!
! EcoSim Biological Model Parameters.
!
!svn $Id: ecosim.in 889 2018-02-10 03:32:52Z arango $
!========================================================= Hernan G. Arango ===
! Copyright (c) 2002-2019 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
! Logical switches (TRUE/FALSE) to increase/decrease horizontal diffusivity
! in specific areas of the application domain (like sponge areas) for the
! desired grid: [Ngrids]
LtracerSponge == 61*F
! 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
! Set lateral boundary conditions keyword. Notice that 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.
!
! NOTICE: 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 in 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 (TRUE/FALSE) to activate biological tracers point
! Sources/Sinks (like river runoff) and to specify which tracer variables
! to consider: [NBT,Ngrids] values are expected. See glossary below for
! details.
LtracerSrc == 61*F
! Logical switches (TRUE/FALSE) to read and process biological tracer
! climatology fields: [NBT,Ngrids] values are expected. See glossary below
! for details.
LtracerCLM == 61*F
! Logical switches (TRUE/FALSE) to nudge the desired biological tracer
! climatology field. If not analytical climatology fields, users need to
! turn on the logical switches above to process the fields from the
! climatology NetCDF file that are needed for nudging; [NBT,Ngrids]
! values are expected. See glossary below for details.
LnudgeTCLM == 61*F
! Logical switches (TRUE/FALSE) to write biological fields into HISTORY output
! file, [NBT,Ngrids] values are expected.
Hout(idTvar) == 61*T ! ..., DIC, ... biological tracer
Hout(idTsur) == 61*F ! ..., DIC_sflux, ... surface tracer flux
! Logical switches (TRUE/FALSE) to write biological fields into QUICKSAVE
! output file, [NBT,Ngrids] values are expected.
Qout(idTvar) == 61*F ! ..., DIC, ... biological tracer
Qout(idsurT) == 61*F ! ..., DIC_sur, ... surface bological tracer
Qout(idTsur) == 61*F ! ..., DIC_sflux, ... surface tracer flux
! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
! into AVERAGE output file, [NBT,Ngrids] values are expected.
Aout(idTvar) == 61*T ! ..., DIC, ... biological tracer
Aout(idTTav) == 61*F ! ..., DIC_2, ... quadratic <t*t> tracer terms
Aout(idUTav) == 61*F ! ..., u_DIC, ... quadratic <u*t> tracer terms
Aout(idVTav) == 61*F ! ..., v_DIC, ... quadratic <v*t> tracer terms
Aout(iHUTav) == 61*F ! ..., Huon_DIC, ... tracer volume flux, <Huon*t>
Aout(iHVTav) == 61*F ! ..., Hvom_DIC, ... tracer volume flux, <Hvom*t>
! Logical switches (TRUE/FALSE) to activate writing of time-averaged,
! biological tracer diagnostic terms into DIAGNOSTIC output file:
! [1:NBT,Ngrids].
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
!
! GLOSSARY:
! =========
!
!==============================================================================
! EcoSim Biological Model Parameters. It is configured with 61 biological
! tracers by default:
!
! idbio( 1) DIC DIC concentration
! idbio( 2) FeO Iron concentration
! idbio( 3) NH4 Ammonium concentration
! idbio( 4) NO3 Nitrate concentration
! idbio( 5) PO4 Phosphate concentration
! idbio( 6) SiO Silica concentration
! idbio( 7) Bac_C1 Bacteria, Carbon Group 1
! idbio( 8) Bac_F1 Bacteria, Iron Group 1
! idbio( 9) Bac_N1 Bacteria, Nitrogen Group 1
! idbio(10) Bac_P1 Bacteria, Phosphorus Group 1
! idbio(11) CDM_C1 Color degradational matter, Carbon Group 1
! idbio(12) DOM_C1 Dissolved organic matter, Carbon Group 1
! idbio(13) DOM_N1 Dissolved organic matter, Nitrogen Group 1
! idbio(14) DOM_P1 Dissolved organic matter, Phosphorus Group 1
! idbio(15) CDM_C2 Color degradational matter, Carbon Group 2
! idbio(16) DOM_C2 Dissolved organic matter, Carbon Group 2
! idbio(17) DOM_N2 Dissolved organic matter, Nitrogen Group 2
! idbio(18) DOM_P2 Dissolved organic matter, Phosphorus Group 2
! idbio(19) Fec_C1 Fecal matter, Carbon Group 1
! idbio(20) Fec_F1 Fecal matter, Iron Group 1
! idbio(21) Fec_N1 Fecal matter, Nitrogen Group 1
! idbio(22) Fec_P1 Fecal matter, Phosphorus Group 1
! idbio(23) Fec_S1 Fecal matter, Silica Group 1
! idbio(24) Fec_C2 Fecal matter, Carbon Group 2
! idbio(25) Fec_F2 Fecal matter, Iron Group 2
! idbio(26) Fec_N2 Fecal matter, Nitrogen Group 2
! idbio(27) Fec_P2 Fecal matter, Phosphorus Group 2
! idbio(28) Fec_S2 Fecal matter, Silica Group 2
! idbio(29) Phy_C1 Small diatom, Carbon Group 1
! idbio(30) Phy_F1 Small diatom, Iron Group 1
