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LunaMod.F90
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LunaMod.F90
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module LunaMod
#include "shr_assert.h"
!**********************************************************************************************************************************************************************
! !DESCRIPTION:
! Calculates the photosynthetic capacities based on a prescribed leaf nitrogen content, using the LUNA model, developed by Chonggang Xu, Ashehad Ali and Rosie Fisher
! Currently only works for C3 plants. See Xu et al 2012; Ali et al 2015a. Ecological Applications. http://dx.doi.org/10.1890/14-2111.1. and Ali et al 2015b.In Review.
! !USES:
use shr_kind_mod , only : r8 => shr_kind_r8
use shr_log_mod , only : errMsg => shr_log_errMsg
use clm_varcon , only : rgas, tfrz,spval
use abortutils , only : endrun
use clm_varctl , only : iulog
use clm_varcon , only : namep
use clm_varpar , only : nlevcan
use decompMod , only : bounds_type
use pftconMod , only : pftcon
use FrictionvelocityMod , only : frictionvel_type
use atm2lndType , only : atm2lnd_type
use CanopyStateType , only : canopystate_type
use PhotosynthesisMod , only : photosyns_type
use TemperatureType , only : temperature_type
use PatchType , only : patch
use GridcellType , only : grc
use SolarAbsorbedType , only : solarabs_type
use SurfaceAlbedoType , only : surfalb_type
use WaterDiagnosticBulkType , only : waterdiagnosticbulk_type
!use EDPhotosynthesisMod , only : vcmaxc, jmaxc
implicit none
save
!------------------------------------------------------------------------------
! PUBLIC MEMBER FUNCTIONS:
public :: LunaReadNML !subroutine to read in the Luna namelist
public :: Update_Photosynthesis_Capacity !subroutine to update the canopy nitrogen profile
public :: Acc24_Climate_LUNA !subroutine to accumulate 24 hr climates
public :: Acc240_Climate_LUNA !subroutine to accumulate 10 day climates
public :: Clear24_Climate_LUNA !subroutine to clear 24 hr climates
public :: readParams
type, private :: params_type
! cp25, kc25, ko25: Bernacchi et al (2001) Plant, Cell & Environment 24:253-259
real(r8) :: cp25_yr2000 ! CO2 compensation point at 25°C at present day O2 (mol/mol)
real(r8) :: kc25_coef ! Michaelis-Menten const. at 25°C for CO2 (unitless)
real(r8) :: ko25_coef ! Michaelis-Menten const. at 25°C for O2 (unitless)
end type params_type
type(params_type), private :: params_inst
! PRIVATE MEMBER FUNCTIONS:
private :: NitrogenAllocation !subroutine to update the Vcmax25 and Jmax25 at the leaf level
private :: NUEref !Calculate the Nitrogen use effieciency based on reference CO2 and leaf temperature
private :: NUE !Calculate the Nitrogen use effieciency based on current CO2 and leaf temperature
private :: JmxTLeuning !Calculate the temperature response for Jmax, based on Leunning 2002 Plant, Cell & Environment
private :: JmxTKattge !Calculate the temperature response for Jmax, based on Kattge and Knorr 2007
private :: VcmxTLeuning !Calculate the temperature response for Vcmax, based on Leunning 2002 Plant, Cell & Environment
private :: VcmxTKattge !Calculate the temperature response for Vcmax, based on Kattge and Knorr 2007
private :: RespTBernacchi !Calculate the temperature response for respiration, following Bernacchi PCE 2001
private :: Photosynthesis_luna !calculate the photosynthetic rate for nitrogen allocation
private :: Quadratic !Calculate the soultion using the quadratic formula
!------------------------------------------------------------------------------
!Constants
real(r8), parameter :: Cv = 1.2e-5_r8 * 3600.0 ! conversion factor from umol CO2 to g carbon
real(r8), parameter :: Fc25 = 294.2_r8 ! Fc25 = 6.22*47.3 #see Rogers (2014) Photosynthesis Research
real(r8), parameter :: Fj25 = 1257.0_r8 ! Fj25 = 8.06*156 # #see COSTE 2005 and Xu et al 2012
real(r8), parameter :: NUEr25 = 33.69_r8 ! nitrogen use efficiency for respiration, see Xu et al 2012
real(r8), parameter :: Cb = 1.78_r8 ! nitrogen use effiency for choloraphyll for light capture, see Evans 1989
real(r8), parameter :: O2ref = 209460.0_r8 ! ppm of O2 in the air
real(r8), parameter :: CO2ref = 380.0_r8 ! reference CO2 concentration for calculation of reference NUE.
real(r8), parameter :: forc_pbot_ref = 101325.0_r8 ! reference air pressure for calculation of reference NUE
real(r8), parameter :: Q10Enz = 2.0_r8 ! Q10 value for enzyme decay rate
real(r8), parameter :: Jmaxb0 = 0.0311_r8 ! the baseline proportion of nitrogen allocated for electron transport (J)
real(r8) :: Jmaxb1 = 0.1_r8 ! the baseline proportion of nitrogen allocated for electron transport (J)
real(r8), parameter :: Wc2Wjb0 = 0.8054_r8 ! the baseline ratio of rubisco limited rate vs light limited photosynthetic rate (Wc:Wj)
real(r8), parameter :: relhExp = 6.0999_r8 ! electron transport parameters related to relative humidity
real(r8), parameter :: Enzyme_turnover_daily = 0.1_r8 ! the daily turnover rate for photosynthetic enzyme at 25oC in view of ~7 days of half-life time for Rubisco (Suzuki et al. 2001)
real(r8), parameter :: NMCp25 = 0.715_r8 ! estimated by assuming 80% maintenance respiration is used for photosynthesis enzyme maintenance
real(r8), parameter :: Trange1 = 5.0_r8 ! lower temperature limit (oC) for nitrogen optimization
real(r8), parameter :: Trange2 = 42.0_r8 ! upper temperature limit (oC) for nitrogen optimization
real(r8), parameter :: SNC = 0.004_r8 ! structural nitrogen concentration (g N g-1 dry mass carbon)
real(r8), parameter :: mp = 9.0_r8 ! slope of stomatal conductance; this is used to estimate model parameter, but may need to be updated from the physiology file,
real(r8), parameter :: PARLowLim = 200.0_r8 ! minimum photosynthetically active radiation for nitrogen optimization
real(r8), parameter :: minrelh = 0.25_r8 ! minimum relative humdity for nitrogen optimization
character(len=*), parameter, private :: sourcefile = &
__FILE__
!------------------------------------------------------------------------------
contains
!**********************************************************************************************************************************************************************
! Read in LUNA namelist
subroutine LunaReadNML( NLFilename )
!
! !DESCRIPTION:
! Read the namelist for LUNA
!
! !USES:
use fileutils , only : getavu, relavu, opnfil
use shr_nl_mod , only : shr_nl_find_group_name
use spmdMod , only : masterproc, mpicom
use shr_mpi_mod , only : shr_mpi_bcast
use clm_varctl , only : iulog
use shr_log_mod , only : errMsg => shr_log_errMsg
use abortutils , only : endrun
!
! !ARGUMENTS:
character(len=*), intent(in) :: NLFilename ! Namelist filename
!
! !LOCAL VARIABLES:
integer :: ierr ! error code
integer :: unitn ! unit for namelist file
character(len=*), parameter :: subname = 'lunaReadNML'
character(len=*), parameter :: nmlname = 'luna'
!-----------------------------------------------------------------------
namelist /luna/ Jmaxb1
! Initialize options to default values, in case they are not specified in
! the namelist
if (masterproc) then
unitn = getavu()
write(iulog,*) 'Read in '//nmlname//' namelist'
call opnfil (NLFilename, unitn, 'F')
call shr_nl_find_group_name(unitn, nmlname, status=ierr)
if (ierr == 0) then
read(unitn, nml=luna, iostat=ierr)
if (ierr /= 0) then
call endrun(msg="ERROR reading "//nmlname//"namelist"//errmsg(__FILE__, __LINE__))
end if
else
call endrun(msg="ERROR could NOT find "//nmlname//"namelist"//errmsg(__FILE__, __LINE__))
end if
call relavu( unitn )
end if
call shr_mpi_bcast (Jmaxb1, mpicom)
if (masterproc) then
write(iulog,*) ' '
write(iulog,*) nmlname//' settings:'
write(iulog,nml=luna)
write(iulog,*) ' '
end if
end subroutine lunaReadNML
!----------------------------------------------------------------------------
subroutine readParams( ncid )
!
