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revision 1.10 by cnh, Thu Apr 6 20:03:45 2006 UTC revision 1.38 by cnh, Wed Jun 28 15:36:02 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 298  in content: Horizontal Dissipation: 2 ti Line 314  in content: Horizontal Dissipation: 2 ti
314    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
315    Eastward, Northward direction.    Eastward, Northward direction.
316    + mention horizGridFile= in file "data" (PARM04)    + mention horizGridFile= in file "data" (PARM04)
317  - add cylindrical grid description  - add cylindrical polar grid description
318     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
319    
320    
# Line 325  in content: Horizontal Dissipation: 2 ti Line 341  in content: Horizontal Dissipation: 2 ti
341      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
342        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
343        scaling (not cos()2)        scaling (not cos()2)
344     - need to reference the smag/leith section.
345    
346  2.13.6 Vertical dissipation  2.13.6 Vertical dissipation
347   - 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 360  in content: Horizontal Dissipation: 2 ti
360    
361  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
362   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
363     - fix equations 2.202 & 2.203 (thanks to Martin)
364    
365  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
366  - does not use std notation  - does not use std notation
367  - would be better as an appendix of section 2.20:  - would be better as an appendix of section 2.20:
368  (e.g changing the tile to:  (e.g changing the tile to:
369    - talk to Baylor
370   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
371    
 JM  
   
 >>>> From Ed  
372    
373  Here are the remaining bits for Chap 4 :  Diagrams of grid locations etc.... and what variables and output files
374    and/or netcdf variable names are not very easy to figure out and follow.
375   - The grammar/flow could still use some work.  Boo was an English  It would be good to redo and extend these diagrams and align with GRID.h
376     major and has experience editing/proofing technical papers.  I  content.
377     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  
378    
379    JM
380    
 andrea  
381    
382  >>>> From Andrea  >>>> From Andrea
383    
# Line 482  Chapter 3 Line 386  Chapter 3
386    
387  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
388    
 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?)  
   
389  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)
390      - link to htdig is broken      - link to htdig is broken
391    
# Line 531  divide chapter 3 more clearly into 2 sec Line 431  divide chapter 3 more clearly into 2 sec
431          are written.          are written.
432  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
433    
 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  
   
