Difference between revisions of "nemuro.in"
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*Logical switches to activate writing of biological tracers into history output file: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected. Currently, '''NEMURO''' has [[Variables#NBT|NBT]]=11 ecosystem compartments. The 11 switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page. | *Logical switches to activate writing of biological tracers into history output file: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected. Currently, '''NEMURO''' has [[Variables#NBT|NBT]]=11 ecosystem compartments. The 11 switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page. | ||
:<div class="box">[[Variables#Hout(idTvar)|Hout(idTvar)]] == 11* | :<div class="box">[[Variables#Hout|Hout(idTvar)]] == 11*T ! ..., NO3, ... biological tracers<br />[[Variables#Hout|Hout(idTsur)]] == 11*F ! ..., NO3_sflux, ... surface tracer flux</div> | ||
*Logical switches to activate writing of biological tracers into quicksave output file: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected. Currently, '''NEMURO''' has [[Variables#NBT|NBT]]=11 ecosystem compartments. The 11 switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page. | |||
:<div class="box">[[Variables#Qout|Qout(idTvar)]] == 11*F ! ..., NO3, ... biological tracers<br />[[Variables#Qout|Qout(idsurT)]] == 11*F ! ..., NO3_sur, ... surface biological tracers<br />[[Variables#Qout|Qout(idTsur)]] == 11*F ! ..., NO3_sflux, ... surface tracer flux</div> | |||
*Logical switches to activate writing of time-averaged fields into averages file. [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected. | *Logical switches to activate writing of time-averaged fields into averages file. [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected. |
Revision as of 01:31, 18 August 2016
The nemuro.in file sets the parameters for the NEMURO model. The name of this file is set by the BPARNAM keyword in the ocean.in file. A default nemuro.in standard input ASCII file can be found in the User/External subdirectory of the ROMS source code. In order to include the NEMURO model in ROMS you must set BPARNAM correctly and activate the NEMURO CPP option.
# | index | Description | Units | NetCDF variable |
---|---|---|---|---|
1 | iSphy | Small Phytoplankton biomass | mmol/m3 | nanophytoplankton |
2 | iLphy | Large Phytoplankton biomass | mmol/m3 | diatom |
3 | iSzoo | Small Zooplankton biomass | mmol/m3 | microzooplankton |
4 | iLzoo | Large Zooplankton biomass | mmol/m3 | mesozooplankton |
5 | iPzoo | Predator Zooplankton biomass | mmol/m3 | Pzooplankton |
6 | iNO3_ | Nitrate concentration | mmol/m3 | NO3 |
7 | iNH4_ | Ammonium concentration | mmol/m3 | NH4 |
8 | iPON_ | Particulate Organic Nitrogen | mmol/m3 | PON |
9 | iDON_ | Dissolved Organic Nitrogen | mmol/m3 | DON |
10 | iSiOH | Silicate concentration | mmol/m3 | SiOH4 |
11 | iopal | Particulate organic silica | mmol/m3 | opal |
The "#" column denotes the internal index number within the idbio array while the "index" column is the index within the tracer array t(:,:,:,:,index).
NEMURO equations and representative parameters may be found in:
Notice: Detailed information about ROMS input script file syntax can be found here.
Biological Model Parameters
- This switch to control the computation of NEMURO within nested and/or multiple connected grids. By default this switch is set to TRUE in mod_scalars.F 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.F. In order to make the model more efficient in memory usage, NBT(:) should be zero in such grids.
- Lbiology == T
- Maximum number of iterations to achieve convergence of the nonlinear solution.
- BioIter == 1
Light Parameters
Input parameter units are specified within brackets ([ ]). Unless specified, [1:Ngrids] values expected for each parameter.
- Light attenuation due to seawater [1/m].
- AttSW == 0.04d0
- Light attenuation due to phytoplankton, self-shading coefficient, [m2/millimole_N].
- 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].
- Phytoplankton photoinhibition coefficient, [1/(W/m2) 1/day].
Phytoplankton Parameters
Input parameter units are specified within brackets ([ ]). Unless specified, [1:Ngrids] values expected for each parameter.
- Phytoplankton maximum photosynthetic rate at 0 Celsius [1/day].
- Phytoplankton half saturation constant for Nitrate [millimole_N/m3].
- Phytoplankton half saturation constant for Ammonium [millimole_N/m3].
- Phytoplankton half saturation constant for Silicate [millimole_Si/m3].
- KSiL == 6.0d0 ! large biomass
- Phytoplankton Ammonium inhibition coefficient [m3/millimole_N].
- Phytoplankton temperature coefficient for photosynthetic rate [1/Celsius].
- Phytoplankton respiration rate at 0 Celsius [1/day].
- Phytoplankton temperature coefficient for respiration [1/Celsius].
- Phytoplankton ratio of extracellular excretion to photosynthesis [nondimensional].
- Phytoplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].
- Phytoplankton temperature coefficient for mortality [1/Celsius].
Zooplankton Parameters
Input parameter units are specified within brackets ([ ]). Unless specified, [1:Ngrids] values expected for each parameter.
- 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].
Zooplankton Ivlev constant [m3/millimole_N].
- 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].
- Zooplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].
- Zooplankton temperature coefficient for mortality [1/Celsius].
- Zooplankton assimilation efficiency [nondimemsional].
- Zooplankton growth efficiency [nondimensional].
Nutrient Parameters
Input parameter units are specified within brackets ([ ]). Unless specified, [1:Ngrids] values expected for each parameter.
- Decomposition rates at 0 Celsius [1/day].
- Temperature coefficients for decomposition [1/Celsius]
- Si:N ratio [millimole_Si/millimole_N].
- RSiN == 2.0d0
- Settling (sinking) velocities [m/day].
Other Parameters
Unless specified, [1:NBT,Ngrids] values expected for each parameter.
- Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer for nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids] values expected. The 11 values correspond to the Variable Index Table at the top of this page.
- Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids] values expected. The 11 values correspond to the Variable Index Table at the top of this page.
- Nudging/relaxation time scale. Inverse scale will be computed internally: [1:NBT,Ngrids] values expected. The 11 values correspond to the Variable Index Table at the top of this page.
- TNUDG == 11*0.0d0 ! days
- The lateral boundary conditions are entered with a keyword. 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 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 to specify which variables to process for tracers climatology: [1:NBT,Ngrids] values expected. The 11 switches correspond to the Variable Index Table at the top of this page.
- LtracerCLM == 11*F
- Logical switches to specify which variables to consider on tracers point Sources/Sinks (like river runoff): [1:NBT,Ngrids] values expected. The 11 switches correspond to the Variable Index Table at the top of this page.
- LtracerSrc == 11*F
- Logical switches to activate writing of biological tracers into history output file: [1:NBT,Ngrids] values expected. Currently, NEMURO has NBT=11 ecosystem compartments. The 11 switches correspond to the Variable Index Table at the top of this page.
- Hout(idTvar) == 11*T ! ..., NO3, ... biological tracers
Hout(idTsur) == 11*F ! ..., NO3_sflux, ... surface tracer flux
- Logical switches to activate writing of biological tracers into quicksave output file: [1:NBT,Ngrids] values expected. Currently, NEMURO has NBT=11 ecosystem compartments. The 11 switches correspond to the Variable Index Table at the top of this page.
- Qout(idTvar) == 11*F ! ..., NO3, ... biological tracers
Qout(idsurT) == 11*F ! ..., NO3_sur, ... surface biological tracers
Qout(idTsur) == 11*F ! ..., NO3_sflux, ... surface tracer flux
- Logical switches to activate writing of time-averaged fields into averages file. [1:NBT,Ngrids] values expected.
- Aout(idTvar) == 11*T ! ..., NO3, ... biological tracer
- Logical switches to activate writing of time-averaged, biological tracer diagnostic terms into the diagnostic output file. [1:NBT,Ngrids] values expected.
- 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