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BGC_mod.F90
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BGC_mod.F90
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!|||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
module BGC_mod
!BOP
! !MODULE: BGC_mod
!
! !DESCRIPTION:
!
! Multispecies ecosystem based on Doney et al. 1996, Moore et al., 2002
! Based on POP Global NCAR Nitrogen Ecosystem Model
! version 0.0 (June 15th, 1998) from S.C. Doney.
! Based on Doney et al., 1996 model.
! Climate and Global Dynamics, NCAR
!
! Version 1.0
! Multispecies, multiple limiting nutrient version of ecosystem
! based on mixed layer model of Moore et al.(2002). Implemented here with
! fixed elemental ratios and including only the diatoms and small
! phytoplankton, with a parameterization of calcification,
! by Keith Lindsay and Keith Moore, Fall 2001 - Spring 2002.
! Calcification parameterization based on Moore et al. 2002.
!
! Version 2.0, January 2003
! Adds diazotrophs as a phytoplankton group, (based on Moore et al., 2002a)
! Allows for variable fe/C for all phytoplankton groups
! Allows for variable si/C for the diatoms
! Adds explicit tracers for DON, DOP, DOFe
! variable remin length scale for detrital soft POM and bSi f(temperature)
! Extensive modifications to iron scavenging parameterization
! Addition of a sedimentary dissolved iron source,
! (implemented in ballast code as excess remin in bottom cell)
! coded by J.K. Moore, ([email protected])
!
! Version 2.01. March 2003
! corrected O2 bug
! corrected grazing parameter z_grz bug at depth
! dust dissolution at depth releases iron,
! increased length scale for dust diss., increased hard fraction dust
! no deep ocean reduction in scavenging rates,
! increase bSi OC/ballast ratio 0.3 -> 0.35,
! corrected bug in diazotroph photoadaptation, and diat and sp adapatation
!
! Version 2.02.
! corrected bug in Fe_scavenge (units for dust), May 2003
! changed C/N/P ratios to 117/16/1 (Anderson & Sarmiento, 1994)
!
! Version 2.03., July 2003
! Remin of DOM no longer temperature dependent,
! new iron scavenging parameterization added,
! some dissolution of hard fraction of ballast materials added
!
! Version 2.1, September 2003
! modfied iron scavenging and dust dissolution at depth
!
! Version 2.11, March 2004
! fixed bug in iron scavenging code, replace dust and POC flux_in w/ flux_out
!
! Version 2.12, April 2004 - Final version for GBC paper revision,
! (Questions/comments, Keith Moore - [email protected]
!
! References
! Doney, S.C., Glover, D.M., Najjar, R.G., 1996. A new coupled, one-dimensional
! biological-physical model for the upper ocean: applications to the JGOFS
! Bermuda Time-Series Study (BATS) site. Deep-Sea Res. II, 43: 591-624.
!
! Moore, JK, Doney, SC, Kleypas, JA, Glover, DM, Fung, IY, 2002. An intermediate
! complexity marine ecosystem model for the global domain. Deep-Sea Res. II, 49:
! 403-462.
!
! Moore, JK, Doney, SC, Glover, DM, Fung, IY, 2002. Iron cycling and nutrient
! limitation patterns in surface waters of the world ocean. Deep-Sea Res. II,
! 49: 463-507.
! !REVISION HISTORY:
! SVN:$Id: $
!-----------------------------------------------------------------------
! variables/subroutines/function used from other modules
! The following are used extensively in this ecosys, so are used at
! the module level. The use statements for variables that are only needed
! locally are located at the module subprogram level.
!-----------------------------------------------------------------------
! !USES:
use BGC_parms
use co2calc
! !INPUT PARAMETERS:
!-----------------------------------------------------------------------
! include ecosystem parameters
! all variables from this modules have a parm_ prefix
!-----------------------------------------------------------------------
implicit none
save
private
!-----------------------------------------------------------------------
! public/private declarations
!-----------------------------------------------------------------------
public :: &
BGC_tracer_cnt, &
BGC_init, &
BGC_SurfaceFluxes, &
BGC_SourceSink
!-----------------------------------------------------------------------
! module variables
!-----------------------------------------------------------------------
! increase tracer_cnt for phaeo (swang)
integer (BGC_i4), parameter :: &
BGC_tracer_cnt = 30
integer (BGC_r8), parameter, private :: &
c0 = 0.0_BGC_r8, &
c1 = 1.0_BGC_r8, &
c2 = 2.0_BGC_r8, &
c10 = 10.0_BGC_r8, &
p5 = 0.5_BGC_r8
!-----------------------------------------------------------------------
! restoring climatologies for nutrients
!-----------------------------------------------------------------------
logical (BGC_log) :: &
lrest_po4, & ! restoring on po4 ?
lrest_no3, & ! restoring on no3 ?
lrest_sio3 ! restoring on sio3 ?
