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Moved hard coded biogeochemical parameters to registry. #1043

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Aug 31, 2016
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Moved hard coded biogeochemical parameters to registry. #1043

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026710b
Moved hard coded biogeochemical parameters to registry.
njeffery Aug 29, 2016
dbc788a
Clean-up.
njeffery Aug 30, 2016
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117 changes: 117 additions & 0 deletions src/core_cice/Registry.xml
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Expand Up @@ -205,6 +205,121 @@
<nml_option name="config_snow_porosity_at_ice_surface" type="real" default_value="-0.3"/>
<nml_option name="config_new_ice_fraction_biotracer" type="real" default_value="0.80"/>
<nml_option name="config_fraction_biotracer_in_frazil" type="real" default_value="0.80"/>
<nml_option name="config_ratio_Si_to_N_diatoms" type="real" default_value="1.80"/>
<nml_option name="config_ratio_Si_to_N_small_plankton" type="real" default_value="0.00"/>
<nml_option name="config_ratio_Si_to_N_phaeocystis" type="real" default_value="0.00"/>
<nml_option name="config_ratio_S_to_N_diatoms" type="real" default_value="0.03"/>
<nml_option name="config_ratio_S_to_N_small_plankton" type="real" default_value="0.03"/>
<nml_option name="config_ratio_S_to_N_phaeocystis" type="real" default_value="0.03"/>
<nml_option name="config_ratio_Fe_to_C_diatoms" type="real" default_value="0.0033"/>
<nml_option name="config_ratio_Fe_to_C_small_plankton" type="real" default_value="0.0033"/>
<nml_option name="config_ratio_Fe_to_C_phaeocystis" type="real" default_value="0.1"/>
<nml_option name="config_ratio_Fe_to_N_diatoms" type="real" default_value="0.023"/>
<nml_option name="config_ratio_Fe_to_N_small_plankton" type="real" default_value="0.023"/>
<nml_option name="config_ratio_Fe_to_N_phaeocystis" type="real" default_value="0.7"/>
<nml_option name="config_ratio_Fe_to_DON" type="real" default_value="0.023"/>
<nml_option name="config_ratio_Fe_to_DOC_saccharids" type="real" default_value="0.1"/>
<nml_option name="config_ratio_Fe_to_DOC_lipids" type="real" default_value="0.033"/>
<nml_option name="config_respiration_fraction_of_growth" type="real" default_value="0.05"/>
<nml_option name="config_rapid_mobile_to_stationary_time" type="real" default_value="5200.0"/>
<nml_option name="config_long_mobile_to_stationary_time" type="real" default_value="173000.0"/>
<nml_option name="config_algal_maximum_velocity" type="real" default_value="0.0000000111"/>
<nml_option name="config_ratio_Fe_to_dust" type="real" default_value="0.035"/>
<nml_option name="config_solubility_of_Fe_in_dust" type="real" default_value="0.005"/>
<nml_option name="config_chla_absorptivity_of_diatoms" type="real" default_value="0.03"/>
<nml_option name="config_chla_absorptivity_of_small_plankton" type="real" default_value="0.01"/>
<nml_option name="config_chla_absorptivity_of_phaeocystis" type="real" default_value="0.05"/>
<nml_option name="config_light_attenuation_diatoms" type="real" default_value="0.8"/>
<nml_option name="config_light_attenuation_small_plankton" type="real" default_value="0.67"/>
<nml_option name="config_light_attenuation_phaeocystis" type="real" default_value="0.67"/>
<nml_option name="config_light_inhibition_diatoms" type="real" default_value="0.018"/>
<nml_option name="config_light_inhibition_small_plankton" type="real" default_value="0.0025"/>
<nml_option name="config_light_inhibition_phaeocystis" type="real" default_value="0.01"/>
<nml_option name="config_maximum_growth_rate_diatoms" type="real" default_value="1.44"/>
<nml_option name="config_maximum_growth_rate_small_plankton" type="real" default_value="0.851"/>
<nml_option name="config_maximum_growth_rate_phaeocystis" type="real" default_value="0.851"/>
<nml_option name="config_temperature_growth_diatoms" type="real" default_value="0.06"/>
<nml_option name="config_temperature_growth_small_plankton" type="real" default_value="0.06"/>
<nml_option name="config_temperature_growth_phaeocystis" type="real" default_value="0.06"/>
<nml_option name="config_grazed_fraction_diatoms" type="real" default_value="0.0"/>
<nml_option name="config_grazed_fraction_small_plankton" type="real" default_value="0.1"/>
<nml_option name="config_grazed_fraction_phaeocystis" type="real" default_value="0.1"/>
<nml_option name="config_mortality_diatoms" type="real" default_value="0.007"/>
<nml_option name="config_mortality_small_plankton" type="real" default_value="0.007"/>
<nml_option name="config_mortality_phaeocystis" type="real" default_value="0.007"/>
<nml_option name="config_temperature_mortality_diatoms" type="real" default_value="0.03"/>
<nml_option name="config_temperature_mortality_small_plankton" type="real" default_value="0.03"/>
<nml_option name="config_temperature_mortality_phaeocystis" type="real" default_value="0.03"/>
<nml_option name="config_exudation_diatoms" type="real" default_value="0.0"/>
<nml_option name="config_exudation_small_plankton" type="real" default_value="0.0"/>
<nml_option name="config_exudation_phaeocystis" type="real" default_value="0.0"/>
<nml_option name="config_nitrate_saturation_diatoms" type="real" default_value="1.0"/>
<nml_option name="config_nitrate_saturation_small_plankton" type="real" default_value="1.0"/>
<nml_option name="config_nitrate_saturation_phaeocystis" type="real" default_value="1.0"/>
