ecosim.in

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EcoSim Model Input Script - ecosim.in

The ecosim.in file sets the parameters for the EcoSim model. The name of this file is set by the BPARNAM keyword in the roms.in file. A default ecosim.in standard input ASCII file can be found in the User/External subdirectory of the ROMS source code. In order to include the EcoSim model in ROMS you must set BPARNAM correctly and activate the ECOSIM CPP option.


EcoSim equations and representative parameters may be found in:


Note Notice: Detailed information about ROMS input script file syntax can be found here.



Biological Model Control Parameters

  • This switch to control the computation of EcoSim within nested and/or multiple connected grids. By default this switch is set to TRUE in mod_scalars.F for all grids. Ngrids values are expected. The user has the option, for example, to compute the biology in just one of the nested grids.
Lbiology == T
  • Maximum number of iterations to achieve convergence of the nonlinear solution.
BioIter == 1
  • Calculation control switches.
RtUVR_flag == T  ! calculate CDOC UV photolysis
NFIX_flag == F  ! calculate temperature based nitrogen fixation
Regen_flag == T  ! calculate fecal matter regeneration

Phytoplankton Group Parameters

Unless specified, [1:Nphy,1:Ngrids] values are expected for each parameter. This file is configured for Nphy=1 and Ngrids=1. The order of phytoplankton are:

