You are here

EcoSim in SELFE User Manual

Important: in order to run EcoSim with SELFE, you need to first compile the code with USE_ECO turned on in Makefile! Then you'll need to prepare 3 input files:

  1. tracer_param.in
  2. atmos.in
  3. ecosim.in

Below are detailed descriptions for each file.


 

Input file format


tracer_param.in

Ecological Model !Descriptive line
2 !Type of model (1-Sediments Model, 2-Ecological Model, 3-Oil Spill Model)
01 06 2007 00 00 00 !Date in the format: dd mm aa hh mm ss
3 !Type of initial conditions (1,2 or 3; similar to icst; "3" is for analytical form)


atmos.in

This files has only 1 line; note that currently only a uniform value can be used for meteological variables.
Uwind Vwind Pair Hair Tair cloud

Uwind, Vwind: components u and v of wind velocity and direction (m/s)
Pair: atmospheric pressure (mbar)
Hair: relative humidity
Tair: air temperature (K)
cloud: cloud cover (fraction 0-1)

Example:
0 5 1018 72 293.15 0.2


ecosim.in

This is the main input for the ecological model, and the descriptions below are adapted from ROMS model. The numbers Nphy, Nbac etc are set in bio_param.F90. So the following statement:
HsNH4 == value1 value2 ... valueNphy
means that Nphy values are expected for the parameter HsNH4. See the sample files in the biotoy test for detals. Note that you can give more values than expected and the program will read them in order until all are read in.

 

