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gotm_ismer
Commit a5d329e7 authored by Dany Dumont's avatar Dany Dumont
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Merge branch 'snow' of gitlasso.uqar.ca:dumoda01/gotm_ismer

parents 11b18235 c946efdb
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nml/bio_polynow.nml 0 → 100644
View file @ a5d329e7
#$Id$
!-------------------------------------------------------------------------------
! Fasham et al. biological model with modifications by Kuehn and Radach
!
! numc= number of compartments for geobiochemical model
!
! p_initial= initial phytoplankton concentration [mmol n/m3]
! z_initial= initial zooplakton concentration [mmol n/m3]
! b_initial= initial bacteria concentration [mmol n/m3]
! dph_initial= initial dph concentration [mmol n/m3]
! dzo_initial= initial dzo concentration [mmol n/m3]
! fp_initial= initial fp concentration [mmol n/m3]
! msn_initial= initial dzo concentration [mmol n/m3]
! n_initial= *** see obs.nml *** [mmol n/m3]
! a_initial= *** see obs.nml *** [mmol n/m3]
! l_initial= initial LDON concentration [mmol n/m3]
! p0 = minimum phytoplankton concentration [mmol n/m3]
! z0 = minimum zooplakton concentration [mmol n/m3]
! b0 = minimum bacteria concentration [mmol n/m3]
! mu5 = nitrification rate [1/day] !!GG-CHG1
! vp = maximum phytoplankton uptake rate [1/day]
! alpha = slope of the PI-curvea [m2/(W day)]
! inib = inhibition slope of the PI-curve (positive) [m2/(W day)]
! kc = attenuation constant for the self shading effect [m**2/mmol N]
! k1 = half saturation constant nitrate uptake [mmol n/m3]
! k2 = half saturation constant ammonium uptake [mmol n/m3]
! mu1 = phytoplankton mortality rate [1/day]
! k5 = half saturation constant phytoplankton mortality [mmol n/m3]
! gamma = exudation fraction [-]
! capt = Percentage of living phyto. captured in msn [%/day] - GG-D
! sp_mort = Phytoplankton non grazing mortality [1/day] - GG-D
! sp_mort2 = Quadratic mortality/aggrgation rate coefficient [1/day] - GG-D
! w_p = phytoplankton settling velocity [m/day]
! stip = Stickiness of choosen Phytoplankton species [-] - GG-D
! stidph = Stickiness of dead Phytoplankton [-] - GG-D
! gmax = maximum ingestion rate [1/day]
! k3 = half saturation constant ingestion [mmol n/m3]
! beta = grazing efficiency [-]
! betamsn = grazing efficiency on marine snow [-] - GG-D
! mu2 = maximum zooplankton loss rate [1/day]
! k6 = half saturation zooplankton loss [mmol n/m3]
! delta = fractional zooplankton loss to LDON [-]
! epsi = fractional zooplankton loss to ammonium [-]
! r1 = grazing preference phytoplankton [-]
! r2 = grazing preference bacteria [-]
! r3 = grazing preference dead phytoplankton (dph) [-] - GG-D
! r4 = grazing preference dead zooplankton (dzo) [-] - GG-D
! r5 = grazing preference fecal pellets (fp) [-] - GG-D
! r6 = grazing preference marine snow (msn) [-] - GG-D
!zingest = Proportion of grazed matter added to zoo. biomass [-] - GG-D
! eg = Percentage of eggestion [%/day] - GG-D
! stidzo = Stickiness of choosen zooplankton species [-] - GG-D
! stifp = Stickiness of fecal pellets [-] - GG-D
! pmin = intensity rariadtion in the water column
! w_zmax = Max. swimming speed for zoo (not exceed 320) [1/day]
