/[MITgcm]/manual/manual_todo.txt

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-revision 1.21 by cnh,
Thu Apr  6 20:51:30 2006 UTC
+revision 1.45 by cnh,
Thu Jun 29 17:45:14 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 185 
 o Latex
+Line 205 
 o Latex
            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
-Line 212 
 In general:
+Line 233 
 In general:
  - would be nice to have an active link to the fortran-file
    for all the S/R & eq.Number in the "calling-tree" boxes
  - search for CALC_MOM_RHS and replace it by the appropriate S/R
-   (mom_flux_form, mom_vecinv, dynamics)
+   (mom_flux_form, mom_vecinv, dynamics) <- DONE
  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
-Line 223 
 at the beginning of section.2 and to men
+Line 244 
 at the beginning of section.2 and to men
  the 2 sections.
  in content: Horizontal Dissipation: 2 times in vector-invariant section
+ <- DONE
 .1 time-stepping (part2/time_stepping.tex)
-Line 231 
 in content: Horizontal Dissipation: 2 ti
+Line 253 
 in content: Horizontal Dissipation: 2 ti
  >> In all the above configurations it is also possible to substitute the
  >> Adams-Bashforth with an alternative time-stepping scheme for terms
  >> evaluated explicitly in time
+ <- Leave it general.
 .2 rigid-lid:
  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
    to stay closer to the code.
- - mention section 2.5 implicit-Time-stepping (for vertical viscosity)
+ - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
 .3 linear free-surface:
  - add ref(+link) to S/R names:
- - add ref(+link) to Crank-Nickelson section 2.9.1
+ - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
 .4 Adams-Bashforth
- - add stability diagrams (I have some figures that I can put)
+ - add stability diagrams (I have some figures that I can put) <- DONE
- - add link for var. forcing_In_AB
+ - add link for var. forcing_In_AB and epsil_AB <- half DONE
- - add S/R link for S/R ADAMS_BASHFORTH2
+ - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
 .5 Implicit time-stepping
  - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
-Line 264 
 in content: Horizontal Dissipation: 2 ti
+Line 287 
 in content: Horizontal Dissipation: 2 ti
  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
 .9 Variants on Free-Surface
- - Delta.t mis-written (eq.2.73)
+ - Delta.t mis-written (eq.2.73) <- DONE
- - Eq.Num missing (has been fixed since)
+ - Eq.Num missing <- DONE
- - u* is stored in gU (and not in gUnm1)
+ - u* is stored in gU (and not in gUnm1) <- DONE
- - Phi_nh in NH_VARS.h
+ - Phi_nh in NH_VARS.h <- DONE
  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
    INI_CG2D, INI_CG3D
-Line 277 
 in content: Horizontal Dissipation: 2 ti
+Line 300 
 in content: Horizontal Dissipation: 2 ti
 .9.2 NLFS
  - eq.Nb are wrong in html
  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
+  <- DONE
 .10.1 Notation
  - Area definition is not really used like this
-Line 285 
 in content: Horizontal Dissipation: 2 ti
+Line 309 
 in content: Horizontal Dissipation: 2 ti
    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
    the model variables) are used (e.g., see section 2.10.5)
+ <- DONE
 .10.5 Horizontal grid:
  - fig.2.8 : should use Aw,As consistently in this figure description,
-   in the figure itself, as it is in the text.
+   in the figure itself, as it is in the text. <- DONE
  - curvilinear:
    to add: mention the angle of the grid direction relative to
    Eastward, Northward direction.
-Line 339 
 in content: Horizontal Dissipation: 2 ti
+Line 364 
 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) <- DONE
 .20.2 mercator, non-dimensional Equations:
  - does not use std notation
-Line 346 
 in content: Horizontal Dissipation: 2 ti
+Line 372 
 in content: Horizontal Dissipation: 2 ti
  (e.g changing the tile to:
  - talk to Baylor
   Appendix: non-dimensional Equations on Spherical-Polar grid.)
