! ! EcoSim Biological Model Parameters. ! !svn $Id$ !========================================================= Hernan G. Arango === ! Copyright (c) 2002-2009 The ROMS/TOMS Group W. Paul Bissett ! ! Licensed under a MIT/X style license ! ! See License_ROMS.txt ! !============================================================================== ! ! ! Input parameters can be entered in ANY order, provided that the parameter ! ! KEYWORD (usually, upper case) is typed correctly followed by "=" or "==" ! ! symbols. Any comment lines are allowed and must begin with an exclamation ! ! mark (!) in column one. Comments may appear to the right of a parameter ! ! specification to improve documentation. Comments will be ignored during ! ! reading. Blank lines are also allowed and ignored. Continuation lines in ! ! a parameter specification are allowed and must be preceded by a backslash ! ! (\). In some instances, more than one value is required for a parameter. ! ! If fewer values are provided, the last value is assigned for the entire ! ! parameter array. The multiplication symbol (*), without blank spaces in ! ! between, is allowed for a parameter specification. For example, in a two ! ! grids nested application: ! ! ! ! AKT_BAK == 2*1.0d-6 2*5.0d-6 ! m2/s ! ! ! ! indicates that the first two entries of array AKT_BAK, in fortran column- ! ! major order, will have the same value of "1.0d-6" for grid 1, whereas the ! ! next two entries will have the same value of "5.0d-6" for grid 2. ! ! ! ! In multiple levels of nesting and/or multiple connected domains step-ups, ! ! "Ngrids" entries are expected for some of these parameters. In such case, ! ! the order of the entries for a parameter is extremely important. It must ! ! follow the same order (1:Ngrids) as in the state variable declaration. The ! ! USER may follow the above guidelines for specifying his/her values. These ! ! parameters are marked by "==" plural symbol after the KEYWORD. ! ! ! !=============================================================================! ! ! Switch to control the computation of EcoSim within nested and/or multiple ! connected grids. Lbiology == T ! Maximum number of iterations to achieve convergence of the nonlinear ! solution. BioIter == 1 ! Logical switch (T/F) to calculate CDOC UV photolysis. RtUVR_flag == T ! Logical switch (T/F) to calculate temperature based nitrogen fixation. NFIX_flag == F ! Logical switch (T/F) to calculate fecal matter regeneration. Regen_flag == T !----------------------------------------------------------------------------- ! Phytoplankton group parameters. !----------------------------------------------------------------------------- ! ! Half-saturation for phytoplankton NO3 uptake (micromole_NO3/liter), ! [Nphy,Ngrids] values are expected. HsNO3 == 8.2400d-01 4.1200d-01 8.2400d-01 1.6700d-01 ! Half-saturation for phytoplankton NH4 uptake (micromole_NH4/liter), ! [Nphy,Ngrids] values are expected. HsNH4 == 4.1400d-01 2.0800d-01 4.1400d-01 8.3000d-02 ! Half-saturation for phytoplankton SiO uptake (micromole_SiO/liter), ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. HsPO4 == 5.1500d-02 2.5750d-02 5.1500d-02 1.0438d-02 ! Half-saturation for phytoplankton Fe uptake (micromole_Fe/liter), ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. GtALG_max == 3.7000d+00 3.7000d+00 2.0000d+00 2.0000d+00 ! Phytoplankton temperature base for exponential response to temperature ! (Celsius), [Nphy,Ngrids] values are expected. PhyTbase == 4*27.0d0 ! Phytoplankton exponential temperature factor (1/Celsius), ! [Nphy,Ngrids] values are expected. PhyTfac == 4*0.0633d0 ! Nitrate uptake inhibition for NH4 (l/micromole), ! [Nphy,Ngrids] values are expected. BET_ == 1.2800d+00 2.6000d+00 1.2800d+00 6.5000d+00 ! Maximum phytoplankton C:N ratio (micromole_C/micromole_N), ! [Nphy,Ngrids] values are expected. maxC2nALG == 1.4000d+01 1.7750d+01 1.7000d+01 6.6250d+00 ! Balanced phytoplankton C:N ratio (micromole_C/micromole_N), ! [Nphy,Ngrids] values are expected. minC2nALG == 6.6250d+00 6.6250d+00 6.6250d+00 6.6250d+00 ! Absolute minimum phytoplankton C:N ratio (micromole_C/micromole_N), ! [Nphy,Ngrids] values are expected. C2nALGminABS == 5.5000d+00 5.5000d+00 5.5000d+00 5.5000d+00 ! Maximum phytoplankton C:Si ratio (micromole_C/micromole_Si), ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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) ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. minC2pALG == 1.0600d+02 1.0600d+02 1.0600d+02 1.0600d+02 ! Absolute minimum phytoplankton C:P ratio (micromole_C/micromole_P), ! [Nphy,Ngrids] values are expected. C2pALGminABS == 8.800d+01 8.800d+01 8.800d+01 8.800d+01 ! Maximum phytoplankton C:Fe ratio (micromole_C/micromole_Fe), ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. qu_yld == 8.3300d-02 8.3300d-02 8.3300d-02 8.3300d-02 ! Compensation light level (micromole_quanta), ! [Nphy,Ngrids] values are expected. E0_comp == 1.0000d+01 1.0000d+01 1.0000d+01 6.0000d+00 ! Light level for onset of photoinhibition (micromole_quanta), ! [Nphy,Ngrids] values are expected. E0_inhib == 1.0000d+04 1.0000d+04 1.0500d+02 1.0000d+04 ! Exponential decay factor for light limited growth (1/micromole_quanta), ! [Nphy,Ngrids] values are expected. 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), [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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), [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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)], ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. 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), [Nphy,Ngrids] values are expected. FecDOC == 3.3330d-01 3.3330d-01 3.3330d-01 4.1670d-01 ! Proportion of grazing stress that is apportioned to fecal ! (nondimensional), [Nphy,Nfec,Ngrids] values are expected. FecPEL == 3*1.6670d-01 8.3350d-02 3*1.6670d-01 8.3350d-02 ! Proportion of grazing stress that is recycled (nondimensional), ! [Nphy,Ngrids] values are expected. FecCYC == 3.3330d-01 3.3330d-01 3.3330d-01 4.1660d-01 ! Proportion of daily production that is lost to excretion ! (nondimensional), [Nphy,Ngrids] values are expected. ExALG == 5.0000d-03 5.0000d-03 5.0000d-03 5.0000d-03 ! Phytoplankton sinking speed (meters/day), ! [Nphy,Ngrids] values are expected. WS == 0.0000d+00 0.0000d+00 0.0000d+00 0.0000d+00 ! Phytoplankton grazing parameter (nondimensional). ! [Nphy,Ngrids] values are expected. HsGRZ == 0.0100d+00 0.0100d+00 0.0100d+00 0.0100d+00 ! Refuge Phytoplankton population (micromole_C/liter), ! [Nphy,Ngrids] values are expected. MinRefuge == 2.0000d-02 2.0000d-02 2.0000d-02 2.0000d-02 ! Maximum Refuge Phytoplankton depth (meters), ! [Nphy,Ngrids] values are expected. RefugeDep == 4.0000d+01 4.0000d+01 4.0000d+01 4.0000d+01 ! Normalized Volume factor (nondimensional), ! [Nphy,Ngrids] values are expected. (1 micron diameter cell = 1). Norm_Vol == 7.2398d+01 7.2398d+01 7.2398d+01 4.6370d+00 ! Normalized Surface Area factor (nondimensional), ! [Nphy,Ngrids] values are expected. (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), ! [Nphy,Ngrids] values are expected. HsDOP == 1.0000d-05 1.0000d-05 2.0000d+00 1.0000d-05 ! C:P ratio where DOP uptake begins (micromole_C/micromole_P), ! [Nphy,Ngrids] values are expected. 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), ! [Nphy,Ngrids] values are expected. HsDON == 1.0000d-05 1.0000d-05 2.0000d+00 1.0000d-05 ! C:N ratio where DON uptake begins (micromole_C/micromole_N), ! [Nphy,Ngrids] values are expected. Values above maxC2nALG denote ! no DOP uptake. C2nNupDON == 5.0000d+02 5.0000d+02 1.4000d+01 5.0000d+02 !----------------------------------------------------------------------------- ! Bacteria group parameters. !----------------------------------------------------------------------------- ! ! Half saturation constant for bacteria DOC uptake (micromole_DOC/liter), ! [Nbac,Ngrids] values are expected. HsDOC_ba == 130.0d+00 ! Maximum 24 hour bacterial growth rate (1/day), ! [Nbac,Ngrids] values are expected. GtBAC_max == 2.0d+00 ! Bacteria temperature base for exponential response to temperature ! (Celsius), [Nbac,Ngrids] values are expected. BacTbase == 27.0d+0 ! Bacteria exponential temperature factor (1/Celsius), ! [Nbac,Ngrids] values are expected. BacTfac == 0.092d+00 ! Carbon to Nitrogen ratio of Bacteria (micromole_C/micromole_N), ! [Ngrids] values are expected. C2nBAC == 5.0d+00 ! Carbon to Phosphorus ratio of Bacteria (micromole_C/micromole_P) ! [Ngrids] values are expected. C2pBAC == 60.0d+00 ! Carbon to Iron ratio of Bacteria (micromole_C/micromole_Fe), ! [Ngrids] values are expected. C2FeBAC == 1000.0d+00 ! Proportion of bacteria grazing stress that is apportioned to DOM ! (nondimensional), [Ngrids] values are expected. BacDOC == 4.583d-01 ! Proportion of bacteria grazing stress that is apportioned to fecal ! (nondimensional), [Ngrids] values are expected. BacPEL == 8.340d-02 ! Proportion of bacteria grazing stress that is recycled ! (nondimensional), [Ngrids] values are expected. BacCYC == 4.583d-01 ! Bacterial recalcitrant carbon excretion as a proportion of uptake ! (nondimensional), [Ngrids] values are expected. ExBAC_c == 4.0d-02 ! Bacterial recalcitrant excretion carbon to nitrogen ratio ! (micromole_C/micromole_N), [Ngrids] values are expected. ExBacC2N == 15.0d0 ! Bacterial gross growth carbon efficiency (nondimensional), ! [Ngrids] values are expected. Bac_Ceff == 0.3d0 ! Maximum nitrification rate (1/day), ! [Ngrids] values are expected. RtNIT == 0.4d0 ! Half-saturation constant for bacterial nitrification (micromole_NH4/liter), ! [Ngrids] values are expected. HsNIT == 0.1d0 !----------------------------------------------------------------------------- ! DOM group parameters. !----------------------------------------------------------------------------- ! ! Colored fraction of DOC from phytoplankton and bacterial losses ! (nondimensional), [Ndom,Ngrids] values are expected cDOCfrac_c == 0.0323d0 0.0930d0 ! UV degradation of DOC into DIC ! (micromole/meter/liter/hour at 410 nm), ! [Ngrids] values are expected. RtUVR_DIC == 0.0193d0 ! UV degradation of DOC to colorless labile DOC ! (micromole/meter/liter/hour at 410 nm), ! [Ngrids] values are expected. RtUVR_DOC == 0.0034d0 !----------------------------------------------------------------------------- ! Fecal and detritus group parameters. !----------------------------------------------------------------------------- ! ! Fecal sinking flux (meters/day), ! [Nfec,Ngrids] values are expected. WF == 0.0d0 100.0d0 ! Fecal regeneration temp base for exponential response to tempemperaute ! (Celsius), [Nfec,Ngrids] values are expected. RegTbase == 2*27.0d0 ! Fecal regeneration exponential temperature factor, ! (1/Celsius), [Nfec,Ngrids] values are expected. RegTfac == 2*0.092d0 ! Fecal carbon regeneration rate (1/day), ! [Nfec,Ngrids] values are expected. RegCR == 0.10d0 0.0d0 ! Fecal nitrogen regeneration rate (1/day), ! [Nfec,Ngrids] values are expected. RegNR == 0.10d0 0.0d0 ! Fecal silica regeneration rate (1/day), ! [Nfec,Ngrids] values are expected. RegSR == 0.13d0 0.0d0 ! Fecal phosphorus regeneration rate (1/day), ! [Nfec,Ngrids] values are expected. RegPR == 0.10d0 0.0d0 ! Fecal iron regeneration rate (1/day), ! [Nfec,Ngrids] values are expected. RegFR == 0.10d0 0.0d0 !----------------------------------------------------------------------------- ! Physical and output parameters !----------------------------------------------------------------------------- ! Harmonic/biharmonic horizontal diffusion of biological tracer for ! nonlinear model and adjoint-based algorithms: [NBT,Ngrids] values are ! 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 for nonlinear model and ! basic state scale factor in adjoint-based algorithms: [NBT,Ngrids] values ! are expected. AKT_BAK == 61*1.0d-6 ! m2/s ad_AKT_BAK == 61*1.0d0 ! nondimensional ! Nudging/relaxation time scales, inverse scales will be computed internally, ! [NBT,Ngrids] values are expected. TNUDG == 61*0.0d0 ! days ! Logical switches (TRUE/FALSE) to specify which variables to consider on ! tracers point Sources/Sinks (like river runoff): [NBT,Ngrids] values are ! expected. See glossary below for details. LtracerSrc == 61*F ! Logical switches (T/F) to write biological tracers into output NetCDF ! files, [NBT,Ngrids] values are expected. Hout(idTvar) == 61*T ! biological tracer Hout(idTsur) == 61*F ! surface tracer flux ! ! GLOSSARY: ! ========= ! !