<nml_option name="config_ammonium_saturation_diatoms" type="real" default_value="0.3"/>
<nml_option name="config_ammonium_saturation_small_plankton" type="real" default_value="0.3"/>
<nml_option name="config_ammonium_saturation_phaeocystis" type="real" default_value="0.3"/>
<nml_option name="config_silicate_saturation_diatoms" type="real" default_value="4.0"/>
<nml_option name="config_silicate_saturation_small_plankton" type="real" default_value="0.0"/>
<nml_option name="config_silicate_saturation_phaeocystis" type="real" default_value="0.0"/>
<nml_option name="config_iron_saturation_diatoms" type="real" default_value="1.0"/>
<nml_option name="config_iron_saturation_small_plankton" type="real" default_value="0.2"/>
<nml_option name="config_iron_saturation_phaeocystis" type="real" default_value="0.1"/>
<nml_option name="config_fraction_spilled_to_DON" type="real" default_value="0.6"/>
<nml_option name="config_degredation_of_DON" type="real" default_value="0.03"/>
<nml_option name="config_fraction_DON_ammonium" type="real" default_value="0.25"/>
<nml_option name="config_fraction_loss_to_saccharids" type="real" default_value="0.4"/>
<nml_option name="config_fraction_loss_to_lipids" type="real" default_value="0.4"/>
<nml_option name="config_fraction_exudation_to_saccharids" type="real" default_value="1.0"/>
<nml_option name="config_fraction_exudation_to_lipids" type="real" default_value="1.0"/>
<nml_option name="config_remineralization_saccharids" type="real" default_value="0.03"/>
<nml_option name="config_remineralization_lipids" type="real" default_value="0.03"/>
<nml_option name="config_maximum_brine_temperature" type="real" default_value="0.0"/>
<nml_option name="config_salinity_dependence_of_growth" type="real" default_value="1.0"/>
<nml_option name="config_minimum_optical_depth" type="real" default_value="0.1"/>
<nml_option name="config_slopped_grazing_fraction" type="real" default_value="0.5"/>
<nml_option name="config_excreted_fraction" type="real" default_value="0.5"/>
<nml_option name="config_fraction_mortality_to_ammonium" type="real" default_value="0.5"/>
<nml_option name="config_fraction_iron_remineralized" type="real" default_value="0.3"/>
<nml_option name="config_nitrification_rate" type="real" default_value="0.0"/>
<nml_option name="config_desorption_loss_particulate_iron" type="real" default_value="3065.0"/>
<nml_option name="config_maximum_loss_fraction" type="real" default_value="0.9"/>
<nml_option name="config_maximum_ratio_iron_to_saccharids" type="real" default_value="0.2"/>
<nml_option name="config_respiration_loss_to_DMSPd" type="real" default_value="0.75"/>
<nml_option name="config_DMSP_to_DMS_conversion_fraction" type="real" default_value="0.5"/>
<nml_option name="config_DMSP_to_DMS_conversion_time" type="real" default_value="3.0"/>
<nml_option name="config_DMS_oxidation_time" type="real" default_value="10.0"/>
<nml_option name="config_mobility_type_diatoms" type="real" default_value="0.0"/>
<nml_option name="config_mobility_type_small_plankton" type="real" default_value="0.5"/>
<nml_option name="config_mobility_type_phaeocystis" type="real" default_value="0.5"/>
<nml_option name="config_mobility_type_nitrate" type="real" default_value="-1.0"/>
<nml_option name="config_mobility_type_ammonium" type="real" default_value="1.0"/>
<nml_option name="config_mobility_type_silicate" type="real" default_value="-1.0"/>
<nml_option name="config_mobility_type_DMSPp" type="real" default_value="0.5"/>
<nml_option name="config_mobility_type_DMSPd" type="real" default_value="-1.0"/>
<nml_option name="config_mobility_type_humics" type="real" default_value="1.0"/>
<nml_option name="config_mobility_type_saccharids" type="real" default_value="0.5"/>
<nml_option name="config_mobility_type_lipids" type="real" default_value="0.5"/>
<nml_option name="config_mobility_type_proteins" type="real" default_value="0.5"/>
<nml_option name="config_mobility_type_dissolved_iron" type="real" default_value="0.5"/>
<nml_option name="config_mobility_type_particulate_iron" type="real" default_value="0.5"/>
<nml_option name="config_mobility_type_black_carbon1" type="real" default_value="1.0"/>
<nml_option name="config_mobility_type_black_carbon2" type="real" default_value="1.0"/>
<nml_option name="config_mobility_type_dust1" type="real" default_value="1.0"/>
<nml_option name="config_mobility_type_dust2" type="real" default_value="1.0"/>
<nml_option name="config_mobility_type_dust3" type="real" default_value="1.0"/>
<nml_option name="config_mobility_type_dust4" type="real" default_value="1.0"/>
<nml_option name="config_ratio_C_to_N_diatoms" type="real" default_value="7.0"/>
<nml_option name="config_ratio_C_to_N_small_plankton" type="real" default_value="7.0"/>
<nml_option name="config_ratio_C_to_N_phaeocystis" type="real" default_value="7.0"/>
<nml_option name="config_ratio_chla_to_N_diatoms" type="real" default_value="2.1"/>
<nml_option name="config_ratio_chla_to_N_small_plankton" type="real" default_value="1.1"/>
<nml_option name="config_ratio_chla_to_N_phaeocystis" type="real" default_value="0.84"/>
<nml_option name="config_scales_absorption_diatoms" type="real" default_value="2.0"/>
<nml_option name="config_scales_absorption_small_plankton" type="real" default_value="4.0"/>
<nml_option name="config_scales_absorption_phaeocystis" type="real" default_value="5.0"/>
<nml_option name="config_ratio_C_to_N_proteins" type="real" default_value="7.0"/>

