/[MITgcm]/manual/manual_todo.txt

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-revision 1.12 by cnh,
Thu Apr  6 20:12:55 2006 UTC
+revision 1.32 by edhill,
Tue Jun 27 15:13:26 2006 UTC
 Line 14 
 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
-Line 30 
 o HTML, scripts and front content
+Line 25 
 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 298 
 in content: Horizontal Dissipation: 2 ti
+Line 283 
 in content: Horizontal Dissipation: 2 ti
    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
-Line 325 
 in content: Horizontal Dissipation: 2 ti
+Line 310 
 in content: Horizontal Dissipation: 2 ti
      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.
 .13.6 Vertical dissipation
   - mention the implicit vertical viscosity option and ref to section 2.5
-Line 343 
 in content: Horizontal Dissipation: 2 ti
+Line 329 
 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 362 
 Chapter 3
+Line 349 
 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?)
 .1 - don't need a link to the outside of the document (remove it)
      - link to htdig is broken
-Line 411 
 divide chapter 3 more clearly into 2 sec
+Line 394 
 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 449 
 the verification directory
+Line 429 
 the verification directory
       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 :
-  - 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}
-Line 478 
 Chapter 6
+Line 512 
 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_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/           - 6.6 (no content yet)
+ 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)
+ cd_code/              - chapter 2 (JM check add a reference to paper,
- cfc/                  - not sure
+                           mention parameter in data)
- chronos/              - AM to check
+ cfc/                  - not sure  (CNH to talk to Steph and Helen)
- compon_communic/      - 6.6 (no content yet)
+ 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/                  - not sure
+ ebm/                  - (check with PH)
  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)
+ 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 tapering
+                         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 - JM to fix)
+ land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
  matrix/               - Samar
  mdsio/                - 7.3.1
  mnc/                  - 7.2.1
-Line 526 
 mom_fluxform/         - in chapter 2 (JM
+Line 558 
 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:
+.1.1 - links to section 7.1.4: the text of the first
-.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
+         one should read "see MITgcm Kernel Diagnostics Menu"
          the links are pointing to the proper place
-.5.1 - add Graphix to the list of stuff in utils/matlab
+.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
-.5.2 - empty
+.5.2 - get bathymetry pre-processing stuff from Patrick
+         and then describe it
  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
+ Bibliography
+  tidy up from misc - .tex

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