Manual revision 2022

Revision of NEMO manuals in view of 4.2 official release.

NEMO MANUAL TODO LIST

List of pending items compiled by @acoward

MANUAL

• Documenting restart options 2.6 Start/restart strategy has no mention of options: nn_stocklist; ln_mskland; ln_cfmeta; nn_write; nn_chunksz; ln_xios_read; nn_wxios

• Updating Space domain sections 3.2.[2-3] (align with information in the migration guide) Space Domain sections are out-of-date w.r.t. contents of the domcfg.nc file (correct in the migration guide)

• Possible simplification of wetting and drying 5.9 Wetting and drying two limiters detailed -time to simplify to one recommended method?

• Address highlighted comments in LDF chapter Chap LDF some highlighted comments/questions circa page 125 resolve and amend

• Refresh XIOS chapter 10.1 XIOS out-of-date -mentions key_iomput and XIOS2.5 Needs revising

• Checking SAO: 11.4 SAO Has anyone tested this recently? 11.4.2 In using the standalone observation operator Build instructions has old directory names

• Update stochastic parameterisation documentation 13.2 Stochastic parameterization most of the variables now in the namelist are not mentioned

• Tidy chapter 15 : 15.2 key_c1d key no longer in code - check accuracy of section 15.3 ORCA2 zenodo link to old configuration file 15.3.2 Pre-defined resolution orphaned last sentence?

Additions, deletions and corrections

• 14.4.1 key_nosignedzero Add recommendation to add this key via the arch files
• 14.3.1 closed sea formatting error with extra \
• 5.5.3 dynspg_flt section should be removed
• 6.13.5 Interface to CICE No longer supported -delete
• 10.5 key_floats no longer supported? - delete
• 10.6 key_diadct no longer supported? - delete
• 15.5 AMM formatting error extra \

Coding rules refresh

• G.4.4.1 Coding rules: argument list should now include time pointer arguments
• G4.2 Array syntax update with tiling in mind?
• G4.7 F90 standard update to F2003?
• G4.10 Loops introduce DO LOOP macros?
• G5.1 Configurations discourage use of keys
• G5.7 PRINT ln_prt outdated
• G.5.8 Precision does this need a statemnet on mixed precision?
• G6.1 Bounds checking key_vecopt_loop mentioned
• G6.4 Memory management UGH!
• G6.5 Optimisation key_vecopt_loop
• G6.7 Parallelism key_mpp_mpi outdated

keys that need checking/changing

• all keys revised

in the code but not in the manual	in the manual but not in the code	Clean up CICE interface
key_RK3 key_RK3all key_cpl key_cyclone key_diabio key_diainstant key_gyre key_iom key_isf key_linssh key_loop_fusion key_mpi_isend key_oa3mct_v3 key_orca_lev10 key_osmldpth1 key_qco key_qcoTest_FluxForm key_sed_off key_single key_trabbc key_xios	key_c1d key_diadct key_dynspg_exp key_dynspg_flt key_dynspg_ts key_floats key_iomput key_mpp_mpi key_traldf_c2d key_traldf_eiv key_vvl	remove CICE interface from manual Remove from code key_cice key_cice4 key_nemocice_decomp

Instructions for 'manual_build.sh' usage in this branch

Usage:
------
./manual_build.sh [-p] [-r version ] manual
Mandatory
          Chose one model manual among NEMO SI3 TOP or all (if not provided compile "NEMO")
Optional
   -p     Produce manual with figures and disable draft watermark
   -r     Specify the release version number of the manual(s) instead of the branch name

The latex function \nlstlocal allows to load specific namelists from the component folder (e.g. doc/latex/TOP/namelists) rather than from the main one in doc/namelists (added in in doc/latex/global/highlighting.tex)

arch/CMCC/arch-X64_ZEUS.fcm

@@ -3,8 +3,8 @@
 #
 # NCDF_INC    netcdf4 include file
 # NCDF_LIB    netcdf4 library
-# XIOS_INC    xios include file    (taken into accound only if key_iomput is activated)
-# XIOS_LIB    xios library         (taken into accound only if key_iomput is activated)
+# XIOS_INC    xios include file    (taken into accound only if key_xios is activated)
+# XIOS_LIB    xios library         (taken into accound only if key_xios is activated)
 #
 # CPP         Pre-processor
 # FC          Fortran compiler command