Difference between revisions of "nemuro.in"

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:<div class="box">      [[Variables#TNUDG|TNUDG]] == 11*0.0d0                  ! days</div>
 
:<div class="box">      [[Variables#TNUDG|TNUDG]] == 11*0.0d0                  ! days</div>
  
*Set horizontal and vertical advection schemes for biological tracers. A different advection scheme is allowed for each tracer. For example, a positive-definite (monotonic) algorithm can be activated for salinity and biological tracers, while a different one is set for temperature.<div class="box">Keyword    Advection Algorithm<br /><br />A4        4th-order Akima (horizontal/vertical)<br />C2        2nd-order centered differences (horizontal/vertical)<br />C4        4th-order centered differences (horizontal/vertical)<br />HSIMT      3th-order HSIMT with TVD limiter (horizontal/vertical)<br />MPDATA    recursive flux corrected MPDATA (horizontal/vertical)<br />SPLINES    parabolic splines reconstruction (only vertical)<br />SU3        split third-order upstream (horizontal/vertical)<br />U3        3rd-order upstresm-bias (only horizontal)</div>The user has the option of specifying the full Keyword or the first two letters, regardless if using uppercase or lowercase. If nested grids, specify values for each grid. For more details please read the [[roms.in#Tracer_Advection_Schemes|roms.in Tracer Advection Schemes]] section. [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values are expected.<div class="box">  [[Variables#Hadvection|Hadvection]] == HSIMT    \                    ! idbio( 1), nanophyto<br />                HSIMT    \                    ! idbio( 2), diatom<br />                HSIMT    \                    ! idbio( 3), microzoo<br />                HSIMT    \                    ! idbio( 4), mesozoo<br />                HSIMT    \                    ! idbio( 5), Pzooplankton<br />                HSIMT    \                    ! idbio( 6), NO3<br />                HSIMT    \                    ! idbio( 7), NH4<br />                HSIMT    \                    ! idbio( 8), PON<br />                HSIMT    \                    ! idbio( 9), DON<br />                HSIMT    \                    ! idbio(10), SiOH4<br />                HSIMT                          ! idbio(11), opal<br /><br />  [[Variables#Vadvection|Vadvection]] == HSIMT    \                    ! idbio( 1), nanophyto<br />                HSIMT    \                    ! idbio( 2), diatom<br />                HSIMT    \                    ! idbio( 3), microzoo<br />                HSIMT    \                    ! idbio( 4), mesozoo<br />                HSIMT    \                    ! idbio( 5), Pzooplankton<br />                HSIMT    \                    ! idbio( 6), NO3<br />                HSIMT    \                    ! idbio( 7), NH4<br />                HSIMT    \                    ! idbio( 8), PON<br />                HSIMT    \                    ! idbio( 9), DON<br />                HSIMT    \                    ! idbio(10), SiOH4<br />                HSIMT                          ! idbio(11), opal</div>
+
*Set horizontal and vertical advection schemes for biological tracers. A different advection scheme is allowed for each tracer. For example, a positive-definite (monotonic) algorithm can be activated for salinity and biological tracers, while a different one is set for temperature.<div class="box">Keyword    Advection Algorithm<br /><br />A4        4th-order Akima (horizontal/vertical)<br />C2        2nd-order centered differences (horizontal/vertical)<br />C4        4th-order centered differences (horizontal/vertical)<br />HSIMT      3th-order HSIMT with TVD limiter (horizontal/vertical)<br />MPDATA    recursive flux corrected MPDATA (horizontal/vertical)<br />SPLINES    parabolic splines reconstruction (only vertical)<br />SU3        split third-order upstream (horizontal/vertical)<br />U3        3rd-order upstresm-bias (only horizontal)</div>The user has the option of specifying the full Keyword or the first two letters, regardless if using uppercase or lowercase. If nested grids, specify values for each grid. For more details please read the [[roms.in#Tracer_Advection_Schemes|roms.in Tracer Advection Schemes]] section. [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values are expected.<div class="box">  [[Variables#Hadvection|Hadvection]] == HSIMT    \                    ! [[Variables#idbio|idbio]]( 1), nanophyto<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 2), diatom<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 3), microzoo<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 4), mesozoo<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 5), Pzooplankton<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 6), NO3<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 7), NH4<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 8), PON<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 9), DON<br />                HSIMT    \                    ! [[Variables#idbio|idbio]](10), SiOH4<br />                HSIMT                          ! [[Variables#idbio|idbio]](11), opal<br /><br />  [[Variables#Vadvection|Vadvection]] == HSIMT    \                    ! [[Variables#idbio|idbio]]( 1), nanophyto<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 2), diatom<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 3), microzoo<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 4), mesozoo<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 5), Pzooplankton<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 6), NO3<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 7), NH4<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 8), PON<br />                HSIMT    \                    ! [[Variables#idbio|idbio]]( 9), DON<br />                HSIMT    \                    ! [[Variables#idbio|idbio]](10), SiOH4<br />                HSIMT                          ! [[Variables#idbio|idbio]](11), opal</div>
  
