! NEMURO Ecosystem Model Parameters.
!
!git $Id$
!svn $Id: nemuro.in 1151 2023-02-09 03:08:53Z arango $
!========================================================= Hernan G. Arango ===
! Copyright (c) 2002-2023 The ROMS/TOMS Group !
! Licensed under a MIT/X style license !
! See License_ROMS.md !
!==============================================================================
! !
! 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. !
! !
!==============================================================================
!
! NOTICE: Input parameter units are specified within brackets and default
! ****** values are specified within braces.
!
! Switch to control the computation of biology within nested and/or multiple
! connected grids.
Lbiology == T
! Maximum number of iterations to achieve convergence of the nonlinear
! solution.
BioIter == 1
! Light attenuation due to seawater [1/m].
AttSW == 0.04d0
! Light attenuation due to phytoplankton, self-shading coefficient,
! [m2/millimole_N].
AttPS == 0.04d0 ! small biomass
AttPL == 0.04d0 ! large biomass
! Fraction of shortwave radiation that is photosynthetically active,
! [nondimensional].
PARfrac == 0.43d0
! Phytoplankton photochemical reaction coefficient, initial slope of
! the P-I curve [1/(W/m2) 1/day].
AlphaPS == 0.01d0 ! small biomass
AlphaPL == 0.01d0 ! large biomass
! Phytoplankton photoinhibition coefficient, [1/(W/m2) 1/day].
BetaPS == 4.5d-4 ! small biomass
BetaPL == 4.5d-4 ! large biomass
! Phytoplankton maximum photosynthetic rate at 0 Celsius [1/day].
VmaxS == 0.4d0 ! small biomass
VmaxL == 0.8d0 ! large biomass
! Phytoplankton half saturation constant for Nitrate [millimole_N/m3].
KNO3S == 1.0d0 ! small biomass
KNO3L == 3.0d0 ! large biomass
! Phytoplankton half saturation constant for Ammonium [millimole_N/m3].
KNH4S == 0.1d0 ! small biomass
KNH4L == 0.3d0 ! large biomass
! Phytoplankton half saturation constant for Silicate [millimole_Si/m3].
KSiL == 6.0d0 ! large biomass
! Phytoplankton Ammonium inhibition coefficient [m3/millimole_N].
PusaiS == 1.5d0 ! small biomass
PusaiL == 1.5d0 ! large biomass
! Phytoplankton temperature coefficient for photosynthetic rate [1/Celsius].
KGppS == 6.93d-2 ! small biomass
KGppL == 6.93d-2 ! large biomass
! Phytoplankton respiration rate at 0 Celsius [1/day].
ResPS0 == 0.03d0 ! small biomass
ResPL0 == 0.03d0 ! large biomass
! Phytoplankton temperature coefficient for respiration [1/Celsius].
KResPS == 0.0519d0 ! small biomass
KResPL == 0.0519d0 ! large biomass
! Phytoplankton ratio of extracellular excretion to photosynthesis
! [nondimensional].
GammaS == 0.135d0 ! small biomass
GammaL == 0.135d0 ! large biomass
! Phytoplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].
MorPS0 == 58.5d-3 ! small biomass
MorPL0 == 29.0d-3 ! large biomass
! Phytoplankton temperature coefficient for mortality [1/Celsius].
KMorPS == 6.93d-2 ! small biomass
KMorPL == 6.93d-2 ! large biomass
! Zooplankton maximum grazing rate at 0 Celsius [1/day].
GRmaxSps == 0.40d0 ! small Zoo on small phy
GRmaxLps == 0.10d0 ! large Zoo on small Phy
GRmaxLpl == 0.40d0 ! large Zoo on large Phy
GRmaxLzs == 0.40d0 ! large Zoo on small Zoo
GRmaxPpl == 0.20d0 ! predator Zoo on large Phy
GRmaxPzs == 0.20d0 ! predator Zoo on small Zoo
GRmaxPzl == 0.20d0 ! predator Zoo on large Zoo
! Zooplankton temperature coefficient for grazing [1/Celsius].