! EcoSim Biological Model Parameters.
!
!!======================================================================
!! April/May, 2007 !
!!======================================================Marta Rodrigues=
!! !
!! This file is adapted from ROMS: !
!! !
!!=====================================================================
!================================================= Hernan G. Arango ===
! Copyright (c) 2002-2007 The ROMS/TOMS Group W. Paul Bissett !
! Licensed under a MIT/X style license !
! See License_ROMS.txt !
!========================================================================
!
! Maximum number of iterations to achieve convergence of the nonlinear
! solution.
!
BioIter == value
!
! Logical switch (T/F) to calculate CDOC UV photolysis.
!
RtUVR_flag == T or F
!
! Logical switch (T/F) to calculate temperature based nitrogen fixation.
!
NFIX_flag == T or F
!
! Logical switch (T/F) to calculate fecal matter regeneration.
!
Regen_flag == T or F
!
!------------------------------------------------------------------------
! Phytoplankton group parameters.
!------------------------------------------------------------------------
!
! Half-saturation for phytoplankton NO3 uptake (micromole_NO3/liter),
! [Nphy] values are expected.
!
HsNO3 == value1 value2 ... valueNphy
!
! Half-saturation for phytoplankton NH4 uptake (micromole_NH4/liter),
! [Nphy] values are expected.
!
HsNH4 == value1 value2 ... valueNphy
!
! Half-saturation for phytoplankton SiO uptake (micromole_SiO/liter),
! [Nphy] values are expected. A value of 1.0d+30 denotes no SiO
! uptake being calculated for that phytoplankton group.
!
HsSiO == value1 value2 ... valueNphy
!
! Half-saturation for phytoplankton PO4 uptake (micromole_PO4/liter),
! [Nphy] values are expected.
!
HsPO4 == value1 value2 ... valueNphy
!
! Half-saturation for phytoplankton Fe uptake (micromole_Fe/liter),
! [Nphy] values are expected. A value of 1.0d+30 denotes no Fe
! uptake being calculated for that phytoplankton group.
!
HsFe == value1 value2 ... valueNphy
!
! Maximum phytoplankton 24 hour growth rate (1/d),
! [Nphy] values are expected.
!
GtALG_max == value1 value2 ... valueNphy
!
! Phytoplankton temperature base for exponential response to temperature
! (Celsius), [Nphy] values are expected.
!
PhyTbase == value1 value2 ... valueNphy
!
! Phytoplankton exponential temperature factor (1/Celsius),
! [Nphy] values are expected.
!
PhyTfac == value1 value2 ... valueNphy
!
! Nitrate uptake inhibition for NH4 (l/micromole),
! [Nphy] values are expected.
!
BET_ == value1 value2 ... valueNphy
!
! Maximum phytoplankton C:N ratio (micromole_C/micromole_N),
! [Nphy] values are expected.
!
maxC2nALG == value1 value2 ... valueNphy
!
! Balanced phytoplankton C:N ratio (micromole_C/micromole_N),
! [Nphy] values are expected.
!
minC2nALG == value1 value2 ... valueNphy
!
! Absolute minimum phytoplankton C:N ratio (micromole_C/micromole_N),
! [Nphy] values are expected.
!
C2nALGminABS == value1 value2 ... valueNphy
!
! Maximum phytoplankton C:Si ratio (micromole_C/micromole_Si),
! [Nphy] values are expected. A value of 0.0 denotes no silica used.
!
maxC2SiALG == value1 value2 ... valueNphy
!
! Balanced phytoplankton C:Si ratio (micromole_C/micromole_Si),
! [Nphy] values are expected. A value of 1.0 denotes no silica used.
!
minC2SiALG == value1 value2 ... valueNphy
!
! Absolute minimum phytoplankton C:Si ratio (micromole_C/micromole_Si)
! [Nphy] values are expected. A value of 1.0 denotes no silica used.
!
C2SiALGminABS == value1 value2 ... valueNphy
!
! Maximum phytoplankton C:P ratio (micromole_C/micromole_P),
! [Nphy] values are expected. A value of 1.0 denotes no silica used.
!
maxC2pALG == value1 value2 ... valueNphy
!
! Balanced phytoplankton C:P ratio (micromole_C/micromole_P),
! [Nphy] values are expected.
!
minC2pALG == value1 value2 ... valueNphy
!
! Absolute minimum phytoplankton C:P ratio (micromole_C/micromole_P),
! [Nphy] values are expected.
!
C2pALGminABS == value1 value2 ... valueNphy
!
! Maximum phytoplankton C:Fe ratio (micromole_C/micromole_Fe),
! [Nphy] values are expected. A value of 1.0d+30 denotes no Fe
! uptake being calculated.
!
maxC2FeALG == value1 value2 ... valueNphy
!
! Balanced phytoplankton C:Fe ratio (micromole_C/micromole_Fe),
! [Nphy] values are expected. A value of 1.0d+30 denotes no Fe
! uptake being calculated.
!
minC2FeALG == value1 value2 ... valueNphy
!
! Absolute minimum phytoplankton C:Fe ratio (micromole_C/micromole_Fe),