*Adjoint-based algorithms can have different horizontal and vertical schemes for biological tracers.[1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values are expected.<div class="box">[[Variables#ad_Hadvection|ad_Hadvection]] == U3                            ! idbio(:), compact<br /><br />[[Variables#ad_Vadvection|ad_Vadvection]] == C4                            ! idbio(:), compact</div>
+
*Adjoint-based algorithms can have different horizontal and vertical schemes for biological tracers.[1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values are expected.<div class="box">[[Variables#ad_Hadvection|ad_Hadvection]] == U3                            ! [[Variables#idbio|idbio]](:), compact<br /><br />[[Variables#ad_Vadvection|ad_Vadvection]] == C4                            ! [[Variables#idbio|idbio]](:), compact</div>
  
*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:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values. The boundary order is: '''1'''=west, '''2'''=south, '''3'''=east, and '''4'''=north. That is, anticlockwise starting at the western boundary.<br /><br />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.<br /><br />{{note}}'''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.<div class="box"><span class="twilightBlue">!  Keyword    Lateral Boundary Condition Type<br />!<br />!  Cla        Clamped                                _____N_____    j=Mm<br />!  Clo        Closed                                |    4    |<br />!  Gra        Gradient                              |          |<br />!  Nes        Nested                              1 W          E 3<br />!  Nud        Nudging                              |          |<br />!  Per        Periodic                              |_____S_____|<br />!  Rad        Radiation                                  2          j=1<br />!                                                  i=1        i=Lm<br />!                  W      S      E      N<br />!                  e      o      a      o<br />!                  s      u      s      r<br />!                  t      t      t      t<br />!                          h              h<br />!<br />!                  1      2      3      4</span><br /><br />  [[Variables#LBC|LBC(isTvar)]] ==  Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 1), nanophyto<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 2), diatom<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 3), microzoo<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 4), mesozoo<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 5), Pzooplankton<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 6), NO3<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 7), NH4<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 8), PON<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 9), DON<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]](10), SiOH4<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]](11), opal</div>
+
*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:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values. The boundary order is: '''1'''=west, '''2'''=south, '''3'''=east, and '''4'''=north. That is, anticlockwise starting at the western boundary.<br /><br />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.<br /><br />{{note}}'''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.<div class="box"><span class="twilightBlue">!  Keyword    Lateral Boundary Condition Type<br />!<br />!  Cla        Clamped                                _____N_____    j=Mm<br />!  Clo        Closed                                |    4    |<br />!  Gra        Gradient                              |          |<br />!  Nes        Nested                              1 W          E 3<br />!  Nud        Nudging                              |          |<br />!  Per        Periodic                              |_____S_____|<br />!  Rad        Radiation                                  2          j=1<br />!                                                  i=1        i=Lm<br />!                  W      S      E      N<br />!                  e      o      a      o<br />!                  s      u      s      r<br />!                  t      t      t      t<br />!                          h              h<br />!<br />!                  1      2      3      4</span><br /><br />  [[Variables#LBC|LBC]](isTvar) ==  Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 1), nanophyto<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 2), diatom<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 3), microzoo<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 4), mesozoo<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 5), Pzooplankton<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 6), NO3<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 7), NH4<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 8), PON<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 9), DON<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]](10), SiOH4<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]](11), opal</div>
  
