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revision 1.9 by cnh, Thu Apr 6 19:54:06 2006 UTC revision 1.11 by cnh, Thu Apr 6 20:04:27 2006 UTC
# Line 207  o Latex Line 207  o Latex
207            o Gas giant?            o Gas giant?
208    
209    
 Master list of packages  
   
 admtlm/               - autodiff (chapter 5)  
 aim/                  - 6.4.1 (content needs fixing - JM to do)  
 aim_compon_interf/    - 6.6 (no content yet)  
 aim_ocn_coupler/      - 6.6 (no content yet)  
 aim_v23/              - retired  
 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  
   
   
 >>>> From Ed  
   
 Here are the remaining bits for Chap 4 :  
   
  - 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.  
   
  - 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)  
   
   
 >>>> 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  
   
   
 andrea  
   
 >>>> From Andrea  
   
 Chapter 3  
 --------  
   
 Almost all of the 'math mode' text is dropped down as subscripts  
   
 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?)  
   
 3.1 - don't need a link to the outside of the document (remove it)  
     - link to htdig is broken  
   
 3.2.1 - link at bottom to source code points to section 3.2.1  
    (ie, to itself) - link should point to cvs code archive  
   
 3.2.2.1  - ('upgrading from an earlier version') belongs under  
       the cvs part, ie, should be 3.2.1.1  
   
 3.3 - remove reference to 'diags' section under MITgcm  
     - remove reference to 'exe' and 'bin' sections also  
       (remove the .cvsignore file under these directories in cvs)  
     - add a 'jobs' section, and a description as examples of run scripts  
     - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions  
     - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'  
     - under 'tools' the adjoint points to section 5 - this is now section 8  
       (but should be a floating reference)  
     - under 'utils' add a reference to exch2 - stuff for different resolutions  
     - the description of the pkg section refers directly to  
       section 3. should be section 6 (actually should be a floating reference)  
   
 3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)  
 3.4.1 - links to the following experiments don't exist or are broken:  
           exp2 - should link to section 3.9  
           hs94.cs-32x32x5 - link to section 3.12  
           add 'convection' to the list, link to section 3.13  
           add 'plume on slope` to the list, link to section 3.14  
           add '??' link to section 3.15  
           add 'dic_example on slope` to the list, link to section 3.16  
           add '??' link to section 3.17  
           add 'offline' and link to section 3.18  
           clean up others and make links where they are needed  
 3.4.2 - text suggests to see section 2 for details about what is in the 'code'  
         and 'input' directories - should refer to the examples in this section  
       - add 'build' bullet - this is where the model is compiled and exectuable lives  
   
 3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options  
       as the place where they live (add a link?)  
   
 3.6.1 - Add some general 'approach' text - ie, output is controlled either by the  
         'data' file in the input directory or by the data.[pkg name] file for any  
         package running. And there is some default behavior when the 'state' dumps  
         are written.  
 3.6.1.2 - needs to be moved to inside section 3.6.2  
   
 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  
   
 All the 'overview' sections need some reference to the name of the experiment in  
 the verification directory  
   
 3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript  
      - is this experiment in the list from section 3.4???  
 3.10.3.1 - refers to figures and equations, links are broken  
   
 3.11.3.2 - line 43: link to equation is broken  
          - line 51-53: link to equation is broken  
          - there is some mess of text hanging around the end of this section. remove? reformat?  
   
 3.12.4.1 - line 34 - link to equation is broken  
          - lines 60,61 - 1st (take out the 'r' in the superscript)  
   
 3.13.2 - link to theta-equation is broken  
 3.13.5.4 -- ALL of the bold links to variable names are broken  
             line 34: link to equation is broken  
   
 3.15.1 - reference to 'fourth experiment' should be removed  
   
 3.16.4 - strange formatting, presence of '>' symbols - remove them  
   
 3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4  
 3.17.3.1 - nothing filled in under file input/data - needs description  
   
 3.18.2 - point to section 2 for details - need hyperlink  
   
 3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!  
          section 3.5 has the 'build' directory in the example  
   
 3.20.1 - link to doc at end of section points to this section  
 3.20.2 - link to doc at end of section points to this section  
   
      offline - duplicate inputs, what is it, tidy up cfc v.  
                other offline. JM thinks these need tidying up.  
   