! idbio(31) Phy_N1 Small diatom, Nitrogen Group 1
! idbio(32) Phy_P1 Small diatom, Phosphorus Group 1
! idbio(33) Phy_C2 Large diatom, Carbon Group 2
! idbio(34) Phy_F2 Large diatom, Iron Group 2
! idbio(35) Phy_N2 Large diatom, Nitrogen Group 2
! idbio(36) Phy_P2 Large diatom, Phosphorus Group 2
! idbio(37) Phy_C3 Large dinoflagellate, Carbon Group 3
! idbio(38) Phy_F3 Large dinoflagellate, Iron Group 3
! idbio(39) Phy_N3 Large dinoflagellate, Nitrogen Group 3
! idbio(40) Phy_P3 Large dinoflagellate, Phosphorus Group 3
! idbio(41) Phy_C4 Synechococcus, Carbon Group 4
! idbio(42) Phy_F4 Synechococcus, Iron Group 4
! idbio(43) Phy_N4 Synechococcus, Nitrogen Group 4
! idbio(44) Phy_P4 Synechococcus, Phosphorus Group 4
! idbio(45) Phy_S1 Small diatom, Silica Group 1
! idbio(46) Phy_S2 Large diatom, Silica Group 2
! idbio(47) Pigs_11 Small diatom, chlorophyll-a
! idbio(48) Pigs_21 Large diatom, chlorophyll-a
! idbio(49) Pigs_31 Large dinoflagellate, chlorophyll-a
! idbio(50) Pigs_41 Synechococcus, chlorophyll-a
! idbio(51) Pigs_13 Small diatom, chlorophyll-c
! idbio(52) Pigs_23 Large diatom, chlorophyll-c
! idbio(53) Pigs_33 Large dinoflagellate, chlorophyll-c
! idbio(54) Pigs_14 Small diatom, photosynthetic carotenoids
! idbio(55) Pigs_24 Large diatom, photosynthetic carotenoids
! idbio(56) Pigs_34 Large dinoflagellate, photosynthetic carotenoids
! idbio(57) Pigs_15 Small diatom, photoprotective carotenoids
! idbio(58) Pigs_25 Large diatom, photoprotective carotenoids
! idbio(59) Pigs_35 Large dinoflagellate, photoprotective carotenoids
! idbio(60) Pigs_45 Synechococcus, photoprotective carotenoids
! idbio(61) Pigs_47 Synechococcus, 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.
!
! LtracerSponge Logical switches (TRUE/FALSE) to increase/decrease horizontal
! diffusivity of biological tracers in specific areas of the
! domain. It can be used to specify sponge areas with larger
! horizontal mixing coefficients for damping of high
! frequency noise due to open boundary conditions or nesting.
! The CPP option SPONGE is now deprecated and replaced with
! this switch to facilitate or not sponge areas over a
! particular nested grid; [1:NBT,1:Ngrids] values are
! expected.
!
! The horizontal mixing distribution is specified in
! "ini_hmixcoef.F" as:
!
! diff2(i,j,itrc) = diff_factor(i,j) * diff2(i,j,itrc)
! diff4(i,j,itrc) = diff_factor(i,j) * diff4(i,j,itrc)
!
! The variable "diff_factor" can be read from the grid
! NetCDF file. Alternately, the horizontal diffusion in the
! sponge area can be set-up with analytical functions in
! "ana_sponge.h" using CPP ANA_SPONGE when these switches
! are turned ON for a particular grid.
!
! 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.
!
!------------------------------------------------------------------------------
! Lateral boundary conditions parameters.
!------------------------------------------------------------------------------
!
! The lateral boundary conditions are now specified with logical switches
! instead of CPP flags to allow nested grid configurations. Their values are
! load into structured array:
!
! LBC(1:4, nLBCvar, Ngrids)
!
! where 1:4 are the number of boundary edges, nLBCvar are the number LBC state
! variables, and Ngrids is the number of nested grids. For Example, to apply
! gradient boundary conditions to any tracer we use:
!
! LBC(iwest, isTvar(itrc), ng) % gradient
! LBC(ieast, isTvar(itrc), ng) % gradient
! LBC(isouth, isTvar(itrc), ng) % gradient
! LBC(inorth, isTvar(itrc), ng) % gradient
!
! The lateral boundary conditions for biological tracers are entered with
! a keyword. This 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.
!
! It is possible to specify the lateral boundary conditions for all biological
! tracers in a compact form with a single entry. for example, in a East-West
! periodic application we can just have:
!
! 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
!
! Then, the standard input processing routine will assume that all the
! biological tracers have the same lateral boundary condition specified by
! 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
!
! LBC(isTvar) Biological Tracers, [1:4, 1:NBT, Ngrids] values are expected.
!
! Similarly, the adjoint-based algorithms (ADM, TLM, RPM) can have different
! lateral boundary conditions keywords:
!
! ad_LBC(isTvar) Biological Tracers, [1:4, 1:NBT, Ngrids] values are expected.
!
!------------------------------------------------------------------------------
! Tracer point Sources/Sink sources switches: [1:NBT,1:Ngrids].
!------------------------------------------------------------------------------
!
! LtracerSrc Logical switches (T/F) to activate biological tracer
! variables point Sources/Sinks.
!
! LtracerSrc(idbio( 1),ng)
! ... ...
! LtracerSrc(idbio(NBT),ng)
!
! Recall that these switches are 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.
!
! These logical switches 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.
!
!------------------------------------------------------------------------------
! Tracer climatology processing switches: [1:NBT,1:Ngrids].
!------------------------------------------------------------------------------
!
! LtracerCLM Logical switches (T/F) to process biological tracer variables
! climatology. The CPP option TCLIMATOLOGY is now obsolete
! and replaced with these switches to facilitate nesting
! applications. Currently, the CLIMA(ng)%tclm is used for
! horizontal mixing, sponges, and nudging.
!
! LtracerCLM(idbio( 1),ng)
! ... ...
! LtracerCLM(idbio(NBT),ng)
!
! These switches also controls which climatology tracer
! fields needs to be processed. So we may reduce the
! memory allocation for the CLIMA(ng)%tclm array.
!
!------------------------------------------------------------------------------
! Logical switches for nudging to climatology: [1:NBT,1:Ngrids].
!------------------------------------------------------------------------------
!
! LnudgeTCLM Logical switches (T/F) to activate the nugding of biological
! tracer variables climatology. These switches also control
! which biological tracer variables to nudge. The CPP option
! TCLM_NUDGING is now obsolete and replaced with these
! switches to facilitate nesting.
!
! LnudgeTCLM(idbio( 1),ng)
! ... ...
! LnudgeTCLM(idbio(NBT),ng)
!
! User also needs to TURN ON the respective logical switches
! "LtracerCLM", described above, to process the required 3D
! biological tracer climatology data. This data can be set
! with analytical functions (ANA_TCLIMA) or read from input
! climatology NetCDF file(s).
!
! The nudging coefficients CLIMA(ng)%Tnudgcof can be set
! with analytical functions in "ana_nudgcoef.h" using CPP
! option ANA_NUDGCOEF. Otherwise, it will be read from
! NetCDF file NUDNAME.
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate writing of fields into HISTORY file.
!------------------------------------------------------------------------------
!
! Hout Logical switches to write out biological fields into
! output HISTORY NetCDF file, [1:NBT,1:Ngrids] values
! are expected:
!
! Hout(idTvar) biological tracers
! Hout(idTsur) biological tracers surface flux
!
! The idTvar(idbio(:)) and idTsur(idbio(:)) indices are
! provided above.
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate writing of fields into QUICKSAVE file.
!------------------------------------------------------------------------------
!
! Qout Logical switches to write out biological fields into
! output QUICKSAVE NetCDF file, [1:NBT,1:Ngrids] values
! are expected:
!
! Qout(idTvar) biological tracers
! Qout(idsurT) surface biological tracers
! Qout(idTsur) biological tracers surface flux
!
! The idTvar(idbio(:)), idsurR(idbio(:)), and
! idTsur(idbio(:)) indices are provided above.
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate writing of fields into AVERAGE file.
!------------------------------------------------------------------------------
!
! Aout Logical switches to write out biological fields into
! output AVERAGE NetCDF file, [1:NBT,1:Ngrids] values
! are expected:
!
! Aout(idTvar) biological tracers
!
! Aout(idTTav) quadratic <t*t> tracers terms
! Aout(idUTav) quadratic <u*t> tracers terms
! Aout(idVTav) quadratic <v*t> tracers terms
! Aout(iHUTav) tracer u-volume flux, <Huon*t>
! Aout(iHVTav) tracer v-volume flux, <Hvom*t>
!
! The idTvar(idbio(:)) indices are provided above.
!
!------------------------------------------------------------------------------
! Logical switches (T/F) to activate writing of time-averaged fields into
! DIAGNOSTIC file.
!------------------------------------------------------------------------------
!
! Time-averaged, biological tracers diagnostic terms, [1:NBT,Ngrids] values
! expected: (if DIAGNOSTICS_TS)
!
! Dout(idDtrc(idbio(1:NBT),iT....),1:Ngrids)
!
! Dout(iTrate) Write out time rate of change.
! Dout(iThadv) Write out horizontal total advection.
! Dout(iTxadv) Write out horizontal XI-advection.
! Dout(iTyadv) Write out horizontal ETA-advection.
! Dout(iTvadv) Write out vertical advection.
! Dout(iThdif) Write out horizontal total diffusion, if TS_DIF2 or TS_DIF4
! Dout(iTxdif) Write out horizonta1 XI-diffusion, if TS_DIF2 or TS_DIF4.
! Dout(iTydif) Write out horizontal ETA-diffusion, if TS_DIF2 or TS_DIF4.
! Dout(iTsdif) Write out horizontal S-diffusion, if TS_DIF2 or TS_DIF4
! and rotated tensor (MIX_GEO_TS or MIX_ISO_TS).
! Dout(iTvdif) Write out vertical diffusion.
!