| 207 |
o Gas giant? |
o Gas giant? |
| 208 |
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| 209 |
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Master list of packages |
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admtlm/ - autodiff (chapter 5) |
|
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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) |
|
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bulk_force/ - 6.3.3 |
|
|
cal/ - 6.3.5 |
|
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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 |
|
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dic/ - 6.7.2 |
|
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ebm/ - not sure |
|
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ecco/ - chapter 8 |
|
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embed_files/ - add something to chapter 7 |
|
|
ex3/ - rename to exch3 |
|
|
exch2/ - 6.2.2 |
|
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exf/ - 6.3.4 |
|
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fizhi/ - 6.4.3 |
|
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flt/ - in chapter 2 (JM check) |
|
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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 |
|
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kpp/ - 6.3.2 |
|
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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) |
|
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Possible for chap 7 - Daniels grafix/ stuff |
|
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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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>>>> From Ed |
|
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|
Here are the remaining bits for Chap 4 : |
|
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|
|
- 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: |
|
|
|
|
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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" |
|
|
the links are pointing to the proper place |
|
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|
|
|
7.5.1 - add Graphix to the list of stuff in utils/matlab |
|
|
7.5.2 - empty |
|
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|
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|
|
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: |
| 348 |
- does not use std notation |
- does not use std notation |
| 349 |
- would be better as an appendix of section 2.20: |
- would be better as an appendix of section 2.20: |
| 350 |
(e.g changing the tile to: |
(e.g changing the tile to: |
| 351 |
|
- talk to Baylor |
| 352 |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
| 353 |
|
|
| 354 |
|
|
| 355 |
JM |
JM |
| 356 |
|
|
| 357 |
|
|
| 358 |
|
>>>> From Andrea |
| 359 |
|
|
| 360 |
|
Chapter 3 |
| 361 |
|
-------- |
| 362 |
|
|
| 363 |
|
Almost all of the 'math mode' text is dropped down as subscripts |
| 364 |
|
|
| 365 |
|
divide chapter 3 more clearly into 2 sections? |
| 366 |
|
(ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |
| 367 |
|
then 3.19 and 3.20 are informational again - rearrange subsections?) |
| 368 |
|
|
| 369 |
|
3.1 - don't need a link to the outside of the document (remove it) |
| 370 |
|
- link to htdig is broken |
| 371 |
|
|
| 372 |
|
3.2.1 - link at bottom to source code points to section 3.2.1 |
| 373 |
|
(ie, to itself) - link should point to cvs code archive |
| 374 |
|
|
| 375 |
|
3.2.2.1 - ('upgrading from an earlier version') belongs under |
| 376 |
|
the cvs part, ie, should be 3.2.1.1 |
| 377 |
|
|
| 378 |
|
3.3 - remove reference to 'diags' section under MITgcm |
| 379 |
|
- remove reference to 'exe' and 'bin' sections also |
| 380 |
|
(remove the .cvsignore file under these directories in cvs) |
| 381 |
|
- add a 'jobs' section, and a description as examples of run scripts |
| 382 |
|
- add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions |
| 383 |
|
- under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |
| 384 |
|
- under 'tools' the adjoint points to section 5 - this is now section 8 |
| 385 |
|
(but should be a floating reference) |
