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revision 1.17 by edhill, Thu Apr 6 20:38:43 2006 UTC revision 1.36 by edhill, Tue Jun 27 22:34:55 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    
# Line 25  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 67  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 339  in content: Horizontal Dissipation: 2 ti Line 359  in content: Horizontal Dissipation: 2 ti
359    
360  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
361   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
362     - fix equations 2.202 & 2.203 (thanks to Martin)
363    
364  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
365  - does not use std notation  - does not use std notation
# Line 346  in content: Horizontal Dissipation: 2 ti Line 367  in content: Horizontal Dissipation: 2 ti
367  (e.g changing the tile to:  (e.g changing the tile to:
368  - talk to Baylor  - talk to Baylor
369   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
370    
371    
372    Diagrams of grid locations etc.... and what variables and output files
373    and/or netcdf variable names are not very easy to figure out and follow.
374    It would be good to redo and extend these diagrams and align with GRID.h
375    content.
376    
377    
378  JM  JM
# Line 358  Chapter 3 Line 385  Chapter 3
385    
386  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
387    
 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?)  
 [DONE]  
   
388  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)
389      - link to htdig is broken      - link to htdig is broken
390    
# Line 408  divide chapter 3 more clearly into 2 sec Line 430  divide chapter 3 more clearly into 2 sec
430          are written.          are written.
431  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
432    
 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  
   
433  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
434  the verification directory  the verification directory
435    
# Line 448  the verification directory Line 467  the verification directory
467                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
468    
469  Which of the following are which tutorial?  Which of the following are which tutorial?
470  ! MLAdjust  adjustment.128x64x1
 adjust_nlfs.cs-32x32x1  
 aim.5l_XZ_Equatorial_Slice  
 biogeo  
 aim.5l_zon-ave  
 coupled_ucla  
 cfc_offline  
 exp3  
 global2x2_tot  
 global1x1_tot  
 global_ocean.cubed_wEXF  
 global_with_CFC11  
 goz  
 gop  
 natl_box_obcs  
 natl_box_forward  
 spinup_optim  
 tutorial_held_suarez_cs  
 vero  
 inverted_barometer  
 global_ocean.cubed32x32x30  
 exp1  
 advect_cs  
 dic_example  
 fizhi-gridalt-hs  
 global_ocean_pressure  
 matrix_example  
 exp4  
 solid-body.cs-32x32x1  
 cfc_example  
 flt_example  
471  adjustment.cs-32x32x1  adjustment.cs-32x32x1
472    advect_cs
473    advect_xy
474  advect_xz  advect_xz
475  rotating_tank  aim.5l_cs
476  ideal_2D_oce  aim.5l_Equatorial_Channel
 global_ocean.90x40x15  
 front_relax  
477  aim.5l_LatLon  aim.5l_LatLon
478  lab_sea  biogeo
479  hs94.cs-32x32x5  bottom_ctrl_5x5
480  global_with_exf  cfc_example
481    cpl_aim+ocn
482    dome
483  exp2  exp2
484  tidal_basin_2d  exp4
 fizhi-cs-32x32x10  
485  exp5  exp5
486    fizhi-cs-32x32x10
487    fizhi-cs-aqualev20
488    fizhi-gridalt-hs
489    flt_example
490    front_relax
491    global1x1_tot
492    global2x2_tot
493    global_ocean.90x40x15
494  global_ocean.cs32x15  global_ocean.cs32x15
495  OpenAD  global_ocean.cubed32x32x30
 hs94.1x64x5  
 fizhi-cs-aqualev10  
 exp0  
 dome  
 aim.5l_Equatorial_Channel  
 aim.5l_cs  
 hs94.128x64x5  
 prm  
 carbon  
 plume_on_slope  
 natl_box_adjoint  
 vermix  
 cpl_aim+ocn  
496  global_ocean_ebm  global_ocean_ebm
497    global_with_exf
498    hs94.128x64x5
499    hs94.1x64x5
500    hs94.cs-32x32x5
501    ideal_2D_oce
502  internal_wave  internal_wave
503  advect_xy  inverted_barometer
504    lab_sea
505    matrix_example
506    MLAdjust
507  natl_box  natl_box
508  adjustment.128x64x1  natl_box_adjoint
509    OpenAD
510    rotating_tank
511    solid-body.cs-32x32x1
512    tidal_basin_2d
513    tutorial_baroclinic_gyre
514    tutorial_barotropic_gyre
515    tutorial_cfc_offline
516    tutorial_deep_convection
517    tutorial_global_oce_biogeo
518    tutorial_global_oce_in_p
519    tutorial_global_oce_latlon
520    tutorial_global_oce_optim
521    tutorial_held_suarez_cs
522    tutorial_offline
523    tutorial_plume_on_slope
524    tutorial_tracer_adjsens
525    vermix
526    
527  >>>> From Ed  >>>> From Ed
528    
# Line 538  Chapter 6 Line 548  Chapter 6
548    
549     the master package diagram does not appear in the document     the master package diagram does not appear in the document
550    
    pkg/ptracers doesn't seem to have any documentation (see packages list below)  
                 martin volunteered - get martin to ask steph  
   
