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revision 1.9 by cnh, Thu Apr 6 19:54:06 2006 UTC revision 1.41 by molod, Wed Jun 28 17:21:21 2006 UTC
# Line 1  Line 1 
1    Editors
2    
3     Overall       - JM, AM, PH, CNH, EH3
4    
5     Front content - EH3
6    
7     Chapter 1     - CNH
8    
9     Chapter 2     - JMC
10    
11     Chapter 3     -  AM
12    
13     Chapter 4     - CNH
14    
15     Chapter 5     -  PH
16    
17     Chapter 6     -  AM
18    
19     Chapter 7     - EH3
20    
21     Chapter 8     -  PH
22    
23     Chapter 9     - CNH (Applications)
24    
25     Chapter 10    - JMC (Under development chapter)
26    
27     Biblio        - EH3
28    
29  Rebuild and set to do cron build - DONE on hugo  Rebuild and set to do cron build - DONE on hugo
30    
31  To do  To do
# Line 8  To do Line 36  To do
36      Add an "Under development, chapter" - shortish description of what      Add an "Under development, chapter" - shortish description of what
37      is available (last chapter)      is available (last chapter)
38    
39      - add in example latex for formatting author names in different pieces.
40        this aknowledges peoples contributions and gives ref for who
41        to talk to.
42    
43  o HTML, scripts and front content  o HTML, scripts and front content
44    
45    - pick a URL    - pick a URL
46      TBD      TBD
47    
   - 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  
   
48    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
49      o add another short-cut for quick download      o add another short-cut for quick download
50    
# Line 30  o HTML, scripts and front content Line 56  o HTML, scripts and front content
56        Tutorials (broken)        Tutorials (broken)
57        Browse Code        Browse Code
58    
     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?  
   
59      o words on http://mitgcm.org/r2_web_testing/latest      o words on http://mitgcm.org/r2_web_testing/latest
60        change to        change to
61         "access on-line Auser manual/A and Atable of contents/A         "access on-line Auser manual/A and Atable of contents/A
# Line 72  o Latex Line 88  o Latex
88    
89        o List of key papers needs to be updated and reformatted        o List of key papers needs to be updated and reformatted
90    
   
91        o Global atmosphere: `Held Suarez',        o Global atmosphere: `Held Suarez',
92          update Adcroft reference          update Adcroft reference
93          fix up ingrid link and frame (ingrid movies seem to be broken?)          fix up ingrid link and frame (ingrid movies seem to be broken?)
# Line 190  o Latex Line 205  o Latex
205            o coupled aqua, ridge world etc...            o coupled aqua, ridge world etc...
206              - links to ingrid output              - links to ingrid output
207                get stuff from Daniel                get stuff from Daniel
208                  Davids donut movie
209    
210            o constrained lab simulation            o constrained lab simulation
211              - links to ingrid output for model and lab              - links to ingrid output for model and lab
# Line 207  o Latex Line 223  o Latex
223            o Gas giant?            o Gas giant?
224    
225    
 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:  
   
   
 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  
   
 7.5.1 - add Graphix to the list of stuff in utils/matlab  
 7.5.2 - 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?)  
   
 3.1 - don't need a link to the outside of the document (remove it)  
     - link to htdig is broken  
   
 3.2.1 - link at bottom to source code points to section 3.2.1  
    (ie, to itself) - link should point to cvs code archive  
   
 3.2.2.1  - ('upgrading from an earlier version') belongs under  
       the cvs part, ie, should be 3.2.1.1  
   
 3.3 - 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)  
   
 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)  
 3.4.1 - 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  
 3.4.2 - 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  
   
 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options  
       as the place where they live (add a link?)  
   
 3.6.1 - 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.  
 3.6.1.2 - needs to be moved to inside section 3.6.2  
   
 3.7 - 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  
   
 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript  
      - is this experiment in the list from section 3.4???  
 3.10.3.1 - refers to figures and equations, links are broken  
   
 3.11.3.2 - 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?  
   
 3.12.4.1 - line 34 - link to equation is broken  
          - lines 60,61 - 1st (take out the 'r' in the superscript)  
   
 3.13.2 - link to theta-equation is broken  
 3.13.5.4 -- ALL of the bold links to variable names are broken  
             line 34: link to equation is broken  
   
 3.15.1 - reference to 'fourth experiment' should be removed  
   
 3.16.4 - strange formatting, presence of '>' symbols - remove them  
   
 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4  
 3.17.3.1 - nothing filled in under file input/data - needs description  
   
 3.18.2 - point to section 2 for details - need hyperlink  
   
 3.19.1 - 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  
   
 3.20.1 - link to doc at end of section points to this section  
 3.20.2 - 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.  
   
