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revision 1.41 by molod, Wed Jun 28 17:21:21 2006 UTC revision 1.50 by cnh, Thu Jan 17 17:35:59 2008 UTC
# Line 26  Editors Line 26  Editors
26    
27   Biblio        - EH3   Biblio        - EH3
28    
29    
30  Rebuild and set to do cron build - DONE on hugo  Rebuild and set to do cron build - DONE on hugo
31    
32  To do  To do
# Line 42  To do Line 43  To do
43    
44  o HTML, scripts and front content  o HTML, scripts and front content
45    
46    - pick a URL    - pick a URL:  mitgcm.org/r2  <-- EH3's preferred base URL
     TBD  
47    
48    - mitgcm.org/r2_web_testing/latest    - mitgcm.org/r2_web_testing/latest
49      o add another short-cut for quick download      
50        o --DONE--  add another short-cut for quick download
51    
52        o --DONE--  add another short-cut
53                      About
54                      Installation
55                      Contents
56                      Overview
57                      Tutorials (broken)
58                      Browse Code
59    
60        o --DONE--  words on http://mitgcm.org/r2_web_testing/latest change to
61    
62        o --DONE--  finite-volume doesn't leap to FV figure
63    
64        o -- DONE ??? --  have another go at pnmcrop et al.
65    
66      o add another short-cut           I've tried making a small change in latex2html which fixes
67        About           the oddball-lower-alignment issue that we were seeing with
68        Installation           most in-line expressions (that is, math embedded in text).
69        Contents           The fix results in some things being slightly raised but I
70        Overview           thin this is more asthetically pleasing than being somewhat
71        Tutorials (broken)           lowered as before. --EH3
       Browse Code  
   
     o words on http://mitgcm.org/r2_web_testing/latest  
       change to  
        "access on-line Auser manual/A and Atable of contents/A  
         and browse the Aoverview section/A"  
72    
73      o finite-volume doesn't leap to FV figure           To view the altered alignment, see:
74    
75      o have another go at pnmcrop et al.              http://eddy.csail.mit.edu/r2/latest/
76    
77      o Need an empty package as part of distribution. Check out atm_common      o Need an empty package as part of distribution. Check out atm_common
78    
79    
80  o Latex    o Latex  
81    
82      Chapter 1                 - CNH      Chapter 1                 - CNH
# Line 255  in content: Horizontal Dissipation: 2 ti Line 265  in content: Horizontal Dissipation: 2 ti
265  >> evaluated explicitly in time  >> evaluated explicitly in time
266  <- Leave it general.  <- Leave it general.
267    
268     o Time-stepping outline
269       - what gets called when
270    
271    
272  2.2 rigid-lid:  2.2 rigid-lid:
273    
274  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"  - At some point, would be better to replace "g \eta" with "\Phi_s (cg2d_x)"
275    to stay closer to the code.    to stay closer to the code.
276  - mention section 2.5 implicit-Time-stepping (for vertical viscosity)  - mention section 2.5 implicit-Time-stepping (for vertical viscosity) <- DONE
277    
278  2.3 linear free-surface:  2.3 linear free-surface:
279  - add ref(+link) to S/R names:  - add ref(+link) to S/R names:
280  - add ref(+link) to Crank-Nickelson section 2.9.1  - add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE
281    
282  2.4 Adams-Bashforth  2.4 Adams-Bashforth
283  - add stability diagrams (I have some figures that I can put)  - add stability diagrams (I have some figures that I can put) <- DONE
284  - add link for var. forcing_In_AB  - add link for var. forcing_In_AB and epsil_AB <- half DONE
285  - add S/R link for S/R ADAMS_BASHFORTH2  - add S/R link for S/R ADAMS_BASHFORTH2 <-DONE
286    
287  2.5 Implicit time-stepping  2.5 Implicit time-stepping
288  - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R  - add name of S/R: IMPLDIFF, GAD_IMPLICIT_R, MOM_U_IMPLICIT_R
# Line 391  Chapter 3 Line 404  Chapter 3
404    
405  Almost all of the 'math mode' text is dropped down as subscripts  Almost all of the 'math mode' text is dropped down as subscripts
406    
407  3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript  3.11.3.1 - refers to figures and equations, links are broken
      - is this experiment in the list from section 3.4???  
 3.10.3.1 - refers to figures and equations, links are broken  
408    
409  3.11.3.2 - line 43: link to equation is broken  3.12.3.2 - line 43: link to equation is broken
410           - line 51-53: link to equation is broken           - line 51-53: link to equation is broken
411           - there is some mess of text hanging around the end of this section. remove? reformat?           - there is some mess of text hanging around the end of this section. remove? reformat?
412    
413  3.12.4.1 - line 34 - link to equation is broken  3.13.4.1 - line 34 - link to equation is broken
414           - lines 60,61 - 1st (take out the 'r' in the superscript)           - lines 60,61 - 1st (take out the 'r' in the superscript)
415    
416  3.13.2 - link to theta-equation is broken  3.14.2 - link to theta-equation is broken
417  3.13.5.4 -- ALL of the bold links to variable names are broken  3.14.5.4 -- ALL of the bold links to variable names are broken
418              line 34: link to equation is broken              line 34: link to equation is broken
419    
420  3.15.1 - reference to 'fourth experiment' should be removed   o Update basic intro with one and four layer gyres
421       - include advection options
422       - conservation analysis
423       - diagnostics
424    
425  3.16.4 - strange formatting, presence of '>' symbols - remove them   o Four degree adjoint
426       - both TAF and OpenAD based.
