Updated user manual.

docs/manual/meteorological-input-data.md

@@ -10,52 +10,52 @@ The MPTRAC model needs meteorological input data (winds, temperature, ...) to pe
      <basename>_<YYYY>_<MM>_<DD>_<HH>.nc
 ```
 
-At a minimum, MPTRAC needs temperature (T), zonal wind (U), meridional wind (V), and vertical velocity (W). Additionally, many applications need specific humidity (Q), ozone (O3), cloud liquid water content (CLWC), and cloud ice water content (CIWC).
+At a minimum, MPTRAC needs temperature (netCDF variable name: T), zonal wind (U), and meridional wind (V). Additionally, many applications need the vertical velocity (W), specific humidity (Q) or relative humidity (RH), ozone (O3), cloud liquid/rain water content (CLWC/CRWC), cloud ice/snow water content (CIWC/CSWC), and cloud cover (CC).
 
-It is also necessary to download the surface pressure (PS or LNSP) and the surface geopotential height (Z). Optionally, surface temperature (T2M) and winds (U10M, V10M) are read in.
+It is also necessary to provide the surface pressure (LNSP, PS, or SP) and the surface geopotential height (Z or ZM). Optionally, the surface temperature (T2M). the wind components (U10M, V10M), the land-sea mask (LSM), and sea surface temperature (SSTK) are read in.
 
-It is possible to provide meteo data on model levels rather than pressure levels. In this case, pressure (PL) on model levels is required as an additional input variable in order to perform a vertical interpolation from model levels to pressure levels.
+It is possible to provide meteo data on model levels rather than pressure levels. In this case, pressure on model levels (PL) is required as an additional input variable in order to perform a vertical interpolation from model levels to pressure levels.
 
-See the example/meteo/ directory in the MPTRAC repository for an example of the meteo data netCDF files.
+See the tests/data/ directory in the MPTRAC repository for examples of meteo data netCDF files.
 
 ## The ECMWF reanalyses
 
 ### Overview
 
 As an example, we discuss the use of [ERA-Interim](https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era-interim) and [ERA5](https://www.ecmwf.int/en/forecasts/datasets/reanalysis-datasets/era5) reanalysis data provided by the European Centre for Medium-Range Weather Forecasts (ECMWF) to run the MPTRAC model.
 
-ERA-Interim is a global atmospheric reanalysis that is available from 1 January 1979 to 31 August 2019. The data assimilation system used to produce ERA-Interim is based on a 2006 release of the IFS (Cy31r2). The system includes a 4-dimensional variational analysis (4D-Var) with a 12-hour analysis window. The spatial resolution of the data set is approximately 80 km (T255 spectral) on 60 levels in the vertical from the surface up to 0.1 hPa.
+ERA-Interim is a global atmospheric reanalysis that is available from 1 January 1979 to 31 August 2019. The data assimilation system used to produce ERA-Interim is based on a 2006 release of the IFS (Cy31r2). The system includes a 4-dimensional variational analysis (4D-Var) with a 12-hour analysis window. The spatial resolution of the data set is approximately 80 km (T255 spectral grid) on 60 levels in the vertical from the surface up to 0.1 hPa.
 
-A first segment of the ERA5 dataset is now available for public use (1979 to within 5 days of real time). ERA5 provides hourly estimates of a large number of atmospheric, land and oceanic climate variables. The data cover the Earth on a 30 km grid and resolve the atmosphere using 137 levels from the surface up to a height of 80 km. ERA5 includes information about uncertainties for all variables at reduced spatial and temporal resolutions.
+ERA5 provides hourly estimates of a large number of atmospheric, land and oceanic climate variables from 1950 to present. The data cover the Earth on a 30 km grid (T639 triangular truncation) and resolve the atmosphere using 137 levels from the surface up to a height of about 80 km. ERA5 includes information about uncertainties for all variables at reduced spatial and temporal resolutions.
 
-### Download of ERA-Interim data
+### Download of ECMWF data
 
 The first step is to download the ERA-Interim data from [ECMWF's data archive](https://apps.ecmwf.int/datasets/data/interim-full-daily). It is recommended to download the data in grib file format at 0.75°x0.75° horizontal resolution, on all 60 model levels, and at 6-hourly time intervals.
 
-*Alternatively, download ERA5 from the [Copernicus Climate Change Service (C3S) Climate Date Store](https://cds.climate.copernicus.eu/#!/search?text=ERA5&type=dataset). It is recommended to download the data in grib file format at 0.3°x0.3° horizontal resolution, on all 137 model levels, and at hourly time intervals.
+Alternatively, download ERA5 data from the [Copernicus Climate Change Service (C3S) Climate Date Store](https://cds.climate.copernicus.eu/#!/search?text=ERA5&type=dataset). It is recommended to download the data in grib file format at 0.3°x0.3° horizontal resolution, on all 137 model levels, and at hourly time intervals.
 
 ### Interpolation to pressure levels
 
 The second step is to interpolate the ERA-Interim data from model levels to pressure levels. Here, a set of target pressure levels needs to be selected. It is recommended to use a set of 60 pressure levels that matches the vertical sampling of the model level data (as defined by a fixed surface pressure of 1013.25 hPa and [ECMWF's a and b level coefficients](https://www.ecmwf.int/en/forecasts/documentation-and-support/60-model-levels)).
 
-For ERA5 a different set of [a and be level coeffients](https://www.ecmwf.int/en/forecasts/documentation-and-support/137-model-levels) should be considered. Potentially, the vertical sampling of the target pressure levels in the lower troposphere and the number of levels in the mesosphere can be reduced to reduce the amount of data.
+For ERA5 a different set of [a and be level coefficients](https://www.ecmwf.int/en/forecasts/documentation-and-support/137-model-levels) should be considered. Potentially, the vertical sampling of the target pressure levels in the lower troposphere and the number of levels in the mesosphere can be reduced to reduce the amount of data.
 
-The CDO tools can be used to perform the vertical interpolation from model levels to pressure levels and to convert from grib to netCDF file format. For example:
+The [CDO tools](https://code.mpimet.mpg.de/projects/cdo) can be used to perform the vertical interpolation from model levels to pressure levels and to convert from grib to netCDF file format. For example:
 
