Updates bgc case settings documentation take 2 #4
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-Updates bgc environment variables -Corrects and updates BGC namelist parameter table -Corrects and updates BGC parameter arrays table BFB
| "``alpha2max_low_diatoms``", "real", "light limitation diatoms 1/(W/m^2)", "0.3" | ||
| "``alpha2max_low_phaeo``", "real", "light limitation phaeocystis 1/(W/m^2)", "0.17" | ||
| "``alpha2max_low_sp``", "real", "light limitation small plankton 1/(W/m^2)", "0.2" | ||
| "``ammoniumtype``", "real", "mobility type between stationary and mobile ammonium", "0.0" | ||
| "``beta2max_diatoms``", "real", "light inhibition diatoms 1/(W/m^2)", "0.001" | ||
| "``beta2max_phaeo``", "real", "light inhibition phaeocystis 1/(W/m^2)", "0.04" | ||
| "``beta2max_sp``", "real", "light inhibition small plankton 1/(W/m^2)", "0.001" | ||
| "``bgc_flux_type``", "``constant``", "constant ice–ocean flux velocity", "``Jin2006``" | ||
| "", "``Jin2006``", "ice–ocean flux velocity of :cite:`Jin06`", "" | ||
| "``bgc_data_type``", "``clim``", "bgc climatological data", "``default``" |
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bgc_data_type is in forcing_nml in Icepack and CICE. Please check the definitions there and remove it here.
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@apcraig : Okay, this last commit removes bgc_data_type. Should be good now. This field isn't used in mpas-seaice. So if the options are good for cice & icepack, then that's fine. |
| "``alpha2max_low_diatoms``", "real", "light limitation diatoms 1/(W/m^2)", "0.3" | ||
| "``alpha2max_low_phaeo``", "real", "light limitation phaeocystis 1/(W/m^2)", "0.17" | ||
| "``alpha2max_low_sp``", "real", "light limitation small plankton 1/(W/m^2)", "0.2" | ||
| "``ammoniumtype``", "real", "mobility type between stationary and mobile ammonium", "0.0" | ||
| "``beta2max_diatoms``", "real", "light inhibition diatoms 1/(W/m^2)", "0.001" | ||
| "``beta2max_phaeo``", "real", "light inhibition phaeocystis 1/(W/m^2)", "0.04" | ||
| "``beta2max_sp``", "real", "light inhibition small plankton 1/(W/m^2)", "0.001" | ||
| "``bgc_flux_type``", "``constant``", "constant ice–ocean flux velocity", "``Jin2006``" | ||
| "``bgc_flux_type``", "``constant``", "constant ice–ocean flux velocity", "``Jin2006``" |
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looks like there is an extra space at the start of the line.
| @@ -472,14 +476,14 @@ zbgc_nml | |||
| "``K_Sil_phaeo``", "real", "silicate half saturation phaeocystis mmol/m^3", "0.0" | |||
| "``K_Sil_sp``", "real", "silicate half saturation small plankton mmol/m^3", "0.0" | |||
| "``kn_bac_protein``", "real", "bacterial degradation of DON per day", "0.2" | |||
| "``l_sk``", "real", "characteristic diffusive scale in m", "20.0" | |||
| "``l_sk``", "real", "characteristic diffusive scale in m", "2.0" | |||
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The default in Icepack and in namelist is currently 20 and we use 20. Should it be 2?
| @@ -488,20 +492,20 @@ zbgc_nml | |||
| "``mu_max_sp``", "real", "maximum growth rate small plankton per day", "0.41" | |||
| "``nitratetype``", "real", "mobility type between stationary and mobile nitrate", "-1.0" | |||
| "``op_dep_min``", "real", "light attenuates for optical depths exceeding min", "0.1" | |||
| "``phi_snow``", "real", "snow porosity for brine height tracer", "-0.3" | |||
| "``phi_snow``", "real", "snow porosity for brine height tracer (compute from snow density if negative)", "-1.0" | |||
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What is going on here. Our default is -0.3. Is it the case that any negative value has the same impact? Should we change the value to -1.0 in the code and namelist?
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Any negative value does the same thing. Snow porosity is computed from snow density.
| "``solve_zsal``", "logical", "DEPRECATED", "``.false.``" | ||
| "``tau_max``", "real", "long time mobile to stationary exchanges", "7776000." | ||
| "``tau_min``", "real", "rapid module to stationary exchanges", "3600." | ||
| "``tau_max``", "real", "long time mobile to stationary exchanges (s)", "604800.0" |
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The Icepack default is 7776000 and that's what we run with. Is that value correct?
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I've changed it to be consistent with MPAS-Si.
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We're not documenting MPAS-Si. What should the default be in Icepack? Should we be using 604800 in Icepack and CICE then? We'll need to update the code too if these defaults should change.
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@apcraig : i'm making this changes because this is what I think should be in the icepack documentation. But if you'd like to keep it as is, that's fine with me.
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Happy to make the change, just want to make sure.
For detailed information about submitting Pull Requests (PRs) to the CICE-Consortium,
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PR checklist
updates to documentation of bgc namelist and env variables
njeffery, ehunke, apcraig
apcraig
visual check in html
-Updates bgc environment variables
-Corrects and updates BGC namelist parameter table
-Corrects and updates BGC parameter arrays table
BFB