! bertha = amplitud coefficient
! parcrit =min. phyto concentration needed for zooplankton
! vb = maximum bacterial uptake rate [1/day]
! k4 = half saturation bacterial uptake [mmol n/m3]
! mu3 = bacteria excretion rate [1/day]
! eta = uptake ratio ammonium:LDON [-]
! mbac = Percentage of bacerias captured in msn [%/day] - GG-D
! dphlossl = Dph breakdown rate [%/day] - GG-D
! dzolossl = Percentage of Dzo loss in LDON [%/day] - GG-D
! dzolossb = Percentage of Dzo loss in bacteria respiration [%/day] - GG-D
! fplossl = Percentage of fp loss in LDON [%/day] - GG-D
! fplossb = Percentage of fp loss in bacteria respiration [%/day] - GG-D
! w_d1 = [1/day]
! w_d2 = [1/day]
! w_d3 = [1/day]
! w_d4 = [1/day]
! mldon = Percentage of LDON used to constitute matrice of msn [%/day] - GG-D
!lmin = LDON limit concentration to become the matrix of msn [mmol n/m3]- GG-D
!Coag_coef = Specification by user of utilisation of model calculated Coagulation coefficient(false) or given parameter(true) [true.false] - GG-D
!betap = Coagulation coefficient of Phytoplankton [1/day]- GG-D
!betadph = Coagulation coefficient of dead Phytoplankton [1/day]- GG-D
!betadzo = Coagulation coefficient of deadzooplankton [1/day]- GG-D
!betafp = Coagulation coefficient of fecal pellets [1/day]- GG-D
!-------------------------------------------------------------------------------
&bio_polynow_nml
numc= 10
p_initial= 0.012
z_initial= 0.012
b_initial= 0.001
dph_initial= 0.012
dzo_initial= 0.012
fp_initial= 0.012
msn_initial= 0.012
l_initial= 0.1
p0= 0.0001
z0= 0.0001
b0= 0.0001
mu5= 0.1
vp= 0.3
alpha= 0.04
inib= 0.06
kc= 0.03
k1= 1.0
k2= 0.8
mu1= 0.05
k5= 0.2
gamma= 0.0
capt= 0.0
sp_mort= 0.0
sp_mort2= 0.0
w_p= 0.5
stip= 0.0
stidph= 0.0
gmax= 0.6
k3= 1.0
beta= 0.625
betamsn= 0.0
mu2= 0.3
k6= 0.2
delta= 0.0
epsi= 0.70
r1= 0.1
r2= 0.2
r3= 0.3
r4= 0.1
r5= 0.2
r6= 0.1
zingest= 0.0
eg= 0.0
stidzo= 0.0
stifp= 0.0
pmin= 0.7
w_zmax= 320
bertha= 0.05
parcrit= 10
vb= 0.
k4= 0.5
mu3= 0.03
eta= 0.0
mbac= 0.0
dphlossl= 0.0
dzolossl= 0.0
dzolossb= 0.0
fplossl= 0.0
fplossb= 0.0
w_d1= 0
w_d2= 0
w_d3= 0
w_d4= 0
mldon= 0.0
lmin= 0.0
coag_coef= .false.
betap= 0.0
betadph= 0.0
betadzo= 0.0
betafp= 0.0
/
src/extras/bio/Makefile
View file @ a5d329e7
......@@ -16,8 +16,9 @@ bio_sed.F90 \
bio_fasham.F90 \
bio_ismer.F90 \
bio_gsj.F90 \
bio_save.F90 \
bio_nocera.F90 \
bio_polynow.F90 \
bio_save.F90 \
bio_npzd4.F90 \
nitrate.F90 \
ammonium.F90 \
......@@ -34,6 +35,7 @@ ${LIB}(bio_ismer.o) \
${LIB}(bio_gsj.o) \
${LIB}(bio_fasham.o) \
${LIB}(bio_nocera.o) \
${LIB}(bio_polynow.o) \
${LIB}(bio_npzd4.o) \
${LIB}(bio_sed.o) \
${LIB}(bio_save.o) \
......
src/extras/bio/ammonium.F90
View file @ a5d329e7
......@@ -180,6 +180,11 @@
do i=1,nlev
amm(i) = cc(6,i)
end do
else if (bio_model.eq.9) then ! GG-A
do i=1,nlev
amm(i) = cc(6,i)
end do
end if
#endif
......
src/extras/bio/bio.F90
View file @ a5d329e7
......@@ -48,9 +48,13 @@
use bio_mab, only : init_bio_mab,init_var_mab,var_info_mab
use bio_mab, only : light_mab,surface_fluxes_mab,do_bio_mab
use bio_polynow, only : init_bio_polynow,init_var_polynow,var_info_polynow !GG-A
use bio_polynow, only : light_polynow,do_bio_polynow !GG-A
use output, only : out_fmt,write_results,ts
use util
!
