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aed2_nitrogen.F90
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!###############################################################################
! .-----------------. .----------------. .----------------. !
! | .--------------. || .--------------. || .--------------. | !
! | | ____ _____ | || | _____ | || | _________ | | !
! | ||_ \|_ _| | || | |_ _| | || | | _ _ | | | !
! | | | \ | | | || | | | | || | |_/ | | \_| | | !
! | | | |\ \| | | || | | | | || | | | | | !
! | | _| |_\ |_ | || | _| |_ | || | _| |_ | | !
! | ||_____|\____| | || | |_____| | || | |_____| | | !
! | | | || | | || | | | !
! | '--------------' || '--------------' || '--------------' | !
! '----------------' '----------------' '----------------' !
!###############################################################################
!# #
!# aed2_nitrogen.F90 #
!# #
!# Developed by : #
!# AquaticEcoDynamics (AED) Group #
!# School of Agriculture and Environment #
!# The University of Western Australia #
!# #
!# http://aquatic.science.uwa.edu.au/ #
!# #
!# Copyright 2013 - 2019 - The University of Western Australia #
!# #
!# GLM is free software: you can redistribute it and/or modify #
!# it under the terms of the GNU General Public License as published by #
!# the Free Software Foundation, either version 3 of the License, or #
!# (at your option) any later version. #
!# #
!# GLM is distributed in the hope that it will be useful, #
!# but WITHOUT ANY WARRANTY; without even the implied warranty of #
!# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
!# GNU General Public License for more details. #
!# #
!# You should have received a copy of the GNU General Public License #
!# along with this program. If not, see <http://www.gnu.org/licenses/>. #
!# #
!# ---------------------------------------------------------------------- #
!# #
!# Created 9 May 2011 #
!# #
!###############################################################################
#include "aed2.h"
!
MODULE aed2_nitrogen
!------------------------------------------------------------------------------+
! aed2_nitrogen --- nitrogen biogeochemical model
!
! Nitrogen module contains equations for nitrification and denitrification
!------------------------------------------------------------------------------+
USE aed2_core
USE aed2_util, ONLY: aed2_gas_piston_velocity, aed2_n2o_sat
IMPLICIT NONE
PRIVATE ! By default make everything private
!
PUBLIC aed2_nitrogen_data_t
!
TYPE,extends(aed2_model_data_t) :: aed2_nitrogen_data_t
!# Variable identifiers
INTEGER :: id_nox, id_amm, id_n2o, id_no2
INTEGER :: id_oxy, id_ph, id_temp, id_salt, id_denit_product
INTEGER :: id_wind, id_E_depth, id_E_tau, id_E_dens, id_E_rain
INTEGER :: id_Fsed_amm, id_Fsed_nit, id_Fsed_n2o, id_Fsed_no2
INTEGER :: id_nitrf, id_denit, id_n2op, id_anammox, id_dnra
INTEGER :: id_sed_amm, id_sed_nit, id_sed_n2o, id_sed_no2
INTEGER :: id_atm_n2o, id_atm_dep
INTEGER :: id_cell_vel
!# Model parameters
AED_REAL :: Rnitrif,Rdenit,Ranammox,Rn2o,Rdnra
AED_REAL :: Knitrif,Kdenit,Kanmx_nit,Kanmx_amm,Kdnra_oxy
AED_REAL :: Kpart_ammox, Kin_deamm, Rno2o2, Rnh4o2, Rnh4no2
AED_REAL :: theta_nitrif,theta_denit,theta_sed_amm,theta_sed_nit
AED_REAL :: Fsed_amm,Fsed_nit,Fsed_n2o,Fsed_no2,Ksed_amm,Ksed_nit,Ksed_n2o
AED_REAL :: atm_din_dd, atm_din_conc, atm_pn_dd, f_dindep_nox
AED_REAL :: atm_n2o
LOGICAL :: use_oxy, use_ph
LOGICAL :: use_sed_model_amm,use_sed_model_nit,use_sed_model_n2o,use_sed_model_no2
LOGICAL :: simNitrfpH,simNitrfLight,simDryDeposition,simWetDeposition
INTEGER :: oxy_lim, simN2O, n2o_piston_model
CONTAINS
PROCEDURE :: define => aed2_define_nitrogen
PROCEDURE :: calculate => aed2_calculate_nitrogen
PROCEDURE :: calculate_benthic => aed2_calculate_benthic_nitrogen
PROCEDURE :: calculate_surface => aed2_calculate_surface_nitrogen
! PROCEDURE :: mobility => aed2_mobility_nitrogen
! PROCEDURE :: light_extinction => aed2_light_extinction_nitrogen
! PROCEDURE :: delete => aed2_delete_nitrogen
END TYPE
! MODULE GLOBALS
INTEGER :: diag_level = 10
!===============================================================================
CONTAINS
!###############################################################################
SUBROUTINE aed2_define_nitrogen(data, namlst)
!------------------------------------------------------------------------------+
! Initialise the AED model
!
! Here, the aed namelist is read and te variables exported
! by the model are registered with AED2.
!------------------------------------------------------------------------------+
!ARGUMENTS
INTEGER,INTENT(in) :: namlst
CLASS (aed2_nitrogen_data_t),INTENT(inout) :: data
!
