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ECOSMO an ECOSystem Model coupled physics-lower trophic level dynamics
General Overview
Basic equations Towards model equations: vertical integration Model equations and approximations Air-sea and air-ice-ocean fluxes Lower trophic level dynamics Numerical schemes Grid- and slab information Model flow, main program Literature Additional features New set-up Irina
Basic equations
Reynolds equations, hydrostatic approximation, conservation equation: mass (volume), salt mass, heat and tracer mass (nutrients, biomass etc…)
Vertical integration and boundary conditions results in model equations
Basic equations:
Approximations
Transport model equations : subroutines motmit, druxav, konv
Transport model equations: boundary conditions
Model equations for T and S(and other tracers) subroutine strom3
More model equations
subroutine konti
subroutine sor, sorcof
subroutine estate
Turbulence closure
Stationarity
local production and local dissipation of turbulent kinetic energy balance,
advection and diffusion of turbulent kinetic energy can be neglected
Vertical integration for one model layer k from zk-zk-1:Horizontal transport
Turbulence closure
Turbulence closure
Turbulence closure
subroutine druxav
Dynamic sea ice model: subroutine icemod, icevel
• 3 state variables:
-Ice compactness Ai,
-level ice thickness hi
- ridging ice thickness hr
• continuum approach, conservation equations for open water area, level ice thickness, ridging ice thickness
• Hibler type ice dynamics: viscous-plastic, elliptical yield curve, normal flow rule
Ice transports
Conservation equation for ice stages: compactness (open water and thin ice), level ice, ridged ice
Mechanic deformation functions
1. Ai<1 and convergent or divergent flow field, or divergent flow field ice transport change only ice concentration
2. Ai=1, ice thickness below critical value (0.1m), convergent flow field ice transport results in rafting: level ice thickness change
3. Ai=1, ice thickness above critical value, convergent flow field
ice transport results in ridging: level ice thickness change
3 cases:
Fluxes
Air sea fluxes : subroutine fluxes
Based on Monin-Obukhov similarity theory:
- MONIN and OBUKHOV, 1954
- LAUNIAINEN and VIHMA, 1990
•2m Tair, spec. humidity are up-scaled to 10m-ref heights
•Upscaling, cd exchange coefficients and fluxes depend on
atmospheric stability
Ice thermo-dynamics: subroutine trmice
Ice thermodynamics
Lower trophic level dynamics: coupling vs. transport equations subroutine strom3 calls subroutine bio
12 biological and chemical variables:
Phytoplankton: Pd - diatoms; Pf - flagellates;
Zooplankton: Zs, Z l – micro and macro-zooplankton;
Nitrogen: NH4 - ammonium; NO2 - nitrite; NO3 - nitrate;
Phosphorus: PO4 - phosphate;
Silica: SiO2 - silicate; SiO2•2H2O - biogenic opal;
O2 – Oxygen, D - detritus
NO3
Pf Z s
Z l Pd
NH4
D
O2
SiO2 PO4
NO2
N2
SiO2•2H2O
Nitrification Denitrification
Lower trophic level dynamics: subroutine bio
Biological state variables
parameter (nbio=14) dimension Tc(ndrei,nbio)
ibio=1,nbio
ibio = 1,2 reserved for T,S
ibio = 3,nbio: 3 4Phytoplankton: Ps – flagellates; Pl - diatoms;
5 6Zooplankton: Zs, Z l – micro and macro-zooplankton;
7 D - detritus;
8 9 10Nitrogen: NH4 - ammonium; NO2 - nitrite; NO3 - nitrate;
11 Phosphorus: PO4 - phosphate;
12 14Silica: SiO2 - silicate; SiO2•2H2O - biogenic opal;