+  <- No (Chris said)
+ 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 391 
 Chapter 3
  Almost all of the 'math mode' text is dropped down as subscripts
- divide chapter 3 more clearly into 2 sections?
+.11.3.1 - refers to figures and equations, links are broken
-    (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
-.2.1 - link at bottom to source code points to section 3.2.1
-    (ie, to itself) - link should point to cvs code archive
-.2.2.1  - ('upgrading from an earlier version') belongs under
-       the cvs part, ie, should be 3.2.1.1
-.3 - remove reference to 'diags' section under MITgcm
-     - remove reference to 'exe' and 'bin' sections also
-       (remove the .cvsignore file under these directories in cvs)
-     - add a 'jobs' section, and a description as examples of run scripts
-     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
-     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
-     - under 'tools' the adjoint points to section 5 - this is now section 8
-       (but should be a floating reference)
-     - under 'utils' add a reference to exch2 - stuff for different resolutions
-     - the description of the pkg section refers directly to
-       section 3. should be section 6 (actually should be a floating reference)
-.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
-.4.1 - links to the following experiments don't exist or are broken:
-           exp2 - should link to section 3.9
-           hs94.cs-32x32x5 - link to section 3.12
-           add 'convection' to the list, link to section 3.13
-           add 'plume on slope` to the list, link to section 3.14
-           add '??' link to section 3.15
-           add 'dic_example on slope` to the list, link to section 3.16
-           add '??' link to section 3.17
-           add 'offline' and link to section 3.18
-           clean up others and make links where they are needed
-.4.2 - text suggests to see section 2 for details about what is in the 'code'
-         and 'input' directories - should refer to the examples in this section
-       - add 'build' bullet - this is where the model is compiled and exectuable lives
-.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
-       as the place where they live (add a link?)
-.6.1 - Add some general 'approach' text - ie, output is controlled either by the
-         'data' file in the input directory or by the data.[pkg name] file for any
-         package running. And there is some default behavior when the 'state' dumps
-         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
-.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
-      - is this experiment in the list from section 3.4???
-.10.3.1 - refers to figures and equations, links are broken
-.11.3.2 - line 43: link to equation is broken
+.12.3.2 - line 43: link to equation is broken
           - line 51-53: link to equation is broken
           - there is some mess of text hanging around the end of this section. remove? reformat?
-.12.4.1 - line 34 - link to equation is broken
+.13.4.1 - line 34 - link to equation is broken
           - lines 60,61 - 1st (take out the 'r' in the superscript)
-.13.2 - link to theta-equation is broken
+.14.2 - link to theta-equation is broken
-.13.5.4 -- ALL of the bold links to variable names are broken
+.14.5.4 -- ALL of the bold links to variable names are broken
              line 34: link to equation is broken
-.15.1 - reference to 'fourth experiment' should be removed
-.16.4 - strange formatting, presence of '>' symbols - remove them
-.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
-.17.3.1 - nothing filled in under file input/data - needs description
-.18.2 - point to section 2 for details - need hyperlink
-.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
-          section 3.5 has the 'build' directory in the example
-.20.1 - link to doc at end of section points to this section
-.20.2 - link to doc at end of section points to this section
-      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?
- ! MLAdjust
- 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_xz
- rotating_tank
- ideal_2D_oce
- global_ocean.90x40x15
- front_relax
- aim.5l_LatLon
- lab_sea
- hs94.cs-32x32x5
- global_with_exf
- exp2
- tidal_basin_2d
- fizhi-cs-32x32x10
- exp5
- global_ocean.cs32x15
- OpenAD
- 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
- internal_wave
- advect_xy
- natl_box
- adjustment.128x64x1
  >>>> From Ed
  Here are the remaining bits for Chap 4 :
-Line 597 
 ptracers/             - JM + SD + Martin
+Line 487 
 ptracers/             - JM + SD + Martin
  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)
  list an expeiment which uses package? CNH
- 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
 .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
+ add in gmaze PV calculation scripts plus write up on how it is calculated
+ http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
  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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