  1. larger diatoms
  2. small diatoms
  3. dinoflagellates
  4. synechococcus.
  • Half-saturation for phytoplankton NO3 uptake (micromole_NO3/liter).
HsNO3 == 8.2400d-01 4.1200d-01 8.2400d-01 1.6700d-01
  • Half-saturation for phytoplankton NH4 uptake (micromole_NH4/liter).
HsNH4 == 4.1400d-01 2.0800d-01 4.1400d-01 8.3000d-02
  • Half-saturation for phytoplankton SiO uptake (micromole_SiO/liter). A value of 1.0d+30 denotes no SiO uptake being calculated for that phytoplankton group.
HsSiO == 1.8240d+00 1.4120d+00 1.0000d+30 1.0000d+30
  • Half-saturation for phytoplankton PO4 uptake (micromole_PO4/liter)
HsPO4 == 5.1500d-02 2.5750d-02 5.1500d-02 1.0438d-02
  • Half-saturation for phytoplankton Fe uptake (micromole_Fe/liter). A value of 1.0d+30 denotes no Fe uptake being calculated for that phytoplankton group.
HsFe == 1.0000d+30 1.0000d+30 1.0000d+30 1.0000d+30
  • Maximum phytoplankton 24 hour growth rate (1/d).
GtALG_max == 3.7000d+00 3.7000d+00 2.0000d+00 2.0000d+00
  • Phytoplankton temperature base for exponential response to temperature (Celsius).
PhyTbase == 4*27.0d0
  • Phytoplankton exponential temperature factor (1/Celsius).
PhyTfac == 4*0.0633d0
  • Nitrate uptake inhibition for NH4 (1/micromole).
BET_ == 1.2800d+00 2.6000d+00 1.2800d+00 6.5000d+00
  • Maximum phytoplankton C:N ratio (micromole_C/micromole_N).
maxC2nALG == 1.4000d+01 1.7750d+01 1.7000d+01 6.6250d+00
  • Balanced phytoplankton C:N ratio (micromole_C/micromole_N).
minC2nALG == 6.6250d+00 6.6250d+00 6.6250d+00 6.6250d+00
  • Absolute minimum phytoplankton C:N ratio (micromole_C/micromole_N).
C2nALGminABS == 5.5000d+00 5.5000d+00 5.5000d+00 5.5000d+00
  • Maximum phytoplankton C:Si ratio (micromole_C/micromole_Si). A value of 0.0 denotes no silica used.
maxC2SiALG == 5.5210d+00 5.5210d+00 0.0000d+00 0.0000d+00
  • Balanced phytoplankton C:Si ratio (micromole_C/micromole_Si). A value of 1.0 denotes no silica used.
minC2SiALG == 5.5210d+00 5.5210d+00 1.0000d+00 1.0000d+00
  • Absolute minimum phytoplankton C:Si ratio (micromole_C/micromole_Si). A value of 1.0 denotes no silica used.
C2SiALGminABS == 4.5831d+00 4.5831d+00 1.0000d+00 1.0000d+00
  • Maximum phytoplankton C:P ratio (micromole_C/micromole_P). A value of 1.0 denotes no silica used.
maxC2pALG == 1.0600d+02 1.0600d+02 1.3000d+02 1.0600d+02
  • Balanced phytoplankton C:P ratio (micromole_C/micromole_P).
minC2pALG == 1.0600d+02 1.0600d+02 1.0600d+02 1.0600d+02
  • Absolute minimum phytoplankton C:P ratio (micromole_C/micromole_P).
C2pALGminABS == 8.800d+01 8.800d+01 8.800d+01 8.800d+01
  • Maximum phytoplankton C:Fe ratio (micromole_C/micromole_Fe). A value of 1.0d+30 denotes no Fe uptake being calculated.
maxC2FeALG == 1.0000d+30 1.0000d+30 1.0000d+30 1.0000d+30
  • Balanced phytoplankton C:Fe ratio (micromole_C/micromole_Fe). A value of 1.0d+30 denotes no Fe uptake being calculated.
minC2FeALG == 1.0000d+30 1.0000d+30 1.0000d+30 1.0000d+30
  • Absolute minimum phytoplankton C:Fe ratio (micromole_C/micromole_Fe). A value of 1.0d+30 denotes no Fe uptake being calculated.
C2FeALGminABS == 1.0000d+30 1.0000d+30 1.0000d+30 1.0000d+30
  • Maximum quantum yield (micromole_C/micromole_quanta).
qu_yld == 8.3300d-02 8.3300d-02 8.3300d-02 8.3300d-02
  • Compensation light level (micromole_quanta).
E0_comp == 1.0000d+01 1.0000d+01 1.0000d+01 6.0000d+00
  • Light level for onset of photoinhibition (micromole_quanta).
E0_inhib == 1.0000d+04 1.0000d+04 1.0500d+02 1.0000d+04
  • Exponential decay factor for light limited growth (1/micromole_quanta).
inhib_fac == 0.0000d+00 0.0000d+00 1.0000d-03 0.0000d+00
  • Maximum lighted limited (nutrient replete) C:Chl ratio (microgram_C/microgram_Chl).
C2CHL_max == 6.0000d+01 4.2000d+01 1.2400d+02 1.6000d+02
  • Rate of change in light limited C:Chl ratio (microgram_C/microgram_Chl/micromole_quanta).
mxC2Cl == 1.2000d-01 1.1440d-01 4.7790d-01 1.0000d-01
  • Minimum lighted limited (nutrient replete) C:Chl ratio (microgram_C/microgram_Chl)
b_C2Cl == 2.5000d+01 1.4800d+01 4.7530d+01 3.0000d+01
  • Rate of change in nutient limited C:Chl ratio [(microgram_C/microgram_Chl)/(micromole_C/micromole_N)]. A value of 0.0 denotes no change in C:Chl with nutrient status.
mxC2Cn == 1.2200d+01 6.8315d+00 1.0350d+01 0.0000d+00
  • Minimum nutrient limited C:Chl ratio (microgram_C/microgram_Chl). A value of 0.0 denotes no change in C:Chl with nutrient status.
b_C2Cn == 6.0000d+01 4.2000d+01 1.2400d+02 0.0000d+00
  • Rate of change in package effect [1/(microgram_C/microgram_Chl)]. A value of 0.0 denotes no change in package effect.
mxPacEff == 1.4290d-02 1.8380d-02 0.0000d+00 0.0000d+00
  • Maximum package effect [1/(microgram_C/microgram_Chl)]. A value of 0.0 denotes no change in package effect.
b_PacEff == 5.0000d-01 5.0000d-01 0.0000d+00 0.0000d+00
  • Rate of change in the Chl_b:Chl_a ratio [(microgram_Chl_b/microgram_Chl_a)/[microgram_C/microgram_Chl_ a)]. A value of 0.0 denotea no change in Chl_b:Chl_a ratio.
mxChlB == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00

Maximum Chl_b:Chl_a ratio (microgram_Chl_b/microgram_Chl_a). A value of 0.0 denotes no Chl_b.

