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revision 1.10 by cnh, Thu Apr 6 20:03:45 2006 UTC revision 1.33 by cnh, Tue Jun 27 15:22:03 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    
30    
31  Rebuild and set to do cron build - DONE on hugo  Rebuild and set to do cron build - DONE on hugo
32    
33  To do  To do
# Line 8  To do Line 38  To do
38      Add an "Under development, chapter" - shortish description of what      Add an "Under development, chapter" - shortish description of what
39      is available (last chapter)      is available (last chapter)
40    
41      - add in example latex for formatting author names in different pieces.
42        this aknowledges peoples contributions and gives ref for who
43        to talk to.
44    
45    
46  o HTML, scripts and front content  o HTML, scripts and front content
47    
48    - pick a URL    - pick a URL
49      TBD      TBD
50    
   - 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  
   
51    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
52      o add another short-cut for quick download      o add another short-cut for quick download
53    
# Line 30  o HTML, scripts and front content Line 59  o HTML, scripts and front content
59        Tutorials (broken)        Tutorials (broken)
60        Browse Code        Browse Code
61    
     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?  
   
62      o words on http://mitgcm.org/r2_web_testing/latest      o words on http://mitgcm.org/r2_web_testing/latest
63        change to        change to
64         "access on-line Auser manual/A and Atable of contents/A         "access on-line Auser manual/A and Atable of contents/A
# Line 298  in content: Horizontal Dissipation: 2 ti Line 317  in content: Horizontal Dissipation: 2 ti
317    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
318    Eastward, Northward direction.    Eastward, Northward direction.
319    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
320  - add cylindrical grid description  - add cylindrical polar grid description
321     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
322    
323    
# Line 325  in content: Horizontal Dissipation: 2 ti Line 344  in content: Horizontal Dissipation: 2 ti
344      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
345        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
346        scaling (not cos()2)        scaling (not cos()2)
347     - need to reference the smag/leith section.
348    
349  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
350   - 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 343  in content: Horizontal Dissipation: 2 ti Line 363  in content: Horizontal Dissipation: 2 ti
363    
364  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
365   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
366     - fix equations 2.202 & 2.203 (thanks to Martin)
367    
368  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
369  - does not use std notation  - does not use std notation
370  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
371  (e.g changing the tile to:  (e.g changing the tile to:
372    - talk to Baylor
373   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
374    
375    
376  JM  JM
377    
 >>>> 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)  
   
   
 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_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)  
 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  
   
 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  
  Figure 6.8 is missing  
   
   
 >>>> 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  
378    
379  >>>> From Andrea  >>>> From Andrea
380    
# Line 482  Chapter 3 Line 383  Chapter 3
383    
384  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
385    
 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?)  
   
386  3.1 - don't need a link to the outside of the document (remove it)  3.1 - don't need a link to the outside of the document (remove it)
387      - link to htdig is broken      - link to htdig is broken
388    
# Line 531  divide chapter 3 more clearly into 2 sec Line 428  divide chapter 3 more clearly into 2 sec
428          are written.          are written.
429  3.6.1.2 - needs to be moved to inside section 3.6.2  3.6.1.2 - needs to be moved to inside section 3.6.2
430    
 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  
   