! !USES:
use ncdio_pio, only: file_desc_t
use paramUtilMod, only: readNcdioScalar
!
! !ARGUMENTS:
implicit none
type(file_desc_t),intent(inout) :: ncid ! pio netCDF file id
!
! !LOCAL VARIABLES:
character(len=*), parameter :: subname = 'readParams_Luna'
!--------------------------------------------------------------------
! CO2 compensation point at 25°C at present day O2 levels
call readNcdioScalar(ncid, 'cp25_yr2000', subname, params_inst%cp25_yr2000)
params_inst%cp25_yr2000 = params_inst%cp25_yr2000 * 1.e5_r8 ! from mol/mol to Luna units
! Michaelis-Menten constant at 25°C for O2 (unitless)
call readNcdioScalar(ncid, 'ko25_coef', subname, params_inst%ko25_coef)
params_inst%ko25_coef = params_inst%ko25_coef * 1.e5_r8 ! from mol/mol to Luna units
! Michaelis-Menten constant at 25°C for CO2 (unitless)
call readNcdioScalar(ncid, 'kc25_coef', subname, params_inst%kc25_coef)
params_inst%kc25_coef = params_inst%kc25_coef * 1.e5_r8 ! from mol/mol to Luna units
end subroutine readParams
!**********************************************************************************************************************************************************************
! this subroutine updates the photosynthetic capacity as determined by Vcmax25 and Jmax25
subroutine Update_Photosynthesis_Capacity(bounds, fn, filterp, &
dayl_factor, atm2lnd_inst, temperature_inst, canopystate_inst, photosyns_inst, &
surfalb_inst, solarabs_inst, waterdiagnosticbulk_inst, frictionvel_inst)
!
! !DESCRIPTION:
! Calculates Nitrogen fractionation within the leaf, based on optimum calculated fractions in rubisco, cholorophyll,
! Respiration and Storage. Based on Xu et al. 2012 and Ali et al 2015.In Review
!
! !REVISION HISTORY:
! version 1.0, by Chonggang Xu, Ashehad Ali and Rosie Fisher. July 14 2015.
! version 0.1, by Chonggang Xu, Ashehad Ali and Rosie Fisher. October 30 2014.
! CALLED FROM:
! subroutine CanopyFluxes
! !USES:
use clm_time_manager , only : get_step_size_real, is_end_curr_day
use clm_varpar , only : nlevsoi, mxpft
use perf_mod , only : t_startf, t_stopf
use clm_varctl , only : use_cn
use quadraticMod , only : quadratic
use CNSharedParamsMod , only : CNParamsShareInst
use shr_infnan_mod, only : isnan => shr_infnan_isnan
implicit none
! !ARGUMENTS:
type(bounds_type) , intent(in) :: bounds
integer , intent(in) :: fn ! size of pft filter
integer , intent(in) :: filterp(fn) ! pft filter
real(r8) , intent(in) :: dayl_factor( bounds%begp: ) ! scalar (0-1) for daylength
type(atm2lnd_type) , intent(in) :: atm2lnd_inst
type(temperature_type) , intent(inout) :: temperature_inst
type(canopystate_type) , intent(inout) :: canopystate_inst
type(photosyns_type) , intent(inout) :: photosyns_inst
type(surfalb_type) , intent(in) :: surfalb_inst
type(solarabs_type) , intent(inout) :: solarabs_inst
type(waterdiagnosticbulk_type) , intent(inout) :: waterdiagnosticbulk_inst
type(frictionvel_type) , intent(inout) :: frictionvel_inst
! !LOCAL VARIABLES:
!
! local pointers to implicit in variables
integer :: c,CL,f,g,iv,j,p,ps ! indices
integer :: NCL_p ! number of canopy layers in patch
integer :: ft ! plant functional type
integer :: z ! the index across leaf layers
real (r8) :: PNstoreopt,PNlcopt,PNetopt,PNrespopt,PNcbopt ! the optimal nitrogen allocations
real (r8) :: PNstoreold,PNlcold,PNetold,PNrespold,PNcbold ! the previous time step nitrogen allocations
real (r8) :: delta_fn ! daily change in nitrogen investiment
real (r8) :: relCLNCa ! the relative factor for LNCa due to canopy location and seasonal growth
real (r8) :: relSLNCa ! the relative factor for LNCa due to seasonal growth
real (r8) :: relRad ! the realtive radiation to the top of the canopy
real (r8) :: FNCmtar ! target functional nitrogen content (g N/g leaf c)
real (r8) :: LMA ! leaf mass per unit area (g leaf c/m2 leaf)
real (r8) :: PARTop ! photosynthetic active radiation on the top of canopy (umol/m2/s)
real (r8) :: RadTop ! short-wave radiation on the top of canopy (w/m2)
real (r8) :: TRad ! total short-wave radiation on the top of canopy (w/m2)
real (r8) :: PARi10 ! 10-day mean photosynthetic active radiation on in the canopy (umol/m2/s)
real (r8) :: PARimx10 ! 10-day mean maximum photosynthetic active radiation on in the canopy (umol/m2/s)
real (r8) :: tleaf10 ! 10-day mean leaf temperature (oC)
real (r8) :: tleafd10 ! 10-day mean daytime leaf temperature (oC)
real (r8) :: tleafn10 ! 10-day mean nighttime leaf temperature (oC)
real (r8) :: hourpd ! hours per day (hours)
real (r8) :: CO2a10 ! 10-day mean air co2 concentration (pa)
real (r8) :: O2a10 ! 10-day mean air o2 concentration (pa)
real (r8) :: max_daily_pchg ! maximum daily percentrage change for nitrogen allocation
real (r8) :: max_daily_decay ! maximum daily decay for nitrogen allocation
real (r8) :: radk ! light extintion factor
real (r8) :: FNCa ! leaf functional nitrogen content (g/m2)
real (r8) :: FNCa_z(1:nlevcan) ! profile of leaf functional nitrogen content (g/m2)
real (r8) :: fnps ! fraction of light absorbed by non-photosynthetic pigments
real (r8) :: radmax2mean ! ratio of max radiation to mean
real (r8) :: qabs ! PAR absorbed by PS II (umol photons/m**2/s)
real (r8) :: EnzTurnoverTFactor ! temperature adjust factor for enzyme decay
real (r8) :: vcmax25 ! Predicted vcmax25 from EDN model umol CO2/m**2/s
real (r8) :: jmax25 ! Predicted jmax25 from EDN model umol electrons/m**2/s
real (r8) :: dtime ! stepsize in seconds
real (r8) :: rb10v ! 10-day mean boundary layer resistance
real (r8) :: relh10 ! 10-day mean relative humidity (unitless)
real (r8) :: tair10 ! 10-day running mean of the 2m temperature (oC)
real (r8) :: rabsorb ! ratio of absorbed raditation to the total incident radiation
real (r8) :: tlaii ! total leaf area index for a certain canopy layer
real (r8) :: SNCa ! structural leaf nitrogen content (g N/m2 leaf)
real (r8) :: vcmx25_opt ! optimal Vc,max25 (umol CO2/m**2/s)
real (r8) :: jmx25_opt ! optimal Jmax25 (umol electron/m**2/s)
real (r8) :: chg ! change in Vcmax25 or Jmax25
real (r8) :: chg_constrn ! constrained change in Vcmax25 or Jmax25
