Data output

Data output#

Data output is handled by the DataOutput class and configured in the model config file. Output is to a series of text files:

  • summary.md: A plain-text summary of the model simulation, including compartmental mean PECs. These means are simply a summary of what is output in the following CSV files.

  • output_water.csv: Output data for every waterbody.

  • output_sediment.csv: Output data for each waterbody’s bed sediment.

  • output_soil.csv: Output for each soil profile.

Configuration#

The &output group in the model config file is responsible for configuring data output. The following options are available:

  • write_metadata_as_comment: Should metadata (largely column descriptions) be writen to the header of each CSV file as # delimited comments? Top tip: If you turn metadata on and are using Pandas to read the data, then make sure to use the comment argument when reading the CSV: df = pd.read_csv('output_water.csv', comment='#'). Defaults to true.

  • include_waterbody_breakdown: For surface waters, should data for each waterbody be output, or should it be aggregated to grid cell level? Defaults to true.

  • include_sediment_layer_breakdown: Should data for each sediment layer be output, or only summaries of the whole sediment profile? Defaults to true.

  • include_soil_layer_breakdown: Should data for each soil layer be output, or only summaries of the whole soil profile? Defaults to true.

  • include_soil_state_breakdown: Should the breakdown of soil NM into free and attached states be output? Bear in mind that outputting a layer and state breakdown may result in particularly large output files. Defaults to false.

  • include_sediment_fluxes: Should the fluxes of sediment from/to waterbodies be included in the output (e.g. soil erosion, bank erosion, deposition/resuspension).

In addition, two options to specific the units for concentrations (kg/m3 or kg/kg) in soils and sediments will soon be available: soil_pec_units and sediment_pec_units. Watch this space.

Output files#

Column descriptions are given in the file metadata (if write_metadata_as_comment is set to .true.). For water, each row represents an individual waterbody on a timestep, if include_waterbody_breakdown is .true., or aggregated to grid cell level if .false.. For soils and sediment, each row represents the entire soil/sediment profile in a grid cell on a particular timestep.

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