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README

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Coupling with the Biogeochemical Flux Model (BFM)
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Author: M. Vichi, BFM system team and NEMO system team
INFO HELPDESK: info@bfm-community.eu
WEB SITE: www.bfm-community.eu
REVISION DATE: October 2013

Please address any technical query to the BFM System Team 
bfm_st@lists.cmcc.it
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What is the BFM?
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The Biogeochemical Flux Model (BFM) is a numerical model for the 
simulation of the dynamics of major biogeochemical properties 
in marine ecosystems.  The BFM is open source software freely available 
under the GNU Public License. The model can be used in standalone mode 
to simulate a 0-D system or coupled with other OGCM.
The coupling with NEMO is maintained by CMCC as part of the 
NEMO system team activity

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How to get the BFM code
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The code can be downloaded from http://www.bfm-community.eu after
the registration of a new user. Follow the instructions on how to 
install the code. It is recommended to run the STANDALONE test cases 
before using the NEMO-BFM coupled system.

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Compile NEMO with the BFM 
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NEMO-BFM is compiled from the BFM configuration script relying on the
NEMO FCM compilation environment. This is done to allow BFM users to
use new configurations in NEMO that are not part of the NEMO
standard distribution code.
The BFM configuration shipped with NEMO is GYRE_BFM (see next section)

Make sure that the BFMDIR variable is defined in your environment
and define the variable NEMODIR pointing to the root of NEMO source code
It is assumed here that you have expanded the bfm in /home/user/bfm
and the root of this NEMO directory in /home/user/nemo then
and that you have already adjusted the appropriate ARCHFILE that
is used for the NEMO compilation with makenemo in ../../ARCH

Execute the following commands:
>> export BFMDIR=/home/user/bfm
>> export NEMODIR=/home/user/nemo
>> cd $BFMDIR/build
>> ./bfm_config.sh -gcd -p GYRE_BFM

The script will generate (-g) the BFM code, then launch 
makenemo for compilation (-c) and create the run directory
(-d) in $BFMDIR/run.

to get information on how to use the BFM configuration script run
>> ./bfm_config.sh -h

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Standard test case
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The distributed standard test case is GYRE_BFM, a version of GYRE
with a full-blown BFM. It is a demnstration simulation and it is not
meant to produce any published result. 
GYRE_BFM runs with analytical input data only.
The namelists for the BFM are not distributed with NEMO but are 
generated directly by the BFM, in directory $BFMDIR/run/gyre_bfm. 
The generation of the BFM namelist also copy the required NEMO
namelist and namelist_top files to this directory. 
This is why there are no namelist files found in the standard 
run directory $NEMODIR/NEMOGCM/CONFIG/GYRE_BFM/EXP00 

Note for expert users:
If a user prefers to work in the NEMO directory than she has to
copy the generated namelists there 
>> cp $BFMDIR/run/gyre_bfm/* $NEMODIR/NEMOGCM/CONFIG/GYRE_BFM/EXP00
Once the BFM code has been generated the first time, the code can be 
also rebuilt with the standard NEMO command:
>> ./makenemo -n GYRE_BFM -m ARCHFILE -e $BFMDIR/src/nemo 

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Other examples
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Other couplings with NEMO are available in $BFMDIR/build/configurations.
Run the command 
>> ./bfm_config.sh -P
to get a list of available presets
Please refer to the README file in each directory for more information.
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