.. _`ch-inputfiles`: Input files =========== This chapter provides an overview on the necessary input files to run the EMEP/MSC-W model. A complete set of input files is provided as part of the EMEP/MSC-W Open Source release to allow model runs for the meteorological year 2015. :numref:`tab-inputdata` lists the input files. In the latest release, meteorology is provided for 2 different model domains and resolutions: - `EECCA` domain with a horizontal resolution of 50x50 km2 (at 60°N), on polar stereographic projection, and 20 vertical levels; - `EMEP01` domain with a 0.1x0.1 degrees on long-lat projection, and 34 vertical levels. Download the input via the catalog tool (:numref:`sec-ModelCode`) as follows: .. code-block:: bash # download 2015 meteorology for the EECCA domain catalog.py -Y 2015 -m --met-domain EECCA # download 2015 meteorology for the EMEP01 domain catalog.py -Y 2015 -m --met-domain EMEP01 # download other input files catalog.py --input The meteorology files will be placed under ``EMEP_MSC-W_model.rv4.45.OpenSource/meteo2015/``, and the remaining input files will be placed under ``EMEP_MSC-W_model.rv4.45.OpenSource/input/`` This are all input files needed to run the EMEP/MSC-W model, except the aircraft emissions (``AircraftEmis_FL.nc``), and forest fire emissions (``FINN_ForestFireEmis_2015.nc``). See sections :numref:`emisair` and :numref:`emisff` for details about these emissions data. IMPORTANT: The input data available in the EMEP/MSC-W Open Source Web site should be appropriately acknowledged when used for model runs. If nothing else is specified according to references further in this chapter, please acknowledge EMEP/MSC-W in any use of these data. .. csv-table:: List of input data files :name: tab-inputdata :header: **Data**, **Name**, **Format** :delim: & **Meteorology data**& ``meteoYYYY/GRID``& Meteorology & ``meteoYYYYMMDD.nc`` (365+1 files) & netCDF [#YMD]_ Degree-day factor & ``DegreeDayFactors.nc`` & netCDF **Other Input files**& ``input/``& Global Ozone & ``GLOBAL_O3.nc`` & netCDF New Global Ozone & ``Logan_P.nc`` & netCDF [#NewO3]_ BVOC emissions & ``EMEP_EuroBVOC.nc`` & netCDF Landuse & ``glc2000xCLMf18.nc`` and ``Landuse_PS_5km_LC.nc``& netCDF N depositions & ``AnnualNdep_PS50x_EECCA2005_2009.nc`` & netCDF Road dust & ``RoadMap.nc`` and ``AVG_SMI_2005_2010.nc`` & netCDF [#Optional]_ Aircraft emissions& ``AircraftEmis_FL.nc`` & netCDF [#Optional]_ Surface Pressure & ``SurfacePressure.nc`` & netCDF [#Optional]_ Forest Fire & ``FINN_ForestFireEmis_YYYY.nc`` & netCDF [#Optional]_ Dust files & ``Soil_Tegen.nc`` & netCDF [#Optional]_ & ``SoilTypes_IFS.nc`` & netCDF [#Optional]_ Emissions & ``EECCA/emislist.POLL`` (7 files, EMEP 50km PS grid) & ASCII [#POLL]_ & ``EMEP01/GNFRemis_EMEP01_2015.nc`` (regional, :math:`0.1\times 0.1` lon-lat) & netCDF [#Optional]_ Vertical level distribution & ``Vertical_levels20_EC.txt`` (for 20lev runs) & ASCII Time factors for monthly emissions & ``MonthlyFac.POLL`` (7 files) & ASCII [#POLL]_ Time factors for daily emissions & ``DailyFac.POLL`` (7 files) & ASCII [#POLL]_ Time factors for hourly emissions & ``HourlyFacs.INERIS`` & ASCII Natural |SO2| & ``DMS.nc`` & netCDF Volcanoes & ``columnsource_emission.csv`` & ASCII & ``columnsource_location.csv`` & ASCII Lightning emissions & ``lt21-nox.datMM`` (12 files) & ASCII [#YMD]_ Emissions speciation & ``emissplit.defaults.POLL`` & ASCII [#POLL]_ & ``emissplit.specials.POLL`` & ASCII [#POLL]_ [#Optional]_ Emission factors for scenario runs & ``femis.dat`` & ASCII Photo-dissociation rates & ``jclear.SEASON`` (4 files) & ASCII [#SEASON]_ & ``jcl1.SEASON`` (4 files) & ASCII [#SEASON]_ & ``jcl3.SEASON`` (4 files) & ASCII [#SEASON]_ Landuse definitions & ``Inputs_LandDefs.csv`` & ASCII Stomatal conductance & ``Inputs_DO3SE.csv`` & ASCII Sites locations for surface output & ``sites.dat`` & ASCII Sondes locations for vertical output& ``sondes.dat`` & ASCII .. rubric:: Footnotes .. [#YMD] ``YYYY``: year, ``MM``: month, ``DD``: day. .. [#NewO3] New |O3| boundary condition data in 30 levels. Can be used with ``NewLogan=.true.