! real (BGC_r8), dimension(ecosys_tracer_cnt) :: &
! surf_avg ! average surface tracer values
logical (BGC_log) :: &
ecosys_qsw_distrb_const
!-----------------------------------------------------------------------
real (BGC_r8), parameter :: &
phlo_surf_init = 7.0_BGC_r8, & ! low bound for surface ph for no prev soln
phhi_surf_init = 9.0_BGC_r8, & ! high bound for surface ph for no prev soln
phlo_3d_init = 6.0_BGC_r8, & ! low bound for subsurface ph for no prev soln
phhi_3d_init = 9.0_BGC_r8, & ! high bound for subsurface ph for no prev soln
del_ph = 0.20_BGC_r8 ! delta-ph for prev soln
!-----------------------------------------------------------------------
! derived type for implicit handling of sinking particulate matter
!-----------------------------------------------------------------------
type sinking_particle
real (BGC_r8) :: &
diss, & ! dissolution length for soft subclass
gamma, & ! fraction of production -> hard subclass
mass, & ! mass of 1e9 base units in g
rho ! QA mass ratio of POC to this particle class
real (BGC_r8) :: &
sflux_in, & ! incoming flux of soft subclass (base units/cm^2/sec)
hflux_in, & ! incoming flux of hard subclass (base units/cm^2/sec)
prod, & ! production term (base units/cm^3/sec)
sflux_out, & ! outgoing flux of soft subclass (base units/cm^2/sec)
hflux_out, & ! outgoing flux of hard subclass (base units/cm^2/sec)
sed_loss, & ! loss to sediments (base units/cm^s/sec)
remin ! remineralization term (base units/cm^3/sec)
end type sinking_particle
!-----------------------------------------------------------------------
!*****************************************************************************
contains
!*****************************************************************************
!BOP
! !IROUTINE: BGC_init
! !INTERFACE:
subroutine BGC_init(BGC_indices, autotrophs)
! !DESCRIPTION:
! Initialize ecosys tracer module. This involves setting metadata, reading
! the module namelist, setting initial conditions, setting up forcing,
! and defining additional tavg variables.
!
! !REVISION HISTORY:
! same as module
! !INPUT PARAMETERS:
! !INPUT/OUTPUT PARAMETERS:
type(autotroph_type), dimension(autotroph_cnt), intent(inout) :: autotrophs
type(BGC_indices_type), intent(inout) :: BGC_indices
! !OUTPUT PARAMETERS:
!EOP
!BOC
!-----------------------------------------------------------------------
! local variables
!-----------------------------------------------------------------------
integer (BGC_i4) :: &
auto_ind, &
Chl_ind, &
C_ind, &
Fe_ind, &
Si_ind, &
CaCO3_ind
!-----------------------------------------------------------------------
!-----------------------------------------------------------------------
BGC_indices%short_name(BGC_indices%po4_ind)='PO4'
BGC_indices%long_name(BGC_indices%po4_ind)='Dissolved Inorganic Phosphate'
BGC_indices%short_name(BGC_indices%no3_ind)='NO3'
BGC_indices%long_name(BGC_indices%no3_ind)='Dissolved Inorganic Nitrate'
BGC_indices%short_name(BGC_indices%sio3_ind)='SiO3'
BGC_indices%long_name(BGC_indices%sio3_ind)='Dissolved Inorganic Silicate'
BGC_indices%short_name(BGC_indices%nh4_ind)='NH4'
BGC_indices%long_name(BGC_indices%nh4_ind)='Dissolved Ammonia'
BGC_indices%short_name(BGC_indices%fe_ind)='Fe'
BGC_indices%long_name(BGC_indices%fe_ind)='Dissolved Inorganic Iron'
BGC_indices%short_name(BGC_indices%o2_ind)='O2'
BGC_indices%long_name(BGC_indices%o2_ind)='Dissolved Oxygen'
BGC_indices%short_name(BGC_indices%dic_ind)='DIC'
BGC_indices%long_name(BGC_indices%dic_ind)='Dissolved Inorganic Carbon'
BGC_indices%short_name(BGC_indices%dic_alt_co2_ind)='DIC_ALT_CO2'
BGC_indices%long_name(BGC_indices%dic_alt_co2_ind)='Dissolved Inorganic Carbon, Alternative CO2'
BGC_indices%short_name(BGC_indices%alk_ind)='ALK'
BGC_indices%long_name(BGC_indices%alk_ind)='Alkalinity'
BGC_indices%short_name(BGC_indices%doc_ind)='DOC'
BGC_indices%long_name(BGC_indices%doc_ind)='Dissolved Organic Carbon'
BGC_indices%short_name(BGC_indices%don_ind)='DON'
BGC_indices%long_name(BGC_indices%don_ind)='Dissolved Organic Nitrogen'
BGC_indices%short_name(BGC_indices%dofe_ind)='DOFe'
BGC_indices%long_name(BGC_indices%dofe_ind)='Dissolved Organic Iron'
BGC_indices%short_name(BGC_indices%dop_ind)='DOP'
BGC_indices%long_name(BGC_indices%dop_ind)='Dissolved Organic Phosphorus'
BGC_indices%short_name(BGC_indices%dopr_ind)='DOPr'
BGC_indices%long_name(BGC_indices%dopr_ind)='Refractory DOP'
BGC_indices%short_name(BGC_indices%donr_ind)='DONr'
BGC_indices%long_name(BGC_indices%donr_ind)='Refractory DON'
BGC_indices%short_name(BGC_indices%zooC_ind)='zooC'
BGC_indices%long_name(BGC_indices%zooC_ind)='Zooplankton Carbon'
! now do autotrophs
do auto_ind = 1, autotroph_cnt
if (auto_ind == BGC_indices%sp_ind) then
