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add the ICM SAV epiphytes module
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@wzhengui
wzhengui committed Jul 29, 2024
1 parent e209a4f commit dc4c6bf
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Showing 8 changed files with 558 additions and 355 deletions.
111 changes: 79 additions & 32 deletions sample_inputs/icm.nml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@
!---------------------------------------------------------------------------------
!---------------------------state variables in ICM--------------------------------
!---------------------------------------------------------------------------------
!Core Module
!Core Module (1)
! 1 PB1 : Diatom g/m^3
! 2 PB2 : Green Algae g/m^3
! 3 PB3 : Cyanobacteria g/m^3
Expand All @@ -32,26 +32,27 @@
! 15 PO4 : Total Phosphate g/m^3
! 16 COD : Chemical Oxygen Demand g/m^3
! 17 DOX : Dissolved Oxygen g/m^3
!Silica Module
!Silica Module (2)
! 1 SU : Particulate Biogenic Silica g/m^3
! 2 SA : Available Silica g/m^3
!Zooplankton Module
!Zooplankton Module (3)
! 1 ZB1 : 1st zooplankton g/m^3
! 2 ZB2 : 2nd zooplankton g/m^3
!pH Module
!pH Module (4)
! 1 TIC : Total Inorganic Carbon g/m^3
! 2 ALK : Alkalinity g[CaCO3]/m^3
! 3 CA : Dissolved Calcium g[CaCO3]/m^3
! 4 CACO3 : Calcium Carbonate g[CaCO3]/m^3
!CBP Module
!CBP Module (5)
! 1 SRPOC : Slow Refractory Particulate Organic Carbon g/m^3
! 2 SRPON : Slow Refractory Particulate Organic Nitro. g/m^3
! 3 SRPOP : Slow Refractory Particulate Organic Phosp. g/m^3
! 4 PIP : Particulate Inorganic Phosphate g/m^3
!SAV Module (no transport variables)
!MARSH Module (no transport variables)
!SFM Module (no transport variables)
!BA Module (no transport variables)
!SAV Module (no transport variables) (6)
!MARSH Module (no transport variables) (7)
!SFM Module (no transport variables) (8)
!BA Module (no transport variables) (9)
!CLAM Module (no transport variables) (10)
!---------------------------------------------------------------------------------

&MARCO
Expand Down Expand Up @@ -117,14 +118,14 @@ iPh = 0
iCBP = 0

!-----------------------------------------------------------------------
!Submerged Aquatic Vegetation switch
!Submerged Aquatic Vegetation switch (0: OFF; 1: SAV; 2: SAV+epiphytes)
!-----------------------------------------------------------------------
isav_icm = 0

!-----------------------------------------------------------------------
!Intertidal marsh switch; nmarsh: number of marsh species
!-----------------------------------------------------------------------
imarsh_icm = 0 !0: off; 1: on
imarsh_icm = 0 !0: off; 1: mechanistic model; 2: simple formulation
nmarsh = 3 !parameters in marsh module must be consistent with

!-----------------------------------------------------------------------
Expand Down Expand Up @@ -167,6 +168,13 @@ ibflux = 0
iout_icm = 0
nspool_icm = 24

!-----------------------------------------------------------------------
!ICM diagnostic outputs of sub-modules (0: OFF; 1: ON)
!Note: it can output any model-related variables, but may need coding (developers)
!-----------------------------------------------------------------------
! Core Silica ZB pH CBP SAV Marsh SFM BA Clam
idbg = 0 0 0 0 0 0 0 0 0 0

!-----------------------------------------------------------------------
!options of nutrient limitation on phytoplankton growth
! iLimit=0: f=min[f(N),f(P)]*f(I); iLimit=1: f=min[f(N),f(P),f(I)]
Expand Down Expand Up @@ -437,28 +445,30 @@ inu_ph = 0 !nudge option for pH model
!-----------------------------------------------------------------------
!Submerged Aquatic Vegetation (SAV) parameters
!-----------------------------------------------------------------------
spatch0 = -999 !region flag for SAV. (1: ON all elem.; -999: spatial)
sav0 = 100.0 50.0 10.0 !init. SAV leaf/stem/root conc. (g[C].m-2)
spatch0 = -999 !region flag for SAV. (1: ON all elem.; -999: spatial)
sav0 = 100.0 50.0 10.0 20.0 !init. SAV leaf/stem/root/tuber conc. (g[C].m-2)