   
551  Master list of packages (add this to beginning of chap 6)  Master list of packages (add this to beginning of chap 6)
552    
553  admtlm/               - autodiff (chapter 5)  admtlm/               - autodiff (chapter 5)
# Line 569  embed_files/          - add something to Line 575  embed_files/          - add something to
575  exch2/                - 6.2.2  exch2/                - 6.2.2
576  exf/                  - 6.3.4  exf/                  - 6.3.4
577  fizhi/                - 6.4.3  fizhi/                - 6.4.3
578  flt/                  - in chapter 2 (JM check)  flt/                  - (PH check)
579  gchem/                - 6.7.1  gchem/                - 6.7.1
580  generic_advdiff/      - in chapter 2 (JM check)  generic_advdiff/      - in chapter 2 (JM check)
581  ggl90/                - nothing, (Martin?)  ggl90/                - nothing, (Martin?)
582  gmredi/               - in chapter 2 (JM check). also need  gmredi/               - in chapter 2 (JM check). also need
583                          Ferrari & Mc tapering                          Ferrari & Mc transition zone stuff (Samar doing this)
584                            get dfer to read this
585  grdchk/               - grdchk (chapter 5 - check with PH)  grdchk/               - grdchk (chapter 5 - check with PH)
586  gridalt/              - 6.2.4  gridalt/              - 6.2.4
587  kpp/                  - 6.3.2  kpp/                  - 6.3.2
588  land/                 - 6.4.2 (not connected to code - JM to fix)  land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix)
589  matrix/               - Samar  matrix/               - Samar
590  mdsio/                - 7.3.1  mdsio/                - 7.3.1
591  mnc/                  - 7.2.1  mnc/                  - 7.2.1
# Line 587  mom_fluxform/         - in chapter 2 (JM Line 594  mom_fluxform/         - in chapter 2 (JM
594  mom_vecinv/           - in chapter 2 (JM check)  mom_vecinv/           - in chapter 2 (JM check)
595  monitor/              - 7.4  monitor/              - 7.4
596  my82/                 - nothing, (martin?)  my82/                 - nothing, (martin?)
597  obcs/                 - 6.3 (needs a check)  obcs/                 - 6.3 (needs a check - ask PH to read)
598  ocn_compon_interf/    - 6.6 (no content yet)  ocn_compon_interf/    - 6.6 (no content yet)
599  offline/              - nothing, tutorials that need work but no package   section entry  offline/              - nothing, tutorials that need work but no package   section entry
600                            trivial to document (CNH to do)
601  opps/                 - nothing, (martin?)  opps/                 - nothing, (martin?)
602  pp81/                 - nothing, (martin?)  pp81/                 - nothing, (martin?)
603  profiles/             - GAEL  profiles/             - GAEL
604  ptracers/             - JM + SD to write something  ptracers/             - JM + SD + Martin to write something (nothing for this
605  rbcs/                 - talk to steph                            at the moment)
606  runclock/             - runclock                          AM has diagnostics table for this.
607  rw/                   - not sure  rbcs/                 - CNH to talk to steph
608    runclock/             - runclock - CNH
609    rw/                   - not sure - going to stay says JMC. quick IO calls
610                            JMC to write a quick note for that.
611  sbo/                  - text in sbo_descruption.tex but not linked into  sbo/                  - text in sbo_descruption.tex but not linked into
612                          part6                          part6 - CNH
613  seaice/               - 6.5.2 - no equations, dimitris has promised some  seaice/               - 6.5.2 - no equations, dimitris has promised some
614  shap_filt/            - chapter 2, JM to check  shap_filt/            - chapter 2, JM to check
615  shelfice/             - nothing yet (martin?)  shelfice/             - nothing yet (martin?)
616  solver/               - empty  solver/               - empty (go away?)
617  sphere/               - chapter 5 or 8 (PH to check)  sphere/               - chapter 5 or 8 (PH to check)
618  therm_seaice/         - empty  therm_seaice/         - empty (go away?)
619  thsice/               - 6.5.1 (JM to update?)  thsice/               - 6.5.1 (JM to update?)
620  timeave/              - retiring......  timeave/              - retiring......
621  zonal_filt/           - chapter 2 (JM to check)  zonal_filt/           - chapter 2 (JM to check)
622    
623  Possible for chap 7 - Daniels grafix/ stuff  list an expeiment which uses package? CNH
   
 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  
624    
625  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
626   Figure 6.8 is missing   Figure 6.8 is missing
627    
628    
629  >>>> From Andrea  =====  Chapter 7  =====  [EH3 editing] :
   
 to do list for chap 7:  
630    
631    7.1.x - JMC: please add description of:
632            - diagstat
633            - new temporal averaging feature
634    
635  7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"  7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)
         the links are pointing to the proper place  
636    
637  7.5.1 - add Graphix to the list of stuff in utils/matlab  7.5.2 - get bathymetry pre-processing stuff from Patrick
638  7.5.2 - empty          and then describe it
639    
640    
641  andrea  andrea
642    
643    
644  9. Model uses  9. Publications using MITgcm --> "Previous Applications of MITgcm"
645     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
646     (check in support for more names)     (check in support for more names)
647    
648    10. Under development
649    
650    Constantinos LCML
651    
652    
653    Bibliography
654    
655     tidy up from misc - .tex
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