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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 |
20 |
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21 |
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Chapter 8 - PH |
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Chapter 9 - CNH (Applications) |
24 |
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Chapter 10 - JMC (Under development chapter) |
26 |
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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. |
40 |
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this aknowledges peoples contributions and gives ref for who |
41 |
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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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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?) |
205 |
o coupled aqua, ridge world etc... |
o coupled aqua, ridge world etc... |
206 |
- links to ingrid output |
- links to ingrid output |
207 |
get stuff from Daniel |
get stuff from Daniel |
208 |
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Davids donut movie |
209 |
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210 |
o constrained lab simulation |
o constrained lab simulation |
211 |
- links to ingrid output for model and lab |
- links to ingrid output for model and lab |
233 |
- would be nice to have an active link to the fortran-file |
- would be nice to have an active link to the fortran-file |
234 |
for all the S/R & eq.Number in the "calling-tree" boxes |
for all the S/R & eq.Number in the "calling-tree" boxes |
235 |
- 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 |
236 |
(mom_flux_form, mom_vecinv, dynamics) |
(mom_flux_form, mom_vecinv, dynamics) <- DONE |
237 |
- 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}) |
238 |
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}} |
239 |
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 |
244 |
the 2 sections. |
the 2 sections. |
245 |
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246 |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
in content: Horizontal Dissipation: 2 times in vector-invariant section |
247 |
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<- DONE |
248 |
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249 |
2.1 time-stepping (part2/time_stepping.tex) |
2.1 time-stepping (part2/time_stepping.tex) |
250 |
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253 |
>> In all the above configurations it is also possible to substitute the |
>> In all the above configurations it is also possible to substitute the |
254 |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
>> Adams-Bashforth with an alternative time-stepping scheme for terms |
255 |
>> evaluated explicitly in time |
>> evaluated explicitly in time |
256 |
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<- Leave it general. |
257 |
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258 |
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259 |
2.2 rigid-lid: |
2.2 rigid-lid: |
287 |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
- add link & S/R names: CALC_GW, SOLVE_FOR_PRESSURE, CG3D |
288 |
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289 |
2.9 Variants on Free-Surface |
2.9 Variants on Free-Surface |
290 |
- Delta.t mis-written (eq.2.73) |
- Delta.t mis-written (eq.2.73) <- DONE |
291 |
- Eq.Num missing (has been fixed since) |
- Eq.Num missing <- DONE |
292 |
- u* is stored in gU (and not in gUnm1) |
- u* is stored in gU (and not in gUnm1) <- DONE |
293 |
- Phi_nh in NH_VARS.h |
- Phi_nh in NH_VARS.h <- DONE |
294 |
- 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, |
295 |
INI_CG2D, INI_CG3D |
INI_CG2D, INI_CG3D |
296 |
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300 |
2.9.2 NLFS |
2.9.2 NLFS |
301 |
- eq.Nb are wrong in html |
- eq.Nb are wrong in html |
302 |
- 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) |
303 |
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<- DONE |
304 |
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305 |
2.10.1 Notation |
2.10.1 Notation |
306 |
- Area definition is not really used like this |
- Area definition is not really used like this |
309 |
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310 |
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
Instead, in the following section, Ac,Aw,As,A_zeta (= corresponding to |
311 |
the model variables) are used (e.g., see section 2.10.5) |
the model variables) are used (e.g., see section 2.10.5) |
312 |
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<- DONE |
313 |
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314 |
2.10.5 Horizontal grid: |
2.10.5 Horizontal grid: |
315 |
- fig.2.8 : should use Aw,As consistently in this figure description, |
- fig.2.8 : should use Aw,As consistently in this figure description, |
316 |
in the figure itself, as it is in the text. |
in the figure itself, as it is in the text. <- DONE |
317 |
- curvilinear: |
- curvilinear: |
318 |
to add: mention the angle of the grid direction relative to |
to add: mention the angle of the grid direction relative to |
319 |
Eastward, Northward direction. |
Eastward, Northward direction. |
345 |
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 |
346 |
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 |
347 |
scaling (not cos()2) |
scaling (not cos()2) |
348 |
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- need to reference the smag/leith section. |
349 |
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350 |
2.13.6 Vertical dissipation |
2.13.6 Vertical dissipation |
351 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
