Update reference manual for 4.0 release

[clevy]

Reference manual updates for 4.0 release

Updates to be committed in the trunk, see below

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 Tuesday 23 July 2019 . Add a "Done" in your line below once your work is done

Tex files to be reviewed/updated when needed	PI
Introduction	Sébastien Masson
chap_model_basics	Mike Bell	Done
chap_time_domain Time discretisation (time stepping strategy)	Jérôme Chanut	Done
chap_DOM Space discretisation	Simon Müller Andrew Coward	Done
chap_TRA Tracer advection/diffusion equation	Christian Ethé	Done
chap_DYN Dynamics : momentum equation	Gurvan Madec
chap_SBC Surface Boundary Conditions	Guillaume Samson	Done
chap_LBC Lateral Boundary Conditions	Stefania Ciliberti	Done
chap_LDF Lateral diffusion	Jérôme Chanut	Done
chap_ZDF Vertical diffusion	Romain Bourdalle Badie	Done
chap_DIA Outputs and Diagnostics	Drudi, Iovino	Done
chap_OBS Observation operator	Dan Lea	Done
chap_ASM Assimilation increments	Dan Lea	Done
chap_STO Stochastic param.	Claire Lévy	Done
chap_misc Miscellaneous topics	Andrew Coward	Done
chap_CONFIG Predefined configurations	Silvia Mocavero	Done
annex_A Generalised vertical coordinate	Mike Bell	Done
annex_B Diffusive operator	Dave Storkey	Done
annex_C Discrete invariants of the eqs.	Gurvan Madec
annex_iso Isoneutral diffusion using triads	George Nurser
annex_DOMAINcfg Notes on DOMAINcfg tool	Andrew Coward	Done
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You can find the output of manuals_checking.sh that pointing out the missing namelists and the out-of-date chapters (references to source code are not valid)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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[mocavero]

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[sciliberti]

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