! [Nphy] values are expected. A value of 1.0d+30 denotes no Fe
! uptake being calculated.
!
C2FeALGminABS == value1 value2 ... valueNphy
!
! Maximum quantum yield (micromole_C/micromole_quanta),
! [Nphy] values are expected.
!
qu_yld == value1 value2 ... valueNphy
!
! Compensation light level (micromole_quanta),
! [Nphy] values are expected.
!
E0_comp == value1 value2 ... valueNphy
!
! Light level for onset of photoinhibition (micromole_quanta),
! [Nphy] values are expected.
!
E0_inhib == value1 value2 ... valueNphy
!
! Exponential decay factor for light limited growth (1/micromole_quanta),
! [Nphy] values are expected.
!
inhib_fac == value1 value2 ... valueNphy
!
! Maximum lighted limited (nutrient replete) C:Chl ratio
! (microgram_C/microgram_Chl), [Nphy] values are expected.
!
C2CHL_max == value1 value2 ... valueNphy
!
! Rate of change in light limited C:Chl ratio
! (microgram_C/microgram_Chl/micromole_quanta),
! [Nphy] values are expected.
!
mxC2Cl == value1 value2 ... valueNphy
!
! Minimum lighted limited (nutrient replete) C:Chl ratio
! (microgram_C/microgram_Chl), [Nphy] values are expected.
!
b_C2Cl == value1 value2 ... valueNphy
!
! Rate of change in nutient limited C:Chl ratio
! [(microgram_C/microgram_Chl)/(micromole_C/micromole_N)],
! [Nphy] values are expected. A value of 0.0 denotes no change
! in C:Chl with nutrient status.
!
mxC2Cn == value1 value2 ... valueNphy
!
! Minimum nutrient limited C:Chl ratio (microgram_C/microgram_Chl),
! [Nphy] values are expected. A value of 0.0 denotes no change
! in C:Chl with nutrient status.
!
b_C2Cn == value1 value2 ... valueNphy
!
! Rate of change in package effect [1/(microgram_C/microgram_Chl)],
! [Nphy] values are expected. A value of 0.0 denotes no change
! in package effect.
!
mxPacEff == value1 value2 ... valueNphy
!
! Maximum package effect [1/(microgram_C/microgram_Chl)],
! [Nphy] values are expected. A value of 0.0 denotes no change
! in package effect.
!
b_PacEff == value1 value2 ... valueNphy
!
! Rate of change in the Chl_b:Chl_a ratio
! [(microgram_Chl_b/microgram_Chl_a)/[microgram_C/microgram_Chl_ a)],
! [Nphy] values are expected. A value of 0.0 denotea no change
! in Chl_b:Chl_a ratio.
!
mxChlB == value1 value2 ... valueNphy
!
! Maximum Chl_b:Chl_a ratio (microgram_Chl_b/microgram_Chl_a),
! [Nphy] values are expected. A value of 0.0 denotes no Chl_b.
!
b_ChlB == value1 value2 ... valueNphy
!
! Rate of change in the Chl_c:Chl_a ratio.
! [(microgram_Chl_c/microgram_Chl_a)/(microgram_C/microgram_Chl_a)],
! [Nphy] values are expected. A value of 0.0 denotes no change
! in Chl_c:Chl_a ratio.
!
mxChlC == value1 value2 ... valueNphy
!
! Maximum Chl_c:Chl_a ratio (microgram_Chl_c/microgram_Chl_a),
! [Nphy] values are expected. A value of 0.0 denotes no Chl_c.
!
b_ChlC == value1 value2 ... valueNphy
!
! Rate of change in the PSC:Chl_a ratio
! [(microgram_PSC/microgram_Chl_a)/microgram_C/microgram_Chl_a)],
! [Nphy] values are expected. A value of 0.0 denotes no change
! in PSC:Chl_a ratio.
!
mxPSC == value1 value2 ... valueNphy
!
! Maximum PSC:Chl_a ratio (microgram_PSC/microgram_Chl_a),
! [Nphy] values are expected. A value of 0.0 denotes no
! Photosynthetic Caroteniods.
!
b_PSC == value1 value2 ... valueNphy
!
! Rate of change in the PPC:Chl_a ratio
! [(microgram_PPC/microgram_Chl_a)/(microgram_C/microgram_Chl_ a)],
! [Nphy] values are expected. A value of 0.0 denotes no change
! in PPC:Chl_a ratio.
!
mxPPC == value1 value2 ... valueNphy
!
! Maximum PPC:Chl_a ratio (microgram_Chl_c/microgram_Chl_a),
! [Nphy] values are expected. A value of 0.0 denotes no
! Photoprotective Caroteniods.
!
b_PPC == value1 value2 ... valueNphy
!
! Rate of change in the LPUb:Chl_a ratio
! [(microgram_LPUb/microgram_Chl_a)/(microgram_C/microgram_Chl_a)],
! [Nphy] values are expected. A value of 0.0 denotes no change
! in LPUb:Chl_a ratio.
!
mxLPUb == value1 value2 ... valueNphy
!
! Maximum LPUb:Chl_a ratio (migrogram_HPUb/microgram_Chl_a),
! [Nphy] values are expected. A value of 0.0 denotes no LPUb.
!
b_LPUb == value1 value2 ... valueNphy
!
! Rate of change in the HPUb:Chl_a ratio
! [(microgram_HPUb/microgram_Chl_a)/(microgram_C/microgram_Chl_a)],
! [Nphy] values are expected. A value of 0.0 denotes no change
! in HPUb:Chl_a ratio.
!
mxHPUb == value1 value2 ... valueNphy
!
! Maximum HPUb:Chl_a ratio (microgram_HPUb/microgram_Chl_a),
! [Nphy] values are expected. A value of 0.0 denotes no HPUb.
!
b_HPUb == value1 value2 ... valueNphy
!
