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Branch 2019/dev_r10721_KERNEL-02_Storkey_Coward_IMMERSE_first_steps. Merge changes to doc from trunk r10740 through r11740

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1*****************
2Data assimilation
3*****************
4
5.. todo::
6
7
8
9.. contents::
10   :local:
11
12The assimilation interface to NEMO is split into three modules.
13
14- ``OBS`` for the observation operator
15- ``ASM`` for the application of increments and model bias correction
16  (based on the assimilation increments).
17- ``TAM`` the tangent linear and adjoint model.
18
19Please see |DOI man OCE|_ for more details including information about the input file formats and
20the namelist settings.
21
22Observation and model comparison (``OBS``)
23==========================================
24
25The observation and model comparison code (OBS) reads in observation files
26(profile temperature and salinity, sea surface temperature, sea level anomaly, sea ice concentration,
27and velocity) and calculates an interpolated model equivalent value at
28the observation location and nearest model timestep.
29The resulting data are saved in a feedback file (or files).
30The code was originally developed for use with the NEMOVAR data assimilation code, but
31can be used for validation or verification of model or any other data assimilation system.
32This is all controlled by the namelist.
33To build with the OBS code active ``key_diaobs`` must be set.
34
35More details in |DOI man OCE|_ "Observation and Model Comparison (``OBS``)" chapter.
36
37Standalone observation operator (``SAO``)
38-----------------------------------------
39
40The OBS code can also be run after a model run using saved NEMO model data.
41This is accomplished using the standalone observation operator (SAO)
42(previously known the offline observation operator).
43
44To build the SAO use makenemo.
45This means compiling NEMO once (in the normal way) for the chosen configuration.
46Then include ``SAO`` at the end of the relevant line in :file:`cfg.txt` file.
47Then recompile with the replacement main program in :file:`./src/SAO`.
48This is a special version of :file:`nemogcm.F90` (which doesn't run the model,
49but reads in the model fields, and observations and runs the OBS code.
50See "Standalone observation operator (``SAO``)" section in |DOI man OCE|_.
51
52Apply assimilation increments (``ASM``)
53=======================================
54
55The ASM code adds the functionality to apply increments to the model variables:
56temperature, salinity, sea surface height, velocity and sea ice concentration.
57These are read into the model from a NetCDF file which
58may be produced by separate data assimilation code.
59The code can also output model background fields which are used as an input to data assimilation code.
60This is all controlled by the namelist ``&nam_asminc``.
61To build the ASM code ``key asminc`` must be set.
62
63More details in |DOI man OCE|_ "Apply Assimilation Increments (``ASM``)" chapter.
64
65Tangent linear and adjoint (``TAM``)
66====================================
67
68This is the tangent linear and adjoint code of NEMO which is useful to 4D VAR assimilation.
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