364 |
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365 |
2.16 & 2.17 & 2.18 : |
2.16 & 2.17 & 2.18 : |
366 |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
367 |
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- fix equations 2.202 & 2.203 (thanks to Martin) <- DONE |
368 |
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369 |
2.20.2 mercator, non-dimensional Equations: |
2.20.2 mercator, non-dimensional Equations: |
370 |
- does not use std notation |
- does not use std notation |
372 |
(e.g changing the tile to: |
(e.g changing the tile to: |
373 |
- talk to Baylor |
- talk to Baylor |
374 |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
375 |
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<- No (Chris said) |
376 |
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377 |
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378 |
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Diagrams of grid locations etc.... and what variables and output files |
379 |
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and/or netcdf variable names are not very easy to figure out and follow. |
380 |
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It would be good to redo and extend these diagrams and align with GRID.h |
381 |
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content. |
382 |
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383 |
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384 |
JM |
JM |
391 |
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392 |
Almost all of the 'math mode' text is dropped down as subscripts |
Almost all of the 'math mode' text is dropped down as subscripts |
393 |
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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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3.1 - don't need a link to the outside of the document (remove it) |
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- link to htdig is broken |
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3.2.1 - link at bottom to source code points to section 3.2.1 |
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(ie, to itself) - link should point to cvs code archive |
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3.2.2.1 - ('upgrading from an earlier version') belongs under |
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the cvs part, ie, should be 3.2.1.1 |
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3.3 - remove reference to 'diags' section under MITgcm |
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- remove reference to 'exe' and 'bin' sections also |
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(remove the .cvsignore file under these directories in cvs) |
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- add a 'jobs' section, and a description as examples of run scripts |
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- add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions |
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- under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |
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- under 'tools' the adjoint points to section 5 - this is now section 8 |
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(but should be a floating reference) |
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- under 'utils' add a reference to exch2 - stuff for different resolutions |
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- the description of the pkg section refers directly to |
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section 3. should be section 6 (actually should be a floating reference) |
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394 |
3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |
3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |
395 |
3.4.1 - links to the following experiments don't exist or are broken: |
3.4.1 - links to the following experiments don't exist or are broken: |
396 |
exp2 - should link to section 3.9 |
exp2 - should link to section 3.9 |
415 |
are written. |
are written. |
416 |
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 |
417 |
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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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418 |
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 |
419 |
the verification directory |
the verification directory |
420 |
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450 |
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451 |
offline - duplicate inputs, what is it, tidy up cfc v. |
offline - duplicate inputs, what is it, tidy up cfc v. |
452 |
other offline. JM thinks these need tidying up. |
other offline. JM thinks these need tidying up. |
453 |
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454 |
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Which of the following are which tutorial? |
455 |
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adjustment.128x64x1 |
456 |
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adjustment.cs-32x32x1 |
457 |
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advect_cs |
458 |
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advect_xy |
459 |
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advect_xz |
460 |
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aim.5l_cs |
461 |
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aim.5l_Equatorial_Channel |
462 |
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aim.5l_LatLon |
463 |
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biogeo |
464 |