13 O2 – Oxygen.
Biological reactionssPlssssPsPs PmZPGZPGPФR
ss )()( 21
lPllsllPlPl PmZPG)Z(PGPΦσRll
)(21
ssZsslssslsZs ZmZμ)Z(ZG(D)ZGZ)(PG)(PGγR 2111 ][
lZllllsls ZmZ(D)ZGZ)(ZG)(PG)(PGγRl
2222 ][Zl
DZmZmPmPm
(D)ZGZ)(ZG)(PG)(PG
(D)ZGZ)(PG)(PGR
lZsZlPsP
llsls
sslsD
lsls
2222
111
1
1
])[(
][)(
44
4
1(z)NHΩZμZμεD
β
βPΦPΦ
REDFR allss
N
NHlPlsPs
NCNH ls
:
2324 NOzNOzNOzNHzR drna )()()()(2NO
323
3
1(z)NOΩ(z)NOΩ
β
βPΦPΦ
REDFR rn
N
NO
lPlsPsNC
NO ls
:
llsslPlsPsPC
PO ZμZμεDPΦPΦREDF
Rls
:
14
Biological reactions in the model : term RC is Dxbi(ndrei,nbio)
*------------------BIOLOGICAL SOURCES------------------------------------ *Ps DXbi(ll,3)= ( BioC(2)*Ps_prod-BioC(10) )*Tc(ll,3) !1 prod & - ZsonPs*Tc(ll,5) ! & - ZlonPs*Tc(ll,6) ! *Pl DXbi(ll,4)= ( BioC(1)*Pl_prod-BioC(9 ) )*Tc(ll,4) !2 prod, c & - ZsonPl*Tc(ll,5) ! & - ZlonPl*Tc(ll,6) ! *Zs DXbi(ll,5)= ( BioC(20)*(ZsonPs+ZsonPl) !3,4,5 & + BioC(21)*ZsonD & - BioC(16) !c & - BioC(18)) *Tc(ll,5) !c & - ZlonZs*Tc(ll,6) ! *Zl DXbi(ll,6)= ( BioC(19)*(ZlonPs+ZlonPl+ZlonZs) !6,7,8,9 & + BioC(21)*ZlonD & - BioC(15) !c & - BioC(17) ) *Tc(ll,6) !c *D DXbi(ll,7)= ( (1.-BioC(20))*(ZsonPs+ZsonPl) !3,4,5 & + (1.-BioC(21))*ZsonD & + BioC(16) )*Tc(ll,5) !c & +( (1.-BioC(19))*(ZlonPs+ZlonPl+ZlonZs) !6,7,8,9 & + (1.-BioC(21))*ZlonD & + BioC(15) )*Tc(ll,6) !c & + BioC(10)*Tc(ll,3) !c & + BioC(9)*Tc(ll,4) !c & - ZsonD*Tc(ll,5) !5 & - ZlonD*Tc(ll,6) !9 & - BioC(22)*Tc(ll,7) !reminiralization !10 *NH4 DXbi(ll,8)= - UP_NH4/UP_N*Prod !11 & + BioC(18)*Tc(ll,5)+BioC(17)*Tc(ll,6) !c,c & + BioC(22)*Tc(ll,7) !reminiralization !c & - BioOM1*Tc(ll,8) !oxydation !13 BioOM1 *NO2 DXbi(ll,9)= BioOM1*Tc(ll,8)-(BioOM2+BioOM4)* !14, 16 BioOM2,BioOM4 & Tc(ll,9)+BioOM3*Tc(ll,10) !15 BioOM3 *NO3 DXbi(ll,10)=- UP_NO3/UP_N*Prod !NO3 !12 & + BioOM2*Tc(ll,9)-BioOM3*Tc(ll,10) !14,15 *PO4 DXbi(ll,11)=(-Prod !1+2 & + BioC(18)*Tc(ll,5)+BioC(17)*Tc(ll,6) & + BioC(22)*Tc(ll,7) ) !reminiralization !10 *SiO2 DXbi(ll,12)=- BioC(1)*Pl_prod *Tc(ll,4) & + BioC(27)*Tc(ll,14) !regeneration SiO2 !17 *O2 DXbi(ll,13)= ((6.625*UP_NH4+8.125*UP_NO3)/UP_N*Prod !O2 !18 O2 from production & - 6.625*(BioC(18)*Tc(ll,5)+BioC(17)*Tc(ll,6)) !zoo exctrition ! & - 6.625*BioC(22)*Tc(ll,7) !detritus mineralization ! & - BioOM1*Tc(ll, 8) !NH4-NO2 ! & -0.5*BioOM2*Tc(ll, 9) !NO2-NO3 ! & +0.5*BioOM3*Tc(ll,10) !NO3-NO2 ! & + BioOM4*Tc(ll, 9))*REDF(11) !NO2-N2 !29 DXbi(ll,14)= + BioC(9 )*Tc(ll,4) & + ZsonPl*Tc(ll,5) & + ZlonPl*Tc(ll,6) & - BioC(27)*Tc(ll,14) !regeneration SiO2
do ibio=3,nbio Tc(ll,ibio) = Tc(ll,ibio)+DXbi(ll,ibio)*dt end do
Subroutine bio (Tc,dd,dz,sh_wave,sh_depth)
Numerics: basic information
Semi-implicit:
-implicit: barotropic pressure gradients, turbulent vertical exchange
-explicit: convective terms, baroclinic pressure gradients, horizontal
turbulent diffusion
Convective or nonlinear terms: energy and enstrophy conserving
scheme Arakawa J7
Rotation of corriolis term (C-grid)
Upstream advection scheme (2d) for T,S and bio-parameter
Free surface and bottom depth resolving coordinates application of
kinematic boundary conditions necessary
Model grid: Arakawa C-grid horizontal
•TC(i,j) •TC(i,j+1)
