Difference between revisions of "bio Fennel.in"

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m (moved bioFasham.in to bio Fennel.in: Fasham model renamed to Fennel.)   (change visibility)
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<div class="title">Fasham Model Input Script - <span class="red">bioFasham.in</span></div>
<div class="title">Fennel Model Input Script - <span class="red">bioFennel.in</span></div>


The <span class="red">bioFasham.in</span> file sets the parameters for the '''bioFasham''' model. The name of this file is set by the [[Variables#bparnam|BPARNAM]] keyword in the [[ocean.in]] file. A default <span class="red">bioFasham.in</span> standard input ASCII file can be found in the '''User/External''' subdirectory of the ROMS source code. In order to include the '''bioFasham''' model in ROMS you must set [[Variables#bparnam|BPARNAM]] correctly and activate the [[BIO_FASHAM]] [[Options|CPP option]].
The <span class="red">bioFennel.in</span> file sets the parameters for the '''bioFennel''' (formerly bioFasham) model. The name of this file is set by the [[Variables#bparnam|BPARNAM]] keyword in the [[ocean.in]] file. A default <span class="red">bioFennel.in</span> standard input ASCII file can be found in the '''User/External''' subdirectory of the ROMS source code. In order to include the '''bioFennel''' model in ROMS you must set [[Variables#bparnam|BPARNAM]] correctly and activate the [[BIO_FENNEL]] [[Options|CPP option]].




The Fasham model equations and representative parameters may be found in:
The Fennel model equations and representative parameters may be found in:
*[[Bibliography#FashamMJR_1990a|Fasham et al. 1990a]]
*[[Bibliography#FashamMJR_1990a|Fasham et al. 1990a]]


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Input parameter units are specified within brackets (<span class="olive">[ ]</span>)and default values are specified within braces (<span class="olive">{ }</span>).
Input parameter units are specified within brackets (<span class="olive">[ ]</span>)and default values are specified within braces (<span class="olive">{ }</span>).


*This switch to control the computation of bioFasham within nested and/or multiple connected grids. By default this switch is set to TRUE in <span class="red">mod_scalars.F</span> for all grids. [[Variables#Ngrids|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 [[Variables#NBT|NBT]] in <span class="red">mod_param.F</span>. In order to make the model more efficient in memory usage, [[Variables#NBT|NBT(:)]] should be zero in such grids.
*This switch controls the computation of bioFennel within nested and/or multiple connected grids. By default this switch is set to TRUE in <span class="red">mod_scalars.F</span> for all grids. [[Variables#Ngrids|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 [[Variables#NBT|NBT]] in <span class="red">mod_param.F</span>. In order to make the model more efficient in memory usage, [[Variables#NBT|NBT(:)]] should be zero in such grids.
:<div class="box">    [[Variables#Lbiology|Lbiology]] == T</div>
:<div class="box">    [[Variables#Lbiology|Lbiology]] == T</div>


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:<div class="box">    [[Variables#pCO2air|pCO2air]] == 370.0d0</div>
:<div class="box">    [[Variables#pCO2air|pCO2air]] == 370.0d0</div>


*Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
*Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer for nonlinear model and adjoint-based algorithms: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
:<div class="box">        [[Variables#TNU2|TNU2]] == 12*0.0d0              ! m<sup>2</sup>/s<br />        [[Variables#TNU4|TNU4]] == 12*0.0d0              ! m<sup>4</sup>/s</div>
:<div class="box">        [[Variables#TNU2|TNU2]] == 12*0.0d0              ! m<sup>2</sup>/s<br />        [[Variables#TNU4|TNU4]] == 12*0.0d0              ! m<sup>4</sup>/s<br /><br />    [[Variables#ad_TNU2|ad_TNU2]] == 12*0.0d0              ! m<sup>2</sup>/s<br />    [[Variables#ad_TNU4|ad_TNU4]] == 12*0.0d0              ! m<sup>4</sup>/s</div>


*Vertical mixing coefficients for biological tracers: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
*Vertical mixing coefficients for biological tracers: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
:<div class="box">    [[Variables#AKT_BAK|AKT_BAK]] == 12*1.0d-6            ! m<sup>2</sup>/s</div>
:<div class="box">    [[Variables#AKT_BAK|AKT_BAK]] == 12*1.0d-6            ! m<sup>2</sup>/s<br /><br />  [[Variables#ad_AKT_fac|ad_AKT_fac]] == 12*1.0d0              ! nondimensional</div>


*Nudging/relaxation time scales, inverse scales will be computed internally: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
*Nudging/relaxation time scales, inverse scales will be computed internally: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
:<div class="box">      [[Variables#TNUDG|TNUDG]] == 12*0.0d0              ! days</div>
:<div class="box">      [[Variables#TNUDG|TNUDG]] == 12*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.
:<div class="box">  [[Variables#LtracerSrc|LtracerSrc]] == 12*F</div>


*Logical switches to activate writing of biological tracers into history output file: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
*Logical switches to activate writing of biological tracers into history output file: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.

Revision as of 14:35, 3 December 2009

Fennel Model Input Script - bioFennel.in

The bioFennel.in file sets the parameters for the bioFennel (formerly bioFasham) model. The name of this file is set by the BPARNAM keyword in the ocean.in file. A default bioFennel.in standard input ASCII file can be found in the User/External subdirectory of the ROMS source code. In order to include the bioFennel model in ROMS you must set BPARNAM correctly and activate the BIO_FENNEL CPP option.


