source: NEMO/trunk/src/OCE/CRS/README.rst @ 10201

Last change on this file since 10201 was 10201, checked in by nicolasmartin, 3 years ago

Various modifications related to the setting of a NEMO Quick Start Guide

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