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revision 1.13 by cnh, Thu Apr 6 20:13:23 2006 UTC revision 1.31 by jmc, Mon Jun 26 00:41:02 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 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 343  in content: Horizontal Dissipation: 2 ti Line 329  in content: Horizontal Dissipation: 2 ti
329    
330  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
331   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
332     - fix equations 2.202 & 2.203 (thanks to Martin)
333    
334  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
335  - does not use std notation  - does not use std notation
# Line 362  Chapter 3 Line 349  Chapter 3
349    
350  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
351    
 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?)  
   
352  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)
353      - link to htdig is broken      - link to htdig is broken
354    
# Line 411  divide chapter 3 more clearly into 2 sec Line 394  divide chapter 3 more clearly into 2 sec
394          are written.          are written.
395  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
396    
 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  
   
397  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
398  the verification directory  the verification directory
399    
# Line 449  the verification directory Line 429  the verification directory
429    
430       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
431                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
432    
433    Which of the following are which tutorial?
434    adjustment.128x64x1
435    adjustment.cs-32x32x1
436    advect_cs
437    advect_xy
438    advect_xz
439    aim.5l_cs
440    aim.5l_Equatorial_Channel
441    aim.5l_LatLon
442    biogeo
443    bottom_ctrl_5x5
444    cfc_example
445    cpl_aim+ocn
446    dome
447    exp2
448    exp4
449    exp5
450    fizhi-cs-32x32x10
451    fizhi-cs-aqualev20
452    fizhi-gridalt-hs
453    flt_example
454    front_relax
455    global1x1_tot
456    global2x2_tot
457    global_ocean.90x40x15
458    global_ocean.cs32x15
459    global_ocean.cubed32x32x30
460    global_ocean_ebm
461    global_with_exf
462    hs94.128x64x5
463    hs94.1x64x5
464    hs94.cs-32x32x5
465    ideal_2D_oce
466    internal_wave
467    inverted_barometer
468    lab_sea
469    matrix_example
470    MLAdjust
471    natl_box
472    natl_box_adjoint
473    OpenAD
474    rotating_tank
475    solid-body.cs-32x32x1
476    tidal_basin_2d
477    tutorial_baroclinic_gyre
478    tutorial_barotropic_gyre
479    tutorial_cfc_offline
480    tutorial_deep_convection
481    tutorial_global_oce_biogeo
482    tutorial_global_oce_in_p
483    tutorial_global_oce_latlon
484    tutorial_global_oce_optim
485    tutorial_held_suarez_cs
486    tutorial_offline
487    tutorial_plume_on_slope
488    tutorial_tracer_adjsens
489    vermix
490    
491  >>>> From Ed  >>>> From Ed
492    
493  Here are the remaining bits for Chap 4 :  Here are the remaining bits for Chap 4 :
494    
  - 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.  
   
495   - missing references (if you point me towards URLs, I'll add them   - missing references (if you point me towards URLs, I'll add them
496     to the bibliography):     to the bibliography):
497       \ref{ref hoe and hill, ecmwf}       \ref{ref hoe and hill, ecmwf}
# Line 478  Chapter 6 Line 512  Chapter 6
512    
513     the master package diagram does not appear in the document     the master package diagram does not appear in the document
514    
    pkg/ptracers doesn't seem to have any documentation (see packages list below)  
   