! Proportion of grazing stress that is apportioned to DOM
! (nondimensional), [Nphy] values are expected.
!
FecDOC == value1 value2 ... valueNphy
!
! Proportion of grazing stress that is apportioned to fecal
! (nondimensional), [Nphy,Nfec] values are expected.
!
FecPEL == value1_1 value2_1 ... valueNphy_1 ? value1_Nfec value2_Nfec ? valueNphy_Nfec
!
! Proportion of grazing stress that is recycled (nondimensional),
! [Nphy] values are expected.
!
FecCYC == value1 value2 ... valueNphy
!
! Proportion of daily production that is lost to excretion
! (nondimensional), [Nphy] values are expected.
!
ExALG == value1 value2 ... valueNphy
!
! Phytoplankton sinking speed (meters/day),
! [Nphy] values are expected.
!
WS == value1 value2 ... valueNphy
!
! Phytoplankton grazing parameter (nondimensional).
! [Nphy] values are expected.
!
HsGRZ == value1 value2 ... valueNphy
!
! Refuge Phytoplankton population (micromole_C/liter),
! [Nphy] values are expected.
!
MinRefuge == value1 value2 ... valueNphy
!
! Maximum Refuge Phytoplankton depth (meters),
! [Nphy] values are expected.
!
RefugeDep == value1 value2 ... valueNphy
!
! Normalized Volume factor (nondimensional),
! [Nphy] values are expected. (1 micron diameter cell = 1).
!
Norm_Vol == value1 value2 ... valueNphy
!
! Normalized Surface Area factor (nondimensional),
! [Nphy] values are expected. (1 micron diameter cell = 1).
!
Norm_Surf == value1 value2 ... valueNphy
!
! Half Saturation Constant for DOP uptake (micromole_DOP/liter),
! [Nphy] values are expected.
!
HsDOP == value1 value2 ... valueNphy
!
! C:P ratio where DOP uptake begins (micromole_C/micromole_P),
! [Nphy] values are expected. Values above maxC2pALG denote
! no DOP uptake.
!
C2pALKPHOS == value1 value2 ... valueNphy
!
! Half Saturation constant for DON uptake (micromole_DON/liter),
! [Nphy] values are expected.
!
HsDON == value1 value2 ... valueNphy
!
! C:N ratio where DON uptake begins (micromole_C/micromole_N),
! [Nphy] values are expected. Values above maxC2nALG denote
! no DOP uptake.
!
C2nNupDON == value1 value2 ... valueNphy
!
!-----------------------------------------------------------------------------
! Bacteria group parameters.
!-----------------------------------------------------------------------------
!
! Half saturation constant for bacteria DOC uptake (micromole_DOC/liter),
! [Nbac] values are expected.
!
HsDOC_ba == value1 ... valueNbac
!
! Maximum 24 hour bacterial growth rate (1/day),
! [Nbac] values are expected.
!
GtBAC_max == value1 ... valueNbac
!
! Bacteria temperature base for exponential response to temperature
! (Celsius), [Nbac] values are expected.
!
BacTbase == value1 ... valueNbac
!
! Bacteria exponential temperature factor (1/Celsius),
! [Nbac] values are expected.
!
BacTfac == value1 ... valueNbac
!
! Carbon to Nitrogen ratio of Bacteria (micromole_C/micromole_N),
! [1] values are expected.
!
C2nBAC == value1 ... valueNbac
!
! Carbon to Phosphorus ratio of Bacteria (micromole_C/micromole_P)
! [1] values are expected.
!
C2pBAC == value1 ... valueNbac
!
! Carbon to Iron ratio of Bacteria (micromole_C/micromole_Fe),
! [1] values are expected.
!
C2FeBAC == value
!
! Proportion of bacteria grazing stress that is apportioned to DOM
! (nondimensional), [1] values are expected.
!
BacDOC == value
!
! Proportion of bacteria grazing stress that is apportioned to fecal
! (nondimensional), [1] values are expected.
!
BacPEL == value
!
! Proportion of bacteria grazing stress that is recycled
! (nondimensional), [1] values are expected.
!
BacCYC == value
!
! Bacterial recalcitrant carbon excretion as a proportion of uptake
! (nondimensional), [1] values are expected.
!
ExBAC_c == value
!
! Bacterial recalcitrant excretion carbon to nitrogen ratio
! (micromole_C/micromole_N), [1] values are expected.
!
ExBacC2N == value
!
! Bacterial gross growth carbon efficiency (nondimensional),
! [1] values are expected.
!
Bac_Ceff == value
!
! Maximum nitrification rate (1/day),
! [1] values are expected.
!
RtNIT == value
!
! Half-saturation constant for bacterial nitrification (micromole_NH4/liter),
! [1] values are expected.
!
HsNIT == value
!
!-----------------------------------------------------------------------------
! DOM group parameters.
!-----------------------------------------------------------------------------
!
! Colored fraction of DOC from phytoplankton and bacterial losses
! (nondimensional), [Ndom] values are expected
!
cDOCfrac_c == value1 ... valueNdom