`` in ``BoundaryConditions_mod.f90``. .. [#Optional] Optional, in most cases. .. [#POLL] ``POLL``: pollutant type (|NH3|\ , CO, |NOx|\ , |SOx|\ , NMVOC, |PM25| and |PMco|\ ). .. [#SEASON] ``SEASON``: seasonal files (jan, apr, jul, oct). NetCDF files ------------ Meteorology ~~~~~~~~~~~ The daily meteorological input data (``meteoYYYYMMDD.nc``, where ``YYYY`` is year, ``MM`` is month and ``DD`` is day) used for the EMEP/MSC-W Model are based on forecast experiment runs with the Integrated Forecast System (IFS), a global operational forecasting model from the European Centre for Medium-Range Weather Forecasts (ECMWF). The IFS forecasts has been run by MSC-W as independent experiments on the HPCs at ECMWF with special requests on some output parameters. The meteorological fields are retrieved on a :math:`0.1^\circ\times 0.1^\circ` longitude latitude coordinates and interpolated to :math:`50\times 50 km^2` polar-stereographic grid projection. Vertically, the fields on 60 eta (\ :math:`\eta`\ ) levels from the IFS model are interpolated onto the 37 EMEP sigma (\ :math:`\sigma`\ ) levels. The meteorology is prepared into 37 sigma levels since the model is under test for a finer vertical resolution. The open source code is released with 20 sigma levels and to make the model read the meteorology properly, a description of the 20 vertical sigma levels is needed. This is provided in an ASCII file called ``Vertical_levels.txt`` together with the other input data (:numref:`tab-inputdata`). The version of the IFS model used for preparing these fields, Cycle 38r2, is documented in http://www.ecmwf.int/research/ifsdocs/index.html. Previous years are based on Cycle 36r1 with a resolution of :math:`0.2^\circ\times 0.2^\circ` on a spherical grid. Meteorological fields currently used for EMEP/MSC-W Model runs are given in :numref:`tab-metinput`. Some verification and description of these meteorological fields are given in Chapter 2 of the EMEP Status Report 1/2016. Acknowledgement: ECMWF, met.no .. csv-table:: Input meteorological data used in the EMEP/MSC-W Model :name: tab-metinput :header: **Parameter**, **Unit**, **Description** :delim: & **3D fields** && for 37 :math:`\sigma` :math:`u, v` & :math:`m/s` & Horizontal wind velocity components :math:`q` & :math:`kg/kg` & Specific humidity :math:`\theta` & :math:`K` & Potential temperature :math:`CW` & :math:`kg/kg` & Cloud water :math:`CL` & :math:`\%` & 3D Cloud cover :math:`cnvuf` & :math:`kg/sm^2` & Convective updraft flux :math:`cnvdf` & :math:`kg/sm^2` & Convective downdraft flux :math:`PR` & :math:`mm` & Precipitation **2D fields** && for surface :math:`PS` & :math:`hPa` & Surface pressure :math:`T2` & :math:`K` & Temperature at :math:`2 m` height :math:`Rh2` & :math:`\%` & Relative humidity at :math:`2 m` height :math:`SH` & :math:`W/m^2` & Surface flux of sensible heat :math:`LH` & :math:`W/m^2` & Surface flux of latent heat :math:`\tau` & :math:`N/m^2` & Surface stress :math:`SST` & :math:`K` & Sea surface temperature :math:`SWC` & :math:`m^3/m^3` & Soil water content :math:`lspr` & :math:`m` & Large scale precipitation :math:`cpr` & :math:`m` & Convective precipitation :math:`sdepth` & :math:`m` & Snow depth :math:`ice` & :math:`\%` & Fraction of ice :math:`SMI1` & & Soil moisture index level 1 :math:`SMI3` & & Soil moisture index level 3 :math:`u10, v10` & :math:`m/s` & Wind at :math:`10 m` height .. _`emisnew`: Gridded emissions ~~~~~~~~~~~~~~~~~ Gridded emissions in NetCDF care be used in conjunction with sector definitions. See section ``Defining own sectors`` and ``Country Variable (CV) format`` The main advantage of NetCDF emissions is that all the information about the data (projection, units) is given in the same file. This allows the code to reproject the emissions to any grid projection on the fly. It is easy to visualize the emissions of one country with simple tools, like ncview. The data is simple to interpret and it is possible to add new countries to an existing file (with appropriate tools). Global Ozone ~~~~~~~~~~~~ Initial concentration of ozone are required in order to initialize the model runs. Boundary conditions along the sides of the model domain and at the top of the domain are then required as the model is running. The ``Logan_P.nc`` file contains monthly averaged fields in NetCDF format. The initial and background concentrations are based on the Logan (1998) climatology. The Logan climatology is scaled on run time according to the Mace Head measurements as described in Simpson *et al.