 
*Adjoint-based algorithms can have different lateral boundary conditions keywords.<div class="box">[[Variables#ad_LBC|ad_LBC(isTvar)]] ==  Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 1), nanophyto<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 2), diatom<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 3), microzoo<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 4), mesozoo<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 5), Pzooplankton<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 6), NO3<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 7), NH4<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 8), PON<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 9), DON<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]](10), SiOH4<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]](11), opal</div>
 
*Adjoint-based algorithms can have different lateral boundary conditions keywords.<div class="box">[[Variables#ad_LBC|ad_LBC(isTvar)]] ==  Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 1), nanophyto<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 2), diatom<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 3), microzoo<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 4), mesozoo<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 5), Pzooplankton<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 6), NO3<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 7), NH4<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 8), PON<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]]( 9), DON<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]](10), SiOH4<br />                    Per    Clo    Per    Clo \    ! [[Variables#idbio|idbio]](11), opal</div>
  
 
*Logical switches to specify which variables to process for tracers climatology: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected. The 11 switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page.
 
*Logical switches to specify which variables to process for tracers climatology: [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected. The 11 switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page.
:<div class="box"> [[Variables#LtracerCLM|LtracerCLM]] == 11*F</div>
+
:<div class="box">   [[Variables#LtracerCLM|LtracerCLM]] == 11*F</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. The 11 switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page.
 
*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 11 switches correspond to the [[#var_tab|Variable Index Table]] at the top of this page.
:<div class="box"> [[Variables#LtracerSrc|LtracerSrc]] == 11*F</div>
+
:<div class="box">   [[Variables#LtracerSrc|LtracerSrc]] == 11*F</div>
  
 
*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|Hout(idTvar)]] == 11*T    ! ..., NO3, ...          biological tracers<br />[[Variables#Hout|Hout(idTsur)]] == 11*F    ! ..., NO3_sflux, ...    surface tracer flux</div>
+
:<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.
 
*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>
+
:<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.
:<div class="box">[[Variables#Aout|Aout(idTvar)]] == 11*T    ! ..., NO3, ...          biological tracer</div>
+
:<div class="box"> [[Variables#Aout|Aout]](idTvar) == 11*T    ! ..., NO3, ...          biological tracer</div>
  
 
*Logical switches to activate writing of time-averaged, biological tracer diagnostic terms into the diagnostic output file. [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
 
*Logical switches to activate writing of time-averaged, biological tracer diagnostic terms into the diagnostic output file. [1:[[Variables#NBT|NBT]],[[Variables#Ngrids|Ngrids]]] values expected.
:<div class="box">[[Variables#Dout|Dout(iTrate)]] == 11*T    ! ..., NO3_rate, ...    time rate of change<br />[[Variables#Dout|Dout(iThadv)]] == 11*T    ! ..., NO3_hadv, ...    horizontal total advection<br />[[Variables#Dout|Dout(iTxadv)]] == 11*T    ! ..., NO3_xadv, ...    horizontal XI-advection<br />[[Variables#Dout|Dout(iTyadv)]] == 11*T    ! ..., NO3_yadv, ...    horizontal ETA-advection<br />[[Variables#Dout|Dout(iTvadv)]] == 11*T    ! ..., NO3_vadv, ...    vertical advection<br />[[Variables#Dout|Dout(iThdif)]] == 11*T    ! ..., NO3_hdiff, ...    horizontal total diffusion<br />[[Variables#Dout|Dout(iTxdif)]] == 11*T    ! ..., NO3_xdiff, ...    horizontal XI-diffusion<br />[[Variables#Dout|Dout(iTydif)]] == 11*T    ! ..., NO3_ydiff, ...    horizontal ETA-diffusion<br />[[Variables#Dout|Dout(iTsdif)]] == 11*T    ! ..., NO3_sdiff, ...    horizontal S-diffusion<br />[[Variables#Dout|Dout(iTvdif)]] == 11*T    ! ..., NO3_vdiff, ...    vertical diffusion</div>
+
:<div class="box"> [[Variables#Dout|Dout]](iTrate) == 11*T    ! ..., NO3_rate, ...    time rate of change<br /> [[Variables#Dout|Dout]](iThadv) == 11*T    ! ..., NO3_hadv, ...    horizontal total advection<br /> [[Variables#Dout|Dout]](iTxadv) == 11*T    ! ..., NO3_xadv, ...    horizontal XI-advection<br /> [[Variables#Dout|Dout]](iTyadv) == 11*T    ! ..., NO3_yadv, ...    horizontal ETA-advection<br /> [[Variables#Dout|Dout]](iTvadv) == 11*T    ! ..., NO3_vadv, ...    vertical advection<br /> [[Variables#Dout|Dout]](iThdif) == 11*T    ! ..., NO3_hdiff, ...    horizontal total diffusion<br /> [[Variables#Dout|Dout]](iTxdif) == 11*T    ! ..., NO3_xdiff, ...    horizontal XI-diffusion<br /> [[Variables#Dout|Dout]](iTydif) == 11*T    ! ..., NO3_ydiff, ...    horizontal ETA-diffusion<br /> [[Variables#Dout|Dout]](iTsdif) == 11*T    ! ..., NO3_sdiff, ...    horizontal S-diffusion<br /> [[Variables#Dout|Dout]](iTvdif) == 11*T    ! ..., NO3_vdiff, ...    vertical diffusion</div>