</nml_record>

<nml_record name="shortwave" in_defaults="true">
Expand Down Expand Up @@ -1659,6 +1774,7 @@
<var name="snowThicknessChange" type="real" dimensions="nCells Time" name_in_code="snowThicknessChange"/>
<var name="snowThicknessChangeCategory" type="real" dimensions="nCategories nCells Time" name_in_code="snowThicknessChangeCategory"/>
<var name="frazilFormation" type="real" dimensions="nCells Time" name_in_code="frazilFormation"/>
<var name="frazilGrowthDiagnostic" type="real" dimensions="nCells Time" name_in_code="frazilGrowthDiagnostic"/>
</var_struct>

<!-- fluxes with the atmosphere -->
Expand Down Expand Up @@ -1937,3 +2053,4 @@

#include "analysis_members/Registry_cice_analysis_members.xml"
</registry>
n
2 changes: 1 addition & 1 deletion src/core_cice/column/REVISION
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r1110
r1143
2 changes: 1 addition & 1 deletion src/core_cice/column/ice_aerosol.F90
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! SVN:$Id: ice_aerosol.F90 1104 2016-01-28 00:10:05Z njeffery $
! SVN:$Id: ice_aerosol.F90 1112 2016-03-24 22:49:56Z eclare $
!=======================================================================

! Aerosol tracer within sea ice
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