KGraS == 6.93d-2 ! small biomass
KGraL == 6.93d-2 ! large biomass
KGraP == 6.93d-2 ! predator biomass
! Zooplankton Ivlev constant [m3/millimole_N].
LamS == 1.4d0 ! small biomass
LamL == 1.4d0 ! large biomass
LamP == 1.4d0 ! predator biomass
! Zooplankton half-saturation coefficient (squared) for ingestion used
! only when the Holling-type grazing formulation is activated
! [millimole_N/m3]^2.
KPS2ZS == 0.16d0 ! small Zoo on small Phy
KPS2ZL == 0.16d0 ! large Zoo on small Phy
KPL2ZL == 0.16d0 ! large Zoo on large Phy
KZS2ZL == 0.16d0 ! large Zoo on small Zoo
KPL2ZP == 0.16d0 ! predator Zoo on large Phy
KZS2ZP == 0.16d0 ! predator Zoo on small Zoo
KZL2ZP == 0.16d0 ! predator Zoo on large Zoo
! Zooplankton threshold value for grazing [millimole_N/m3].
PS2ZSstar == 4.3d-2 ! small Zoo on small Phy
PS2ZLstar == 4.0d-2 ! large Zoo on small Phy
PL2ZLstar == 4.0d-2 ! large Zoo on large Phy
ZS2ZLstar == 4.0d-2 ! large Zoo on small Zoo
PL2ZPstar == 4.0d-2 ! predator Zoo on large Phy
ZS2ZPstar == 4.0d-2 ! predator Zoo on small Zoo
ZL2ZPstar == 4.0d-2 ! predator Zoo on large Zoo
! Zooplankton grazing inhibition coefficient [m3/millimole_N].
PusaiPL == 4.605d0 ! predator Zoo on large Phy
PusaiZS == 3.010d0 ! predator Zoo on small Zoo
! Zooplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].
MorZS0 == 58.5d-3 ! small biomass
MorZL0 == 58.5d-3 ! large biomass
MorZP0 == 58.5d-3 ! predator biomass
! Zooplankton temperature coefficient for mortality [1/Celsius].
KMorZS == 0.0693d0 ! small biomass
KMorZL == 0.0693d0 ! large biomass
KMorZP == 0.0693d0 ! predator biomass
! Zooplankton assimilation efficiency [nondimemsional].
AlphaZS == 0.70d0 ! small biomass
AlphaZL == 0.70d0 ! large biomass
AlphaZP == 0.70d0 ! predator biomass
! Zooplankton growth efficiency [nondimensional].
BetaZS == 0.30d0 ! small biomass
BetaZL == 0.30d0 ! large biomass
BetaZP == 0.30d0 ! predator biomass
! Decomposition rates at 0 Celsius [1/day].
Nit0 == 0.03d0 ! NH4 nitrification
VP2N0 == 0.10d0 ! PON to NH4
VP2D0 == 0.10d0 ! PON to DON
VD2N0 == 0.20d0 ! DON to NH4
VO2S0 == 0.10d0 ! Opal to Silicate
! Temperature coefficients for decomposition [1/Celsius]
KNit == 6.93d-2 ! NH4 nitrification
KP2D == 6.93d-2 ! PON to DON
KP2N == 6.93d-2 ! PON to NH4
KD2N == 6.93d-2 ! DON to NH4
KO2S == 6.93d-2 ! Opal to Silicate
! Si:N ratio [millimole_Si/millimole_N].
RSiN == 2.0d0
! Settling (sinking) velocities [m/day].
setVPON == 40.0d0 ! PON
setVOpal == 40.0d0 ! Opal
! Harmonic/biharmonic horizontal diffusion of biological tracer for
! nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids].
TNU2 == 11*0.0d0 ! m2/s
TNU4 == 11*0.0d0 ! m4/s
ad_TNU2 == 11*0.0d0 ! m2/s
ad_TNU4 == 11*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 == 11*F
! Vertical mixing coefficients for biological tracers for nonlinear
! model and basic state scale factor in adjoint-based algorithms:
! [1:NBT,Ngrids].
AKT_BAK == 11*1.0d-6 ! m2/s
ad_AKT_fac == 11*1.0d0 ! nondimensional
! Nudging/relaxation time scales, inverse scales will be computed
! internally: [1:NBT,Ngrids].
