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Manual revision 2022

Tomas Lovato requested to merge manual_revision_2022 into main

Revision of NEMO manuals in view of 4.2 official release.


List of pending items compiled by @acoward


  • 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  • Updating Space domain sections 3.2.[2-3] (align with information in the migration guide) Space Domain sections are out-of-date w.r.t. contents of the file (correct in the migration guide)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  • Refresh XIOS chapter 10.1 XIOS out-of-date -mentions key_iomput and XIOS2.5 Needs revising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  • G5.7 PRINT ln_prt outdated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  • G6.7 Parallelism key_mpp_mpi outdated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 '' usage in this branch

./ [-p] [-r version ] manual
          Chose one model manual among NEMO SI3 TOP or all (if not provided compile "NEMO")
   -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)

Edited by Nicolas Martin

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