226  >>>> from JM  >>>> from JM
227    
228    
   
229  manual, section.2 :  manual, section.2 :
230    
231  In general:  In general:
# Line 433  In general: Line 233  In general:
233  - would be nice to have an active link to the fortran-file  - would be nice to have an active link to the fortran-file
234    for all the S/R & eq.Number in the "calling-tree" boxes    for all the S/R & eq.Number in the "calling-tree" boxes
235  - search for CALC_MOM_RHS and replace it by the appropriate S/R  - search for CALC_MOM_RHS and replace it by the appropriate S/R
236    (mom_flux_form, mom_vecinv, dynamics)    (mom_flux_form, mom_vecinv, dynamics) <- DONE
237  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
238  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
239  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
# Line 444  at the beginning of section.2 and to men Line 244  at the beginning of section.2 and to men
244  the 2 sections.  the 2 sections.
245    
246  in content: Horizontal Dissipation: 2 times in vector-invariant section  in content: Horizontal Dissipation: 2 times in vector-invariant section
247    <- DONE
248    
249  2.1 time-stepping (part2/time_stepping.tex)  2.1 time-stepping (part2/time_stepping.tex)
250    
# Line 452  in content: Horizontal Dissipation: 2 ti Line 253  in content: Horizontal Dissipation: 2 ti
253  >> In all the above configurations it is also possible to substitute the  >> In all the above configurations it is also possible to substitute the
254  >> Adams-Bashforth with an alternative time-stepping scheme for terms  >> Adams-Bashforth with an alternative time-stepping scheme for terms
255  >> evaluated explicitly in time  >> evaluated explicitly in time
256    <- Leave it general.
257    
258    
259  2.2 rigid-lid:  2.2 rigid-lid:
# Line 485  in content: Horizontal Dissipation: 2 ti Line 287  in content: Horizontal Dissipation: 2 ti
287  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
288    
289  2.9 Variants on Free-Surface  2.9 Variants on Free-Surface
290  - Delta.t mis-written (eq.2.73)  - Delta.t mis-written (eq.2.73) <- DONE
291  - Eq.Num missing (has been fixed since)  - Eq.Num missing <- DONE
292  - u* is stored in gU (and not in gUnm1)  - u* is stored in gU (and not in gUnm1) <- DONE
293  - Phi_nh in NH_VARS.h  - Phi_nh in NH_VARS.h <- DONE
294  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
295    INI_CG2D, INI_CG3D    INI_CG2D, INI_CG3D
296    
# Line 498  in content: Horizontal Dissipation: 2 ti Line 300  in content: Horizontal Dissipation: 2 ti
300  2.9.2 NLFS  2.9.2 NLFS
301  - eq.Nb are wrong in html  - eq.Nb are wrong in html
302  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
303     <- DONE
304    
305  2.10.1 Notation  2.10.1 Notation
306  - Area definition is not really used like this  - Area definition is not really used like this
# Line 506  in content: Horizontal Dissipation: 2 ti Line 309  in content: Horizontal Dissipation: 2 ti
309    
310    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
311    the model variables) are used (e.g., see section 2.10.5)    the model variables) are used (e.g., see section 2.10.5)
312    <- DONE
313    
314  2.10.5 Horizontal grid:  2.10.5 Horizontal grid:
315  - fig.2.8 : should use Aw,As consistently in this figure description,  - fig.2.8 : should use Aw,As consistently in this figure description,
316    in the figure itself, as it is in the text.    in the figure itself, as it is in the text. <- DONE
317  - curvilinear:  - curvilinear:
318    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
319    Eastward, Northward direction.    Eastward, Northward direction.
320    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
321  - add cylindrical grid description  - add cylindrical polar grid description
322     need to do a better job of relating model variables to this diagram     need to do a better job of relating model variables to this diagram
323    
324    
# Line 541  in content: Horizontal Dissipation: 2 ti Line 345  in content: Horizontal Dissipation: 2 ti
345      o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags      o need to relate c11, c12 etc.. to COSFAC, USE_COS etc... flags
346        in code need to explain why cos()3/2 turns out to be        in code need to explain why cos()3/2 turns out to be
347        scaling (not cos()2)        scaling (not cos()2)
348     - need to reference the smag/leith section.
349    
350  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
351   - mention the implicit vertical viscosity option and ref to section 2.5   - mention the implicit vertical viscosity option and ref to section 2.5
# Line 559  in content: Horizontal Dissipation: 2 ti Line 364  in content: Horizontal Dissipation: 2 ti
364    
