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revision 1.10 by cnh, Thu Apr 6 20:03:45 2006 UTC revision 1.34 by cnh, Tue Jun 27 15:28:10 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    
 JM  
   
 >>>> 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  
   
375    
376  >>>> From Andrea  Diagrams of grid locations etc.... and what variables and output files
377    and/or netcdf variable names are not very easy to figure out and follow.
378  to do list for chap 7:  It would be good to redo and extend these diagrams and align with GRID.h
379    content.
380    
 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  
381    
382    JM
383    
 andrea  
384    
385  >>>> From Andrea  >>>> From Andrea
386    
# Line 482  Chapter 3 Line 389  Chapter 3
389    
390  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
391    
 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?)  
   
392  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)
393      - link to htdig is broken      - link to htdig is broken
394    
# Line 531  divide chapter 3 more clearly into 2 sec Line 434  divide chapter 3 more clearly into 2 sec
434          are written.          are written.
435  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
436    
 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  
   
437  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
438  the verification directory  the verification directory
439    
# Line 570  the verification directory Line 470  the verification directory
470       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
471                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
472    
473    Which of the following are which tutorial?
474    adjustment.128x64x1
475    adjustment.cs-32x32x1
476    advect_cs
477    advect_xy
478    advect_xz
479    aim.5l_cs
480    aim.5l_Equatorial_Channel
481    aim.5l_LatLon
482    biogeo
483    bottom_ctrl_5x5
484    cfc_example
485    cpl_aim+ocn
486    dome
487    exp2
488    exp4
489    exp5
490    fizhi-cs-32x32x10
491    fizhi-cs-aqualev20
492    fizhi-gridalt-hs
493    flt_example
494    front_relax
495    global1x1_tot
496    global2x2_tot
497    global_ocean.90x40x15
498    global_ocean.cs32x15
499    global_ocean.cubed32x32x30
500    global_ocean_ebm
501    global_with_exf
502    hs94.128x64x5
503    hs94.1x64x5
504    hs94.cs-32x32x5
505    ideal_2D_oce
506    internal_wave
507    inverted_barometer
508    lab_sea
509    matrix_example
510    MLAdjust
511    natl_box
512    natl_box_adjoint
513    OpenAD
514    rotating_tank
515    solid-body.cs-32x32x1
516    tidal_basin_2d
517    tutorial_baroclinic_gyre
518    tutorial_barotropic_gyre
519    tutorial_cfc_offline
520    tutorial_deep_convection
521    tutorial_global_oce_biogeo
522    tutorial_global_oce_in_p
523    tutorial_global_oce_latlon
524    tutorial_global_oce_optim
525    tutorial_held_suarez_cs
526    tutorial_offline
527    tutorial_plume_on_slope
528    tutorial_tracer_adjsens
529    vermix
530    
531    >>>> From Ed
532    
533    Here are the remaining bits for Chap 4 :
534    
535     - missing references (if you point me towards URLs, I'll add them
536       to the bibliography):
537         \ref{ref hoe and hill, ecmwf}
538         \ref{magicgarden}
539         \ref{IBMLAPI}
540         \ref{Memorychannel}
541         \ref{hoe-hill:99}
542    
543     - There are a few empty sub-sections at the end of Chap 4 that
544       should either be commented out or fleshed out.
545    
546  9. Model uses  and thats about it for Chap 4.
547    
548    
549    Add more to quick links on front page
550    
551    Chapter 6
552    
553       the master package diagram does not appear in the document
554    
555    Master list of packages (add this to beginning of chap 6)
556    
557    admtlm/               - autodiff (chapter 5)
558    aim/                  - retired
559    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
560    aim_ocn_coupler/      - 6.6 (no content yet)
561    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
562    atm_common/           - nothing in this package (6.4.1 related)
563    autodiff/             - autodiff (chapter 5)
564    bulk_force/           - 6.3.3
565    cal/                  - 6.3.5
566    cd_code/              - chapter 2 (JM check add a reference to paper,
567                              mention parameter in data)
568    cfc/                  - not sure  (CNH to talk to Steph and Helen)
569    chronos/              - AM to check (not being used - Andrea to kill it)
570    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
571    cost/                 - not sure, check with PH
572    ctrl/                 - not sure, check with PH
573    debug/                - JM may do something in chapter 7 (utilities)
574    diagnostics/          - 7.1
575    dic/                  - 6.7.2
576    ebm/                  - (check with PH)
577    ecco/                 - chapter 8
578    embed_files/          - add something to chapter 7
579    exch2/                - 6.2.2
580    exf/                  - 6.3.4
581    fizhi/                - 6.4.3
582    flt/                  - (PH check)
583    gchem/                - 6.7.1
584    generic_advdiff/      - in chapter 2 (JM check)
585    ggl90/                - nothing, (Martin?)
586    gmredi/               - in chapter 2 (JM check). also need
587                            Ferrari & Mc transition zone stuff (Samar doing this)
588                            get dfer to read this
589    grdchk/               - grdchk (chapter 5 - check with PH)
590    gridalt/              - 6.2.4
591    kpp/                  - 6.3.2
592    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
593    matrix/               - Samar
594    mdsio/                - 7.3.1
595    mnc/                  - 7.2.1
596    mom_common/           - in chapter 2 (JM check)
597    mom_fluxform/         - in chapter 2 (JM check)
598    mom_vecinv/           - in chapter 2 (JM check)
599    monitor/              - 7.4
600    my82/                 - nothing, (martin?)
601    obcs/                 - 6.3 (needs a check - ask PH to read)
602    ocn_compon_interf/    - 6.6 (no content yet)
603    offline/              - nothing, tutorials that need work but no package   section entry
604                            trivial to document (CNH to do)
605    opps/                 - nothing, (martin?)
606    pp81/                 - nothing, (martin?)
607    profiles/             - GAEL
608    ptracers/             - JM + SD + Martin to write something (nothing for this
609                              at the moment)
610                            AM has diagnostics table for this.
611    rbcs/                 - CNH to talk to steph
612    runclock/             - runclock - CNH
613    rw/                   - not sure - going to stay says JMC. quick IO calls
614                            JMC to write a quick note for that.
615    sbo/                  - text in sbo_descruption.tex but not linked into
616                            part6 - CNH
617    seaice/               - 6.5.2 - no equations, dimitris has promised some
618    shap_filt/            - chapter 2, JM to check
619    shelfice/             - nothing yet (martin?)
620    solver/               - empty (go away?)
621    sphere/               - chapter 5 or 8 (PH to check)
622    therm_seaice/         - empty (go away?)
623    thsice/               - 6.5.1 (JM to update?)
624    timeave/              - retiring......
625    zonal_filt/           - chapter 2 (JM to check)
626    
627    list an expeiment which uses package? CNH
628    
629    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
630     Figure 6.8 is missing
631    
632    
633    =====  Chapter 7  =====  [EH3 editing] :
634    
635    7.1.1 - links to section 7.1.4: the text of the first
636            one should read "see MITgcm Kernel Diagnostics Menu"
637            the links are pointing to the proper place
638    
639    7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
640    
641    7.5.2 - get bathymetry pre-processing stuff from Patrick
642            and then describe it
643    
644    
645    andrea
646    
647    
648    9. Publications using MITgcm --> "Previous Applications of MITgcm"
649     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
650     (check in support for more names)     (check in support for more names)
651    
652    10. Under development
653    
654    
655    Bibliography
656    
657     tidy up from misc - .tex
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