TNUDG == 11*0.0d0 ! days
! Set horizontal and vertical advection schemes for biological tracers.
! A different advection scheme is allowed for each tracer. For example,
! a positive-definite (monotonic) algorithm can be activated for
! salinity and biological tracers, while a different one is set for
! temperature. [1:NAT+NPT,Ngrids] values are expected.
!
! Keyword Advection Algorithm
!
! A4 4th-order Akima (horizontal/vertical)
! C2 2nd-order centered differences (horizontal/vertical)
! C4 4th-order centered differences (horizontal/vertical)
! HSIMT 3th-order HSIMT-TVD (horizontal/vertical)
! MPDATA recursive flux corrected MPDATA (horizontal/vertical)
! SPLINES parabolic splines (only vertical)
! SU3 split third-order upstream (horizontal/vertical)
! U3 3rd-order upstream-biased (only horizontal)
!
! The user has the option of specifying the full Keyword or the first
! two letters, regardless if using uppercase or lowercase. If nested
! grids, specify values for each grid.
Hadvection == HSIMT \ ! idbio( 1), nanophyto
HSIMT \ ! idbio( 2), diatom
HSIMT \ ! idbio( 3), microzoo
HSIMT \ ! idbio( 4), mesozoo
HSIMT \ ! idbio( 5), Pzooplankton
HSIMT \ ! idbio( 6), NO3
HSIMT \ ! idbio( 7), NH4
HSIMT \ ! idbio( 8), PON
HSIMT \ ! idbio( 9), DON
HSIMT \ ! idbio(10), SiOH4
HSIMT ! idbio(11), opal
Vadvection == HSIMT \ ! idbio( 1), nanophyto
HSIMT \ ! idbio( 2), diatom
HSIMT \ ! idbio( 3), microzoo
HSIMT \ ! idbio( 4), mesozoo
HSIMT \ ! idbio( 5), Pzooplankton
HSIMT \ ! idbio( 6), NO3
HSIMT \ ! idbio( 7), NH4
HSIMT \ ! idbio( 8), PON
HSIMT \ ! idbio( 9), DON
HSIMT \ ! idbio(10), SiOH4
HSIMT ! idbio(11), opal
! Adjoint-based algorithms can have different horizontal and schemes
! for active and inert tracers.
ad_Hadvection == U3 ! idbio(:), compact
ad_Vadvection == C4 ! idbio(:), compact
! 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( 1), nanophyto
Per Clo Per Clo \ ! idbio( 2), diatom
Per Clo Per Clo \ ! idbio( 3), microzoo
Per Clo Per Clo \ ! idbio( 4), mesozoo
Per Clo Per Clo \ ! idbio( 5), Pzooplankton
Per Clo Per Clo \ ! idbio( 6), NO3
Per Clo Per Clo \ ! idbio( 7), NH4
Per Clo Per Clo \ ! idbio( 8), PON
Per Clo Per Clo \ ! idbio( 9), DON
Per Clo Per Clo \ ! idbio(10), SiOH4
Per Clo Per Clo ! idbio(11), opal
! Adjoint-based algorithms can have different lateral boundary
! conditions keywords.
ad_LBC(isTvar) == Per Clo Per Clo \ ! idbio( 1), nanophyto
Per Clo Per Clo \ ! idbio( 2), diatom
Per Clo Per Clo \ ! idbio( 3), microzoo
Per Clo Per Clo \ ! idbio( 4), mesozoo
Per Clo Per Clo \ ! idbio( 5), Pzooplankton
Per Clo Per Clo \ ! idbio( 6), NO3
Per Clo Per Clo \ ! idbio( 7), NH4
Per Clo Per Clo \ ! idbio( 8), PON
Per Clo Per Clo \ ! idbio( 9), DON
Per Clo Per Clo \ ! idbio(10), SiOH4
Per Clo Per Clo ! idbio(11), opal
! 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 == 11*F
! Logical switches (TRUE/FALSE) to read and process biological tracer
! climatology fields: [NBT,Ngrids] values are expected. See glossary below
! for details.