logical :: is_end_day ! is end of current day
!-------------------------------------------------------------------------------------------------------------------------------------------------
associate( &
c3psn => pftcon%c3psn , & ! photosynthetic pathway: 0. = c4, 1. = c3
slatop => pftcon%slatop , & ! specific leaf area at top of canopy, projected area basis [m^2/gC]
leafcn => pftcon%leafcn , & ! leaf C:N (gC/gN)
forc_pbot10 => atm2lnd_inst%forc_pbot240_downscaled_patch , & ! Input: [real(r8) (:) ] 10 day mean atmospheric pressure(Pa)
CO2_p240 => atm2lnd_inst%forc_pco2_240_patch , & ! Input: [real(r8) (:) ] 10-day mean CO2 partial pressure (Pa)
O2_p240 => atm2lnd_inst%forc_po2_240_patch , & ! Input: [real(r8) (:) ] 10-day mean O2 partial pressure (Pa)
elai => canopystate_inst%elai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index with burying by snow
tlai => canopystate_inst%tlai_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index
tlai_z => surfalb_inst%tlai_z_patch , & ! Input: [real(r8) (:) ] one-sided leaf area index
dayl => grc%dayl , & ! Input: [real(r8) (:) ] daylength (s)
sabv => solarabs_inst%sabv_patch , & ! Input: [real(r8) (:) ] patch solar radiation absorbed by vegetation (W/m**2)
t_veg => temperature_inst%t_veg_patch , & ! Input: [real(r8) (:) ] vegetation temperature (Kelvin)
rhol => pftcon%rhol , & ! Input: [real(r8) (:) ] leaf reflectance: 1=vis, 2=nir
taul => pftcon%taul , & ! Input: [real(r8) (:) ] leaf transmittance: 1=vis, 2=nir
par240d_z => solarabs_inst%par240d_z_patch , & ! Input: [real(r8) (:,:) ] 10-day running mean of daytime patch absorbed PAR for leaves in canopy layer (W/m**2)
par24d_z => solarabs_inst%par24d_z_patch , & ! Input: [real(r8) (:,:) ] daily accumulated absorbed PAR for leaves in canopy layer (W/m**2)
par240x_z => solarabs_inst%par240x_z_patch , & ! Input: [real(r8) (:,:) ] 10-day running mean of maximum patch absorbed PAR for leaves in canopy layer (W/m**2)
par24x_z => solarabs_inst%par24x_z_patch , & ! Input: [real(r8) (:,:) ] daily maximum of patch absorbed PAR for leaves in canopy layer (W/m**2)
nrad => surfalb_inst%nrad_patch , & ! Input: [integer (:) ] pft number of canopy layers, above snow for radiative transfer
lnc => photosyns_inst%lnca_patch , & ! Input: [real(r8) (:) ] top leaf layer leaf N concentration (gN leaf/m^2)
t10 => temperature_inst%t_a10_patch , & ! Input: [real(r8) (:) ] 10-day running mean of the 2 m temperature (K)
t_veg_day => temperature_inst%t_veg_day_patch , & ! Input: [real(r8) (:) ] daytime mean vegetation temperature (Kelvin)
t_veg_night => temperature_inst%t_veg_night_patch , & ! Input: [real(r8) (:) ] nighttime mean vegetation temperature (Kelvin)
t_veg10_day => temperature_inst%t_veg10_day_patch , & ! Input: [real(r8) (:) ] 10-day mean daytime vegetation temperature (Kelvin)
t_veg10_night => temperature_inst%t_veg10_night_patch , & ! Input: [real(r8) (:) ] 10-day mean nighttime vegetation temperature (Kelvin)
rh10_p => waterdiagnosticbulk_inst%rh10_af_patch , & ! Input: [real(r8) (:) ] 10-day mean canopy air relative humidity at the pacth (unitless)
rb10_p => frictionvel_inst%rb10_patch , & ! Input: [real(r8) (:) ] 10-day mean boundary layer resistance at the pacth (s/m)
gpp_day => photosyns_inst%fpsn24_patch , & ! Input: [real(r8) (:) ] patch 24 hours mean gpp(umol CO2/m**2 ground/day) for canopy layer
vcmx25_z => photosyns_inst%vcmx25_z_patch , & ! Output: [real(r8) (:,:) ] patch leaf Vc,max25 (umol/m2 leaf/s) for canopy layer
jmx25_z => photosyns_inst%jmx25_z_patch , & ! Output: [real(r8) (:,:) ] patch leaf Jmax25 (umol electron/m**2/s) for canopy layer
pnlc_z => photosyns_inst%pnlc_z_patch , & ! Output: [real(r8) (:,:) ] patch proportion of leaf nitrogen allocated for light capture for canopy layer
enzs_z => photosyns_inst%enzs_z_patch & ! Output: [real(r8) (:,:) ] enzyme decay status 1.0-fully active; 0-all decayed during stress
)
!----------------------------------------------------------------------------------------------------------------------------------------------------------
!set timestep
!Initialize enzyme decay Q10
dtime = get_step_size_real()
is_end_day = is_end_curr_day()
fnps = 0.15_r8
call t_startf('LUNA')
do f = 1,fn
p = filterp(f)
ft = patch%itype(p)
g = patch%gridcell(p)
c = patch%column(p)
!----------------------------------------------------
!store the daily mean climate conditions
if(t_veg_day(p).ne.spval) then !check whether it is the first day
!------------------------------------------
!get the climate driver
CO2a10 = CO2_p240(p)
O2a10 = O2_p240(p)
hourpd = dayl(g) / 3600._r8
tleafd10 = t_veg10_day(p) - tfrz
tleafn10 = t_veg10_night(p) - tfrz
tleaf10 = (dayl(g)*tleafd10 +(86400._r8-dayl(g)) * tleafd10)/86400._r8
tair10 = t10(p)- tfrz
relh10 = min(1.0_r8, rh10_p(p))
rb10v = rb10_p(p)
!--------------------------------------------------------------------
!calculate the enzyme ternover rate
EnzTurnoverTFactor = Q10Enz**(0.1_r8*(min(40.0_r8, tleaf10) - 25.0_r8))
max_daily_pchg = EnzTurnoverTFactor * Enzyme_turnover_daily
!-----------------------------------------------------------------
rabsorb = 1.0_r8-rhol(ft,1)-taul(ft,1)
!Implemented the nitrogen allocation model
if(tlai(p) > 0.0_r8 .and. lnc(p) > 0._r8)then
RadTop = par240d_z(p,1)/rabsorb
PARTop = RadTop*4.6 !conversion from w/m2 to umol/m2/s. PAR is still in umol photons, not electrons. Also the par240d_z is only for radiation at visible range. Hence 4.6 not 2.3 multiplier.
!-------------------------------------------------------------
!the nitrogen allocation model, may need to be feed from the parameter file in CLM
if (nint(c3psn(ft)) == 1)then
if(gpp_day(p)>0.0 )then !only optimize if there is growth and it is C3 plants
!-------------------------------------------------------------
do z = 1, nrad(p)
if(tlai_z(p,z)>0.0_r8)then
qabs = par240d_z(p,z)/rabsorb
PARi10 = qabs * 4.6_r8
else
PARi10 = 0.01_r8
endif
!-----------------------------------------------------------------------
relRad = PARi10/PARTop
relCLNCa = 0.1802_r8*log(relRad)+1.0_r8 !see Ali et al 2015.
