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Experiment Atlantic Zoo 88

 

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_83][atlantic_genus_9_zoo 83]] with CGT-based ERGOM.

 

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_88/ http://phy-4:8080/thredds/genus/catalog_era_run88.html

 

 

-- Main.MartinSchmidt - 2014-08-21