Difference between revisions of "bio Fennel.in"

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*Light attenuation due to seawater [1/m], {0.04d0}.
*Light attenuation due to seawater [1/m], {0.04d0}.
:<div class="box">      AttSW == 0.04d0</div>
:<div class="box">      [[Variables#AttSW|AttSW]] == 0.04d0</div>


*Light attenuation by chlorophyll [1/(mg_Chl m2)], {0.02486d0}.
*Light attenuation by chlorophyll [1/(mg_Chl m2)], {0.02486d0}.
:<div class="box">      AttChl == 0.02486d0</div>
:<div class="box">      [[Variables#AttChl|AttChl]] == 0.02486d0</div>


*Fraction of shortwave radiation that is photosynthetically active [nondimensional], {0.43d0}.
*Fraction of shortwave radiation that is photosynthetically active [nondimensional], {0.43d0}.
:<div class="box">    PARfrac == 0.43d0</div>
:<div class="box">    [[Variables#PARfrac|PARfrac]] == 0.43d0</div>


*Eppley temperature-limited growth parameter [nondimensional], {1.0d0}.
*Eppley temperature-limited growth parameter [nondimensional], {1.0d0}.
:<div class="box">        Vp0 == 1.0d0</div>
:<div class="box">        [[Variables#Vp0|Vp0]] == 1.0d0</div>


*Radiation threshold for nitrification inhibition [Watts/m2], {0.0095d0}.
*Radiation threshold for nitrification inhibition [Watts/m2], {0.0095d0}.
:<div class="box">    I_thNH4 == 0.0095d0</div>
:<div class="box">    [[Variables#I_thNH4|I_thNH4]] == 0.0095d0</div>


*Half-saturation radiation for nitrification inhibition [Watts/m2], {0.036d0}.
*Half-saturation radiation for nitrification inhibition [Watts/m2], {0.036d0}.
:<div class="box">    D_p5NH4 == 0.1d0</div>
:<div class="box">    [[Variables#D_p5NH4|D_p5NH4]] == 0.1d0</div>


*Nitrification rate: oxidation of NH<sub>4</sub> to NO<sub>3</sub> [1/day], {0.05d0}.
*Nitrification rate: oxidation of NH<sub>4</sub> to NO<sub>3</sub> [1/day], {0.05d0}.
:<div class="box">      NitriR == 0.05d0</div>
:<div class="box">      [[Variables#NitriR|NitriR]] == 0.05d0</div>


*Inverse half-saturation for phytoplankton NO<sub>3</sub> uptake [1/(millimole_N m-3)], {2.0d0}.
*Inverse half-saturation for phytoplankton NO<sub>3</sub> uptake [1/(millimole_N m-3)], {2.0d0}.
:<div class="box">      K_NO3 == 2.0d0</div>
:<div class="box">      [[Variables#K_NO3|K_NO3]] == 2.0d0</div>


*Inverse half-saturation for phytoplankton NH<sub>4</sub> uptake [1/(millimole_N m-3)], {2.0d0}.
*Inverse half-saturation for phytoplankton NH<sub>4</sub> uptake [1/(millimole_N m-3)], {2.0d0}.
:<div class="box">      K_NH4 == 2.0d0</div>
:<div class="box">      [[Variables#K_NH4|K_NH4]] == 2.0d0</div>


*Zooplankton half-saturation constant (squared) for ingestion [millimole_N m-3]^2, {1.0d0}.
*Zooplankton half-saturation constant (squared) for ingestion [millimole_N m-3]^2, {1.0d0}.
:<div class="box">      K_Phy == 2.0d0</div>
:<div class="box">      [[Variables#K_Phy|K_Phy]] == 2.0d0</div>


*Maximum chlorophyll to carbon ratio [mg_Chl/mg_C], {0.0535d0}.
*Maximum chlorophyll to carbon ratio [mg_Chl/mg_C], {0.0535d0}.
:<div class="box">    Chl2C_m == 0.0535d0</div>
:<div class="box">    [[Variables#Chl2C_m|Chl2C_m]] == 0.0535d0</div>


*Chlorophyll minimum threshold value [mg_Chl/m3], {0.0d0}.
*Chlorophyll minimum threshold value [mg_Chl/m3], {0.0d0}.
:<div class="box">      ChlMin == 0.001d0</div>
:<div class="box">      [[Variables#ChlMin|ChlMin]] == 0.001d0</div>


*Phytoplankton Carbon:Nitrogen ratio [mole_C/mole_N] , {6.625d0}.
*Phytoplankton Carbon:Nitrogen ratio [mole_C/mole_N] , {6.625d0}.
:<div class="box">      PhyCN == 6.625d0</div>
:<div class="box">      [[Variables#PhyCN|PhyCN]] == 6.625d0</div>