* (2003). For a number of other species, background/initial conditions are set within the model using functions based on observations (Simpson *et al.*, 2003 and Fagerli *et al.*, 2004). BVOC emissions ~~~~~~~~~~~~~~ Biogenic emissions of isoprene and monoterpene are calculated in the model as a function of temperature and solar radiation, using the landuse datasets. The light and temperature dependencies follow the ideas proposed in Guenther et al (1993,1995), the first step in the emission processing is to define 'standard' emission potentials, which give the emissions of particular land-covers at standard environmental conditions (:math:`30^\circ C` and photosynthetically active radiation of 1000 :math:`\mu mole/m^2/s`). European forests are treated in most detail. For these, BVOC emission potentials have been created from the the map of forest species generated by Koeble and Seufert (2001). This work provided maps for 115 tree species in 30 European countries, based upon a compilation of data from the ICP-forest network. The emission potentials for each species are as given in Simpson *et al.*, 2012, and have been aggregated into the four default forest classes used by EMEP over Europe (DF, CF, NF, BF). The NetCDF file ``EMEP_EuroBVOC.nc`` provides the aggregated emission potenitals for these 4 categories. These emission potentials have unit :math:`\mu g/m^2/h`\ , and refer to emissions per area of the appropriate forest category. On the global scale, new landcover maps were created as a combination of GLC2000 and Community Land Model (CLM) data as described in Simpson *et al.*, 2017. The default emission potentials are given for these extra CLM categories, and for any non-forest land-cover on Europe in the file ``Inputs_LandDefs.csv``. The underlying emission potentials, land-cover data bases, and model coding have however changed substantially since model version v.2011-06. The new approach is documented in Simpson *et al.*, 2012 and Simpson *et al.* 2017. Landuse ~~~~~~~ Landuse data are required for modelling boundary layer processes (i.e. dry deposition, turbulent diffusion). The EMEP/MSC-W model can accept landuse data from any data set covering the whole of the domain, providing reasonable resolution of the vegetation categories. Gridded data sets providing these landuse categories across the EMEP domain have been created based on the data from the Stockholm Environment Institute at York (SEI-Y) and from the Coordinating Center for Effects (CCE). 16 basic landuse classes have been identified for use in the deposition module in the model, and three additional "fake" landuse classes are used for providing results for integrated assessment modeling and effects work. There are two NetCDF files included, one file ``Landuse_PS_5km_LC.nc`` on 5 km resolution over the EMEP domain, and a global ``LanduseGLC.nc`` which combines data from GLC2000 with the Community Land Model (CLM). The different landuse types are desribed in Simpson et al (2012) and Simpson et al. (2017). Degree-day factor ~~~~~~~~~~~~~~~~~ Domestic combustion which contribute to a large part of GNFR C (SNAP 2), varies on the daily mean temperature. The variation is based on the heating degree-day concept. These degree days are pre-calculated for each day and stored in the file ``DegreeDayFactors.nc``. See Simpson et al. (2012) section 6.1.2. |NOx| depositions ~~~~~~~~~~~~~~~~~ Areas with high NO deposition loads have greater soil-NO emissions. To include this in the model, a NetCDF file where pre-calculated N-depositions are included. The file made by the results from the EMEP/MSC-W model runs over a 5-year period. Road Dust ~~~~~~~~~ Road traffic produces dust. These emissions are handled in the EMEP/MSC-W model in the ``Emissions_mod.f90`` module. To include road dust, set ``USE_ROADDUST=.true.`` in ``config_emep.nml``. There are two files included in input data, ``RoadMap.nc`` and ``AVG_SMI_2005-2010.nc``. ``RoadMap.nc`` include gridded roads and PM emissions over Europe, ``AVG_SMI_2005-2010.nc`` are global. .. _`emisair`: Aircraft emissions ~~~~~~~~~~~~~~~~~~ In the EMEP/MSC-W model aircraft emissions are 'OFF' by default. They can be switched 'ON' by setting ``USE_AIRCRAFT_EMIS=.true.