--- manual/manual_todo.txt 2006/04/06 20:03:45 1.10 +++ manual/manual_todo.txt 2006/06/28 15:36:02 1.38 @@ -1,3 +1,31 @@ +Editors + + Overall - JM, AM, PH, CNH, EH3 + + Front content - EH3 + + Chapter 1 - CNH + + Chapter 2 - JMC + + Chapter 3 - AM + + Chapter 4 - CNH + + Chapter 5 - PH + + Chapter 6 - AM + + Chapter 7 - EH3 + + Chapter 8 - PH + + Chapter 9 - CNH (Applications) + + Chapter 10 - JMC (Under development chapter) + + Biblio - EH3 + Rebuild and set to do cron build - DONE on hugo To do @@ -8,17 +36,15 @@ Add an "Under development, chapter" - shortish description of what is available (last chapter) + - add in example latex for formatting author names in different pieces. + this aknowledges peoples contributions and gives ref for who + to talk to. o HTML, scripts and front content - pick a URL TBD - - mitgcm.org very front page. - o too many clicks to get to model manual. - make doc link go to mitgcm.org/r2_web_testing/latest - and add "HowTo" reference etc... to /latest page - - mitgcm.org/r2_web_testing/latest o add another short-cut for quick download @@ -30,16 +56,6 @@ Tutorials (broken) Browse Code - o mitgcm.org (front content) [DONE] - Get Code (where does this go to?) - get rid of * CVS current bullet - make HTML-enabled CVS code browser leap to MITgcm/MITgcm - - o authors - John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, - Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, - Gael - others? - o words on http://mitgcm.org/r2_web_testing/latest change to "access on-line Auser manual/A and Atable of contents/A @@ -72,7 +88,6 @@ o List of key papers needs to be updated and reformatted - o Global atmosphere: `Held Suarez', update Adcroft reference fix up ingrid link and frame (ingrid movies seem to be broken?) @@ -190,6 +205,7 @@ o coupled aqua, ridge world etc... - links to ingrid output get stuff from Daniel + Davids donut movie o constrained lab simulation - links to ingrid output for model and lab @@ -298,7 +314,7 @@ to add: mention the angle of the grid direction relative to Eastward, Northward direction. + mention horizGridFile= in file "data" (PARM04) -- add cylindrical grid description +- add cylindrical polar grid description need to do a better job of relating model variables to this diagram @@ -325,6 +341,7 @@ o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags in code need to explain why cos()3/2 turns out to be scaling (not cos()2) + - need to reference the smag/leith section. 2.13.6 Vertical dissipation - mention the implicit vertical viscosity option and ref to section 2.5 @@ -343,137 +360,24 @@ 2.16 & 2.17 & 2.18 : - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options + - fix equations 2.202 & 2.203 (thanks to Martin) 2.20.2 mercator, non-dimensional Equations: - does not use std notation - would be better as an appendix of section 2.20: (e.g changing the tile to: +- talk to Baylor Appendix: non-dimensional Equations on Spherical-Polar grid.) -JM - ->>>> From Ed -Here are the remaining bits for Chap 4 : - - - The grammar/flow could still use some work. Boo was an English - major and has experience editing/proofing technical papers. I - could print out a copy and ask her to read it and suggest - improvements. - - - missing references (if you point me towards URLs, I'll add them - to the bibliography): - \ref{ref hoe and hill, ecmwf} - \ref{magicgarden} - \ref{IBMLAPI} - \ref{Memorychannel} - \ref{hoe-hill:99} - - - There are a few empty sub-sections at the end of Chap 4 that - should either be commented out or fleshed out. - -and thats about it for Chap 4. - - -Add more to quick links on front page - -Chapter 6 - - the master package diagram does not appear in the document - - pkg/ptracers doesn't seem to have any documentation (see packages list below) - - -Master list of packages (add this to beginning of chap 6) - -admtlm/ - autodiff (chapter 5) -aim/ - retired -aim_compon_interf/ - 6.6 (no content yet) -aim_ocn_coupler/ - 6.6 (no content yet) -aim_v23/ - 6.4.1 (content