/[MITgcm]/manual/manual_todo.txt

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-revision 1.9 by cnh,
Thu Apr  6 19:54:06 2006 UTC
+revision 1.30 by jmc,
Thu Apr 20 13:10:04 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 207 
 o Latex
+Line 192 
 o Latex
            o Gas giant?
- Master list of packages
- admtlm/               - autodiff (chapter 5)
- aim/                  - 6.4.1 (content needs fixing - JM to do)
- aim_compon_interf/    - 6.6 (no content yet)
- aim_ocn_coupler/      - 6.6 (no content yet)
- aim_v23/              - retired
- 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
- >>>> 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)
- >>>> From Andrea
- to do list for chap 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
-.5.1 - add Graphix to the list of stuff in utils/matlab
-.5.2 - empty
- andrea
- >>>> From Andrea
- 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
-.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
-          - 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
-          - lines 60,61 - 1st (take out the 'r' in the superscript)
-.13.2 - link to theta-equation is broken
-.13.5.4 -- 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.
  >>>> from JM
  manual, section.2 :
  In general:
-Line 514 
 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 541 
 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 559 
 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
  - 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
-. Model uses
+ >>>> From Andrea
+ Chapter 3
+ --------
+ Almost all of the 'math mode' text is dropped down as subscripts
+.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
+ 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
+          - 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
+          - lines 60,61 - 1st (take out the 'r' in the superscript)
+.13.2 - link to theta-equation is broken
+.13.5.4 -- 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 :
+  - 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
+.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
+  Figure 6.8 is missing
+ >>>> From Andrea
+ to do list for chap 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
+.5.1 - add Graphix to the list of stuff in utils/matlab
+.5.2 - empty
+ andrea
+. 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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