relCLNCa = max(0.2_r8,relCLNCa)
relCLNCa = min(1.0_r8,relCLNCa)
relSLNCa = 1.0_r8
!------------------------------------------------------------------
SNCa = 1.0_r8/slatop(ft) * SNC
if(0.9_r8 * lnc(p)> SNCa)then
FNCa_z(z)= relCLNCa*(lnc(p)-SNCa)
else
FNCa_z(z)= relCLNCa*0.1_r8*lnc(p)
endif
enddo
!----------------------------------------------------------------------
!nitrogen allocation model
do z = 1 , nrad(p)
!-------------------------------------------------------------------------------------------
!for different layers of leaves
FNCa = FNCa_z(z)
if(FNCa>15.0_r8) then !boundary condition check for unrealistically high leaf nitrogen content
FNCa = 15.0_r8
write(iulog, *) 'Warning: leaf nitrogen content become unrealistically high (>15.0 g N/m2 leaf) ', &
'for patch=', p, 'z=', z, "pft=", ft
endif
radmax2mean = par240x_z(p,z) / par240d_z(p,z)
if(tlai_z(p,z)>0.0_r8)then
qabs = par240d_z(p,z)/rabsorb
PARi10 = qabs * 4.6_r8
else
PARi10 = 0.01_r8
endif
PARimx10 = PARi10*radmax2mean
!-----------------------------------------------------------------------------------------------------
!nitrogen allocastion model-start
PNlcold = PNlc_z(p,z)
PNetold = 0.0_r8
PNrespold = 0.0_r8
PNcbold = 0.0_r8
call NitrogenAllocation(FNCa,forc_pbot10(p), relh10, CO2a10, O2a10, PARi10, PARimx10, rb10v, hourpd, &
tair10, tleafd10, tleafn10, &
Jmaxb0, Jmaxb1, Wc2Wjb0, relhExp, PNlcold, PNetold, PNrespold, &
PNcbold, PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
vcmx25_opt= PNcbopt * FNCa * Fc25
jmx25_opt= PNetopt * FNCa * Fj25
chg = vcmx25_opt-vcmx25_z(p, z)
chg_constrn = min(abs(chg),vcmx25_z(p, z)*max_daily_pchg)
vcmx25_z(p, z) = vcmx25_z(p, z)+sign(1.0_r8,chg)*chg_constrn
chg = jmx25_opt-jmx25_z(p, z)
chg_constrn = min(abs(chg),jmx25_z(p, z)*max_daily_pchg)
jmx25_z(p, z) = jmx25_z(p, z)+sign(1.0_r8,chg)*chg_constrn
PNlc_z(p, z)= PNlcopt
if(enzs_z(p,z)<1.0) then
enzs_z(p,z) = enzs_z(p,z)* (1.0_r8 + max_daily_pchg)
endif
!nitrogen allocastion model-end
!DML turn off endrun and instead modify vcmx25_z(p,z) and jmx25_z(p,z) to a reasonable value
!-----------------------------------------------------------------------------------------------------
if(isnan(vcmx25_z(p, z)))then
write(iulog, *) 'Error: Vc,mx25 is NaN for patch=', &
p, 'z=', z, "pft=", ft
write(iulog, *) 'LUNA env:',FNCa,forc_pbot10(p), relh10, CO2a10, O2a10, PARi10, PARimx10, rb10v, &
hourpd, tair10, tleafd10, tleafn10
call endrun(msg=errmsg(sourcefile, __LINE__))
endif
if(vcmx25_z(p, z)>1000._r8 .or. vcmx25_z(p, z)<0._r8)then
write(iulog, *) 'Warning: Vc,mx25 become unrealistic (>1000 or negative) for patch=', &
p, 'z=', z, "pft=", ft
write(iulog, *) 'LUNA env:',vcmx25_z(p,z),FNCa,forc_pbot10(p), relh10, CO2a10, &
O2a10, PARi10, PARimx10, rb10v, hourpd, tair10, tleafd10, tleafn10
vcmx25_z(p,z) = 50._r8
endif
if(isnan(jmx25_z(p, z)))then
write(iulog, *) 'Error: Jmx25 is NaN for patch=', &
p, 'z=', z, "pft=", ft
write(iulog, *) 'LUNA env:', FNCa,forc_pbot10(p), relh10, CO2a10, O2a10, PARi10, PARimx10, rb10v, &
hourpd, tair10, tleafd10, tleafn10
call endrun(msg=errmsg(sourcefile, __LINE__))
endif
if(jmx25_z(p, z)>2000._r8 .or. jmx25_z(p, z)<0._r8)then
write(iulog, *) 'Warning: Jmx25 become unrealistic (>2000, or negative) for patch=', &
p, 'z=', z, "pft=", ft
write(iulog, *) 'LUNA env:', jmx25_z(p,z),FNCa,forc_pbot10(p), relh10, CO2a10, &
O2a10, PARi10, PARimx10, rb10v, hourpd, tair10, tleafd10, tleafn10
jmx25_z(p,z) = 85._r8
endif
enddo ! finished loop of leaf layers
else !decay during drought or winter
max_daily_decay = min(0.5_r8, 0.1_r8 * max_daily_pchg)
!assume enzyme turnover under maintenance is 10
!times lower than enzyme change under growth
do z = 1 , nrad(p)
if(enzs_z(p,z)>0.5_r8) then
!decay is set at only 50% of original
!enzyme in view that plant will need to
!maintain their basic functionality
enzs_z(p,z) = enzs_z(p,z)* (1.0_r8 - max_daily_decay)
jmx25_z(p, z) = jmx25_z(p, z)* (1.0_r8 - max_daily_decay)
vcmx25_z(p, z) = vcmx25_z(p, z)* (1.0_r8 - max_daily_decay)
endif
end do
endif !checking for growth
endif !if not C3 plants
else
do z = 1 , nrad(p)
jmx25_z(p, z) = 85._r8
vcmx25_z(p, z) = 50._r8
end do
endif !checking for LAI and LNC
endif !the first daycheck
end do !fn loop
call t_stopf('LUNA')
end associate
end subroutine Update_Photosynthesis_Capacity
subroutine Acc240_Climate_LUNA(bounds, fn, filterp, oair, cair, &
rb,rh, temperature_inst, photosyns_inst, &
surfalb_inst, solarabs_inst, waterdiagnosticbulk_inst, frictionvel_inst)
!
! !DESCRIPTION:
! Accumulate the 10-day running mean climates for LUNA model
!
! !REVISION HISTORY:
! version 1.0, by Chonggang Xu July 14 2015.
! CALLED FROM:
! subroutine CanopyFluxes
! !USES:
use clm_time_manager , only : get_step_size_real, is_end_curr_day
implicit none
! !ARGUMENTS:
type(bounds_type) , intent(in) :: bounds
integer , intent(in) :: fn ! size of pft filter
integer , intent(in) :: filterp(fn) ! pft filter
real(r8) , intent(in) :: oair( bounds%begp: ) ! Atmospheric O2 partial pressure (Pa)
real(r8) , intent(in) :: cair( bounds%begp: ) ! Atmospheric CO2 partial pressure (Pa)
real(r8) , intent(in) :: rb( bounds%begp: ) ! boundary layer resistance (s/m)
real(r8) , intent(in) :: rh( bounds%begp: ) ! canopy air relative humidity
type(temperature_type) , intent(inout) :: temperature_inst
type(photosyns_type) , intent(inout) :: photosyns_inst
type(surfalb_type) , intent(in) :: surfalb_inst
type(solarabs_type) , intent(inout) :: solarabs_inst
type(waterdiagnosticbulk_type) , intent(inout) :: waterdiagnosticbulk_inst
type(frictionvel_type) , intent(inout) :: frictionvel_inst
! !LOCAL VARIABLES:
!
