source: TOOLS/MOSAIX/README.md @ 4757

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1# MOSAIX
2
3## SVN information
4
5    svn propset svn:keywords "Date Revision HeadURL Author Id" *.bash *.xml *.py src/MOSAIX/* Utils/*
6    $Author$
7    $Date$
8    $Revision$
9    $Id$
10    $HeadURL$
11
12All documentation available at https://forge.ipsl.jussieu.fr/igcmg/wiki/IPSLCM6/MOSAIX
13
14Extraction : `svn co http://forge.ipsl.jussieu.fr/igcmg/svn/TOOLS/MOSAIX MOSAIX`
15
16or `svn co svn+ssh://omamce@forge.ipsl.jussieu.fr/ipsl/forge/projets/igcmg/svn/TOOLS/MOSAIX MOSAIX`
17
18### [XIOS ](http://forge.ipsl.jussieu.fr/ioserver/)
19MOSAIC is known to work with XIOS revision 1257
20
21XIOS : http://forge.ipsl.jussieu.fr/ioserver/svn/XIOS/trunk   revision 1257
22
23## MOSAIX
24
25MOSAIX is a small set of fortran routines, bash scripts, python scripts and xml files allowing to generate coupling weights for IPSL Earth System Model. It is under development, and presently not used by the production runs. It aims to replace the old MOSAIC software. It uses XIOS as a library to compute weights. In the present state, it can handle ORCA, LMDZ lon/lat and DYNAMICO grids.
26
27MOSAIX can generate 2nd order conservative interpolation weights. They are used in place of bilinear interpolation by [OASIS-MCT](https://portal.enes.org/oasis)
28
29As MOSAIX uses XIOS, it works in parallel, using MPI distributed memory.
30
31## Compatibility with MOSAIC
32
33-   Weights are generally compatible with the weights generated by MOSAIC. The precision of the interpolation (conservation) is improved.
34
35-   **Run-off** : runoff weights are computed with a different algorithm, the result can be quite different.
36
37-   **Calving** : In IPSLCM6, the calving was integrated for each latitude of the grid on the LMDZ grid. Weights were use to aggregate several latitudes to compute an integral over a latitudinal band.. This is not possible with DYNAMICO, and was abandon for rectilinear LMD grid. The atmosphere model must the integral over a region (presently latitudinal bands). The final result should be the same as with MOSAIC.
38
39## TODO
40
41-   Creates a non-masked grid for atmosphere, to compute integrals of run-off
42-   Creates 2^nd^ order interpolation weights that conserve posivity. They won't be conservative.
43
44## Known problems
45
46-   ?
47
48## Future work
49
50-   Geographical distribution of the calving for the northern hemisphere.
51
52## Code availability
53
54-   Web : [​https://forge.ipsl.jussieu.fr/igcmg/browser/TOOLS/MOSAIX](https://forge.ipsl.jussieu.fr/igcmg/browser/TOOLS/MOSAIX)
55-   SVN : svn co http://forge.ipsl.jussieu.fr/igcmg/svn/TOOLS/MOSAIX MOSAIX
56-   SVN : svn co svn+ssh://<login>@forge.ipsl.jussieu.fr/ipsl/forge/projets/igcmg/svn/TOOLS/MOSAIX MOSAIX
57
58## Portability
59
60MOSAIX has been tested on Curie and Irene ([​TGCC](https://www-tgcc.ccc.cea.fr)) .
61
62## Requirements
63
64-   Fortran compiler, C++ compiler, MPI.
65-   A working [​XIOS](http://forge.ipsl.jussieu.fr/ioserver) library. Revision 1615 is known to work.
66-   fcm version 1.2
67-   NetCDF fortran librairies. See [​XIOS](http://forge.ipsl.jussieu.fr/ioserver) for a suitable version.
68-   Python, version>=3.6 with [​netCDF4](http://unidata.github.io/netcdf4-python/) and [​numpy](http://www.numpy.org) modules. Python version>=2.7 mights work, but has not been tested recently.
69-   Bash version>=4.
70-   [​NCO](http://nco.sourceforge.net). Version 4.6.0 is known to work.
71
72## Input files
73
74MOSAIX needs files describing the grid of the models. See `CreateWeightsMask.bash` and the bottom of this page.
75
76## Output files
77
78All netCDF files have a detailed header.
79
80-   Weight files rmp_*. Should have a rather explicit name. The name is configurable at the beginning of `CreateWeightsMask.bash`.
81-   Diagnostic file used for debug dia_*.nc for each rmp file, except for runoff and calving. Debug information are directly in weight files in this last cases.
82-   Grid description file for OASIS-MCT grids.nc, areas.nc and masks.nc.
83-   A file containing the fraction of ocean in each atmosphere grid box. For instance ICO40\_grid\_maskFrom_eORCA1.2.nc.
84-   A README file. Includes a checksum for each generated files.
85
86## Scripts and codes
87
88*   **CreateWeightsMask.bash**. Creates the weights to interpolate between atmospheric and ocean grid. Weight files are suitable for OASIS-MCT. Creates the fraction of ocean in atmospheric grid cells. Uses parallel processing with MPI. Has a configuration section at the beginning.
89
90-   **CreateOasisGrids.bash**. Creates files `grids.nc`, `areas.nc` and `masks.nc` with information from both models, suitable for OASIS-MCT. Mono CPU. Launched by `CreateWeights.bash`.
91
92-   **update_xml.py**. Python script used to perform on the fly editing of xml files. Used by CreateWeights.bash. More information with `python update_xml.py -h`.