427    
428  3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4   o Coupled with biogeo setup
429  3.17.3.1 - nothing filled in under file input/data - needs description     - based on CCGS setup
430    
 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.  
   
 Which of the following are which tutorial?  
 adjustment.128x64x1  
 adjustment.cs-32x32x1  
 advect_cs  
 advect_xy  
 advect_xz  
 aim.5l_cs  
 aim.5l_Equatorial_Channel  
 aim.5l_LatLon  
 biogeo  
 bottom_ctrl_5x5  
 cfc_example  
 cpl_aim+ocn  
 dome  
 exp2  
 exp4  
 exp5  
 fizhi-cs-32x32x10  
 fizhi-cs-aqualev20  
 fizhi-gridalt-hs  
 flt_example  
 front_relax  
 global1x1_tot  
 global2x2_tot  
 global_ocean.90x40x15  
 global_ocean.cs32x15  
 global_ocean.cubed32x32x30  
 global_ocean_ebm  
 global_with_exf  
 hs94.128x64x5  
 hs94.1x64x5  
 hs94.cs-32x32x5  
 ideal_2D_oce  
 internal_wave  
 inverted_barometer  
 lab_sea  
 matrix_example  
 MLAdjust  
 natl_box  
 natl_box_adjoint  
 OpenAD  
 rotating_tank  
 solid-body.cs-32x32x1  
 tidal_basin_2d  
 tutorial_baroclinic_gyre  
 tutorial_barotropic_gyre  
 tutorial_cfc_offline  
 tutorial_deep_convection  
 tutorial_global_oce_biogeo  
 tutorial_global_oce_in_p  
 tutorial_global_oce_latlon  
 tutorial_global_oce_optim  
 tutorial_held_suarez_cs  
 tutorial_offline  
 tutorial_plume_on_slope  
 tutorial_tracer_adjsens  
 vermix  
431    
432  >>>> From Ed  >>>> From Ed
433    
# Line 504  Add more to quick links on front page Line 451  Add more to quick links on front page
451    
452  Chapter 6  Chapter 6
453    
454     the master package diagram does not appear in the document     update organigramme
455        - include rbcs
456        (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
457    
458  Master list of packages (add this to beginning of chap 6)  Master list of packages (add this to beginning of chap 6)
459     (<- needs an update: e.g. atm2d, salt_plume, shelfice ...)
460    
461  admtlm/               - autodiff (chapter 5)  admtlm/               - autodiff (chapter 5)
462  aim/                  - retired  aim/                  - retired
# Line 533  embed_files/          - add something to Line 483  embed_files/          - add something to
483  exch2/                - 6.2.2  exch2/                - 6.2.2
484  exf/                  - 6.3.4  exf/                  - 6.3.4
485  fizhi/                - 6.4.3  fizhi/                - 6.4.3
486     o Including FIZHI doc
487       - get things up to date
488  flt/                  - (PH check)  flt/                  - (PH check)
489  gchem/                - 6.7.1  gchem/                - 6.7.1
490  generic_advdiff/      - in chapter 2 (JM check)  generic_advdiff/      - in chapter 2 (JM check)
# Line 578  thsice/               - 6.5.1 (JM to upd Line 530  thsice/               - 6.5.1 (JM to upd
530  timeave/              - retiring......  timeave/              - retiring......
531  zonal_filt/           - chapter 2 (JM to check)  zonal_filt/           - chapter 2 (JM to check)
532    
533     o Cost function packages
534       - floats, weights, profiles etc...
535    
536    
537  list an expeiment which uses package? CNH  list an expeiment which uses package? CNH
538    
539  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997
# Line 586  list an expeiment which uses package? CN Line 542  list an expeiment which uses package? CN
542    
543  =====  Chapter 7  =====  [EH3 editing] :  =====  Chapter 7  =====  [EH3 editing] :
544    
545  7.1.x - JMC: please add description of:   + JMC: please add description of:
546          - diagstat          - diagstat
547          - new temporal averaging feature          - new temporal averaging feature
548    
549  7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel)   + update the RW / MDSIO description
550       -> new meta file
551       -> list all RW S/R that one should use instead of calling directly MDSIO
552    
553     + add Graphix to the list of stuff in utils/matlab (Daniel)
554    
555     + get bathymetry pre-processing stuff from Patrick and then describe it
556    
557  7.5.2 - get bathymetry pre-processing stuff from Patrick   + add something on spgrid mesh generator
558          and then describe it   o Grid generation
559       - more explanation and some step-by-step examples
560       - plotting grid examples
561    
562  add something on spgrid mesh generator (maybe)?  
563     + add in gmaze PV calculation scripts plus write up on how it is calculated
564         http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
565    
566    
567  andrea  andrea
# Line 608  andrea Line 574  andrea
574  10. Under development  10. Under development
575    
576  Constantinos LCML  Constantinos LCML
577     o Legend/LCML examples and explanation
578       - examples and explanation!
579    
580    
581    
582  Bibliography  Bibliography
583    
584   tidy up from misc - .tex   tidy up from misc - .tex
585    
586    Also
587    
588    a link to the new manual
589    should appear on the front page (even if it's under construction).
590    
591    updating:
592    http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html
593    which points to a 1.5 years old code. Would be good to generate a
594    new one, and even better, to try to keep it up-to-date.
595    
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