*Phytoplankton, NH<sub>4</sub> inhibition parameter [1/(millimole_N)], {1.5d0}.
*Phytoplankton, NH<sub>4</sub> inhibition parameter [1/(millimole_N)], {1.5d0}.
:<div class="box">      PhyIP == 1.5d0</div>
:<div class="box">      [[Variables#PhyIP|PhyIP]] == 1.5d0</div>


*Phytoplankton, initial slope of P-I curve [mg_C/(mg_Chl Watts m-2 day)], {0.025d0}.
*Phytoplankton, initial slope of P-I curve [mg_C/(mg_Chl Watts m-2 day)], {0.025d0}.
:<div class="box">      PhyIS == 0.025d0</div>
:<div class="box">      [[Variables#PhyIS|PhyIS]] == 0.025d0</div>


*Phytoplankton minimum threshold value [millimole_N/m3], {0.0d0}.
*Phytoplankton minimum threshold value [millimole_N/m3], {0.0d0}.
:<div class="box">      PhyMin == 0.001d0</div>
:<div class="box">      [[Variables#PhyMin|PhyMin]] == 0.001d0</div>


*Phytoplankton mortality rate [1/day], {0.072d0}.
*Phytoplankton mortality rate [1/day], {0.072d0}.
:<div class="box">      PhyMR == 0.15d0</div>
:<div class="box">      [[Variables#PhyMR|PhyMR]] == 0.15d0</div>


*Zooplankton Nitrogen assimilation efficiency [nondimesnional], {0.75d0}.
*Zooplankton Nitrogen assimilation efficiency [nondimesnional], {0.75d0}.
:<div class="box">    ZooAE_N == 0.75d0</div>
:<div class="box">    [[Variables#ZooAE_N|ZooAE_N]] == 0.75d0</div>


*Zooplankton Basal metabolism [1/day], {0.1d0}.
*Zooplankton Basal metabolism [1/day], {0.1d0}.
:<div class="box">      ZooBM == 0.1d0</div>
:<div class="box">      [[Variables#ZooBM|ZooBM]] == 0.1d0</div>


*Zooplankton Carbon:Nitrogen ratio [mole_C/mole_N], {5.0d0}.
*Zooplankton Carbon:Nitrogen ratio [mole_C/mole_N], {5.0d0}.
:<div class="box">      ZooCN == 6.625d0</div>
:<div class="box">      [[Variables#ZooCN|ZooCN]] == 6.625d0</div>


*Zooplankton specific excretion rate [1/day], {0.1d0}.
*Zooplankton specific excretion rate [1/day], {0.1d0}.
:<div class="box">      ZooER == 0.1d0</div>
:<div class="box">      [[Variables#ZooER|ZooER]] == 0.1d0</div>


*Zooplankton maximum growth rate [1/day], {0.75d0}.
*Zooplankton maximum growth rate [1/day], {0.75d0}.
:<div class="box">      ZooGR == 0.6d0</div>
:<div class="box">      [[Variables#ZooGR|ZooGR]] == 0.6d0</div>


*Zooplankton minimum threshold value [millimole_N/m3], {0.0d0}.
*Zooplankton minimum threshold value [millimole_N/m3], {0.0d0}.
:<div class="box">      ZooMin == 0.001d0</div>
:<div class="box">      [[Variables#ZooMin|ZooMin]] == 0.001d0</div>


*Zooplankton mortality rate [1/day], {0.025d0}.
*Zooplankton mortality rate [1/day], {0.025d0}.
:<div class="box">      ZooMR == 0.025d0</div>
:<div class="box">      [[Variables#ZooMR|ZooMR]] == 0.025d0</div>


*Large detritus remineralization rate N-fraction [1/day], {0.01d0}.
*Large detritus remineralization rate N-fraction [1/day], {0.01d0}.
:<div class="box">      LDeRRN == 0.01d0</div>
:<div class="box">      [[Variables#LDeRRN|LDeRRN]] == 0.01d0</div>


*Large detritus remineralization rate C-fraction [1/day].
*Large detritus remineralization rate C-fraction [1/day].
:<div class="box">      LDeRRC == 0.01d0</div>
:<div class="box">      [[Variables#LDeRRC|LDeRRC]] == 0.01d0</div>


*Coagulation rate: aggregation rate of SDeN + Phy ==> LDeN [1/day], {0.005d0}.
*Coagulation rate: aggregation rate of SDeN + Phy ==> LDeN [1/day], {0.005d0}.
:<div class="box">      CoagR == 0.005d0</div>
:<div class="box">      [[Variables#CoagR|CoagR]] == 0.005d0</div>


*Small detritus remineralization rate N-fraction [1/day], {0.03d0}.
*Small detritus remineralization rate N-fraction [1/day], {0.03d0}.
:<div class="box">      SDeRRN == 0.03d0</div>
:<div class="box">      [[Variables#SDeRRN|SDeRRN]] == 0.03d0</div>