! local pointers to implicit in variables
integer :: c,f,g,iv,j,p ! indices
integer :: ft ! plant functional type
integer :: z ! the index across leaf layers
real (r8) :: dtime ! stepsize in seconds
real (r8) :: TRad ! total short-wave radiation on the top of canopy (w/m2)
real (r8) :: tlaii ! total leaf area index for a certain canopy layer
real (r8) :: t_veg_dayi ! daytime mean vegetation temperature (Kelvin)
real (r8) :: t_veg_nighti ! nighttime mean vegetation temperature (Kelvin)
real (r8) :: par24d_z_i(1:nlevcan) ! daytime mean radiation (w/m**2)
logical :: is_end_day ! is end of current day
!-------------------------------------------------------------------------------------------------------------------------------------------------
associate( &
par24d_z => solarabs_inst%par24d_z_patch , & ! Input: [real(r8) (:,:) ] daily accumulated absorbed PAR for leaves in canopy layer (W/m**2)
par24x_z => solarabs_inst%par24x_z_patch , & ! Input: [real(r8) (:,:) ] daily maximum of patch absorbed PAR for leaves in canopy layer (W/m**2)
nrad => surfalb_inst%nrad_patch , & ! Input: [integer (:) ] pft number of canopy layers, above snow for radiative transfer
t_veg_day => temperature_inst%t_veg_day_patch , & ! Input: [real(r8) (:) ] daytime accumulative vegetation temperature (Kelvin*nsteps)
t_veg_night => temperature_inst%t_veg_night_patch , & ! Input: [real(r8) (:) ] nighttime accumulative vegetation temperature (Kelvin*nsteps)
nnightsteps => temperature_inst%nnightsteps_patch , & ! Input: [integer (:) ] number of nighttime steps in 24 hours from mid-night, LUNA specific
ndaysteps => temperature_inst%ndaysteps_patch , & ! Input: [integer (:) ] number of daytime steps in 24 hours from mid-night, LUNA specific
t_veg10_day => temperature_inst%t_veg10_day_patch , & ! Output: [real(r8) (:) ] 10-day mean vegetation temperature (Kelvin)
t_veg10_night => temperature_inst%t_veg10_night_patch , & ! Output: [real(r8) (:) ] 10-day mean vegetation temperature (Kelvin)
rh10_p => waterdiagnosticbulk_inst%rh10_af_patch , & ! Output: [real(r8) (:) ] 10-day mean canopy air relative humidity at the pacth (s/m)
rb10_p => frictionvel_inst%rb10_patch , & ! Output: [real(r8) (:) ] 10-day mean boundary layer resistance at the pacth (s/m)
par240d_z => solarabs_inst%par240d_z_patch , & ! Output: [real(r8) (:,:) ] 10-day running mean of daytime patch absorbed PAR for leaves in canopy layer (W/m**2)
par240x_z => solarabs_inst%par240x_z_patch & ! Output: [real(r8) (:,:) ] 10-day running mean of maximum patch absorbed PAR for leaves in canopy layer (W/m**2)
)
!----------------------------------------------------------------------------------------------------------------------------------------------------------
!set timestep
!Initialize enzyme decay Q10
dtime = get_step_size_real()
is_end_day = is_end_curr_day()
do f = 1,fn
p = filterp(f)
ft = patch%itype(p)
g = patch%gridcell(p)
c = patch%column(p)
if(t_veg_day(p).ne.spval) then !check whether it is the first day
!---------------------------------------------------------
!calculate the 10 day running mean radiations
if(ndaysteps(p)>0.0) then
par24d_z_i=par24d_z(p,:)/(dtime * ndaysteps(p))
else
par24d_z_i = 0._r8
endif
if(par240d_z(p,1).eq. spval)then !first day set as the same of first day environmental conditions
par240x_z(p,:)= par24x_z(p,:)
par240d_z(p,:)= par24d_z_i
else
par240x_z(p,:)= 0.9_r8 * par240x_z(p,:) + 0.1_r8 * par24x_z(p,:)
par240d_z(p,:)= 0.9_r8 * par240d_z(p,:) + 0.1_r8 * par24d_z_i
endif
!-------------------------------------------------------
!calculate the 10 day running mean daytime temperature
if(ndaysteps(p)>0.0)then
t_veg_dayi = t_veg_day(p) / ndaysteps(p)
else
t_veg_dayi = t_veg_night(p) / nnightsteps(p)
endif
if(t_veg10_day(p).eq. spval)then
t_veg10_day(p) = t_veg_dayi
endif
t_veg10_day(p) = 0.9_r8 * t_veg10_day(p)+ 0.1_r8 * t_veg_dayi
!-------------------------------------------------------
!calculate the 10 day running mean nighttime temperature
if(nnightsteps(p)>0)then
t_veg_nighti = t_veg_night(p) / nnightsteps(p)
else
t_veg_nighti = t_veg_day(p) / ndaysteps(p)
endif
if(t_veg10_night(p).eq. spval)then
t_veg10_night(p) = t_veg_nighti
endif
t_veg10_night(p) = 0.9_r8 * t_veg10_night(p) + 0.1_r8 * t_veg_nighti
!--------------------------------------------------------------------
if(rh10_p(p).eq. spval)then
rh10_p(p) = rh(p)
endif
rh10_p(p) = 0.9_r8 * rh10_p(p) + 0.1_r8 * min(1.0_r8, rh(p))
if(rb10_p(p).eq. spval)then
rb10_p(p) = rb(p)
endif
rb10_p(p) = 0.9_r8 * rb10_p(p) + 0.1_r8 * rb(p)
endif !the first day check
end do !fn loop
end associate
end subroutine Acc240_Climate_LUNA
subroutine Acc24_Climate_LUNA(bounds, fn, filterp, canopystate_inst, photosyns_inst, &
surfalb_inst, solarabs_inst,temperature_inst)
!
! !DESCRIPTION:
! Accumulate the 24 hr climates for LUNA model
!
! !REVISION HISTORY:
! version 1.0, by Chonggang Xu July 14 2015.
! CALLED FROM:
! subroutine CanopyFluxes
! !USES:
use clm_time_manager , only : get_step_size_real
implicit none
! !ARGUMENTS:
type(bounds_type) , intent(in) :: bounds
integer , intent(in) :: fn ! size of pft filter
integer , intent(in) :: filterp(fn) ! pft filter
type(canopystate_type) , intent(inout) :: canopystate_inst
type(photosyns_type) , intent(inout) :: photosyns_inst
type(surfalb_type) , intent(in) :: surfalb_inst
type(solarabs_type) , intent(inout) :: solarabs_inst
type(temperature_type) , intent(inout) :: temperature_inst
! !LOCAL VARIABLES:
!