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bottom_ctrl_5x5 |
465 |
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cfc_example |
466 |
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cpl_aim+ocn |
467 |
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dome |
468 |
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exp2 |
469 |
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exp4 |
470 |
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exp5 |
471 |
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fizhi-cs-32x32x10 |
472 |
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fizhi-cs-aqualev20 |
473 |
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fizhi-gridalt-hs |
474 |
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flt_example |
475 |
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front_relax |
476 |
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global1x1_tot |
477 |
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global2x2_tot |
478 |
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global_ocean.90x40x15 |
479 |
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global_ocean.cs32x15 |
480 |
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global_ocean.cubed32x32x30 |
481 |
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global_ocean_ebm |
482 |
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global_with_exf |
483 |
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hs94.128x64x5 |
484 |
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hs94.1x64x5 |
485 |
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hs94.cs-32x32x5 |
486 |
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ideal_2D_oce |
487 |
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internal_wave |
488 |
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inverted_barometer |
489 |
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lab_sea |
490 |
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matrix_example |
491 |
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MLAdjust |
492 |
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natl_box |
493 |
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natl_box_adjoint |
494 |
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OpenAD |
495 |
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rotating_tank |
496 |
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solid-body.cs-32x32x1 |
497 |
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tidal_basin_2d |
498 |
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tutorial_baroclinic_gyre |
499 |
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tutorial_barotropic_gyre |
500 |
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tutorial_cfc_offline |
501 |
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tutorial_deep_convection |
502 |
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tutorial_global_oce_biogeo |
503 |
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tutorial_global_oce_in_p |
504 |
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tutorial_global_oce_latlon |
505 |
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tutorial_global_oce_optim |
506 |
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tutorial_held_suarez_cs |
507 |
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tutorial_offline |
508 |
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tutorial_plume_on_slope |
509 |
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tutorial_tracer_adjsens |
510 |
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vermix |
511 |
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512 |
>>>> From Ed |
>>>> From Ed |
513 |
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514 |
Here are the remaining bits for Chap 4 : |
Here are the remaining bits for Chap 4 : |
515 |
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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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516 |
- missing references (if you point me towards URLs, I'll add them |
- missing references (if you point me towards URLs, I'll add them |
517 |
to the bibliography): |
to the bibliography): |
518 |
\ref{ref hoe and hill, ecmwf} |
\ref{ref hoe and hill, ecmwf} |
533 |
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534 |
the master package diagram does not appear in the document |
the master package diagram does not appear in the document |
535 |
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pkg/ptracers doesn't seem to have any documentation (see packages list below) |
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536 |
Master list of packages (add this to beginning of chap 6) |
Master list of packages (add this to beginning of chap 6) |
537 |
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538 |
admtlm/ - autodiff (chapter 5) |
admtlm/ - autodiff (chapter 5) |
539 |
aim/ - retired |
aim/ - retired |
540 |
aim_compon_interf/ - 6.6 (no content yet) |
aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) |
541 |
aim_ocn_coupler/ - 6.6 (no content yet) |
aim_ocn_coupler/ - 6.6 (no content yet) |
542 |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
543 |
atm_common/ - 6.6 (no content yet) |
atm_common/ - nothing in this package (6.4.1 related) |
544 |
autodiff/ - autodiff (chapter 5) |
autodiff/ - autodiff (chapter 5) |
545 |
bulk_force/ - 6.3.3 |
bulk_force/ - 6.3.3 |
546 |
cal/ - 6.3.5 |
cal/ - 6.3.5 |
547 |
cd_code/ - chapter 2 (JM check) |
cd_code/ - chapter 2 (JM check add a reference to paper, |
548 |
cfc/ - not sure |
mention parameter in data) |
549 |
chronos/ - AM to check |
cfc/ - not sure (CNH to talk to Steph and Helen) |
550 |
