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Editors |
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Overall - JM, AM, PH, CNH, EH3 |
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Front content - EH3 |
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Chapter 1 - CNH |
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Chapter 2 - JMC |
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Chapter 3 - AM |
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Chapter 4 - CNH |
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Chapter 5 - PH |
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Chapter 6 - AM |
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Chapter 7 - EH3 |
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Chapter 8 - PH |
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Chapter 9 - CNH (Applications) |
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Chapter 10 - JMC (Under development chapter) |
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27 |
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Biblio - EH3 |
28 |
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29 |
Rebuild and set to do cron build - DONE on hugo |
Rebuild and set to do cron build - DONE on hugo |
30 |
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31 |
To do |
To do |
36 |
Add an "Under development, chapter" - shortish description of what |
Add an "Under development, chapter" - shortish description of what |
37 |
is available (last chapter) |
is available (last chapter) |
38 |
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39 |
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- add in example latex for formatting author names in different pieces. |
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this aknowledges peoples contributions and gives ref for who |
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to talk to. |
42 |
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43 |
o HTML, scripts and front content |
o HTML, scripts and front content |
44 |
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45 |
- pick a URL |
- pick a URL |
46 |
TBD |
TBD |
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- mitgcm.org very front page. |
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o too many clicks to get to model manual. |
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make doc link go to mitgcm.org/r2_web_testing/latest |
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and add "HowTo" reference etc... to /latest page |
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48 |
- mitgcm.org/r2_web_testing/latest |
- mitgcm.org/r2_web_testing/latest |
49 |
o add another short-cut for quick download |
o add another short-cut for quick download |
50 |
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56 |
Tutorials (broken) |
Tutorials (broken) |
57 |
Browse Code |
Browse Code |
58 |
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o mitgcm.org (front content) [DONE] |
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Get Code (where does this go to?) |
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get rid of * CVS current bullet |
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make HTML-enabled CVS code browser leap to MITgcm/MITgcm |
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o authors |
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John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, |
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Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, |
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Gael - others? |
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59 |
o words on http://mitgcm.org/r2_web_testing/latest |
o words on http://mitgcm.org/r2_web_testing/latest |
60 |
change to |
change to |
61 |
"access on-line Auser manual/A and Atable of contents/A |
"access on-line Auser manual/A and Atable of contents/A |
88 |
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89 |
o List of key papers needs to be updated and reformatted |
o List of key papers needs to be updated and reformatted |
90 |
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91 |
o Global atmosphere: `Held Suarez', |
o Global atmosphere: `Held Suarez', |
92 |
update Adcroft reference |
update Adcroft reference |
93 |
fix up ingrid link and frame (ingrid movies seem to be broken?) |
fix up ingrid link and frame (ingrid movies seem to be broken?) |
313 |
to add: mention the angle of the grid direction relative to |
to add: mention the angle of the grid direction relative to |
314 |
Eastward, Northward direction. |
Eastward, Northward direction. |
315 |
+ mention horizGridFile= in file "data" (PARM04) |
+ mention horizGridFile= in file "data" (PARM04) |
316 |
- add cylindrical grid description |
- add cylindrical polar grid description |
317 |
need to do a better job of relating model variables to this diagram |
need to do a better job of relating model variables to this diagram |
318 |
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319 |
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340 |
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 |
341 |
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 |
342 |
scaling (not cos()2) |
scaling (not cos()2) |
343 |
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- need to reference the smag/leith section. |
344 |
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345 |
2.13.6 Vertical dissipation |
2.13.6 Vertical dissipation |