*Small detritus remineralization rate C-fraction[1/day].
*Small detritus remineralization rate C-fraction[1/day].
:<div class="box">      SDeRRC == 0.03d0</div>
:<div class="box">      [[Variables#SDeRRC|SDeRRC]] == 0.03d0</div>


*Vertical sinking velocity for phytoplankton [m/day], {0.1d0}.
*Vertical sinking velocity for phytoplankton [m/day], {0.1d0}.
:<div class="box">        wPhy == 0.1d0</div>
:<div class="box">        [[Variables#wPhy|wPhy]] == 0.1d0</div>


*Vertical sinking velocity for large detritus [m/day], {1.0d0}.
*Vertical sinking velocity for large detritus [m/day], {1.0d0}.
:<div class="box">      wLDet == 1.0d0</div>
:<div class="box">      [[Variables#wLDet|wLDet]] == 1.0d0</div>


*Vertical sinking velocity for small detritus [m/day], {0.1d0}.
*Vertical sinking velocity for small detritus [m/day], {0.1d0}.
:<div class="box">      wSDet == 0.1d0</div>
:<div class="box">      [[Variables#wSDet|wSDet]] == 0.1d0</div>


*CO<sub>2</sub> partial pressure in the air (parts per million by volume), {377.0d0}.
*CO<sub>2</sub> partial pressure in the air (parts per million by volume), {377.0d0}.
:<div class="box">    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: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
:<div class="box">        TNU2 == 12*0.0d0              ! m2/s<br />        TNU4 == 12*0.0d0              ! m4/s</div>
:<div class="box">        [[Variables#TNU2|TNU2]] == 12*0.0d0              ! m2/s<br />        [[Variables#TNU4|TNU4]] == 12*0.0d0              ! m4/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">    AKT_BAK == 12*1.0d-6            ! m2/s</div>
:<div class="box">    [[Variables#AKT_BAK|AKT_BAK]] == 12*1.0d-6            ! m2/s</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">      TNUDG == 12*0.0d0              ! days</div>
:<div class="box">      [[Variables#TNUDG|TNUDG]] == 12*0.0d0              ! days</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.
:<div class="box">Hout(idTvar) == 12*T                  ! biological tracer<br />Hout(idTsur) == 12*F                  ! surface tracer flux</div>
:<div class="box">[[Variables#Hout(idTvar)|Hout(idTvar)]] == 12*T                  ! biological tracer<br />[[Variables#Hout(idTsur)|Hout(idTsur)]] == 12*F                  ! surface tracer flux</div>


*Logical switches to activate writing of diagnostics terms into diagnostic output file [1:[[Variables#Ngrids|Ngrids]]] values expected.
*Logical switches to activate writing of diagnostics terms into diagnostic output file [1:[[Variables#Ngrids|Ngrids]]] values expected.
:<div class="box">Hout(iCOfx) == T                      ! air-sea CO<sub>2</sub> flux<br />Hout(iDNIT) == T                      ! denitrification flux<br />Hout(ipCO2) == T                      ! CO<sub>2</sub> partial pressure<br />Hout(iO2fx) == T                      ! air-sea O<sub>2</sub> flux<br />Hout(iPPro) == T                      ! primary production<br />Hout(iNO3u) == T                      ! NO<sub>3</sub> uptake</div>
:<div class="box">[[Variables#Hout(iCOfx)|Hout(iCOfx)]] == T                      ! air-sea CO<sub>2</sub> flux<br />[[Variables#Hout(iDNIT)|Hout(iDNIT)]] == T                      ! denitrification flux<br />[[Variables#Hout(ipCO2)|Hout(ipCO2)]] == T                      ! CO<sub>2</sub> partial pressure<br />[[Variables#Hout(iO2fx)|Hout(iO2fx)]] == T                      ! air-sea O<sub>2</sub> flux<br />[[Variables#Hout(iPPro)|Hout(iPPro)]] == T                      ! primary production<br />[[Variables#Hout(iNO3u)|Hout(iNO3u)]] == T                      ! NO<sub>3</sub> uptake</div>

Revision as of 12:40, 1 April 2008

Fasham Model Input Script - bioFasham.in

The bioFasham.in file sets the parameters for the bioFasham model. The name of this file is set by the BPARNAM keyword in the ocean.in file. A default bioFasham.in 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 BPARNAM correctly and activate the BIO_FASHAM CPP option.


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 bioFasham 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: [1:NBT,Ngrids] values expected.
TNU2 == 12*0.0d0  ! m2/s
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
  • Nudging/relaxation time scales, inverse scales will be computed internally: [1:NBT,Ngrids] values expected.
TNUDG == 12*0.0d0  ! days
  • 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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