nfdata 0.1.0

Compile and edit input data for the NanoFASE model

NanoFASE Data

The NanoFASE Data module is a set of scripts to compile and edit input data for the NanoFASE model.

See the NanoFASE documentation for full documentation.

Still in development. Use with caution!

Getting started

The easiest way to get started is to create a Conda environment using the provided environment.yaml file:

$ conda env create -f environment.yaml
$ activate nanofase-data

If you don't want to use Conda, then this environment.yaml file lists the packages that need to be installed.

Usage

usage: nanofase_data.py [-h] [--output OUTPUT] {create,edit,constants} file

Compile or edit data for the NanoFASE model.

positional arguments:
  {create,edit,constants}
                        do you wish to create from scratch, edit the data or
                        create a constants file?
  file                  path to the config file (create/edit tasks) or
                        constants file (constants task)

optional arguments:
  -h, --help            show this help message and exit
  --output OUTPUT, -o OUTPUT
                        where to create the new constants file (for constants
                        task)

Creating a new dataset

Specifying the "create" option compiles a new NetCDF dataset and Fortran namelist constant file:

$ python nanofase_data.py create /path/to/config.create.yaml

An annotated example config file is given: config.create.example.yaml. The file is quite self-explanatory, but a few further explanations are provided in this document.

The two files will be output to the paths specified in the config file.

Editing an existing dataset

To edit an existing NetCDF dataset, specify the "edit" option:

$ python nanofase_data.py edit /path/to/config.edit.yaml

An annotated example config file is given: config.edit.example.yaml. This is similar (but not identical) in format to the creation config file, except only those variables you with to edit should be specified (all other variables are left as-is).

Certain variables can't be edited: flow_dir, is_estuary. Create a new dataset instead if you wish to change these variables.

The Fortran namelist file cannot be edited using this method and you should instead edit the file directly.

Only creating a new constants file

To simply convert a constants YAML file to a Fortran namelist file, you can use the constants option:

$ python nanofase_data.py constants /path/to/constants.yaml -o /path/to/constants.nml

No config file is required. The location of the newly created constants file is given by the -o or --output argument.

Tips

• For the moment, all rasters must be the same CRS as the flow_dir raster, and this must be a projected raster. We recommend ESPG:27700 (British National Grid). In addition, all rasters except for land_use must be the same resolution as flow_dir. They can cover a large geographical region and the module will automatically clip them to the correct size.
• Support for different file types is a bit sporadic at the moment. I suggest sticking the raster files for spatial variables, raster or CSV files for spatiotemporal variables (with 1 file per timestep for raster files) and shapefiles for point sources. You will trigger errors if you use an unsupported file.
• Example input data files are given in data.example/thames_tio2_2015/. Running the model using the example config files uses these data.