•TC(i+1,j) •TC(i+1,j+1)
X U(i,j)
+V(i,j)
X U(i,j+1)
X U(i+1,j+1)X U(i+1,j)
+V(i+1,j+1)
+V(i,j+1)
+V(i+1,j)
NW=(1,1) Columns n (j)
Rows
m (i)
Model grid: vertical grid
•TC(k)
•TC(k+1)
+w (k+1) Av(k+1)
Surface layer: 1
ilo (k)
+w (k) Av(k)
•Av and w are not defined at the lower boundary of the bottom layer
•Av(1)=0, i.e. at the sea surface
•w(1) is the first guess for solving the equation system for the sea surface elevation
Organisation of slabs: Counting wet grid points
c----------------------------------------------------------------------- c set grid index arrays c----------------------------------------------------------------------- lwe = 0 nwet=0 do k=1,n lwa = lwe+1 lwe = indend(k) do lw=lwa,lwe i = iwet(lw) lump = lazc(lw) jjc(i,k) = 1 iindex(i,k) = nwet id3sur(lw) = nwet+1 do jj=1,lump nwet = nwet+1 enddo izet(i,k) = lw enddo enddo
•Start with NW grid point, at the sea surface
•2-d arrays: outer loop columns, inner loop rows
•3-d arrays: outer loop, columns, than rows, inner loop depth layers
Relevant arrays and dimensions
•compressed 3-d arrays of dimension ndrei UC(ndrei)
•compressed 2-d arrays of dimension khor zac(khor)
•iindex(i,j) help array to address wet grid from i,j,k arrays i,j,k
known respective uc=uc(iindex(i,j)+k)
•jjc(i,k) mask array, =1 if wet, =0 if land point
•lazc(khor): number of layers for compressed 2-d arrays
•iwet (khor): i-index(row) for compressed 2-d arrays
•indend(k): end index of compressed arrays for
Literature model description
Backhaus J. O. (1983) A semi-implicit scheme for the shallow water equations for application to shelf sea modelling. Continental Shelf Research, 3,243-254.
Backhaus J. O. (1985) A three-dimensional model for the simulation of shelf sea dynamics. Deutsche Hydrographische Zeitschrifi, 38, 165-187.
Schrum, C. (1997): Thermohaline stratification and instabilities at tidal mixing fronts. Results of an eddy resolving model for the German Bight. Cont. Shelf. Res., 17(6), 689-716.
Schrum, C, Backhaus, J. O. (1999): Sensitivity of atmosphere-ocean heat exchange and heat content in North Sea and Baltic Sea. A comparitive assessment. Tellus 51A. 526-549.
Schrum, C, Alekseeva, I, St. John, M (2006): Development of a coupled physical–biological ecosystem model ECOSMO Part I: Model description and validation for the North Sea, Journal of Marine Systems, doi:10.1016/j.jmarsys.2006.01.005.
Access to model code and literature
ftp://ftp.uib.no/
path: /var/ftp/pub/gfi/corinna/ECOSMO
Additional features (not in basic version)
3-d wetting and drying, mass conserving
Groundwater runoff module
Particle tracking module (online)
IBM parameterized for larvae fish growing (temperature based
and food consumption)
Setting up a new configuration
Attention required:
•ngro array size to be set in C_model.f, it needs to be
ngro=max((m*(ilo*20+10),(kasor*8)), for current configuration set to
m*(ilo*20+10)
•consider exclusion of boundary points for iteration in kotief!
currently weak programming
•3 frame lines are necessary in the west and north, only 2 frame lines
in the south and east
•consider 3 equal boundary lines at the open boundaries