`` in ``config_emep.nml``. When using aircraft emissions there are two options: Either the dataset provided by the EU-Framework Programme 6 Integrated Project QUANTIFY (http://www.pa.op.dlr.de/quantify), or the more recent CAMS-GLOB-AIR dataset which can be downloaded from the Atmosphere Data Store (https://ads.atmosphere.copernicus.eu/cdsapp#!/dataset/cams-global-emission-inventories?tab=form). However, before using these data a protocol has to be signed, which is why the data file can not be provided directly on the EMEP MSC-W Open Source website. Since rv4.39, CAMS-GLOB-AIR has been the default dataset. Registering at the Atmosphere Data Store is straightforward (https://ads.atmosphere.copernicus.eu/user/register?destination=/cdsapp) (If you rather want to use older QUANTIFY dataset go to http://www.pa.op.dlr.de/quantify, click on 'QUANTIFY emission inventories and scenarios', and then on 'Register'. That page will provide information about the registration process and the protocol that has to be signed. Once you are registered, click 'Login' and provide user name and password. On the new page, search for 'Emissions for EMEP', which links directly to the ``Readme`` file and the emission data file in NetCDF format. Download the emission data file and place it in the input folder.) Natural |SO2| ~~~~~~~~~~~~~~~~~~~~ Natural |SO2| emissions (dimethylsulfide (DMS) from sea) are provided as monthly gridded files. The values are computed taking into account sea surface temperature and wind speed. Surface water concentrations of DMS (needed for the flux calculation) are taken from SOLAS (Surface Ocean Lower Atmosphere Study) and were downloaded from https://www.bodc.ac.uk/solas_integration/implementation_products/group1/dms/. Surface Pressure ~~~~~~~~~~~~~~~~ If ``USE_AIRCRAFT_EMIS=.true``. in ``config_emep.nml``, then in addition to the Aircraft Emission file, there will be need for a ``SurfacePressure.nc`` file, which is already in the ``/input`` folder. The NetCDF file consists of surface pressure fields for each of the months in 2008 called ``surface_pressure``, and one field for the whole year called ``surface_pressure_year``. All fields are given in Pa. .. _`emisff`: Forest Fire ~~~~~~~~~~~ Since model version rv3.9 (November 2011), daily emissions from forest and vegetation fires are taken from the "Fire INventory from NCAR version 1.0" (FINNv1, Wiedinmyer et al. 2011). Data are available from 2005, with daily resolution, on a fine :math:`1 km\times1 km` grid. We store these data on a slightly coarser grid (\ :math:`0.2^\circ\times 0.2^\circ`\ ) globally for access by the EMEP MSC-W model. To include forest fire emissions set ``USE_FOREST_FIRES=.true.`` in ``config_emep.nml`` and download the 2012 GEOS-chem daily data http://bai.acom.ucar.edu/Data/fire/. The data needs to be stored with units mole/day in a NetCDF file called ``FINN_ForestFireEmis_2015.nc`` compatible with the ``ForestFire_mod.f90`` module. Dust files ~~~~~~~~~~ The annual ASCII data for sand and clay fractions as well as the monthly data for boundary and initial conditions for dust from Sahara are replaced with a single NetCDF file ``Soil_Tegen.nc`` since 2013. This covers data for a global domain in :math:`0.5\times 0.5` degree resolution. The variables 'sand' and 'clay' gives the fraction (in %) of sand an clay in the soil for each grid cell over land. The files are used by the module ``DustProd_mod.f90``, which calculates windblown dust emissions from soil erosion. Note that the parametrization is still in the development and testing phase, and is by default 'turned off'. To include it in the model calculations, set ``USE_DUST=.true.`` in ``config_emep.nml``. The user is recommended to read carefully documentation and comments in the module ``DustProd_mod.f90``. There is also a possibility to include boundary and initial conditions for dust from Sahara. The input file gives monthly dust mixing ratios (MM - month, e.g. 01, 02, 03,...) for fine and coarse dust from Sahara. The files are based on calculations from a global CTM at the University of Oslo for 2000. To include Saharan dust, set ``USE_SAHARA=.true.