LtracerCLM == 11*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 == 11*F
! Logical switches (TRUE/FALSE) to activate writing of biological fields
! into HISTORY output file: [1:NBT,Ngrids].
Hout(idTvar) == 11*T ! ..., NO3, ... biological tracers
Hout(idTsur) == 11*F ! ..., NO3_sflux, ... surface tracer flux
! Logical switches (TRUE/FALSE) to activate writing of biological fields
! into QUICKSAVE output file: [1:NBT,Ngrids].
Qout(idTvar) == 11*F ! ..., NO3, ... biological tracers
Qout(idsurT) == 11*F ! ..., NO3_sur, ... surface biological tracer
Qout(idTsur) == 11*F ! ..., NO3_sflux, ... surface tracer flux
! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
! into AVERAGE output file: [1;NBT,Ngrids].
Aout(idTvar) == 11*T ! ..., NO3, ... biological tracer
Aout(idTTav) == 11*F ! ..., NO3_2, ... quadratic <t*t> tracer terms
Aout(idUTav) == 11*F ! ..., u_NO3, ... quadratic <u*t> tracer terms
Aout(idVTav) == 11*F ! ..., v_NO3, ... quadratic <v*t> tracer terms
Aout(iHUTav) == 11*F ! ..., Huon_NO3, ... tracer volume flux, <Huon*t>
Aout(iHVTav) == 11*F ! ..., Hvom_NO3, ... 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) == 11*T ! ..., NO3_rate, ... time rate of change
Dout(iThadv) == 11*T ! ..., NO3_hadv, ... horizontal total advection
Dout(iTxadv) == 11*T ! ..., NO3_xadv, ... horizontal XI-advection
Dout(iTyadv) == 11*T ! ..., NO3_yadv, ... horizontal ETA-advection
Dout(iTvadv) == 11*T ! ..., NO3_vadv, ... vertical advection
Dout(iThdif) == 11*T ! ..., NO3_hdiff, ... horizontal total diffusion
Dout(iTxdif) == 11*T ! ..., NO3_xdiff, ... horizontal XI-diffusion
Dout(iTydif) == 11*T ! ..., NO3_ydiff, ... horizontal ETA-diffusion
Dout(iTsdif) == 11*T ! ..., NO3_sdiff, ... horizontal S-diffusion
Dout(iTvdif) == 11*T ! ..., NO3_vdiff, ... vertical diffusion
!
! GLOSSARY:
! =========
!
!------------------------------------------------------------------------------
! NEMURO Ecosystem Model Parameters, [1:Ngrids] values are expected. Currently,
! it can be configured with 11 biological tracers:
!
! idbio( 1) nanophytoplankton Nanophytoplankton biomass
! idbio( 2) diatom Diatom biomass
! idbio( 3) microzooplankton Microzooplankton biomass
! idbio( 4) mesozooplankton Mesozooplankton biomass
! idbio( 5) Pzooplankton Predactor zooplankton biomass
! idbio( 6) NO3 Nitrate concentration
! idbio( 7) NH4 Ammonium concentration
! idbio( 8) PON Particulate Organic Nitrogen concentration
! idbio( 9) DON Dissolved Organic Nitrogen concentration
! idbio(10) SiOH4 Silicate concentration
! idbio(11) opal Particulate organic silica concentration
!
!------------------------------------------------------------------------------
!
! 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. If so, this switch needs to be consistent with the
! dimension parameter NBT in "mod_param". In order to make
! the model more efficient in memory usage, NBT(:) should
! be zero in such grids.
!
! BioIter Maximum number of iterations to achieve convergence of
! the nonlinear solution.
!
!------------------------------------------------------------------------------
! Light Parameters, [1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
! AttSW Light attenuation due to seawater [1/m].
!
! AttPS Light attenuation due to Small Phytoplankton, self-shading
! coefficient, [m2/millimole_N].
!
! AttPL Light attenuation due to Large Phytoplankton, self-shading
! coefficient, [m2/millimole_N].
!
! PARfrac Fraction of shortwave radiation that is photosynthetically
! active, [nondimensional].
!
! AlphaPS Small Phytoplankton photochemical reaction coefficient:
! initial slope (low light) of the P-I curve (Platt et al,
! 1980), [1/(W/m2) 1/day].
