Update reference manual for 4.0 release

[clevy]

Summary

Action	${ACTION_NAME} Subject
PI(S)	Principal investigator(s)
Digest	Brief description with motivations and main tasks
Dependencies
Branch	NEMO/branches/$YEAR/dev_r{REV}_{ACTION_NAME}
Previewer(s)
Reviewer(s)
Wiki	wiki:${YEAR}WP/...

Reference manual updates for 4.0 release

Files to update : the tex files located in source:/NEMO/trunk/doc/latex/NEMO/subfiles after revision 11023 to get latests useful scripts:
1/ check out the trunk in commit mode , svn+ssh

cd trunk/doc
.//manual_build.sh   # script to clean directory and download in right place for PDF generation figures, logos and namelists

Tex files are now ready for your updates
Use your latex tool to generate NEMO_book.pdf and check your updates
Commit your updated tex files

Work is due 15 June 2019 . Add a comment in this ticket once your work is done

REMAINING TO BE DONE:

Tex files to be reviewed/updated when needed	PI
Introduction	Sébastien Masson
chap_model_basics	Mike Bell
chap_time_domain Time discretisation (time stepping strategy)	Jérôme Chanut
chap_DOM Space discretisation	Nico Bruneau
chap_TRA Tracer advection/diffusion equation	Christian Ethé
chap_DYN Dynamics : momentum equation	Gurvan Madec
chap_SBC Surface Boundary Conditions	Guillaume Samson
chap_LBC Lateral Boundary Conditions	Stefania Ciliberti
chap_LDF Lateral diffusion	Clement Bricaud
chap_ZDF Vertical diffusion	Romain Bourdalle Badie
chap_DIA Outputs and Diagnostics	Massimiliano Drudi
chap_OBS Observation operator	Dan Lea
chap_ASM Assimilation increments	Dan Lea
chap_STO Stochastic param.	Claire Lévy
chap_misc Miscellaneous topics	Andrew Coward
chap_CONFIG Predefined configurations	Silvia Mocavero
annex_A Generalised vertical coordinate	Gurvan Madec
annex_B Diffusive operator	Dave Storkey
annex_C Discrete invariants of the eqs.	Gurvan Madec
annex_iso Isoneutral diffusion using triads	George Nurser
annex_D Coding rules	Nicolas Martin

[nicolasmartin]

You can find the output of manuals_checking.sh that pointing out the missing namelists and the out-of-date chapters (references to source code are not valid)

Missing namelist groups

• namage namagrif namalb
• namc14_fcg namc14_sbc namc14_typ
• namc1d namc1d_dyndmp namc1d_uvd
• namcfc namcrs namdia namdrg namdrg_bot namdrg_top
• namdta_dyn
• namdyn namdyn_rdgrft namdyn_rhg
• namforcing namhsb namini namitd
• namlobdet namlobdom namlobnut namlobopt namlobphy namlobrat namlobsed namlobzoo
• nammpp
• namp4zlim namp4zmes namp4zmort namp4zprod namp4zzoo namp5zlim namp5zmes namp5zmort namp5zprod namp5zquota namp5zzoo
• nampar
• nampisatm nampisbio nampiscal nampisdmp nampisext nampisfer nampisice nampislig nampismass nampismod nampisopt nampispoc nampisrem nampissbc
• namsbc_blk namsbc_iif
• namthd namthd_da namthd_do namthd_pnd namthd_sal namthd_zdf
• namtra_eiv namtra_mle
• namtrc namtrc_adv namtrc_bc namtrc_bdy namtrc_dmp namtrc_dta namtrc_ice namtrc_ldf namtrc_rad namtrc_run namtrc_snk namtrc_trd
• nam_vvl namzdf_iwm

Vanished index entries (\{hf,jp,key,mdl,ngn,nlst,np,rou}{...})