| 386 |
|
- under 'utils' add a reference to exch2 - stuff for different resolutions |
| 387 |
|
- the description of the pkg section refers directly to |
| 388 |
|
section 3. should be section 6 (actually should be a floating reference) |
| 389 |
|
|
| 390 |
|
3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |
| 391 |
|
3.4.1 - links to the following experiments don't exist or are broken: |
| 392 |
|
exp2 - should link to section 3.9 |
| 393 |
|
hs94.cs-32x32x5 - link to section 3.12 |
| 394 |
|
add 'convection' to the list, link to section 3.13 |
| 395 |
|
add 'plume on slope` to the list, link to section 3.14 |
| 396 |
|
add '??' link to section 3.15 |
| 397 |
|
add 'dic_example on slope` to the list, link to section 3.16 |
| 398 |
|
add '??' link to section 3.17 |
| 399 |
|
add 'offline' and link to section 3.18 |
| 400 |
|
clean up others and make links where they are needed |
| 401 |
|
3.4.2 - text suggests to see section 2 for details about what is in the 'code' |
| 402 |
|
and 'input' directories - should refer to the examples in this section |
| 403 |
|
- add 'build' bullet - this is where the model is compiled and exectuable lives |
| 404 |
|
|
| 405 |
|
3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options |
| 406 |
|
as the place where they live (add a link?) |
| 407 |
|
|
| 408 |
|
3.6.1 - Add some general 'approach' text - ie, output is controlled either by the |
| 409 |
|
'data' file in the input directory or by the data.[pkg name] file for any |
| 410 |
|
package running. And there is some default behavior when the 'state' dumps |
| 411 |
|
are written. |
| 412 |
|
3.6.1.2 - needs to be moved to inside section 3.6.2 |
| 413 |
|
|
| 414 |
|
3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |
| 415 |
|
underneath this one and leave the text for 3.7 in place |
| 416 |
|
|
| 417 |
|
All the 'overview' sections need some reference to the name of the experiment in |
| 418 |
|
the verification directory |
| 419 |
|
|
| 420 |
|
3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript |
| 421 |
|
- is this experiment in the list from section 3.4??? |
| 422 |
|
3.10.3.1 - refers to figures and equations, links are broken |
| 423 |
|
|
| 424 |
|
3.11.3.2 - line 43: link to equation is broken |
| 425 |
|
- line 51-53: link to equation is broken |
| 426 |
|
- there is some mess of text hanging around the end of this section. remove? reformat? |
| 427 |
|
|
| 428 |
|
3.12.4.1 - line 34 - link to equation is broken |
| 429 |
|
- lines 60,61 - 1st (take out the 'r' in the superscript) |
| 430 |
|
|
| 431 |
|
3.13.2 - link to theta-equation is broken |
| 432 |
|
3.13.5.4 -- ALL of the bold links to variable names are broken |
| 433 |
|
line 34: link to equation is broken |
| 434 |
|
|
| 435 |
|
3.15.1 - reference to 'fourth experiment' should be removed |
| 436 |
|
|
| 437 |
|
3.16.4 - strange formatting, presence of '>' symbols - remove them |
| 438 |
|
|
| 439 |
|
3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 |
| 440 |
|
3.17.3.1 - nothing filled in under file input/data - needs description |
| 441 |
|
|
| 442 |
|
3.18.2 - point to section 2 for details - need hyperlink |
| 443 |
|
|
| 444 |
|
3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! |
| 445 |
|
section 3.5 has the 'build' directory in the example |
| 446 |
|
|
| 447 |
|
3.20.1 - link to doc at end of section points to this section |
| 448 |
|
3.20.2 - link to doc at end of section points to this section |
| 449 |
|
|
| 450 |
|
offline - duplicate inputs, what is it, tidy up cfc v. |
| 451 |
|
other offline. JM thinks these need tidying up. |
| 452 |
|
>>>> From Ed |
| 453 |
|
|
| 454 |
|
Here are the remaining bits for Chap 4 : |
| 455 |
|
|
| 456 |
|
- The grammar/flow could still use some work. Boo was an English |
| 457 |
|
major and has experience editing/proofing technical papers. I |
| 458 |
|
could print out a copy and ask her to read it and suggest |
| 459 |
|
improvements. |
| 460 |
|
|
| 461 |
|
- missing references (if you point me towards URLs, I'll add them |
| 462 |
|
to the bibliography): |
| 463 |
|
\ref{ref hoe and hill, ecmwf} |
| 464 |
|
\ref{magicgarden} |
| 465 |
|
\ref{IBMLAPI} |
| 466 |
|
\ref{Memorychannel} |
| 467 |
|
\ref{hoe-hill:99} |
| 468 |
