14 |
- pick a URL |
- pick a URL |
15 |
TBD |
TBD |
16 |
|
|
|
- mitgcm.org very front page. |
|
|
o too many clicks to get to model manual. |
|
|
make doc link go to mitgcm.org/r2_web_testing/latest |
|
|
and add "HowTo" reference etc... to /latest page |
|
|
|
|
17 |
- mitgcm.org/r2_web_testing/latest |
- mitgcm.org/r2_web_testing/latest |
18 |
o add another short-cut for quick download |
o add another short-cut for quick download |
19 |
|
|
293 |
to add: mention the angle of the grid direction relative to |
to add: mention the angle of the grid direction relative to |
294 |
Eastward, Northward direction. |
Eastward, Northward direction. |
295 |
+ mention horizGridFile= in file "data" (PARM04) |
+ mention horizGridFile= in file "data" (PARM04) |
296 |
- add cylindrical grid description |
- add cylindrical polar grid description |
297 |
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 |
298 |
|
|
299 |
|
|
320 |
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 |
321 |
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 |
322 |
scaling (not cos()2) |
scaling (not cos()2) |
323 |
|
- need to reference the smag/leith section. |
324 |
|
|
325 |
2.13.6 Vertical dissipation |
2.13.6 Vertical dissipation |
326 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
344 |
- does not use std notation |
- does not use std notation |
345 |
- would be better as an appendix of section 2.20: |
- would be better as an appendix of section 2.20: |
346 |
(e.g changing the tile to: |
(e.g changing the tile to: |
347 |
|
- talk to Baylor |
348 |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
349 |
|
|
350 |
|
|
351 |
JM |
JM |
352 |
|
|
353 |
|
|
354 |
|
>>>> From Andrea |
355 |
|
|
356 |
|
Chapter 3 |
357 |
|
-------- |
358 |
|
|
359 |
|
Almost all of the 'math mode' text is dropped down as subscripts |
360 |
|
|
361 |
|
divide chapter 3 more clearly into 2 sections? |
362 |
|
(ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |
363 |
|
then 3.19 and 3.20 are informational again - rearrange subsections?) |
364 |
|
[DONE] |
365 |
|
|
366 |
|
3.1 - don't need a link to the outside of the document (remove it) |
367 |
|
- link to htdig is broken |
368 |
|
|
369 |
|
3.2.1 - link at bottom to source code points to section 3.2.1 |
370 |
|
(ie, to itself) - link should point to cvs code archive |
371 |
|
|
372 |
|
3.2.2.1 - ('upgrading from an earlier version') belongs under |
373 |
|
the cvs part, ie, should be 3.2.1.1 |
374 |
|
|
375 |
|
3.3 - remove reference to 'diags' section under MITgcm |
376 |
|
- remove reference to 'exe' and 'bin' sections also |
377 |
|
(remove the .cvsignore file under these directories in cvs) |
378 |
|
- add a 'jobs' section, and a description as examples of run scripts |
379 |
|
- add 'lsopt', 'optim' and 'tutorial examples' with brief descriptions |
380 |
|
- under 'tools' add a reference to 'build_options'. refer to the 'optfiles' |
381 |
|
- under 'tools' the adjoint points to section 5 - this is now section 8 |
382 |
|
(but should be a floating reference) |
383 |
|
- under 'utils' add a reference to exch2 - stuff for different resolutions |
384 |
|
- the description of the pkg section refers directly to |
385 |
|
section 3. should be section 6 (actually should be a floating reference) |
386 |
|
|
387 |
|
3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |
388 |
|
3.4.1 - links to the following experiments don't exist or are broken: |
389 |
|
exp2 - should link to section 3.9 |
390 |
|
hs94.cs-32x32x5 - link to section 3.12 |
391 |
|
add 'convection' to the list, link to section 3.13 |
392 |
|
add 'plume on slope` to the list, link to section 3.14 |
393 |
|
add '??' link to section 3.15 |