• chap_DYN.tex:
  • key{dynspg\_exp} key{dynspg\_flt} key{dynspg\_ts} key{trddyn} key{trdvor} key{vvl}
  • mdl{dynspg\_flt} mdl{zpsdhe}
  • nlst{namsplit}
  • np{ln\_bt\_nn\_auto} np{ln\_dynhpg\_djc} np{ln\_dynhpg\_imp} np{ln\_dynhpg\_isf} np{ln\_dynhpg\_prj} np{ln\_dynhpg\_sco} np{ln\_dynhpg\_vec} np{ln\_dynhpg\_zco} np{ln\_dynhpg\_zps} np{ln\_dynldf\_bilap} np{ln\_dynvor\_con} np{ln\_dynzad\_zts} np{ln\_traadv\_tvd\_zts} np{ln\_wd\_dl\_ramp} np{ln\_zdfexp} np{nn\_atfp} np{nn\_dynhpg\_rst} np{nn\_ice\_embd} np{nn\_zdfexp}
• chap_model_basics_zstar.tex:
  • key{dynspg\_exp} key{dynspg\_flt} key{dynspg\_ts} key{vvl}
  • mdl{dynspg\_flt}
  • np{rdtbt} np{rnu}
• chap_DIA.tex:
  • key{diaar5} key{diadct} key{diaharm} key{diahth} key{diainstant} key{floats} key{IOM} key{iomput} key{mpp\_mpi} key{netcdf4} key{trdmld\_trc} key{trdtrc} key{vvl}
  • ngn{namdia\_harm}
  • np{init\_float\_ariane} np{iom\_put} np{jpnflnewflo} np{nb\_ana} np{nit000} np{nitend} np{nn\_debug} np{nn\_diacfl} np{tname}
  • rou{iom\_rstput}
• annex_E.tex: key{traldf\_eiv}
• chap_TRA.tex:
  • jp{lk\_vvl}
  • key{trabbl} key{traTTT} key{zdfddm}
  • mdl{traldf\_lap}
  • ngn{namtra\_bbc}
  • np{ln\_flxqsr} np{ln\_sco} np{ln\_traadv\_NONE} np{ln\_traldf} np{ln\_traldf\_grif} np{ln\_traldf\_NONE} np{ln\_tsd\_tradmp} np{ln\_useCT} np{ln\_zco} np{ln\_zdfexp} np{ln\_zps} np{nn\_chdta} np{nn\_eos} np{nn\_fct\_zts} np{nn\_geoflx\_cst} np{nn\_zdfexp}
  • rou{traldf\_blp} rou{traldf\_lap}
• chap_ASM.tex:
  • key{asminc}
  • ngn{namasm}
• chap_ZDF.tex:
  • key{dynspg\_exp} key{dynspg\_flt} key{dynspg\_ts} key{trabbl} key{vvl} key{zdf} key{zdfcst} key{zdfddm} key{zdfgls} key{zdfosm} key{zdfric} key{zdftke} key{zdftmx} key{zdftmx\_new}
  • mdl{dynbfr} mdl{dynzdf\_imp} mdl{zdfbfr} mdl{zdfini} mdl{zdfkpp}
  • ngn{namzdf\_ddm} ngn{namzdf\_tmx} ngn{namzdf\_tmx\_new}
  • nlst{nambfr} nlst{namzdf_ddm} nlst{namzdf_tmx} nlst{namzdf_tmx_new}
  • np{ln\_bfr2d} np{ln\_bfrimp} np{ln\_crban} np{ln\_tmx\_itf} np{ln\_tranpc} np{ln\_zdfexp} np{ln\_zdftmx\_itf} np{nn\_botfr} np{nn\_clo} np{nn\_ediff} np{nn\_ediss} np{nn\_tkebc\_bot} np{nn\_tkebc\_surf} np{rn\_avevd} np{rn\_bfeb2} np{rn\_bfri1} np{rn\_bfri2} np{rn\_bfri2\_max} np{rn\_bfrien} np{rn\_bfrz0} np{rn\_htmx} np{rn\_me} np{rn\_n2min} np{rn\_tfe} np{rn\_tfe\_itf} np{rn\_tfri2} np{rn\_tfri2\_max} np{rn\_tfrz0}
  • rou{zdf\_bfr}
• chap_misc.tex:
  • key{mpp\_mpi} key{nosignedzero} key{vectopt\_loop}
