/[MITgcm]/manual/manual_todo.txt

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-revision 1.13 by cnh,
Thu Apr  6 20:13:23 2006 UTC
+revision 1.48 by cnh,
Tue Jan 15 14:47:57 2008 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 37 
 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
-   - pick a URL
+   - pick a URL:  mitgcm.org/r2  <-- EH3's preferred base 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
+     o --DONE--  add another short-cut for quick download
+     o --DONE--  add another short-cut
+                   About
+                   Installation
+                   Contents
+                   Overview
+                   Tutorials (broken)
+                   Browse Code
-     o add another short-cut
+     o --DONE--  words on http://mitgcm.org/r2_web_testing/latest change to
-       About
-       Installation
-       Contents
-       Overview
-       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
-         and browse the Aoverview section/A"
-     o finite-volume doesn't leap to FV figure
+     o --DONE--  finite-volume doesn't leap to FV figure
-     o have another go at pnmcrop et al.
+     o -- DONE ??? --  have another go at pnmcrop et al.
+          I've tried making a small change in latex2html which fixes
+          the oddball-lower-alignment issue that we were seeing with
+          most in-line expressions (that is, math embedded in text).
+          The fix results in some things being slightly raised but I
+          thin this is more asthetically pleasing than being somewhat
+          lowered as before. --EH3
+          To view the altered alignment, see:
+             http://eddy.csail.mit.edu/r2/latest/
      o Need an empty package as part of distribution. Check out atm_common
  o Latex
      Chapter 1                 - CNH
-Line 72 
 o Latex
+Line 98 
 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 190 
 o Latex
+Line 215 
 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 217 
 In general:
+Line 243 
 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 228 
 at the beginning of section.2 and to men
+Line 254 
 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 236 
 in content: Horizontal Dissipation: 2 ti
+Line 263 
 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.
+  o Time-stepping outline
+    - what gets called when
 .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 269 
 in content: Horizontal Dissipation: 2 ti
+Line 300 
 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 282 
 in content: Horizontal Dissipation: 2 ti
+Line 313 
 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 290 
 in content: Horizontal Dissipation: 2 ti
+Line 322 
 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 325 
 in content: Horizontal Dissipation: 2 ti
+Line 358 
 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 377 
 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 350 
 in content: Horizontal Dissipation: 2 ti
+Line 385 
 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 362 
 Chapter 3
+Line 404 
 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?)
-.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
+  o Update basic intro with one and four layer gyres
+    - include advection options
+    - conservation analysis
+    - diagnostics
-.16.4 - strange formatting, presence of '>' symbols - remove them
+  o Four degree adjoint
+    - both TAF and OpenAD based.
-.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
+  o Coupled with biogeo setup
-.17.3.1 - nothing filled in under file input/data - needs description
+    - based on CCGS setup
-.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.
  >>>> 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 453 
 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)
+  o Including FIZHI doc
+    - get things up to date
+ 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 501 
 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
+  o Cost function packages
+    - floats, weights, profiles etc...
- 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
+ list an expeiment which uses package? CNH
 .3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
   Figure 6.8 is missing
- >>>> From Andrea
+ =====  Chapter 7  =====  [EH3 editing] :
+  + JMC: please add description of:
+         - diagstat
+         - new temporal averaging feature
+  + add Graphix to the list of stuff in utils/matlab (Daniel)
- to do list for chap 7:
+  + get bathymetry pre-processing stuff from Patrick and then describe it
+  + add something on spgrid mesh generator
+  o Grid generation
+    - more explanation and some step-by-step examples
+    - plotting grid examples
-.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
-.5.1 - add Graphix to the list of stuff in utils/matlab
+  + add in gmaze PV calculation scripts plus write up on how it is calculated
-.5.2 - empty
+      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
+  o Legend/LCML examples and explanation
+    - examples and explanation!
+ Bibliography
+  tidy up from misc - .tex
+ Also
+ a link to the new manual
+ should appear on the front page (even if it's under construction).
+ updating:
+ http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html
+ which points to a 1.5 years old code. Would be good to generate a
+ new one, and even better, to try to keep it up-to-date.

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