|
|
| 469 |
|
- There are a few empty sub-sections at the end of Chap 4 that |
| 470 |
|
should either be commented out or fleshed out. |
| 471 |
|
|
| 472 |
|
and thats about it for Chap 4. |
| 473 |
|
|
| 474 |
|
|
| 475 |
|
Add more to quick links on front page |
| 476 |
|
|
| 477 |
|
Chapter 6 |
| 478 |
|
|
| 479 |
|
the master package diagram does not appear in the document |
| 480 |
|
|
| 481 |
|
pkg/ptracers doesn't seem to have any documentation (see packages list below) |
| 482 |
|
|
| 483 |
|
|
| 484 |
|
Master list of packages (add this to beginning of chap 6) |
| 485 |
|
|
| 486 |
|
admtlm/ - autodiff (chapter 5) |
| 487 |
|
aim/ - retired |
| 488 |
|
aim_compon_interf/ - 6.6 (no content yet) |
| 489 |
|
aim_ocn_coupler/ - 6.6 (no content yet) |
| 490 |
|
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
| 491 |
|
atm_common/ - 6.6 (no content yet) |
| 492 |
|
autodiff/ - autodiff (chapter 5) |
| 493 |
|
bulk_force/ - 6.3.3 |
| 494 |
|
cal/ - 6.3.5 |
| 495 |
|
cd_code/ - chapter 2 (JM check) |
| 496 |
|
cfc/ - not sure |
| 497 |
|
chronos/ - AM to check |
| 498 |
|
compon_communic/ - 6.6 (no content yet) |
| 499 |
|
cost/ - not sure, check with PH |
| 500 |
|
ctrl/ - not sure, check with PH |
| 501 |
|
debug/ - JM may do something in chapter 7 (utilities) |
| 502 |
|
diagnostics/ - 7.1 |
| 503 |
|
dic/ - 6.7.2 |
| 504 |
|
ebm/ - not sure |
| 505 |
|
ecco/ - chapter 8 |
| 506 |
|
embed_files/ - add something to chapter 7 |
| 507 |
|
ex3/ - rename to exch3 |
| 508 |
|
exch2/ - 6.2.2 |
| 509 |
|
exf/ - 6.3.4 |
| 510 |
|
fizhi/ - 6.4.3 |
| 511 |
|
flt/ - in chapter 2 (JM check) |
| 512 |
|
gchem/ - 6.7.1 |
| 513 |
|
generic_advdiff/ - in chapter 2 (JM check) |
| 514 |
|
ggl90/ - nothing, (Martin?) |
| 515 |
|
gmredi/ - in chapter 2 (JM check). also need |
| 516 |
|
Ferrari & Mc tapering |
| 517 |
|
grdchk/ - grdchk (chapter 5 - check with PH) |
| 518 |
|
gridalt/ - 6.2.4 |
| 519 |
|
kpp/ - 6.3.2 |
| 520 |
|
land/ - 6.4.2 (not connected to code - JM to fix) |
| 521 |
|
matrix/ - Samar |
| 522 |
|
mdsio/ - 7.3.1 |
| 523 |
|
mnc/ - 7.2.1 |
| 524 |
|
mom_common/ - in chapter 2 (JM check) |
| 525 |
|
mom_fluxform/ - in chapter 2 (JM check) |
| 526 |
|
mom_vecinv/ - in chapter 2 (JM check) |
| 527 |
|
monitor/ - 7.4 |
| 528 |
|
my82/ - nothing, (martin?) |
| 529 |
|
obcs/ - 6.3 (needs a check) |
| 530 |
|
ocn_compon_interf/ - 6.6 (no content yet) |
| 531 |
|
offline/ - nothing, tutorials that need work but no package section entry |
| 532 |
|
opps/ - nothing, (martin?) |
| 533 |
|
pp81/ - nothing, (martin?) |
| 534 |
|
profiles/ - GAEL |
| 535 |
|
ptracers/ - JM + SD to write something |
| 536 |
|
rbcs/ - talk to steph |
| 537 |
|
runclock/ - runclock |
| 538 |
|
rw/ - not sure |
| 539 |
|
sbo/ - text in sbo_descruption.tex but not linked into |
| 540 |
|
part6 |
| 541 |
|
seaice/ - 6.5.2 - no equations, dimitris has promised some |
| 542 |
|
shap_filt/ - chapter 2, JM to check |
| 543 |
|
shelfice/ - nothing yet (martin?) |
| 544 |
|
solver/ - empty |
| 545 |
|
sphere/ - chapter 5 or 8 (PH to check) |
| 546 |
|
therm_seaice/ - empty |
| 547 |
|
thsice/ - 6.5.1 (JM to update?) |
| 548 |
|
timeave/ - retiring...... |
| 549 |
|
zonal_filt/ - chapter 2 (JM to check) |
| 550 |
|
|
| 551 |
|
Possible for chap 7 - Daniels grafix/ stuff |
| 552 |
|
|
| 553 |
|
Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. |
| 554 |
|
|
| 555 |
|
Figure 6.8 is missing |
| 556 |
|
|
| 557 |
|
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
| 558 |
|
Figure 6.8 is missing |
| 559 |
|
|
| 560 |
|
|
| 561 |
|
>>>> From Andrea |
| 562 |
|
|
| 563 |
|
to do list for chap 7: |
| 564 |
|
|
| 565 |
|
|
| 566 |
|
7.1.1 - links to section 7.1.4: the text of the first one should read "see MITgcm Kernel Diagnostics Menu" |
| 567 |
|
the links are pointing to the proper place |
| 568 |
|
|
| 569 |
|
7.5.1 - add Graphix to the list of stuff in utils/matlab |
| 570 |
|
7.5.2 - empty |
| 571 |
|
|
| 572 |
|
|
| 573 |
|
andrea |
| 574 |
|
|
| 575 |
|
|
| 576 |
9. Model uses |
9. Model uses |
| 577 |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
| 578 |
(check in support for more names) |
(check in support for more names) |
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