b_ChlB == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00
  • Rate of change in the Chl_c:Chl_a ratio [(microgram_Chl_c/microgram_Chl_a)/(microgram_C/microgram_Chl_a)]. A value of 0.0 denotes no change in Chl_c:Chl_a ratio.
mxChlC == -1.3600d-03 -1.2000d-03 0.0000d+00 0.0000d+00
  • Maximum Chl_c:Chl_a ratio (microgram_Chl_c/microgram_Chl_a). A value of 0.0 denotes no Chl_c.
b_ChlC == 3.4000d-01 3.4000d-01 5.6000d-02 0.0000d+00
  • Rate of change in the PSC:Chl_a ratio [(microgram_PSC/microgram_Chl_a)/microgram_C/microgram_Chl_a)]. A value of 0.0 denotes no change in PSC:Chl_a ratio.
mxPSC == -1.2000d-02 -1.0400d-02 0.0000d+00 0.0000d+00
  • Maximum PSC:Chl_a ratio (microgram_PSC/microgram_Chl_a). A value of 0.0 denotes no Photosynthetic Caroteniods.
b_PSC == 2.0000d+00 2.0000d+00 1.1060d+00 0.0000d+00
  • Rate of change in the PPC:Chl_a ratio [(microgram_PPC/microgram_Chl_a)/(microgram_C/microgram_Chl_ a)]. A value of 0.0 denotes no change in PPC:Chl_a ratio.
mxPPC == 0.0000d+00 0.0000d+00 1.8000d-03 9.0000d-03
  • Maximum PPC:Chl_a ratio (microgram_Chl_c/microgram_Chl_a). A value of 0.0 denotes no Photoprotective Caroteniods.
b_PPC == 1.0000d-01 1.0000d-01 1.6000d-01 3.0000d-01
  • Rate of change in the LPUb:Chl_a ratio [(microgram_LPUb/microgram_Chl_a)/(microgram_C/microgram_Chl_a)]. A value of 0.0 denotes no change in LPUb:Chl_a ratio.
mxLPUb == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00
  • Maximum LPUb:Chl_a ratio (migrogram_HPUb/microgram_Chl_a). A value of 0.0 denotes no LPUb.
b_LPUb == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00
  • Rate of change in the HPUb:Chl_a ratio [(microgram_HPUb/microgram_Chl_a)/(microgram_C/microgram_Chl_a)]. A value of 0.0 denotes no change in HPUb:Chl_a ratio.
mxHPUb == 0.0000d+00 0.0000d+00 0.0000d+00 -1.3000d-01
  • Maximum HPUb:Chl_a ratio (microgram_HPUb/microgram_Chl_a). A value of 0.0 denotes no HPUb.
b_HPUb == 0.0000d+00 0.0000d+00 0.0000d+00 2.0000d+01
  • Proportion of grazing stress that is apportioned to DOM (nondimensional).
FecDOC == 3.3330d-01 3.3330d-01 3.3330d-01 4.1670d-01
  • Proportion of grazing stress that is apportioned to fecal (nondimensional).
FecPEL == 3*1.6670d-01 8.3350d-02 3*1.6670d-01 8.3350d-02
  • Proportion of grazing stress that is recycled (nondimensional).
FecCYC == 3.3330d-01 3.3330d-01 3.3330d-01 4.1660d-01
  • Proportion of daily production that is lost to excretion (nondimensional)
ExALG == 5.0000d-03 5.0000d-03 5.0000d-03 5.0000d-03
  • Phytoplankton sinking speed (meters/day)
WS == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00
  • Phytoplankton grazing parameter (nondimensional).
HsGRZ == 0.0100d+00 0.0100d+00 0.0100d+00 0.0100d+00
  • Refuge Phytoplankton population (micromole_C/liter)
MinRefuge == 2.0000d-02 2.0000d-02 2.0000d-02 2.0000d-02
  • Maximum Refuge Phytoplankton depth (meters)
RefugeDep == 4.0000d+01 4.0000d+01 4.0000d+01 4.0000d+01
  • Normalized Volume factor (nondimensional). (1 micron diameter cell = 1).
Norm_Vol == 7.2398d+01 7.2398d+01 7.2398d+01 4.6370d+00
  • Normalized Surface Area factor (nondimensional). (1 micron diameter cell = 1).
Norm_Surf == 1.7361d+01 1.7361d+01 1.7361d+01 2.7781d+00
  • Half Saturation Constant for DOP uptake (micromole_DOP/liter).
HsDOP == 1.0000d-05 1.0000d-05 2.0000d+00 1.0000d-05
  • C:P ratio where DOP uptake begins (micromole_C/micromole_P). Values above maxC2pALG denote no DOP uptake.
C2pALKPHOS == 5.0000d+02 5.0000d+02 1.1000d+02 5.0000d+02
  • Half Saturation constant for DON uptake (micromole_DON/liter).
HsDON == 1.0000d-05 1.0000d-05 2.0000d+00 1.0000d-05
  • C:N ratio where DON uptake begins (micromole_C/micromole_N). Values above maxC2nALG denote no DOP uptake.
C2nNupDON == 5.0000d+02 5.0000d+02 1.4000d+01 5.0000d+02


