==== Objective ====


This is a package containing bash and R code that produces smoother fields from original ones. This has been needed in the past to produce smoother restart fields when the ocean model couldn't cope with too strong gradients. 

  *  [[http://ic3.cat/wikicfu/index.php/Tools/Smoothing#Applying_smoothing_to_GLORYS_ocean_restart_files|Applying smoothing to GLORYS ocean restart files]]


==== Description ====



=== List of functions ===


  *  run_smoothing.bash
  *  smooth_fields.R
  *  replace_variables.bash


==== Requirements ====



==== Use ====


The smoothing package consists of bash and R code that runs in the following order:

1) run_smoothing.bash

---> 2) smooth_fields.R

---> 3) replace_variables.bash

1) The running parameters are set in the bash-script //run_smoothing.bash//. This script launches steps 2) and 3).

2) //smooth_fields.R// produces smooth fields from the input fields specified by the variables list //varlist// in step 1).

[[important_note:]]
At this moment, the smoothing is implemented in **Loop A**, which corresponds to a coastal region with the continent on the west.
The smoothing is performed from the open ocean towards the coast, to bring smoother information into the smaller scales.
If smoothing needs to be applied in a coastal region with a different orientation, a different loop will need to be written and a switch implemented.
(contact isabel.andreu-burillo (at) ic3.cat)

3) //replace_variables.bash// replaces the fields in a file by the corresponding smoothed fields, obtained in step 2).

[[instructions_for_running:]]
For an ORCA1L46 setup, and two start-dates, the script has run on moore in an interactive queue specifying:  qrsh -l h_vmem=20G,s_rt=02:00:00,h_rt=02:00:00


==== Repository ====


The link to the GIT repository is https://dev.cfu.local/cfu_tools.git


==== Contact ====


The coordinator of this project is Domingo Manubens Gil <domingo.manubens@ic3.cat>

Any issues, please contact the developer:  Isabel Andreu-Burillo <isabel.andreu-burillo@ic3.cat>

As a new user, please register to this mailing list: http://cfutools.ic3.cat/mailman/listinfo/cfutools
You'll then have access to the history of all the emails sent to the users and presenting the
functions and their available options.


==== Development ====



=== Package structure ===



=== How to develop ===


Download the repository folder to your computer ( git clone https://dev.cfu.local/cfu_tools.git <local_folder> ) and check-out to the branch you want to develop in.


=== Steps to add a new function to a package ===


  *  Put the code of the function in a file.
  *  Make sure the code of the function follows the style rules (information below header, history, ...).
  *  Fill in the file with the function documentation.


==== Style Guide ====

You can check the style guide for the Smoothing package [[tools:style_guides:bash|here]] and [[tools:style_guides:r|here]]