!
! AlphaPL Large Phytoplankton photochemical reaction coefficient:
! initial slope (low light) of the P-I curve (Platt et al.,
! 1980), [1/(W/m2) 1/day].
!
! BetaPS Small Phytoplankton photoinhibition coefficient (Platt
! et al., 1980), [1/(W/m2) 1/day]. Set it to zero for no
! inhibition.
!
! BetaPL Large Phytoplankton photoinhibition coefficient (Platt
! et al., 1980), [1/(W/m2) 1/day]. Set it to zero for no
! inhibition.
!
!------------------------------------------------------------------------------
! Phytoplankton Parameters, [1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
! VmaxS Maximum Small Phytoplankton photosynthetic rate [1/day] in
! the absence of photoinhibition under optimal light.
!
! VmaxL Maximum Large Phytoplankton photosynthetic rate [1/day] in
! the absence of photoinhibition under optimal light.
!
! KNO3S Small Phytoplankton half saturation constant for Nitrate,
! [millimole_N/m3].
!
! KNO3L Large Phytoplankton half saturation constant for Nitrate,
! [millimole_N/m3].
!
! KNH4S Small Phytoplankton half saturation constant for Ammonium,
! [millimole_N/m3].
!
! KNH4L Large Phytoplankton half saturation constant for Ammonium,
! [millimole_N/m3].
!
! KSiL Large Phytoplankton half saturation constant for Silicate,
! [millimole_Si/m3].
!
! PusaiS Small Phytoplankton Ammonium inhibition coefficient,
! [m3/millimole_N].
!
! PusaiL Large Phytoplankton Ammonium inhibition coefficient,
! [m3/millimole_N].
!
! KGppS Small Phytoplankton temperature coefficient for
! photosynthetic rate, [1/Celsius].
!
! KGppL Large Phytoplankton temperature coefficient for
! photosynthetic rate, [1/Celsius].
!
! ResPS0 Small Phytoplankton respiration rate at 0 Celsius, [1/day].
!
! ResPL0 Large Phytoplankton respiration rate at 0 Celsius, [1/day].
!
! KResPS Small Phytoplankton temperature coefficient for respiration,
! [1/Celsius].
!
! KResPL Large Phytoplankton temperature coefficient for respiration,
! [1/Celsius].
!
! GammaS Small Phytoplankton ratio of extracellular excretion to
! photosynthesis [nondimensional].
!
! GammaL Large Phytoplankton ratio of extracellular excretion to
! photosynthesis [nondimensional].
!
! MorPS0 Small Phytoplankton mortality rate at 0 Celsius,
! [m3/millimole_N 1/day].
!
! MorPL0 Large Phytoplankton mortality rate at 0 Celsius,
! [m3/millimole_N 1/day].
!
! KMorPS Small Phytoplankton temperature coefficient for mortality,
! [1/Celsius].
!
! KMorPL Large Phytoplankton temperature coefficient for mortality,
! [1/Celsius].
!
!------------------------------------------------------------------------------
! Zooplankton parameters, [1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
! GRmaxSps Small Zooplankton maximum grazing rate on Small
! Phytoplankton at 0 Celsius, [1/day].
!
! GRmaxLps Large Zooplankton maximum grazing rate on Small
! Phytoplankton at 0 Celsius, [1/day].
!
! GRmaxLpl Large Zooplankton maximum grazing rate on Large
! Phytoplankton at 0 Celsius, [1/day].
!
! GRmaxLzs Small Zooplankton maximum grazing rate on Small
! Zooplankton at 0 Celsius, [1/day].
!
! GRmaxPpl Predator Zooplankton maximum grazing rate on Large
! Phytoplankton at 0 Celsius, [1/day].
!
! GRmaxPzs Predator Zooplankton maximum grazing rate on Small
! Zooplankton at 0 Celsius, [1/day].
!
! GRmaxPzl Predator Zooplankton maximum grazing rate on Large
! Phytoplankton at 0 Celsius, [1/day].
!
! KGraS Small Zooplankton temperature coefficient for grazing,
! [1/Celsius].
!