93
94-   **iodef\_atm\_to_oce.xml** and **iodef\_oce\_to_atm.xml**. xml files read by `interpol.f90`. These files are edited by update_xml.py.
95
96-   **MOSAIX/src/MOSAIX/interpol.f90**. Fortran source using the XIOS library.
97
98-   **make_mosaix**. Small script for compiling **interpol.f90**. You need to compile XIOS first. Uses compiler, compiler options and librairies defined by XIOS.
99   
100        make_xios \[options\]
101            options :
102                   \[--xios path\] : path to XIOS. Default is ../XIOS
103                   \[--full\]      : to regenerate dependencies and recompile from scratch
104            Example : ./make_mosaix --xios ../XIOS
105   
106
107- **RunoffWeights.py**. Python code to generates weights for run-off. Launched by CreateWeights.bash. More information with python `RunOffWeights.py -h`.
108
109  - Defines a coastal band on land in the atmosphere model. For LMDZ rectilinear grids, the width of this band is parametrized, in grid points. For ico grids, the band contains only point with a fraction of ocean in \]0,1\[.
110
111  - Defines a coastal band on ocean in the ocean model. The width of this band is parametrized.
112
113  - An atmosphere point of the coastal band is linked to an ocean point in the coastal band if the distance between the two is less than searchRadius.
114
115- **CalvingWeights.py**. Python code to generates weights for calving. Launched by `CreateWeights.bash`. More information with python `CalvingWeights.py -h`.
116
117  - The atmosphere model integrate the calving over on specific regions. Presently the regions are three latitudinal bands with limits 90°S/40°S/50°N/90°N.
118
119  - The weights distribute the calving in the ocean in the corresponding latitudinal bands. By default, the distribution is uniform.
120
121  - For the southernmost band, it is possible to use a geographical distribution read in a file. These files are currently available for eORCA1 and eORCA025.
122
123## Grids
124
125-   _\[tuv\]orc_. ORCA grid at _\[TUV\]_ points. Masked on land, with area equal to grid box surface.
126-   _tlmd_. LMD rectilinear grid at scalar (physics) point. Masked on land, with area equal to grid box surface.
127-   _tico_. LMD icosahedron grid at scalar (physics) point. Masked on land, with area equal to grid box surface.
128-   _olmd_. LMD rectilinear grid at scalar (physics) point. Not masked, with areas equal to 1.
129-   _oico_. LMD icosahedron grid at scalar (physics) point. Not masked, with areas equal to 1.
130-   _corc_. ORCA grid at _T_ point. Masked on land, duplicated (from periodicity) point masked, with area equal to grid box surface.
131-   _oorc_. ORCA grid at _T_ point. Masked on land, duplicated (from periodicity) point masked, with area equal 1.
132
133## Generating input grid files
134
135**Generating icosahedral grid in double precision using XIOS:**
136
137Here are the main changes:
138
139-   File `context_lmdz.xml` :
140```xml
141        .....
142         <domain_definition>
143             <domain id="dom_glo" data_dim="2" />
144             <domain id="dom_glo_p8"  domain_ref="dom_glo"  prec="8" />
145             <domain id="geordered"  domain_ref="dom_glo">
146             <reorder_domain invert_lat="true" shift_lon_fraction="0"/>
147            </domain>
148         </domain_definition>
149        .....
150         <grid_definition>
151        .....
152             <grid id="grid_glo">
153                <domain domain_ref="dom_glo" />
154             </grid>
155         
156             <grid id="grid_glo_p8">
157                <domain domain_ref="dom_glo_p8" />
158             </grid>
159        .....
160```
161               
162-   File `field_def_lmdz.xml` :
163```xml
164        <field_definition level="1" prec="4" operation="average" freq_op="1ts" enabled=".true." default_value="9.96921e+36" domain_ref="dom_glo">
165            <field_group id="fields_2D_p8" grid_ref="grid_glo_p8" prec="8">
166              <field id="aire_p8" field_ref="aire" long_name="Grid area p8" unit="-"    />
167              <field id="fract_oce_p8" field_ref="fract_oce" long_name="Fraction oce p8"   unit="1" />
168              <field id="fract_sic_p8" field_ref="fract_sic"   long_name="Fraction sic p8"   unit="1" />
169              <field id="fract_oce_plus_sic_p8" long_name="Fraction oce plus sic p8"   unit="1" />
170              <field id="mask_oce_plus_sic_p8" long_name="Masque oce plus sic p8"  unit="1" />
171            </field_group>
172        ...
173        </field_definition>
174```
175
176-   File `file_def_histmth_lmdz.xml` :
177```xml
178        <file_definition>
179            <file_group id="defile">
180                <file id="grid_p8" name="grid_p8" output_freq="1d" sync_freq="10d" output_level="2" enabled="true" timeseries="none" time_counter="none">
181                  <field_group grid_ref="grid_glo_p8" ts_enabled="true" freq_op="1d" expr="@this"> 
182                      <field field_ref="aire_p8" level="1" operation="once"  />
183                      <field field_ref="fract_oce_p8" level="1" operation="once" />
184                      <field field_ref="fract_sic_p8" level="1" operation="once" /> 
185                  </field_group>                               
186                         
187                  <field_group grid_ref="grid_glo_p8" ts_enabled="true" freq_op="1d" > 
188                      <field field_ref="fract_oce_plus_sic_p8" level="1" > fract_oce + fract_sic </field>   
189                      <field field_ref="mask_oce_plus_sic_p8" level="1" > ((fract_oce + fract_sic) &gt; 0) ? 1 : 0 </field>
190                  </field_group>
191                </file>
192        ..........
193```
194
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