 ```
     # merge surface and model level grib files...
     cdo -P 8 merge 2020010100_sf.grb 2020010100_ml.grb merge.grib
 
     # interpolate to pressure levels and create netCDF file (for ERA-Interim)...
-    cdo -P 8 -a -f nc -t ecmwf ml2pl,101325,101085,100726,100202,99474.7,98514,97298.7,95814.8,94055.1,92018.9,89711.2,87142,84326.3,81283,78034.6,74606.3,71026.3,67324,63530.6,59677.7,55797.3,51920.9,48079.1,44300.9,40613.3,37040.7,33604.4,30321.7,27205.9,24265.2,21502.5,18914.7,16508.9,14290.2,12261.4,10422.9,8772.74,7306.63,6018.02,4906.71,3960.29,3196.42,2579.89,2082.27,1680.64,1356.47,1094.83,883.66,713.22,575.65,464.62,373.97,298.5,234.78,180.58,134.48,95.64,63.65,38.43,20,10 merge.grib ei_2020_01_01_00.nc
+    cdo -P 8 -a -f nc -t ecmwf ml2pl,104613,102853,101094,99334.1,97574.4,95814.8,94055.1,92018.9,89711.2,87142,84326.3,81283,78034.6,74606.3,71026.3,67324,63530.6,59677.7,55797.3,51920.9,48079.1,44300.9,40613.3,37040.7,33604.4,30321.7,27205.9,24265.2,21502.5,18914.7,16508.9,14290.2,12261.4,10422.9,8772.74,7306.63,6018.02,4906.71,3960.29,3196.42,2579.89,2082.27,1680.64,1356.47,1094.83,883.66,713.22,575.65,464.62,373.97,298.5,234.78,180.58,134.48,95.64,63.65,38.43,20,10 merge.grib ei_2020_01_01_00.nc
 