! default: all is private.
private
......@@ -58,6 +62,9 @@
! !PUBLIC MEMBER FUNCTIONS:
public init_bio, set_env_bio, do_bio, get_bio_updates, clean_bio
logical, public :: bio_calc=.false.
! REALTYPE,public, dimension(:), allocatable :: eps_ !GG-T
!
! !REVISION HISTORY:!
! Original author(s): Hans Burchard & Karsten Bolding
......@@ -353,6 +360,17 @@
call var_info_npzd4()
case (10) ! The model for the north Water polynya - NPZD- Sedimentation GG-A
call init_bio_polynow(namlst,'bio_polynow.nml',unit)
call allocate_memory(nlev)
call init_var_polynow(nlev)
call var_info_polynow()
case default
stop "bio: no valid biomodel specified in bio.nml !"
end select
......@@ -448,9 +466,9 @@
! modules
!
! !INTERFACE:
subroutine set_env_bio(nlev,h_,t_,s_,nit_,amm_,hcb_,rho_,nuh_,rad_,wind_, &
subroutine set_env_bio(nlev,h_,t_,s_,nit_,amm_,hcb_,rho_,nuh_,rad_,wind_, &
I_0_,w_,w_adv_ctr_)
!
! !DESCRIPTION:
!
! !USES:
......@@ -471,6 +489,8 @@
REALTYPE, intent(in) :: I_0_
REALTYPE, optional, intent(in) :: w_(0:nlev)
integer, optional, intent(in) :: w_adv_ctr_
!
! !REVISION HISTORY:
! Original author(s): Hans Burchard & Karsten Bolding
......@@ -494,6 +514,9 @@
if (present(w_)) w = w_
if (present(w_adv_ctr_)) w_adv_ctr = w_adv_ctr_
return
end subroutine set_env_bio
!EOC
......@@ -742,6 +765,10 @@
case (9)
call light_npzd4(nlev,bioshade_feedback)
call ode_solver(ode_method,numc,nlev,dt_eff,cc,do_bio_npzd4)
case (10)
call light_polynow(nlev,bioshade_feedback)
call ode_solver(ode_method,numc,nlev,dt_eff,cc,do_bio_polynow)
end select
end do
......@@ -820,6 +847,17 @@
if (allocated(var_units)) deallocate(var_units)
if (allocated(var_long)) deallocate(var_long)
!Stickiness
if (allocated(sti_2p)) deallocate(sti_2p)
if (allocated(sti_pdph)) deallocate(sti_pdph)
if (allocated(sti_pdzo)) deallocate(sti_pdzo)
if (allocated(sti_pfp)) deallocate(sti_pfp)
if (allocated(sti_2dph)) deallocate(sti_2dph)
if (allocated(sti_dphdzo)) deallocate(sti_dphdzo)
if (allocated(sti_dphfp)) deallocate(sti_dphfp)
if (allocated(sti_2dzo)) deallocate(sti_2dzo)
if (allocated(sti_dzofp)) deallocate(sti_dzofp)
if (allocated(sti_2fp)) deallocate(sti_2fp)
!DD
if (allocated(lumlim1)) deallocate(lumlim1)
if (allocated(nitlim1)) deallocate(nitlim1)
......@@ -829,6 +867,15 @@
if (allocated(ammlim2)) deallocate(ammlim2)
if (allocated(ppnet)) deallocate(ppnet)
if (allocated(flux_msn)) deallocate(flux_msn)
if (allocated(Flux_P)) deallocate(Flux_P)
if (allocated(Flux_D1)) deallocate(Flux_D1)
if (allocated(Flux_D2)) deallocate(Flux_D2)
if (allocated(Flux_D3)) deallocate(Flux_D3)
if (allocated(size_msnow)) deallocate(size_msnow)
if (allocated(w_msn_lev)) deallocate(w_msn_lev)
! The external provide arrays
if (allocated(h)) deallocate(h)
if (allocated(nuh)) deallocate(nuh)
......@@ -912,6 +959,29 @@
allocate(var_long(numc),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating var_long)'
!Stickiness
allocate(sti_2p(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_2p)'
allocate(sti_pdph(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_pdph)'
allocate(sti_pdzo(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_pdzo)'
allocate(sti_pfp(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_pfp)'
allocate(sti_2dph(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_2dph)'
allocate(sti_dphdzo(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_dphdzo)'
allocate(sti_dphfp(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_dphfp)'