346 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
359 |
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360 |
2.16 & 2.17 & 2.18 : |
2.16 & 2.17 & 2.18 : |
361 |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
362 |
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- fix equations 2.202 & 2.203 (thanks to Martin) |
363 |
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364 |
2.20.2 mercator, non-dimensional Equations: |
2.20.2 mercator, non-dimensional Equations: |
365 |
- does not use std notation |
- does not use std notation |
367 |
(e.g changing the tile to: |
(e.g changing the tile to: |
368 |
- talk to Baylor |
- talk to Baylor |
369 |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
370 |
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371 |
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372 |
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Diagrams of grid locations etc.... and what variables and output files |
373 |
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and/or netcdf variable names are not very easy to figure out and follow. |
374 |
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It would be good to redo and extend these diagrams and align with GRID.h |
375 |
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content. |
376 |
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377 |
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378 |
JM |
JM |
385 |
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386 |
Almost all of the 'math mode' text is dropped down as subscripts |
Almost all of the 'math mode' text is dropped down as subscripts |
387 |
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divide chapter 3 more clearly into 2 sections? |
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(ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |
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then 3.19 and 3.20 are informational again - rearrange subsections?) |
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388 |
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) |
389 |
- link to htdig is broken |
- link to htdig is broken |
390 |
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430 |
are written. |
are written. |
431 |
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 |
432 |
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3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |
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underneath this one and leave the text for 3.7 in place |
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433 |
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 |
434 |
the verification directory |
the verification directory |
435 |
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465 |
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466 |
offline - duplicate inputs, what is it, tidy up cfc v. |
offline - duplicate inputs, what is it, tidy up cfc v. |
467 |
other offline. JM thinks these need tidying up. |
other offline. JM thinks these need tidying up. |
468 |
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469 |
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Which of the following are which tutorial? |
470 |
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adjustment.128x64x1 |
471 |
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adjustment.cs-32x32x1 |
472 |
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advect_cs |
473 |
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advect_xy |
474 |
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advect_xz |
475 |
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aim.5l_cs |
476 |
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aim.5l_Equatorial_Channel |
477 |
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aim.5l_LatLon |
478 |
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biogeo |
479 |
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bottom_ctrl_5x5 |
480 |
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cfc_example |
481 |
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cpl_aim+ocn |
482 |
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dome |
483 |
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exp2 |
484 |
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exp4 |
485 |
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exp5 |
486 |
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fizhi-cs-32x32x10 |
487 |
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fizhi-cs-aqualev20 |
488 |
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fizhi-gridalt-hs |
489 |
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flt_example |
490 |
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front_relax |
491 |
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global1x1_tot |
492 |
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global2x2_tot |
493 |
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global_ocean.90x40x15 |
494 |
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global_ocean.cs32x15 |
495 |
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global_ocean.cubed32x32x30 |
496 |
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global_ocean_ebm |
497 |
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global_with_exf |
498 |
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hs94.128x64x5 |
499 |
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hs94.1x64x5 |
500 |
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hs94.cs-32x32x5 |
501 |
