/[MITgcm]/manual/manual_todo.txt
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revision 1.14 by edhill, Thu Apr 6 20:14:48 2006 UTC revision 1.29 by molod, Wed Apr 19 22:44:49 2006 UTC
# Line 25  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 320  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 357  Chapter 3 Line 348  Chapter 3
348    
349  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
350    
 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?)  
   
351  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)
352      - link to htdig is broken      - link to htdig is broken
353    
# Line 406  divide chapter 3 more clearly into 2 sec Line 393  divide chapter 3 more clearly into 2 sec
393          are written.          are written.
394  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
395    
 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  
   
396  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
397  the verification directory  the verification directory
398    
# Line 444  the verification directory Line 428  the verification directory
428    
429       offline - duplicate inputs, what is it, tidy up cfc v.       offline - duplicate inputs, what is it, tidy up cfc v.
430                 other offline. JM thinks these need tidying up.                 other offline. JM thinks these need tidying up.
431    
432    Which of the following are which tutorial?
433    ! MLAdjust
434    adjust_nlfs.cs-32x32x1
435    aim.5l_XZ_Equatorial_Slice
436    biogeo
437    aim.5l_zon-ave
438    coupled_ucla
439    cfc_offline
440    exp3
441    global2x2_tot
442    global1x1_tot
443    global_ocean.cubed_wEXF
444    global_with_CFC11
445    goz
446    gop
447    natl_box_obcs
448    natl_box_forward
449    spinup_optim
450    tutorial_held_suarez_cs
451    vero
452    inverted_barometer
453    global_ocean.cubed32x32x30
454    exp1
455    advect_cs
456    dic_example
457    fizhi-gridalt-hs
458    global_ocean_pressure
459    matrix_example
460    exp4
461    solid-body.cs-32x32x1
462    cfc_example
463    flt_example
464    adjustment.cs-32x32x1
465    advect_xz
466    rotating_tank
467    ideal_2D_oce
468    global_ocean.90x40x15
469    front_relax
470    aim.5l_LatLon
471    lab_sea
472    hs94.cs-32x32x5
473    global_with_exf
474    exp2
475    tidal_basin_2d
476    fizhi-cs-32x32x10
477    exp5
478    global_ocean.cs32x15
479    OpenAD
480    hs94.1x64x5
481    fizhi-cs-aqualev10
482    exp0
483    dome
484    aim.5l_Equatorial_Channel
485    aim.5l_cs
486    hs94.128x64x5
487    prm
488    carbon
489    plume_on_slope
490    natl_box_adjoint
491    vermix
492    cpl_aim+ocn
493    global_ocean_ebm
494    internal_wave
495    advect_xy
496    natl_box
497    adjustment.128x64x1
498    
499  >>>> From Ed  >>>> From Ed
500    
501  Here are the remaining bits for Chap 4 :  Here are the remaining bits for Chap 4 :
502    
  - 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.  
   
503   - missing references (if you point me towards URLs, I'll add them   - missing references (if you point me towards URLs, I'll add them
504     to the bibliography):     to the bibliography):
505       \ref{ref hoe and hill, ecmwf}       \ref{ref hoe and hill, ecmwf}
# Line 473  Chapter 6 Line 520  Chapter 6
520    
521     the master package diagram does not appear in the document     the master package diagram does not appear in the document
522    
    pkg/ptracers doesn't seem to have any documentation (see packages list below)  
   