allocate(sti_2dzo(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_2dzo)'
allocate(sti_dzofp(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_dzofp)'
allocate(sti_2fp(0:nlev),stat=rc)
if (rc /= 0) STOP 'init_bio: Error allocating (sti_2fp)'
!DD
allocate(lumlim1(0:nlev),stat=rc)
......@@ -935,6 +1005,28 @@
allocate(ppnet(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (ppnet)'
allocate(flux_msn(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (flux_msn)'
allocate(Flux_P(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (Flux_P)'
allocate(Flux_D1(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (Flux_D1)'
allocate(Flux_D2(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (Flux_D2)'
allocate(Flux_D3(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (Flux_D3)'
allocate(size_msnow(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (size_msnow)'
allocate(w_msn_lev(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (w_msn_lev)'
! The external provide arrays
allocate(h(0:nlev),stat=rc)
if (rc /= 0) stop 'init_bio(): Error allocating (h)'
......
src/extras/bio/bio_polynow.F90 0 → 100644
View file @ a5d329e7
This source diff could not be displayed because it is too large. You can view the blob instead.
src/extras/bio/bio_save.F90
View file @ a5d329e7
This diff is collapsed.
src/extras/bio/bio_var.F90
View file @ a5d329e7
......@@ -23,6 +23,27 @@
REALTYPE, dimension(:), allocatable :: par
REALTYPE, dimension(:), allocatable :: lumlim1,nitlim1,ammlim1,lumlim2,nitlim2,ammlim2 !DD
REALTYPE, dimension(:), allocatable :: ppnet
REALTYPE, dimension(:), allocatable :: flux_msn
integer :: flux_msn_id
REALTYPE, dimension(:), allocatable :: Flux_P
integer :: Flux_P_id
REALTYPE, dimension(:), allocatable :: Flux_D1
integer :: Flux_D1_id
REALTYPE, dimension(:), allocatable :: Flux_D2
integer :: Flux_D2_id
REALTYPE, dimension(:), allocatable :: Flux_D3
integer :: Flux_D3_id
REALTYPE, dimension(:), allocatable :: size_msnow
integer :: size_msnow_id
REALTYPE, dimension(:), allocatable :: w_msn_lev
integer :: w_msn_lev_id
REALTYPE :: dt_eff
REALTYPE, dimension(:,:), allocatable :: cc,ws
integer :: surface_flux_method=-1
integer :: n_surface_fluxes=-1
......@@ -34,11 +55,24 @@
integer, dimension(:,:), allocatable :: particle_indx
REALTYPE, dimension(:,:), allocatable :: particle_pos
!Stickiness
REALTYPE, dimension(:), allocatable :: sti_2p,sti_pdph,sti_pdzo,sti_pfp
integer :: sti_2p_id,sti_pdph_id,sti_pdzo_id,sti_pfp_id
REALTYPE, dimension(:), allocatable :: sti_2dph,sti_dphdzo,sti_dphfp
integer :: sti_2dph_id,sti_dphdzo_id,sti_dphfp_id
REALTYPE, dimension(:), allocatable :: sti_2dzo,sti_dzofp
integer :: sti_2dzo_id,sti_dzofp_id
REALTYPE, dimension(:), allocatable :: sti_2fp
integer :: sti_2fp_id
integer, dimension(:), allocatable :: var_ids
integer :: wp_id,wz_id
integer :: wp_id,wz_id,wd1_id,wd2_id,wd3_id,wd4_id
integer :: par_id
integer :: lumlim1_id,nitlim1_id,ammlim1_id,lumlim2_id,nitlim2_id,ammlim2_id !DD
integer :: ppnet_id
character(len=64), dimension(:), allocatable :: var_names
character(len=64), dimension(:), allocatable :: var_units
character(len=64), dimension(:), allocatable :: var_long
......@@ -58,6 +92,7 @@
REALTYPE, dimension(:), allocatable :: hcb
REALTYPE, dimension(:), allocatable :: hcprof
REALTYPE, dimension(:), allocatable :: rho
integer ::rho_id
REALTYPE, dimension(:), allocatable :: nuh
REALTYPE, dimension(:), allocatable :: w
REALTYPE, dimension(:), allocatable :: rad
......
