Fortran libraries and tools initially created during the COSMO project (CTM2016-79474-R, MINECO/FEDER, UE) and further developed during the MEDOSMOSIS (6MED20_4.1._SP_005) project.

The code has been developed under Ubuntu using the GNU Fortran 9.4.0 compiler and the Fortran 90 netcdf library version 4.3.3 and 4.7.3 and python versions 3.6.3 and 3.8.10. It has been also tested in Centos using python 3.8.12 under anaconda (conda version4.11.10).

Purpose: Build a fortran utilities library and a Lagrangian trajectory integrator (COSMO Lagrangian Model). Requirements: Fortran compiler and the NetCDF F90 library version 4.3.X.X

To have access to all the capabilities of the codes, both a fortran compiler and a Python 3 interpreter are necessary. In addition, the following libraries, utilities and python modules are required:

• FFmpeg: a collection of libraries and programs for handling video and multimedia (Required by cosmo-view to create animations).

• NetCDF-Fortran library for running the Lagrangian model (written in Fortran).
• GEOS
• PROJ
• Shapely

• tkinter
• PIL
• numpy
• scipy
• matplotlib
• netcdf4
• Beautiful Soup
• wget
• psycopg2
• future
• requests
• tkcolorpicker
• py-postgresql
• shapely
• owslib
• tkcalendar
• motuclient
• cartopy

Some of these packages may already be installed in your operational system. Other might need to be installed. Be aware that the actual names of these packages and the commands required for their installation will vary from one system to another. Windows 10 users are strongly encouraged to install a Windows Subsystem for Linux (WSL) that will allow installing a Ubuntu 20.04 LTS environment running directly under windows.

Once all dependencies have been installed, the cosmo code can be retrieved through git:

$ git clone https://github.com/quimbp/cosmo.git

Auxiliary isobath contours, useful for cosmo-view can be downloaded from here:

https://nuvol.cmima.csic.es/owncloud/s/x8fGx5cEyHo7KMt/download

Download this file and save in the cosmo root folder (the folder where the file make.inc is located). Then, install it as

$ tar -xvzf isobaths.tar.gz

This command should extract the isobaths and place them in the folder data/isobaths

Edit the file make.inc and modify the linux sustem (Ubuntu or Centos), the fortran compiler, the fortran compiler options or the paths to the NetCDF modules and libraries. Be aware that, for ubuntu systems, make.inc uses the utility nc-config to obtain the location of the NetCDF files. However, this utility fails to provide the correct paths in Centos.

Then type,

$ make

If compilation succeeds, the COSMO Lagrangian Model will be located in $COSMO/bin/clm

Type

$ $COSMO/bin/clm --help

to obtain the list of options for running the model. A detailed User Documentation will be uploaded shortly.

Three utilities are currently available:

A visualization tool to visualize JSON files with lagrangian trajectories generated during the COSMO project. This tool allows simple selection of initial and final points and to remove undesired locations.

$ python3 cosmo-jason.py

A tool returning the initial position and the release date of a JSON lagrangian trajectory.

$ python3 release_point.py ../data/exp001.json
Opening file ../data/exp0001.json
1.4167 41.0002 2017-11-22T10:35:13

Using the option '-label' the corresponding option names required by the COSMO Lagrangian Model are included.

$ python3 release_point.py -label ../data/exp001.json
Opening file ../data/exp0001.json
-xo  1.4167 -yo  41.0002  -do  2017-11-22T10:35:13

A visualization tool to visualize ocean currents. It can load fields directly from operational providers or from Netcdf files. It can superimpose satellite SST data received by the HPRT station located in the Institut de Ciencies del Mar (ICM/CSIC) and lagrangian trajectories created by the COSMO Lagrangian Model or JSON files from field experiments.

$ $COSMO/bin/cosmo-view

A detailed User Documentation will be uploaded shortly.

• Joaquim Ballabrera (ICM/CSIC) E-mail: [email protected]
• Emilio García (ICM/CSIC) E-mail: [email protected]

This project is licensed under the MIT License - see the LICENSE file for details.

The COSMO project was funded by the Spanish Government Minstry of Economy and Competitivity (CTM2016-79474-R, MINECO/FEDER, UE). The MEDOSMOSIS project (6MED20_4.1._SP_005) was funded by the INTERREG-MED program. This work is the result of the collaboration of ICM-CSIC Research Team: Dr. Jordi Isern, Dr. Jordi Sole, Dr. Justino Martinez and Dr. Jose Antonio Jimenez.