431  All the 'overview' sections need some reference to the name of the experiment in  All the 'overview' sections need some reference to the name of the experiment in
432  the verification directory  the verification directory
433    
# Line 570  the verification directory Line 464  the verification directory
464       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
465                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
466    
467    Which of the following are which tutorial?
468    adjustment.128x64x1
469    adjustment.cs-32x32x1
470    advect_cs
471    advect_xy
472    advect_xz
473    aim.5l_cs
474    aim.5l_Equatorial_Channel
475    aim.5l_LatLon
476    biogeo
477    bottom_ctrl_5x5
478    cfc_example
479    cpl_aim+ocn
480    dome
481    exp2
482    exp4
483    exp5
484    fizhi-cs-32x32x10
485    fizhi-cs-aqualev20
486    fizhi-gridalt-hs
487    flt_example
488    front_relax
489    global1x1_tot
490    global2x2_tot
491    global_ocean.90x40x15
492    global_ocean.cs32x15
493    global_ocean.cubed32x32x30
494    global_ocean_ebm
495    global_with_exf
496    hs94.128x64x5
497    hs94.1x64x5
498    hs94.cs-32x32x5
499    ideal_2D_oce
500    internal_wave
501    inverted_barometer
502    lab_sea
503    matrix_example
504    MLAdjust
505    natl_box
506    natl_box_adjoint
507    OpenAD
508    rotating_tank
509    solid-body.cs-32x32x1
510    tidal_basin_2d
511    tutorial_baroclinic_gyre
512    tutorial_barotropic_gyre
513    tutorial_cfc_offline
514    tutorial_deep_convection
515    tutorial_global_oce_biogeo
516    tutorial_global_oce_in_p
517    tutorial_global_oce_latlon
518    tutorial_global_oce_optim
519    tutorial_held_suarez_cs
520    tutorial_offline
521    tutorial_plume_on_slope
522    tutorial_tracer_adjsens
523    vermix
524    
525    >>>> From Ed
526    
527    Here are the remaining bits for Chap 4 :
528    
529     - missing references (if you point me towards URLs, I'll add them
530       to the bibliography):
531         \ref{ref hoe and hill, ecmwf}
532         \ref{magicgarden}
533         \ref{IBMLAPI}
534         \ref{Memorychannel}
535         \ref{hoe-hill:99}
536    
537     - There are a few empty sub-sections at the end of Chap 4 that
538       should either be commented out or fleshed out.
539    
540  9. Model uses  and thats about it for Chap 4.
541    
542    
543    Add more to quick links on front page
544    
545    Chapter 6
546    
547       the master package diagram does not appear in the document
548    
549    Master list of packages (add this to beginning of chap 6)
550    
551    admtlm/               - autodiff (chapter 5)
552    aim/                  - retired
553    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
554    aim_ocn_coupler/      - 6.6 (no content yet)
555    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
556    atm_common/           - nothing in this package (6.4.1 related)
557    autodiff/             - autodiff (chapter 5)
558    bulk_force/           - 6.3.3
559    cal/                  - 6.3.5
560    cd_code/              - chapter 2 (JM check add a reference to paper,
561                              mention parameter in data)
562    cfc/                  - not sure  (CNH to talk to Steph and Helen)
563    chronos/              - AM to check (not being used - Andrea to kill it)
564    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
565    cost/                 - not sure, check with PH
566    ctrl/                 - not sure, check with PH
567    debug/                - JM may do something in chapter 7 (utilities)
568    diagnostics/          - 7.1
569    dic/                  - 6.7.2
570    ebm/                  - (check with PH)
571    ecco/                 - chapter 8
572    embed_files/          - add something to chapter 7
573    exch2/                - 6.2.2
574    exf/                  - 6.3.4
575    fizhi/                - 6.4.3
576    flt/                  - (PH check)
577    gchem/                - 6.7.1
578    generic_advdiff/      - in chapter 2 (JM check)
579    ggl90/                - nothing, (Martin?)
580    gmredi/               - in chapter 2 (JM check). also need
581                            Ferrari & Mc transition zone stuff (Samar doing this)
582                            get dfer to read this
583    grdchk/               - grdchk (chapter 5 - check with PH)
584    gridalt/              - 6.2.4
585    kpp/                  - 6.3.2
586    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
587    matrix/               - Samar
588    mdsio/                - 7.3.1
589    mnc/                  - 7.2.1
590    mom_common/           - in chapter 2 (JM check)
591    mom_fluxform/         - in chapter 2 (JM check)
592    mom_vecinv/           - in chapter 2 (JM check)
593    monitor/              - 7.4
594    my82/                 - nothing, (martin?)
595    obcs/                 - 6.3 (needs a check - ask PH to read)
596    ocn_compon_interf/    - 6.6 (no content yet)
597    offline/              - nothing, tutorials that need work but no package   section entry
598                            trivial to document (CNH to do)
599    opps/                 - nothing, (martin?)
600    pp81/                 - nothing, (martin?)
601    profiles/             - GAEL
602    ptracers/             - JM + SD + Martin to write something (nothing for this
603                              at the moment)
604                            AM has diagnostics table for this.
605    rbcs/                 - CNH to talk to steph
606    runclock/             - runclock - CNH
607    rw/                   - not sure - going to stay says JMC. quick IO calls
608                            JMC to write a quick note for that.
609    sbo/                  - text in sbo_descruption.tex but not linked into
610                            part6 - CNH
611    seaice/               - 6.5.2 - no equations, dimitris has promised some
612    shap_filt/            - chapter 2, JM to check
613    shelfice/             - nothing yet (martin?)
614    solver/               - empty (go away?)
615    sphere/               - chapter 5 or 8 (PH to check)
616    therm_seaice/         - empty (go away?)
617    thsice/               - 6.5.1 (JM to update?)
618    timeave/              - retiring......
619    zonal_filt/           - chapter 2 (JM to check)
620    
621    list an expeiment which uses package? CNH
622    
623    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
624     Figure 6.8 is missing
625    
626    
627    =====  Chapter 7  =====  [EH3 editing] :
628    
629    7.1.1 - links to section 7.1.4: the text of the first
630            one should read "see MITgcm Kernel Diagnostics Menu"
631            the links are pointing to the proper place
632    
633    7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
634    
635    7.5.2 - get bathymetry pre-processing stuff from Patrick
636            and then describe it
637    
638    
639    andrea
640    
641    
642    9. Publications using MITgcm --> "Previous Applications of MITgcm"
643     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
644     (check in support for more names)     (check in support for more names)
645    
646    10. Under development
647    
648    
649    Bibliography
650    
651     tidy up from misc - .tex

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