`` in ``config_emep.nml``. Another source for dust is an arid surface. This is accounted for by soilmosture calculations in ``DustProd_mod.f90``. Together with Soil Water Index from the meteorology files and permanent wilting point (pwp) from ``SoilTypes_IFS.nc``. This file is global and NetCDF. See Simpson et al. (2012) section 6.10. ASCII files ----------- Volcanoes ~~~~~~~~~ Emissions from volcanic passive degassing of |SO2| are included for the active Italian volcanoes, Etna, Vulcano and Stromboli, and based upon the officially submitted data. To consider these volcanic emissions, we need to feed the locations and heights of volcanoes into the model. The input file ``columnsource_location.csv`` contains the geographical coordinates (latitudes and longitudes) and the heights (in meters) of the included volcanoes, while ``columnsource_emission.csv`` contains the emission parameters. Since 2010 the EMEP/MSC-W model has also been used to model the transport of ash and |SO2| from volcanic eruptions. In addition to data for passive degassing of |SO2|\ , the above two input files also contain locations and emission parameters for two recent eruptions of Icelandic volcanoes (Eyjafjallajökull in 2010 and Grimsvötn in 2011). In order to include emissions from these eruptions one needs to set ``USE_ASH=.true.`` in ``config_emep.nml``. Gridded emissions ~~~~~~~~~~~~~~~~~ The official emission input for the EMEP/MSC-W model consists of gridded annual national emissions based on emission data reported every year to EMEP/MSC-W (until 2005) and to CEIP (from 2006) by each participating country. More details about the emission input with references can be found in Chapter 4 of the EMEP Status Report 1/2003 Part I (Simpson et al., 2003). Since 2015 different formats of gridded emissions can be used and mixed (with some restrictions) in the EMEP model under one common framework. The new emission system is described in :numref:`emisnew`. Here we focus only on the "old style" ASCII emission format. Seven gridded emission input files (``emislist.poll``) are available in ASCII format for the following compounds: CO, |NH3|\ , |NOx|\ , |PM25|\ , |PMco|\ , |SOx| and VOC. The gridded ASCII emission files contain 16 columns where the first column represents the country code (http://www.emep.int/grid/country_numbers.txt), the second and the third columns are the :math:`i` and :math:`j` indices of the EMEP grid, the fourth and fifth columns are the total emissions from low and high sources, and the last 11 columns contain emissions from 10 anthropogenic SNAP sectors (http://reports.eea.eu.int/technical_report_2001_3/en) and 1 source-sector called "Other sources and sinks", which include natural and biogenic emission sources. The data are given with the :math:`Mg`\ . Acknowledgement: EMEP Time factors for emissions ~~~~~~~~~~~~~~~~~~~~~~~~~~ Monthly and daily time factors for emission can be specified for the 7 compounds (CO, |NH3|\ , |NOx|\ , |PM25|\ , |PMco|\ , |SOx| and VOC). There is one file available per compound in ASCII format. The first two columns in the files represent the country code (http://www.emep.int/grid/country_numbers.txt), the second column represents an index that can be referenced by the sector definion (orginally this index corresponded to a SNAP sector). In the monthly files (``MonthlyFacFile``), the 12 consecutive columns represent the time factors corresponding to the months of the year. These time factors are interpolated according to whether the "current" simulation day is in the first or second half of the month. For days in the first half of the month, the monthly factor is a combination of the factor of the previous month and the current month. For days in the second half of the month, the monthly factor combines the factor of the current and the next month (for details, see the source code). In the daily files (``DailyFacFile``) there are 7 consecutive columns representing the time factor for each day of the week. The monthly timefactors are normalized in such a way that when combined with the daily timefactors, the total emission stays the same. The file defined in ``HourlyFacFile`` includes factors for each of the eleven SNAP sectors for every hour (the columns) for each day of the week, see Simpson et al. (2012) section 6.1.2. An additional