! UV degradation of DOC into DIC
! (micromole/meter/liter/hour at 410 nm),
! [1] values are expected.
!
RtUVR_DIC == value
!
! UV degradation of DOC to colorless labile DOC
! (micromole/meter/liter/hour at 410 nm),
! [1] values are expected.
!
RtUVR_DOC == value
!
!-----------------------------------------------------------------------------
! Fecal and detritus group parameters.
!-----------------------------------------------------------------------------
!
! Fecal sinking flux (meters/day),
! [Nfec] values are expected.
!
WF == value1 ... valueNfec
!
! Fecal regeneration temp base for exponential response to tempemperaute
! (Celsius), [Nfec] values are expected.
!
RegTbase == value1 ... valueNfec
!
! Fecal regeneration exponential temperature factor,
! (1/Celsius), [Nfec] values are expected.
!
RegTfac == value1 ... valueNfec
!
! Fecal carbon regeneration rate (1/day),
! [Nfec] values are expected.
!
RegCR == value1 ... valueNfec
!
! Fecal nitrogen regeneration rate (1/day),
! [Nfec] values are expected.
!
RegNR == value1 ... valueNfec
!
! Fecal silica regeneration rate (1/day),
! [Nfec] values are expected.
!
RegSR == value1 ... valueNfec
!
! Fecal phosphorus regeneration rate (1/day),
! [Nfec] values are expected.
!
RegPR == value1 ... valueNfec
!
! Fecal iron regeneration rate (1/day),
! [Nfec] values are expected.
!
RegFR == value1 ... valueNfec
!
! Marta Rodrigues
!-----------------------------------------------------------------------------
! Zooplankton group parameters.
!-----------------------------------------------------------------------------
!
! Zooplankton flag for zooplankton maximum growth rate calculations
! (1-Acartia tonsa, naupilus; 2-Acartia tonsa, copepodites; 3-Acartia clausi,
! naupilus; 4-Acartia clausi, copepodites), [Nzoo] values are expected.
!
zoo_sp == value
!
! Proportion of zooplankton which is apportioned to DOM
! (nondimensional), [Nzoo] values are expected.
!
ZooDOC == value1 ... valueNzoo
!
! Proportion of zooplankton which is apportioned to fecal pellets
! (nondimensional), [Nzoo,NFec] values are expected.
!
ZooPEL == value1_1 ... valueNzoo_1 ? value1_Nfec ? valueNzoo_Nfec
!
! Proportion of zooplankton which is apportioned to direct remineralization
! (nondimensional), [Nzoo] values are expected.
!
ZooCYC == value1 ... valueNzoo
!
! Availability of prey to predator (nondimensional),
! [Nzoo, Nphy] values are expected
!
DeltaZoo == value1_1 ... valueNzoo_1 ? value1_Nphy ? valueNzoo_Nphy
!
! Capture efficiency of zooplankton (nondimensional),
! [Nzoo, Nphy] values are expected
!
EfcCap == value1_1 ... valueNzoo_1 ? value1_Nphy ? valueNzoo_Nphy
!
! Half-saturation constant for total food ingestion
! (micromole_C/liter), [Nzoo] values are expected.
!
HsZoo == value1 ... valueNzoo
!
! Assimilation efficiency of zooplankton's predators
! (nondimensional), [Nzoo] values are expected.
!
EfcPrd == value1 ... valueNzoo
!
! Zooplankton excretion rate (1/day), [Nzoo] values are expected.
!
ExZoo == value1 ... valueNzoo
!
! Zooplankton losses due to natural mortality and predation
! (1/day), [Nzoo] values are expected.
!
GZ == value1 ... valueNzoo
!
!
! GLOSSARY:
! =========
!
!==============================================================================
! EcoSim Biological Model Parameters.
!==============================================================================
!
! 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., 2003.
! 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, submitted.
! (For a PDF preprint, see: www.flenvironmental.org/Publications)
!
!------------------------------------------------------------------------------
! Model switches and flags.
!------------------------------------------------------------------------------