! local pointers to implicit in variables
integer :: c,f,g,iv,j,p ! indices
integer :: ft ! plant functional type
integer :: z ! the index across leaf layers
real (r8) :: dtime ! stepsize in seconds
real (r8) :: TRad ! total short-wave radiation on the top of canopy (w/m2)
real (r8) :: tlaii ! total leaf area index for a certain canopy layer
!-------------------------------------------------------------------------------------------------------------------------------------------------
associate( &
sabv => solarabs_inst%sabv_patch , & ! Input: [real(r8) (:) ] patch solar radiation absorbed by vegetation (W/m**2)
t_veg => temperature_inst%t_veg_patch , & ! Input: [real(r8) (:) ] vegetation temperature (Kelvin)
par_sun_z => solarabs_inst%parsun_z_patch , & ! Input: [real(r8) (:,:) ] par absorbed per unit lai for sunlit canopy layer (w/m**2)
par_sha_z => solarabs_inst%parsha_z_patch , & ! Input: [real(r8) (:,:) ] par absorbed per unit lai for shaded canopy layer (w/m**2)
lai_sun_z => canopystate_inst%laisun_z_patch , & ! Input: [real(r8) (:,:) ] leaf area index for sunlit canopy layer
lai_sha_z => canopystate_inst%laisha_z_patch , & ! Input: [real(r8) (:,:) ] leaf area index for canopy shaded layer
par24d_z => solarabs_inst%par24d_z_patch , & ! Input: [real(r8) (:,:) ] daily accumulated absorbed PAR for leaves in canopy layer (W/m**2)
par24x_z => solarabs_inst%par24x_z_patch , & ! Input: [real(r8) (:,:) ] daily maximum of patch absorbed PAR for leaves in canopy layer (W/m**2)
nrad => surfalb_inst%nrad_patch , & ! Input: [integer (:) ] pft number of canopy layers, above snow for radiative transfer
gpp => photosyns_inst%fpsn_patch , & ! Input: [real(r8) (:) ] patch instaneous gpp (umol CO2/m**2 ground/s) for canopy layer
gpp_day => photosyns_inst%fpsn24_patch , & ! Output: [real(r8) (:) ] patch 24 hours acculative gpp(umol CO2/m**2 ground/day) from mid-night
t_veg_day => temperature_inst%t_veg_day_patch , & ! Output: [real(r8) (:) ] daytime mean vegetation temperature (Kelvin)
t_veg_night => temperature_inst%t_veg_night_patch , & ! Output: [real(r8) (:) ] nighttime mean vegetation temperature (Kelvin)
nnightsteps => temperature_inst%nnightsteps_patch , & ! Output: [integer (:) ] number of nighttime steps in 24 hours from mid-night, LUNA specific
ndaysteps => temperature_inst%ndaysteps_patch & ! Output: [integer (:) ] number of daytime steps in 24 hours from mid-night, LUNA specific
)
!----------------------------------------------------------------------------------------------------------------------------------------------------------
!set timestep
!Initialize enzyme decay Q10
dtime = get_step_size_real()
do f = 1,fn
p = filterp(f)
ft = patch%itype(p)
g = patch%gridcell(p)
c = patch%column(p)
!----------------------------------------------------
!store the daily mean climate conditions
if(t_veg_day(p).ne.spval) then !check whether it is the first day
if(sabv(p)>0)then
t_veg_day(p) = t_veg_day(p) + t_veg(p)
ndaysteps(p) = ndaysteps(p) + 1
else
t_veg_night(p) = t_veg_night(p) + t_veg(p)
nnightsteps(p) = nnightsteps(p) + 1
endif
do z = 1, nrad(p)
!average of sunlit and shaded leaves
tlaii = lai_sun_z(p,z) + lai_sha_z(p,z)
if(tlaii > 0._r8)then
TRad = (par_sun_z(p,z)*lai_sun_z(p,z)+par_sha_z(p,z)*lai_sha_z(p,z))/tlaii
TRad = par_sun_z(p,z) !RF & GBB. Make LUNA predict sunlit fraction N fractionation, scale in PhotosynthesisMod.
par24d_z(p,z)= par24d_z(p,z)+ dtime * TRad
if(TRad > par24x_z(p,z))then
par24x_z(p,z) = TRad
endif
endif
enddo
gpp_day(p) = gpp_day(p) + dtime * gpp(p)
endif !first day check
end do !fn loop
end associate
end subroutine Acc24_Climate_LUNA
subroutine Clear24_Climate_LUNA(bounds, fn, filterp, canopystate_inst, photosyns_inst, &
surfalb_inst, solarabs_inst,temperature_inst)
!
! !DESCRIPTION:
! Zero out the 24 hr climates for LUNA model
!
! !REVISION HISTORY:
! version 1.0, by Chonggang Xu July 14 2015.
! CALLED FROM:
! subroutine CanopyFluxes
! !USES:
use clm_time_manager , only : get_step_size_real, is_end_curr_day
implicit none
! !ARGUMENTS:
type(bounds_type) , intent(in) :: bounds
integer , intent(in) :: fn ! size of pft filter
integer , intent(in) :: filterp(fn) ! pft filter
type(canopystate_type) , intent(inout) :: canopystate_inst
type(photosyns_type) , intent(inout) :: photosyns_inst
type(surfalb_type) , intent(in) :: surfalb_inst
type(solarabs_type) , intent(inout) :: solarabs_inst
type(temperature_type) , intent(inout) :: temperature_inst
! !LOCAL VARIABLES:
!
! local pointers to implicit in variables
integer :: c,f,g,iv,j,p ! indices
integer :: ft ! plant functional type
integer :: z ! the index across leaf layers
real (r8) :: dtime ! stepsize in seconds
logical :: is_end_day ! is end of current day
!-------------------------------------------------------------------------------------------------------------------------------------------------
associate( &
par24d_z => solarabs_inst%par24d_z_patch , & ! Output: [real(r8) (:,:) ] daily accumulated absorbed PAR for leaves in canopy layer (W/m**2)
par24x_z => solarabs_inst%par24x_z_patch , & ! Output: [real(r8) (:,:) ] daily maximum of patch absorbed PAR for leaves in canopy layer (W/m**2)
gpp_day => photosyns_inst%fpsn24_patch , & ! Output: [real(r8) (:) ] patch 24 hours acculative gpp(umol CO2/m**2 ground/day) from mid-night
t_veg_day => temperature_inst%t_veg_day_patch , & ! Output: [real(r8) (:) ] daytime mean vegetation temperature (Kelvin)
t_veg_night => temperature_inst%t_veg_night_patch , & ! Output: [real(r8) (:) ] nighttime mean vegetation temperature (Kelvin)
nnightsteps => temperature_inst%nnightsteps_patch , & ! Output: [integer (:) ] number of nighttime steps in 24 hours from mid-night, LUNA specific
ndaysteps => temperature_inst%ndaysteps_patch & ! Output: [integer (:) ] number of daytime steps in 24 hours from mid-night, LUNA specific
)
!----------------------------------------------------------------------------------------------------------------------------------------------------------
!set timestep
!Initialize enzyme decay Q10
dtime = get_step_size_real()
is_end_day = is_end_curr_day()
do f = 1,fn
p = filterp(f)
ft = patch%itype(p)
g = patch%gridcell(p)
c = patch%column(p)
!------------------------------------------------------------------------------
!clear out the daily state variables at the begining of simulations
t_veg_day(p) = 0.0_r8
t_veg_night(p) = 0.0_r8
par24d_z(p,:) = 0.0_r8
par24x_z(p,:) = 0.0_r8
gpp_day(p) = 0.0_r8
nnightsteps(p) = 0.0_r8
ndaysteps(p) = 0.0_r8
end do !fn loop
end associate
end subroutine Clear24_Climate_LUNA
!************************************************************************************************************************************************
!Use the LUNA model to calculate the Nitrogen partioning
subroutine NitrogenAllocation(FNCa,forc_pbot10, relh10, CO2a10,O2a10, PARi10,PARimx10,rb10, hourpd, tair10, tleafd10, tleafn10, &
Jmaxb0, Jmaxb1, Wc2Wjb0, relhExp,&
PNlcold, PNetold, PNrespold, PNcbold, &
PNstoreopt, PNlcopt, PNetopt, PNrespopt, PNcbopt)
implicit none
real(r8), intent (in) :: FNCa !Area based functional nitrogen content (g N/m2 leaf)
real(r8), intent (in) :: forc_pbot10 !10-day mean air pressure (Pa)
real(r8), intent (in) :: relh10 !10-day mean relative humidity (unitless)
real(r8), intent (in) :: CO2a10 !10-day meanCO2 concentration in the air (Pa)
real(r8), intent (in) :: O2a10 !10-day mean O2 concentration in the air (Pa)
real(r8), intent (in) :: PARi10 !10-day mean photosynthetic active radiation on in a canopy (umol/m2/s)