============================================================================== ! EcoSim Biological Model Parameters. It is configured with 61 biological ! tracers by default: ! ! idbio( 1) DIC concentration ! idbio( 2) Iron concentration ! idbio( 3) Ammonium concentration ! idbio( 4) Nitrate concentration ! idbio( 5) Phosphate concentration ! idbio( 6) Silica concentration ! idbio( 7) Bacteria, Carbon Group 1 ! idbio( 8) Bacteria, Iron Group 1 ! idbio( 9) Bacteria, Nitrogen Group 1 ! idbio(10) Bacteria, Phosphorus Group 1 ! idbio(11) Color degradational matter, Carbon Group 1 ! idbio(12) Dissolved organic matter, Carbon Group 1 ! idbio(13) Dissolved organic matter, Nitrogen Group 1 ! idbio(14) Dissolved organic matter, Phosphorus Group 1 ! idbio(15) Color degradational matter, Carbon Group 2 ! idbio(16) Dissolved organic matter, Carbon Group 2 ! idbio(17) Dissolved organic matter, Nitrogen Group 2 ! idbio(18) Dissolved organic matter, Phosphorus Group 2 ! idbio(19) Fecal matter, Carbon Group 1 ! idbio(20) Fecal matter, Iron Group 1 ! idbio(21) Fecal matter, Nitrogen Group 1 ! idbio(22) Fecal matter, Phosphorus Group 1 ! idbio(23) Fecal matter, Silica Group 1 ! idbio(24) Fecal matter, Carbon Group 2 ! idbio(25) Fecal matter, Iron Group 2 ! idbio(26) Fecal matter, Nitrogen Group 2 ! idbio(27) Fecal matter, Phosphorus Group 2 ! idbio(28) Fecal matter, Silica Group 2 ! idbio(29) Small diatom, Carbon Group ! idbio(30) Small diatom, Iron Group ! idbio(31) Small diatom, Nitrogen Group ! idbio(32) Small diatom, Phosphorus Group ! idbio(33) Large diatom, Carbon Group ! idbio(34) Large diatom, Iron Group ! idbio(35) Large diatom, Nitrogen Group ! idbio(36) Large diatom, Phosphorus Group ! idbio(37) Large dinoflagellate, Carbon Group ! idbio(38) Large dinoflagellate, Iron Group ! idbio(39) Large dinoflagellate, Nitrogen Group ! idbio(40) Large dinoflagellate, Phosphorus Group ! idbio(41) Synechococcus, Carbon Group ! idbio(42) Synechococcus, Iron Group ! idbio(43) Synechococcus, Nitrogen Group ! idbio(44) Synechococcus, Phosphorus Group ! idbio(45) Small diatom, Silica Group ! idbio(46) Large diatom, Silica Group ! idbio(47) Small diatom, chlorophyll-a ! idbio(48) Large diatom, chlorophyll-a ! idbio(49) Large dinoflagellate, chlorophyll-a ! idbio(50) Synechococcus, chlorophyll-a ! idbio(51) Small diatom, chlorophyll-c ! idbio(52) Large diatom, chlorophyll-c ! idbio(53) Large dinoflagellate, chlorophyll-c ! idbio(54) Small diatom, photosynthetic carotenoids ! idbio(55) Large diatom, photosynthetic carotenoids ! idbio(56) Large dinoflagellate, photosynthetic carotenoids ! idbio(57) Small diatom, photoprotective carotenoids ! idbio(58) Large diatom, photoprotective carotenoids ! idbio(59) Large dinoflagellate, photoprotective carotenoids ! idbio(60) Synechococcus, photoprotective carotenoids ! idbio(61) Synechococcus, high urobilin phycoeurythin carotenoids ! !============================================================================== ! ! 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. !------------------------------------------------------------------------------ ! ! Lbiology Switch to control the computation of a particular module ! within nested and/or multiple connected grids. By default ! this switch is set to TRUE in "mod_scalars" 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. ! ! 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,Ngrids] values are ! expected. 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 !------------------------------------------------------------------------------ ! ! 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,Ngrids] 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, [Ngrids] values are expected. This ! file is configured for Nbac=1 and Ngrids=1. !------------------------------------------------------------------------------ ! ! HsDOC_ba Half saturation constant for bacteria DOC uptake, ! (micromole_DOC/liter). ! [Nbac,Ngrids] values are expected. ! ! GtBAC_max Maximum 24 hour bacterial growth rate, ! (1/day). ! [Nbac,Ngrids] values are expected. ! ! BacTbase Phytoplankton temperature base for exponential response to ! temperature, (Celsius). ! [Nbac,Ngrids] values are expected. ! ! BacTfac Phytoplankton exponential temperature factor, ! (1/Celsius). ! [Nbac,Ngrids] 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, [Ngrids] values are expected. This ! file is configured for Ndom=2 and Ngrids=1. !------------------------------------------------------------------------------ ! ! cDOCfrac_c Colored fraction of DOC production from phytoplankton and ! bacterial losses, (nondimensional). ! [Ndom,Ngrids] 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,Ngrids] values are ! expected. This file is configured for Nfec=2 and Ngrids=1. !------------------------------------------------------------------------------ ! ! 