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ideal_2D_oce |
502 |
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internal_wave |
503 |
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inverted_barometer |
504 |
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lab_sea |
505 |
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matrix_example |
506 |
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MLAdjust |
507 |
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natl_box |
508 |
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natl_box_adjoint |
509 |
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OpenAD |
510 |
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rotating_tank |
511 |
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solid-body.cs-32x32x1 |
512 |
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tidal_basin_2d |
513 |
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tutorial_baroclinic_gyre |
514 |
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tutorial_barotropic_gyre |
515 |
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tutorial_cfc_offline |
516 |
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tutorial_deep_convection |
517 |
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tutorial_global_oce_biogeo |
518 |
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tutorial_global_oce_in_p |
519 |
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tutorial_global_oce_latlon |
520 |
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tutorial_global_oce_optim |
521 |
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tutorial_held_suarez_cs |
522 |
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tutorial_offline |
523 |
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tutorial_plume_on_slope |
524 |
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tutorial_tracer_adjsens |
525 |
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vermix |
526 |
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527 |
>>>> From Ed |
>>>> From Ed |
528 |
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529 |
Here are the remaining bits for Chap 4 : |
Here are the remaining bits for Chap 4 : |
530 |
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- The grammar/flow could still use some work. Boo was an English |
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major and has experience editing/proofing technical papers. I |
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could print out a copy and ask her to read it and suggest |
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improvements. |
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531 |
- missing references (if you point me towards URLs, I'll add them |
- missing references (if you point me towards URLs, I'll add them |
532 |
to the bibliography): |
to the bibliography): |
533 |
\ref{ref hoe and hill, ecmwf} |
\ref{ref hoe and hill, ecmwf} |
548 |
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549 |
the master package diagram does not appear in the document |
the master package diagram does not appear in the document |
550 |
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pkg/ptracers doesn't seem to have any documentation (see packages list below) |
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551 |
Master list of packages (add this to beginning of chap 6) |
Master list of packages (add this to beginning of chap 6) |
552 |
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553 |
admtlm/ - autodiff (chapter 5) |
admtlm/ - autodiff (chapter 5) |
554 |
aim/ - retired |
aim/ - retired |
555 |
aim_compon_interf/ - 6.6 (no content yet) |
aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) |
556 |
aim_ocn_coupler/ - 6.6 (no content yet) |
aim_ocn_coupler/ - 6.6 (no content yet) |
557 |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
558 |
atm_common/ - 6.6 (no content yet) |
atm_common/ - nothing in this package (6.4.1 related) |
559 |
autodiff/ - autodiff (chapter 5) |
autodiff/ - autodiff (chapter 5) |
560 |
bulk_force/ - 6.3.3 |
bulk_force/ - 6.3.3 |
561 |
cal/ - 6.3.5 |
cal/ - 6.3.5 |
562 |
cd_code/ - chapter 2 (JM check) |
cd_code/ - chapter 2 (JM check add a reference to paper, |
563 |
cfc/ - not sure |
mention parameter in data) |
564 |
chronos/ - AM to check |
cfc/ - not sure (CNH to talk to Steph and Helen) |
565 |
compon_communic/ - 6.6 (no content yet) |
chronos/ - AM to check (not being used - Andrea to kill it) |
566 |
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compon_communic/ - 6.6 (no content yet)(Daniel + JM) |
567 |
cost/ - not sure, check with PH |
cost/ - not sure, check with PH |
568 |
ctrl/ - not sure, check with PH |
ctrl/ - not sure, check with PH |
569 |
debug/ - JM may do something in chapter 7 (utilities) |
debug/ - JM may do something in chapter 7 (utilities) |
570 |
diagnostics/ - 7.1 |
diagnostics/ - 7.1 |
571 |
dic/ - 6.7.2 |
dic/ - 6.7.2 |
572 |
ebm/ - not sure |
ebm/ - (check with PH) |
573 |
ecco/ - chapter 8 |
ecco/ - chapter 8 |
574 |
embed_files/ - add something to chapter 7 |
embed_files/ - add something to chapter 7 |
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ex3/ - rename to exch3 |
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575 |
exch2/ - 6.2.2 |
exch2/ - 6.2.2 |
576 |
exf/ - 6.3.4 |
exf/ - 6.3.4 |
577 |
fizhi/ - 6.4.3 |
fizhi/ - 6.4.3 |
578 |
flt/ - in chapter 2 (JM check) |
flt/ - (PH check) |
579 |
gchem/ - 6.7.1 |
gchem/ - 6.7.1 |
580 |
generic_advdiff/ - in chapter 2 (JM check) |
generic_advdiff/ - in chapter 2 (JM check) |
581 |