!
! BioIter Maximum number of iterations to achieve convergence of
! the nonlinear solution.
!
! RtUVR_flag Logical switch (T/F) to calculate CDOC UV photolysis.
!
! NFIX_flag Logical switch (T/F) to calculate temperature based nitrogen
! fixation. (Not tested at this time; No nitrogen fixation
! being calculated).
!
! Regen_flag Logical switch (T/F) to calculate fecal matter regeneration.
!
!------------------------------------------------------------------------------
! Phytoplankton Parameters. Unless specified, [Nphy] values are
! expected. This file is configured for Nphy
!------------------------------------------------------------------------
!
! HsNO3 Half-saturation for phytoplankton NO3 uptake,
! (micromole_NO3/liter).
!
! HsNH4 Half-saturation for phytoplankton NH4 uptake,
! (micromole_NH4/liter).
!
! HsSiO Half-saturation for phytoplankton SiO uptake,
! (micromole_SiO/liter).
! << 1.0d+30 denotes no SiO uptake being calculated >>
!
! HsPO4 Half-saturation for phytoplankton PO4 uptake,
! (micromole_PO4/liter).
!
! HsFe Half-saturation for phytoplankton Fe uptake,
! (micromole_Fe/liter).
! << 1.0d+30 denotes no Fe uptake being calculated >>
!
! GtALG_max Maximum 24 hour growth rate,
! (1/day).
!
! PhyTbase Phytoplankton temperature base for exponential response
! to temperature, (Celsius).
!
! PhyTfac Phytoplankton exponential temperature factor,
! (1/Celsius).
!
! BET_ Nitrate uptake inhibition for NH4,
! (l/micromole).
!
! maxC2nALG Maximum phytoplankton C:N ratio,
! (micromole_C/micromole_N).
!
! minC2nALG Balanced phytoplankton C:N ratio,
! (micromole_C/micromole_N).
!
! C2nALGminABS Absolute minimum phytoplankton C:N ratio,
! (micromole_C/micromole_N).
!
! maxC2SiALG Maximum phytoplankton C:Si ratio,
! (micromole_C/micromole_Si).
! (0.0 denotes no silica used)
!
! minC2SiALG Balanced phytoplankton C:Si ratio,
! (micromole_C/micromole_Si).
! << 1.0 denotes no silica used >>
!
! C2SiALGminABS Absolute minimum phytoplankton C:Si ratio,
! (micromole_C/micromole_Si).
! (1.0 denotes no silica used)
!
! maxC2pALG Maximum phytoplankton C:P ratio,
! (micromole_C/micromole_P).
!
! minC2pALG Balanced phytoplankton C:P ratio,
! (micromole_C/micromole_P).
!
! C2pALGminABS Absolute minimum phytoplankton C:P ratio,
! (micromole_C/micromole_P).
!
! maxC2FeALG Maximum phytoplankton C:Fe ratio,
! (micromole_C/micromole_Fe).
! << 1.0d+30 denotes no Fe uptake being calculated >>
!
! minC2FeALG Balanced phytoplankton C:Fe ratio,
! (micromole_C/micromole_Fe).
! << 1.0d+30 denotes no Fe uptake being calculated >>
!
! C2FeALGminABS Absolute minimum phytoplankton C:Fe ratio,
! (micromole_C/micromole_Fe).
! << 1.0d+30 denotes no Fe uptake being calculated >>
!
! qu_yld Maximum quantum yield,
! (micromole_C/micromole_quanta).
!
! E0_comp Compensation light level,
! (micromole_quanta).
!
! E0_inhib Light level for onset of photoinhibition,
! (micromole_quanta).
!
! inhib_fac Exponential decay factor for light limited growth,
! (1/micromole_quanta).
!
! C2Chl_max Maximum lighted limited (nutrient replete) C:Chl ratio,
! (microgram_C/microgram_Chl).
!
! mxC2Cl Rate of change in the lighted limited C:Chl ratio,
! (microgram_C/microgram_Chl/micromole_quanta).
!
! b_C2Cl Minimum lighted limited (nutrient replete) C:Chl ratio,
! (microgram_C/microgram_Chl).
!
! mxC2Cn Rate of change in the nutrient limited C:Chl ratio,
! [(microgram_C/microgram_Chl)/(micromole_C/micromole_N)].
! << Zeros denote no change in C:Chl with nutrient status >>
!
! b_C2Cn Minimum nutrient limited C:Chl ratio,
! (microgram_C/microgram_Chl).
! << Zeros denote no change in C:Chl with nutrient status >>
!
! mxPacEff Rate of change in package effect,
! [1/(microgram_C/microgram_Chl)].