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) ! !------------------------------------------------------------------------------ ! Physical parameters. This file is configured for NBT=61. !------------------------------------------------------------------------------ ! ! TNU2 Nonlinear model lateral, harmonic, constant, mixing ! coefficient (m2/s) for biological tracer variables; ! [1:NBT,1:Ngrids] values are expected. If variable ! horizontal diffusion is activated, TNU2 is the mixing ! coefficient for the largest grid-cell in the domain. ! ! TNU4 Nonlinear model lateral, biharmonic, constant, mixing ! coefficient (m4/s) for biological tracer variables; ! [1:NBT,1:Ngrids] values are expected. If variable ! horizontal diffusion is activated, TNU4 is the mixing ! coefficient for the largest grid-cell in the domain. ! ! ad_TNU2 Adjoint-based algorithms lateral, harmonic, constant, ! mixing coefficient (m2/s) for biological tracer variables; ! [1:NBT,1:Ngrids] values are expected. If variable ! horizontal diffusion is activated, ad_TNU2 is the mixing ! coefficient for the largest grid-cell in the domain. ! ! ad_TNU4 Adjoint-based algorithms lateral, biharmonic, constant, ! mixing coefficient (m4/s) for biological tracer variables; ! [1:NBT,1:Ngrids] values are expected. If variable ! horizontal diffusion is activated, ad_TNU4 is the mixing ! coefficient for the largest grid-cell in the domain. ! ! AKT_BAK Background vertical mixing coefficient (m2/s) for biological ! tracer variables, [1:NBT,1:Ngrids] values are expected. ! ! ! ad_AKT_fac Adjoint-based algorithms vertical mixing, basic state, ! scale factor (nondimensional) for biological tracer ! variables; [1:NBT,1:Ngrids] values are expected. In ! some applications, a smaller/larger values of vertical ! mixing are necessary for stability. It is only used ! when FORWARD_MIXING is activated. ! ! TNUDG Nudging time scale (days), [1:NBT,1:Ngrids]. Inverse scale ! will be computed internally. ! !------------------------------------------------------------------------------ ! Tracer point Sources/Sink sources switches. !------------------------------------------------------------------------------ ! ! LtracerSrc Logical switches (T/F) to specify which tracer variables ! to consider when the option TS_PSOURCE is activated; ! [1:NBT,1:Ngrids] values are expected. ! ! LtracerSrc(idbio( 1),ng) ! ... ... ! LtracerSrc(idbio(NBT),ng) ! ! Recall that TS_PSOURCE is usually activated to add river ! runoff as a point source. At minimum, it is necessary to ! specify both temperature and salinity for all rivers. The ! other tracers are optional. The user needs to know the ! correspondence between biological variables and indices ! idbio(1:NBT) when activating one or more of these switches. ! ! This logical switch REPLACES and ELIMINATES the need to ! have or read the variable "river_flag(river)" in the input ! rivers forcing NetCDF file: ! ! double river_flag(river) ! river_flag:long_name = "river runoff tracer flag" ! river_flag:option_0 = "all tracers are off" ! river_flag:option_1 = "only temperature" ! river_flag:option_2 = "only salinity" ! river_flag:option_3 = "both temperature and salinity" ! river_flag:units = "nondimensional" ! ! This logic was too cumbersome and complicated when ! additional tracers are considered. However, this change ! is backward compatible. ! ! The LtracerSrc switch will be used to activate the reading ! of respective tracer variable from input river forcing ! NetCDF file. If you want to add other tracer variables ! (other than temperature and salinity) as a source for a ! particular river(s), you just need to specify such values ! on those river(s). Then, set the values to ZERO on the ! other river(s) that do NOT require such river forcing for ! that tracer. Recall that you need to specify the tracer ! values for all rivers, even if their values are zero. ! !------------------------------------------------------------------------------ ! Logical switches (T/F) to activate writing of fields into output files. !------------------------------------------------------------------------------ ! ! Hout Logical switches to write out biological tracers into ! output NetCDF files, [1:NBT,1:Ngrids] values are ! expected. ! ! Hout(idTvar) biological tracers ! Hout(idTsur) biological tracers surface flux !