file defined in ``HourlyFacSpecialsFile`` can be created by the user with modified hourly factors to be used for specific countries. The format is the same as for the default factors, except for an additional first column speicifying the country code number. Emission heights ~~~~~~~~~~~~~~~~ In previous versions the emission height distributions was given in a separate file. Now it is part of the code, and can also be modified by the users using config_emep.nml setting (see section "defining own sectors). A set of vertical distribution for different sectors are predefined in the model. The release heights are defined as a set of fractions released into predefined layers. The release height definitions are independent of the layers used by the model. There are 8 predefined release heights distributions. Those can also be defined through the config_emep.nml setting. The following will give exactly the same distributions as the predefined. You can then modify the values, or add new defined distributions. .. code-block:: Fortran :caption: Default definition of emission height distributions Emis_Zlevels(1:)20.0, 50.0, 92.0, 184.0, 324.0, 522.0, 781.0, 1106.0, Emis_h(1:,1) = 0.000, 0.000, 0.000, 0.003, 0.147, 0.400, 0.300, 0.150, Emis_h(1:,2) = 1.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, Emis_h(1:,3) = 0.060, 0.067, 0.093, 0.750, 0.030, 0.000, 0.000, 0.000, Emis_h(1:,4) = 0.050, 0.063, 0.087, 0.700, 0.100, 0.000, 0.000, 0.000, Emis_h(1:,5) = 0.020, 0.034, 0.046, 0.600, 0.300, 0.000, 0.000, 0.000, Emis_h(1:,6) = 0.000, 0.000, 0.000, 0.410, 0.570, 0.020, 0.000, 0.000, Emis_h(1:,7) = 0.200, 0.300, 0.020, 0.044, 0.066, 0.094, 0.123, 0.153, Emis_h(1:,8) = 0.200, 0.800, 0.000, 0.000, 0.000, 0.000, 0.000, 0.000, The ``Emis_Zlevels`` defines the height of the layer boundaries for emissions in meters. (Standard atmosphere is assumed to transform those in Pressure by the model). The first layers is from surface to 20 meters, the second layer from 20 to 50 m... until the eigth and last layer which runs from 781 to 1106 meters. For example sectors defined with the height index "1", will release nothing in the three lowest layers, 0.3% into the fourth layer, 14.7% into the fifth layer etc. The layers defined in Emis_h are independent from the layers used in the model run and do not need to be adapted if the number of model layers is modified. The actual resulting distribution of emissions into model layers is computed by the model and will be shown in the standard output. .. _`sec-femis`: Emission factor for scenario runs ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Scenario run in the case of the EMEP/MSC-W model means a run to test the impact of one or more pollutants from a particular country. Emission factors are applied to specified countries and emission sectors and can be set by changing the ASCII file ``femis.dat``. This file can be changed by the users according to their needs. See the `Source Receptor (SR) Runs `_ section for details. Vertical_levels.txt ~~~~~~~~~~~~~~~~~~~ Defines the vertical model layers. The numbers in Vertical_levels.txt correspond to the "A" and "B" coefficients of the hybrid (eta) coordinates (P=A+B*Psurf). Close to the surface, A should be small, and higher up we should use pressure levels. Then there is a gradual transition from surface to pressure levels. If the file is not provided, the meteorological vertical levels are used. In principle the model levels can be completely different, but it is more sensible to define layer boundaries that match the meteorological levels. NB: it is important not to define a lowest layer thinner than about 45 meters; the deposition scheme will fail if the middle of the lowest layer is smaller than the highest defined vegetation. Chemical speciation of emissions ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Many of the emission files give emissions of a group of compounds, e.g. |NOx| includes NO+|NO2|\ , and VOC can include many compounds. The information needed to retrieve emissions of individual compounds from these the gridded files is given in files labelled ``emissplit.defaults.POLL`` or ``emissplit.specials.POLL``, where ``POLL`` can be |NOx|\ , VOC, etc. The defaults file give the emission split for each sector split index (one per row, with second index being the sector split index), which is applied to all countries by default. For VOC this split was derived from the UK inventory of Passant (2002), as part of the chemical comparison project of Hayman *et al.