! << Zeros denote no change in Package Effect >>
!
! b_PacEff Maximum package effect,
! [1/(microgram_C/microgram_Chl)].
! << Zeros denote no package effect >>
!
! mxChlB Rate of change in the Chl_b:Chl_a ratio,
! [(microgram_Chl_b/microgram_Chl_a)/
! (microgram_C/microgram_Chl_a)].
! << Zeros denote no change in Chl_b:Chl_a ratio >>
!
! b_ChlB Maximum Chl_b:Chl_a ratio,
! (microgram_Chl_b/microgram_Chl_a).
! (Zeros denote no Chl_b)
!
! mxChlC Rate of change in the Chl_c:Chl_a ratio.
! [(microgram_Chl_c/microgram_Chl_a)/
! (microgram_C/microgram_Chl_a)].
! << Zeros denote no change in Chl_c:Chl_a ratio >>
!
! b_ChlC Maximum Chl_c:Chl_a ratio,
! (microgram_Chl_c/microgram_Chl_a).
! << Zeros denote no Chl_c >>
!
! mxPSC Rate of change in the PSC:Chl_a ratio,
! [(microgram_PSC/microgram_Chl_a)/
! (microgram_C/microgram_Chl_a)].
! << Zeros denote no change in PSC:Chla ratio >>
!
! b_PSC Maximum PSC:Chl_a ratio,
! (microgram_Chl_c/microgram_Chl_a).
! << Zeros denote no Photosynthetic Caroteniods >>
!
! mxPPC Rate of change in the PPC:Chl_a ratio,
! [(microgram_PPC/microgram_Chl_a)/
! (microgram_C/microgram_Chl_a)].
! << Zeros denote no change in PPC:Chl_a ratio >>
!
! b_PPC Maximum PPC:Chl_a ratio,
! (microgram_Chl_c/microgram_Chl_a).
! << Zeros denote no Photoprotective Caroteniods >>
!
! mxLPUb Rate of change in the LPUb:Chl_a ratio,
! [(microgram_LPUb/microgram_Chl_a)/
! (microgram_C/microgram_Chl_a)].
! << Zeros denote no change in LPUb:Chl_a ratio >>
!
! b_LPUb Maximum LPUb:Chl_a ratio,
! (microgram_HPUb/microgram_Chl_a).
! << Zeros denote no LPUb >>
!
! mxHPUb Rate of change in the HPUb:Chl_a ratio,
! [(microgram_HPUb/microgram_Chl_a)/
! (microgram_C/microgram_Chl_a)].
! << Zeros denote no change in HPUb:Chl_a ratio >>
!
! b_HPUb Maximum HPUb:Chl_a ratio,
! (microgram_HPUb/microgram_Chl_a).
! << Zeros denote no HPUb >>
!
! FecDOC Proportion of grazing stress which is apportioned to DOM,
! (nondimensional).
!
! FecPEL Proportion of grazing stress which is apportioned to fecal
! pellets, (nondimesional).
! [Nphy,Nfec] values are expected.
!
! FecCYC Proportion of grazing stress which is apportioned to direct
! remineralization, (nondimensional).
!
! ExALG Proportion of daily production that is lost to excretion,
! (nondimensional).
!
! WS Phytoplankton sinking speed,
! (meters/day).
!
! HsGRZ Phytoplankton grazing parameter,
! (nondimensional).
!
! MinRefuge Refuge Phytoplankton population,
! (micromole_C/liter).
!
! RefugeDep Maximum Refuge Phytoplankton depth,
! (meters).
!
! Norm_Vol Normalized Volume factor,
! (nondimensional).
! << 1 micron diameter cell = 1 >>
!
! Norm_Surf Normalized surface area factor,
! (nondimensional).
! << 1 micron diameter cell = 1 >>
!
! HsDOP Half Saturation Constant for DOP uptake,
! (micromole_DOP/liter).
!
! C2pALKPHOS C:P ratio where DOP uptake begins,
! (micromole_C/micromole_P).
! << Values above maxC2pALG denote no DOP uptake >>
!
! HsDON Half Saturation Constant for DON uptake,
! (micromole_DON/liter).
!
! C2nNupDON C:N ratio where DON uptake begins,
! (micromole_C/micromole_N).
! << Values above maxC2nALG denote no DOP uptake >>
!
!------------------------------------------------------------------------------
! Bacteria Parameters. Unless specified, [1] values are expected. This
! file is configured for Nbac.
!------------------------------------------------------------------------------
!
! HsDOC_ba Half saturation constant for bacteria DOC uptake,
! (micromole_DOC/liter).
! [Nbac] values are expected.
!
! GtBAC_max Maximum 24 hour bacterial growth rate,
! (1/day).
! [Nbac] values are expected.
!
! BacTbase Phytoplankton temperature base for exponential response to
! temperature, (Celsius).
! [Nbac] values are expected.
!
! BacTfac Phytoplankton exponential temperature factor,