210  >>>> from JM  >>>> from JM
211    
212    
   
213  manual, section.2 :  manual, section.2 :
214    
215  In general:  In general:
# Line 569  in content: Horizontal Dissipation: 2 ti Line 353  in content: Horizontal Dissipation: 2 ti
353  JM  JM
354    
355    
356    >>>> From Andrea
357    
358    Chapter 3
359    --------
360    
361    Almost all of the 'math mode' text is dropped down as subscripts
362    
363    divide chapter 3 more clearly into 2 sections?
364       (ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and
365        then 3.19 and 3.20 are informational again - rearrange subsections?)
366    
367    3.1 - don't need a link to the outside of the document (remove it)
368        - link to htdig is broken
369    
370    3.2.1 - link at bottom to source code points to section 3.2.1
371       (ie, to itself) - link should point to cvs code archive
372    
373    3.2.2.1  - ('upgrading from an earlier version') belongs under
374          the cvs part, ie, should be 3.2.1.1
375    
376    3.3 - remove reference to 'diags' section under MITgcm
377        - remove reference to 'exe' and 'bin' sections also
378          (remove the .cvsignore file under these directories in cvs)
379        - add a 'jobs' section, and a description as examples of run scripts
380        - add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions
381        - under 'tools' add a reference to 'build_options'. refer to the 'optfiles'
382        - under 'tools' the adjoint points to section 5 - this is now section 8
383          (but should be a floating reference)
384        - under 'utils' add a reference to exch2 - stuff for different resolutions
385        - the description of the pkg section refers directly to
386          section 3. should be section 6 (actually should be a floating reference)
387    
388    3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10)
389    3.4.1 - links to the following experiments don't exist or are broken:
390              exp2 - should link to section 3.9
391              hs94.cs-32x32x5 - link to section 3.12
392              add 'convection' to the list, link to section 3.13
393              add 'plume on slope` to the list, link to section 3.14
394              add '??' link to section 3.15
395              add 'dic_example on slope` to the list, link to section 3.16
396              add '??' link to section 3.17
397              add 'offline' and link to section 3.18
398              clean up others and make links where they are needed
399    3.4.2 - text suggests to see section 2 for details about what is in the 'code'
400            and 'input' directories - should refer to the examples in this section
401          - add 'build' bullet - this is where the model is compiled and exectuable lives
402    
403    3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options
404          as the place where they live (add a link?)
405    
406    3.6.1 - Add some general 'approach' text - ie, output is controlled either by the
407            'data' file in the input directory or by the data.[pkg name] file for any
408            package running. And there is some default behavior when the 'state' dumps
409            are written.
410    3.6.1.2 - needs to be moved to inside section 3.6.2
411    
412    3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18)
413          underneath this one and leave the text for 3.7 in place
414    
415    All the 'overview' sections need some reference to the name of the experiment in
416    the verification directory
417    
418    3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript
419         - is this experiment in the list from section 3.4???
420    3.10.3.1 - refers to figures and equations, links are broken
421    
422    3.11.3.2 - line 43: link to equation is broken
423             - line 51-53: link to equation is broken
424             - there is some mess of text hanging around the end of this section. remove? reformat?
425    
426    3.12.4.1 - line 34 - link to equation is broken
427             - lines 60,61 - 1st (take out the 'r' in the superscript)
428    
429    3.13.2 - link to theta-equation is broken
430    3.13.5.4 -- ALL of the bold links to variable names are broken
431                line 34: link to equation is broken
432    
433    3.15.1 - reference to 'fourth experiment' should be removed
434    
435    3.16.4 - strange formatting, presence of '>' symbols - remove them
436    
437    3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4
438    3.17.3.1 - nothing filled in under file input/data - needs description
439    
440    3.18.2 - point to section 2 for details - need hyperlink
441    
442    3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true!
443             section 3.5 has the 'build' directory in the example
444    
445    3.20.1 - link to doc at end of section points to this section
446    3.20.2 - link to doc at end of section points to this section
447    
448         offline - duplicate inputs, what is it, tidy up cfc v.
449                   other offline. JM thinks these need tidying up.
450    >>>> From Ed