!LOCALS
INTEGER :: status
INTEGER :: oxy_lim = 1
INTEGER :: simN2O = 0
INTEGER :: n2o_piston_model = 4
LOGICAL :: simNitrfpH = .false.
LOGICAL :: simNitrfLight = .false.
LOGICAL :: simDryDeposition = .false.
LOGICAL :: simWetDeposition = .false.
! %% NAMELIST
AED_REAL :: n_min = zero_
AED_REAL :: n_max = 1e6
AED_REAL :: nit_initial = 4.5
AED_REAL :: amm_initial = 4.5
AED_REAL :: n2o_initial = 0.0
AED_REAL :: no2_initial = 0.0
AED_REAL :: Rnitrif = 0.01
AED_REAL :: Rdenit = 0.01
AED_REAL :: Rn2o = 0.0015
AED_REAL :: Ranammox = 0.0
AED_REAL :: Rdnra = 0.0
AED_REAL :: Knitrif = 150.0
AED_REAL :: Kdenit = 150.0
AED_REAL :: Kanmx_nit = 150.0
AED_REAL :: Kanmx_amm = 150.0
AED_REAL :: Kdnra_oxy = 150.0
AED_REAL :: Kpart_ammox = 20.0 !Ko2_4
AED_REAL :: Kin_deamm = 0.886 !Ko2_5
AED_REAL :: Rno2o2
AED_REAL :: Rnh4o2
AED_REAL :: Rnh4no2
AED_REAL :: theta_nitrif = 1.0
AED_REAL :: theta_denit = 1.0
AED_REAL :: Fsed_amm = zero_
AED_REAL :: Fsed_nit = zero_
AED_REAL :: Fsed_n2o = zero_
AED_REAL :: Fsed_no2 = zero_
AED_REAL :: Ksed_amm = 30.0
AED_REAL :: Ksed_nit = 30.0
AED_REAL :: Ksed_n2o = 30.0
AED_REAL :: Ksed_no2 = 30.0
AED_REAL :: theta_sed_amm = 1.0
AED_REAL :: theta_sed_nit = 1.0
AED_REAL :: atm_n2o = 0.32*1e-6 !## recent atmospheric N2O conc (in ppm)
AED_REAL :: atm_din_dd = zero_
AED_REAL :: atm_din_conc = zero_
AED_REAL :: atm_pn_dd = zero_
AED_REAL :: f_dindep_nox = 0.5
CHARACTER(len=64) :: nitrif_reactant_variable=''
CHARACTER(len=64) :: denit_product_variable=''
CHARACTER(len=64) :: nitrif_ph_variable=''
CHARACTER(len=64) :: Fsed_amm_variable=''
CHARACTER(len=64) :: Fsed_nit_variable=''
CHARACTER(len=64) :: Fsed_n2o_variable=''
CHARACTER(len=64) :: Fsed_no2_variable=''
! %% END NAMELIST
NAMELIST /aed2_nitrogen/ n_min, n_max, &
nit_initial, amm_initial, n2o_initial, no2_initial, &
Rnitrif,Rdenit,Fsed_amm,Fsed_nit, &
Knitrif,Kdenit,Ksed_amm,Ksed_nit, &
Kpart_ammox, Kin_deamm, Rno2o2, Rnh4o2, Rnh4no2, &
theta_nitrif,theta_denit,theta_sed_amm,theta_sed_nit, &
nitrif_reactant_variable,denit_product_variable,nitrif_ph_variable,&
Fsed_amm_variable,Fsed_nit_variable,Fsed_n2o_variable,Fsed_no2_variable,&
simN2O, atm_n2o, oxy_lim, Rn2o, Fsed_n2o, Ksed_n2o, n2o_piston_model,&
Ranammox, Rdnra, Kanmx_nit, Kanmx_amm, Kdnra_oxy, &
simNitrfpH, simNitrfLight, simDryDeposition, simWetDeposition, &
atm_din_dd, atm_din_conc, atm_pn_dd, f_dindep_nox
!
!------------------------------------------------------------------------------+
!BEGIN
print *," aed2_nitrogen initialization"
!---------------------------------------------------------------------------+
! Read the namelist
read(namlst,nml=aed2_nitrogen,iostat=status)
IF (status /= 0) STOP 'Error reading namelist aed2_nitrogen'
!---------------------------------------------------------------------------+
! Store config options and parameter values in module's own derived type
! Note: all rates must be provided in values per day in the nml,
! and are converted for internal use as values per second.
data%simNitrfpH = simNitrfpH
data%simNitrfLight = simNitrfLight
data%simN2O = simN2O
data%oxy_lim = oxy_lim
data%Rnitrif = Rnitrif/secs_per_day
data%Rdenit = Rdenit/secs_per_day
data%Rn2o = Rn2o/secs_per_day
data%Ranammox = Ranammox/secs_per_day
data%Rdnra = Rdnra/secs_per_day
data%Knitrif = Knitrif
data%Kdenit = Kdenit
data%Kanmx_nit = Kanmx_nit
data%Kanmx_amm = Kanmx_amm
data%Kdnra_oxy = Kdnra_oxy
data%Kpart_ammox = Kpart_ammox
data%Kin_deamm = Kin_deamm
data%Rno2o2 = Rno2o2/secs_per_day
data%Rnh4o2 = Rnh4o2/secs_per_day
data%Rnh4no2 = Rnh4no2/secs_per_day
data%theta_nitrif = theta_nitrif
data%theta_denit = theta_denit
data%atm_n2o = atm_n2o
data%n2o_piston_model = n2o_piston_model
data%Fsed_amm = Fsed_amm/secs_per_day
data%Fsed_nit = Fsed_nit/secs_per_day
data%Fsed_n2o = Fsed_n2o/secs_per_day
data%Fsed_no2 = Fsed_no2/secs_per_day
data%Ksed_amm = Ksed_amm
data%Ksed_nit = Ksed_nit
data%Ksed_n2o = Ksed_n2o
data%theta_sed_amm = MIN(MAX(0.5,theta_sed_amm),1.5)
data%theta_sed_nit = MIN(MAX(0.5,theta_sed_nit),1.5)
data%simDryDeposition = simDryDeposition
data%simWetDeposition = simWetDeposition
data%atm_din_dd = MAX(zero_,atm_din_dd/secs_per_day)
data%atm_pn_dd = MAX(zero_,atm_pn_dd/secs_per_day) ! Remains unused ?
data%atm_din_conc = MAX(zero_,atm_din_conc)
data%f_dindep_nox = MIN(MAX(zero_,f_dindep_nox),one_)
!---------------------------------------------------------------------------+
! Register state variables
data%id_amm = aed2_define_variable('amm','mmol/m**3','ammonium', &
amm_initial,minimum=n_min, maximum=n_max)
data%id_nox = aed2_define_variable('nit','mmol/m**3','nitrate', &
nit_initial,minimum=n_min, maximum=n_max)
IF( simN2O>0 ) THEN
! TODO check here to see if oxy is simulated if simN2O is also on
IF (nitrif_reactant_variable .NE. '') THEN
print *,' advanced nitrogen redox model linking to ',TRIM(nitrif_reactant_variable)
! this allocation is done below with other state var dependancies
!data%id_oxy = aed2_locate_variable(nitrif_reactant_variable)
print *,' ... found'
ELSE
PRINT *,' ERROR advanced nitrogen redox set (simN2O) but no oxygen target variable is set'
STOP
ENDIF
data%id_n2o = aed2_define_variable('n2o','mmol/m**3','nitrous oxide', &
n2o_initial, minimum=n_min, maximum=n_max)
IF( simN2O>1 ) THEN ! Advanced model requires NO2
data%id_no2 = aed2_define_variable('no2','mmol/m**3','nitrate', &
no2_initial, minimum=n_min, maximum=n_max)
ENDIF
ENDIF
!---------------------------------------------------------------------------+
! Register external state variable dependencies
data%use_oxy = nitrif_reactant_variable .NE. '' !Check for link to OXY module
IF (data%use_oxy) data%id_oxy = aed2_locate_variable(nitrif_reactant_variable)
data%use_ph = nitrif_ph_variable .NE. '' !Check for link to CAR module
IF (.NOT.data%use_ph) data%simNitrfpH = .false. !Disable if no link possible
IF (data%simNitrfpH) data%id_ph = aed2_locate_variable(nitrif_ph_variable)
data%id_Fsed_amm = -1 ; data%id_Fsed_nit = -1
data%id_Fsed_n2o = -1 ; data%id_Fsed_no2 = -1
data%use_sed_model_amm = Fsed_amm_variable .NE. ''
IF (data%use_sed_model_amm) &
data%id_Fsed_amm = aed2_locate_global_sheet(Fsed_amm_variable)
data%use_sed_model_nit = Fsed_nit_variable .NE. ''
IF (data%use_sed_model_nit) &
data%id_Fsed_nit = aed2_locate_global_sheet(Fsed_nit_variable)
data%use_sed_model_n2o = Fsed_n2o_variable .NE. ''
IF (data%use_sed_model_n2o .and. simN2O>0 ) &
data%id_Fsed_n2o = aed2_locate_global_sheet(Fsed_n2o_variable)
data%use_sed_model_no2 = Fsed_no2_variable .NE. ''
IF (data%use_sed_model_no2 .and. simN2O>1 ) &
data%id_Fsed_no2 = aed2_locate_global_sheet(Fsed_no2_variable)
!---------------------------------------------------------------------------+
! Register diagnostic variables
data%id_sed_amm = aed2_define_sheet_diag_variable('sed_amm','mmol/m**2/d','ammonium sediment flux')
data%id_sed_nit = aed2_define_sheet_diag_variable('sed_nit','mmol/m**2/d','nitrate sediment flux')
data%id_nitrf = aed2_define_diag_variable('nitrif','mmol/m**3/d','nitrification rate')
data%id_denit = aed2_define_diag_variable('denit','mmol/m**3/d','de-nitrification rate')
data%id_anammox = aed2_define_diag_variable('anammox','mmol/m**3/d','anammox rate')
data%id_dnra = aed2_define_diag_variable('dnra','mmol/m**3/d','dnra rate')
IF( simN2O>0 ) THEN
data%id_n2op = aed2_define_diag_variable('n2oprod','mmol/m**3/d','n2o prod rate')
data%id_atm_n2o = aed2_define_sheet_diag_variable('atm_n2o_flux','mmol/m**2/d','n2o atmospheric flux')
data%id_sed_n2o = aed2_define_sheet_diag_variable('sed_n2o','mmol/m**2/d','n2o sediment flux')
IF( simN2O>1 ) data%id_sed_no2 = aed2_define_sheet_diag_variable('sed_no2','mmol/m**2/d','no2 sediment flux')
ENDIF
IF( simWetDeposition .OR. simDryDeposition ) THEN
data%id_atm_dep = aed2_define_sheet_diag_variable('atm_din_flux','mmol/m**2/d','din atmospheric deposition flux')
ENDIF
!---------------------------------------------------------------------------+
! Register environmental dependencies
data%id_temp = aed2_locate_global('temperature')
data%id_salt = aed2_locate_global('salinity')
IF( simWetDeposition ) data%id_E_rain = aed2_locate_global_sheet('rain')
IF( simN2O>0 ) data%id_wind = aed2_locate_global_sheet('wind_speed')
IF( simN2O>0 ) data%id_E_depth = aed2_locate_global('layer_ht')
IF( simN2O>0 ) data%id_cell_vel= aed2_locate_global('cell_vel')! needed for k600
!IF( simN2O>0 ) data%id_E_tau = aed2_locate_global('taub') ! tau to be converted to velocity
!IF( simN2O>0 ) data%id_E_dens = aed2_locate_global('density') ! density needed for tau-vel
END SUBROUTINE aed2_define_nitrogen
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!###############################################################################
SUBROUTINE aed2_calculate_nitrogen(data,column,layer_idx)
!------------------------------------------------------------------------------+
! Right hand sides of aed2_nitrogen model
!------------------------------------------------------------------------------+
!ARGUMENTS
CLASS (aed2_nitrogen_data_t),INTENT(in) :: data
TYPE (aed2_column_t),INTENT(inout) :: column(:)
INTEGER,INTENT(in) :: layer_idx
!
!LOCALS
AED_REAL :: amm,nit,n2o,no2 ! State variables
AED_REAL :: oxy,temp,pH ! Dependant variables
AED_REAL :: nitrification,denitrification,anammox,dnra
AED_REAL :: denit_n2o_prod,denit_n2o_cons,nit_n2o_prod
AED_REAL :: nitratation, denitratation, &
nitritation, denitritation, &
deammonification, & !dnra,
nitrousation, denitrousation, &
ammonium_oxidation, ammonium_release
AED_REAL,PARAMETER :: Xon = 3.0 !ratio of O2 to N utilised during nitrification
AED_REAL,PARAMETER :: Knev = 3.0 !Nevison nitrification O2 threshold
AED_REAL,PARAMETER :: aa = 0.26 !Nevison nitrification parameter
AED_REAL,PARAMETER :: bb = -0.0006 !Nevison nitrification parameter
AED_REAL,PARAMETER :: Xnc = 16./106. !OM stoichiomtery
AED_REAL,PARAMETER :: Kn2oc= 0.3 !N2O consumption O2 poisoning
AED_REAL,PARAMETER :: Kno3 = 5.0 !Denit NO3 half-sat
AED_REAL,PARAMETER :: Xon1 = 1.
AED_REAL,PARAMETER :: Xon2 = 1.
AED_REAL,PARAMETER :: Xon3 = 1.!
!------------------------------------------------------------------------------+
!BEGIN
n2o = zero_ ; no2 = zero_
!-----------------------------------------------
! Retrieve current environmental conditions.
temp = _STATE_VAR_(data%id_temp) ! temperature
!-----------------------------------------------
! Set current (local) state variable values.
amm = _STATE_VAR_(data%id_amm) ! ammonium
nit = _STATE_VAR_(data%id_nox) ! nitrate
oxy = 300.0 ; IF( data%id_oxy>0 ) oxy = _STATE_VAR_(data%id_oxy) ! oxygen
ph = 7.0 ; IF( data%simNitrfpH ) ph = _STATE_VAR_(data%id_ph) ! pH
!-----------------------------------------------
!# Define process rates in units mmol N/m3/s, using either the fully resolved
! GHG model, or traditional simple nitrification/denitrification model
IF ( data%simN2O == 2 ) THEN
!# Full N GHG model with NO2 and N2O; hetertrophy is done in OGM
no2 = _STATE_VAR_(data%id_no2) ! nitrite
n2o = _STATE_VAR_(data%id_n2o) ! nitrous oxide
!# Nitrification (autotrophic so done here)
nitratation = data%Rno2o2 * no2*oxy
ammonium_oxidation = data%Rnh4o2 * amm*oxy
nitritation = data%Rnh4o2 * amm*oxy * oxy/(data%Kpart_ammox+oxy)
nitrousation = data%Rnh4o2 * amm*oxy * data%Kpart_ammox/(data%Kpart_ammox+oxy) * 0.5
deammonification = data%Rnh4no2* no2*amm * data%Kin_deamm/(data%Kin_deamm+oxy)
!IF( data%simNitrfpH ) nitrousation = nitrousation * NitrfpHFunction(pH) ! Ask Dan
!# De-nitrification (for info only, they are hetertrophic so are done in OGM)
! denitratation = kom*om * nit/(data%K_nit+nit) * data%Ko2_1/(data%Ko2_1+oxy)
! denitritation = kom*om * nit/(data%K_nit+nit) * data%Ko2_3/(data%Ko2_3+oxy)
! denitrousation = kom*om * n2o/(data%K_n2o+n2o) * data%Ko2_6/(data%Ko2_6+oxy)
! dnra = denitritation * data%K_no2/(data%K_no2+no2)
! nitrous_denitritation = denitritation * no2/(data%K_no2+no2) * data%K_n2o/(data%K_n2o+n2o)
! ammonium_release =(denitratation + denitritation + denitrousation) * data%X_nc
! Update nitrogen pools with the flux calculations
_FLUX_VAR_(data%id_nox) = _FLUX_VAR_(data%id_nox) + nitratation ! - denitratation
_FLUX_VAR_(data%id_no2) = _FLUX_VAR_(data%id_no2) + &
nitritation - nitratation - deammonification ! + denitritation - denitritation
_FLUX_VAR_(data%id_n2o) = _FLUX_VAR_(data%id_n2o) + &
nitrousation ! + nitrous_denitritation - denitrousation
_FLUX_VAR_(data%id_amm) = _FLUX_VAR_(data%id_amm) - &
ammonium_oxidation - deammonification ! + dnra + ammonium_release
!_FLUX_VAR_(data%id_n2 ) = _FLUX_VAR_(data%id_n2 ) + deammonification
!# Take nitrification consumption of oxygen
_FLUX_VAR_(data%id_oxy) = _FLUX_VAR_(data%id_oxy) - &
Xon1*nitrousation - Xon2*nitritation - Xon3*nitratation
!# Set diagnostics, based on this sub-model
_DIAG_VAR_(data%id_nitrf) = ammonium_oxidation * secs_per_day
_DIAG_VAR_(data%id_anammox) = deammonification * secs_per_day
_DIAG_VAR_(data%id_n2op) = nitrousation* secs_per_day
_DIAG_VAR_(data%id_denit) = zero_ * secs_per_day ! Heterotrophic done in OGM
_DIAG_VAR_(data%id_dnra) = zero_ * secs_per_day ! Heterotrophic done in OGM
ELSE
!# Simple model
!# Nitrification
nitrification = amm * NitrfO2Function(data%use_oxy,data%Rnitrif,data%Knitrif,data%theta_nitrif,oxy,temp)
IF( data%simNitrfpH ) nitrification = nitrification * NitrfpHFunction(pH)
!IF( data%simNitrfLight ) nitrification = nitrification* NitrfLightFunction(I) ! Capone Pg 238 add one day
!# De-nitrification
denitrification = nit * DenitO2Function(data%Rdenit, &
data%use_oxy,data%oxy_lim, &
data%Kdenit,data%theta_denit,Kno3, &
oxy,temp,nit)
!# Leakign of N2O, using the Babbin model
IF( data%simN2O == 1 ) THEN
! Babbin style model to capture intermediate N2O pool
n2o = _STATE_VAR_(data%id_n2o) ! nitrous oxide
denit_n2o_prod = 0.5 * denitrification !* Xnc
denit_n2o_cons = data%Rn2o * n2o * exp(-oxy/Kn2oc)
nit_n2o_prod = zero_
IF(oxy>Knev) nit_n2o_prod = ((aa/oxy)+bb)*nitrification
!IF(oxy>Knev) nit_n2o_prod = ((aa/oxy)+bb)*remin*Xnc
ENDIF
!# Anammox (NO2 + NH4 + CO2 -> N2); assuming nit ~ NO2 for now
anammox = zero_
IF( data%use_oxy .AND. oxy < 1e-1*(1e3/32.) ) THEN
anammox = data%Ranammox * nit/(data%Kanmx_nit+nit) * amm/(data%Kanmx_amm+amm)
ENDIF
!## Dissasimilatory nitrate reduction to ammonia (DNRA)
dnra = zero_
IF( data%use_oxy ) THEN
dnra = data%Rdnra * data%Kdnra_oxy/(data%Kdnra_oxy+oxy) * nit
ENDIF
!-----------------------------------------------
! Set temporal derivatives
_FLUX_VAR_(data%id_amm) = _FLUX_VAR_(data%id_amm) - nitrification - anammox + dnra
_FLUX_VAR_(data%id_nox) = _FLUX_VAR_(data%id_nox) &
+ nitrification - denitrification - anammox - dnra
IF( data%simN2O==1 ) &
_FLUX_VAR_(data%id_n2o) = _FLUX_VAR_(data%id_n2o) &
+ (denit_n2o_prod - denit_n2o_cons + nit_n2o_prod)
! If an externally maintained oxygen pool is linked, take nitrification from it
IF (data%use_oxy) &
_FLUX_VAR_(data%id_oxy) = _FLUX_VAR_(data%id_oxy) + (-Xon*nitrification)
!-----------------------------------------------
! Export diagnostic variables
_DIAG_VAR_(data%id_nitrf) = nitrification * secs_per_day
_DIAG_VAR_(data%id_denit) = denitrification * secs_per_day
_DIAG_VAR_(data%id_anammox) = anammox * secs_per_day
_DIAG_VAR_(data%id_dnra) = dnra * secs_per_day
IF( data%simN2O==1 ) THEN
_DIAG_VAR_(data%id_n2op) = (denit_n2o_prod + nit_n2o_prod) * secs_per_day
ENDIF
ENDIF
END SUBROUTINE aed2_calculate_nitrogen
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!###############################################################################
SUBROUTINE aed2_calculate_surface_nitrogen(data,column,layer_idx)
!------------------------------------------------------------------------------+
! Air-water exchange for the aed nitrogen model. Includes N2O atmos exchange
! and wet/dry deposition, depending on the configuration
!------------------------------------------------------------------------------+
!ARGUMENTS
CLASS (aed2_nitrogen_data_t),INTENT(in) :: data
TYPE (aed2_column_t),INTENT(inout) :: column(:)
INTEGER,INTENT(in) :: layer_idx
!
!LOCALS
! Environment
AED_REAL :: temp, salt, wind, depth, rain
AED_REAL :: vel = 0.0001
! State
AED_REAL :: n2o, nox, no2, nh4
! Temporary variables
AED_REAL :: n2o_atm_flux = zero_ ! N2O atmos exchange with water
AED_REAL :: Cn2o_air = zero_ ! N2O in the air phase
AED_REAL :: kn2o_trans = zero_ ! N2O piston velocity
AED_REAL :: wind_hgt = 10. ! Height of wind data, for correction
AED_REAL :: f_pres = 1. ! Pressure correction function (currently
! unused but needed for high altitudes)
!
!------------------------------------------------------------------------------+
!BEGIN
!----------------------------------------------------------------------------+
!# Water-Atmosphere exchange of N2O
IF( data%simN2O>0 ) THEN
!-----------------------------------------------
! Get the necessary environmental variables (from physical driver)
wind_hgt = 10.
wind = _STATE_VAR_S_(data%id_wind) ! Wind speed at 10m above surface (m/s)
temp = _STATE_VAR_(data%id_temp) ! Temperature (degrees Celsius)
salt = _STATE_VAR_(data%id_salt) ! Salinity (psu)
depth = MAX( _STATE_VAR_(data%id_E_depth), one_ )
IF (data%id_cell_vel > 0 ) vel = _STATE_VAR_(data%id_cell_vel)
!-----------------------------------------------
! Retrieve current (local) state variable values.
n2o = _STATE_VAR_(data%id_n2o) ! Concentration of N2O in surface layer
!-----------------------------------------------
! Get the surface piston velocity (Note : THIS IS BASED ON 2D FLOWS)
! transfer velocity k of Ho et al. 2016
!kn2o_trans = 0.77*( (vel**0.5)*(depth**(-0.5)) + 0.266*wind**2. ) / 3.6e5
kn2o_trans = aed2_gas_piston_velocity(wind_hgt,wind,temp,salt,vel=vel, &
depth=depth,schmidt_model=2,piston_model=data%n2o_piston_model)
!-----------------------------------------------
! First get the N2O concentration in the air-phase at atm interface
! C_N2O = F x P ; Capone (2008) pg 56
f_pres = 1.0 ! add function here for altitude correction.
Cn2o_air = data%atm_n2o
Cn2o_air = Cn2o_air * aed2_n2o_sat(salt,temp)
!-----------------------------------------------
! Get the N2O flux: [ mmol/m2/s = m/s * mmol/m3 ]
n2o_atm_flux = kn2o_trans * (n2o - Cn2o_air) * f_pres
!-----------------------------------------------
! Set surface exchange value (mmmol/m2/s) for AED2 ODE solution.
_FLUX_VAR_T_(data%id_n2o) = -n2o_atm_flux
!-----------------------------------------------
! Also store N2O flux across the atm/water interface as a
! diagnostic variable (mmmol/m2/d).
_DIAG_VAR_S_(data%id_atm_n2o) = n2o_atm_flux * secs_per_day
ENDIF
!----------------------------------------------------------------------------+
!# Atmosphere loading of DIN to the water, due to dry or wet deposition
IF( data%simDryDeposition ) THEN
!-----------------------------------------------
! Set surface exchange value (mmmol/m2/s) for AED2 ODE solution.
_FLUX_VAR_T_(data%id_nox) = data%atm_din_dd * data%f_dindep_nox
_FLUX_VAR_T_(data%id_amm) = data%atm_din_dd * (1.-data%f_dindep_nox)
ENDIF
IF( data%simWetDeposition ) THEN
!-----------------------------------------------
! Get the necessary environmental variables (from physical driver)
rain = _STATE_VAR_S_(data%id_E_rain) / secs_per_day ! Rain (m/s)
!-----------------------------------------------
! Set surface exchange value (mmmol/m2/s) for AED2 ODE solution.
_FLUX_VAR_T_(data%id_nox) = _FLUX_VAR_T_(data%id_nox) &
+ rain * data%atm_din_conc * data%f_dindep_nox
_FLUX_VAR_T_(data%id_amm) = _FLUX_VAR_T_(data%id_amm) &
+ rain * data%atm_din_conc *(1.-data%f_dindep_nox)
ENDIF
IF( data%simDryDeposition .OR. data%simWetDeposition ) THEN
!-----------------------------------------------
! Also store deposition across the atm/water interface as a
! diagnostic variable (mmmol/m2/day).
_DIAG_VAR_S_(data%id_atm_dep) = _DIAG_VAR_S_(data%id_atm_dep) &
+ (_FLUX_VAR_T_(data%id_nox) + _FLUX_VAR_T_(data%id_amm)) * secs_per_day
ENDIF
END SUBROUTINE aed2_calculate_surface_nitrogen
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!###############################################################################
SUBROUTINE aed2_calculate_benthic_nitrogen(data,column,layer_idx)
!------------------------------------------------------------------------------+
! Calculate pelagic bottom fluxes and benthic sink / source terms dis nitrogen.
! Everything in units per surface area (not volume!) per time.
!------------------------------------------------------------------------------+
!ARGUMENTS
CLASS (aed2_nitrogen_data_t),INTENT(in) :: data
TYPE (aed2_column_t),INTENT(inout) :: column(:)
INTEGER,INTENT(in) :: layer_idx
!
!LOCALS
! Environment
AED_REAL :: temp
! State
AED_REAL :: amm,nit,n2o,oxy
! Temporary variables
AED_REAL :: amm_flux, nit_flux, n2o_flux, no2_flux
AED_REAL :: Fsed_amm, Fsed_nit, Fsed_n2o, Fsed_no2
AED_REAL :: fTa, fTo
!
!------------------------------------------------------------------------------+
!BEGIN
no2_flux = zero_ ; n2o_flux = zero_ ; amm_flux = zero_ ; nit_flux = zero_
!-----------------------------------------------
! Retrieve local environmental conditions for this bottom water layer.
temp = _STATE_VAR_(data%id_temp) ! local temperature
!-----------------------------------------------
! Set the maximum flux (@20C) to use in this cell, either constant or linked
Fsed_amm = data%Fsed_amm
IF (data%id_Fsed_amm>0) Fsed_amm = _STATE_VAR_S_(data%id_Fsed_amm)
Fsed_nit = data%Fsed_nit ;
IF (data%id_Fsed_nit>0) Fsed_nit = _STATE_VAR_S_(data%id_Fsed_nit)
Fsed_n2o = data%Fsed_n2o ;
IF (data%id_Fsed_n2o>0) Fsed_n2o = _STATE_VAR_S_(data%id_Fsed_n2o)
Fsed_no2 = data%Fsed_no2 ;
IF (data%id_Fsed_no2>0) Fsed_no2 = _STATE_VAR_S_(data%id_Fsed_no2)
!-----------------------------------------------
! Compute temperature scaling
fTa = data%theta_sed_amm**(temp-20.0)
fTo = data%theta_sed_nit**(temp-20.0)
!-----------------------------------------------
! Compute actual flux based on oxygen and temperature
IF (data%use_oxy) THEN
! Sediment flux dependent on oxygen and temperature
oxy = _STATE_VAR_(data%id_oxy)
amm_flux = Fsed_amm * data%Ksed_amm/(data%Ksed_amm+oxy) * fTa
nit_flux = Fsed_nit * oxy/(data%Ksed_nit+oxy) * fTo
IF( data%simN2O>0 ) n2o_flux = Fsed_n2o * data%Ksed_n2o/(data%Ksed_n2o+oxy) * fTa
ELSE
! Sediment flux dependent on temperature only
amm_flux = Fsed_amm * fTa
nit_flux = Fsed_nit * fTo
ENDIF
!-----------------------------------------------
! Set bottom fluxes for the pelagic (change per surface area per second)
! Transfer sediment flux value to AED2.
_FLUX_VAR_(data%id_amm) = _FLUX_VAR_(data%id_amm) + amm_flux
_FLUX_VAR_(data%id_nox) = _FLUX_VAR_(data%id_nox) + nit_flux
IF( data%simN2O>0 ) _FLUX_VAR_(data%id_n2o)=_FLUX_VAR_(data%id_n2o) + n2o_flux
! Needs NO2
IF( data%simN2O>1 ) _FLUX_VAR_(data%id_no2)=_FLUX_VAR_(data%id_no2) + no2_flux
!-----------------------------------------------
! Store sediment flux as diagnostic variable.
_DIAG_VAR_S_(data%id_sed_amm) = amm_flux*secs_per_day
_DIAG_VAR_S_(data%id_sed_nit) = nit_flux*secs_per_day
IF( data%simN2O>0 ) _DIAG_VAR_S_(data%id_sed_n2o) = n2o_flux*secs_per_day
!----------------------------------------------- NEEDS ADDING
! Set sink and source terms for the benthos (change per surface area per sec)
! Note that this must include the fluxes to AND from the pelagic.
!_FLUX_VAR_B_(data%id_ben_amm) = _FLUX_VAR_B_(data%id_ben_amm) &
! + (-amm_flux/secs_per_day)
END SUBROUTINE aed2_calculate_benthic_nitrogen
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!###############################################################################
PURE AED_REAL FUNCTION NitrfO2Function(use_oxy,Rnitrif,Knitrif,theta_nitrif,oxy,temp)
!-------------------------------------------------------------------------------
! Michaelis-Menten formulation for nitrification
!
!-------------------------------------------------------------------------------
!ARGUMENTS
LOGICAL,INTENT(in) :: use_oxy
AED_REAL,INTENT(in) :: Rnitrif,Knitrif,theta_nitrif,oxy,temp
!
!-------------------------------------------------------------------------------
!BEGIN
IF (use_oxy) THEN
NitrfO2Function = Rnitrif * oxy/(Knitrif+oxy) * (theta_nitrif**(temp-20.0))
ELSE
NitrfO2Function = Rnitrif * (theta_nitrif**(temp-20.0))
ENDIF
END FUNCTION NitrfO2Function
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!###############################################################################
PURE AED_REAL FUNCTION DenitO2Function(Rdenit,use_oxy,oxy_lim, &
Kdenit,theta_denit,Kdenitnit,oxy,temp,nit)
!-------------------------------------------------------------------------------
! Michaelis-Menten formulation for denitrification sensitivity to O2, NO3, & T
!
!-------------------------------------------------------------------------------
!ARGUMENTS
LOGICAL, INTENT(in) :: use_oxy
INTEGER, INTENT(in) :: oxy_lim
AED_REAL,INTENT(in) :: Rdenit,Kdenit,theta_denit,oxy,temp,nit,Kdenitnit
AED_REAL :: fT, fDO, fNO3
!
!-------------------------------------------------------------------------------
!BEGIN
fT = (theta_denit**(temp-20.0))
fDO = one_
IF (use_oxy) THEN
IF (oxy_lim == 1) fDO = Kdenit/(Kdenit+oxy)
IF (oxy_lim == 2) fDO = exp(-oxy/Kdenit)
ENDIF
IF(Kdenitnit==zero_)THEN
fNO3 = one_
ELSE
fNO3 = nit/(Kdenitnit+nit)
ENDIF
DenitO2Function = Rdenit * fDO * fT * fNO3
END FUNCTION DenitO2Function
!+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
!###############################################################################
FUNCTION NitrfpHFunction(pH) RESULT(limitation)
!------------------------------------------------------------------------------+
! Dependence of nitrification rate on pH
!------------------------------------------------------------------------------+
!-- Incoming
AED_REAL, INTENT(IN) :: pH ! pH in the water column
!-- Returns the salinity function
AED_REAL :: limitation
!-- Local
AED_REAL, PARAMETER :: NITpHOptMin = 7.1 ! min pH of optimum range
AED_REAL, PARAMETER :: NITpHOptMax = 7.9 ! max pH of optimum range
AED_REAL, PARAMETER :: NITpHTolMax = 9.0 ! upper pH tolerance
AED_REAL, PARAMETER :: NITpHTolMin = 5.5 ! lower pH tolerance
AED_REAL :: tmp1,tmp2
!____________________________________________________________________!
! !
! =1 .!---------------!. !
! ! ! !
! ! ! !
! ! ! !
! ! ! !
! ! ! !
! ! ! !
!_______________!___________________________________!________________!
! ! ! ! ! !
! NITpHOptMin NITpHOptMax !
! NITpHTolMax NITpHTolMax !
!____________________________________________________________________!
!---------------------------------------------------------------------------+
! pH is within the tolerance; no limitation.
IF(pH >= NITpHOptMin .AND. pH <= NITpHOptMax) THEN
limitation = one_
ENDIF
! pH is greater than the upper bound of the optimum region
IF(pH > NITpHOptMax) THEN
limitation = (-pH*pH+2.0*NITpHOptMax*pH - &
2.0*NITpHOptMax*NITpHTolMax+NITpHTolMax*NITpHTolMax)/ &
((NITpHOptMax)*(NITpHOptMax))
ENDIF
! pH is less than the lower bound of optimum region (NITpHOptMin)
! but greater than minimum tolerance NITpHTolMin
tmp1 = zero_
tmp2 = zero_
IF(pH < NITpHOptMin .AND. pH > NITpHTolMin) THEN
tmp1 = pH-NITpHTolMin
tmp2 = NITpHOptMin-NITpHTolMin
limitation = (2.0*tmp1/NITpHOptMin-(tmp1*tmp1/(NITpHOptMin*NITpHOptMin))) &
/ (2.0*tmp2/NITpHOptMin-(tmp2*tmp2/(NITpHOptMin*NITpHOptMin)))
ENDIF
! pH is less than the NITpHTolMin
IF(pH <= NITpHTolMin) THEN
limitation = zero_
ENDIF
! ensure we don't go negative
IF(limitation <= zero_) THEN
limitation = zero_
ENDIF
END FUNCTION NitrfpHFunction
!------------------------------------------------------------------------------!
!###############################################################################
FUNCTION NitrfLightFunction(light) RESULT(limitation)
!----------------------------------------------------------------------------
! Dependence of nitrification rate on light
!----------------------------------------------------------------------------
!-- Incoming
AED_REAL, INTENT(IN) :: light ! pH in the water column
!-- Returns the function between 0 and 1
AED_REAL :: limitation
!-- Local
limitation = one_ ! TO BE COMPLETED - SEE CAPONE 2008
END FUNCTION NitrfLightFunction
!------------------------------------------------------------------------------!
END MODULE aed2_nitrogen