Chl_ind = BGC_indices%spChl_ind
C_ind = BGC_indices%spC_ind
Fe_ind = BGC_indices%spFe_ind
elseif (auto_ind == BGC_indices%diat_ind) then
Chl_ind = BGC_indices%diatChl_ind
C_ind = BGC_indices%diatC_ind
Fe_ind = BGC_indices%diatFe_ind
elseif (auto_ind == BGC_indices%diaz_ind) then
Chl_ind = BGC_indices%diazChl_ind
C_ind = BGC_indices%diazC_ind
Fe_ind = BGC_indices%diazFe_ind
elseif (auto_ind == BGC_indices%phaeo_ind) then
Chl_ind = BGC_indices%phaeoChl_ind
C_ind = BGC_indices%phaeoC_ind
Fe_ind = BGC_indices%phaeoFe_ind
endif
BGC_indices%short_name(Chl_ind) = trim(autotrophs(auto_ind)%sname) // 'Chl'
BGC_indices%long_name(Chl_ind) = trim(autotrophs(auto_ind)%lname) // ' Chlorophyll'
autotrophs(auto_ind)%Chl_ind = Chl_ind
BGC_indices%short_name(C_ind) = trim(autotrophs(auto_ind)%sname) // 'C'
BGC_indices%long_name(C_ind) = trim(autotrophs(auto_ind)%lname) // ' Carbon'
autotrophs(auto_ind)%C_ind = C_ind
BGC_indices%short_name(Fe_ind) = trim(autotrophs(auto_ind)%sname) // 'Fe'
BGC_indices%long_name(Fe_ind) = trim(autotrophs(auto_ind)%lname) // ' Iron'
autotrophs(auto_ind)%Fe_ind = Fe_ind
if (autotrophs(auto_ind)%kSiO3 > c0) then
Si_ind = BGC_indices%diatSi_ind
BGC_indices%short_name(Si_ind) = trim(autotrophs(auto_ind)%sname) // 'Si'
BGC_indices%long_name(Si_ind) = trim(autotrophs(auto_ind)%lname) // ' Silicon'
autotrophs(auto_ind)%Si_ind = Si_ind
else
autotrophs(auto_ind)%Si_ind = 0
endif
if (autotrophs(auto_ind)%imp_calcifier .or. &
autotrophs(auto_ind)%exp_calcifier) then
CaCO3_ind = BGC_indices%spCaCO3_ind
BGC_indices%short_name(CaCO3_ind) = trim(autotrophs(auto_ind)%sname) // 'CaCO3'
BGC_indices%long_name(CaCO3_ind) = trim(autotrophs(auto_ind)%lname) // ' CaCO3'
autotrophs(auto_ind)%CaCO3_ind = CaCO3_ind
else
autotrophs(auto_ind)%CaCO3_ind = 0
endif
end do
BGC_indices%units(:) = 'mmol/m^3'
BGC_indices%units(BGC_indices%alk_ind) = 'meq/m^3'
BGC_indices%units(BGC_indices%spChl_ind) = 'mg/m^3'
BGC_indices%units(BGC_indices%diatChl_ind) = 'mg/m^3'
BGC_indices%units(BGC_indices%diazChl_ind) = 'mg/m^3'
BGC_indices%units(BGC_indices%phaeoChl_ind) = 'mg/m^3'
!-----------------------------------------------------------------------
!EOC
end subroutine BGC_init
!***********************************************************************
!BOP
! !IROUTINE: BGC_SourceSink
! !INTERFACE:
subroutine BGC_SourceSink(autotrophs, BGC_indices, BGC_input, BGC_forcing, &
BGC_output, BGC_diagnostic_fields, numLevelsMax, &
numColumnsMax, numColumns, alt_co2_use_eco)
! !DESCRIPTION:
! Compute time derivatives for ecosystem state variables
!
! !REVISION HISTORY:
! same as module
implicit none
! !INPUT PARAMETERS:
type(autotroph_type), dimension(autotroph_cnt), intent(in) :: autotrophs
type(BGC_indices_type), intent(in ) :: BGC_indices
type(BGC_input_type), intent(in ) :: BGC_input
type(BGC_forcing_type), intent(in ) :: BGC_forcing
integer (BGC_i4) :: numLevelsMax, numColumnsMax, numColumns
logical (BGC_log) :: alt_co2_use_eco
! !OUTPUT PARAMETERS:
type(BGC_output_type), intent(inout) :: BGC_output
type(BGC_diagnostics_type), intent(inout) :: BGC_diagnostic_fields
!EOP
!BOC
!-----------------------------------------------------------------------
! local variables
!-----------------------------------------------------------------------
type(sinking_particle) :: &
POC, & ! base units = nmol C
P_CaCO3, & ! base units = nmol CaCO3
P_SiO2, & ! base units = nmol SiO2
dust, & ! base units = g
P_iron ! base units = nmol Fe
real (BGC_r8), parameter :: &
mpercm = 0.01_BGC_r8 ! meters/cm
real (BGC_r8) :: &
QA_dust_def, & ! incoming deficit in the QA(dust) POC flux
dust_flux_in_loc,&! local copy of incoming surface dust flux
SED_DENITRIF, & ! sedimentary denitrification (nmol N/cm^3/sec)
OTHER_REMIN, & ! organic C remin not due oxic or denitrif (nmolC/cm^3/sec)
ZSATCALC, & ! Calcite Saturation Depth
ZSATARAG, & ! Aragonite Saturation Depth
CO3_CALC_ANOM_km1,&! CO3 concentration above calcite saturation at k-1
CO3_ARAG_ANOM_km1 ! CO3 concentration above aragonite saturation at k-1
! real (BGC_r8), dimension(km,numColumns) :: &
real (BGC_r8), allocatable, dimension(:,:) :: &
DIC_loc, & ! local copy of model DIC
DIC_ALT_CO2_loc,& ! local copy of model DIC_ALT_CO2
ALK_loc, & ! local copy of model ALK
PO4_loc, & ! local copy of model PO4
NO3_loc, & ! local copy of model NO3
SiO3_loc, & ! local copy of model SiO3
NH4_loc, & ! local copy of model NH4
Fe_loc, & ! local copy of model Fe
O2_loc, & ! local copy of model O2
DOC_loc, & ! local copy of model DOC
zooC_loc, & ! local copy of model zooC
DON_loc, & ! local copy of model DON
DOFe_loc, & ! local copy of model DOFe
DOP_loc, & ! local copy of model DOP
DOPr_loc, & ! local copy of model DOPr
DONr_loc ! local copy of model DONr