src/extras/bio/nitrate.F90
View file @ a5d329e7
......@@ -186,6 +186,10 @@
do i=1,nlev
nit(i) = cc(5,i)
end do
else if (bio_model.eq.9) then ! GG-A
do i=1,nlev
nit(i) = cc(5,i)
end do
end if
#endif
......
src/observations/observations.F90
View file @ a5d329e7
......@@ -85,6 +85,10 @@
! relaxation times for hydrocarbon
REALTYPE, public, dimension(:), allocatable :: HCRelaxTau
!TEST
! relaxation times for phy
REALTYPE, public, dimension(:), allocatable :: phyRelaxTau
! sea surface elevation, sea surface gradients and height of velocity obs.
REALTYPE, public :: zeta=0.,dpdx=0.,dpdy=0.,h_press=0
......@@ -259,6 +263,8 @@
integer, parameter :: n_prof_unit=41 !CHG3
integer, parameter :: a_prof_unit=42 !CHG5
integer, parameter :: hc_prof_unit=43
!!!!!TEST
!integer, parameter :: phy_prof_unit=44
! pre-defined parameters
integer, parameter :: READ_SUCCESS=1
......@@ -448,6 +454,9 @@
read(namlst,nml=aprofile,err=94)
read(namlst,nml=tprofile,err=82)
read(namlst,nml=hcprofile,err=95)
!TEST
! read(namlst,nml=phyprofile,err=95)
read(namlst,nml=ext_pressure,err=83)
read(namlst,nml=int_pressure,err=84)
read(namlst,nml=extinct,err=85)
......@@ -559,12 +568,16 @@
NRelaxTau(0)=NRelaxTauB !CHG3
ARelaxTau(0)=ARelaxTauB !CHG3
HCRelaxTau(0)=HCRelaxTauB
!phyRelaxTau(0)=phyRelaxTauB ! TEST
do i=1,nlev
TRelaxTau(i)=TRelaxTauM
SRelaxTau(i)=SRelaxTauM
NRelaxTau(i)=NRelaxTauM !CHG3
ARelaxTau(i)=ARelaxTauM !CHG3
HCRelaxTau(i)=HCRelaxTauM
! phyRelaxTau(i)=phyRelaxTauM ! TEST
db=db+0.5*h(i)
ds=ds-0.5*h(i)
if (db.le.SRelaxBott) SRelaxTau(i)=SRelaxTauB
......@@ -577,6 +590,10 @@
if (ds.le.ARelaxSurf) ARelaxTau(i)=ARelaxTauS !CHG5
if (db.le.HCRelaxBott) HCRelaxTau(i)=HCRelaxTauB
if (ds.le.HCRelaxSurf) HCRelaxTau(i)=HCRelaxTauS
!TEST
! if (db.le.phyRelaxBott) phyRelaxTau(i)=phyRelaxTauB
! if (ds.le.phyRelaxSurf) phyRelaxTau(i)=phyRelaxTauS
db=db+0.5*h(i)
ds=ds-0.5*h(i)
if ((s_prof_method.ne.0).and.(SRelaxTau(i).le.0.)) then
......@@ -624,6 +641,7 @@
LEVEL2 '***************************************************'
stop 'init_observations'
end if
end do
allocate(o2_prof(0:nlev),stat=rc)
......@@ -1269,7 +1287,7 @@
close(t_prof_unit)
close(n_prof_unit) !CHG3
close(a_prof_unit) !CHG5
close(hc_prof_unit) !CHG5
close(hc_prof_unit)
close(ext_press_unit)
close(int_press_unit)
close(extinct_unit)
......
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