real(r8), intent (in) :: PARimx10 !10-day mean 24hr maximum photosynthetic active radiation on in a canopy (umol/m2/s)
real(r8), intent (in) :: rb10 !10-day mean boundary layer resistance
real(r8), intent (in) :: hourpd !hours of light in a the day (hrs)
real(r8), intent (in) :: tair10 !10-day running mean of the 2m temperature (oC)
real(r8), intent (in) :: tleafd10 !10-day running mean of daytime leaf temperature (oC)
real(r8), intent (in) :: tleafn10 !10-day running mean of nighttime leaf temperature (oC)
real(r8), intent (in) :: Jmaxb0 !baseline proportion of nitrogen allocated for electron transport rate (unitless)
real(r8), intent (in) :: Jmaxb1 !coefficient determining the response of electron transport rate to light availability (unitless)
real(r8), intent (in) :: Wc2Wjb0 !the baseline ratio of rubisco-limited rate vs light-limited photosynthetic rate (Wc:Wj)
real(r8), intent (in) :: relhExp !specifies the impact of relative humidity on electron transport rate (unitless)
real(r8), intent (in) :: PNlcold !old value of the proportion of nitrogen allocated to light capture (unitless)
real(r8), intent (in) :: PNetold !old value of the proportion of nitrogen allocated to electron transport (unitless)
real(r8), intent (in) :: PNrespold !old value of the proportion of nitrogen allocated to respiration (unitless)
real(r8), intent (in) :: PNcbold !old value of the proportion of nitrogen allocated to carboxylation (unitless)
real(r8), intent (out):: PNstoreopt !optimal proportion of nitrogen for storage
real(r8), intent (out):: PNlcopt !optimal proportion of nitrogen for light capture
real(r8), intent (out):: PNetopt !optimal proportion of nitrogen for electron transport
real(r8), intent (out):: PNrespopt !optimal proportion of nitrogen for respiration
real(r8), intent (out):: PNcbopt !optial proportion of nitrogen for carboxyaltion
!-------------------------------------------------------------------------------------------------------------------------------
!intermediate variables
real(r8) :: Carboncost1 !absolute amount of carbon cost associated with maintenance respiration due to deccrease in light capture nitrogen(g dry mass per day)
real(r8) :: Carboncost2 !absolute amount of carbon cost associated with maintenance respiration due to increase in light capture nitrogen(g dry mass per day)
real(r8) :: Carbongain1 !absolute amount of carbon gain associated with maintenance respiration due to deccrease in light capture nitrogen(g dry mass per day)
real(r8) :: Carbongain2 !absolute amount of carbon gain associated with maintenance respiration due to increase in light capture nitrogen(g dry mass per day)
real(r8) :: Fc !the temperature adjustment factor for Vcmax
real(r8) :: Fj !the temperature adjustment factor for Jmax
real(r8) :: PNlc !the current nitrogen allocation proportion for light capture
real(r8) :: Jmax !the maximum electron transport rate (umol/m2/s)
real(r8) :: JmaxCoef !coefficient determining the response of electron transport rate to light availability (unitless) and humidity
real(r8) :: Jmaxb0act !base value of Jmax (umol/m2/s)
real(r8) :: JmaxL !the electron transport rate with maximum daily radiation (umol/m2/s)
real(r8) :: JmeanL !the electron transport rate with mean radiation (umol/m2/s)
real(r8) :: Nstore !absolute amount of nitrogen allocated to storage (gN/m2 leaf)
real(r8) :: Nresp !absolute amount of nitrogen allocated to respiration (gN/m2 leaf)
real(r8) :: Nlc !absolute amount of nitrogen allocated to light capture (gN/m2 leaf)
real(r8) :: Net !absolute amount of nitrogen allocated to electron transport (gN/m2 leaf)
real(r8) :: Ncb !absolute amount of nitrogen allocated to carboxylation (gN/m2 leaf)
real(r8) :: Nresp1 !absolute amount of nitrogen allocated to respiration due to increase in light capture nitrogen(gN/m2 leaf)
real(r8) :: Nlc1 !absolute amount of nitrogen allocated to light capture due to increase in light capture nitrogen(gN/m2 leaf)
real(r8) :: Net1 !absolute amount of nitrogen allocated to electron transport due to increase in light capture nitrogen(gN/m2 leaf)
real(r8) :: Ncb1 !absolute amount of nitrogen allocated to carboyxlation due to increase in light capture nitrogen(gN/m2 leaf)
real(r8) :: Nresp2 !absolute amount of nitrogen allocated to respiration due to decrease in light capture nitrogen(gN/m2 leaf)
real(r8) :: Nlc2 !absolute amount of nitrogen allocated to light capture due to decrease in light capture nitrogen(gN/m2 leaf)
real(r8) :: Net2 !absolute amount of nitrogen allocated to electron transport due to decrease in light capture nitrogen(gN/m2 leaf)
real(r8) :: Ncb2 !absolute amount of nitrogen allocated to carboxylation due to increase in light capture nitrogen(gN/m2 leaf)
real(r8) :: PSN !g carbon photosynthesized per day per unit(m2) of leaf
real(r8) :: RESP !g carbon respired per day per unit(m2) of leaf due to increase in light capture nitrogen(gN/m2 leaf)
real(r8) :: PSN1 !g carbon photosynthesized per day per unit(m2) of leaf due to increase in light capture nitrogen(gN/m2 leaf)
real(r8) :: RESP1 !g carbon respired per day per unit(m2) of leaf due to decrease in light capture nitrogen(gN/m2 leaf)
real(r8) :: PSN2 !g carbon photosynthesized per day per unit(m2) of leaf due to decrease in light capture nitrogen(gN/m2 leaf)
real(r8) :: RESP2 !g carbon respired per day per unit(m2) of leaf
real(r8) :: Npsntarget !absolute amount of target nitrogen for photosynthesis(gN/m2 leaf)
real(r8) :: Npsntarget1 !absolute amount of target nitrogen for photosynthesis due to increase in light capture nitrogen(gN/m2 leaf)
real(r8) :: Npsntarget2 !absolute amount of target nitrogen for photosynthesis due to decrease in light capture nitrogen(gN/m2 leaf)
real(r8) :: NUEj !nitrogen use efficiency for electron transport under current environmental conditions
real(r8) :: NUEc !nitrogen use efficiency for carboxylation under current environmental conditions
real(r8) :: NUEjref !nitrogen use efficiency for electron transport under reference environmental conditions (25oC and 385ppm Co2)
real(r8) :: NUEcref !nitrogen use efficiency for carboxylation under reference environmental conditions (25oC and 385ppm Co2)
real(r8) :: NUEr !nitrogen use efficiency for respiration
real(r8) :: PARi10c !10-day mean constrained photosynthetic active radiation on in a canopy (umol/m2/s)
real(r8) :: PARimx10c !10-day mean constrained 24hr maximum photosynthetic active radiation on in a canopy (umol/m2/s)
real(r8) :: Kj2Kcref !the ratio of rubisco-limited photosynthetic rate (Wc) to light limited photosynthetic rate (Wj)
real(r8) :: PNlcoldi !old value of the proportion of nitrogen allocated to light capture (unitless)
real(r8) :: Kj2Kc !the ratio of Wc to Wj under changed conditions
real(r8) :: Kc !conversion factors for Vc,max to Wc
real(r8) :: Kj !conversion factor for electron transport rate to Wj
real(r8) :: theta !efficiency of light energy conversion (unitless)
real(r8) :: chg_per_step !the nitrogen change per interation
real(r8) :: Vcmaxnight !Vcmax during night (umol/m2/s)
real(r8) :: ci !inter-cellular CO2 concentration (Pa)
real(r8) :: theta_cj !interpolation coefficient
real(r8) :: tleafd10c !10-day mean daytime leaf temperature, contrained for physiological range (oC)
real(r8) :: tleafn10c !10-day mean leaf temperature for night, constrained for physiological range (oC)
real(r8) :: Vcmax !the maximum carboxyaltion rate (umol/m2/s)
integer :: KcKjFlag !flag to indicate whether to update the Kc and Kj using the photosynthesis subroutine; 0--Kc and Kj need to be calculated; 1--Kc and Kj is prescribed.
