Output files

Output files from a model run are written out in either ASCII, or (for most data outputs) in NetCDF format. The different NetCDF files are named after the runlabel1 parameter set in modrun.sh. The model output is written to the same directory as where the runscript where submitted, as described in ch-submitarun.

To check your model run, already prepared model result files can be downloaded using the catalog tool (sec-ModelCode) as follows:

# download the output
catalog.py -R rv4_10 --output

Unpacked files are placed in an output directory with model run results for a whole year, and sometimes with a smaller test run for e.g. April.

Table 5 List of model output files

Output data files	Short description	Format
Base_hour.nc	Gridded hourly values of a	NetCDF
	selection of compounds
Base_day.nc	Gridded daily values of a	NetCDF
	selection of compounds
Base_month.nc	Gridded monthly values of a	NetCDF
	selection of compounds
Base_fullrun.nc	Gridded yearly values of a	NetCDF
	selection of compounds
sites_YYYY.nc	Surface daily values of a	NetCDF [1]
	selection of stations and compounds
sondes_YYYY.nc	Vertical daily values of a	NetCDF [1]
	selection of stations and compounds
sites_YYYY.cvs	ASCII version of sites_YYYY.nc	ASCII [2]
sondes_YYYY.csv	ASCII version of sondes_YYYY.nc	ASCII [2]
Additional files
RunLog.out	Summary log of runs, including total emissions	ASCII
	of different air pollutants per country
Timing.out	Timing log file	ASCII

Footnotes

[1]	(1, 2) YYYY: year.

[2]	(1, 2) Deprecated output.

Output parameters NetCDF files

Parameters to be written out Base_day.nc, Base_month.nc and Base_year.nc are defined in My_Derived_ml.f90 and Derived_ml.f90. In My_Derived_ml.f90, the use can specify the output species (air concentrations, depositions, column values), units and temporal resolution of the outputs (daily, monthly, yearly).

The name of output parameter provides some information about data. The names start with TYPE of the parameter, namely SURF (surface air concentrations), DDEP (Dry deposition), WDEP (Wet deposition), COLUMN (Vertically integrated parameters), Area (Surface area) etc.

For surface air concentrations, the general name pattern is SURF_UNITS_COMPONENT. Here, UNITS can e.g. be “ug” (\(\mu g/m^3\)), “ugS” (\(\mu g(S)/m^3\)), “ugN” (\(\mu g(N)/m^3\)), or “ppb”. Note that the components are classified either as “SPEC” (species) or “GROUP”. The content of complex GROUP components can be found in CM_ChemGroups_ml.f90.

For column integrated parameters, the names are COLUMN_COMPONENT_kNLAYERS, where NLAYERS is the number of layers from model top included in the integration. The units for column outputs are “ugm2” (\(\mu g/m^2\)), “mcm2” (\(molec/m^2\)) or “e15mcm2” (\(10^{15} molec/m^2\)).

For dry depositions, given per \(1 m^2\) of specified landuse, the names look like DDEP_COMPONENT_m2LANDUSE, where LANDUSE can be either a specific landuse type or a cell average. For wet depositions, the names are WDEP_COMPONENT. The units for dry and wet depositions are \(mg/m^2\), \(mg(S)/m^2\) or \(mg(N)/m^2\).

Surface concentrations, column integrated, wet and dry deposition outputs are defined by the user in config_emep.nml file. Surface concentrations and column integrated outputs are described in OutputConcs_config namelist, Dry and wet deposition outputs are described in OutputDep_config namelist.

VG_COMPONENT_LANDUSE are the dry deposition velocities on various landuse types, typically in \(cm/s\).

Table 6 lists most of output parameters, providing additional explanation to the complex components. For a complete suit of currently selected output parameters, see provided output NetCDF files, or My_Derived_ml.f90 module.