compon_communic/ - 6.6 (no content yet) |
chronos/ - AM to check (not being used - Andrea to kill it) |
551 |
|
compon_communic/ - 6.6 (no content yet)(Daniel + JM) |
552 |
cost/ - not sure, check with PH |
cost/ - not sure, check with PH |
553 |
ctrl/ - not sure, check with PH |
ctrl/ - not sure, check with PH |
554 |
debug/ - JM may do something in chapter 7 (utilities) |
debug/ - JM may do something in chapter 7 (utilities) |
555 |
diagnostics/ - 7.1 |
diagnostics/ - 7.1 |
556 |
dic/ - 6.7.2 |
dic/ - 6.7.2 |
557 |
ebm/ - not sure |
ebm/ - (check with PH) |
558 |
ecco/ - chapter 8 |
ecco/ - chapter 8 |
559 |
embed_files/ - add something to chapter 7 |
embed_files/ - add something to chapter 7 |
|
ex3/ - rename to exch3 |
|
560 |
exch2/ - 6.2.2 |
exch2/ - 6.2.2 |
561 |
exf/ - 6.3.4 |
exf/ - 6.3.4 |
562 |
fizhi/ - 6.4.3 |
fizhi/ - 6.4.3 |
563 |
flt/ - in chapter 2 (JM check) |
flt/ - (PH check) |
564 |
gchem/ - 6.7.1 |
gchem/ - 6.7.1 |
565 |
generic_advdiff/ - in chapter 2 (JM check) |
generic_advdiff/ - in chapter 2 (JM check) |
566 |
ggl90/ - nothing, (Martin?) |
ggl90/ - nothing, (Martin?) |
567 |
gmredi/ - in chapter 2 (JM check). also need |
gmredi/ - in chapter 2 (JM check). also need |
568 |
Ferrari & Mc tapering |
Ferrari & Mc transition zone stuff (Samar doing this) |
569 |
|
get dfer to read this |
570 |
grdchk/ - grdchk (chapter 5 - check with PH) |
grdchk/ - grdchk (chapter 5 - check with PH) |
571 |
gridalt/ - 6.2.4 |
gridalt/ - 6.2.4 |
572 |
kpp/ - 6.3.2 |
kpp/ - 6.3.2 |
573 |
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) |
574 |
matrix/ - Samar |
matrix/ - Samar |
575 |
mdsio/ - 7.3.1 |
mdsio/ - 7.3.1 |
576 |
mnc/ - 7.2.1 |
mnc/ - 7.2.1 |
579 |
mom_vecinv/ - in chapter 2 (JM check) |
mom_vecinv/ - in chapter 2 (JM check) |
580 |
monitor/ - 7.4 |
monitor/ - 7.4 |
581 |
my82/ - nothing, (martin?) |
my82/ - nothing, (martin?) |
582 |
obcs/ - 6.3 (needs a check) |
obcs/ - 6.3 (needs a check - ask PH to read) |
583 |
ocn_compon_interf/ - 6.6 (no content yet) |
ocn_compon_interf/ - 6.6 (no content yet) |
584 |
offline/ - nothing, tutorials that need work but no package section entry |
offline/ - nothing, tutorials that need work but no package section entry |
585 |
|
trivial to document (CNH to do) |
586 |
opps/ - nothing, (martin?) |
opps/ - nothing, (martin?) |
587 |
pp81/ - nothing, (martin?) |
pp81/ - nothing, (martin?) |
588 |
profiles/ - GAEL |
profiles/ - GAEL |
589 |
ptracers/ - JM + SD to write something |
ptracers/ - JM + SD + Martin to write something (nothing for this |
590 |
rbcs/ - talk to steph |
at the moment) |
591 |
runclock/ - runclock |
AM has diagnostics table for this. |
592 |
rw/ - not sure |
rbcs/ - CNH to talk to steph |
593 |
|
runclock/ - runclock - CNH |
594 |
|
rw/ - not sure - going to stay says JMC. quick IO calls |
595 |
|
JMC to write a quick note for that. |
596 |
sbo/ - text in sbo_descruption.tex but not linked into |
sbo/ - text in sbo_descruption.tex but not linked into |
597 |
part6 |
part6 - CNH |
598 |
seaice/ - 6.5.2 - no equations, dimitris has promised some |
seaice/ - 6.5.2 - no equations, dimitris has promised some |
599 |
shap_filt/ - chapter 2, JM to check |
shap_filt/ - chapter 2, JM to check |
600 |
shelfice/ - nothing yet (martin?) |
shelfice/ - nothing yet (martin?) |
601 |
solver/ - empty |
solver/ - empty (go away?) |
602 |
sphere/ - chapter 5 or 8 (PH to check) |
sphere/ - chapter 5 or 8 (PH to check) |
603 |
therm_seaice/ - empty |
therm_seaice/ - empty (go away?) |
604 |
thsice/ - 6.5.1 (JM to update?) |
thsice/ - 6.5.1 (JM to update?) |
605 |
timeave/ - retiring...... |
timeave/ - retiring...... |
606 |
zonal_filt/ - chapter 2 (JM to check) |
zonal_filt/ - chapter 2 (JM to check) |
607 |
|
|
608 |
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 |
|
609 |
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610 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
611 |
Figure 6.8 is missing |
Figure 6.8 is missing |
612 |
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613 |
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614 |
>>>> From Andrea |
===== Chapter 7 ===== [EH3 editing] : |
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to do list for chap 7: |
7.1.x - JMC: please add description of: |
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- diagstat |
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- new temporal averaging feature |
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7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) |
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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 |
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the links are pointing to the proper place |
and then describe it |
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7.5.1 - add Graphix to the list of stuff in utils/matlab |
add something on spgrid mesh generator (maybe)? |
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7.5.2 - empty |
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andrea |
andrea |
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9. Model uses |
9. Publications using MITgcm --> "Previous Applications of MITgcm" |
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Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
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(check in support for more names) |
(check in support for more names) |
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10. Under development |
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Constantinos LCML |
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Bibliography |
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tidy up from misc - .tex |