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revision 1.10 by cnh, Thu Apr 6 20:03:45 2006 UTC revision 1.28 by edhill, Fri Apr 7 02:35:23 2006 UTC
# Line 14  o HTML, scripts and front content Line 14  o HTML, scripts and front content
14    - pick a URL    - pick a URL
15      TBD      TBD
16    
   - 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  
   
17    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
18      o add another short-cut for quick download      o add another short-cut for quick download
19    
# Line 30  o HTML, scripts and front content Line 25  o HTML, scripts and front content
25        Tutorials (broken)        Tutorials (broken)
26        Browse Code        Browse Code
27    
     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?  
   
28      o words on http://mitgcm.org/r2_web_testing/latest      o words on http://mitgcm.org/r2_web_testing/latest
29        change to        change to
30         "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 283  in content: Horizontal Dissipation: 2 ti
283    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
284    Eastward, Northward direction.    Eastward, Northward direction.
285    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
286  - add cylindrical grid description  - add cylindrical polar grid description
287     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
288    
289    
# Line 325  in content: Horizontal Dissipation: 2 ti Line 310  in content: Horizontal Dissipation: 2 ti
310      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
311        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
312        scaling (not cos()2)        scaling (not cos()2)
313     - need to reference the smag/leith section.
314    
315  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
316   - 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 348  in content: Horizontal Dissipation: 2 ti Line 334  in content: Horizontal Dissipation: 2 ti
334  - does not use std notation  - does not use std notation
335  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
336  (e.g changing the tile to:  (e.g changing the tile to:
337    - talk to Baylor
338   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
339    
340    
341  JM  JM
342    
 >>>> 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  
343    
344  >>>> From Andrea  >>>> From Andrea
345    
# Line 485  Almost all of the 'math mode' text is dr Line 351  Almost all of the 'math mode' text is dr
351  divide chapter 3 more clearly into 2 sections?  divide chapter 3 more clearly into 2 sections?
352     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and     (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
353      then 3.19 and 3.20 are informational again - rearrange subsections?)      then 3.19 and 3.20 are informational again - rearrange subsections?)
354    [DONE]
355    
356  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)
357      - link to htdig is broken      - link to htdig is broken
# Line 570  the verification directory Line 437  the verification directory
437       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
438                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
439    
440    Which of the following are which tutorial?
441    ! MLAdjust
442    adjust_nlfs.cs-32x32x1
443    aim.5l_XZ_Equatorial_Slice
444    biogeo
445    aim.5l_zon-ave
446    coupled_ucla
447    cfc_offline
448    exp3
449    global2x2_tot
450    global1x1_tot
451    global_ocean.cubed_wEXF
452    global_with_CFC11
453    goz
454    gop
455    natl_box_obcs
456    natl_box_forward
457    spinup_optim
458    tutorial_held_suarez_cs
459    vero
460    inverted_barometer
461    global_ocean.cubed32x32x30
462    exp1
463    advect_cs
464    dic_example
465    fizhi-gridalt-hs
466    global_ocean_pressure
467    matrix_example
468    exp4
469    solid-body.cs-32x32x1
470    cfc_example
471    flt_example
472    adjustment.cs-32x32x1
473    advect_xz
474    rotating_tank
475    ideal_2D_oce
476    global_ocean.90x40x15
477    front_relax
478    aim.5l_LatLon
479    lab_sea
480    hs94.cs-32x32x5
481    global_with_exf
482    exp2
483    tidal_basin_2d
484    fizhi-cs-32x32x10
485    exp5
486    global_ocean.cs32x15
487    OpenAD
488    hs94.1x64x5
489    fizhi-cs-aqualev10
490    exp0
491    dome
492    aim.5l_Equatorial_Channel
493    aim.5l_cs
494    hs94.128x64x5
495    prm
496    carbon
497    plume_on_slope
498    natl_box_adjoint
499    vermix
500    cpl_aim+ocn
501    global_ocean_ebm
502    internal_wave
503    advect_xy
504    natl_box
505    adjustment.128x64x1
506    
507  9. Model uses  >>>> From Ed
508    
509    Here are the remaining bits for Chap 4 :
510    
511     - missing references (if you point me towards URLs, I'll add them
512       to the bibliography):
513         \ref{ref hoe and hill, ecmwf}
514         \ref{magicgarden}
515         \ref{IBMLAPI}
516         \ref{Memorychannel}
517         \ref{hoe-hill:99}
518    
519     - There are a few empty sub-sections at the end of Chap 4 that
520       should either be commented out or fleshed out.
