Experiment Atlantic Zoo 388
General Information
Purpose of the Experiment
The purpose of the experiment is simulation of the nitrogen cycle in the Atlantic eastern boundary currents. It repeats [[Model.ZoO_88][atlantic_genus_9_zoo 88]] with vertical zooplankton migration switched off.
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: 2012.05.12
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_388/ | http://phy-4:8080/thredds/genus/catalog_era_run388.html |
-- Main.MartinSchmidt - 2014-08-21