  • np{iom\_get} np{jpjdta} np{jpjglo} np{nn\_bench} np{nn\_bit\_cmp} np{open\_ocean\_jstart}
• chap_LDF.tex:
  • hf{dynldf\_cNd} hf{ldfdyn\_substitute} hf{ldftra\_substitute} hf{traldf\_c1d} hf{traldf\_cNd}
  • key{dynldf\_c1d} key{dynldf\_c2d} key{dynldf\_c3d} key{traldf\_c1d} key{traldf\_c2d} key{traldf\_c3d} key{traldf\_cNd} key{traldf\_eiv}
  • mdl{ldfdyn\_c2d} mdl{ldfeiv} mdl{traadv\_eiv}
  • np{ln\_dynldf\_bilap} np{ln\_sco} np{nn\_eos} np{rn\_aeih\_0} np{rn\_aeiv} np{rn\_aeiv\_0} np{rn\_ahm0} np{rn\_ahmb0} np{rn\_aht0} np{rn\_ahtb0} np{traldf\_grif} np{traldf\_grif\_iso}
  • rou{ldf\_dyn\_c2d\_orca} rou{ldfslp\_init}
• chap_LBC.tex:
  • jp{jpreci}
  • key{mpp\_mpi}
  • np{jperio} np{jpiglo} np{jpindt} np{jpinft} np{jpjglo} np{jpjnob} np{nbdysegn} np{nn\_bdy\_jpk} np{nn\_msh} np{nn\_tra}
  • rou{inimpp2}
• chap_DOM.tex:
  • key{mpp\_mpi}
  • ngn{namzgr} ngn{namzgr\_sco}
  • nlst{namzgr} nlst{namzgr_sco}
  • np{jperio} np{jpiglo} np{jpjglo} np{jpkglo} np{ln\_sco} np{ln\_sigcrit} np{ln\_s\_SF12} np{ln\_s\_SH94} np{ln\_tsd\_ini} np{ln\_zco} np{ln\_zps} np{nn\_bathy} np{nn\_msh} np{ppa0} np{ppa1} np{ppacr} np{ppdzmin} np{pphmax} np{ppkth} np{ppsur} np{rn\_alpha} np{rn\_bb} np{rn\_e3zps\_min} np{rn\_e3zps\_rat} np{rn\_hc} np{rn\_rmax} np{rn\_sbot\_max} np{rn\_sbot\_min} np{rn\_theta} np{rn\_zb\_a} np{rn\_zb\_b} np{rn\_zs}
  • rou{istate\_t\_s}
• chap_conservation.tex: key{\_}
• annex_iso.tex:
  • key{trabbl} key{traldf\_eiv}
  • np{ln\_traldf\_eiv} np{ln\_traldf\_gdia}
• chap_time_domain.tex: np{ln\_zdfexp} np{nn\_dynhpg\_rst} np{nn\_zdfexp}
• chap_CONFIG.tex:
  • key{agrif} key{c1d} key{dynspg\_ts} key{orca\_r12} key{orca\_r8} key{vvl} key{zdfgls}
  • ngn{namusr\_def}
  • np{jpiglo} np{jpizoom} np{jpjglo} np{jpjzoom} np{ln\_bench} np{nn\_GYRE} np{ORCA\_index}
• chap_SBC.tex:
  • key{cice} key{coupled} key{cpl\_carbon\_cycle} key{lim3} key{mpp\_mpi} key{nemocice\_decomp} key{oasis3} key{pisces} key{top} key{vvl}
  • mdl{sbcana} mdl{sbc\_ana\_gyre} mdl{sbcsas} ngn{namsbc\_ana} ngn{namsbc\_clio} ngn{namsbc\_core}
  • nlst{namsbc_ana} nlst{namsbc_clio} nlst{namsbc_core}
  • np{clim} np{ln\_ana} np{ln\_blk\_clio} np{ln\_blk\_core} np{ln\_clio} np{ln\_core} np{ln\_rnf\_temp} np{nn\_nit000} np{nn\_tau000} np{nn\_test\_box} np{nz\_rnf} np{rn\_emp0} np{rn\_fiscpl} np{rn\_qns0} np{rn\_qsr0} np{rn\_utau0} np{rn\_vtau0}

[diovino]

Revision of chap_LBC by Ciliberti

[clevy]

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