394 |
|
add 'dic_example on slope` to the list, link to section 3.16 |
395 |
|
add '??' link to section 3.17 |
396 |
|
add 'offline' and link to section 3.18 |
397 |
|
clean up others and make links where they are needed |
398 |
|
3.4.2 - text suggests to see section 2 for details about what is in the 'code' |
399 |
|
and 'input' directories - should refer to the examples in this section |
400 |
|
- add 'build' bullet - this is where the model is compiled and exectuable lives |
401 |
|
|
402 |
|
3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options |
403 |
|
as the place where they live (add a link?) |
404 |
|
|
405 |
|
3.6.1 - Add some general 'approach' text - ie, output is controlled either by the |
406 |
|
'data' file in the input directory or by the data.[pkg name] file for any |
407 |
|
package running. And there is some default behavior when the 'state' dumps |
408 |
|
are written. |
409 |
|
3.6.1.2 - needs to be moved to inside section 3.6.2 |
410 |
|
|
411 |
|
3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |
412 |
|
underneath this one and leave the text for 3.7 in place |
413 |
|
|
414 |
|
All the 'overview' sections need some reference to the name of the experiment in |
415 |
|
the verification directory |
416 |
|
|
417 |
|
3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript |
418 |
|
- is this experiment in the list from section 3.4??? |
419 |
|
3.10.3.1 - refers to figures and equations, links are broken |
420 |
|
|
421 |
|
3.11.3.2 - line 43: link to equation is broken |
422 |
|
- line 51-53: link to equation is broken |
423 |
|
- there is some mess of text hanging around the end of this section. remove? reformat? |
424 |
|
|
425 |
|
3.12.4.1 - line 34 - link to equation is broken |
426 |
|
- lines 60,61 - 1st (take out the 'r' in the superscript) |
427 |
|
|
428 |
|
3.13.2 - link to theta-equation is broken |
429 |
|
3.13.5.4 -- ALL of the bold links to variable names are broken |
430 |
|
line 34: link to equation is broken |
431 |
|
|
432 |
|
3.15.1 - reference to 'fourth experiment' should be removed |
433 |
|
|
434 |
|
3.16.4 - strange formatting, presence of '>' symbols - remove them |
435 |
|
|
436 |
|
3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 |
437 |
|
3.17.3.1 - nothing filled in under file input/data - needs description |
438 |
|
|
439 |
|
3.18.2 - point to section 2 for details - need hyperlink |
440 |
|
|
441 |
|
3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! |
442 |
|
section 3.5 has the 'build' directory in the example |
443 |
|
|
444 |
|
3.20.1 - link to doc at end of section points to this section |
445 |
|
3.20.2 - link to doc at end of section points to this section |
446 |
|
|
447 |
|
offline - duplicate inputs, what is it, tidy up cfc v. |
448 |
|
other offline. JM thinks these need tidying up. |
449 |
|
|
450 |
|
Which of the following are which tutorial? |
451 |
|
! MLAdjust |
452 |
|
adjust_nlfs.cs-32x32x1 |
453 |
|
aim.5l_XZ_Equatorial_Slice |
454 |
|
biogeo |
455 |
|
aim.5l_zon-ave |
456 |
|
coupled_ucla |
457 |
|
cfc_offline |
458 |
|
exp3 |
459 |
|
global2x2_tot |
460 |
|
global1x1_tot |
461 |
|
global_ocean.cubed_wEXF |
462 |
|
global_with_CFC11 |
463 |
|
goz |
464 |
|
gop |
465 |
|
natl_box_obcs |
466 |
|
natl_box_forward |
467 |
|
spinup_optim |
468 |
|
tutorial_held_suarez_cs |
469 |
|
vero |
470 |
|
inverted_barometer |
471 |
|
global_ocean.cubed32x32x30 |
472 |
|
exp1 |
473 |
|
advect_cs |
474 |
|
dic_example |
475 |
|
fizhi-gridalt-hs |
476 |
|
global_ocean_pressure |
477 |
|
matrix_example |
478 |
|
exp4 |
479 |
|
solid-body.cs-32x32x1 |
480 |
|
cfc_example |
481 |
|
flt_example |
482 |
|
adjustment.cs-32x32x1 |
483 |
|
advect_xz |
