Opened 19 months ago

Last modified 4 months ago

#2216 closed Enhancement

Update reference manual for 4.0 release — at Version 27

Reported by: clevy Owned by: systeam
Priority: high Milestone: Documentation
Component: doc Version:
Severity: critical Keywords: manual
Cc: smasson, mikebell, jchanut, cetlod, gm, gsamson, sciliberti, cbricaud, rbourdal, mdrudi, djlea, clevy, acc, mocavero, davestorkey, agn, Nicolas_MARTIN Review:
MP ready?:

Description (last modified by 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
.//   # 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
chap_time_domain Time discretisation (time stepping strategy) Jérôme Chanut Done
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 Done
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

Commit History (13)


#2216 revision of LBC chapter: main ones in bdy description and geometry


#2216, correct description of grid scale dependent mixing coefficient


#2216: updates to STO reference manual


#2216: updates to STO reference manual


Update LDF chapter, #2216


#2216: update SBC chapter with corresponding bibliography


#2216, wrong namelist name in ZDF chapter


#2216, Finalize ZDF chapter - OSMOSIS and Adaptive vertical advection subsections to be updated


#2216: add AGRIF_DEMO test case in place of Agulhas and remove cpp keys


#2216: Add Romain's update of ZDF chapter


Add new flowchart figure, #2216


Update time domain chapter, #2216


Update the chapter on reference configurations for 4.0 release, see #2216

Change History (28)

comment:1 Changed 19 months ago by nicolasmartin

  • Keywords reference release-4.0 removed

Changed 19 months ago by nicolasmartin

comment:2 Changed 19 months ago by nicolasmartin

You can find the output of 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}

comment:3 Changed 19 months ago by nicolasmartin

  • Summary changed from Update refernce manual for 4.0 release to Update reference manual for 4.0 release

comment:4 Changed 18 months ago by mathiot

  • Description modified (diff)

comment:5 Changed 18 months ago by nicolasmartin

  • Description modified (diff)

comment:6 Changed 18 months ago by acc

  • Description modified (diff)

comment:7 Changed 18 months ago by clevy

  • Description modified (diff)
  • Type changed from Task to Bug
  • Version trunk deleted

comment:8 Changed 18 months ago by clevy

  • Type changed from Bug to Enhancement

comment:9 Changed 17 months ago by gsamson

  • Description modified (diff)

comment:10 Changed 17 months ago by clevy

  • Description modified (diff)

comment:11 Changed 17 months ago by jchanut

  • Description modified (diff)

comment:12 Changed 17 months ago by mathiot

  • Description modified (diff)

comment:13 Changed 17 months ago by gsamson

  • Description modified (diff)

comment:14 Changed 17 months ago by epico

  • Description modified (diff)

comment:15 Changed 17 months ago by epico

  • Description modified (diff)

comment:16 Changed 16 months ago by clevy

  • Description modified (diff)

comment:17 Changed 15 months ago by clevy

  • Description modified (diff)

comment:18 Changed 15 months ago by diovino

  • Description modified (diff)

comment:19 Changed 15 months ago by diovino

Revision of chap_LBC by Ciliberti

comment:20 Changed 15 months ago by clevy

  • Cc smasson mikebell jchanut cetlod gm gsamson sciliberti cbricaud rbourdal mdrudi djlea clevy acc mocavero davestorkey agn Nicolas_MARTIN added
  • Description modified (diff)


comment:21 Changed 14 months ago by mocavero

In 11112:

Update the chapter on reference configurations for 4.0 release, see #2216

comment:22 Changed 14 months ago by francesca

  • Description modified (diff)

comment:23 Changed 14 months ago by jchanut

In 11184:

Update time domain chapter, #2216

comment:24 Changed 14 months ago by jchanut

In 11185:

Add new flowchart figure, #2216

comment:25 Changed 13 months ago by jchanut

In 11213:

#2216: Add Romain's update of ZDF chapter

comment:26 Changed 13 months ago by jchanut

In 11214:

#2216: add AGRIF_DEMO test case in place of Agulhas and remove cpp keys

comment:27 Changed 13 months ago by clevy

  • Description modified (diff)
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