Latest revision as of 17:19, 16 January 2020

NEMURO Model Input Script - nemuro.in

The nemuro.in file sets the parameters for the NEMURO model. The name of this file is set by the BPARNAM keyword in the roms.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:


Note 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].
AttPS == 0.04d0  ! small biomass
AttPL == 0.04d0  ! large biomass
  • 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].
AlphaPS == 0.01d0  ! small biomass
AlphaPL == 0.01d0  ! large biomass
  • Phytoplankton photoinhibition coefficient, [1/(W/m2) 1/day].
BetaPS == 4.5d-4  ! small biomass
BetaPL == 4.5d-4  ! large biomass


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].
VmaxS == 0.4d0  ! small biomass
VmaxL == 0.8d0  ! large biomass
  • Phytoplankton half saturation constant for Nitrate [millimole_N/m3].
KNO3S == 1.0d0  ! small biomass
KNO3L == 3.0d0  ! large biomass
  • Phytoplankton half saturation constant for Ammonium [millimole_N/m3].
KNH4S == 0.1d0  ! small biomass
KNH4L == 0.3d0  ! large biomass
  • Phytoplankton half saturation constant for Silicate [millimole_Si/m3].
KSiL == 6.0d0  ! large biomass
  • Phytoplankton Ammonium inhibition coefficient [m3/millimole_N].
PusaiS == 1.5d0  ! small biomass
PusaiL == 1.5d0  ! large biomass
  • Phytoplankton temperature coefficient for photosynthetic rate [1/Celsius].
KGppS == 6.93d-2  ! small biomass
KGppL == 6.93d-2  ! large biomass
  • Phytoplankton respiration rate at 0 Celsius [1/day].
ResPS0 == 0.03d0  ! small biomass
ResPL0 == 0.03d0  ! large biomass
  • Phytoplankton temperature coefficient for respiration [1/Celsius].
KResPS == 0.0519d0  ! small biomass
KResPL == 0.0519d0  ! large biomass
  • Phytoplankton ratio of extracellular excretion to photosynthesis [nondimensional].
GammaS == 0.135d0  ! small biomass
GammaL == 0.135d0  ! large biomass
  • Phytoplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].
MorPS0 == 58.5d-3  ! small biomass
MorPL0 == 29.0d-3  ! large biomass
  • Phytoplankton temperature coefficient for mortality [1/Celsius].
KMorPS == 6.93d-2  ! small biomass
KMorPL == 6.93d-2  ! large biomass


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].
KGraS == 6.93d-2  ! small biomass
KGraL == 6.93d-2  ! large biomass
KGraP == 6.93d-2  ! predator biomass

Zooplankton Ivlev constant [m3/millimole_N].

