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| 2 | Coupling with the Biogeochemical Flux Model (BFM) |
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| 3 | ----------------------------------------------------------------------- |
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| 4 | Author: M. Vichi, BFM system team and NEMO system team |
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| 5 | INFO HELPDESK: info@bfm-community.eu |
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| 6 | WEB SITE: www.bfm-community.eu |
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| 7 | REVISION DATE: October 2013 |
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| 8 | |
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| 9 | Please address any technical query to the BFM System Team |
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| 10 | bfm_st@lists.cmcc.it |
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| 11 | ----------------------------------------------------------------------- |
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| 12 | |
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| 13 | ----------------------------------------------------------------------- |
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| 14 | What is the BFM? |
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| 15 | ----------------------------------------------------------------------- |
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| 16 | The Biogeochemical Flux Model (BFM) is a numerical model for the |
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| 17 | simulation of the dynamics of major biogeochemical properties |
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| 18 | in marine ecosystems. The BFM is open source software freely available |
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| 19 | under the GNU Public License. The model can be used in standalone mode |
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| 20 | to simulate a 0-D system or coupled with other OGCM. |
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| 21 | The coupling with NEMO is maintained by CMCC as part of the |
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| 22 | NEMO system team activity |
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| 23 | |
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| 24 | ----------------------------------------------------------------------- |
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| 25 | How to get the BFM code |
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| 26 | ----------------------------------------------------------------------- |
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| 27 | The code can be downloaded from http://www.bfm-community.eu after |
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| 28 | the registration of a new user. Follow the instructions on how to |
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| 29 | install the code. It is recommended to run the STANDALONE test cases |
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| 30 | before using the NEMO-BFM coupled system. |
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| 31 | |
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| 32 | ----------------------------------------------------------------------- |
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| 33 | Compile NEMO with the BFM |
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| 34 | ----------------------------------------------------------------------- |
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| 35 | NEMO-BFM is compiled from the BFM configuration script relying on the |
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| 36 | NEMO FCM compilation environment. This is done to allow BFM users to |
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| 37 | use new configurations in NEMO that are not part of the NEMO |
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| 38 | standard distribution code. |
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| 39 | The BFM configuration shipped with NEMO is GYRE_BFM (see next section) |
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| 40 | |
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| 41 | Make sure that the BFMDIR variable is defined in your environment |
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| 42 | and define the variable NEMODIR pointing to the root of NEMO source code |
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| 43 | It is assumed here that you have expanded the bfm in /home/user/bfm |
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| 44 | and the root of this NEMO directory in /home/user/nemo then |
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| 45 | and that you have already adjusted the appropriate ARCHFILE that |
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| 46 | is used for the NEMO compilation with makenemo in ../../ARCH |
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| 47 | |
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| 48 | Execute the following commands: |
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| 49 | >> export BFMDIR=/home/user/bfm |
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| 50 | >> export NEMODIR=/home/user/nemo |
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| 51 | >> cd $BFMDIR/build |
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| 52 | >> ./bfm_config.sh -gcd -p GYRE_BFM |
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| 53 | |
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| 54 | The script will generate (-g) the BFM code, then launch |
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| 55 | makenemo for compilation (-c) and create the run directory |
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| 56 | (-d) in $BFMDIR/run. |
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| 57 | |
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| 58 | to get information on how to use the BFM configuration script run |
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| 59 | >> ./bfm_config.sh -h |
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| 60 | |
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| 61 | ----------------------------------------------------------------------- |
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| 62 | Standard test case |
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| 63 | ----------------------------------------------------------------------- |
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| 64 | The distributed standard test case is GYRE_BFM, a version of GYRE |
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| 65 | with a full-blown BFM. It is a demnstration simulation and it is not |
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| 66 | meant to produce any published result. |
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| 67 | GYRE_BFM runs with analytical input data only. |
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| 68 | The namelists for the BFM are not distributed with NEMO but are |
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| 69 | generated directly by the BFM, in directory $BFMDIR/run/gyre_bfm. |
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| 70 | The generation of the BFM namelist also copy the required NEMO |
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| 71 | namelist and namelist_top files to this directory. |
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| 72 | This is why there are no namelist files found in the standard |
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| 73 | run directory $NEMODIR/NEMOGCM/CONFIG/GYRE_BFM/EXP00 |
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| 74 | |
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| 75 | Note for expert users: |
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| 76 | If a user prefers to work in the NEMO directory than she has to |
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| 77 | copy the generated namelists there |
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| 78 | >> cp $BFMDIR/run/gyre_bfm/* $NEMODIR/NEMOGCM/CONFIG/GYRE_BFM/EXP00 |
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| 79 | Once the BFM code has been generated the first time, the code can be |
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| 80 | also rebuilt with the standard NEMO command: |
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| 81 | >> ./makenemo -n GYRE_BFM -m ARCHFILE -e $BFMDIR/src/nemo |
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| 82 | |
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| 83 | ----------------------------------------------------------------------- |
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| 84 | Other examples |
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| 85 | ----------------------------------------------------------------------- |
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| 86 | Other couplings with NEMO are available in $BFMDIR/build/configurations. |
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| 87 | Run the command |
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| 88 | >> ./bfm_config.sh -P |
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| 89 | to get a list of available presets |
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| 90 | Please refer to the README file in each directory for more information. |
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