Table 6 List of output parameters

Parameter name	Short description	Comments
Surface Concentrations
SURF_ppb_O3	O3 [ppb]
SURF_ugN_NO	NO [\(\mu g(N)/m^3\)]	Available also in ppb
SURF_ugN_NO2	NO2 [\(\mu g(N)/m^3\)]	Available also in ppb
SURF_ugN_HNO3	HNO3 [\(\mu g(N)/m^3\)]	Available also in ppb
SURF_ugN_NH3	NH3 [\(\mu g(N)/m^3\)]	Available also in ppb
SURF_ugS_SO2	SO2 [\(\mu g(S)/m^3\)]	Available also in ppb
SURF_ug_SO4	SO\(_4^{2-}\) [\(\mu g/m^3\)]
SURF_ug_NO3_F	NO\(_3^-\) fine aerosol [\(\mu g/m^3\)]	As ammonium nitrate
SURF_ug_NO3_C	NO\(_3^-\) coarse aerosol [\(\mu g/m^3\)]	Associated with sea salt and mineral dust
SURF_ug_TNO3	NO\(_3^-\) total [\(\mu g/m^3\)]	Sum of fine and coarse nitrate
SURF_ug_NH4_F	NH\(_4^+\) fine aerosol [\(\mu g/m^3\)]	As ammonium sulphate and ammonium nitrate
SURF_ug_SIA	SIA [\(\mu g/m^3\)]	Secondary Inorganic Aerosol
SURF_ug_SIA	SIA [\(\mu g/m^3\)]	Secondary Inorganic Aerosol
SURF_ug_ECFINE	EC fine [\(\mu g/m^3\)]	Elemental carbon
SURF_ug_ECCOARSE	EC coarse [\(\mu g/m^3\)]	Elemental carbon
SURF_ug_PM_OM25	OM fine [\(\mu g/m^3\)]	Organic Matter fine aerosol
SURF_ug_PM_OMCOARSE	OM coarse [\(\mu g/m^3\)]	Organic Matter coarse aerosol
SURF_ug_SEASALT_F	Sea salt fine aerosol [\(\mu g/m^3\)]
SURF_ug_SEASALT_C	Sea salt coarse aerosol [\(\mu g/m^3\)]
SURF_ug_SEASALT	Sea salt [\(\mu g/m^3\)]	Sum of fine and coarse sea salt
SURF_ug_DUST_ROAD_F	Road dust fine aerosol [\(\mu g/m^3\)]
SURF_ug_DUST_ROAD_C	Road dust coarse aerosol [\(\mu g/m^3\)]
SURF_ug_DUST_WB_F	Windblown dust fine [\(\mu g/m^3\)]
SURF_ug_DUST_WB_C	Windblown dust coarse [\(\mu g/m^3\)]
SURF_ug_DUST_SAH_F	Saharan dust fine [\(\mu g/m^3\)]	From Boundary conditions
SURF_ug_DUST_SAH_C	Saharan dust coarse [\(\mu g/m^3\)]	From Boundary conditions
SURF_ug_DUST_NAT_F	Natural dust fine [\(\mu g/m^3\)]	Windblown and Saharan
SURF_ug_DUST_NAT_C	Natural dust coarse [\(\mu g/m^3\)]	Windblown and Saharan
SURF_ug_DUST	Mineral dust [\(\mu g/m^3\)]	From all sources
SURF_ug_PM10	PM10 dry [\(\mu g/m^3\)]
SURF_ug_PM10_rh50	PM10 wet [\(\mu g/m^3\)]	PM10 particle water at 50 %rh
SURF_ug_PM25	PM2.5 dry [\(\mu g/m^3\)]	Includes fine PM and 27% of coarse NO\(_3^-\)
SURF_ug_PM25_rh50	PM2.5 wet [\(\mu g/m^3\)]	PM2.5 particle water at 50 %rh
SURF_ug_PM25X	PM2.5 dry [\(\mu g/m^3\)]	Includes fine PM and 27% of coarse NO\(_3^-\), EC and OM
SURF_ug_PM25X_rh50	PM2.5 [\(\mu g/m^3\)]	As PM25X + particle water at 50 %rh
SURF_ug_PMFINE	Fine PM [\(\mu g/m^3\)]	Sum of all fine aerosols
SURF_ug_PPM25	Primary P|PM25| [\(\mu g/m^3\)]	Anthropogenic emissions
SURF_ug_PPM_C	Primary coarse PM [\(\mu g/m^3\)]	Anthropogenic emissions
SURF_ug_PM25_FIRE	PM2.5 from forest fires [\(\mu g/m^3\)]	Sum of BC, OC and rest PM2.5
Dry Depositions
DDEP_SOX_m2Grid	Oxidized sulphur [\(mg(S)/m^2\)]	For a grid cell landuse area weighted
DDEP_SOX_m2Conif	Oxidized sulphur [\(mg(S)/m^2\)]	To coniferous forest
DDEP_NOX_m2Grid	Oxidized nitrogen [\(mg(N)/m^2\)]	For a grid cell landuse area weighted
DDEP_NOX_m2Decid	Oxidized nitrogen [\(mg(N)/m^2\)]	To decideous forest
DDEP_RDN_m2Grid	Reduced nitrogen [\(mg(N)/m^2\)]	For a grid cell landuse area weighted
DDEP_RDN_m2Seminat	Reduced nitrogen [\(mg(N)/m^2\)]	To semi-natural
Wet Depositions
WDEP_PREC	Precipitation [mm]
WDEP_SOX	Oxidized sulphur [\(mg(S)/m^2\)]
WDEP_SS	Sea salt [\(mg/m^2\)]
Others
AOD	Aerosol Optical Depth at 550nm	Experimental
Area_Crops_Frac	Area fraction of crops	Available for several landuses
VG_NO3_F_Grid	Dry deposition velocity of fine NO\(_3^-\)	Grid cell average
Meteorological parameters
USTAR_GRID	\(U^*\) grid averaged	Available for several landuses
T2m	Temperature at 2m [\(^\circ C\)]
rh2m	Fractional relative humidity at 2m