! KGraL Large Zooplankton temperature coefficient for grazing,
! [1/Celsius].
!
! KGraP Predator Zooplankton temperature coefficient for grazing,
! [1/Celsius].
!
! LamS Small Zooplankton Ivlev constant, [m3/millimole_N].
!
! LamL Large Zooplankton Ivlev constant, [m3/millimole_N].
!
! LamP Predator Zooplankton Ivlev constant, [m3/millimole_N].
!
! KPS2ZS Small Zooplankton half-saturation, squared coefficient for
! ingestion on Small Phytoplankton [millimole_N/m3]^2.
!
! KPS2ZL Large Zooplankton half-saturation, squared coefficient for
! ingestion on Small Phytoplankton [millimole_N/m3]^2.
!
! KPL2ZL Large Zooplankton half-saturation, squared coefficient for
! ingestion on Large Phytoplankton [millimole_N/m3]^2.
!
! KZS2ZL Large Zooplankton half-saturation, squared coefficient for
! ingestion on Small Phytoplankton [millimole_N/m3]^2.
!
! KPL2ZP Predator Zooplankton half-saturation, squared coefficient for
! ingestion on Large Phytoplankton [millimole_N/m3]^2.
!
! KZS2ZP Predator Zooplankton half-saturation, squared coefficient for
! ingestion on Small Zooplankton [millimole_N/m3]^2.
!
! KZL2ZP Predator Zooplankton half-saturation, squared coefficient for
! ingestion on Large Zooplankton [millimole_N/m3]^2.
!
! PS2ZSstar Small Zooplankton threshold value for grazing on
! Small Phytoplankton, [millimole_N/m3].
!
! PS2ZLstar Large Zooplankton threshold value for grazing on
! Small Phytoplankton, [millimole_N/m3].
!
! PL2ZLstar Large Zooplankton threshold value for grazing on
! Large Phytoplankton, [millimole_N/m3].
!
! ZS2ZLstar Large Zooplankton threshold value for grazing on
! Small Zooplankton, [millimole_N/m3].
!
! PL2ZPstar Predator Zooplankton threshold value for grazing on
! Large Phytoplankton, [millimole_N/m3].
!
! ZS2ZPstar Predator Zooplankton threshold value for grazing on
! Small Zooplankton, [millimole_N/m3].
!
! ZL2ZPstar Small Zooplankton threshold value for grazing on
! Small Phytoplankton, [millimole_N/m3].
!
! PusaiPL Predator Zooplankton grazing on Large Phytoplankton
! inhibition coefficient, [m3/millimole_N].
!
! PusaiZS Predator Zooplankton grazing on Small Zooplankton
! inhibition coefficient, [m3/millimole_N].
!
! MorZS0 Small Zooplankton mortality rate at 0 Celsius,
! [m3/millimole_N 1/day].
!
! MorZL0 Large Zooplankton mortality rate at 0 Celsius,
! [m3/millimole_N 1/day].
!
! MorZP0 Predator Zooplankton mortality rate at 0 Celsius,
! [m3/millimole_N 1/day].
!
! KMorZS Small Zooplankton temperature coefficient for mortality,
! [1/Celsius].
!
! KMorZL Large Zooplankton temperature coefficient for mortality,
! [1/Celsius].
!
! KMorZP Predator Zooplankton temperature coefficient for mortality,
! [1/Celsius].
!
! AlphaZS Small Zooplankton assimilation efficiency
! [nondimemsional].
!
! AlphaZL Large Zooplankton assimilation efficiency
! [nondimemsional].
!
! AlphaZP Predator Zooplankton assimilation efficiency
! [nondimemsional].
!
! BetaZS Small Zooplankton growth efficiency
! [nondimensional].
!
! BetaZL Large Zooplankton growth efficiency
! [nondimensional].
!
! BetaZP Predator Zooplankton growth efficiency
! [nondimensional].
!
!------------------------------------------------------------------------------
! Nutrient parameters.
!------------------------------------------------------------------------------
!
! Nit0 Nitrification (NH4 to NO3) rate at 0 Celsius, [1/day].
!
! VP2N0 PON to NH4 decomposition rate at 0 Celsius, [1/day].