!growth coefficients
sGPM = 0.1 !maximum growth rate (day-1)
sTGP = 32 !optimal growth temperature (oC)
sKTGP = 0.003 0.005 !temp. dependence for growth (T<=sTGP & T>sTGP)
sFAM = 0.2 !fraction of leaf production to active metabolism
sFCP = 0.6 0.3 0.1 !fractions of production to leaf/stem/root biomass
sGPM = 0.1 !maximum growth rate (day-1)
sTGP = 32 !optimal growth temperature (oC)
sKTGP = 0.003 0.005 !temp. dependence for growth (T<=sTGP & T>sTGP)
sFAM = 0.2 !fraction of leaf production to active metabolism
sFCP = 0.55 0.3 0.1 0.05 !fractions of production to leaf/stem/root/tuber biomass

!metabolism coefficients
sMTB = 0.02 0.02 0.02 !metabolism rates of leaf/stem/root (day-1)
sTMT = 20 20 20 !reference temp. for leaf/stem/root metabolism (oC)
sKTMT = 0.069 0.069 0.069 !temp. dependence of leaf/stem/root metabolism (oC-1)
sFCM = 0.05 0.15 0.3 0.5 !fractions of metabolism leaf/stem C into (RPOC,LPOC,DOC,CO2)
sFNM = 0.05 0.15 0.3 0.5 !fractions of metabolism leaf/stem N into (RPON,LPON,DON,NH4)
sFPM = 0.05 0.1 0.35 0.5 !fractions of metabolism leaf/stem P into (RPOP,LPOP,DOP,PO4)
sFCMb = 0.65 0.255 0.095 0.0 !fractions of metabolism root C into (G1/G2/G3 POC, CO2) in sediment
sFNMb = 0.65 0.300 0.050 0.0 !fractions of metabolism root N into (G1/G2/G3 PON, NH4) in sediment
sFPMb = 0.65 0.255 0.095 0.0 !fractions of metabolism root P into (G1/G2/G3 POP, PO4) in sediment
sMTB = 0.02 0.02 0.02 0.02 !metabolism rates of leaf/stem/root/tuber (day-1)
sTMT = 20 20 20 20 !reference temp. for leaf/stem/root/tuber metabolism (oC)
sKTMT = 0.069 0.069 0.069 0.069 !temp. dependence of leaf/stem/root/tuber metabolism (oC-1)
sFCM = 0.05 0.15 0.3 0.5 !fractions of metabolism leaf/stem C into (RPOC,LPOC,DOC,CO2)
sFNM = 0.05 0.15 0.3 0.5 !fractions of metabolism leaf/stem N into (RPON,LPON,DON,NH4)
sFPM = 0.05 0.1 0.35 0.5 !fractions of metabolism leaf/stem P into (RPOP,LPOP,DOP,PO4)
sFCMb = 0.65 0.255 0.095 0.0 !fractions of metabolism root C into (G1/G2/G3 POC, CO2) in sediment
sFNMb = 0.65 0.300 0.050 0.0 !fractions of metabolism root N into (G1/G2/G3 PON, NH4) in sediment
sFPMb = 0.65 0.255 0.095 0.0 !fractions of metabolism root P into (G1/G2/G3 POP, PO4) in sediment

!misc. coefficients
sKTB = 0.1 !mass transfer rate from tuber to leaves (day-1)
sDoy = 60 150 !range of day_of_year for mass transfer of tuber
sKhN = 0.01 0.1 !reference N conc. in water and sediment (mg/L)
sKhP = 0.001 0.01 !reference P conc. in water and sediment (mg/L)
salpha = 0.006 !init. slope of P-I curve (g[C].m2.g[Chl]-1.E-1)
Expand All @@ -468,15 +478,43 @@ s2ht = 0.0036 0.0036 0.0 !coeffs. converting (leaf,stem,root) to canopy heigh
sc2dw = 0.38 !carbon to dry weight ratio of sav
sn2c = 0.09 !nitrogen to carbon ratio of sav
sp2c = 0.01 !phosphorus to carbon ratio
so2c = 2.67 !oxygen to carbon ratio