ASCII outputs: sites and sondes

Two main options are available for the output of ASCII files for comparison with measurements or detailed model analysis. These are

sites

output of surface concentrations for a set of specified measurement site locations.

sondes

output of concentrations for the vertical column above a set of specified locations.

Both sites and sondes are specified and handled in similar ways, in the module Sites_ml.f90, so we treat them both together below. Locations are specified in the input files sites.dat and sondes.dat. The files start with a description of its content followed by a list of the stations. For example, a sondes.dat input file may look like this:

Listing 2 Minimum modrun.sh example.

# "Sondes: names, locations, elevations"
# "Area: EMEP-Europe"
# "ix: x coordinate"
# "iy: y coordinate"
# "lev: vertical coordinate (20=ground)"
: Units index
: Coords LatLong
: VertCoords EMEPsigma
: DomainName NA
#
name lat long lev #HEADERS
-    deg deg level #SKIP
#DATA:
Uccle             50.80    4.35  20  ! comment
Lerwick           60.13   -1.18  20  ! comment
Sodankyla         67.39   26.65  20  ! comment
Ny_Alesund        78.93   11.88  20  ! comment
Hohenpeissenberg  47.80   11.02  20  ! comment

The first line in each file is a header with file content. Then, the contents are described in more detail. Text strings after # are just clarifying comments. ‘Area’, e.g., is the domain to which the stations belong, e.g. ‘Northern Hemisphere’.

Text after : is read in by the model:

Units

Either ‘deg’ (degrees) or ‘index’ (model grid indices).

Coords

Either ‘LatLong’ (latitudes/longitudes) or ‘ModelCoords’ (indices of the grid box in which the station is located).

VertCoords

Vertical coordinate system that is used in the model (usually ‘EMEPsigma’).

Both sites.dat and sondes.dat files are optional, but recommended. The species and meteorological data requested for site and sonde output are specified in My_Outputs.f90 by the use of arrays. Only a few met fields are defined so far but more can be added into Sites_ml.f90 as required.

The output files sites_2014.csv and sondes_2010.csv are comma separated files that can be read by excel. If you include the whole year, or the 31^st December, sites_2015.csv and sondes_2015.csv are also included in the output.