Experiment Atlantic Zoo 101
General Information
Purpose of the Experiment
The purpose of the experiment is simulation of the nitrogen cycle in the Atlantic eastern boundary currents. It tests the influence of zooplankton vertical migration on the oxygen in the open ocean oxygen minimum zones. It repeats [[Model.ZoO_88][atlantic_genus_9_zoo 88]]. The following parameters are modified:
- reduced sink and sedimentation velocity of detritus
- enhanced sink velocity of large phytoplankton
- reduced tolerance of low oxygen conditions by both krill types.
Area and time coverage
- regional model: 10°W - 18°E, 33°S - 8°N
- initialisation time: 1999,07,20,0,0,0
- first output time stamp: 1999.08.19
- last output time stamp: 2009.05.27
Specific information
The model is integrated over about 10 model years. Important parameterisations:
- positive mdfl swebe advection
- kpp vertical mixing scheme
- additional passive model tracer
- Manizza shortwave radiation scheme - chlorophyll from ecosystem dynamics
- wave model and resuspension of sediments enabled
- tidal mixing switched on
- the sea level air pressure does not act onto the ocean
Specific namelist setup
Atmospheric forcing and OBC
- Data.QuikSCAT daily winds combined with ERA 6-hourly data
- ERA interim amosphere temperature, pressure and humidity for heat flux and moisture flux calculation, ERA precipitation
- ERA interim clouds for short wave radiation
- baroclinic OBC: 10 day temperature and salinity from ECCO simulations
- barotropic OBC: 12 hourly sea level from ECCO simulations
Known errors and shortcomings and corrections
- zmax_pen=800 in ocean_shortwave_gfdl_nml is changed to zmax_pen=1800
- dn_sed=0.001 in genus_nml is changed to dn_sed=0.002
- frac_dn_anoxic=0.3 in genus_nml does not exist any more. Default is 1
Configuration files
- [[%ATTACHURL%/input.nml][input.nml]]: input.nml
- [[%ATTACHURL%/data_table][data_table]]: data_table
- [[%ATTACHURL%/field_table][field_table]]: field_table
- [[%ATTACHURL%/diag_table][diag_table]]: diag_table
Output Variables
| xu_ocean | ucell longitude |
| yu_ocean | ucell latitude |
| time | time |
| nv | vertex number |
| xt_ocean | tcell longitude |
| yt_ocean | tcell latitude |
| st_ocean | tcell zstar depth |
| st_edges_ocean | tcell zstar depth edges |
| sw_ocean | ucell zstar depth |
| sw_edges_ocean | ucell zstar depth edges |
| drag_coeff | Dimensionless bottom drag coefficient |
| geolon_t | tracer longitude |
| geolat_t | tracer latitude |
| geolon_c | uv longitude |
| geolat_c | uv latitude |
| area_t | tracer cell area |
| area_u | velocity cell area |
| ht | ocean depth on t-cells |
| hu | ocean depth on u-cells |
| dzt | t-cell thickness |
| eta_t | surface height on T cells [Boussinesq (volume conserving) model] |
| eta_u | surface height on U cells |
| eta_t_bar | surface height on T cells averaged over bar loop |
| mld | mixed layer depth determined by density criteria |
| hblt | T-cell boundary layer depth from KPP |
| urhod | depth and density weighted u |
| vrhod | depth and density weighted v |
| runoff | mass flux of liquid river runoff entering ocean |
| windx_wave | zonal wind speed for waves |
| windy_wave | meridional wind speed for waves |
| xmom | zonal wave momentum |
| ymom | meridional wave momentum |
| height | significant wave height |
| wave_p | peak frequency |
| wave_k | wave number |
| wave_s | wave skin friction velocity |
| wave_u | wave friction velocity |
| iter | number of ustar iterations |
| current_wave_stress | combined current wave bottom stress |
| temp | Potential temperature |