484 |
|
rotating_tank |
485 |
|
ideal_2D_oce |
486 |
|
global_ocean.90x40x15 |
487 |
|
front_relax |
488 |
|
aim.5l_LatLon |
489 |
|
lab_sea |
490 |
|
hs94.cs-32x32x5 |
491 |
|
global_with_exf |
492 |
|
exp2 |
493 |
|
tidal_basin_2d |
494 |
|
fizhi-cs-32x32x10 |
495 |
|
exp5 |
496 |
|
global_ocean.cs32x15 |
497 |
|
OpenAD |
498 |
|
hs94.1x64x5 |
499 |
|
fizhi-cs-aqualev10 |
500 |
|
exp0 |
501 |
|
dome |
502 |
|
aim.5l_Equatorial_Channel |
503 |
|
aim.5l_cs |
504 |
|
hs94.128x64x5 |
505 |
|
prm |
506 |
|
carbon |
507 |
|
plume_on_slope |
508 |
|
natl_box_adjoint |
509 |
|
vermix |
510 |
|
cpl_aim+ocn |
511 |
|
global_ocean_ebm |
512 |
|
internal_wave |
513 |
|
advect_xy |
514 |
|
natl_box |
515 |
|
adjustment.128x64x1 |
516 |
|
|
517 |
>>>> From Ed |
>>>> From Ed |
518 |
|
|
519 |
Here are the remaining bits for Chap 4 : |
Here are the remaining bits for Chap 4 : |
520 |
|
|
|
- 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. |
|
|
|
|
521 |
- missing references (if you point me towards URLs, I'll add them |
- missing references (if you point me towards URLs, I'll add them |
522 |
to the bibliography): |
to the bibliography): |
523 |
\ref{ref hoe and hill, ecmwf} |
\ref{ref hoe and hill, ecmwf} |
539 |
the master package diagram does not appear in the document |
the master package diagram does not appear in the document |
540 |
|
|
541 |
pkg/ptracers doesn't seem to have any documentation (see packages list below) |
pkg/ptracers doesn't seem to have any documentation (see packages list below) |
542 |
|
martin volunteered - get martin to ask steph |
543 |
|
|
544 |
|
|
545 |
Master list of packages (add this to beginning of chap 6) |
Master list of packages (add this to beginning of chap 6) |
546 |
|
|
547 |
admtlm/ - autodiff (chapter 5) |
admtlm/ - autodiff (chapter 5) |
548 |
aim/ - retired |
aim/ - retired |
549 |
aim_compon_interf/ - 6.6 (no content yet) |
aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) |
550 |
aim_ocn_coupler/ - 6.6 (no content yet) |
aim_ocn_coupler/ - 6.6 (no content yet) |
551 |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
552 |
atm_common/ - 6.6 (no content yet) |
atm_common/ - nothing in this package (6.4.1 related) |
553 |
autodiff/ - autodiff (chapter 5) |
autodiff/ - autodiff (chapter 5) |
554 |
bulk_force/ - 6.3.3 |
bulk_force/ - 6.3.3 |
555 |
cal/ - 6.3.5 |
cal/ - 6.3.5 |
556 |
cd_code/ - chapter 2 (JM check) |
cd_code/ - chapter 2 (JM check add a reference to paper, |
557 |
cfc/ - not sure |
mention parameter in data) |
558 |
chronos/ - AM to check |
cfc/ - not sure (CNH to talk to Steph and Helen) |
559 |
compon_communic/ - 6.6 (no content yet) |
chronos/ - AM to check (not being used - Andrea to kill it) |
560 |
|
compon_communic/ - 6.6 (no content yet)(Daniel + JM) |
561 |
cost/ - not sure, check with PH |
cost/ - not sure, check with PH |
562 |
ctrl/ - not sure, check with PH |
ctrl/ - not sure, check with PH |
563 |
debug/ - JM may do something in chapter 7 (utilities) |
debug/ - JM may do something in chapter 7 (utilities) |
564 |
diagnostics/ - 7.1 |
diagnostics/ - 7.1 |
565 |
dic/ - 6.7.2 |
dic/ - 6.7.2 |
566 |
ebm/ - not sure |
ebm/ - (check with PH) |
567 |
ecco/ - chapter 8 |
ecco/ - chapter 8 |
568 |
embed_files/ - add something to chapter 7 |
embed_files/ - add something to chapter 7 |
|
ex3/ - rename to exch3 |
|
569 |
exch2/ - 6.2.2 |
exch2/ - 6.2.2 |
570 |
exf/ - 6.3.4 |
exf/ - 6.3.4 |
571 |
fizhi/ - 6.4.3 |
fizhi/ - 6.4.3 |
633 |
|
|
634 |
andrea |
andrea |
635 |
|
|
|
>>>> 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. |
|
|
|
|
636 |
|
|
637 |
9. Model uses |
9. Model uses |
638 |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |