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revision 1.21 by cnh, Thu Apr 6 20:51:30 2006 UTC revision 1.50 by cnh, Thu Jan 17 17:35:59 2008 UTC
# Line 1  Line 1 
1    Editors
2    
3     Overall       - JM, AM, PH, CNH, EH3
4    
5     Front content - EH3
6    
7     Chapter 1     - CNH
8    
9     Chapter 2     - JMC
10    
11     Chapter 3     -  AM
12    
13     Chapter 4     - CNH
14    
15     Chapter 5     -  PH
16    
17     Chapter 6     -  AM
18    
19     Chapter 7     - EH3
20    
21     Chapter 8     -  PH
22    
23     Chapter 9     - CNH (Applications)
24    
25     Chapter 10    - JMC (Under development chapter)
26    
27     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 8  To do Line 37  To do
37      Add an "Under development, chapter" - shortish description of what      Add an "Under development, chapter" - shortish description of what
38      is available (last chapter)      is available (last chapter)
39    
40      - add in example latex for formatting author names in different pieces.
41        this aknowledges peoples contributions and gives ref for who
42        to talk to.
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 add another short-cut      o --DONE--  words on http://mitgcm.org/r2_web_testing/latest change to
       About  
       Installation  
       Contents  
       Overview  
       Tutorials (broken)  
       Browse Code  
   
     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?  
   
     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"  
61    
62      o finite-volume doesn't leap to FV figure      o --DONE--  finite-volume doesn't leap to FV figure
63    
64      o have another go at pnmcrop et al.      o -- DONE ??? --  have another go at pnmcrop et al.
65    
66             I've tried making a small change in latex2html which fixes
67             the oddball-lower-alignment issue that we were seeing with
68             most in-line expressions (that is, math embedded in text).
69             The fix results in some things being slightly raised but I
70             thin this is more asthetically pleasing than being somewhat
71             lowered as before. --EH3
72    
73             To view the altered alignment, see:
74    
75                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 67  o Latex Line 98  o Latex
98    
99        o List of key papers needs to be updated and reformatted        o List of key papers needs to be updated and reformatted
100    
   
101        o Global atmosphere: `Held Suarez',        o Global atmosphere: `Held Suarez',
102          update Adcroft reference          update Adcroft reference
103          fix up ingrid link and frame (ingrid movies seem to be broken?)          fix up ingrid link and frame (ingrid movies seem to be broken?)
# Line 185  o Latex Line 215  o Latex
215            o coupled aqua, ridge world etc...            o coupled aqua, ridge world etc...
216              - links to ingrid output              - links to ingrid output
217                get stuff from Daniel                get stuff from Daniel
218                  Davids donut movie
219    
220            o constrained lab simulation            o constrained lab simulation
221              - links to ingrid output for model and lab              - links to ingrid output for model and lab
# Line 212  In general: Line 243  In general:
243  - would be nice to have an active link to the fortran-file  - would be nice to have an active link to the fortran-file
244    for all the S/R & eq.Number in the "calling-tree" boxes    for all the S/R & eq.Number in the "calling-tree" boxes
245  - search for CALC_MOM_RHS and replace it by the appropriate S/R  - search for CALC_MOM_RHS and replace it by the appropriate S/R
246    (mom_flux_form, mom_vecinv, dynamics)    (mom_flux_form, mom_vecinv, dynamics) <- DONE
247  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})  - Problem with notation: in section.1 \vec{\bf v_h} (or \vec{\mathbf{v}}_{h})
248  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}  was used for the horizontal velocity vector, and the 3.D vector was \vec{\mathbf{v}}
249  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is  in section.2, \vec{\bf v} is used instead and 3.D velocity vector is
# Line 223  at the beginning of section.2 and to men Line 254  at the beginning of section.2 and to men
254  the 2 sections.  the 2 sections.
255    
256  in content: Horizontal Dissipation: 2 times in vector-invariant section  in content: Horizontal Dissipation: 2 times in vector-invariant section
257    <- DONE
258    
259  2.1 time-stepping (part2/time_stepping.tex)  2.1 time-stepping (part2/time_stepping.tex)
260    
# Line 231  in content: Horizontal Dissipation: 2 ti Line 263  in content: Horizontal Dissipation: 2 ti
263  >> In all the above configurations it is also possible to substitute the  >> In all the above configurations it is also possible to substitute the
264  >> Adams-Bashforth with an alternative time-stepping scheme for terms  >> Adams-Bashforth with an alternative time-stepping scheme for terms
265  >> evaluated explicitly in time  >> evaluated explicitly in time
266    <- 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 264  in content: Horizontal Dissipation: 2 ti Line 300  in content: Horizontal Dissipation: 2 ti
300  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D  - add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D
301    
302  2.9 Variants on Free-Surface  2.9 Variants on Free-Surface
303  - Delta.t mis-written (eq.2.73)  - Delta.t mis-written (eq.2.73) <- DONE
304  - Eq.Num missing (has been fixed since)  - Eq.Num missing <- DONE
305  - u* is stored in gU (and not in gUnm1)  - u* is stored in gU (and not in gUnm1) <- DONE
306  - Phi_nh in NH_VARS.h  - Phi_nh in NH_VARS.h <- DONE
307  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,  - add link to S/R file: SOLVE_FOR_PRESSURE, CALC_DIV_GHAT, CG2D, CG3D,
308    INI_CG2D, INI_CG3D    INI_CG2D, INI_CG3D
309    
# Line 277  in content: Horizontal Dissipation: 2 ti Line 313  in content: Horizontal Dissipation: 2 ti
313  2.9.2 NLFS  2.9.2 NLFS
314  - eq.Nb are wrong in html  - eq.Nb are wrong in html
315  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)  - 2.9.2.4 : set of eq. appears wrong in html (but right in .dvi)
316     <- DONE
317    
318  2.10.1 Notation  2.10.1 Notation
319  - Area definition is not really used like this  - Area definition is not really used like this
# Line 285  in content: Horizontal Dissipation: 2 ti Line 322  in content: Horizontal Dissipation: 2 ti
322    
323    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to    Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to
324    the model variables) are used (e.g., see section 2.10.5)    the model variables) are used (e.g., see section 2.10.5)
325    <- DONE
326    
327  2.10.5 Horizontal grid:  2.10.5 Horizontal grid:
328  - fig.2.8 : should use Aw,As consistently in this figure description,  - fig.2.8 : should use Aw,As consistently in this figure description,
329    in the figure itself, as it is in the text.    in the figure itself, as it is in the text. <- DONE
330  - curvilinear:  - curvilinear:
331    to add: mention the angle of the grid direction relative to    to add: mention the angle of the grid direction relative to
332    Eastward, Northward direction.    Eastward, Northward direction.
# Line 339  in content: Horizontal Dissipation: 2 ti Line 377  in content: Horizontal Dissipation: 2 ti
377    
378  2.16 & 2.17 & 2.18 :  2.16 & 2.17 & 2.18 :
379   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options   - add 1rst Order upwind option & DST-2 (Lax-Wendroff) options
380     - fix equations 2.202 & 2.203 (thanks to Martin) <- DONE
381    
382  2.20.2 mercator, non-dimensional Equations:  2.20.2 mercator, non-dimensional Equations:
383  - does not use std notation  - does not use std notation
# Line 346  in content: Horizontal Dissipation: 2 ti Line 385  in content: Horizontal Dissipation: 2 ti
385  (e.g changing the tile to:  (e.g changing the tile to:
386  - talk to Baylor  - talk to Baylor
387   Appendix: non-dimensional Equations on Spherical-Polar grid.)   Appendix: non-dimensional Equations on Spherical-Polar grid.)
388     <- No (Chris said)
389    
390    
391    Diagrams of grid locations etc.... and what variables and output files
392    and/or netcdf variable names are not very easy to figure out and follow.
393    It would be good to redo and extend these diagrams and align with GRID.h
394    content.
395    
396    
397  JM  JM
# Line 358  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  divide chapter 3 more clearly into 2 sections?  3.11.3.1 - refers to figures and equations, links are broken
    (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?)  
 [DONE]  
   
 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  
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?  
 ! MLAdjust  
 adjust_nlfs.cs-32x32x1  
 aim.5l_XZ_Equatorial_Slice  
 biogeo  
 aim.5l_zon-ave  
 coupled_ucla  
 cfc_offline  
 exp3  
 global2x2_tot  
 global1x1_tot  
 global_ocean.cubed_wEXF  
 global_with_CFC11  
 goz  
 gop  
 natl_box_obcs  
 natl_box_forward  
 spinup_optim  
 tutorial_held_suarez_cs  
 vero  
 inverted_barometer  
 global_ocean.cubed32x32x30  
 exp1  
 advect_cs  
 dic_example  
 fizhi-gridalt-hs  
 global_ocean_pressure  
 matrix_example  
 exp4  
 solid-body.cs-32x32x1  
 cfc_example  
 flt_example  
 adjustment.cs-32x32x1  
 advect_xz  
 rotating_tank  
 ideal_2D_oce  
 global_ocean.90x40x15  
 front_relax  
 aim.5l_LatLon  
 lab_sea  
 hs94.cs-32x32x5  
 global_with_exf  
 exp2  
 tidal_basin_2d  
 fizhi-cs-32x32x10  
 exp5  
 global_ocean.cs32x15  
 OpenAD  
 hs94.1x64x5  
 fizhi-cs-aqualev10  
 exp0  
 dome  
 aim.5l_Equatorial_Channel  
 aim.5l_cs  
 hs94.128x64x5  
 prm  
 carbon  
 plume_on_slope  
 natl_box_adjoint  
 vermix  
 cpl_aim+ocn  
 global_ocean_ebm  
 internal_wave  
 advect_xy  
 natl_box  
 adjustment.128x64x1  
431    
432  >>>> From Ed  >>>> From Ed
433    
# Line 536  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 565  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 597  ptracers/             - JM + SD + Martin Line 517  ptracers/             - JM + SD + Martin
517  rbcs/                 - CNH to talk to steph  rbcs/                 - CNH to talk to steph
518  runclock/             - runclock - CNH  runclock/             - runclock - CNH
519  rw/                   - not sure - going to stay says JMC. quick IO calls  rw/                   - not sure - going to stay says JMC. quick IO calls
520                            JMC to write a quick note for that.
521  sbo/                  - text in sbo_descruption.tex but not linked into  sbo/                  - text in sbo_descruption.tex but not linked into
522                          part6                          part6 - CNH
523  seaice/               - 6.5.2 - no equations, dimitris has promised some  seaice/               - 6.5.2 - no equations, dimitris has promised some
524  shap_filt/            - chapter 2, JM to check  shap_filt/            - chapter 2, JM to check
525  shelfice/             - nothing yet (martin?)  shelfice/             - nothing yet (martin?)
526  solver/               - empty  solver/               - empty (go away?)
527  sphere/               - chapter 5 or 8 (PH to check)  sphere/               - chapter 5 or 8 (PH to check)
528  therm_seaice/         - empty  therm_seaice/         - empty (go away?)
529  thsice/               - 6.5.1 (JM to update?)  thsice/               - 6.5.1 (JM to update?)
530  timeave/              - retiring......  timeave/              - retiring......
531  zonal_filt/           - chapter 2 (JM to check)  zonal_filt/           - chapter 2 (JM to check)
532    
533  list an expeiment which uses package? CNH   o Cost function packages
534       - floats, weights, profiles etc...
 Possible for chap 7 - Daniels grafix/ stuff  
535    
 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started.  
536    
537  Figure 6.8 is missing  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
540   Figure 6.8 is missing   Figure 6.8 is missing
541    
542    
543  >>>> From Andrea  =====  Chapter 7  =====  [EH3 editing] :
544    
545     + JMC: please add description of:
546            - diagstat
547            - new temporal averaging feature
548    
549     + 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  to do list for chap 7:   + get bathymetry pre-processing stuff from Patrick and then describe it
556    
557     + add something on spgrid mesh generator
558     o Grid generation
559       - more explanation and some step-by-step examples
560       - plotting grid examples
561    
 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  
562    
563  7.5.1 - add Graphix to the list of stuff in utils/matlab   + add in gmaze PV calculation scripts plus write up on how it is calculated
564  7.5.2 - empty       http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/
565    
566    
567  andrea  andrea
568    
569    
570  9. Model uses  9. Publications using MITgcm --> "Previous Applications of MITgcm"
571     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...     Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc...
572     (check in support for more names)     (check in support for more names)
573    
574    10. Under development
575    
576    Constantinos LCML
577     o Legend/LCML examples and explanation
578       - examples and explanation!
579    
580    
581    
582    Bibliography
583    
584     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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