r8) :: z_fr ! rooting depth of a cohort [cm]
real(r8) :: v_leaf_donate(1:n_hypool_leaf) ! the volume that leaf will donate to xylem
! We allow the transporting root to donate a fraction of its volume to the absorbing
! roots to help mitigate numerical issues due to very small volumes. This is the
! fraction the transporting roots donate to those layers
real(r8), parameter :: t2aroot_vol_donate_frac = 0.65_r8
real(r8), parameter :: l2sap_vol_donate_frac = 0.5_r8 ! Junyan added
real(r8), parameter :: min_leaf_frac = 0.1_r8 ! Fraction of maximum leaf carbon that
! we set as our lower cap on leaf volume
real(r8), parameter :: min_trim = 0.1_r8 ! The lower cap on trimming function used
! to estimate maximum leaf carbon
ccohort_hydr => ccohort%co_hydr
ft = ccohort%pft
nlevrhiz = csite_hydr%nlevrhiz
leaf_c = ccohort%prt%GetState(leaf_organ, carbon12_element)
sapw_c = ccohort%prt%GetState(sapw_organ, carbon12_element)
fnrt_c = ccohort%prt%GetState(fnrt_organ, carbon12_element)
struct_c = ccohort%prt%GetState(struct_organ, carbon12_element)
roota = prt_params%fnrt_prof_a(ft)
rootb = prt_params%fnrt_prof_b(ft)
! Leaf Volumes
! -----------------------------------------------------------------------------------
! NOTE: SLATOP currently does not use any vertical scaling functions
! but that may not be so forever. ie sla = slatop (RGK-082017)
! m2/gC * cm2/m2 -> cm2/gC
sla = prt_params%slatop(ft) * cm2_per_m2
! empirical regression data from leaves at Caxiuana (~ 8 spp)
denleaf = -2.3231_r8*sla/prt_params%c2b(ft) + 781.899_r8
! Leaf volumes
! Note: Leaf volumes of zero is problematic for two reasons. Zero volumes create
! numerical difficulties, and they could also create problems when a leaf is trying
! to re-flush.
! Therefore, if the leaf is in an "off" status, then we do not update the leaf
! volume. This way the volume is where it was when it dropped, and this is consistent
! with the theory that leaf water potentials drive growth and re-flushing, not the
! other way around. However, it is possible that we may have recruits with an
! "off" status (due to external seed rain active during a dry or cold season). If a
! cohort is newly created, we must give it a starting volume.
! We also place a lower bound on how low the leaf volume is allowed to go, which is 10%
! of the plant's carrying capacity.
! [kgC] * [kg/kgC] / [kg/m3] -> [m3]
! Get the target, or rather, maximum leaf carrying capacity of plant
! Lets also avoid super-low targets that have very low trimming functions
! efleaf_coh hard-coded to 1 in the call below to avoid zero leaf volume
call bleaf(ccohort%dbh,ccohort%pft,ccohort%crowndamage, &
max(ccohort%canopy_trim,min_trim),1.0_r8, leaf_c_target)
ccohort_hydr%v_ag(1:n_hypool_leaf) = max(leaf_c,min_leaf_frac*leaf_c_target) * &
prt_params%c2b(ft) / denleaf/ real(n_hypool_leaf,r8)
! Step sapwood volume