   
515  Master list of packages (add this to beginning of chap 6)  Master list of packages (add this to beginning of chap 6)
516    
517  admtlm/               - autodiff (chapter 5)  admtlm/               - autodiff (chapter 5)
518  aim/                  - retired  aim/                  - retired
519  aim_compon_interf/    - 6.6 (no content yet)  aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
520  aim_ocn_coupler/      - 6.6 (no content yet)  aim_ocn_coupler/      - 6.6 (no content yet)
521  aim_v23/              - 6.4.1 (content needs fixing - JM to do)  aim_v23/              - 6.4.1 (content needs fixing - JM to do)
522  atm_common/           - 6.6 (no content yet)  atm_common/           - nothing in this package (6.4.1 related)
523  autodiff/             - autodiff (chapter 5)  autodiff/             - autodiff (chapter 5)
524  bulk_force/           - 6.3.3  bulk_force/           - 6.3.3
525  cal/                  - 6.3.5  cal/                  - 6.3.5
526  cd_code/              - chapter 2 (JM check)  cd_code/              - chapter 2 (JM check add a reference to paper,
527  cfc/                  - not sure                            mention parameter in data)
528  chronos/              - AM to check  cfc/                  - not sure  (CNH to talk to Steph and Helen)
529  compon_communic/      - 6.6 (no content yet)  chronos/              - AM to check (not being used - Andrea to kill it)
530    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
531  cost/                 - not sure, check with PH  cost/                 - not sure, check with PH
532  ctrl/                 - not sure, check with PH  ctrl/                 - not sure, check with PH
533  debug/                - JM may do something in chapter 7 (utilities)  debug/                - JM may do something in chapter 7 (utilities)
534  diagnostics/          - 7.1  diagnostics/          - 7.1
535  dic/                  - 6.7.2  dic/                  - 6.7.2
536  ebm/                  - not sure  ebm/                  - (check with PH)
537  ecco/                 - chapter 8  ecco/                 - chapter 8
538  embed_files/          - add something to chapter 7  embed_files/          - add something to chapter 7
 ex3/                  - rename to exch3  
539  exch2/                - 6.2.2  exch2/                - 6.2.2
540  exf/                  - 6.3.4  exf/                  - 6.3.4
541  fizhi/                - 6.4.3  fizhi/                - 6.4.3
542  flt/                  - in chapter 2 (JM check)  flt/                  - (PH check)
543  gchem/                - 6.7.1  gchem/                - 6.7.1
544  generic_advdiff/      - in chapter 2 (JM check)  generic_advdiff/      - in chapter 2 (JM check)
545  ggl90/                - nothing, (Martin?)  ggl90/                - nothing, (Martin?)
546  gmredi/               - in chapter 2 (JM check). also need  gmredi/               - in chapter 2 (JM check). also need
547                          Ferrari & Mc tapering                          Ferrari & Mc transition zone stuff (Samar doing this)
548                            get dfer to read this
549  grdchk/               - grdchk (chapter 5 - check with PH)  grdchk/               - grdchk (chapter 5 - check with PH)
550  gridalt/              - 6.2.4  gridalt/              - 6.2.4
551  kpp/                  - 6.3.2  kpp/                  - 6.3.2
552  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)
553  matrix/               - Samar  matrix/               - Samar
554  mdsio/                - 7.3.1  mdsio/                - 7.3.1
555  mnc/                  - 7.2.1  mnc/                  - 7.2.1
# Line 526  mom_fluxform/         - in chapter 2 (JM Line 558  mom_fluxform/         - in chapter 2 (JM
558  mom_vecinv/           - in chapter 2 (JM check)  mom_vecinv/           - in chapter 2 (JM check)
559  monitor/              - 7.4  monitor/              - 7.4
560  my82/                 - nothing, (martin?)  my82/                 - nothing, (martin?)
561  obcs/                 - 6.3 (needs a check)  obcs/                 - 6.3 (needs a check - ask PH to read)
562  ocn_compon_interf/    - 6.6 (no content yet)  ocn_compon_interf/    - 6.6 (no content yet)
563  offline/              - nothing, tutorials that need work but no package   section entry  offline/              - nothing, tutorials that need work but no package   section entry
564                            trivial to document (CNH to do)
565  opps/                 - nothing, (martin?)  opps/                 - nothing, (martin?)
566  pp81/                 - nothing, (martin?)  pp81/                 - nothing, (martin?)
567  profiles/             - GAEL  profiles/             - GAEL
568  ptracers/             - JM + SD to write something  ptracers/             - JM + SD + Martin to write something (nothing for this
569  rbcs/                 - talk to steph                            at the moment)
570  runclock/             - runclock                          AM has diagnostics table for this.
571  rw/                   - not sure  rbcs/                 - CNH to talk to steph
572    runclock/             - runclock - CNH
573    rw/                   - not sure - going to stay says JMC. quick IO calls
574                            JMC to write a quick note for that.
575  sbo/                  - text in sbo_descruption.tex but not linked into  sbo/                  - text in sbo_descruption.tex but not linked into
576                          part6                          part6 - CNH
577  seaice/               - 6.5.2 - no equations, dimitris has promised some  seaice/               - 6.5.2 - no equations, dimitris has promised some
578  shap_filt/            - chapter 2, JM to check  shap_filt/            - chapter 2, JM to check
579  shelfice/             - nothing yet (martin?)  shelfice/             - nothing yet (martin?)
580  solver/               - empty  solver/               - empty (go away?)
581  sphere/               - chapter 5 or 8 (PH to check)  sphere/               - chapter 5 or 8 (PH to check)
582  therm_seaice/         - empty  therm_seaice/         - empty (go away?)
583  thsice/               - 6.5.1 (JM to update?)  thsice/               - 6.5.1 (JM to update?)
584  timeave/              - retiring......  timeave/              - retiring......
585  zonal_filt/           - chapter 2 (JM to check)  zonal_filt/           - chapter 2 (JM to check)
586    
587  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  
588    
589  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
590   Figure 6.8 is missing   Figure 6.8 is missing
# Line 573  to do list for chap 7: Line 605  to do list for chap 7:
605  andrea  andrea
606    
607    
608  9. Model uses  9. Publications using MITgcm --> "Previous Applications of MITgcm"
609     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
610     (check in support for more names)     (check in support for more names)
611    
612    10. Under development
613    
614    
615    Bibliography
616    
617     tidy up from misc - .tex
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