! Hypoxia Simple Respiration Model Biological Parameters.
!
!svn $Id: hypoxia_srm.in 889 2018-02-10 03:32:52Z arango $
!========================================================= Hernan G. Arango ===
! Copyright (c) 2002-2019 The ROMS/TOMS Group !
! 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. !
! !
!==============================================================================
!
! 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
! Total constant respiration rate [1/day].
ResRate == 1.1d-4
! Harmonic/biharmonic horizontal diffusion of biological tracer for
! nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids].
TNU2 == 5.0d0 ! m2/s
TNU4 == 0.0d0 ! m4/s
ad_TNU2 == 0.0d0 ! m2/s
ad_TNU4 == 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 == F
! Vertical mixing coefficients for biological tracers for nonlinear
! model and basic state scale factor in adjoint-based algorithms:
! [1:NBT,Ngrids].
AKT_BAK == 1.0d-6 ! m2/s
ad_AKT_fac == 1.0d0 ! nondimensional
! Nudging/relaxation time scales, inverse scales will be computed
! internally: [1:NBT,Ngrids].
TNUDG == 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) == Gra Gra Gra Clo ! idbio(1), dissolved oxygen
! Adjoint-based algorithms can have different lateral boundary
! conditions keywords.
ad_LBC(isTvar) == Gra Gra Gra Clo ! idbio(1), dissolved oxygen
! 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 == F
! Logical switches (TRUE/FALSE) to read and process biological tracer
! climatology fields: [NBT,Ngrids] values are expected. See glossary below
! for details.
LtracerCLM == 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 == F
! Logical switches (TRUE/FALSE) to activate writing of biological fields
! into HISTORY output files: [1:NBT,Ngrids].
Hout(idTvar) == T ! ..., oxygen biological tracer
Hout(idTsur) == F ! ..., oxygen_sflux surface tracer flux
! Logical switches (TRUE/FALSE) to activate writing of time-averaged fields
! into AVERAGE output file: [1:NBT,Ngrids].
Aout(idTvar) == T ! ..., oxygen biological tracer
Aout(idTTav) == F ! ..., oxygen_2 quadratic <t*t> tracer terms
Aout(idUTav) == F ! ..., u_oxygen quadratic <u*t> tracer terms
Aout(idVTav) == F ! ..., v_oxygen quadratic <v*t> tracer terms
Aout(iHUTav) == F ! ..., Huon_oxygen tracer volume flux, <Huon*t>
Aout(iHVTav) == F ! ..., Hvom_oxygen 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) == T ! ..., oxygen_rate time rate of change
Dout(iThadv) == T ! ..., oxygen_hadv horizontal total advection
Dout(iTxadv) == T ! ..., oxygen_xadv horizontal XI-advection
Dout(iTyadv) == T ! ..., oxygen_yadv horizontal ETA-advection
Dout(iTvadv) == T ! ..., oxygen_vadv vertical advection
Dout(iThdif) == T ! ..., oxygen_hdiff horizontal total diffusion
Dout(iTxdif) == T ! ..., oxygen_xdiff horizontal XI-diffusion
Dout(iTydif) == T ! ..., oxygen_ydiff horizontal ETA-diffusion
Dout(iTsdif) == T ! ..., oxygen_sdiff horizontal S-diffusion
Dout(iTvdif) == T ! ..., oxygen_vdiff vertical diffusion
!
! GLOSSARY:
! =========
!
!------------------------------------------------------------------------------
! Red Tide (Stock et al., 2005; He et al., 2008) Biological Model Parameters.
! Currently, it is configured with one biological tracer (NBT=1):
!
! idbio(1) oxygen dissolved oxigen concetration
!
!------------------------------------------------------------------------------
!
! 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 implicit solution.
!
!
! ResRate Total resporation rate (constant; 1/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.
!
!------------------------------------------------------------------------------
! 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) == Gra Gra Gra 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) Dinoflagellate concetration
!
! 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) Dinoflagellate concetration
!
! 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) Dinoflagellate concetration
!
! 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))=iDino Dinoflagellate concentration
!
!------------------------------------------------------------------------------
! 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.
!