   
523  Master list of packages (add this to beginning of chap 6)  Master list of packages (add this to beginning of chap 6)
524    
525  admtlm/               - autodiff (chapter 5)  admtlm/               - autodiff (chapter 5)
526  aim/                  - retired  aim/                  - retired
527  aim_compon_interf/    - 6.6 (no content yet)  aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
528  aim_ocn_coupler/      - 6.6 (no content yet)  aim_ocn_coupler/      - 6.6 (no content yet)
529  aim_v23/              - 6.4.1 (content needs fixing - JM to do)  aim_v23/              - 6.4.1 (content needs fixing - JM to do)
530  atm_common/           - 6.6 (no content yet)  atm_common/           - nothing in this package (6.4.1 related)
531  autodiff/             - autodiff (chapter 5)  autodiff/             - autodiff (chapter 5)
532  bulk_force/           - 6.3.3  bulk_force/           - 6.3.3
533  cal/                  - 6.3.5  cal/                  - 6.3.5
534  cd_code/              - chapter 2 (JM check)  cd_code/              - chapter 2 (JM check add a reference to paper,
535  cfc/                  - not sure                            mention parameter in data)
536  chronos/              - AM to check  cfc/                  - not sure  (CNH to talk to Steph and Helen)
537  compon_communic/      - 6.6 (no content yet)  chronos/              - AM to check (not being used - Andrea to kill it)
538    compon_communic/      - 6.6 (no content yet)(Daniel + JM)
539  cost/                 - not sure, check with PH  cost/                 - not sure, check with PH
540  ctrl/                 - not sure, check with PH  ctrl/                 - not sure, check with PH
541  debug/                - JM may do something in chapter 7 (utilities)  debug/                - JM may do something in chapter 7 (utilities)
542  diagnostics/          - 7.1  diagnostics/          - 7.1
543  dic/                  - 6.7.2  dic/                  - 6.7.2
544  ebm/                  - not sure  ebm/                  - (check with PH)
545  ecco/                 - chapter 8  ecco/                 - chapter 8
546  embed_files/          - add something to chapter 7  embed_files/          - add something to chapter 7
 ex3/                  - rename to exch3  
547  exch2/                - 6.2.2  exch2/                - 6.2.2
548  exf/                  - 6.3.4  exf/                  - 6.3.4
549  fizhi/                - 6.4.3  fizhi/                - 6.4.3
550  flt/                  - in chapter 2 (JM check)  flt/                  - (PH check)
551  gchem/                - 6.7.1  gchem/                - 6.7.1
552  generic_advdiff/      - in chapter 2 (JM check)  generic_advdiff/      - in chapter 2 (JM check)
553  ggl90/                - nothing, (Martin?)  ggl90/                - nothing, (Martin?)
554  gmredi/               - in chapter 2 (JM check). also need  gmredi/               - in chapter 2 (JM check). also need
555                          Ferrari & Mc tapering                          Ferrari & Mc transition zone stuff (Samar doing this)
556                            get dfer to read this
557  grdchk/               - grdchk (chapter 5 - check with PH)  grdchk/               - grdchk (chapter 5 - check with PH)
558  gridalt/              - 6.2.4  gridalt/              - 6.2.4
559  kpp/                  - 6.3.2  kpp/                  - 6.3.2
560  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)
561  matrix/               - Samar  matrix/               - Samar
562  mdsio/                - 7.3.1  mdsio/                - 7.3.1
563  mnc/                  - 7.2.1  mnc/                  - 7.2.1
# Line 521  mom_fluxform/         - in chapter 2 (JM Line 566  mom_fluxform/         - in chapter 2 (JM
566  mom_vecinv/           - in chapter 2 (JM check)  mom_vecinv/           - in chapter 2 (JM check)
567  monitor/              - 7.4  monitor/              - 7.4
568  my82/                 - nothing, (martin?)  my82/                 - nothing, (martin?)
569  obcs/                 - 6.3 (needs a check)  obcs/                 - 6.3 (needs a check - ask PH to read)
570  ocn_compon_interf/    - 6.6 (no content yet)  ocn_compon_interf/    - 6.6 (no content yet)
571  offline/              - nothing, tutorials that need work but no package   section entry  offline/              - nothing, tutorials that need work but no package   section entry
572                            trivial to document (CNH to do)
573  opps/                 - nothing, (martin?)  opps/                 - nothing, (martin?)
574  pp81/                 - nothing, (martin?)  pp81/                 - nothing, (martin?)
575  profiles/             - GAEL  profiles/             - GAEL
576  ptracers/             - JM + SD to write something  ptracers/             - JM + SD + Martin to write something (nothing for this
577  rbcs/                 - talk to steph                            at the moment)
578  runclock/             - runclock                          AM has diagnostics table for this.
579  rw/                   - not sure  rbcs/                 - CNH to talk to steph
580    runclock/             - runclock - CNH
581    rw/                   - not sure - going to stay says JMC. quick IO calls
582                            JMC to write a quick note for that.
583  sbo/                  - text in sbo_descruption.tex but not linked into  sbo/                  - text in sbo_descruption.tex but not linked into
584                          part6                          part6 - CNH
585  seaice/               - 6.5.2 - no equations, dimitris has promised some  seaice/               - 6.5.2 - no equations, dimitris has promised some
586  shap_filt/            - chapter 2, JM to check  shap_filt/            - chapter 2, JM to check
587  shelfice/             - nothing yet (martin?)  shelfice/             - nothing yet (martin?)
588  solver/               - empty  solver/               - empty (go away?)
589  sphere/               - chapter 5 or 8 (PH to check)  sphere/               - chapter 5 or 8 (PH to check)
590  therm_seaice/         - empty  therm_seaice/         - empty (go away?)
591  thsice/               - 6.5.1 (JM to update?)  thsice/               - 6.5.1 (JM to update?)
592  timeave/              - retiring......  timeave/              - retiring......
593  zonal_filt/           - chapter 2 (JM to check)  zonal_filt/           - chapter 2 (JM to check)
594    
595  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  
596    
597  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
598   Figure 6.8 is missing   Figure 6.8 is missing
# Line 568  to do list for chap 7: Line 613  to do list for chap 7:
613  andrea  andrea
614    
615    
616  9. Model uses  9. Publications using MITgcm --> "Previous Applications of MITgcm"
617     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
618     (check in support for more names)     (check in support for more names)
619    
620    10. Under development
621    
622    
623    Bibliography
624    
625     tidy up from misc - .tex
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