!
! VP2D0 PON to DON decomposition rate at 0 Celsius, [1/day].
!
! VD2N0 DON to NH4 decomposition rate at 0 Celsius, [1/day].
!
! VO2S0 Opal to Silicate decomposition rate at 0 Celsius, [1/day].
!
! KNit Temperature coefficient for nitrification (NH4 -> NO3)
! decomposition, [1/Celsius].
!
! KP2D Temperature coefficient for PON to DON decomposition,
! [1/Celsius].
!
! KP2N Temperature coefficient for PON to NH4 decomposition,
! [1/Celsius].
!
! KD2N Temperature coefficient for DON to NH4 decomposition,
! [1/Celsius].
!
! KO2S Temperature coefficient for Opal to Silicate decomposition,
! [1/Celsius].
!
! RSiN Si:N ratio [millimole_Si/millimole_N].
!
! setVPON PON Settling (sinking) velocity [m/day].
!
! setVOpal Opal Settling (sinking) velocity [m/day].
!
!------------------------------------------------------------------------------
! Physical Parameters, [1:NBT,1:Ngrids] values are expected.
!------------------------------------------------------------------------------
!
! 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.
!
!------------------------------------------------------------------------------
! Tracer advection scheme.
!------------------------------------------------------------------------------
!
! It is more advantageous to set the horizontal and vertical advection schemes
! for each tracer with switches instead of a single CPP flag for all of them.
! Positive-definite and monotonic algorithms (i.e., MPDATA and HSIMT) are
! appropriate and useful for positive fields like salinity, inert, biological,
! and sediment tracers. However, since the temperature has a dynamic range
! with negative and positive values in the ocean, other advection schemes are
! more appropriate.
!
! Currently, the following tracer advection schemes are available and are
! activated using the associated Keyword:
!
! Keyword Advection Algorithm
!
! A4 4th-order Akima (horizontal/vertical)
! C2 2nd-order centered differences (horizontal/vertical)
! C4 4th-order centered differences (horizontal/vertical)
! HSIMT 3th-order HSIMT with TVD limiter (horizontal/vertical)
! MPDATA recursive flux corrected MPDATA (horizontal/vertical)
! SPLINES parabolic splines reconstruction (only vertical)
! SU3 split third-order upstream (horizontal/vertical)
! U3 3rd-order upstresm-bias (only horizontal)
!
! The user has the option of specifying the full Keyword or the first
! two letters, regardless if using uppercase or lowercase.
!
! If using either HSIMT (Wu and Zhu, 2010) or MPDATA (Margolin and
! Smolarkiewicz, 1998) options, the user needs to set the same scheme
! for both horizontal and vertical advection to preserve monotonicity.
!
! Hadvection Horizontal advection for each active (temperature and
! salinity) and inert tracers, [1:NAT+NPT,Ngrids]
! values are expected.
!
! Vadvection Vertical advection for each active (temperature and
! salinity) and inert tracers, [1:NAT+NPT,Ngrids]
! values are expected.
!
! ad_Hadvection Horizontal advection for each active (temperature and
! salinity) and inert tracers in the adjoint-based
! algorithms, [1:NAT+NPT,Ngrids] values are expected.
!
! ad_Vadvection Vertical advection for each active (temperature and
! salinity) and inert tracers in the adjoint-based
! algorithms, [1:NAT+NPT,Ngrids] values are expected.
!
! Examples:
!
! Hadvection == A4 \ ! temperature
! MPDATA \ ! salinity
! HSIMT \ ! dye_01, inert(1)
! HSIMT ! dy2_02, inert(2)
!
! Vadvection == A4 \ ! temperature
! MPDATA \ ! salinity
! HSIMT \ ! dye_01, inert(1)
! HSIMT ! dye_02, inert(2)
!
! or in nested applications
!
! Hadvection == U3 \ ! temperature, Grid 1
! HSIMT \ ! salinity, Grid 1
! U3 \ ! temperature, Grid 2
! HSIMT \ ! salinity, Grid 2
! U3 \ ! temperature, Grid 3
! HSIMT ! salinity, Grid 3
!
