Opened 9 months ago

Last modified 6 weeks ago

#2216 new Enhancement

Update reference manual for 4.0 release

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

Description (last modified by nicolasmartin)

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

Commit History (13)

ChangesetAuthorTimeChangeLog
11445sciliberti2019-08-19T09:18:20+02:00

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

11386jchanut2019-08-01T17:26:28+02:00

#2216, correct description of grid scale dependent mixing coefficient

11344clevy2019-07-25T10:52:10+02:00

#2216: updates to STO reference manual

11340clevy2019-07-24T18:35:12+02:00

#2216: updates to STO reference manual

11336jchanut2019-07-24T12:30:54+02:00

Update LDF chapter, #2216

11333gsamson2019-07-23T17:17:14+02:00

#2216: update SBC chapter with corresponding bibliography

11318jchanut2019-07-22T11:24:56+02:00

#2216, wrong namelist name in ZDF chapter

11225jchanut2019-07-08T14:42:50+02:00

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

11214jchanut2019-07-04T12:30:41+02:00

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

11213jchanut2019-07-04T11:29:44+02:00

#2216: Add Romain's update of ZDF chapter

11185jchanut2019-06-26T16:58:13+02:00

Add new flowchart figure, #2216

11184jchanut2019-06-26T16:56:21+02:00

Update time domain chapter, #2216

11112mocavero2019-06-14T15:57:28+02:00

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

Attachments (1)

NEMO_manual_state.txt (11.4 KB) - added by nicolasmartin 9 months ago.

Download all attachments as: .zip

Change History (49)

comment:1 Changed 9 months ago by nicolasmartin

  • Keywords reference release-4.0 removed

Changed 9 months ago by nicolasmartin

comment:2 Changed 9 months ago by 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}

comment:3 Changed 9 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 8 months ago by mathiot

  • Description modified (diff)

comment:5 Changed 8 months ago by nicolasmartin

  • Description modified (diff)

comment:6 Changed 8 months ago by acc

  • Description modified (diff)

comment:7 Changed 8 months ago by clevy

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

comment:8 Changed 8 months ago by clevy

  • Type changed from Bug to Enhancement

comment:9 Changed 8 months ago by gsamson

  • Description modified (diff)

comment:10 Changed 8 months ago by clevy

  • Description modified (diff)

comment:11 Changed 7 months ago by jchanut

  • Description modified (diff)

comment:12 Changed 7 months ago by mathiot

  • Description modified (diff)

comment:13 Changed 7 months ago by gsamson

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comment:14 Changed 7 months ago by epico

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comment:15 Changed 7 months ago by epico

  • Description modified (diff)

comment:16 Changed 6 months ago by clevy

  • Description modified (diff)

comment:17 Changed 5 months ago by clevy

  • Description modified (diff)

comment:18 Changed 5 months ago by diovino

  • Description modified (diff)

comment:19 Changed 5 months ago by diovino

Revision of chap_LBC by Ciliberti

comment:20 Changed 5 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 4 months ago by mocavero

In 11112:

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

comment:22 Changed 4 months ago by francesca

  • Description modified (diff)

comment:23 Changed 4 months ago by jchanut

In 11184:

Update time domain chapter, #2216

comment:24 Changed 4 months ago by jchanut

In 11185:

Add new flowchart figure, #2216

comment:25 Changed 3 months ago by jchanut

In 11213:

#2216: Add Romain's update of ZDF chapter

comment:26 Changed 3 months ago by jchanut

In 11214:

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

comment:27 Changed 3 months ago by clevy

  • Description modified (diff)

comment:28 Changed 3 months ago by jchanut

In 11225:

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

comment:29 Changed 3 months ago by jchanut

In 11318:

#2216, wrong namelist name in ZDF chapter

comment:30 Changed 3 months ago by davestorkey

  • Description modified (diff)

comment:31 Changed 3 months ago by acc

  • Description modified (diff)

comment:32 Changed 3 months ago by gsamson

In 11333:

#2216: update SBC chapter with corresponding bibliography

comment:33 Changed 3 months ago by gsamson

  • Description modified (diff)

comment:34 Changed 3 months ago by jchanut

In 11336:

Update LDF chapter, #2216

comment:35 Changed 3 months ago by jchanut

  • Description modified (diff)

comment:36 Changed 3 months ago by clevy

In 11340:

#2216: updates to STO reference manual

comment:37 Changed 3 months ago by clevy

  • Description modified (diff)

comment:38 Changed 3 months ago by clevy

In 11344:

#2216: updates to STO reference manual

comment:39 Changed 3 months ago by mdrudi

  • Description modified (diff)

comment:40 Changed 3 months ago by diovino

  • Description modified (diff)

comment:41 Changed 3 months ago by diovino

  • Description modified (diff)

comment:42 Changed 3 months ago by mathiot

  • Description modified (diff)

comment:43 Changed 3 months ago by acc

  • Description modified (diff)

comment:44 Changed 3 months ago by mathiot

  • Description modified (diff)

comment:45 Changed 2 months ago by jchanut

In 11386:

#2216, correct description of grid scale dependent mixing coefficient

comment:46 Changed 8 weeks ago by sciliberti

In 11445:

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

comment:47 Changed 8 weeks ago by sciliberti

  • Description modified (diff)

comment:48 Changed 6 weeks ago by nicolasmartin

  • Description modified (diff)
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