| salt | Practical Salinity |
| u | i-current |
| v | j-current |
| wrhot | rho*dia-surface velocity T-points |
| passive_angola | passive (angola) |
| passive_south | passive (south) |
| passive_south1 | passive (south1) |
| passive_north | passive (north) |
| age_global | Age (global) |
| t_n2 | dissolved molecular nitrogen |
| t_o2 | dissolved oxygen |
| t_dic | dissolved inorganic carbon, treated as carbon dioxide |
| t_nh4 | ammonium |
| t_no3 | nitrate |
| t_po4 | phosphate |
| t_spp | small-cell phytoplankton |
| t_h2s | hydrogen sulfide |
| t_sul | sulfur |
| t_alk | total alkalinity |
| t_ipw | suspended iron phosphate |
| t_lpp | large-cell phytoplankton |
| t_cya | diazotroph cyanobacteria |
| t_det | detritus |
| t_cop | copepods |
| t_kr1 | small krill |
| t_kr2 | large krill |
| p_no3_assim_lpp | layer integral of assimilation of nitrate by large-cell phytoplankton |
| p_nh4_assim_lpp | layer integral of assimilation of ammonium by large-cell phytoplankton |
| p_no3_assim_spp | layer integral of assimilation of nitrate by small-cell phytoplankton |
| p_nh4_assim_spp | layer integral of assimilation of ammonium by small-cell phytoplankton |
| p_n2_assim_cya | layer integral of fixation of dinitrogen by diazotroph cyanobacteria |
| p_lpp_resp_nh4 | layer integral of respiration of large-cell phytoplankton |
| p_spp_resp_nh4 | layer integral of respiration of small-cell phytoplankton |
| p_cya_resp_nh4 | layer integral of respiration of diazotroph cyanobacteria |
| p_lpp_mort_det | layer integral of mortality of large-cell phytoplankton |
| p_spp_mort_det | layer integral of mortality of small-cell phytoplankton |
| p_cya_mort_det | layer integral of mortality of diazotroph cyanobacteria |
| p_nh4_nit_no3 | layer integral of nitrification |
| p_det_resp_nh4 | layer integral of recycling of detritus using oxygen (respiration) |
| p_det_denit_nh4 | layer integral of recycling of detritus using nitrate (denitrification) |
| p_det_sulf_nh4 | layer integral of recycling of detritus using sulfate (sulfate reduction) |
| p_sed_resp_nh4 | recycling of sedimentary detritus to ammonium using oxygen (respiration) |
| p_nh4_nitdenit_n2 | coupled nitrification and denitrification after mineralization of detritus in oxic sediments |
| p_sed_denit_nh4 | recycling of sedimentary detritus to ammonium using nitrate (denitrification) |
| p_sed_sulf_nh4 | recycling of sedimentary detritus to ammonium using sulfate (sulfate reduction) |
| p_po4_retent_ips | retention of phosphate in the sediment under oxic conditions |
| p_ips_liber_po4 | liberation of phosphate from the sediment under anoxic conditions |
| p_h2s_oxo2_sul | layer integral of oxidation of hydrogen sulfide with oxygen |
| p_h2s_oxno3_sul | layer integral of oxidation of hydrogen sulfide with nitrate |
| p_sul_oxo2_so4 | layer integral of oxidation of elemental sulfur with oxygen |
| p_sul_oxno3_so4 | layer integral of oxidation of elemental sulfur with nitrate |
| p_det_sedi_sed | detritus sedimentation |
| p_ipw_sedi_ips | sedimentation of iron PO4 |
| p_sed_ero_det | sedimentary detritus erosion |
| p_ips_ero_ipw | erosion of iron PO4 |
| p_sed_biores_det | bio resuspension of sedimentary detritus |
| p_sed_burial | burial of benthos deeper than max_sed |
| p_dia_graz_cop | layer integral of grazing of copepods eating diatoms |
| p_fla_graz_cop | layer integral of grazing of copepods eating flagellates |
| p_cya_graz_cop | layer integral of grazing of copepods eating cyanobacteria |
| p_det_graz_cop | layer integral of grazing of copepods eating detritus |