521    
522    and thats about it for Chap 4.
523    
524    
525    Add more to quick links on front page
526    
527    Chapter 6
528    
529       the master package diagram does not appear in the document
530    
531    Master list of packages (add this to beginning of chap 6)
532    
533    admtlm/               - autodiff (chapter 5)
534    aim/                  - retired
535    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
536    aim_ocn_coupler/      - 6.6 (no content yet)
537    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
538    atm_common/           - nothing in this package (6.4.1 related)
539    autodiff/             - autodiff (chapter 5)
540    bulk_force/           - 6.3.3
541    cal/                  - 6.3.5
542    cd_code/              - chapter 2 (JM check add a reference to paper,
543                              mention parameter in data)
544    cfc/                  - not sure  (CNH to talk to Steph and Helen)
545    chronos/              - AM to check (not being used - Andrea to kill it)
546    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
547    cost/                 - not sure, check with PH
548    ctrl/                 - not sure, check with PH
549    debug/                - JM may do something in chapter 7 (utilities)
550    diagnostics/          - 7.1
551    dic/                  - 6.7.2
552    ebm/                  - (check with PH)
553    ecco/                 - chapter 8
554    embed_files/          - add something to chapter 7
555    exch2/                - 6.2.2
556    exf/                  - 6.3.4
557    fizhi/                - 6.4.3
558    flt/                  - (PH check)
559    gchem/                - 6.7.1
560    generic_advdiff/      - in chapter 2 (JM check)
561    ggl90/                - nothing, (Martin?)
562    gmredi/               - in chapter 2 (JM check). also need
563                            Ferrari & Mc transition zone stuff (Samar doing this)
564                            get dfer to read this
565    grdchk/               - grdchk (chapter 5 - check with PH)
566    gridalt/              - 6.2.4
567    kpp/                  - 6.3.2
568    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
569    matrix/               - Samar
570    mdsio/                - 7.3.1
571    mnc/                  - 7.2.1
572    mom_common/           - in chapter 2 (JM check)
573    mom_fluxform/         - in chapter 2 (JM check)
574    mom_vecinv/           - in chapter 2 (JM check)
575    monitor/              - 7.4
576    my82/                 - nothing, (martin?)
577    obcs/                 - 6.3 (needs a check - ask PH to read)
578    ocn_compon_interf/    - 6.6 (no content yet)
579    offline/              - nothing, tutorials that need work but no package   section entry
580                            trivial to document (CNH to do)
581    opps/                 - nothing, (martin?)
582    pp81/                 - nothing, (martin?)
583    profiles/             - GAEL
584    ptracers/             - JM + SD + Martin to write something (nothing for this
585                              at the moment)
586                            AM has diagnostics table for this.
587    rbcs/                 - CNH to talk to steph
588    runclock/             - runclock - CNH
589    rw/                   - not sure - going to stay says JMC. quick IO calls
590                            JMC to write a quick note for that.
591    sbo/                  - text in sbo_descruption.tex but not linked into
592                            part6 - CNH
593    seaice/               - 6.5.2 - no equations, dimitris has promised some
594    shap_filt/            - chapter 2, JM to check
595    shelfice/             - nothing yet (martin?)
596    solver/               - empty (go away?)
597    sphere/               - chapter 5 or 8 (PH to check)
598    therm_seaice/         - empty (go away?)
599    thsice/               - 6.5.1 (JM to update?)
600    timeave/              - retiring......
601    zonal_filt/           - chapter 2 (JM to check)
602    
603    list an expeiment which uses package? CNH
604    
605    [DONE]Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
606    
607    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
608     Figure 6.8 is missing
609    
610    
611    >>>> From Andrea
612    
613    to do list for chap 7:
614    
615    
616    7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
617            the links are pointing to the proper place
618    
619    7.5.1 - add Graphix to the list of stuff in utils/matlab
620    7.5.2 - empty
621    
622    
623    andrea
624    
625    
626    9. Publications using MITgcm --> "Previous Applications of MITgcm"
627     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
628     (check in support for more names)     (check in support for more names)
629    
630    10. Under development
631    
632    
633    Bibliography
634    
635     tidy up from misc - .tex
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