* (2011). The specials files are in general optional, and can be used to specify speciation for particular countries or sectors. The 1\ :sup:`st` column specifies the country code of interest, the second the sector index. If forest fires are used, then the file ``emissplit.specials.voc`` is required (not optional), and the country-code 101 used to specify the VOC speciation of forest fires in this file. Lightning emissions ~~~~~~~~~~~~~~~~~~~ Emissions of |NOx| from lightning are included in the model as monthly averages on T21 (\ :math:`5.65^\circ\times 5.65^\circ`\ ) resolution (Køhler *et al.*, 1995). The lightning emissions are defined on a :math:`64\times 32` grid with 17 vertical levels, with global coverage, and are provided as 12 ASCII files ``lightningMM.dat``. Landuse definitions ~~~~~~~~~~~~~~~~~~~ For the vegetative landuse categories where stomatal modelling is undertaken, the start and end of the growing season (SGS, EGS, in days) must be specified. The calculation of SGS and EGS with respect to latitude is done in the module ``LandDefs_mod.f90``. The parameters needed to specify the development of the leaf area index (LAI) within the growing season are given in the ASCII file ``Inputs_LandDefs.csv``. For more information, see chapter 5 of the EMEP Status Report 1/2003 Part I (Simpson *et al.*, 2003). The file, designed to be opened with excel or gnumeric, contains a header briefly explaining the contents of the 14 columns. The first three columns are representing the landuse name, code (which are consistent with those in ``Landuse.Input`` file) and type (grouping of the landuse classes). The fourth column (PFT) gives a plant-functional type code (for future use), the fifth gives the maximum height of vegetation (m), the sixth indicates albedo (%) and the seventh indicates possible source of |NHx| (0 off/1 on, curently not used). Columns 8 to 11 define the growing season (day number), column 12 and 13 lists the LAI minimum and maximum (\ :math:`m^2/m^2`\ ) and columns 14 and 15 defines the length of the LAI increase and decline periods (no. of days). Finally, the last four columns give default values of foliar biomass and biogenic VOC emission potentials. See Simpson et al., (2012) for details. Stomatal conductance ~~~~~~~~~~~~~~~~~~~~ Parameters for the stomatal conductance model, deposition of |O3| and stomatal exchange (DO3SE) must be specified. That are based upon the ideas in Emberson *et al.*, 2000, and are discussed in Simpson and Emberson, 2006 and Tuovinen et al. 2004. The ASCII file ``Inputs_DO3SE.csv`` provides land-phenology data of each landuse type for stomatal conductance calculations. The data are summarised in Table 5.1 in Chapter 5 of the EMEP Status Report 1/2003 Part I (Simpson *et al.*, 2003). The file contains a **header** with the contents of the file, with different factors needed for each of the landuse classes used in the EMEP/MSC-W model. The first two columns represent the landuse code (which are consistent with those in ``Landuse.Input`` file) and name. The next 22 values are different phenology factors. Photo-dissociation rates ~~~~~~~~~~~~~~~~~~~~~~~~ The photo-dissociation rates (J-values) are provided as lookup tables. The method is previously described in Jonson *et al.*, (2001). J-values are provided as clear sky, light cloud and dense cloud conditions, and the model interpolates between these according to cloudiness from the meteorological input data. In the lookup tables data are listed for every 10 degree latitude at an interval of 1 degree zenith angle at every model height. For the two types of cloud conditions there are one ASCII file averaged for each season (``SS``); 01, 02, 03 and 04. For light cloud the four seasonal files are called ``jcl1kmSS.dat``, for dense cloud conditions the four seasonal files are called ``jcl3kmSS.dat``, and then for clear sky four files called ``jclearSS.dat``. In addittion there are two files for June called ``jcl1.jun`` and ``jcl3.jun``. Each file contains 18 columns. The first column is latitude of zenith angle and then the next 17 are the values for the model levels with the 1/s. For more details about these rates, please read Chapter 7.2 of the EMEP Status Report 1/2003 Part I (Simpson *et al.