ggl90/ - nothing, (Martin?) |
ggl90/ - nothing, (Martin?) |
582 |
gmredi/ - in chapter 2 (JM check). also need |
gmredi/ - in chapter 2 (JM check). also need |
583 |
Ferrari & Mc tapering |
Ferrari & Mc transition zone stuff (Samar doing this) |
584 |
|
get dfer to read this |
585 |
grdchk/ - grdchk (chapter 5 - check with PH) |
grdchk/ - grdchk (chapter 5 - check with PH) |
586 |
gridalt/ - 6.2.4 |
gridalt/ - 6.2.4 |
587 |
kpp/ - 6.3.2 |
kpp/ - 6.3.2 |
588 |
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) |
589 |
matrix/ - Samar |
matrix/ - Samar |
590 |
mdsio/ - 7.3.1 |
mdsio/ - 7.3.1 |
591 |
mnc/ - 7.2.1 |
mnc/ - 7.2.1 |
594 |
mom_vecinv/ - in chapter 2 (JM check) |
mom_vecinv/ - in chapter 2 (JM check) |
595 |
monitor/ - 7.4 |
monitor/ - 7.4 |
596 |
my82/ - nothing, (martin?) |
my82/ - nothing, (martin?) |
597 |
obcs/ - 6.3 (needs a check) |
obcs/ - 6.3 (needs a check - ask PH to read) |
598 |
ocn_compon_interf/ - 6.6 (no content yet) |
ocn_compon_interf/ - 6.6 (no content yet) |
599 |
offline/ - nothing, tutorials that need work but no package section entry |
offline/ - nothing, tutorials that need work but no package section entry |
600 |
|
trivial to document (CNH to do) |
601 |
opps/ - nothing, (martin?) |
opps/ - nothing, (martin?) |
602 |
pp81/ - nothing, (martin?) |
pp81/ - nothing, (martin?) |
603 |
profiles/ - GAEL |
profiles/ - GAEL |
604 |
ptracers/ - JM + SD to write something |
ptracers/ - JM + SD + Martin to write something (nothing for this |
605 |
rbcs/ - talk to steph |
at the moment) |
606 |
runclock/ - runclock |
AM has diagnostics table for this. |
607 |
rw/ - not sure |
rbcs/ - CNH to talk to steph |
608 |
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runclock/ - runclock - CNH |
609 |
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rw/ - not sure - going to stay says JMC. quick IO calls |
610 |
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JMC to write a quick note for that. |
611 |
sbo/ - text in sbo_descruption.tex but not linked into |
sbo/ - text in sbo_descruption.tex but not linked into |
612 |
part6 |
part6 - CNH |
613 |
seaice/ - 6.5.2 - no equations, dimitris has promised some |
seaice/ - 6.5.2 - no equations, dimitris has promised some |
614 |
shap_filt/ - chapter 2, JM to check |
shap_filt/ - chapter 2, JM to check |
615 |
shelfice/ - nothing yet (martin?) |
shelfice/ - nothing yet (martin?) |
616 |
solver/ - empty |
solver/ - empty (go away?) |
617 |
sphere/ - chapter 5 or 8 (PH to check) |
sphere/ - chapter 5 or 8 (PH to check) |
618 |
therm_seaice/ - empty |
therm_seaice/ - empty (go away?) |
619 |
thsice/ - 6.5.1 (JM to update?) |
thsice/ - 6.5.1 (JM to update?) |
620 |
timeave/ - retiring...... |
timeave/ - retiring...... |
621 |
zonal_filt/ - chapter 2 (JM to check) |
zonal_filt/ - chapter 2 (JM to check) |
622 |
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623 |
Possible for chap 7 - Daniels grafix/ stuff |
list an expeiment which uses package? CNH |
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Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. |
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Figure 6.8 is missing |
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624 |
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625 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
626 |
Figure 6.8 is missing |
Figure 6.8 is missing |
627 |
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628 |
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629 |
>>>> From Andrea |
===== Chapter 7 ===== [EH3 editing] : |
630 |
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631 |
to do list for chap 7: |
7.1.x - JMC: please add description of: |
632 |
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- diagstat |
633 |
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- new temporal averaging feature |
634 |
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635 |
|
7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) |
636 |
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637 |
7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
7.5.2 - get bathymetry pre-processing stuff from Patrick |
638 |
the links are pointing to the proper place |
and then describe it |
639 |
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640 |
7.5.1 - add Graphix to the list of stuff in utils/matlab |
add something on spgrid mesh generator (maybe)? |
|
7.5.2 - empty |
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641 |
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642 |
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643 |
andrea |
andrea |
644 |
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645 |
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646 |
9. Model uses |
9. Publications using MITgcm --> "Previous Applications of MITgcm" |
647 |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
648 |
(check in support for more names) |
(check in support for more names) |
649 |
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650 |
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10. Under development |
651 |
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652 |
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Constantinos LCML |
653 |
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654 |
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655 |
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Bibliography |
656 |
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657 |
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tidy up from misc - .tex |