! Vadvection == C4 \ ! temperature, Grid 1
! HSIMT \ ! salinity, Grid 1
! C4 \ ! temperature, Grid 2
! HSIMT \ ! salinity, Grid 2
! C4 \ ! temperature, Grid 3
! HSIMT ! salinity, Grid 3
!
! It is convinient to use the compact specification format for biological and
! sediment passive tracers as:
!
! Hadvection == HSIMT ! idbio(:), compact
!
! Vadvection == HSIMT ! idbio(:), compact
!
! when all the passive tracers have the same horizontal and vertical tracer
! advection scheme.
!
!------------------------------------------------------------------------------
! 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) Small Phytoplankton biomass
! LtracerSrc(idbio( 2),ng) Large Phytoplankton biomass
! LtracerSrc(idbio( 3),ng) Small Zooplankton biomass
! LtracerSrc(idbio( 4),ng) Large Zooplankton biomass
! LtracerSrc(idbio( 5),ng) Predator Zooplankton biomass
! LtracerSrc(idbio( 6),ng) Nitrate concentration
! LtracerSrc(idbio( 7),ng) Ammonium concentration
! LtracerSrc(idbio( 8),ng) Particulate Organic Nitrogen
! LtracerSrc(idbio( 9),ng) Dissolved Organic Nitrogen
! LtracerSrc(idbio(10),ng) Silicate concentration
! LtracerSrc(idbio(11),ng) Particulate organic silica
!
! 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) Small Phytoplankton biomass
! LtracerCLM(idbio( 2),ng) Large Phytoplankton biomass
! LtracerCLM(idbio( 3),ng) Small Zooplankton biomass
! LtracerCLM(idbio( 4),ng) Large Zooplankton biomass
! LtracerCLM(idbio( 5),ng) Predator Zooplankton biomass
! LtracerCLM(idbio( 6),ng) Nitrate concentration
! LtracerCLM(idbio( 7),ng) Ammonium concentration
! LtracerCLM(idbio( 8),ng) Particulate Organic Nitrogen
! LtracerCLM(idbio( 9),ng) Dissolved Organic Nitrogen
! LtracerCLM(idbio(10),ng) Silicate concentration
! LtracerCLM(idbio(11),ng) Particulate organic silica
!
! 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) Small Phytoplankton biomass
! LnudgeTCLM(idbio( 2),ng) Large Phytoplankton biomass
! LnudgeTCLM(idbio( 3),ng) Small Zooplankton biomass
! LnudgeTCLM(idbio( 4),ng) Large Zooplankton biomass
! LnudgeTCLM(idbio( 5),ng) Predator Zooplankton biomass
! LnudgeTCLM(idbio( 6),ng) Nitrate concentration
! LnudgeTCLM(idbio( 7),ng) Ammonium concentration
! LnudgeTCLM(idbio( 8),ng) Particulate Organic Nitrogen
! LnudgeTCLM(idbio( 9),ng) Dissolved Organic Nitrogen
! LnudgeTCLM(idbio(10),ng) Silicate concentration
! LnuegeTCLM(idbio(11),ng) Particulate organic silica
!
! 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 files.
!------------------------------------------------------------------------------
!
! 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
!
! idTvar(idbio( 1))=iSphy Small Phytoplankton biomass
! idTvar(idbio( 2))=iLphy Large Phytoplankton biomass
! idTvar(idbio( 3))=iSzoo Small Zooplankton biomass
! idTvar(idbio( 4))=iLzoo Large Zooplankton biomass
! idTvar(idbio( 5))=iPzoo Predator Zooplankton biomass
! idTvar(idbio( 6))=iNO3_ Nitrate concentration
! idTvar(idbio( 7))=iNH4_ Ammonium concentration
! idTvar(idbio( 8))=iPON_ Particulate Organic Nitrogen
! idTvar(idbio( 9))=iDON_ Dissolved Organic Nitrogen
! idTvar(idbio(10))=iSiOH Silicate concentration
! idTvar(idbio(11))=iopal Particulate organic silica
!
!------------------------------------------------------------------------------
! 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(:)) are the same to those in the HISTORY
! file.
!
!------------------------------------------------------------------------------
! 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.
!