*, 2003). .. _`sec-sitessondes-input`: Site and Sonde files ~~~~~~~~~~~~~~~~~~~~ The model provides a possibility for extra output data of surface concentration for a set of specified measurement site locations and concentrations for the vertical column above a set of specified locations. These site and sonde locations are listed in the ASCII files ``sites.dat`` and ``sondes.dat`` files. These files can be changed by the user, and provide the outputs described in :numref:`sec-sitesonde`. 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_mod.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: .. literalinclude:: sites.dat :caption: Site location definition (``sites.dat``) example. .. literalinclude:: sitesLLHrel.dat :caption: Site location definition, LatLonHrel Coords example. .. literalinclude:: sitesLLZ.dat :caption: Site location definition, LatLonZm Coords example. 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 Vertical coordinate system that is used in the model - see below. The VertCoords system was changed in rv4.36, to allow several options. Specifying altitude rather than model coordinate is of course an obvious alternative to the model layer number that was previously used, but it is also easily mis-used and mis-understood too. For example, a site at 500m might need vertical profile and/or deposition correction if sitting on a 500m high plateau (hence it has a relative altitude of 0m, and should use iz=KMAX_MID), but if sitting on an isolated mountain in terrain of height 0m, the relative altitude would indeed to 500m and we should pick from some model level which represents that. Tricky! (Best might be to give station altitude and relative altitude in separate columns, so it is explicit at least.) Briefly though, one can now set the "Coords" parameter (in the header of the sites.dat input file, used to be just "LatLong") to be one of: 1. LatLonKdown - same as older LatLong, with lat/lon coordinates, then k-number with ground level being e.g. 20 2. LatLonZm - give lat, long, then altitude in metres. The model will then compare that altitude with the model's topography, to estimate a relative altitude (Hrel). It then calculates which model layer corresponds to that altitude. 3. LatLonHrel - give lat, long, and then your own preferred relative altitude (Hrel). This relative altitude may be calculated by comparison to digital elevation model (see for example, Loibl, W.; Winiwarter, W.; Kopsca, A.; Zufger, J. & Baumann, R. Estimating the spatial distribution of ozone concentrations in complex terrain Atmos. Environ., 1994, 28, 2557-2566). 4. IJKdown - does everything in model's i, j and k coordinates In principle (3) should produce the best results, with relative altitudes calculated compared to local topography (e.g. < 5km). Option (3) also allows the same Hrel to be used regardless of the underlying meteo resolution. One can also get Hrel from the TOAR database for some sites (Schultz, MG, et al 2017 Tropospheric Ozone Assessment Report: Database and metrics data of global surface ozone observations. Elem Sci Anth, 5: 58, DOI: https://doi.org/10.1525/elementa.244). However, testing of these systems against e.g. diunral profiles of ozone shows rather unpredictable results in some cases, and often just using the model's surface concentrations procudes results which are as good as those based upon altitude. The new systems are very fliexble thouhg, and allow the user to explore different methodologies. 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 ``Config_module.f90`` by the use of arrays. Only a few met fields are defined so far but more can be added into ``Sites_mod.f90`` as required. The output files ``sites_2015.csv`` and ``sondes_2015.csv`` are comma separated files that can be read by excel. netcdf versions of these files are also provided, ``sites_2015.nc`` and ``sondes_2015.nc``. If you include the whole year, or the 31\ :sup:`st` December, ``sites_2016.csv`` and ``sondes_2016.csv`` are also included in the output.