434  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
435  the verification directory  the verification directory
436    
# Line 570  the verification directory Line 467  the verification directory
467       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
468                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
469    
470    Which of the following are which tutorial?
471    adjustment.128x64x1
472    adjustment.cs-32x32x1
473    advect_cs
474    advect_xy
475    advect_xz
476    aim.5l_cs
477    aim.5l_Equatorial_Channel
478    aim.5l_LatLon
479    biogeo
480    bottom_ctrl_5x5
481    cfc_example
482    cpl_aim+ocn
483    dome
484    exp2
485    exp4
486    exp5
487    fizhi-cs-32x32x10
488    fizhi-cs-aqualev20
489    fizhi-gridalt-hs
490    flt_example
491    front_relax
492    global1x1_tot
493    global2x2_tot
494    global_ocean.90x40x15
495    global_ocean.cs32x15
496    global_ocean.cubed32x32x30
497    global_ocean_ebm
498    global_with_exf
499    hs94.128x64x5
500    hs94.1x64x5
501    hs94.cs-32x32x5
502    ideal_2D_oce
503    internal_wave
504    inverted_barometer
505    lab_sea
506    matrix_example
507    MLAdjust
508    natl_box
509    natl_box_adjoint
510    OpenAD
511    rotating_tank
512    solid-body.cs-32x32x1
513    tidal_basin_2d
514    tutorial_baroclinic_gyre
515    tutorial_barotropic_gyre
516    tutorial_cfc_offline
517    tutorial_deep_convection
518    tutorial_global_oce_biogeo
519    tutorial_global_oce_in_p
520    tutorial_global_oce_latlon
521    tutorial_global_oce_optim
522    tutorial_held_suarez_cs
523    tutorial_offline
524    tutorial_plume_on_slope
525    tutorial_tracer_adjsens
526    vermix
527    
528    >>>> From Ed
529    
530    Here are the remaining bits for Chap 4 :
531    
532     - missing references (if you point me towards URLs, I'll add them
533       to the bibliography):
534         \ref{ref hoe and hill, ecmwf}
535         \ref{magicgarden}
536         \ref{IBMLAPI}
537         \ref{Memorychannel}
538         \ref{hoe-hill:99}
539    
540     - There are a few empty sub-sections at the end of Chap 4 that
541       should either be commented out or fleshed out.
542    
543    and thats about it for Chap 4.
544    
545    
546    Add more to quick links on front page
547    
548    Chapter 6
549    
550       the master package diagram does not appear in the document
551    
552    Master list of packages (add this to beginning of chap 6)
553    
554    admtlm/               - autodiff (chapter 5)
555    aim/                  - retired
556    aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
557    aim_ocn_coupler/      - 6.6 (no content yet)
558    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
559    atm_common/           - nothing in this package (6.4.1 related)
560    autodiff/             - autodiff (chapter 5)
561    bulk_force/           - 6.3.3
562    cal/                  - 6.3.5
563    cd_code/              - chapter 2 (JM check add a reference to paper,
564                              mention parameter in data)
565    cfc/                  - not sure  (CNH to talk to Steph and Helen)
566    chronos/              - AM to check (not being used - Andrea to kill it)
567    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
568    cost/                 - not sure, check with PH
569    ctrl/                 - not sure, check with PH
570    debug/                - JM may do something in chapter 7 (utilities)
571    diagnostics/          - 7.1
572    dic/                  - 6.7.2
573    ebm/                  - (check with PH)
574    ecco/                 - chapter 8
575    embed_files/          - add something to chapter 7
576    exch2/                - 6.2.2
577    exf/                  - 6.3.4
578    fizhi/                - 6.4.3
579    flt/                  - (PH check)
580    gchem/                - 6.7.1
581    generic_advdiff/      - in chapter 2 (JM check)
582    ggl90/                - nothing, (Martin?)
583    gmredi/               - in chapter 2 (JM check). also need
584                            Ferrari & Mc transition zone stuff (Samar doing this)
585                            get dfer to read this
586    grdchk/               - grdchk (chapter 5 - check with PH)
587    gridalt/              - 6.2.4
588    kpp/                  - 6.3.2
589    land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
590    matrix/               - Samar
591    mdsio/                - 7.3.1
592    mnc/                  - 7.2.1
593    mom_common/           - in chapter 2 (JM check)
594    mom_fluxform/         - in chapter 2 (JM check)
595    mom_vecinv/           - in chapter 2 (JM check)
596    monitor/              - 7.4
597    my82/                 - nothing, (martin?)
598    obcs/                 - 6.3 (needs a check - ask PH to read)
599    ocn_compon_interf/    - 6.6 (no content yet)
600    offline/              - nothing, tutorials that need work but no package   section entry
601                            trivial to document (CNH to do)
602    opps/                 - nothing, (martin?)
603    pp81/                 - nothing, (martin?)
604    profiles/             - GAEL
605    ptracers/             - JM + SD + Martin to write something (nothing for this
606                              at the moment)
607                            AM has diagnostics table for this.
608    rbcs/                 - CNH to talk to steph
609    runclock/             - runclock - CNH
610    rw/                   - not sure - going to stay says JMC. quick IO calls
611                            JMC to write a quick note for that.
612    sbo/                  - text in sbo_descruption.tex but not linked into
613                            part6 - CNH
614    seaice/               - 6.5.2 - no equations, dimitris has promised some
615    shap_filt/            - chapter 2, JM to check
616    shelfice/             - nothing yet (martin?)
617    solver/               - empty (go away?)
618    sphere/               - chapter 5 or 8 (PH to check)
619    therm_seaice/         - empty (go away?)
620    thsice/               - 6.5.1 (JM to update?)
621    timeave/              - retiring......
622    zonal_filt/           - chapter 2 (JM to check)
623    
624    list an expeiment which uses package? CNH
625    
626    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
627     Figure 6.8 is missing
628    
629    
630    =====  Chapter 7  =====  [EH3 editing] :
631    
632    7.1.x - JMC: please add description of:
633            - diagstat
634            - new temporal averaging feature
635    
636  9. Model uses  7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
637    
638    7.5.2 - get bathymetry pre-processing stuff from Patrick
639            and then describe it
640    
641    add something on spgrid mesh generator (maybe)?
642    
643    
644    andrea
645    
646    
647    9. Publications using MITgcm --> "Previous Applications of MITgcm"
648     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
649     (check in support for more names)     (check in support for more names)
650    
651    10. Under development
652    
653    Constantinos LCML
654    
655    
656    Bibliography
657    
658     tidy up from misc - .tex
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