451    
452    Here are the remaining bits for Chap 4 :
453    
454     - The grammar/flow could still use some work.  Boo was an English
455       major and has experience editing/proofing technical papers.  I
456       could print out a copy and ask her to read it and suggest
457       improvements.
458    
459     - missing references (if you point me towards URLs, I'll add them
460       to the bibliography):
461         \ref{ref hoe and hill, ecmwf}
462         \ref{magicgarden}
463         \ref{IBMLAPI}
464         \ref{Memorychannel}
465         \ref{hoe-hill:99}
466    
467     - There are a few empty sub-sections at the end of Chap 4 that
468       should either be commented out or fleshed out.
469    
470    and thats about it for Chap 4.
471    
472    
473    Add more to quick links on front page
474    
475    Chapter 6
476    
477       the master package diagram does not appear in the document
478    
479       pkg/ptracers doesn't seem to have any documentation (see packages list below)
480    
481    
482    Master list of packages (add this to beginning of chap 6)
483    
484    admtlm/               - autodiff (chapter 5)
485    aim/                  - retired
486    aim_compon_interf/    - 6.6 (no content yet)
487    aim_ocn_coupler/      - 6.6 (no content yet)
488    aim_v23/              - 6.4.1 (content needs fixing - JM to do)
489    atm_common/           - 6.6 (no content yet)
490    autodiff/             - autodiff (chapter 5)
491    bulk_force/           - 6.3.3
492    cal/                  - 6.3.5
493    cd_code/              - chapter 2 (JM check)
494    cfc/                  - not sure
495    chronos/              - AM to check
496    compon_communic/      - 6.6 (no content yet)
497    cost/                 - not sure, check with PH
498    ctrl/                 - not sure, check with PH
499    debug/                - JM may do something in chapter 7 (utilities)
500    diagnostics/          - 7.1
501    dic/                  - 6.7.2
502    ebm/                  - not sure
503    ecco/                 - chapter 8
504    embed_files/          - add something to chapter 7
505    ex3/                  - rename to exch3
506    exch2/                - 6.2.2
507    exf/                  - 6.3.4
508    fizhi/                - 6.4.3
509    flt/                  - in chapter 2 (JM check)
510    gchem/                - 6.7.1
511    generic_advdiff/      - in chapter 2 (JM check)
512    ggl90/                - nothing, (Martin?)
513    gmredi/               - in chapter 2 (JM check). also need
514                            Ferrari & Mc tapering
515    grdchk/               - grdchk (chapter 5 - check with PH)
516    gridalt/              - 6.2.4
517    kpp/                  - 6.3.2
518    land/                 - 6.4.2 (not connected to code - JM to fix)
519    matrix/               - Samar
520    mdsio/                - 7.3.1
521    mnc/                  - 7.2.1
522    mom_common/           - in chapter 2 (JM check)
523    mom_fluxform/         - in chapter 2 (JM check)
524    mom_vecinv/           - in chapter 2 (JM check)
525    monitor/              - 7.4
526    my82/                 - nothing, (martin?)
527    obcs/                 - 6.3 (needs a check)
528    ocn_compon_interf/    - 6.6 (no content yet)
529    offline/              - nothing, tutorials that need work but no package   section entry
530    opps/                 - nothing, (martin?)
531    pp81/                 - nothing, (martin?)
532    profiles/             - GAEL
533    ptracers/             - JM + SD to write something
534    rbcs/                 - talk to steph
535    runclock/             - runclock
536    rw/                   - not sure
537    sbo/                  - text in sbo_descruption.tex but not linked into
538                            part6
539    seaice/               - 6.5.2 - no equations, dimitris has promised some
540    shap_filt/            - chapter 2, JM to check
541    shelfice/             - nothing yet (martin?)
542    solver/               - empty
543    sphere/               - chapter 5 or 8 (PH to check)
544    therm_seaice/         - empty
545    thsice/               - 6.5.1 (JM to update?)
546    timeave/              - retiring......
547    zonal_filt/           - chapter 2 (JM to check)
548    
549    Possible for chap 7 - Daniels grafix/ stuff
550    
551    Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.
552    
553    Figure 6.8 is missing
554    
555    6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
556     Figure 6.8 is missing
557    
558    
559    >>>> From Andrea
560    
561    to do list for chap 7:
562    
563    
564    7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu"
565            the links are pointing to the proper place
566    
567    7.5.1 - add Graphix to the list of stuff in utils/matlab
568    7.5.2 - empty
569    
570    
571    andrea
572    
573    
574  9. Model uses  9. Model uses
575     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
576     (check in support for more names)     (check in support for more names)

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