365  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
366   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
367     - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
368    
369  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
370  - does not use std notation  - does not use std notation
371  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
372  (e.g changing the tile to:  (e.g changing the tile to:
373    - talk to Baylor
374   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
375     <- No (Chris said)
376    
377    
378    Diagrams of grid locations etc.... and what variables and output files
379    and/or netcdf variable names are not very easy to figure out and follow.
380    It would be good to redo and extend these diagrams and align with GRID.h
381    content.
382    
383    
384  JM  JM
385    
386    
387  9. Model uses  >>>> From Andrea
388    
389    Chapter 3
390    --------
391    
392    Almost all of the 'math mode' text is dropped down as subscripts
393    
394    3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
395         - is this experiment in the list from section 3.4???
396    3.10.3.1 - refers to figures and equations, links are broken
397    
398    3.11.3.2 - line 43: link to equation is broken
399             - line 51-53: link to equation is broken
400             - there is some mess of text hanging around the end of this section. remove? reformat?
401    
402    3.12.4.1 - line 34 - link to equation is broken
403             - lines 60,61 - 1st (take out the 'r' in the superscript)
404    
405    3.13.2 - link to theta-equation is broken
406    3.13.5.4 -- ALL of the bold links to variable names are broken
407                line 34: link to equation is broken
408    
409    3.15.1 - reference to 'fourth experiment' should be removed
410    
411    3.16.4 - strange formatting, presence of '>' symbols - remove them
412    
413    3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
414    3.17.3.1 - nothing filled in under file input/data - needs description
415    
416    3.18.2 - point to section 2 for details - need hyperlink
417    
418    3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
419             section 3.5 has the 'build' directory in the example
420    
421    3.20.1 - link to doc at end of section points to this section
422    3.20.2 - link to doc at end of section points to this section
423    
424         offline - duplicate inputs, what is it, tidy up cfc v.
425                   other offline. JM thinks these need tidying up.
426    
427    Which of the following are which tutorial?
428    adjustment.128x64x1
429    adjustment.cs-32x32x1
430    advect_cs
431    advect_xy
432    advect_xz
433    aim.5l_cs
434    aim.5l_Equatorial_Channel
435    aim.5l_LatLon
436    biogeo
437    bottom_ctrl_5x5
438    cfc_example
439    cpl_aim+ocn
440    dome
441    exp2
442    exp4
443    exp5
444    fizhi-cs-32x32x10
445    fizhi-cs-aqualev20
446    fizhi-gridalt-hs
447    flt_example
448    front_relax
449    global1x1_tot
450    global2x2_tot
451    global_ocean.90x40x15
452    global_ocean.cs32x15
453    global_ocean.cubed32x32x30
454    global_ocean_ebm
455    global_with_exf
456    hs94.128x64x5
457    hs94.1x64x5
458    hs94.cs-32x32x5
459    ideal_2D_oce
460    internal_wave
461    inverted_barometer
462    lab_sea
463    matrix_example
464    MLAdjust
465    natl_box
466    natl_box_adjoint
467    OpenAD
468    rotating_tank
469    solid-body.cs-32x32x1
470    tidal_basin_2d
471    tutorial_baroclinic_gyre
472    tutorial_barotropic_gyre
473    tutorial_cfc_offline
474    tutorial_deep_convection
475    tutorial_global_oce_biogeo
476    tutorial_global_oce_in_p
477    tutorial_global_oce_latlon
478    tutorial_global_oce_optim
479    tutorial_held_suarez_cs
480    tutorial_offline
481    tutorial_plume_on_slope
482    tutorial_tracer_adjsens
483    vermix
484    
485    >>>> From Ed
486    
487    Here are the remaining bits for Chap 4 :
488    
489     - missing references (if you point me towards URLs, I'll add them
490       to the bibliography):
491         \ref{ref hoe and hill, ecmwf}
492         \ref{magicgarden}
493         \ref{IBMLAPI}
494         \ref{Memorychannel}
495         \ref{hoe-hill:99}
496    
497     - There are a few empty sub-sections at the end of Chap 4 that
498       should either be commented out or fleshed out.
499    
500    and thats about it for Chap 4.
501    
502    
503    Add more to quick links on front page
504    
505    Chapter 6
506    
507       the master package diagram does not appear in the document
508    
509    Master list of packages (add this to beginning of chap 6)
510    
511    admtlm/               - autodiff (chapter 5)
