Opened 19 months ago

Last modified 4 months ago

#2216 closed Enhancement

Update reference manual for 4.0 release — at Version 18

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?:
Progress:

Description (last modified by diovino)

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 located in source:/NEMO/trunk/doc/latex/NEMO/subfiles

REMAINING TO BE DONE:

 Tex files to be reviewed/updated when needed PI PI proposed by Claire
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
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
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

Change History (19)

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 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 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)
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