| 27 |
Biblio - EH3 |
Biblio - EH3 |
| 28 |
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| 29 |
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|
| 30 |
Rebuild and set to do cron build - DONE on hugo |
Rebuild and set to do cron build - DONE on hugo |
| 31 |
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| 32 |
To do |
To do |
| 41 |
this aknowledges peoples contributions and gives ref for who |
this aknowledges peoples contributions and gives ref for who |
| 42 |
to talk to. |
to talk to. |
| 43 |
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|
|
| 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 |
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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 |
|
| 50 |
|
o --DONE-- add another short-cut for quick download |
| 51 |
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| 52 |
|
o --DONE-- add another short-cut |
| 53 |
|
About |
| 54 |
|
Installation |
| 55 |
|
Contents |
| 56 |
|
Overview |
| 57 |
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Tutorials (broken) |
| 58 |
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Browse Code |
| 59 |
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| 60 |
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o --DONE-- words on http://mitgcm.org/r2_web_testing/latest change to |
| 61 |
|
|
| 62 |
o add another short-cut |
o --DONE-- finite-volume doesn't leap to FV figure |
|
About |
|
|
Installation |
|
|
Contents |
|
|
Overview |
|
|
Tutorials (broken) |
|
|
Browse Code |
|
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|
|
|
o words on http://mitgcm.org/r2_web_testing/latest |
|
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change to |
|
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"access on-line Auser manual/A and Atable of contents/A |
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and browse the Aoverview section/A" |
|
| 63 |
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| 64 |
o finite-volume doesn't leap to FV figure |
o -- DONE ??? -- have another go at pnmcrop et al. |
| 65 |
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| 66 |
o have another go at pnmcrop et al. |
I've tried making a small change in latex2html which fixes |
| 67 |
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the oddball-lower-alignment issue that we were seeing with |
| 68 |
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most in-line expressions (that is, math embedded in text). |
| 69 |
|
The fix results in some things being slightly raised but I |
| 70 |
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thin this is more asthetically pleasing than being somewhat |
| 71 |
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lowered as before. --EH3 |
| 72 |
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| 73 |
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To view the altered alignment, see: |
| 74 |
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| 75 |
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http://eddy.csail.mit.edu/r2/latest/ |
| 76 |
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| 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 |
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| 79 |
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| 80 |
o Latex |
o Latex |
| 81 |
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| 82 |
Chapter 1 - CNH |
Chapter 1 - CNH |
| 98 |
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| 99 |
o List of key papers needs to be updated and reformatted |
o List of key papers needs to be updated and reformatted |
| 100 |
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| 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?) |
| 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 |
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Davids donut movie |
| 219 |
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|
| 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 |
| 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 |
| 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 |
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|
| 259 |
2.1 time-stepping (part2/time_stepping.tex) |
2.1 time-stepping (part2/time_stepping.tex) |
| 260 |
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|
| 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 |
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|
| 268 |
|
o Time-stepping outline |
| 269 |
|
- what gets called when |
| 270 |
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| 271 |
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| 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 |
| 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 |
|
|
| 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 |
| 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. |
| 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) |
- 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 |
| 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 |
Diagrams of grid locations etc.... and what variables and output files |
| 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 |
3.1 - don't need a link to the outside of the document (remove it) |
3.11.3.1 - refers to figures and equations, links are broken |
|
- 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 |
|
| 408 |
|
|
| 409 |
3.2.2.1 - ('upgrading from an earlier version') belongs under |
3.12.3.2 - line 43: link to equation is broken |
|
