Usage

There are four tools available in pyNEMO. These are “boundary file generation” where boundary data files are generated from a parent grid along the boundary of a child grid. Boundary data can comprise of tracers such as temperature and salinity. Or tidal data from global tide models. Sea surface height and ocean currents are also supported. PyNEMO now has an integrated CMEMS repository downloader. Invoking this option will download data of interest (as specified in NCML file) for a region of interest (as specified in BDY file). PyNEMO uses NCML files to define variable names and data location. this allows multiple netcdf input files to appear as one. This commonmly used on THREDDS servers but is also used locally for CMEMS boundary data input. The GUI allows this NCML files to be generated. Finally there is a settings editor that allows you to edit the pynemo configuration file (BDY file)

Boundary file generation

This command line tool reads a BDY file, extracts boundary data and prepares the data for a NEMO simulation. The bdy file is a plain text file containing key value pairs. Please look at the sample namelists in the github repository. They are stored in the inputs directory.

PyNEMO now also requires an NCML file (Netcdf markup) that defines the variables and remaps their names so that they are compatable with PyNEMO. This is most commonly required with CMEMS runs as the variable names are different. In previous versions PyNEMO was able to scan a local directory for netcdf files, this is now no longer supported and an NCML file MUST be referenced in the bdy file.

Note

PyNEMO now requires an NCML file as well as a BDY file to run, this can be adapted from the examples in the inputs folder or generated using the NCML GUI.

There are three examples of ncml files and they all use the same child grid but ultilise different data sources. One uses local data, the other uses data hosted on a THREDDS server. The last one is configured to download CMEMS data first and then run using the downloaded data. The namelist file shares common syntax with the NEMO simulation namelist input file.

Note

Directory paths in bdy file can be relative or absolute. The application picks the relative path from the current working directory.

Syntax for pynemo command is

> pynemo [-g] -s <bdy file>

For help

> pynemo -h
> usage: pynemo [-g] -s -d <namelist.bdy>
>        -g (optional) will open settings editor before extracting the data
>        -s <bdy filename> namelist file to use to generate boundary data
>        -d <bdy filename> namelist file to use to download CMEMS data

Example comamnd

> pynemo -g -s namelist.bdy

CMEMS data download

To download CMEMS data, the flag -d needs to be specified when running pynemo. This will use the specified namelist file and download the relevent CMEMS data. Once successful the same namelist file can be used to generate the boundary conditions by running PyNEMO with the -s flag. Example command.:

$ pynemo -d /PyNEMO/inputs/namelist_cmems.bdy

To use the CMEMS download service an account needs to be created at http://marine.copernicus.eu/services-portfolio/access-to-products/ Once created the user name and password need to be added to PyNEMO. To do this a file with the name CMEMS_cred.py in the utils folder needs to be created with two defined strings one called user and the other called pwd to define the user name and password.:

$ touch pynemo/utils/CMEMS_cred.py
$ vim pynemo/utils/CMEMS_cred.py
press i
user='username goes here'
pwd='password goes here'
press esc and then :wq

IMPORTANT This will create a py file in the right place with the parameters required to download CMEMS, the password is stored as plain text so please do not reuse any existing password you use!

The CMEMS download usage page has more information about how to configure the namelist file.

GUI NCML Generator

This GUI tool facilitates the creation of a virtual dataset for input into PyNEMO. The virtual dataset is defined using NetCDF Markup Language (NcML ).

Using NcML, it is possible to:

  • modify metadata
  • modify and restructure variables
  • combine or aggregate data from multiple datasets. The datasets may reside in the local file system or in a remote OPeNDAP (http://www.opendap.org/) server.

Please see NcML generator usage page for more information in using the GUI.

pynemo settings editor

This tool will open a window where you can edit the mask and change the values of bdy parameters.

Syntax for pynemo_settings_editor command is

> pynemo_settings_editor [-s <bdy filename>]

Note

If no file name is specified then a file dialog box will open to select a file.

For help

> pynemo_settings_editor -h
> usage: pynemo_settings_editor -s <namelist.bdy>

Example:

pynemo_settings_editor -s namelist.bdy