!----------------------
!Epiphytes (activated when isav_icm=2)
!----------------------
EP0 = 0.05 !epiphytes abundane (g[C_EP].g-1[C_sleaf])
eGPM = 0.5 !EP growth rate (day-1)
eTGP = 30 !optimal growth temperature (oC)
eKTGP = 0.005 0.005 !temp. dependence for growth (oC-2)
eKe = 0.05 !light attenuation from EP (g-1[C_EP].g[C_sleaf])
ealpha= 2 !init. slope of P-I curve (g[C].m2.g[Chl]-1.E-1)
eMTB = 0.2 !EP metabolism rate (day-1)
eTMT = 20 !reference temp. for EP metabolism (oC)
eKTMT = 0.069 !temp. dependence of EP metabolism (oC-1)
ePRR = 0.1 !predation rate of EP (day-1.g-1[C_EP].g[C_sleaf])
eFCM = 0.1 0.5 0.2 0.2 !fractions of EP metabolism C. into (RPOC,LPOC,DOC,CO2)
eFNM = 0.1 0.7 0.2 0.0 !fractions of EP metabolism N. into (RPON,LPON,DON,NH4)
eFPM = 0.1 0.7 0.2 0.0 !fractions of EP metabolism P. into (RPOP,LPOP,DOP,PO4)
eFCP = 0.1 0.9 0.0 0.0 !fractions of EP predation C. into (RPOC,LPOC,DOC,CO2)
eFNP = 0.1 0.9 0.0 0.0 !fractions of EP predation N. into (RPON,LPON,DON,NH4)
eFPP = 0.1 0.9 0.0 0.0 !fractions of EP predation P. into (RPOP,LPOP,DOP,PO4)
en2c = 0.167 !nitrogen to carbon ratio
ep2c = 0.02 !phosphorus to carbon ratio
eKhN = 0.01 !half N. concentration for EP growth (mg/L)
eKhP = 0.001 !half P. concentration for EP growth (mg/L)
eKhE = 0.01 !EP abundance at which growth halves (g[C_EP].g-1[C_sleaf])
/

&MARSH
!-----------------------------------------------------------------------
!Marsh modele, paramters
!Marsh model: 1). fully dynamic; 2). simple formulation
!-----------------------------------------------------------------------
iNmarsh = 1 !whether turn on nitrogen/phosphorus dynamics in Marsh kenetics (0: OFF; 1: ON)
vpatch0 = -999 !region flag for marsh. (1: ON all elem.; -999: spatial)

!----------------------
!mechanistic model (imarsh=1)
!----------------------
iNmarsh = 1 !whether turn on nitrogen/phosphorus dynamics in Marsh kenetics (0: OFF; 1: ON)
vmarsh0 = 100.0 100.0 100.0 100.0 100.0 100.0 30.0 30.0 30.0 !init. leaf/stem/root conc. (g[C].m-3) [nmarsh,3]

!growth coefficients
Expand Down Expand Up @@ -511,7 +549,17 @@ v2ht = 0.0036 0.0036 0.0036 0.001 0.001 0.001 !coefs. convert leaf/stem to
vc2dw = 0.38 0.38 0.38 !dry to wet ratio of marsh biomass [nmarsh]
vn2c = 0.09 0.09 0.09 !nitrogen to carbon ratio [nmarsh]
vp2c = 0.01 0.01 0.01 !phosphorus to carbon ratio [nmarsh]
vo2c = 2.67 2.67 2.67 !oxygen to carbon ratio [nmarsh]

!----------------------
!simple wetland model (imarsh=2)
!----------------------
vAw = 0.1 !ratio between marsh area to adjacent water volume (m-1)
vKNO3 = 0.01 !mass-transfer coefficient for NO3 removal (m.day-1)
vKPOM = 0.05 !settling velocity caused by marsh (m.day-1)
vKTw = 0.069 !temperature dependence for wetland effect (oC-1)
vRTw = 20 !reference temperature for wetland effect (oC)
vKhDO = 1.0 !half saturation for wetland effect (mg/L)
vOCw = 0.1 !wetland oxygen consumption rate (g.m-2.day-1)
/

