/[MITgcm]/manual/manual_todo.txt
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revision 1.13 by cnh, Thu Apr 6 20:13:23 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 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 365  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 449  the verification directory Line 446  the verification directory
446    
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  >>>> From Ed
518    
519  Here are the remaining bits for Chap 4 :  Here are the remaining bits for Chap 4 :
520    
  - 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.  
   
521   - missing references (if you point me towards URLs, I'll add them   - missing references (if you point me towards URLs, I'll add them
522     to the bibliography):     to the bibliography):
523       \ref{ref hoe and hill, ecmwf}       \ref{ref hoe and hill, ecmwf}
# Line 478  Chapter 6 Line 538  Chapter 6
538    
539     the master package diagram does not appear in the document     the master package diagram does not appear in the document
540    
    pkg/ptracers doesn't seem to have any documentation (see packages list below)  
   
   
541  Master list of packages (add this to beginning of chap 6)  Master list of packages (add this to beginning of chap 6)
542    
543  admtlm/               - autodiff (chapter 5)  admtlm/               - autodiff (chapter 5)
544  aim/                  - retired  aim/                  - retired
545  aim_compon_interf/    - 6.6 (no content yet)  aim_compon_interf/    - 6.6 (no content yet)(Daniel + JM)
546  aim_ocn_coupler/      - 6.6 (no content yet)  aim_ocn_coupler/      - 6.6 (no content yet)
547  aim_v23/              - 6.4.1 (content needs fixing - JM to do)  aim_v23/              - 6.4.1 (content needs fixing - JM to do)
548  atm_common/           - 6.6 (no content yet)  atm_common/           - nothing in this package (6.4.1 related)
549  autodiff/             - autodiff (chapter 5)  autodiff/             - autodiff (chapter 5)
550  bulk_force/           - 6.3.3  bulk_force/           - 6.3.3
551  cal/                  - 6.3.5  cal/                  - 6.3.5
552  cd_code/              - chapter 2 (JM check)  cd_code/              - chapter 2 (JM check add a reference to paper,
553  cfc/                  - not sure                            mention parameter in data)
554  chronos/              - AM to check  cfc/                  - not sure  (CNH to talk to Steph and Helen)
555  compon_communic/      - 6.6 (no content yet)  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  cost/                 - not sure, check with PH
558  ctrl/                 - not sure, check with PH  ctrl/                 - not sure, check with PH
559  debug/                - JM may do something in chapter 7 (utilities)  debug/                - JM may do something in chapter 7 (utilities)
560  diagnostics/          - 7.1  diagnostics/          - 7.1
561  dic/                  - 6.7.2  dic/                  - 6.7.2
562  ebm/                  - not sure  ebm/                  - (check with PH)
563  ecco/                 - chapter 8  ecco/                 - chapter 8
564  embed_files/          - add something to chapter 7  embed_files/          - add something to chapter 7
 ex3/                  - rename to exch3  
565  exch2/                - 6.2.2  exch2/                - 6.2.2
566  exf/                  - 6.3.4  exf/                  - 6.3.4
567  fizhi/                - 6.4.3  fizhi/                - 6.4.3
568  flt/                  - in chapter 2 (JM check)  flt/                  - (PH check)
569  gchem/                - 6.7.1  gchem/                - 6.7.1
570  generic_advdiff/      - in chapter 2 (JM check)  generic_advdiff/      - in chapter 2 (JM check)
571  ggl90/                - nothing, (Martin?)  ggl90/                - nothing, (Martin?)
572  gmredi/               - in chapter 2 (JM check). also need  gmredi/               - in chapter 2 (JM check). also need
573                          Ferrari & Mc tapering                          Ferrari & Mc transition zone stuff (Samar doing this)
574                            get dfer to read this
575  grdchk/               - grdchk (chapter 5 - check with PH)  grdchk/               - grdchk (chapter 5 - check with PH)
576  gridalt/              - 6.2.4  gridalt/              - 6.2.4
577  kpp/                  - 6.3.2  kpp/                  - 6.3.2
578  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)
579  matrix/               - Samar  matrix/               - Samar
580  mdsio/                - 7.3.1  mdsio/                - 7.3.1
581  mnc/                  - 7.2.1  mnc/                  - 7.2.1
# Line 526  mom_fluxform/         - in chapter 2 (JM Line 584  mom_fluxform/         - in chapter 2 (JM
584  mom_vecinv/           - in chapter 2 (JM check)  mom_vecinv/           - in chapter 2 (JM check)
585  monitor/              - 7.4  monitor/              - 7.4
586  my82/                 - nothing, (martin?)  my82/                 - nothing, (martin?)
587  obcs/                 - 6.3 (needs a check)  obcs/                 - 6.3 (needs a check - ask PH to read)
588  ocn_compon_interf/    - 6.6 (no content yet)  ocn_compon_interf/    - 6.6 (no content yet)
589  offline/              - nothing, tutorials that need work but no package   section entry  offline/              - nothing, tutorials that need work but no package   section entry
590                            trivial to document (CNH to do)
591  opps/                 - nothing, (martin?)  opps/                 - nothing, (martin?)
592  pp81/                 - nothing, (martin?)  pp81/                 - nothing, (martin?)
593  profiles/             - GAEL  profiles/             - GAEL
594  ptracers/             - JM + SD to write something  ptracers/             - JM + SD + Martin to write something (nothing for this
595  rbcs/                 - talk to steph                            at the moment)
596  runclock/             - runclock                          AM has diagnostics table for this.
597  rw/                   - not sure  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  sbo/                  - text in sbo_descruption.tex but not linked into
602                          part6                          part6 - CNH
603  seaice/               - 6.5.2 - no equations, dimitris has promised some  seaice/               - 6.5.2 - no equations, dimitris has promised some
604  shap_filt/            - chapter 2, JM to check  shap_filt/            - chapter 2, JM to check
605  shelfice/             - nothing yet (martin?)  shelfice/             - nothing yet (martin?)
606  solver/               - empty  solver/               - empty (go away?)
607  sphere/               - chapter 5 or 8 (PH to check)  sphere/               - chapter 5 or 8 (PH to check)
608  therm_seaice/         - empty  therm_seaice/         - empty (go away?)
609  thsice/               - 6.5.1 (JM to update?)  thsice/               - 6.5.1 (JM to update?)
610  timeave/              - retiring......  timeave/              - retiring......
611  zonal_filt/           - chapter 2 (JM to check)  zonal_filt/           - chapter 2 (JM to check)
612    
613  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.  
614    
615  Figure 6.8 is missing  [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  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
618   Figure 6.8 is missing   Figure 6.8 is missing

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