LamS == 1.4d0  ! small biomass
LamL == 1.4d0  ! large biomass
LamP == 1.4d0  ! predator biomass
  • 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].
PusaiPL == 4.605d0  ! predator Zoo on large Phy
PusaiZS == 3.010d0  ! predator Zoo on small Zoo
  • Zooplankton mortality rate at 0 Celsius [m3/millimole_N 1/day].
MorZS0 == 58.5d-3  ! small biomass
MorZL0 == 58.5d-3  ! large biomass
MorZP0 == 58.5d-3  ! predator biomass
  • Zooplankton temperature coefficient for mortality [1/Celsius].
KMorZS == 0.0693d0  ! small biomass
KMorZL == 0.0693d0  ! large biomass
KMorZP == 0.0693d0  ! predator biomass
  • Zooplankton assimilation efficiency [nondimemsional].
AlphaZS == 0.70d0  ! small biomass
AlphaZL == 0.70d0  ! large biomass
AlphaZP == 0.70d0  ! predator biomass
  • Zooplankton growth efficiency [nondimensional].
BetaZS == 0.30d0  ! small biomass
BetaZL == 0.30d0  ! large biomass
BetaZP == 0.30d0  ! predator biomass

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].
Nit0 == 0.03d0  ! NH4 nitrification
VP2N0 == 0.10d0  ! PON to NH4
VP2D0 == 0.10d0  ! PON to DON
VD2N0 == 0.20d0  ! DON to NH4
VO2S0 == 0.10d0  ! Opal to Silicate
  • Temperature coefficients for decomposition [1/Celsius]
KNit == 6.93d-2  ! NH4 nitrification
KP2D == 6.93d-2  ! PON to DON
KP2N == 6.93d-2  ! PON to NH4
KD2N == 6.93d-2  ! DON to NH4
KO2S == 6.93d-2  ! Opal to Silicate
  • Si:N ratio [millimole_Si/millimole_N].
RSiN == 2.0d0
  • Settling (sinking) velocities [m/day].
setVPON == 40.0d0  ! PON
setVOpal == 40.0d0  ! Opal

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.
TNU2 == 11*0.0d0  ! m2/s
TNU4 == 11*0.0d0  ! m4/s

ad_TNU2 == 11*0.0d0  ! m2/s
ad_TNU4 == 11*0.0d0  ! m4/s
  • 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.
AKT_BAK == 11*1.0d-6  ! m2/s

ad_AKT_fac == 11*1.0d0  ! nondimensional
  • 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
  • Set horizontal and vertical advection schemes for biological tracers. A different advection scheme is allowed for each tracer. For example, a positive-definite (monotonic) algorithm can be activated for salinity and biological tracers, while a different one is set for temperature.
    Keyword Advection Algorithm

    A4 4th-order Akima (horizontal/vertical)
    C2 2nd-order centered differences (horizontal/vertical)
    C4 4th-order centered differences (horizontal/vertical)
    HSIMT 3th-order HSIMT with TVD limiter (horizontal/vertical)
    MPDATA recursive flux corrected MPDATA (horizontal/vertical)
    SPLINES parabolic splines reconstruction (only vertical)
    SU3 split third-order upstream (horizontal/vertical)
    U3 3rd-order upstresm-bias (only horizontal)
    The user has the option of specifying the full Keyword or the first two letters, regardless if using uppercase or lowercase. If nested grids, specify values for each grid. For more details please read the roms.in Tracer Advection Schemes section. [1:NBT,Ngrids] values are expected.
    Hadvection == HSIMT \  ! idbio( 1), nanophyto
    HSIMT \  ! idbio( 2), diatom
    HSIMT \  ! idbio( 3), microzoo
    HSIMT \  ! idbio( 4), mesozoo
    HSIMT \  ! idbio( 5), Pzooplankton
    HSIMT \  ! idbio( 6), NO3
    HSIMT \  ! idbio( 7), NH4
    HSIMT \  ! idbio( 8), PON
    HSIMT \  ! idbio( 9), DON
    HSIMT \  ! idbio(10), SiOH4
    HSIMT  ! idbio(11), opal

    Vadvection == HSIMT \  ! idbio( 1), nanophyto
    HSIMT \  ! idbio( 2), diatom
    HSIMT \  ! idbio( 3), microzoo
    HSIMT \  ! idbio( 4), mesozoo
    HSIMT \  ! idbio( 5), Pzooplankton
    HSIMT \  ! idbio( 6), NO3
    HSIMT \  ! idbio( 7), NH4
    HSIMT \  ! idbio( 8), PON
    HSIMT \  ! idbio( 9), DON
    HSIMT \  ! idbio(10), SiOH4
    HSIMT  ! idbio(11), opal
  • 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.

    NoteNotice: 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