&BAG
Expand All @@ -534,7 +582,6 @@ gKhN = 0.01 !nitrogen half saturation for BA growth (g[N]/m3)
gKhP = 0.001 !phosphorus half saturation for BA growth (g[P]/m3)
gp2c = 0.0167 !phosphorus to carbon ratio
gn2c = 0.167 !nitrogen to carbon ratio
go2c = 2.67 !oxygen to carbon ratio
gFCP = 0.5 0.45 0.05 !fraction of predation BA C into 3G classes in sediment
gFNP = 0.5 0.45 0.05 !fraction of predation BA N into 3G classes in sediment
gFPP = 0.5 0.45 0.05 !fraction of predation BA P into 3G classes in sediment
Expand Down
3 changes: 0 additions & 3 deletions sample_inputs/param.nml
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Expand Up @@ -1042,9 +1042,6 @@
! !clam biomass(1:nclam) (g[C]/m^2)
! !-------------------------------------------------------------
! iof_icm_clam = 1
!
! !ICM Debug Outputs (need coding, for developers)
! iof_icm_dbg = 1 !2D/3D ICM debug variables

!-----------------------------------------------------------------------
! CoSINE outputs: all 3D
Expand Down
1 change: 0 additions & 1 deletion src/Core/scribe_io.F90
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Expand Up @@ -134,7 +134,6 @@ subroutine scribe_init(indir,iths,ntime)
!call mpi_recv(nout_d3d,1,itype,0,143,comm_schism,rrqst,ierr)
!allocate(iof_icm(nout_icm))
!call mpi_recv(iof_icm,nout_icm,itype,0,144,comm_schism,rrqst,ierr)
!call mpi_recv(iof_icm_dbg,2,itype,0,145,comm_schism,rrqst,ierr)
#endif
call mpi_recv(ics,1,itype,0,146,comm_schism,rrqst,ierr)
call mpi_recv(iof_ugrid,1,itype,0,147,comm_schism,rrqst,ierr)
Expand Down
5 changes: 2 additions & 3 deletions src/Hydro/schism_init.F90
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Expand Up @@ -212,7 +212,7 @@ subroutine schism_init(iorder,indir,iths,ntime)

namelist /SCHOUT/nc_out,iof_hydro,iof_wwm,iof_gen,iof_age,iof_sed,iof_eco,iof_icm_core, &
&iof_icm_silica,iof_icm_zb,iof_icm_ph,iof_icm_cbp,iof_icm_sav,iof_icm_marsh,iof_icm_sed, &
&iof_icm_ba,iof_icm_clam,iof_icm_dbg,iof_cos,iof_fib,iof_sed2d,iof_ice,iof_ana,iof_marsh,iof_dvd, &
&iof_icm_ba,iof_icm_clam,iof_cos,iof_fib,iof_sed2d,iof_ice,iof_ana,iof_marsh,iof_dvd, &
&nhot,nhot_write,iout_sta,nspool_sta,iof_ugrid

!-------------------------------------------------------------------------------
Expand Down Expand Up @@ -509,7 +509,7 @@ subroutine schism_init(iorder,indir,iths,ntime)
iof_hydro=0; iof_wwm=0; iof_gen=0; iof_age=0; iof_sed=0; iof_eco=0; iof_dvd=0
iof_hydro(1)=1; iof_hydro(25:26)=1
iof_icm_core=0; iof_icm_silica=0; iof_icm_zb=0; iof_icm_ph=0; iof_icm_cbp=0; iof_icm_sav=0
iof_icm_marsh=0; iof_icm_sed=0; iof_icm_ba=0; iof_icm_clam=0; iof_icm_dbg=0; iof_cos=0; iof_fib=0; iof_sed2d=0
iof_icm_marsh=0; iof_icm_sed=0; iof_icm_ba=0; iof_icm_clam=0; iof_cos=0; iof_fib=0; iof_sed2d=0
iof_ice=0; iof_ana=0; iof_marsh=0; nhot=0; nhot_write=8640; iout_sta=0; nspool_sta=10; iof_ugrid=0

read(15,nml=OPT)
Expand Down Expand Up @@ -6792,7 +6792,6 @@ subroutine schism_init(iorder,indir,iths,ntime)
call mpi_send(nout_icm_3d,2,itype,nproc_schism-i,142,comm_schism,ierr)
!call mpi_send(nout_d3d,1,itype,nproc_schism-i,143,comm_schism,ierr)
!call mpi_send(iof_icm,nout_icm,itype,nproc_schism-i,144,comm_schism,ierr)
!call mpi_send(iof_icm_dbg,2,itype,nproc_schism-i,145,comm_schism,ierr)
#endif
call mpi_send(ics,1,itype,nproc_schism-i,146,comm_schism,ierr)
call mpi_send(iof_ugrid,1,itype,nproc_schism-i,147,comm_schism,ierr)
Expand Down
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