| p_dia_graz_kr1 | layer integral of grazing of small krill eating diatoms |
| p_fla_graz_kr1 | layer integral of grazing of small krill eating flagellates |
| p_cya_graz_kr1 | layer integral of grazing of small krill eating cyanobacteria |
| p_cop_graz_kr1 | layer integral of grazing of small krill eating copepods |
| p_det_graz_kr1 | layer integral of grazing of small krill eating detritus |
| p_cop_graz_kr2 | layer integral of grazing of large krill eating copepods |
| p_kr1_graz_kr2 | layer integral of grazing of large krill eating small krill |
| p_kr2_graz_kr2 | layer integral of grazing of large krill eating itself (cannibalism) |
| p_det_graz_kr2 | layer integral of grazing of large krill eating detritus |
| p_cop_resp_nh4 | layer integral of respiration of copepods |
| p_kr1_resp_nh4 | layer integral of respiration of small krill |
| p_kr2_resp_nh4 | layer integral of respiration of large krill |
| p_cop_mort_det | layer integral of mortality of copepods |
| p_kr1_mort_det | layer integral of mortality of small krill |
| p_kr2_mort_det | layer integral of mortality of large krill |
| p_det_anam_n2 | layer integral of anammox recycling |
| p_det_denit_nh4_2 | layer integral of recycling of detritus using nitrate, because no ammonium exists for anammox |
| p_sed_dnra_nh4 | recycling of sediment detritus to ammonium using nitrate (DNRA process) |
| btf_n2 | bottom tracer flux of molecular nitrogen (positive upward) [mol/m2/day] |
| btf_o2 | bottom tracer flux of oxygen (positive upward) [mol/m2/day] |
| btf_dic | bottom tracer flux of dic (positive upward) [mol/m2/day] |
| btf_nh4 | bottom tracer flux of ammonium (positive upward) [mol/m2/day] |
| btf_no3 | bottom tracer flux of nitrate (positive upward) [mol/m2/day] |
| btf_po4 | bottom tracer flux of phosphate (positive upward) [mol/m2/day] |
| btf_h2s | bottom tracer flux of hydrogen sulfide (positive upward) [mol/m2/day] |
| btf_det | bottom tracer flux of detritus (positive upward) [mol/m2/day] |
| btf_ipw | bottom tracer flux of iron phosphate (positive upward) [mol/m2/day] |
| t_sed_1 | sediment detritus concentration in sediment layer 1 |
| t_sed_2 | sediment detritus concentration in sediment layer 2 |
| t_ips_1 | iron phosphate in sediment concentration in sediment layer 1 |
| t_ips_2 | iron phosphate in sediment concentration in sediment layer 2 |
| t_sed2_1 | buried sediment detritus concentration in sediment layer 1 |
| t_sed2_2 | buried sediment detritus concentration in sediment layer 2 |
| runoff_flux_t_dic | dissolved inorganic carbon, treated as carbon dioxide runoff flux to the ocean |
| runoff_flux_t_alk | total alkalinity runoff flux to the ocean |
| dep_wet_t_nh4 | Wet Deposition of ammonium to the ocean |
| dep_wet_t_no3 | Wet Deposition of nitrate to the ocean |
| dep_wet_t_po4 | Wet Deposition of phosphate to the ocean |
| sfc_flux_t_n2 | Total flux oft_n2 into Ocean Surface |
| sfc_flux_t_o2 | Total flux oft_o2 into Ocean Surface |
| sfc_flux_t_dic | Total flux oft_dic into Ocean Surface |
| chl | Chlorophyll |
| opacity_water | Opacity of pure water |
| opacity_bio | Opacity of water ingredients |
| average_T1 | Start time for average period |
| average_T2 | End time for average period |
| average_DT | Length of average period |
| time_bounds | time axis boundaries |
Storage of the results
| PERM at HLRN | IOW storage | THREDDS |
| No | /silod2/models/south_atlantic/atlantic_genus_10_era/workdir_101/ | http://phy-4:8080/thredds/genus/catalog_era_run101.html |
-- Main.MartinSchmidt - 2014-08-21