512    aim/                  - retired
513    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
514    aim_ocn_coupler/      - 6.6 (no content yet)
515    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
516    atm_common/           - nothing in this package (6.4.1 related)
517    autodiff/             - autodiff (chapter 5)
518    bulk_force/           - 6.3.3
519    cal/                  - 6.3.5
520    cd_code/              - chapter 2 (JM check add a reference to paper,
521                              mention parameter in data)
522    cfc/                  - not sure  (CNH to talk to Steph and Helen)
523    chronos/              - AM to check (not being used - Andrea to kill it)
524    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
525    cost/                 - not sure, check with PH
526    ctrl/                 - not sure, check with PH
527    debug/                - JM may do something in chapter 7 (utilities)
528    diagnostics/          - 7.1
529    dic/                  - 6.7.2
530    ebm/                  - (check with PH)
531    ecco/                 - chapter 8
532    embed_files/          - add something to chapter 7
533    exch2/                - 6.2.2
534    exf/                  - 6.3.4
535    fizhi/                - 6.4.3
536    flt/                  - (PH check)
537    gchem/                - 6.7.1
538    generic_advdiff/      - in chapter 2 (JM check)
539    ggl90/                - nothing, (Martin?)
540    gmredi/               - in chapter 2 (JM check). also need
541                            Ferrari & Mc transition zone stuff (Samar doing this)
542                            get dfer to read this
543    grdchk/               - grdchk (chapter 5 - check with PH)
544    gridalt/              - 6.2.4
545    kpp/                  - 6.3.2
546    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
547    matrix/               - Samar
548    mdsio/                - 7.3.1
549    mnc/                  - 7.2.1
550    mom_common/           - in chapter 2 (JM check)
551    mom_fluxform/         - in chapter 2 (JM check)
552    mom_vecinv/           - in chapter 2 (JM check)
553    monitor/              - 7.4
554    my82/                 - nothing, (martin?)
555    obcs/                 - 6.3 (needs a check - ask PH to read)
556    ocn_compon_interf/    - 6.6 (no content yet)
557    offline/              - nothing, tutorials that need work but no package   section entry
558                            trivial to document (CNH to do)
559    opps/                 - nothing, (martin?)
560    pp81/                 - nothing, (martin?)
561    profiles/             - GAEL
562    ptracers/             - JM + SD + Martin to write something (nothing for this
563                              at the moment)
564                            AM has diagnostics table for this.
565    rbcs/                 - CNH to talk to steph
566    runclock/             - runclock - CNH
567    rw/                   - not sure - going to stay says JMC. quick IO calls
568                            JMC to write a quick note for that.
569    sbo/                  - text in sbo_descruption.tex but not linked into
570                            part6 - CNH
571    seaice/               - 6.5.2 - no equations, dimitris has promised some
572    shap_filt/            - chapter 2, JM to check
573    shelfice/             - nothing yet (martin?)
574    solver/               - empty (go away?)
575    sphere/               - chapter 5 or 8 (PH to check)
576    therm_seaice/         - empty (go away?)
577    thsice/               - 6.5.1 (JM to update?)
578    timeave/              - retiring......
579    zonal_filt/           - chapter 2 (JM to check)
580    
581    list an expeiment which uses package? CNH
582    
583    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
584     Figure 6.8 is missing
585    
586    
587    =====  Chapter 7  =====  [EH3 editing] :
588    
589    7.1.x - JMC: please add description of:
590            - diagstat
591            - new temporal averaging feature
592    
593    7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
594    
595    7.5.2 - get bathymetry pre-processing stuff from Patrick
596            and then describe it
597    
598    add something on spgrid mesh generator (maybe)?
599    
600    
601    andrea
602    
603    
604    9. Publications using MITgcm --> "Previous Applications of MITgcm"
605     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
606     (check in support for more names)     (check in support for more names)
607    
608    10. Under development
609    
610    Constantinos LCML
611    
612    
613    Bibliography
614    
615     tidy up from misc - .tex
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