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revision 1.10 by cnh, Thu Apr 6 20:03:45 2006 UTC revision 1.23 by cnh, Thu Apr 6 20:54:14 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 298  in content: Horizontal Dissipation: 2 ti Line 293  in content: Horizontal Dissipation: 2 ti
293    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
294    Eastward, Northward direction.    Eastward, Northward direction.
295    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
296  - add cylindrical grid description  - add cylindrical polar grid description
297     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
298    
299    
# Line 325  in content: Horizontal Dissipation: 2 ti Line 320  in content: Horizontal Dissipation: 2 ti
320      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
321        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
322        scaling (not cos()2)        scaling (not cos()2)
323     - need to reference the smag/leith section.
324    
325  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
326   - 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 344  in content: Horizontal Dissipation: 2 ti
344  - does not use std notation  - does not use std notation
345  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
346  (e.g changing the tile to:  (e.g changing the tile to:
347    - talk to Baylor
348   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
349    
350    
351  JM  JM
352    
 >>>> 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  
353    
354  >>>> From Andrea  >>>> From Andrea
355    
# Line 485  Almost all of the 'math mode' text is dr Line 361  Almost all of the 'math mode' text is dr
361  divide chapter 3 more clearly into 2 sections?  divide chapter 3 more clearly into 2 sections?
362     (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
363      then 3.19 and 3.20 are informational again - rearrange subsections?)      then 3.19 and 3.20 are informational again - rearrange subsections?)
364    [DONE]
365    
366  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)
367      - link to htdig is broken      - link to htdig is broken
# Line 570  the verification directory Line 447  the verification directory
447       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
448                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
449    
450    Which of the following are which tutorial?
451    ! MLAdjust
452    adjust_nlfs.cs-32x32x1
453    aim.5l_XZ_Equatorial_Slice
454    biogeo
455    aim.5l_zon-ave
456    coupled_ucla
457    cfc_offline
458    exp3
459    global2x2_tot
460    global1x1_tot
461    global_ocean.cubed_wEXF
462    global_with_CFC11
463    goz
464    gop
465    natl_box_obcs
466    natl_box_forward
467    spinup_optim
468    tutorial_held_suarez_cs
469    vero
470    inverted_barometer
471    global_ocean.cubed32x32x30
472    exp1
473    advect_cs
474    dic_example
475    fizhi-gridalt-hs
476    global_ocean_pressure
477    matrix_example
478    exp4
479    solid-body.cs-32x32x1
480    cfc_example
481    flt_example
482    adjustment.cs-32x32x1
483    advect_xz
484    rotating_tank
485    ideal_2D_oce
486    global_ocean.90x40x15
487    front_relax
488    aim.5l_LatLon
489    lab_sea
490    hs94.cs-32x32x5
491    global_with_exf
492    exp2
493    tidal_basin_2d
494    fizhi-cs-32x32x10
495    exp5
496    global_ocean.cs32x15
497    OpenAD
498    hs94.1x64x5
499    fizhi-cs-aqualev10
500    exp0
501    dome
502    aim.5l_Equatorial_Channel
503    aim.5l_cs
504    hs94.128x64x5
505    prm
506    carbon
507    plume_on_slope
508    natl_box_adjoint
509    vermix
510    cpl_aim+ocn
511    global_ocean_ebm
512    internal_wave
513    advect_xy
514    natl_box
515    adjustment.128x64x1
516    
517    >>>> From Ed
518    
519    Here are the remaining bits for Chap 4 :
520    
521     - missing references (if you point me towards URLs, I'll add them
522       to the bibliography):
523         \ref{ref hoe and hill, ecmwf}
524         \ref{magicgarden}
525         \ref{IBMLAPI}
526         \ref{Memorychannel}
527         \ref{hoe-hill:99}
528    
529     - There are a few empty sub-sections at the end of Chap 4 that
530       should either be commented out or fleshed out.
531    
532    and thats about it for Chap 4.
