source: NEMO/branches/2019/dev_ASINTER-01-05_merged/src/OCE/CRS/README.rst

Last change on this file was 12165, checked in by davestorkey, 11 months ago

2019/dev_ASINTER-01-05_merged: Update to r12072 of trunk.

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Line 
1**********************************
2On line biogeochemistry coarsening
3**********************************
4
5.. todo::
6
7
8
9.. contents::
10   :local:
11
12Presentation
13============
14
15A capacity of coarsening physics to force a BGC model coupled to NEMO has been developed.
16This capacity allow to run 'online' a BGC model coupled to OCE-SI3 with a lower resolution,
17to reduce the CPU cost of the BGC model, while preserving the effective resolution of the dynamics.
18
19A presentation is available [attachment:crs_wiki_1.1.pdf​ here], where the methodology is presented.
20
21What is available and working for now in this version
22=====================================================
23
24[To be completed]
25
26Description of the successful validation tests
27==============================================
28
29[To be completed]
30
31What is not working yet with on line coarsening of biogeochemistry
32==================================================================
33
34[To be completed]
35
36''should include precise explanation on MPI decomposition problems too''
37
38How to set up and use on line biogeochemistry
39=============================================
40
41Extract the on line biogeochemistry branch
42------------------------------------------
43
44To get the appropriate source code with the on line coarsening of biogeochemistry feature:
45
46.. code-block:: console
47
48   $ svn co https://forge.ipsl.jussieu.fr/nemo/browser/NEMO/branches/2018/dev_r5003_MERCATOR6_CRS
49
50
51How to activate coarsening?
52---------------------------
53
54To activate the coarsening, ``key_crs`` should be added to list of CPP keys.
55This key will only activate the coarsening of dynamics.
56
57Some parameters are available in the namelist_cfg:
58
59.. code-block:: fortran
60
61                  !   passive tracer coarsened online simulations
62   !-----------------------------------------------------------------------
63      nn_factx    = 3         !  Reduction factor of x-direction
64      nn_facty    = 3         !  Reduction factor of y-direction
65      nn_msh_crs  = 0         !  create (=1) a mesh file or not (=0)
66      nn_crs_kz   = 3         ! 0, volume-weighted MEAN of KZ
67                              ! 1, MAX of KZ
68                              ! 2, MIN of KZ
69                              ! 3, 10^(MEAN(LOG(KZ))
70                              ! 4, MEDIANE of KZ
71      ln_crs_wn   = .false.   ! wn coarsened (T) or computed using horizontal divergence ( F )
72                              !                           !
73      ln_crs_top = .true.     !coarsening online for the bio
74   /
75
76- Only ``nn_factx = 3`` is available and the coarsening only works for grids with a T-pivot point for
77  the north-fold lateral boundary condition (ORCA025, ORCA12, ORCA36, ...).
78- ``nn_msh_crs = 1`` will activate the generation of the coarsened grid meshmask.
79- ``nn_crs_kz`` is the operator to coarsen the vertical mixing coefficient.
80- ``ln_crs_wn``
81
82  - when ``key_vvl`` is activated, this logical has no effect;
83    the coarsened vertical velocities are computed using horizontal divergence.
84  - when ``key_vvl`` is not activated,
85
86    - coarsened vertical velocities are computed using horizontal divergence (``ln_crs_wn = .false.``)
87    - or coarsened vertical velocities are computed with an average operator (``ln_crs_wn = .true.``)
88- ``ln_crs_top = .true.``: should be activated to run BCG model in coarsened space;
89  so only works when ``key_top`` is in the cpp list and eventually ``key_pisces`` or ``key_my_trc``.
90
91Choice of operator to coarsene KZ
92---------------------------------
93
94A sensiblity test has been done with an Age tracer to compare the different operators.
95The 3 and 4 options seems to provide the best results.
96
97Some results can be found [xxx here]
98
99Example of xml files to output coarsened variables with XIOS
100------------------------------------------------------------
101
102In the [attachment:iodef.xml iodef.xml]  file, a "nemo" context is defined and
103some variable defined in [attachment:file_def.xml file_def.xml] are writted on the ocean-dynamic grid.
104To write variables on the coarsened grid, and in particular the passive tracers,
105a "nemo_crs" context should be defined in [attachment:iodef.xml iodef.xml] and
106the associated variable are listed in [attachment:file_crs_def.xml file_crs_def.xml ].
107
108Passive tracers tracers initial conditions
109------------------------------------------
110
111When initial conditions are provided in NetCDF files, the field might be:
112
113- on the coarsened grid
114- or they can be on another grid and
115  interpolated `on-the-fly <http://forge.ipsl.jussieu.fr/nemo/wiki/Users/SetupNewConfiguration/Weight-creator>`_.
116  Example of namelist for PISCES :
117
118   .. code-block:: fortran
119
120      !-----------------------------------------------------------------------
121      &namtrc_dta      !    Initialisation from data input file
122      !-----------------------------------------------------------------------
123      !
124         sn_trcdta(1)  = 'DIC_REG1'        ,        -12        ,  'DIC'     ,    .false.   , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
125         sn_trcdta(2)  = 'ALK_REG1'        ,        -12        ,  'ALK'     ,    .false.   , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
126         sn_trcdta(3)  = 'O2_REG1'         ,        -1         ,  'O2'      ,    .true.    , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
127         sn_trcdta(5)  = 'PO4_REG1'        ,        -1         ,  'PO4'     ,    .true.    , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
128         sn_trcdta(7)  = 'Si_REG1'         ,        -1         ,  'Si'      ,    .true.    , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
129         sn_trcdta(10) = 'DOC_REG1'        ,        -12        ,  'DOC'     ,    .false.   , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
130         sn_trcdta(14) = 'Fe_REG1'         ,        -12        ,  'Fe'      ,    .false.   , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
131         sn_trcdta(23) = 'NO3_REG1'        ,        -1         ,  'NO3'     ,    .true.    , .true. , 'yearly'  , 'reshape_REG1toeORCA075_bilin.nc'       , ''   , ''
132         rn_trfac(1)   =   1.0e-06  !  multiplicative factor
133         rn_trfac(2)   =   1.0e-06  !  -      -      -     -
134         rn_trfac(3)   =  44.6e-06  !  -      -      -     -
135         rn_trfac(5)   = 122.0e-06  !  -      -      -     -
136         rn_trfac(7)   =   1.0e-06  !  -      -      -     -
137         rn_trfac(10)  =   1.0e-06  !  -      -      -     -
138         rn_trfac(14)  =   1.0e-06  !  -      -      -     -
139         rn_trfac(23)  =   7.6e-06  !  -      -      -     -
140
141         cn_dir        =  './'      !  root directory for the location of the data files
142
143PISCES forcing files
144--------------------
145
146They might be on the coarsened grid.
147
148Perspectives
149============
150
151For the future, a few options are on the table to implement coarsening for biogeochemistry in 4.0 and
152future releases.
153Those will be discussed in Autumn 2018
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