integer :: jj !index record fo the number of iterations
integer :: increase_flag !whether to increase or decrease
call NUEref(NUEjref, NUEcref, Kj2Kcref)
theta_cj = 0.95_r8
Nlc = PNlcold * FNCa !proportion of light capturing nitrogen in functional nitrogen
Net = PNetold * FNCa !proportion of light harvesting (electron transport) nitrogen in functional nitrogen
Nresp = PNrespold * FNCa !proportion of respirational nitrogen in functional nitrogen
Ncb = PNcbold * FNCa !proportion of carboxylation nitrogen in functional nitrogen
if (Nlc > FNCa * 0.5_r8) Nlc = 0.5_r8 * FNCa
chg_per_step = 0.02* FNCa
PNlc = PNlcold
PNlcoldi = PNlcold - 0.001_r8
PARi10c = max(PARLowLim, PARi10)
PARimx10c = max(PARLowLim, PARimx10)
increase_flag = 0
jj = 1
tleafd10c = min(max(tleafd10, Trange1), Trange2) !constrain the physiological range
tleafn10c = min(max(tleafn10, Trange1), Trange2) !constrain the physiological range
ci = 0.7_r8 * CO2a10
JmaxCoef = Jmaxb1 * ((hourpd / 12.0_r8)**2.0_r8) * (1.0_r8 - exp(-relhExp * max(relh10 - minrelh, 0.0_r8) / &
(1.0_r8 - minrelh)))
do while (PNlcoldi .NE. PNlc .and. jj < 100)
Fc = VcmxTKattge(tair10, tleafd10c) * Fc25
Fj = JmxTKattge(tair10, tleafd10c) * Fj25
NUEr = Cv * NUEr25 * (RespTBernacchi(tleafd10c) * hourpd + RespTBernacchi(tleafn10c) * (24.0_r8 - hourpd)) !nitrogen use efficiency for respiration (g biomass/m2/day/g N)
!****************************************************
!Nitrogen Allocation Scheme: store the initial value
!****************************************************
KcKjFlag = 0
call NUE(O2a10, ci, tair10, tleafd10c, NUEj, NUEc, Kj2Kc)
call Nitrogen_investments (KcKjFlag,FNCa, Nlc, forc_pbot10, relh10, CO2a10,O2a10, PARi10c, PARimx10c,rb10, hourpd, tair10, &
tleafd10c,tleafn10c, &
Kj2Kc, Wc2Wjb0, JmaxCoef, Fc,Fj, NUEc, NUEj, NUEcref, NUEjref, NUEr, Kc, Kj, ci, &
Vcmax, Jmax,JmeanL,JmaxL, Net, Ncb, Nresp, PSN, RESP)
Npsntarget = Nlc + Ncb + Net !target nitrogen allocated to photosynthesis, which may be lower or higher than Npsn_avail
PNlcoldi = Nlc / FNCa
Nstore = FNCa - Npsntarget - Nresp
!------------------------------------------------------------------------------------
!test the increase of light capture nitrogen
if (Nstore > 0.0_r8 .and.(increase_flag .eq. 1 .or. jj .eq. 1)) then
Nlc2 = Nlc + chg_per_step
if (Nlc2 / FNCa > 0.95_r8) Nlc2 = 0.95_r8 * FNCa
KcKjFlag = 1
call Nitrogen_investments (KcKjFlag,FNCa, Nlc2, forc_pbot10, relh10, CO2a10,O2a10, PARi10c, PARimx10c,rb10, hourpd, &
tair10, tleafd10c,tleafn10c, &
Kj2Kc, Wc2Wjb0, JmaxCoef, Fc,Fj, NUEc, NUEj, NUEcref, NUEjref,NUEr, Kc, Kj, ci, &
Vcmax, Jmax,JmeanL,JmaxL, Net2, Ncb2, Nresp2, PSN2, RESP2)
Npsntarget2 = Nlc2 + Ncb2 + Net2
!update the nitrogen change
Carboncost2 = (Npsntarget2 - Npsntarget) * NMCp25 * Cv * (RespTBernacchi(tleafd10c) * hourpd + &
RespTBernacchi(tleafn10c) * (24.0_r8 - hourpd))
Carbongain2 = PSN2 - PSN
if(Carbongain2 > Carboncost2 .and. (Npsntarget2 + Nresp2 < 0.95_r8 * FNCa))then
Nlc = Nlc2
Net = Net2
Ncb = Ncb2
Nstore = FNCa - Npsntarget2 - Nresp2
if (jj == 1) increase_flag = 1
end if
end if
!------------------------------------------------------------------------------------
!test the decrease of light capture nitrogen
if (increase_flag == 0) then
if (Nstore < 0.0_r8) then
Nlc1 = Nlc * 0.8_r8 !bigger step of decrease if it is negative
else
Nlc1 = Nlc - chg_per_step
end if
if (Nlc1 < 0.05_r8) Nlc1 = 0.05_r8
KcKjFlag = 1
call Nitrogen_investments (KcKjFlag,FNCa, Nlc1,forc_pbot10, relh10, CO2a10,O2a10, PARi10c, PARimx10c,rb10, hourpd, &
tair10, tleafd10c,tleafn10c, &
Kj2Kc, Wc2Wjb0, JmaxCoef, Fc,Fj, NUEc, NUEj, NUEcref, NUEjref,NUEr, Kc, Kj, ci,&
Vcmax, Jmax,JmeanL,JmaxL, Net1, Ncb1, Nresp1, PSN1, RESP1)
Npsntarget1 = Nlc1 + Ncb1 + Net1
Carboncost1 = (Npsntarget - Npsntarget1) * NMCp25 * Cv * (RespTBernacchi(tleafd10c) * hourpd + &
RespTBernacchi(tleafn10c) * (24.0_r8 - hourpd))
Carbongain1 = PSN - PSN1
if((Carbongain1 < Carboncost1 .and. Nlc1 > 0.05_r8) .or. (Npsntarget + Nresp) > 0.95_r8 * FNCa)then
Nlc = Nlc1
Net = Net1
Ncb = Ncb1
Nstore = FNCa - Npsntarget1 - Nresp1
end if
end if
PNlc = Nlc / FNCa
jj = jj + 1
end do
PNlcopt = Nlc / FNCa
PNstoreopt = Nstore / FNCa
PNcbopt = Ncb / FNCa
PNetopt = Net / FNCa
PNrespopt = Nresp / FNCa
end subroutine NitrogenAllocation
!*****************************************************************************************************************
!calcualte the nitrogen investment for electron transport, carb10oxylation, respiration given a specified value
!of nitrogen allocation in light capture [Nlc]. This equation are based on Ali et al 2015b.
subroutine Nitrogen_investments (KcKjFlag, FNCa, Nlc, forc_pbot10, relh10, &
CO2a10, O2a10, PARi10, PARimx10, rb10, hourpd, tair10, tleafd10, tleafn10, &
Kj2Kc, Wc2Wjb0, JmaxCoef, Fc, Fj, NUEc, NUEj, NUEcref, NUEjref, NUEr, Kc, &
Kj, ci, Vcmax, Jmax, JmeanL, JmaxL, Net, Ncb, Nresp, PSN, RESP)
implicit none
integer, intent (in) :: KcKjFlag !flag to indicate whether to update the Kc and Kj using the photosynthesis subroutine; 0--Kc and Kj need to be calculated; 1--Kc and Kj is prescribed.
real(r8), intent (in) :: FNCa !Area based functional nitrogen content (g N/m2 leaf)
real(r8), intent (in) :: Nlc !nitrogen content for light capture(g N/m2 leaf)
real(r8), intent (in) :: forc_pbot10 !10-day mean air pressure (Pa)
real(r8), intent (in) :: relh10 !10-day mean relative humidity (unitless)
real(r8), intent (in) :: CO2a10 !10-day mean CO2 concentration in the air (Pa)
real(r8), intent (in) :: O2a10 !10-day mean O2 concentration in the air (Pa)
real(r8), intent (in) :: PARi10 !10-day mean photosynthetic active radiation on in a canopy (umol/m2/s)
real(r8), intent (in) :: PARimx10 !10-day mean 24hr maximum photosynthetic active radiation on in a canopy (umol/m2/s)
real(r8), intent (in) :: rb10 !10-day mean boundary layer resistance (s/m)
real(r8), intent (in) :: hourpd !hours of light in a the day (hrs)
real(r8), intent (in) :: tair10 !10-day running mean of the 2m temperature (oC)
real(r8), intent (in) :: tleafd10 !10-day mean daytime leaf temperature (oC)