update IO for VVL compatibility

[smasson]

IO are reviewed for VVL/non-VVL compatibility.

This changes require xios-1.0 rev 562 or higher to work.

Temporal average weighted by the cell thickness is done outside of the code by the means of xios and the xml files. Weighted temporal average is required for all variables used any type of integral computation (transport, msf, bsf, global mean...). Weighted temporal average is not necessary for variables that will just be used for "basic" diagnostics (map, section, hovmoeller...).

Today we propose examples of weighted temporal average only for toce, soce, uoce, voce and woce. Feel free to add others...

NEMOGCM/CONFIG/SHARED/field_def.xml has been be updated:

• cellthc variable is replaced by e3t variable.
• e3u, e3v and e3w have been added
• suoce and svoce have been replaced bu ssu and ssv
• temperature, salinity and currents at the bottom of the ocean have been added

ORCA2_LIM/EXP00/iodef.xml and ORCA2_LIM3/EXP00/iodef.xml show and example of the use of:

• Weighted temporal average
• online computation of mean diurnal cycle
• online computation of standard deviation

In these 2 ORCA2_LIM configurations, we decided to provide by default in iodef.xml weighted temporal average as vvl is targeted as the default option in the near future and as it is harmless (but more expensive) for non-vvl case.

Other xml file have been updated only to keep compatibility with the new field_def.xml file. Feel free to update the xml file you are using if you want to take advantage of the new functionalities of xios...

The new features offered by xios have been added to the doc.

[smasson]

done, see changeset:5107