Bacteria Group Parameters

Unless specified, [1:Ngrids] values are expected for each parameter. This file is configured for Nbac=1 and Ngrids=1.

  • Half saturation constant for bacteria DOC uptake (micromole_DOC/liter), [1:Nbac,1:Ngrids] values expected.
HsDOC_ba == 130.0d+00
  • Maximum 24 hour bacterial growth rate (1/day), [1:Nbac,1:Ngrids] values expected.
GtBAC_max == 2.0d+00
  • Bacteria temperature base for exponential response to temperature (Celsius), [1:Nbac,1:Ngrids] values expected.
BacTbase == 27.0d+0
  • Bacteria exponential temperature factor (1/Celsius), [1:Nbac,1:Ngrids] values expected.
BacTfac == 0.092d+00
  • Carbon to Nitrogen ratio of Bacteria (micromole_C/micromole_N).
C2nBAC == 5.0d+00
  • Carbon to Phosphorus ratio of Bacteria (micromole_C/micromole_P).
C2pBAC == 60.0d+00
  • Carbon to Iron ratio of Bacteria (micromole_C/micromole_Fe).
C2FeBAC == 1000.0d+00

Proportion of bacteria grazing stress which is apportioned to DOM (nondimensional).

BacDOC == 4.583d-01
  • Proportion of bacteria grazing stress which is apportioned to fecal pellets (nondimensional).
BacPEL == 8.340d-02
  • Proportion of bacteria grazing stress which is apportioned to direct remineralization (nondimensional).
BacCYC == 4.583d-01
  • Bacterial recalcitrant carbon excretion as a proportion of uptake (nondimensional).
ExBAC_c == 4.0d-02
  • Bacterial recalcitrant excretion carbon to nitrogen ratio (micromole_C/micromole_N).
ExBacC2N == 15.0d0
  • Bacterial gross growth carbon efficiency (nondimensional).
Bac_Ceff == 0.3d0
  • Maximum nitrification rate (1/day).
RtNIT == 0.4d0
  • Half-saturation constant for bacterial nitrification (micromole_NH4/liter).
HsNIT == 0.1d0


DOM Group Parameters

Unless specified, [1:Ngrids] values are expected. This file is configured for Ndom=2 and Ngrids=1.

  • Colored fraction of DOC from phytoplankton and bacterial losses (nondimensional), [1:Ndom,1:Ngrids] values are expected.
cDOCfrac_c == 0.0323d0 0.0930d0
  • UV degradation of DOC into DIC (micromole/meter/liter/hour at 410 nm).
RtUVR_DIC == 0.0193d0
  • UV degradation of DOC to colorless labile DOC (micromole/meter/liter/hour at 410nm).
RtUVR_DOC == 0.0034d0

Fecal and Detritus Group Parameters

Unless specified, [1:Nfec,1:Ngrids] values are expected. This file is configured for Nfec=2 and Ngrids=1.

  • Fecal sinking flux (meters/day).
WF == 0.0d0 100.0d0
  • Fecal regeneration temperature base for exponential response to temperature (Celsius).
RegTbase == 2*27.0d0
  • Fecal regeneration exponential temperature factor (1/Celsius).
RegTfac == 2*0.092d0
  • Fecal carbon regeneration rate (1/day).
RegCR == 0.10d0 0.0d0
  • Fecal nitrogen regeneration rate (1/day).
RegNR == 0.10d0 0.0d0
  • Fecal silica regeneration rate (1/day).
RegSR == 0.13d0 0.0d0
  • Fecal phosphorus regeneration rate (1/day).
RegPR == 0.10d0 0.0d0

Fecal iron regeneration rate (1/day).

RegFR == 0.10d0 0.0d0

Physical and Output Parameters

Unless specified, [1:NBT,1:Ngrids] values are expected for each parameter. This file is configured for NBT=63.

  • Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer for nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids] values expected.
TNU2 == 61*0.0d0  ! m2/s
TNU4 == 61*0.0d0  ! m4/s

ad_TNU2 == 61*0.0d0  ! m2/s
ad_TNU4 == 61*0.0d0  ! m4/s
  • Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids] values expected.
AKT_BAK == 61*1.0d-6  ! m2/s

ad_AKT_fac == 61*1.0d0  ! nondimensional
  • Nudging time scale (days); inverse scale will be computed internally.
TNUDG == 61*0.0d0  ! days
  • The lateral boundary conditions are entered with a keyword. A value is expected for each boundary segment per nested grid for each state variable. The biological tracer variables require [1:4,1:NBT,Ngrids] values. The boundary order is: 1=west, 2=south, 3=east, and 4=north. That is, anticlockwise starting at the western boundary.

    The keyword is case insensitive and usually has three characters. However, it is possible to have compound keywords, if applicable. For example, the keyword RadNud implies radiation boundary condition with nudging. This combination is usually used in active/passive radiation conditions.

    NoteNotice: It is possible to specify the lateral boundary conditions for all biological tracers in a compact form with a single entry. If so, all the biological tracers are assumed to have the same boundary condition as the single entry.
    ! Keyword Lateral Boundary Condition Type
    !
    ! Cla Clamped _____N_____ j=Mm
    ! Clo Closed | 4 |
    ! Gra Gradient | |
    ! Nes Nested 1 W E 3
    ! Nud Nudging | |
    ! Per Periodic |_____S_____|
    ! Rad Radiation 2 j=1
    ! i=1 i=Lm
    ! W S E N
    ! e o a o
    ! s u s r
    ! t t t t
    ! h h
    !
    ! 1 2 3 4


    LBC(isTvar) == Per Clo Per Clo  ! idbio(:), compact
  • Adjoint-based algorithms can have different lateral boundary conditions keywords.
    ad_LBC(isTvar) == Per Clo Per Clo  ! idbio(:), compact
  • Logical switches to specify which variables to process for tracers climatology: [1:NBT,Ngrids] values expected.
LtracerCLM == 61*F
  • Logical switches to specify which variables to consider on tracers point Sources/Sinks (like river runoff): [1:NBT,Ngrids] values expected.
LtracerSrc == 61*F
  • Logical switches to activate writing of biological tracers into history output file: [1:NBT,Ngrids] values expected.
Hout(idTvar) == 61*T  ! DIC, ... biological tracer
Hout(idTsur) == 61*F  ! DIC_sflux, ... surface tracer flux
  • Logical switches to activate writing of biological tracers into quicksave output file: [1:NBT,Ngrids] values expected.
Qout(idTvar) == 61*F  ! DIC, ... biological tracer
Qout(idsurT) == 61*F  ! DIC_sur, ... surface biological tracer
Qout(idTsur) == 61*F  ! DIC_sflux, ... surface tracer flux
  • Logical switches to activate writing of time-averaged fields into averages file. [1:NBT,Ngrids] values expected.
Aout(idTvar) == 61*T  ! DIC, ... biological tracer
  • Logical switches to activate writing of time-averaged, biological tracer diagnostic terms into the diagnostic output file. [1:NBT,Ngrids] values expected.
Dout(iTrate) == 61*T  ! DIC_rate, ... time rate of change
Dout(iThadv) == 61*T  ! DIC_hadv, ... horizontal total advection
Dout(iTxadv) == 61*T  ! DIC_xadv, ... horizontal XI-advection
Dout(iTyadv) == 61*T  ! DIC_yadv, ... horizontal ETA-advection
Dout(iTvadv) == 61*T  ! DIC_vadv, ... vertical advection
Dout(iThdif) == 61*T  ! DIC_hdiff, ... horizontal total diffusion
Dout(iTxdif) == 61*T  ! DIC_xdiff, ... horizontal XI-diffusion
Dout(iTydif) == 61*T  ! DIC_ydiff, ... horizontal ETA-diffusion
Dout(iTsdif) == 61*T  ! DIC_sdiff, ... horizontal S-diffusion
Dout(iTvdif) == 61*T  ! DIC_vdiff, ... vertical diffusion