Difference between revisions of "npzd Powell.in"

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The <span class="red">npzd_Powell.in</span> file sets the parameters for the '''Powell et al. NPZD''' model. The name of this file is set by the [[Variables#bparnam|BPARNAM]] keyword in the [[ocean.in]] file. A default <span class="red">npzd_Powell.in</span> standard input ASCII file can be found in the '''User/External''' subdirectory of the ROMS source code. In order to include the '''Powell et al. NPZD''' model in ROMS you must set [[Variables#bparnam|BPARNAM]] correctly and activate the [[NPZD_POWELL]] [[Options|CPP option]].
 
The <span class="red">npzd_Powell.in</span> file sets the parameters for the '''Powell et al. NPZD''' model. The name of this file is set by the [[Variables#bparnam|BPARNAM]] keyword in the [[ocean.in]] file. A default <span class="red">npzd_Powell.in</span> standard input ASCII file can be found in the '''User/External''' subdirectory of the ROMS source code. In order to include the '''Powell et al. NPZD''' model in ROMS you must set [[Variables#bparnam|BPARNAM]] correctly and activate the [[NPZD_POWELL]] [[Options|CPP option]].
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 +
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{| id="var_tab" border="1" cellspacing="0" cellpadding="5" align="center"
 +
!#
 +
!index
 +
! align="left" | Description
 +
!Units
 +
! align="left" | NetCDF variable
 +
|-
 +
| align="right" | 1
 +
|iNO3_
 +
|Nitrate concentration
 +
|mmol/m<sup>3</sup>
 +
|NO3
 +
|-
 +
|align="right" | 2
 +
|iPhyt
 +
|Phytoplankton biomass
 +
|mmol/m<sup>3</sup>
 +
|phytoplankton
 +
|-
 +
|align="right" | 3
 +
|iZoop
 +
|Zooplankton biomass
 +
|mmol/m<sup>3</sup>
 +
|zooplankton
 +
|-
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|align="right" | 4
 +
|iSDet
 +
|Detritus concentration
 +
|mmol/m<sup>3</sup>
 +
|detritus
 +
|}
 +
 +
 +
The "'''#'''" column denotes the internal index number within the idbio array while the "'''index'''" column is the index within the tracer array '''t'''(:,:,:,:,'''index''').
  
  
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:<div class="box">        [[Variables#TNUDG|TNUDG]] == 4*0.0d0                        ! days</div>
 
:<div class="box">        [[Variables#TNUDG|TNUDG]] == 4*0.0d0                        ! days</div>
  
*Logical switches to specify which variables to consider on tracers point Sources/Sinks (like river runoff): [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
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*Logical switches to specify which variables to consider on tracers point Sources/Sinks (like river runoff): [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.The switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page.<div class="box">  [[Variables#LtracerSrc|LtracerSrc]] == 4*F</div><!--As an example, if you wanted to exclude '''zooplankton biomass''' from the tracers you would do the following:<div class="box">  [[Variables#LtracerSrc|LtracerSrc]] == 2*T F T</div-->
:<div class="box">  [[Variables#LtracerSrc|LtracerSrc]] == 4*F</div>
 
  
*Logical switches to activate writing of biological tracers into history/average output file: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
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*Logical switches to activate writing of biological tracers into history/average output file: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected. The switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page.
:<div class="box">[[Variables#Hout|Hout(idTvar)]] == 4*T                  ! biological tracer<br />[[Variables#Hout|Hout(idTsur)]] == 4*F                 ! surface tracer flux<br /><br />!    idTvar(idbio(1))=iNO3_    Nitrate concentration<br />!    idTvar(idbio(2))=iPhyt    Phytoplankton biomass<br />!    idTvar(idbio(3))=iZoop    Zooplankton biomass<br />!    idTvar(idbio(4))=iSdet    Detritus concentration</div>
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:<div class="box">[[Variables#Hout|Hout(idTvar)]] == 4*T                  ! biological tracer<br />[[Variables#Hout|Hout(idTsur)]] == 4*F</div>
<!--:As an example, if you only wanted to write '''zooplankton biomass''' to the history and averages files you would do the following:
 
:<div class="box">[[Variables#Hout|Hout(idTvar)]] == 2*F T F</div>-->
 

Revision as of 18:44, 7 December 2009

Powell NPZD Biological Model Input Script - npzd_Powell.in

The npzd_Powell.in file sets the parameters for the Powell et al. NPZD model. The name of this file is set by the BPARNAM keyword in the ocean.in file. A default npzd_Powell.in standard input ASCII file can be found in the User/External subdirectory of the ROMS source code. In order to include the Powell et al. NPZD model in ROMS you must set BPARNAM correctly and activate the NPZD_POWELL CPP option.


# index Description Units NetCDF variable
1 iNO3_ Nitrate concentration mmol/m3 NO3
2 iPhyt Phytoplankton biomass mmol/m3 phytoplankton
3 iZoop Zooplankton biomass mmol/m3 zooplankton
4 iSDet Detritus concentration mmol/m3 detritus


The "#" column denotes the internal index number within the idbio array while the "index" column is the index within the tracer array t(:,:,:,:,index).


The Powell NPZD model equations and representative parameters may be found in:


Note Notice: Detailed information about ROMS input script file syntax can be found here.


Biological Model Parameters

Input parameter units are specified within brackets ([ ])and default values are specified within braces ({ }).

  • This switch to control the computation of npzd_Franks 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
  • Initial concentration for analytical uniform initial conditions, [millimole/m3]. It is only used when ANA_BIOLOGY is activated.
BioIni(iNO3_) == 17.0d0  ! nitrate
BioIni(iPhyt) == 1.0d0  ! phytoplankton
BioIni(iZoop) == 1.0d0  ! zooplankton
BioIni(iSDet) == 1.0d0  ! detritus
  • Fraction of shortwave radiation that is photosynthetically active, [nondimensional], {0.43d0}.
PARfrac == 0.43d0
  • Light attenuation due to seawater, [1/m], {0.067d0}.
AttSW == 0.0067d0  ! k_ext
  • Light attenuation due to phytoplankton, self-shading coefficient, [m2/millimole_N], {0.0095d0}.
AttPhy == 0.0095d0  ! k_extP
  • Phytoplankton, initial slope of P-I curve [m2/W], {0.025d0}.
PhyIS == 0.025d0  ! alpha
  • Nitrate uptake rate, [1/day], {1.5d0}.
Vm_NO3 == 1.5d0  ! Vm
  • Phytoplankton mortality rate to Detritus pool, [1/day], {0.1d0}.
PhyMRD == 0.1d0  ! sigmaD
  • Phytoplankton mortality rate to Nitrogen pool, [1/day], {0.0d0}.
PhyMRN == 0.0d0  ! sigmaN
  • Half-saturation for phytoplankton nitrate uptake [millimole_N m-3], {1.0d0}.
K_NO3 == 1.0d0  ! k_N
  • Ivlev constant for zooplankton grazing parameterization [Nondimensional], {14*0.06=0.84d0}
Ivlev == 0.84d0
  • Zooplankton grazing rate, [1/day], {0.52}.
ZooGR == 0.52d0  ! R_m
  • Zooplankton excretion efficiency to Detritus pool [nondimensional], {0.3d0}
ZooEED == 0.0d0  ! gammaD
  • Zooplankton excretion efficiency to Nitrogen pool [nondimensional], {0.3d0}
ZooEEN == 0.3d0  ! gammaN
  • Zooplankton mortality rate to Detritus pool, [1/day], {0.0d0}.
ZooMRD == 0.145d0  ! zetaD
  • Zooplankton mortality rate to Nitrogen pool, [1/day], {0.145d0}.
ZooMRN == 0.0d0  ! zetaN
  • Detritus remineralization rate, [1/day], {0.1d0}.
DetRR == 1.03d0  ! delta
  • Vertical sinking velocity for phytoplankton [m/day], {0.0d0}.
wPhy == 0.0d0  ! wP
  • Detrital sinking rate, [m/day], {8.0d0}.
wDet == 8.0d0  ! wD
  • Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer for nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids] values expected.
TNU2 == 4*5.0d0  ! m2/s
TNU4 == 4*0.0d0  ! m4/s

ad_TNU2 == 4*0.0d0  ! m2/s
ad_TNU4 == 4*0.0d0  ! m4/s
  • Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids] values expected.
AKT_BAK == 4*1.0d-6  ! m2/s

ad_AKT_fac == 4*1.0d0  ! nondimensional
  • Nudging/relaxation time scales, inverse scales will be computed internally: [1:NBT,Ngrids] values expected.
TNUDG == 4*0.0d0  ! days
  • Logical switches to specify which variables to consider on tracers point Sources/Sinks (like river runoff): [1:NBT,Ngrids] values expected.The switches correspond to the Variable Index Table at the top of this page.
    LtracerSrc == 4*F
  • Logical switches to activate writing of biological tracers into history/average output file: [1:NBT,Ngrids] values expected. The switches correspond to the Variable Index Table at the top of this page.
Hout(idTvar) == 4*T  ! biological tracer
Hout(idTsur) == 4*F