     # interpolate to pressure levels and create netCDF file (for ERA5)...
-    cdo -P 8 -a -f nc -t ecmwf ml2pl,101325,98660.4,93476.7,84269.6,81208.5,79564,77846.6,76060,74208.6,72297.9,70334.7,68326.2,66280.8,64207.6,62116.2,60016.7,57919.3,55834.3,53772,51742,49758.4,47831,45963.2,44153.9,42401.9,40705.8,39064.5,37476.7,35941.1,34456.6,33022,31636.1,30297.6,29005.5,27758.5,26555.6,25395.5,24277.2,23199.5,22161.5,21161.9,20199.7,19273.9,18383.4,17527.3,16704.5,15914,15154.9,14426.2,13727,13056.4,12413.4,11797.1,11206.8,10641.5,10100.5,9582.8,9087.74,8614.5,8161.82,7728.1,7311.87,6911.87,6526.95,6156.07,5798.34,5452.99,5119.9,4799.15,4490.82,4194.93,3911.49,3640.47,3381.74,3135.12,2900.39,2677.35,2465.77,2265.43,2076.1,1897.52,1729.45,1571.62,1423.77,1285.61,1156.85,1037.2,926.34,823.97,729.74,643.34,564.41,492.62,427.59,368.98,316.42,269.54,227.97,191.34,159.28,131.43,107.42,86.9,69.52,54.96,42.88,32.99,24.99,18.61,13.61,9.75 -selname,lnsp,z,t,u,v,w,q,o3 merge.grib ea5_2020_01_01_00.nc
+    cdo -P 8 -a -f nc -t ecmwf ml2pl,104445,103725,103006,102286,101567,100847,100128,99408.1,98688.6,97969,97249.5,96529.9,95810.4,95090.8,94314,93476.7,92575.7,91608.1,90571.2,89462.2,88279.1,87020,85683.8,84269.6,82777.6,81208.5,79564,77846.6,76060,74208.6,72297.9,70334.7,68326.2,66280.8,64207.6,62116.2,60016.7,57919.3,55834.3,53772,51742,49758.4,47831,45963.2,44153.9,42401.9,40705.8,39064.5,37476.7,35941.1,34456.6,33022,31636.1,30297.6,29005.5,27758.5,26555.6,25395.5,24277.2,23199.5,22161.5,21161.9,20199.7,19273.9,18383.4,17527.3,16704.5,15914,15154.9,14426.2,13727,13056.4,12413.4,11797.1,11206.8,10641.5,10100.5,9582.8,9087.74,8614.5,8161.82,7728.1,7311.87,6911.87,6526.95,6156.07,5798.34,5452.99,5119.9,4799.15,4490.82,4194.93,3911.49,3640.47,3381.74,3135.12,2900.39,2677.35,2465.77,2265.43,2076.1,1897.52,1729.45,1571.62,1423.77,1285.61,1156.85,1037.2,926.34,823.97,729.74,643.34,564.41,492.62,427.59,368.98,316.42,269.54,227.97,191.34,159.28,131.43,107.42,86.9,69.52,54.96,42.88,32.99,24.99,18.61,13.61,9.75,6.83,4.67,3.1,2,1 -selname,lnsp,z,t,u,v,w,q,o3 merge.grib ea5_2020_01_01_00.nc
 ```
 
 ## Other meteorological data sets
 
-The MPTRAC model has also been tested with a number of other meteorological data sets.
+The MPTRAC model has also been tested with other meteorological data sets.
 
 The [Modern-Era Retrospective analysis for Research and Applications, Version 2](https://gmao.gsfc.nasa.gov/reanalysis/MERRA-2/) (MERRA-2) provides data beginning in 1980. It was introduced to replace the original MERRA dataset because of the advances made in the assimilation system that enable the assimilation of modern hyperspectral radiance and microwave observations, along with GPS-Radio Occultation datasets. It also uses NASA's ozone profile observations that began in late 2004. Additional advances in both the GEOS model and the GSI assimilation system are included in MERRA-2. The spatial resolution remains about the same (about 50 km in the latitudinal direction) as in MERRA.
 

docs/manual/tropopause-data.md

@@ -38,11 +38,11 @@ MPTRAC provides the tool "tropo" that generates tropopause data files from given
 
 The tropopause data are provided as netCDF files. Each data file may contain one or more time steps of the reanalysis.
 
-The data files provide geopotential height, pressure, temperature, and water vapor volume mixing ratios for the cold point, WMNO 1st and 2nd tropopause, and the dynamical tropopause.
+The data files provide geopotential height, pressure, temperature, and water vapor volume mixing ratios for the cold point, WMO first and second tropopause, and the dynamical tropopause.
 
 The tool "tropo_sample" can be used to extract tropopause data from the netCDF files created by "tropo" for a set of locations specified as a particle data file (atm.tab file).
 
-Tropopause data files for various meteorological reanalyses can be found in the meteocloud data archive in Jülich:
+Tropopause data files for various meteorological reanalyses can be found in the [Reanalysis Tropopause Data Repository](https://datapub.fz-juelich.de/slcs/tropopause) or locally in the Meteocloud data archive in Jülich:
 
 ```
     /p/fastdata/slmet/slmet111/met_data/tropo