533    
534    
535    Add more to quick links on front page
536    
537    Chapter 6
538    
539       the master package diagram does not appear in the document
540    
541    Master list of packages (add this to beginning of chap 6)
542    
543    admtlm/               - autodiff (chapter 5)
544    aim/                  - retired
545    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
546    aim_ocn_coupler/      - 6.6 (no content yet)
547    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
548    atm_common/           - nothing in this package (6.4.1 related)
549    autodiff/             - autodiff (chapter 5)
550    bulk_force/           - 6.3.3
551    cal/                  - 6.3.5
552    cd_code/              - chapter 2 (JM check add a reference to paper,
553                              mention parameter in data)
554    cfc/                  - not sure  (CNH to talk to Steph and Helen)
555    chronos/              - AM to check (not being used - Andrea to kill it)
556    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
557    cost/                 - not sure, check with PH
558    ctrl/                 - not sure, check with PH
559    debug/                - JM may do something in chapter 7 (utilities)
560    diagnostics/          - 7.1
561    dic/                  - 6.7.2
562    ebm/                  - (check with PH)
563    ecco/                 - chapter 8
564    embed_files/          - add something to chapter 7
565    exch2/                - 6.2.2
566    exf/                  - 6.3.4
567    fizhi/                - 6.4.3
568    flt/                  - (PH check)
569    gchem/                - 6.7.1
570    generic_advdiff/      - in chapter 2 (JM check)
571    ggl90/                - nothing, (Martin?)
572    gmredi/               - in chapter 2 (JM check). also need
573                            Ferrari & Mc transition zone stuff (Samar doing this)
574                            get dfer to read this
575    grdchk/               - grdchk (chapter 5 - check with PH)
576    gridalt/              - 6.2.4
577    kpp/                  - 6.3.2
578    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
579    matrix/               - Samar
580    mdsio/                - 7.3.1
581    mnc/                  - 7.2.1
582    mom_common/           - in chapter 2 (JM check)
583    mom_fluxform/         - in chapter 2 (JM check)
584    mom_vecinv/           - in chapter 2 (JM check)
585    monitor/              - 7.4
586    my82/                 - nothing, (martin?)
587    obcs/                 - 6.3 (needs a check - ask PH to read)
588    ocn_compon_interf/    - 6.6 (no content yet)
589    offline/              - nothing, tutorials that need work but no package   section entry
590                            trivial to document (CNH to do)
591    opps/                 - nothing, (martin?)
592    pp81/                 - nothing, (martin?)
593    profiles/             - GAEL
594    ptracers/             - JM + SD + Martin to write something (nothing for this
595                              at the moment)
596                            AM has diagnostics table for this.
597    rbcs/                 - CNH to talk to steph
598    runclock/             - runclock - CNH
599    rw/                   - not sure - going to stay says JMC. quick IO calls
600                            JMC to write a quick note for that.
601    sbo/                  - text in sbo_descruption.tex but not linked into
602                            part6 - CNH
603    seaice/               - 6.5.2 - no equations, dimitris has promised some
604    shap_filt/            - chapter 2, JM to check
605    shelfice/             - nothing yet (martin?)
606    solver/               - empty (go away?)
607    sphere/               - chapter 5 or 8 (PH to check)
608    therm_seaice/         - empty (go away?)
609    thsice/               - 6.5.1 (JM to update?)
610    timeave/              - retiring......
611    zonal_filt/           - chapter 2 (JM to check)
612    
613    list an expeiment which uses package? CNH
614    
615    [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.
616    
617    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
618     Figure 6.8 is missing
619    
620    
621    >>>> From Andrea
622    
623    to do list for chap 7:
624    
625    
626    7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
627            the links are pointing to the proper place
628    
629    7.5.1 - add Graphix to the list of stuff in utils/matlab
630    7.5.2 - empty
631    
632    
633    andrea
634    
635    
636  9. Model uses  9. Model uses
637     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
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