needs fixing - JM to do) -atm_common/ - 6.6 (no content yet) -autodiff/ - autodiff (chapter 5) -bulk_force/ - 6.3.3 -cal/ - 6.3.5 -cd_code/ - chapter 2 (JM check) -cfc/ - not sure -chronos/ - AM to check -compon_communic/ - 6.6 (no content yet) -cost/ - not sure, check with PH -ctrl/ - not sure, check with PH -debug/ - JM may do something in chapter 7 (utilities) -diagnostics/ - 7.1 -dic/ - 6.7.2 -ebm/ - not sure -ecco/ - chapter 8 -embed_files/ - add something to chapter 7 -ex3/ - rename to exch3 -exch2/ - 6.2.2 -exf/ - 6.3.4 -fizhi/ - 6.4.3 -flt/ - in chapter 2 (JM check) -gchem/ - 6.7.1 -generic_advdiff/ - in chapter 2 (JM check) -ggl90/ - nothing, (Martin?) -gmredi/ - in chapter 2 (JM check). also need - Ferrari & Mc tapering -grdchk/ - grdchk (chapter 5 - check with PH) -gridalt/ - 6.2.4 -kpp/ - 6.3.2 -land/ - 6.4.2 (not connected to code - JM to fix) -matrix/ - Samar -mdsio/ - 7.3.1 -mnc/ - 7.2.1 -mom_common/ - in chapter 2 (JM check) -mom_fluxform/ - in chapter 2 (JM check) -mom_vecinv/ - in chapter 2 (JM check) -monitor/ - 7.4 -my82/ - nothing, (martin?) -obcs/ - 6.3 (needs a check) -ocn_compon_interf/ - 6.6 (no content yet) -offline/ - nothing, tutorials that need work but no package section entry -opps/ - nothing, (martin?) -pp81/ - nothing, (martin?) -profiles/ - GAEL -ptracers/ - JM + SD to write something -rbcs/ - talk to steph -runclock/ - runclock -rw/ - not sure -sbo/ - text in sbo_descruption.tex but not linked into - part6 -seaice/ - 6.5.2 - no equations, dimitris has promised some -shap_filt/ - chapter 2, JM to check -shelfice/ - nothing yet (martin?) -solver/ - empty -sphere/ - chapter 5 or 8 (PH to check) -therm_seaice/ - empty -thsice/ - 6.5.1 (JM to update?) -timeave/ - retiring...... -zonal_filt/ - chapter 2 (JM to check) - -Possible for chap 7 - Daniels grafix/ stuff - -Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. - -Figure 6.8 is missing - -6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 - Figure 6.8 is missing - - ->>>> From Andrea - -to do list for chap 7: - - -7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" - the links are pointing to the proper place - -7.5.1 - add Graphix to the list of stuff in utils/matlab -7.5.2 - empty +Diagrams of grid locations etc.... and what variables and output files +and/or netcdf variable names are not very easy to figure out and follow. +It would be good to redo and extend these diagrams and align with GRID.h +content. + +JM -andrea >>>> From Andrea @@ -482,10 +386,6 @@ Almost all of the 'math mode' text is dropped down as subscripts -divide chapter 3 more clearly into 2 sections? - (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and - then 3.19 and 3.20 are informational again - rearrange subsections?) - 3.1 - don't need a link to the outside of the document (remove it) - link to htdig is broken @@ -531,9 +431,6 @@ are written. 3.6.1.2 - needs to be moved to inside section 3.6.2 -3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) - underneath this one and leave the text for 3.7 in place - All the 'overview' sections need some reference to the name of the experiment in the verification directory @@ -570,7 +467,192 @@ offline - duplicate inputs, what is it, tidy up cfc v. other offline. JM thinks these need tidying up. +Which of the following are which tutorial? +adjustment.128x64x1 +adjustment.cs-32x32x1 +advect_cs +advect_xy +advect_xz +aim.5l_cs +aim.5l_Equatorial_Channel +aim.5l_LatLon +biogeo +bottom_ctrl_5x5 +cfc_example +cpl_aim+ocn +dome +exp2 +exp4 +exp5 +fizhi-cs-32x32x10 +fizhi-cs-aqualev20 +fizhi-gridalt-hs +flt_example +front_relax +global1x1_tot +global2x2_tot +global_ocean.90x40x15 +global_ocean.cs32x15 +global_ocean.cubed32x32x30 +global_ocean_ebm +global_with_exf +hs94.128x64x5 +hs94.1x64x5 +hs94.cs-32x32x5 +ideal_2D_oce +internal_wave +inverted_barometer +lab_sea +matrix_example +MLAdjust +natl_box +natl_box_adjoint +OpenAD +rotating_tank +solid-body.cs-32x32x1 +tidal_basin_2d +tutorial_baroclinic_gyre +tutorial_barotropic_gyre +tutorial_cfc_offline +tutorial_deep_convection +tutorial_global_oce_biogeo +tutorial_global_oce_in_p +tutorial_global_oce_latlon +tutorial_global_oce_optim +tutorial_held_suarez_cs +tutorial_offline +tutorial_plume_on_slope +tutorial_tracer_adjsens +vermix + +>>>> From Ed + +Here are the remaining bits for Chap 4 : + + - missing references (if you point me towards URLs, I'll add them + to the bibliography): + \ref{ref hoe and hill, ecmwf} + \ref{magicgarden} + \ref{IBMLAPI} + \ref{Memorychannel} + \ref{hoe-hill:99} + + - There are a few empty sub-sections at the end of Chap 4 that + should either be commented out or fleshed out. + +and thats about it for Chap 4. + + +Add more to quick links on front page + +Chapter 6 + + the master package diagram does not appear in the document + +Master list of packages (add this to beginning of chap 6) + +admtlm/ - autodiff (chapter 5) +aim/ - retired +aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) +aim_ocn_coupler/ - 6.6 (no content yet) +aim_v23/ - 6.4.1 (content needs fixing - JM to do) +atm_common/ - nothing in this package (6.4.1 related) +autodiff/ - autodiff (chapter 5) +bulk_force/ - 6.3.3 +cal/ - 6.3.5 +cd_code/ - chapter 2 (JM check add a reference to paper, + mention parameter in data) +cfc/ - not sure (CNH to talk to Steph and Helen) +chronos/ - AM to check (not being used - Andrea to kill it) +compon_communic/ - 6.6 (no content yet)(Daniel + JM) +cost/ - not sure, check with PH +ctrl/ - not sure, check with PH +debug/ - JM may do something in chapter 7 (utilities) +diagnostics/ - 7.1 +dic/ - 6.7.2 +ebm/ - (check with PH) +ecco/ - chapter 8 +embed_files/ - add something to chapter 7 +exch2/ - 6.2.2 +exf/ - 6.3.4 +fizhi/ - 6.4.3 +flt/ - (PH check) +gchem/ - 6.7.1 +generic_advdiff/ - in chapter 2 (JM check) +ggl90/ - nothing, (Martin?) +gmredi/ - in chapter 2 (JM check). also need + Ferrari & Mc transition zone stuff (Samar doing this) + get dfer to read this +grdchk/ - grdchk (chapter 5 - check with PH) +gridalt/ - 6.2.4 +kpp/ - 6.3.2 +land/ - 6.4.2 (not connected to code Rong's notes - JM to fix) +matrix/ - Samar +mdsio/ - 7.3.1 +mnc/ - 7.2.1 +mom_common/ - in chapter 2 (JM check) +mom_fluxform/ - in chapter 2 (JM check) +mom_vecinv/ - in chapter 2 (JM check) +monitor/ - 7.4 +my82/ - nothing, (martin?) +obcs/ - 6.3 (needs a check - ask PH to read) +ocn_compon_interf/ - 6.6 (no content yet) +offline/ - nothing, tutorials that need work but no package section entry + trivial to document (CNH to do) +opps/ - nothing, (martin?) +pp81/ - nothing, (martin?) +profiles/ - GAEL +ptracers/ - JM + SD + Martin to write something (nothing for this + at the moment) + AM has diagnostics table for this. +rbcs/ - CNH to talk to steph +runclock/ - runclock - CNH +rw/ - not sure - going to stay says JMC. quick IO calls + JMC to write a quick note for that. +sbo/ - text in sbo_descruption.tex but not linked into + part6 - CNH +seaice/ - 6.5.2 - no equations, dimitris has promised some +shap_filt/ - chapter 2, JM to check +shelfice/ - nothing yet (martin?) +solver/ - empty (go away?) +sphere/ - chapter 5 or 8 (PH to check) +therm_seaice/ - empty (go away?) +thsice/ - 6.5.1 (JM to update?) +timeave/ - retiring...... +zonal_filt/ - chapter 2 (JM to check) + +list an expeiment which uses package? CNH + +6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 + Figure 6.8 is missing + + +===== Chapter 7 ===== [EH3 editing] : + +7.1.x - JMC: please add description of: + - diagstat + - new temporal averaging feature -9. Model uses +7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) + +7.5.2 - get bathymetry pre-processing stuff from Patrick + and then describe it + +add something on spgrid mesh generator (maybe)? + + +andrea + + +9. Publications using MITgcm --> "Previous Applications of MITgcm" Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... (check in support for more names) + +10. Under development + +Constantinos LCML + + +Bibliography + + tidy up from misc - .tex