/[MITgcm]/manual/manual_todo.txt

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-revision 1.18 by cnh,
Thu Apr  6 20:39:25 2006 UTC
+revision 1.37 by cnh,
Wed Jun 28 15:11:42 2006 UTC
 Line 1
+ 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
-Line 8 
 To do
+Line 36 
 To do
      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
-Line 25 
 o HTML, scripts and front content
+Line 56 
 o HTML, scripts and front content
        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
-Line 67 
 o Latex
+Line 88 
 o Latex
        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?)
-Line 339 
 in content: Horizontal Dissipation: 2 ti
+Line 359 
 in content: Horizontal Dissipation: 2 ti
 .16 & 2.17 & 2.18 :
   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
+  - fix equations 2.202 & 2.203 (thanks to Martin)
 .20.2 mercator, non-dimensional Equations:
  - does not use std notation
-Line 346 
 in content: Horizontal Dissipation: 2 ti
+Line 367 
 in content: Horizontal Dissipation: 2 ti
  (e.g changing the tile to:
  - talk to Baylor
   Appendix: non-dimensional Equations on Spherical-Polar grid.)
+ 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
-Line 358 
 Chapter 3
+Line 385 
 Chapter 3
  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?)
- [DONE]
 .1 - don't need a link to the outside of the document (remove it)
      - link to htdig is broken
-Line 408 
 divide chapter 3 more clearly into 2 sec
+Line 430 
 divide chapter 3 more clearly into 2 sec
          are written.
 .6.1.2 - needs to be moved to inside section 3.6.2
-.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
-Line 448 
 the verification directory
+Line 467 
 the verification directory
                 other offline. JM thinks these need tidying up.
  Which of the following are which tutorial?
- ! MLAdjust
+ adjustment.128x64x1
- adjust_nlfs.cs-32x32x1
- aim.5l_XZ_Equatorial_Slice
- biogeo
- aim.5l_zon-ave
- coupled_ucla
- cfc_offline
- exp3
- global2x2_tot
- global1x1_tot
- global_ocean.cubed_wEXF
- global_with_CFC11
- goz
- gop
- natl_box_obcs
- natl_box_forward
- spinup_optim
- tutorial_held_suarez_cs
- vero
- inverted_barometer
- global_ocean.cubed32x32x30
- exp1
- advect_cs
- dic_example
- fizhi-gridalt-hs
- global_ocean_pressure
- matrix_example
- exp4
- solid-body.cs-32x32x1
- cfc_example
- flt_example
  adjustment.cs-32x32x1
+ advect_cs
+ advect_xy
  advect_xz
- rotating_tank
+ aim.5l_cs
- ideal_2D_oce
+ aim.5l_Equatorial_Channel
- global_ocean.90x40x15
- front_relax
  aim.5l_LatLon
- lab_sea
+ biogeo
- hs94.cs-32x32x5
+ bottom_ctrl_5x5
- global_with_exf
+ cfc_example
+ cpl_aim+ocn
+ dome
  exp2
- tidal_basin_2d
+ exp4
- fizhi-cs-32x32x10
  exp5
+ fizhi-cs-32x32x10
+ fizhi-cs-aqualev20
+ fizhi-gridalt-hs
+ flt_example
+ front_relax
+ global1x1_tot
+ global2x2_tot
+ global_ocean.90x40x15
  global_ocean.cs32x15
- OpenAD
+ global_ocean.cubed32x32x30
- hs94.1x64x5
- fizhi-cs-aqualev10
- exp0
- dome
- aim.5l_Equatorial_Channel
- aim.5l_cs
- hs94.128x64x5
- prm
- carbon
- plume_on_slope
- natl_box_adjoint
- vermix
- cpl_aim+ocn
  global_ocean_ebm
+ global_with_exf
+ hs94.128x64x5
+ hs94.1x64x5
+ hs94.cs-32x32x5
+ ideal_2D_oce
  internal_wave
- advect_xy
+ inverted_barometer
+ lab_sea
+ matrix_example
+ MLAdjust
  natl_box
- adjustment.128x64x1
+ 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
-Line 538 
 Chapter 6
+Line 548 
 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)
-                 martin volunteered - get martin to ask steph
  Master list of packages (add this to beginning of chap 6)
  admtlm/               - autodiff (chapter 5)
-Line 588 
 mom_fluxform/         - in chapter 2 (JM
+Line 594 
 mom_fluxform/         - in chapter 2 (JM
  mom_vecinv/           - in chapter 2 (JM check)
  monitor/              - 7.4
  my82/                 - nothing, (martin?)
- obcs/                 - 6.3 (needs a check)
+ 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 to write something
+ ptracers/             - JM + SD + Martin to write something (nothing for this
- rbcs/                 - talk to steph
+                           at the moment)
- runclock/             - runclock
+                         AM has diagnostics table for this.
- rw/                   - not sure
+ 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
+                         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
+ solver/               - empty (go away?)
  sphere/               - chapter 5 or 8 (PH to check)
- therm_seaice/         - empty
+ therm_seaice/         - empty (go away?)
  thsice/               - 6.5.1 (JM to update?)
  timeave/              - retiring......
  zonal_filt/           - chapter 2 (JM to check)
- Possible for chap 7 - Daniels grafix/ stuff
+ list an expeiment which uses package? CNH
- 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
 .3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
   Figure 6.8 is missing
- >>>> From Andrea
+ =====  Chapter 7  =====  [EH3 editing] :
- to do list for chap 7:
+.1.x - JMC: please add description of:
+         - diagstat
+         - new temporal averaging feature
+.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
-.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
+.5.2 - get bathymetry pre-processing stuff from Patrick
-         the links are pointing to the proper place
+         and then describe it
-.5.1 - add Graphix to the list of stuff in utils/matlab
+ add something on spgrid mesh generator (maybe)?
-.5.2 - empty
  andrea
-. Model uses
+. Publications using MITgcm --> "Previous Applications of MITgcm"
     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
     (check in support for more names)
+. Under development
+ Constantinos LCML
+ Bibliography
+  tidy up from misc - .tex

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