ecosim.in

Sediment 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 ocean.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:

• Bissett, W.P., J.J. Walsh, D.A. Dieterle, K.L. Carder, 1999: Carbon cycling in the upper waters of the Sargasso Sea: I. Numerical simulation of differential carbon and nitrogen fluxes, Deep-Sea Res., 46, 205-269.
• Bissett, W.P., K.L. Carder, J.J. Walsh, D.A. Dieterle, 1999: Carbon cycling in the upper waters of the Sargasso Sea: II. Numerical simulation of apparent and inherent optical properties, Deep-Sea Res., 46, 271-317.
• Bissett, W., Arnone, R., DeBra, S., Dieterle, D., Dye, D., Kirkpatrick, G., Schofield, O. and Vargo, G., 2005. Predicting the optical properties of the West Florida Shelf: Resolving the potential impacts of a terrestrial boundary condition on the distribution of colored dissolved and particulate matter. Marine Chemistry, 95(3-4), 199-233.

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, Laplacian, constant, mixing coefficient (m2/s) for biological tracer variables. If variable horizontal diffusion is activated, TNU2 is the mixing coefficient for the largest grid-cell in the domain.

TNU2 == 63*0.0d0

• Lateral, biharmonic, constant, mixing coefficient (m4/s) for biological tracer variables. If variable horizontal diffusion is activated, TNU4 is the mixing coefficient for the largest grid-cell in the domain.

TNU4 == 63*0.0d0

• Background vertical mixing coefficients (m2/s) for biological tracer variables.

AKT_BAK == 63*1.0d-6

• Nudging time scale (days); inverse scale will be computed internally.

TNUDG == 63*0.0d0

• Logical switches to write out biological tracers into output NetCDF files.

Hout(idTvar) == 63*T  ! biological tracer
Hout(idTsur) == 63*F  ! surface tracer flux