The Biogeochemical Flux Model (BFM) is numerical model to simulate the dynamics of major biogeochemical properties in lower trophic levels of marine ecosystems.
The BFM is open source software freely available under the GNU Public License. The model description and documentation is available on the BFM website http://www.bfm-community.eu.
In the doc/ folder of the repository are also available the manuals and logos.
The development of the BFM is supported by a system team through a formal agreement (see https://bfm-community.github.io/www.bfm-community.eu/bfm-consortium/). The agreement establishes a program for model development that is discussed and prepared every year by the participants. Model developments are inserted by the system team into the different releases of the model. The agreement is open to entrance of more contributors and more information can be addressed to the BFM system Team at bfm_st(at)cmcc.it
Current members of the consortium are: CMCC, OGS, UNIBO, UCT, SYKE
Supported architectures:
- Linux
- Mac OSX (Darwin)
Software requirements:
- PERL (version 5.8.2 and above), including Switch module (to install it launch
cpanand typeinstall Switch). - FORTRAN 90/95 compiler. Under linux and Mac OSX the model can be currently compiled with gfortran (version 4.6 or higher) and ifort.
- NetCDF Libraries (https://www.unidata.ucar.edu/software/netcdf). It is mandatory that the library has been compiled with the same compiler used for the model compilation (as F90 netcdf module is used).
- GNU make. Makefile only works with GNU make, therefore substitute your system make or use an alias to ensure that the right one is set in case you are not on a linux machine.
Configuration and deployment of the model is done automatically by the script bfm_configure.sh found in the build directory. The minimal user local settings for compilation is provided by means of the environmental shell variable $BFMDIR
$> export BFMDIR=/path/to/bfm
$> cd $BFMDIR/build
[$BFMDIR/build]> ./bfm_configure.sh -hThe user-dependent options are set either through the command line of the script or by adjusting (or adding) an architecture file in directory $BFMDIR/compilers. Default file is gfortran.inc. The standard GNU gmake variables are used for compiler and archiver names. Remember to add the right path for the NetCDF library files in the appropriate .inc file.
If preset is not specified, the STANDALONE zero-dimensional configuration is compiled by default with the command
[$BFMDIR/build]> ./bfm_configure.sh -gcd(see the script help for details on the options) and if successful will produce the following output
.................................. Makefile is ready.
STANDALONE generation done!
Starting STANDALONE compilation...
STANDALONE compilation done!
Go to $BFMDIR/run/standalone and execute command:
./bfm_standalone.xThe configuration script creates in $BFMDIR/run/standalone the executable link, a copy of the namelists, and the running environment.
To launch a simulation go to the experiment run folder and execute the following
$> cd $BFMDIR/run/standalone
[$BFMDIR/run/standalone]> ./bfm_standalone.xTIP: use ./bfm_standalone.x &> outputfile to redirect the screen output messages to a file in bash.
Finally, realize an organized set of plots for BFM STANDALONE preset using the standalone_diag python script from the execution folder (usage details in tools README) :
[$BFMDIR/run/standalone]> python ../../tools/standalone_diag/standalone_diag.py BFM_Standalone.nc`A list of the available presets can be obtained using the command
[$BFMDIR/build]> ./bfm_configure.sh -P Refer to the model documentation for a description of the available presets.
To compile a specific preset use the following
[$BFMDIR/build]> ./bfm_configure.sh -gcd -p <preset_name>