Experiment Atlantic Zoo 83
General Information
Purpose of the Experiment
The purpose of the experiment is simulation of the nitrogen cycle in the Atlantic eastern boundary currents
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: 2009.01.28
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 is changed to frac_dn_anoxic=1.0
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) |
| light | |
| alk_boron | boron alkalinity [mol/kg] |
| alk_h2s | hydrogen sulfide alkalinity [mol/kg] |
| alk_water | water alkalinity [mol/kg] |
| alk_po4 | phosphate alkalinity [mol/kg] |
| alk_co2 | carbonate alkalinity [mol/kg] |
| residual_alk | error in total alkalinity calculation at the assumed pH [mol/kg] |
| dalkp_dh3o | derivative of phosphate alkalinity over h3o [1] |
| dalkc_dh3o | derivative of carbonate alkalinity over h3o [1] |
| dresidualalk_dpH | derivative of residual_alk over pH [mol/kg] |
| new_pH | newly determined pH value [1] |
| h3o | h3o ion concentration [mol/kg] |
| w_kr1 | vertical speed of small krill [m/day] |
| growth_n_p | layer integral of growth of diatoms eating nitrate |
| growth_a_p | layer integral of growth of diatoms eating ammonium |
| growth_n_f | layer integral of growth of flaggelates eating nitrate |
| growth_a_f | layer integral of growth of flaggelates eating ammonium |
| growth_b | layer integral of growth of cyanobacteria |
| resp_p | layer integral of respiration of diatoms |
| resp_f | layer integral of respiration of flaggelates |
| resp_b | layer integral of respiration of cyanobacteria |
| resp_cop | layer integral of respiration of copepods |
| resp_kr1 | layer integral of respiration of small krill |
| resp_kr2 | layer integral of respiration of large krill |
| recycle_d_o | layer integral of recycling of detritus using oxygen |
| recycle_d_n | layer integral of recycling of detritus using nitrate |
| recycle_d_s | layer integral of recycling of detritus using sulfate, because no nitrate exists |
| recycle_d_a | layer integral of anammox recycling |
| oxidation_h2s_o2 | layer integral of oxidation of hydrogen sulfide with oxygen |
| oxidation_h2s_no3 | layer integral of oxidation of hydrogen sulfide with nitrate |
| n2 | dissolved molecular nitrogen |
| o2 | oxygen |
| dic | dissolved inorganic carbon, treated as carbon dioxide |
| nh4 | ammonium |
| no3 | nitrate |
| po4 | phosphate |
| fla | flagellates |
| cop | copepods |
| h2s | hydrogen sulfide |
| sul | sulfur |
| alk_t | total alkalinity |
| cya | cyanobacteria |
| kr1 | small krill |
| kr2 | large krill |
| det | detritus |
| ipw | suspended iron phosphate |
| dia | diatoms |
| sed_1 | sediment detritus concentration in sediment layer 1 |
| sed_2 | sediment detritus concentration in sediment layer 2 |
| ips_1 | iron phosphate in sediment concentration in sediment layer 1 |
| ips_2 | iron phosphate in sediment concentration in sediment layer 2 |
| runoff_flux_dic | dissolved inorganic carbon, treated as carbon dioxide runoff flux to the ocean |
| runoff_flux_alk_t | total alkalinity runoff flux to the ocean |
| dep_wet_nh4 | Wet Deposition of ammonium to the ocean |
| dep_wet_no3 | Wet Deposition of nitrate to the ocean |
| dep_wet_po4 | Wet Deposition of phosphate to the ocean |
| chl | Chlorophyll |
| opacity_water | Opacity of pure water |
| opacity_bio | Opacity of water ingredients |
| sfc_flux_o2 | Total flux ofo2 into Ocean Surface |
| sfc_flux_n2 | Total flux ofn2 into Ocean Surface |
| sfc_flux_dic | Total flux ofdic into Ocean Surface |
| sfc_flux_no3 | Total flux ofno3 into Ocean Surface |
| sfc_flux_nh4 | Total flux ofnh4 into Ocean Surface |
| sfc_flux_po4 | Total flux ofpo4 into Ocean Surface |
| btf_o2 | bottom tracer flux of oxygen (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_nh4 | bottom tracer flux of ammonium (positive upward) [mol/m2/day] |
| btf_dic | bottom tracer flux of dic (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] |
| ergom_is_eroding | switch for sediment erosion |
| 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_83/ | http://phy-4:8080/thredds/genus/catalog_era_run83.html |
-- Main.MartinSchmidt - 2014-08-21