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 |
|
|
|
|
|
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 |
|
| 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 |
3.16.4 - strange formatting, presence of '>' symbols - remove them |
- conservation analysis |
| 423 |
|
- diagnostics |
| 424 |
|
|
| 425 |
3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 |
o Four degree adjoint |
| 426 |
3.17.3.1 - nothing filled in under file input/data - needs description |
- both TAF and OpenAD based. |
| 427 |
|
|
| 428 |
3.18.2 - point to section 2 for details - need hyperlink |
o Coupled with biogeo setup |
| 429 |
|
- based on CCGS setup |
| 430 |
|
|
|
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? |
|
|
adjustment.128x64x1 |
|
|
adjustment.cs-32x32x1 |
|
|
advect_cs |
|
|
advect_xy |
|
|
advect_xz |
|
|
aim.5l_cs |
|
|
aim.5l_Equatorial_Channel |
|
|
aim.5l_LatLon |
|
|
biogeo |
|
|
bottom_ctrl_5x5 |
|
|
cfc_example |
|
|
cpl_aim+ocn |
|
|
dome |
|
|
exp2 |
|
|
exp4 |
|
|
exp5 |
|
|
fizhi-cs-32x32x10 |
|
|
fizhi-cs-aqualev20 |
|
|
fizhi-gridalt-hs |
|
|
flt_example |
|
|
front_relax |
|
|
global1x1_tot |
|
|
global2x2_tot |
|
|
global_ocean.90x40x15 |
|
|
global_ocean.cs32x15 |
|
|
global_ocean.cubed32x32x30 |
|
|
global_ocean_ebm |
|
|
global_with_exf |
|
|
hs94.128x64x5 |
|
|
hs94.1x64x5 |
|
|
hs94.cs-32x32x5 |
|
|
ideal_2D_oce |
|
|
internal_wave |
|
|
inverted_barometer |
|
|
lab_sea |
|
|
matrix_example |
|
|
MLAdjust |
|
|
natl_box |
|
|
natl_box_adjoint |
|
|
OpenAD |
|
|
rotating_tank |
|
|
solid-body.cs-32x32x1 |
|
|
tidal_basin_2d |
|
|
tutorial_baroclinic_gyre |
|
|
tutorial_barotropic_gyre |
|
|
tutorial_cfc_offline |
|
|
tutorial_deep_convection |
|
|
tutorial_global_oce_biogeo |
|
|
tutorial_global_oce_in_p |
|
|
tutorial_global_oce_latlon |
|
|
tutorial_global_oce_optim |
|
|
tutorial_held_suarez_cs |
|
|
tutorial_offline |
|
|
tutorial_plume_on_slope |
|
|
tutorial_tracer_adjsens |
|
|
vermix |
|
| 431 |
|
|
| 432 |
>>>> From Ed |
>>>> From Ed |
| 433 |
|
|
| 451 |
|
|
| 452 |
Chapter 6 |
Chapter 6 |
| 453 |
|
|
| 454 |
the master package diagram does not appear in the document |
the master package diagram does not appear in the document <- done |
| 455 |
|
(<- needs an update: e.g. atm2d, salt_plume, shelfice ...) |
| 456 |
|
|
| 457 |
Master list of packages (add this to beginning of chap 6) |
Master list of packages (add this to beginning of chap 6) |
| 458 |
|
(<- needs an update: e.g. atm2d, salt_plume, shelfice ...) |
| 459 |
|
|
| 460 |
admtlm/ - autodiff (chapter 5) |
admtlm/ - autodiff (chapter 5) |
| 461 |
aim/ - retired |
aim/ - retired |
| 482 |
exch2/ - 6.2.2 |
exch2/ - 6.2.2 |
| 483 |
exf/ - 6.3.4 |
exf/ - 6.3.4 |
| 484 |
fizhi/ - 6.4.3 |
fizhi/ - 6.4.3 |
| 485 |
|
o Including FIZHI doc |
| 486 |
|
- get things up to date |
| 487 |
flt/ - (PH check) |
flt/ - (PH check) |
| 488 |
gchem/ - 6.7.1 |
gchem/ - 6.7.1 |
| 489 |
generic_advdiff/ - in chapter 2 (JM check) |
generic_advdiff/ - in chapter 2 (JM check) |
| 529 |
timeave/ - retiring...... |
timeave/ - retiring...... |
| 530 |
zonal_filt/ - chapter 2 (JM to check) |
zonal_filt/ - chapter 2 (JM to check) |
| 531 |
|
|
| 532 |
|
o Cost function packages |
| 533 |
|
- floats, weights, profiles etc... |
| 534 |
|
|
| 535 |
|
|
| 536 |
list an expeiment which uses package? CNH |
list an expeiment which uses package? CNH |
| 537 |
|
|
| 538 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
| 541 |
|
|
| 542 |
===== Chapter 7 ===== [EH3 editing] : |
===== Chapter 7 ===== [EH3 editing] : |
| 543 |
|
|
| 544 |
7.1.1 - links to section 7.1.4: the text of the first |
+ JMC: please add description of: |
| 545 |
one should read "see MITgcm Kernel Diagnostics Menu" |
- diagstat |
| 546 |
the links are pointing to the proper place |
- new temporal averaging feature |
| 547 |
|
|
| 548 |
|
+ update the RW / MDSIO description |
| 549 |
|
-> new meta file |
| 550 |
|
-> list all RW S/R that one should use instead of calling directly MDSIO |
| 551 |
|
|
| 552 |
|
+ add Graphix to the list of stuff in utils/matlab (Daniel) |
| 553 |
|
|
| 554 |
|
+ get bathymetry pre-processing stuff from Patrick and then describe it |
| 555 |
|
|
| 556 |
|
+ add something on spgrid mesh generator |
| 557 |
|
o Grid generation |
| 558 |
|
- more explanation and some step-by-step examples |
| 559 |
|
- plotting grid examples |
| 560 |
|
|
|
7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) |
|
| 561 |
|
|
| 562 |
7.5.2 - get bathymetry pre-processing stuff from Patrick |
+ add in gmaze PV calculation scripts plus write up on how it is calculated |
| 563 |
and then describe it |
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/ |
| 564 |
|
|
| 565 |
|
|
| 566 |
andrea |
andrea |
| 572 |
|
|
| 573 |
10. Under development |
10. Under development |
| 574 |
|
|
| 575 |
|
Constantinos LCML |
| 576 |
|
o Legend/LCML examples and explanation |
| 577 |
|
- examples and explanation! |
| 578 |
|
|
| 579 |
|
|
| 580 |
|
|
| 581 |
Bibliography |
Bibliography |
| 582 |
|
|
| 583 |
tidy up from misc - .tex |
tidy up from misc - .tex |
| 584 |
|
|
| 585 |
|
Also |
| 586 |
|
|
| 587 |
|
a link to the new manual |
| 588 |
|
should appear on the front page (even if it's under construction). |
| 589 |
|
|
| 590 |
|
updating: |
| 591 |
|
http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html |
| 592 |
|
which points to a 1.5 years old code. Would be good to generate a |
| 593 |
|
new one, and even better, to try to keep it up-to-date. |
| 594 |
|
|
Parent Directory
| 
Revision Log
| 
Revision Graph
| 
Patch