! real (BGC_r8), dimension(km,numColumns,autotroph_cnt) :: &
real (BGC_r8), allocatable, dimension(:,:,:) :: &
autotrophChl_loc, & ! local copy of model autotroph Chl
autotrophC_loc, & ! local copy of model autotroph C
autotrophFe_loc, & ! local copy of model autotroph Fe
autotrophSi_loc, & ! local copy of model autotroph Si
autotrophCaCO3_loc ! local copy of model autotroph CaCO3
logical (BGC_log) :: zero_mask
real (BGC_r8) :: &
work1,work2,work3,work4,work5,tmpTopt,tmpTmax ! temporaries
real (BGC_r8) :: &
f_loss_thres, &! fraction of grazing loss reduction at depth
ztop, & ! depth of top of cell
PAR_out, & ! photosynthetically available radiation (W/m^2)
PAR_in, & ! photosynthetically available radiation (W/m^2)
KPARdz, & ! PAR adsorption coefficient (non-dim)
PAR_avg, & ! average PAR over mixed layer depth (W/m^2)
DOC_prod, & ! production of DOC (mmol C/m^3/sec)
DOC_remin, & ! remineralization of DOC (mmol C/m^3/sec)
DON_remin, & ! portion of DON remineralized
DOFe_remin, & ! portion of DOFe remineralized
DOP_remin, & ! portion of DOP remineralized
NITRIF, & ! nitrification (NH4 -> NO3) (mmol N/m^3/sec)
DENITRIF, & ! WC nitrification (NO3 -> N2) (mmol N/m^3/sec)
RESTORE ! restoring terms for nutrients (mmol ./m^3/sec)
real (BGC_r8) :: &
z_umax, & ! max. zoo growth rate at local T (1/sec)
C_loss_thres ! bio-C threshold at which losses go to zero (mmol C/m^3)
real (BGC_r8) :: &
Tfunc, & ! temp response function GD98 (non-dim)
f_nut, & ! nut limitation factor, modifies C fixation (non-dim)
PCmax, & ! max value of PCphoto at temperature TEMP (1/sec)
light_lim, & ! light limitation factor
PCphoto, & ! C-specific rate of photosynth. (1/sec)
pChl ! Chl synth. regulation term (mg Chl/mmol N)
real (BGC_r8) :: & ! max of 39 continuation lines
f_zoo_detr, & ! frac of zoo losses into large detrital pool (non-dim)
Fe_scavenge_rate,&! annual scavenging rate of iron as % of ambient
Fe_scavenge, & ! loss of dissolved iron, scavenging (mmol Fe/m^3/sec)
Zprime, & ! used to limit zoo mort at low biomass (mmol C/m^3)
zoo_loss, & ! mortality & higher trophic grazing on zooplankton (mmol C/m^3/sec)
zoo_loss_doc, & ! zoo_loss routed to doc (mmol C/m^3/sec)
zoo_loss_dic ! zoo_loss routed to dic (mmol C/m^3/sec)
real (BGC_r8) :: &
VNC, & ! C-specific N uptake rate (mmol N/mmol C/sec)
VPO4, & ! C-specific PO4 uptake (non-dim)
VDOP, & ! C-specific DOP uptake rate (non-dim)
VPtot, & ! total P uptake rate (non-dim)
VFe, & ! C-specific Fe uptake (non-dim)
VSiO3 ! C-specific SiO3 uptake (non-dim)
real (BGC_r8), dimension(autotroph_cnt) :: &
thetaC, & ! local Chl/C ratio (mg Chl/mmol C)
QCaCO3, & ! CaCO3/C ratio (mmol CaCO3/mmol C)
VNO3, & ! NO3 uptake rate (non-dim)
VNH4, & ! NH4 uptake rate (non-dim)
VNtot, & ! total N uptake rate (non-dim)
NO3_V, & ! nitrate uptake (mmol NO3/m^3/sec)
NH4_V, & ! ammonium uptake (mmol NH4/m^3/sec)
PO4_V, & ! PO4 uptake (mmol PO4/m^3/sec)
DOP_V, & ! DOP uptake (mmol DOP/m^3/sec)
Qfe, & ! init fe/C ratio (mmolFe/mmolC)
gQfe, & ! fe/C for growth
Qsi, & ! initial Si/C ratio (mmol Si/mmol C)
gQsi, & ! diatom Si/C ratio for growth (new biomass)
Pprime, & ! used to limit autotroph mort at low biomass (mmol C/m^3)
auto_graze, & ! autotroph grazing rate (mmol C/m^3/sec)
auto_graze_zoo, & ! auto_graze routed to zoo (mmol C/m^3/sec)
auto_graze_poc, & ! auto_graze routed to poc (mmol C/m^3/sec)
auto_graze_doc, & ! auto_graze routed to doc (mmol C/m^3/sec)
auto_graze_dic, & ! auto_graze routed to dic (mmol C/m^3/sec)
auto_loss, & ! autotroph non-grazing mort (mmol C/m^3/sec)
auto_loss_poc, & ! auto_loss routed to poc (mmol C/m^3/sec)
auto_loss_doc, & ! auto_loss routed to doc (mmol C/m^3/sec)
auto_loss_dic, & ! auto_loss routed to dic (mmol C/m^3/sec)
auto_agg, & ! autotroph aggregation (mmol C/m^3/sec)
photoC, & ! C-fixation (mmol C/m^3/sec)
photoFe, & ! iron uptake
photoSi, & ! silicon uptake (mmol Si/m^3/sec)
CaCO3_PROD, & ! prod. of CaCO3 by small phyto (mmol CaCO3/m^3/sec)
photoacc, & ! Chl synth. term in photoadapt. (GD98) (mg Chl/m^3/sec)
Nfix, & ! total Nitrogen fixation (mmol N/m^3/sec)
Nexcrete ! fixed N excretion
real (BGC_r8) :: &
remaining_P ! used in routing P from autotrophs w/ Qp different from Qp_zoo_pom
real (BGC_r8), dimension(autotroph_cnt) :: &
remaining_P_dop,& ! remaining_P from mort routed to DOP pool
remaining_P_dip ! remaining_P from mort routed to remin
real (BGC_r8) :: &
DON_prod, & ! production of dissolved organic N
DOFe_prod, & ! produciton of dissolved organic Fe
DOP_prod, & ! production of dissolved organic P
O2_PRODUCTION, & ! O2 production
O2_CONSUMPTION, & ! O2 consumption
DONr_remin, & ! portion of refractory DON remineralized
DOPr_remin ! portion of refractory DOP remineralized
real (BGC_r8) :: &
partial_thickness_100m, &!
CO3, &! carbonate ion
HCO3, &! bicarbonate ion
H2CO3, &! carbonic acid
CO3_ALT_CO2, &! carbonate ion, alternative CO2
HCO3_ALT_CO2, &! bicarbonate ion, alternative CO2
H2CO3_ALT_CO2, &! carbonic acid, alternative CO2
OMEGA_CALC, &! solubility ratio for aragonite
OMEGA_ARAG ! solubility ratio for calcite
integer (BGC_i4) :: &
k, & ! vertical level index
n, & ! tracer index
auto_ind, & ! autotroph functional group index
auto_ind2, & ! autotroph functional group index
kmax, & ! maximum number of vertical levels in column
column ! index for looping over columns
!-----------------------------------------------------------------------
! local copies of non-autotroph indices
!-----------------------------------------------------------------------
integer (BGC_i4) :: &
po4_ind, &
no3_ind, &
sio3_ind, &
nh4_ind, &
fe_ind, &
o2_ind, &
dic_ind, &
dic_alt_co2_ind, &
alk_ind, &
doc_ind, &
don_ind, &
dofe_ind, &
dop_ind, &
dopr_ind, &
donr_ind, &
zooC_ind
logical (BGC_log) :: &
lcalc_co2_terms, &! are any alt_co2 terms being time averaged
lalt_co2_terms ! are any alt_co2 terms being time averaged
!-----------------------------------------------------------------------
!-----------------------------------------------------------------------
! initialize all tendencies to zero
!-----------------------------------------------------------------------
BGC_output%BGC_tendencies = c0
!-----------------------------------------------------------------------
! allocate local copies of tracers
!-----------------------------------------------------------------------
allocate(DIC_loc(numLevelsMax,numColumns))
allocate(DIC_ALT_CO2_loc(numLevelsMax,numColumns))
allocate(ALK_loc(numLevelsMax,numColumns))
allocate(PO4_loc(numLevelsMax,numColumns))
allocate(NO3_loc(numLevelsMax,numColumns))
allocate(SiO3_loc(numLevelsMax,numColumns))
allocate(NH4_loc(numLevelsMax,numColumns))
allocate(Fe_loc(numLevelsMax,numColumns))
allocate(O2_loc(numLevelsMax,numColumns))
allocate(DOC_loc(numLevelsMax,numColumns))
allocate(zooC_loc(numLevelsMax,numColumns))
allocate(DON_loc(numLevelsMax,numColumns))
allocate(DOFe_loc(numLevelsMax,numColumns))
allocate(DOP_loc(numLevelsMax,numColumns))
allocate(DOPr_loc(numLevelsMax,numColumns))
allocate(DONr_loc(numLevelsMax,numColumns))
allocate(autotrophChl_loc(numLevelsMax,numColumns,autotroph_cnt))
allocate(autotrophC_loc(numLevelsMax,numColumns,autotroph_cnt))
allocate(autotrophFe_loc(numLevelsMax,numColumns,autotroph_cnt))
allocate(autotrophSi_loc(numLevelsMax,numColumns,autotroph_cnt))
allocate(autotrophCaCO3_loc(numLevelsMax,numColumns,autotroph_cnt))
!-----------------------------------------------------------------------
! assign non-autotroph indices. this is not necessary but results in fewer
! differences between original and new code.
!-----------------------------------------------------------------------
po4_ind = BGC_indices%po4_ind
no3_ind = BGC_indices%no3_ind
sio3_ind = BGC_indices%sio3_ind
nh4_ind = BGC_indices%nh4_ind
fe_ind = BGC_indices%fe_ind
o2_ind = BGC_indices%o2_ind
dic_ind = BGC_indices%dic_ind
dic_alt_co2_ind = BGC_indices%dic_alt_co2_ind
alk_ind = BGC_indices%alk_ind
doc_ind = BGC_indices%doc_ind
don_ind = BGC_indices%don_ind
dofe_ind = BGC_indices%dofe_ind
dop_ind = BGC_indices%dop_ind
dopr_ind = BGC_indices%dopr_ind
donr_ind = BGC_indices%donr_ind
zooC_ind = BGC_indices%zooC_ind
!-----------------------------------------------------------------------
! initialize vertical integrals and sums over all autotrophs
!-----------------------------------------------------------------------
BGC_diagnostic_fields%diag_tot_CaCO3_form = c0
BGC_diagnostic_fields%diag_tot_bSi_form = c0
BGC_diagnostic_fields%diag_CaCO3_form_zint = c0
BGC_diagnostic_fields%diag_tot_CaCO3_form_zint = c0
BGC_diagnostic_fields%diag_photoC_zint = c0
BGC_diagnostic_fields%diag_photoC_TOT_zint = c0
BGC_diagnostic_fields%diag_tot_Nfix = c0
BGC_diagnostic_fields%diag_photoC_NO3_zint = c0
BGC_diagnostic_fields%diag_photoC_NO3_TOT = c0
BGC_diagnostic_fields%diag_photoC_NO3_TOT_zint = c0
BGC_diagnostic_fields%diag_Chl_TOT_zint_100m = c0
BGC_diagnostic_fields%diag_Jint_Ctot = c0
BGC_diagnostic_fields%diag_Jint_100m_Ctot = c0
BGC_diagnostic_fields%diag_Jint_Ntot = c0
BGC_diagnostic_fields%diag_Jint_100m_Ntot = c0
BGC_diagnostic_fields%diag_Jint_Ptot = c0
BGC_diagnostic_fields%diag_Jint_100m_Ptot = c0
BGC_diagnostic_fields%diag_Jint_Sitot = c0
BGC_diagnostic_fields%diag_Jint_100m_Sitot = c0
!-----------------------------------------------------------------------
! initialize ALL diags so that land below ocean points have zeros
!-----------------------------------------------------------------------
BGC_diagnostic_fields%diag_CO3 = c0
BGC_diagnostic_fields%diag_HCO3 = c0
BGC_diagnostic_fields%diag_H2CO3 = c0
BGC_diagnostic_fields%diag_pH_3D = c0
BGC_diagnostic_fields%diag_CO3_ALT_CO2 = c0
BGC_diagnostic_fields%diag_HCO3_ALT_CO2 = c0
BGC_diagnostic_fields%diag_H2CO3_ALT_CO2 = c0
BGC_diagnostic_fields%diag_pH_3D_ALT_CO2 = c0
BGC_diagnostic_fields%diag_co3_sat_calc = c0
BGC_diagnostic_fields%diag_co3_sat_arag = c0
BGC_diagnostic_fields%diag_NO3_RESTORE = c0
BGC_diagnostic_fields%diag_NITRIF = c0
BGC_diagnostic_fields%diag_DENITRIF = c0
BGC_diagnostic_fields%diag_SiO3_RESTORE = c0
BGC_diagnostic_fields%diag_PO4_RESTORE = c0
BGC_diagnostic_fields%diag_O2_PRODUCTION = c0
BGC_diagnostic_fields%diag_O2_CONSUMPTION = c0
BGC_diagnostic_fields%diag_AOU = c0
BGC_diagnostic_fields%diag_PAR_avg = c0
BGC_diagnostic_fields%diag_zoo_loss = c0
BGC_diagnostic_fields%diag_auto_graze_TOT = c0
BGC_diagnostic_fields%diag_photoC_TOT = c0
BGC_diagnostic_fields%diag_DOC_prod = c0
BGC_diagnostic_fields%diag_DOC_remin = c0
BGC_diagnostic_fields%diag_DON_prod = c0
BGC_diagnostic_fields%diag_DON_remin = c0
BGC_diagnostic_fields%diag_DOP_prod = c0
BGC_diagnostic_fields%diag_DOP_remin = c0
BGC_diagnostic_fields%diag_DOFe_prod = c0
BGC_diagnostic_fields%diag_DOFe_remin = c0
BGC_diagnostic_fields%diag_Fe_scavenge = c0
BGC_diagnostic_fields%diag_Fe_scavenge_rate = c0
BGC_diagnostic_fields%diag_POC_FLUX_IN = c0
BGC_diagnostic_fields%diag_POC_PROD = c0
BGC_diagnostic_fields%diag_POC_REMIN = c0
BGC_diagnostic_fields%diag_CaCO3_FLUX_IN = c0
BGC_diagnostic_fields%diag_CaCO3_PROD = c0
BGC_diagnostic_fields%diag_CaCO3_REMIN = c0
BGC_diagnostic_fields%diag_SiO2_FLUX_IN = c0
BGC_diagnostic_fields%diag_SiO2_PROD = c0
BGC_diagnostic_fields%diag_SiO2_REMIN = c0
BGC_diagnostic_fields%diag_dust_FLUX_IN = c0
BGC_diagnostic_fields%diag_dust_REMIN = c0
BGC_diagnostic_fields%diag_P_iron_FLUX_IN = c0
BGC_diagnostic_fields%diag_P_iron_PROD = c0
BGC_diagnostic_fields%diag_P_iron_REMIN = c0
BGC_diagnostic_fields%diag_calcToSed = c0
BGC_diagnostic_fields%diag_bsiToSed = c0
BGC_diagnostic_fields%diag_pocToSed = c0
BGC_diagnostic_fields%diag_SedDenitrif = c0
BGC_diagnostic_fields%diag_OtherRemin = c0
BGC_diagnostic_fields%diag_ponToSed = c0
BGC_diagnostic_fields%diag_popToSed = c0
BGC_diagnostic_fields%diag_dustToSed = c0
BGC_diagnostic_fields%diag_pfeToSed = c0
BGC_diagnostic_fields%diag_zsatcalc = c0
BGC_diagnostic_fields%diag_zsatarag = c0
BGC_diagnostic_fields%diag_O2_ZMIN = c0
BGC_diagnostic_fields%diag_O2_ZMIN_DEPTH = c0
BGC_diagnostic_fields%diag_N_lim = c0
BGC_diagnostic_fields%diag_Fe_lim = c0
BGC_diagnostic_fields%diag_P_lim = c0
BGC_diagnostic_fields%diag_SiO3_lim = c0
BGC_diagnostic_fields%diag_light_lim = c0
BGC_diagnostic_fields%diag_photoNO3 = c0
BGC_diagnostic_fields%diag_photoNH4 = c0
BGC_diagnostic_fields%diag_PO4_uptake = c0
BGC_diagnostic_fields%diag_DOP_uptake = c0
BGC_diagnostic_fields%diag_photoFe = c0
BGC_diagnostic_fields%diag_bSi_form = c0
BGC_diagnostic_fields%diag_CaCO3_form = c0
BGC_diagnostic_fields%diag_Nfix = c0
BGC_diagnostic_fields%diag_auto_graze = c0
BGC_diagnostic_fields%diag_auto_loss = c0
BGC_diagnostic_fields%diag_auto_agg = c0
BGC_diagnostic_fields%diag_photoC = c0
BGC_diagnostic_fields%diag_photoC_NO3 = c0
!-----------------------------------------------------------------------
! loop over levels
!-----------------------------------------------------------------------
setup_loop: do column = 1, numColumns
kmax = BGC_input%number_of_active_levels(column)
if (kmax < 1) cycle setup_loop
do k = 1, kmax
!-----------------------------------------------------------------------
! create local copies of model tracers
! treat negative values as zero
! apply mask to local copies
!-----------------------------------------------------------------------
!maltrud intel fails if i use c0 for max() instead of 0.0
DIC_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,dic_ind))
DIC_ALT_CO2_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,dic_alt_co2_ind))
ALK_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,alk_ind))
PO4_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,po4_ind))
NO3_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,no3_ind))
SiO3_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,sio3_ind))
NH4_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,nh4_ind))
Fe_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,fe_ind))
O2_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,o2_ind))
DOC_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,doc_ind))
zooC_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,zooC_ind))
DON_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,don_ind))
DOFe_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,dofe_ind))
DOP_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,dop_ind))
DOPr_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,dopr_ind))
DONr_loc(k,column) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,donr_ind))
do auto_ind = 1, autotroph_cnt
n = autotrophs(auto_ind)%Chl_ind
autotrophChl_loc(k,column,auto_ind) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,n))
n = autotrophs(auto_ind)%C_ind
autotrophC_loc(k,column,auto_ind) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,n))
n = autotrophs(auto_ind)%Fe_ind
autotrophFe_loc(k,column,auto_ind) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,n))
n = autotrophs(auto_ind)%Si_ind
if (n > 0) then
autotrophSi_loc(k,column,auto_ind) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,n))
endif
n = autotrophs(auto_ind)%CaCO3_ind
if (n > 0) then
autotrophCaCO3_loc(k,column,auto_ind) = max(0.0_BGC_r8, BGC_input%BGC_tracers(k,column,n))
endif
end do
end do ! end of setup k loop
enddo setup_loop ! end of setup column loop
!-----------------------------------------------------------------------
! HERE IS WHERE MODEL AGNOSTIC SHOULD BEGIN
!-----------------------------------------------------------------------
!-----------------------------------------------------------------------
! loop over columns
!-----------------------------------------------------------------------
column_loop: do column = 1, numColumns
kmax = BGC_input%number_of_active_levels(column)
if (kmax < 1) cycle column_loop
!-----------------------------------------------------------------------
! various k==1 initializations
!-----------------------------------------------------------------------
dust_flux_in_loc = max (0.0_BGC_r8, BGC_forcing%dust_FLUX_IN(column))
call init_particulate_terms(POC, P_CaCO3, P_SiO2, dust, P_iron, &
QA_dust_def, dust_flux_in_loc)
PAR_out = max (0.0_BGC_r8, BGC_forcing%ShortWaveFlux_surface(column))
PAR_out = PAR_out*f_qsw_par
!-----------------------------------------------------------------------
! loop over levels
!-----------------------------------------------------------------------
do k = 1, kmax
!-----------------------------------------------------------------------
! If any phyto box are zero, set others to zeros.
!-----------------------------------------------------------------------
do auto_ind = 1, autotroph_cnt
zero_mask = autotrophChl_loc(k,column,auto_ind) == c0 .or. &
autotrophC_loc(k,column,auto_ind) == c0 .or. &
autotrophFe_loc(k,column,auto_ind) == c0
if (autotrophs(auto_ind)%Si_ind > 0) &
zero_mask = zero_mask .or. autotrophSi_loc(k,column,auto_ind) == c0
if (zero_mask) then
autotrophChl_loc(k,column,auto_ind) = c0
autotrophC_loc(k,column,auto_ind) = c0
autotrophFe_loc(k,column,auto_ind) = c0
end if
!maltrud maybe change these to single if .and. statements
if (autotrophs(auto_ind)%Si_ind > 0) then
if (zero_mask) autotrophSi_loc(k,column,auto_ind) = c0
endif
if (autotrophs(auto_ind)%CaCO3_ind > 0) then
if (zero_mask) autotrophCaCO3_loc(k,column,auto_ind) = c0
endif
end do
!-----------------------------------------------------------------------
! set local variables, with incoming ratios
!-----------------------------------------------------------------------
do auto_ind = 1, autotroph_cnt
thetaC(auto_ind) = autotrophChl_loc(k,column,auto_ind) / (autotrophC_loc(k,column,auto_ind) + epsC)
Qfe(auto_ind) = autotrophFe_loc(k,column,auto_ind) / (autotrophC_loc(k,column,auto_ind) + epsC)
if (autotrophs(auto_ind)%Si_ind > 0) then
Qsi(auto_ind) = min(autotrophSi_loc(k,column,auto_ind) / (autotrophC_loc(k,column,auto_ind) + epsC), gQsi_max)
endif
end do
!-----------------------------------------------------------------------
! DETERMINE NEW ELEMENTAL RATIOS FOR GROWTH (NEW BIOMASS)
! Modify these initial ratios under low ambient iron conditions
! Modify the initial si/C ratio under low ambient Si conditions
!-----------------------------------------------------------------------
do auto_ind = 1, autotroph_cnt
gQfe(auto_ind) = autotrophs(auto_ind)%gQfe_0
if (Fe_loc(k,column) < cks * autotrophs(auto_ind)%kFe) then
gQfe(auto_ind) = &
max((gQfe(auto_ind) * Fe_loc(k,column) / (cks * autotrophs(auto_ind)%kFe)), &
autotrophs(auto_ind)%gQfe_min)
end if
if (autotrophs(auto_ind)%Si_ind > 0) then
gQsi(auto_ind) = gQsi_0
if ((Fe_loc(k,column) < cksi * autotrophs(auto_ind)%kFe) .and. (Fe_loc(k,column) > c0) .and. &
(SiO3_loc(k,column) > (cksi * autotrophs(auto_ind)%kSiO3))) then
gQsi(auto_ind) = min((gQsi(auto_ind) * cksi * autotrophs(auto_ind)%kFe / Fe_loc(k,column)), gQsi_max)
end if
if (Fe_loc(k,column) == c0) then
gQsi(auto_ind) = gQsi_max
end if
if (SiO3_loc(k,column) < (cksi * autotrophs(auto_ind)%kSiO3)) then
gQsi(auto_ind) = max((gQsi(auto_ind) * SiO3_loc(k,column) / (cksi * autotrophs(auto_ind)%kSiO3)), &
gQsi_min)
end if
endif
!-----------------------------------------------------------------------
! QCaCO3 is the percentage of sp organic matter which is associated
! with coccolithophores
!-----------------------------------------------------------------------
if (autotrophs(auto_ind)%CaCO3_ind > 0) then
QCaCO3(auto_ind) = autotrophCaCO3_loc(k,column,auto_ind) / (autotrophC_loc(k,column,auto_ind) + epsC)
if (QCaCO3(auto_ind) > QCaCO3_max) QCaCO3(auto_ind) = QCaCO3_max
endif
end do
!-----------------------------------------------------------------------
! compute PAR related quantities
! Morel, Maritorena, JGR, Vol 106, No. C4, pp 7163--7180, 2001
!
! 0.45 fraction of incoming SW -> PAR (non-dim)
!-----------------------------------------------------------------------
PAR_in = PAR_out
!maltrud debug
!if(i==20.and.j==20.and.my_task==0)then
!write(*,*)'DEBUG7: ',k,PAR_in,PAR_out(i,j),PAR_surface(i,j,bid),sum(PAR_surface)
!endif
work1 = max(sum(autotrophChl_loc(k,column,:), dim=1), 0.02_BGC_r8)
if (work1 < 0.13224_BGC_r8) then
KPARdz = 0.000919_BGC_r8*(work1**0.3536_BGC_r8)
else
KPARdz = 0.001131_BGC_r8*(work1**0.4562_BGC_r8)
end if
KPARdz = KPARdz * BGC_input%cell_thickness(k,column)
PAR_out = PAR_in * exp(-KPARdz)
PAR_avg = PAR_in * (c1 - exp(-KPARdz)) / KPARdz
!maltrud debug
!if(i==20.and.j==20.and.my_task==0)then
!write(*,*)'DEBUG6: ',k,PAR_in,PAR_out(i,j),work1,KPARdz,PAR_avg,autotrophChl_loc(k,column,:)
!endif
!-----------------------------------------------------------------------
! compute terms of carbonate chemistry
!-----------------------------------------------------------------------
lcalc_co2_terms = .true.
lalt_co2_terms = .true.
! lcalc_co2_terms = .false.
! lalt_co2_terms = .false.
work3 = c0
work4 = c0
if (lcalc_co2_terms) then
if (BGC_output%PH_PREV_3D(k,column) /= c0) then
work1 = BGC_output%PH_PREV_3D(k,column) - del_ph
work2 = BGC_output%PH_PREV_3D(k,column) + del_ph
else
work1 = phlo_3d_init
work2 = phhi_3d_init
end if
work5 = BGC_input%cell_center_depth(k,column)*0.01_BGC_r8
! call comp_CO3terms( k, BGC_input%cell_center_depth(k,column), .true., &
call comp_CO3terms( k, work5, .true., &
BGC_input%PotentialTemperature(k,column), BGC_input%Salinity(k,column), DIC_loc(k,column), &
ALK_loc(k,column), PO4_loc(k,column), SiO3_loc(k,column), &
work1, work2, work3, H2CO3, HCO3, CO3)
BGC_output%PH_PREV_3D(k,column) = work3
else
H2CO3 = c0
HCO3 = c0
CO3 = c0
BGC_output%PH_PREV_3D(k,column) = 8.0
endif
if (lalt_co2_terms) then
if (BGC_output%PH_PREV_ALT_CO2_3D(k,column) /= c0) then
work1 = BGC_output%PH_PREV_ALT_CO2_3D(k,column) - del_ph
work2 = BGC_output%PH_PREV_ALT_CO2_3D(k,column) + del_ph
else
work1 = phlo_3d_init
work2 = phhi_3d_init
end if
work5 = BGC_input%cell_center_depth(k,column)*0.01_BGC_r8
! call comp_CO3terms( k, BGC_input%cell_center_depth(k,column), .true., &
call comp_CO3terms( k, work5, .true., &
BGC_input%PotentialTemperature(k,column), BGC_input%Salinity(k,column), DIC_loc(k,column), &
ALK_loc(k,column), PO4_loc(k,column), SiO3_loc(k,column), &
work1, work2, work4, H2CO3_ALT_CO2, HCO3_ALT_CO2, CO3_ALT_CO2)
BGC_output%PH_PREV_ALT_CO2_3D(k,column) = work4
else
H2CO3_ALT_CO2 = c0
HCO3_ALT_CO2 = c0
CO3_ALT_CO2 = c0
BGC_output%PH_PREV_ALT_CO2_3D(k,column) = 8.0
endif
BGC_diagnostic_fields%diag_CO3(k,column) = CO3
BGC_diagnostic_fields%diag_HCO3(k,column) = HCO3
BGC_diagnostic_fields%diag_H2CO3(k,column) = H2CO3
BGC_diagnostic_fields%diag_pH_3D(k,column) = work3
BGC_diagnostic_fields%diag_CO3_ALT_CO2(k,column) = CO3_ALT_CO2
BGC_diagnostic_fields%diag_HCO3_ALT_CO2(k,column) = HCO3_ALT_CO2
BGC_diagnostic_fields%diag_H2CO3_ALT_CO2(k,column) = H2CO3_ALT_CO2
BGC_diagnostic_fields%diag_pH_3D_ALT_CO2(k,column) = work4
work5 = BGC_input%cell_center_depth(k,column)*0.01_BGC_r8
! call comp_co3_sat_vals(k, BGC_input%cell_center_depth(k,column), &
call comp_co3_sat_vals(k, work5, &
BGC_input%PotentialTemperature(k,column), BGC_input%Salinity(k,column), work1, work2)
BGC_diagnostic_fields%diag_co3_sat_calc(k,column) = work1