! (1/Celsius).
! [Nbac] values are expected.
!
! C2nBAC Carbon to Nitrogen ratio of Bacteria,
! (micromole_C/micromole_N).
!
! C2pBAC Carbon to Phosphorus ratio of Bacteria,
! (micromole_C/micromole_P).
!
! C2FeBAC Carbon to Iron ratio of Bacteria,
! (micromole_C/micromole_Fe).
!
! BacDOC Proportion of bacterial grazing stress which is apportioned
! to DOM, (nondimensional).
!
! BacPEL Proportion of bacterial grazing stress which is apportioned
! to fecal pellets, (nondimensional).
!
! BacCYC Proportion of bacterial grazing stress which is apportioned
! to direct remineralization, (nondimensional).
!
! ExBAC_c Bacterial recalcitrant carbon excretion as a proportion
! of uptake, (nondimensional)
!
! ExBacC2N Bacterial recalcitrant excretion carbon to nitrogen ratio,
! (micromole_C/micromole_N).
!
! Bac_Ceff Bacterial gross growth carbon efficiency,
! (nondimensional).
!
! RtNIT Maximum nitrification rate,
! (1/day).
!
! HsNIT Half-saturation constant for bacterial nitrification,
! (micromole_NH4/liter).
!
!------------------------------------------------------------------------------
! DOM Parameters. Unless specified, [1] values are expected. This
! file is configured for Ndom.
!------------------------------------------------------------------------------
!
! cDOCfrac_c Colored fraction of DOC production from phytoplankton and
! bacterial losses, (nondimensional).
! [Ndom] values are expected.
!
! RtUVR_DIC UV degradation of DOC into DIC,
! (micromole/meter/liter/hour at 410 nanometer).
!
! RtUVR_DOC UV degradation of DOC into colorless labile DOC,
! (micromole/meter/liter/hour at 410 nanometer).
!
!------------------------------------------------------------------------------
! Fecal and detritus Parameters. Unless specified, [Nfec] values are
! expected. This file is configured for Nfec.
!------------------------------------------------------------------------------
!
! WF Fecal sinking flux,
! (meters/day)
!
! RegTbase Fecal regeneration temperature base for exponential response
! to temperature, (Celsius).
!
! RegTfac Fecal regeneration exponential temperature factor,
! (1/Celsius).
!
! RegCR Fecal carbon regeneration rate,
! (1/day).
!
! RegNR Fecal nitrogen regeneration rate,
! (1/day).
!
! RegSR Fecal silica regeneration rate,
! (1/day).
!
! RegPR Fecal phosphorus regeneration rate,
! (1/day).
!
! RegFR Fecal iron regeneration rate,
! (1/day)
!
! Marta Rodrigues
!-----------------------------------------------------------------------------
! Zooplankton group parameters. Unless specified [Nzoo] values are expected.
! This file is configured for Nzoo
!-----------------------------------------------------------------------------
!
! zoo_sp Zooplankton flag for zooplankton maximum growth rate
! calculations(1-Acartia tonsa, naupilus; 2-Acartia tonsa,
! copepodites; 3-Acartia clausi, naupilus; 4-Acartia clausi,
! copepodites).
!
! ZooDOC Proportion of zooplankton which is apportioned to DOM
! (nondimensional), [Nzoo] values are expected.
!
! ZooPEL Proportion of zooplankton which is apportioned to fecal
! pellets (nondimensional), [Nzoo,NFec] values are expected.
!
! ZooCYC Proportion of zooplankton which is apportioned to direct
! remineralization (nondimensional).
!
! DeltaZoo Availability of prey to predator (nondimensional),
! [Nzoo, Nphy] values are expected.
!
! EfcCap Capture efficiency of zooplankton (nondimensional),
! [Nzoo, Nphy] values are expected.
!
! HsZoo Half-saturation constant for total food ingestion
! (micromole_C/liter).
!
! EfcPrd Assimilation efficiency of zooplankton's predators
! (nondimensional).
!
! ExZoo Zooplankton excretion rate (1/day).
!
! GZ Zooplankton losses due to natural mortality and predation
! (1/day).