The Fennel 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 controls the computation of bioFennel 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 attenuation due to seawater [1/m], {0.04d0}.
AttSW == 0.04d0
  • Light attenuation by chlorophyll [1/(mg_Chl m2)], {0.02486d0}.
AttChl == 0.02486d0
  • Fraction of shortwave radiation that is photosynthetically active [nondimensional], {0.43d0}.
PARfrac == 0.43d0
  • Eppley temperature-limited growth parameter [nondimensional], {1.0d0}.
Vp0 == 1.0d0
  • Radiation threshold for nitrification inhibition [Watts/m2], {0.0095d0}.
I_thNH4 == 0.0095d0
  • Half-saturation radiation for nitrification inhibition [Watts/m2], {0.036d0}.
D_p5NH4 == 0.1d0
  • Nitrification rate: oxidation of NH4 to NO3 [1/day], {0.05d0}.
NitriR == 0.05d0
  • Inverse half-saturation for phytoplankton NO3 uptake [1/(millimole_N m-3)], {2.0d0}.
K_NO3 == 2.0d0
  • Inverse half-saturation for phytoplankton NH4 uptake [1/(millimole_N m-3)], {2.0d0}.
K_NH4 == 2.0d0
  • Zooplankton half-saturation constant (squared) for ingestion [millimole_N m-3]2, {1.0d0}.
K_Phy == 2.0d0
  • Maximum chlorophyll to carbon ratio [mg_Chl/mg_C], {0.0535d0}.
Chl2C_m == 0.0535d0
  • Chlorophyll minimum threshold value [mg_Chl/m3], {0.0d0}.
ChlMin == 0.001d0
  • Phytoplankton Carbon:Nitrogen ratio [mole_C/mole_N] , {6.625d0}.
PhyCN == 6.625d0
  • Phytoplankton, NH4 inhibition parameter [1/(millimole_N)], {1.5d0}.
PhyIP == 1.5d0
  • Phytoplankton, initial slope of P-I curve [mg_C/(mg_Chl Watts m-2 day)], {0.025d0}.
PhyIS == 0.025d0
  • Phytoplankton minimum threshold value [millimole_N/m3], {0.0d0}.
PhyMin == 0.001d0
  • Phytoplankton mortality rate [1/day], {0.072d0}.
PhyMR == 0.15d0
  • Zooplankton Nitrogen assimilation efficiency [nondimesnional], {0.75d0}.
ZooAE_N == 0.75d0
  • Zooplankton Basal metabolism [1/day], {0.1d0}.
ZooBM == 0.1d0
  • Zooplankton Carbon:Nitrogen ratio [mole_C/mole_N], {5.0d0}.
ZooCN == 6.625d0
  • Zooplankton specific excretion rate [1/day], {0.1d0}.
ZooER == 0.1d0
  • Zooplankton maximum growth rate [1/day], {0.75d0}.
ZooGR == 0.6d0
  • Zooplankton minimum threshold value [millimole_N/m3], {0.0d0}.
ZooMin == 0.001d0
  • Zooplankton mortality rate [1/day], {0.025d0}.
ZooMR == 0.025d0
  • Large detritus remineralization rate N-fraction [1/day], {0.01d0}.
LDeRRN == 0.01d0
  • Large detritus remineralization rate C-fraction [1/day].
LDeRRC == 0.01d0
  • Coagulation rate: aggregation rate of SDeN + Phy ==> LDeN [1/day], {0.005d0}.
CoagR == 0.005d0
  • Small detritus remineralization rate N-fraction [1/day], {0.03d0}.
SDeRRN == 0.03d0
  • Small detritus remineralization rate C-fraction[1/day].
SDeRRC == 0.03d0
  • Vertical sinking velocity for phytoplankton [m/day], {0.1d0}.
wPhy == 0.1d0
  • Vertical sinking velocity for large detritus [m/day], {1.0d0}.
wLDet == 1.0d0
  • Vertical sinking velocity for small detritus [m/day], {0.1d0}.
wSDet == 0.1d0
  • CO2 partial pressure in the air (parts per million by volume), {377.0d0}.
pCO2air == 370.0d0
  • Lateral, constant, harmonic/biharmonic horizontal diffusion of biological tracer for nonlinear model and adjoint-based algorithms: [1:NBT,Ngrids] values expected.
TNU2 == 12*0.0d0  ! m2/s
TNU4 == 12*0.0d0  ! m4/s

ad_TNU2 == 12*0.0d0  ! m2/s
ad_TNU4 == 12*0.0d0  ! m4/s
  • Vertical mixing coefficients for biological tracers: [1:NBT,Ngrids] values expected.
AKT_BAK == 12*1.0d-6  ! m2/s

ad_AKT_fac == 12*1.0d0  ! nondimensional
  • Nudging/relaxation time scales, inverse scales will be computed internally: [1:NBT,Ngrids] values expected.
TNUDG == 12*0.0d0  ! days
  • Logical switches to specify which variables to consider on tracers point Sources/Sinks (like river runoff): [1:NBT,Ngrids] values expected.
LtracerSrc == 12*F
  • Logical switches to activate writing of biological tracers into history output file: [1:NBT,Ngrids] values expected.
Hout(idTvar) == 12*T  ! biological tracer
Hout(idTsur) == 12*F  ! surface tracer flux
  • Logical switches to activate writing of diagnostics terms into diagnostic output file [1:Ngrids] values expected.
Hout(iCOfx) == T  ! air-sea CO2 flux
Hout(iDNIT) == T  ! denitrification flux
Hout(ipCO2) == T  ! CO2 partial pressure
Hout(iO2fx) == T  ! air-sea O2 flux
Hout(iPPro) == T  ! primary production
Hout(iNO3u) == T  ! NO3 uptake
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