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Biblio - EH3 |
Biblio - EH3 |
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Rebuild and set to do cron build - DONE on hugo |
Rebuild and set to do cron build - DONE on hugo |
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To do |
To do |
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o HTML, scripts and front content |
o HTML, scripts and front content |
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| 46 |
- pick a URL |
- pick a URL: mitgcm.org/r2 <-- EH3's preferred base URL |
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TBD |
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| 48 |
- mitgcm.org/r2_web_testing/latest |
- mitgcm.org/r2_web_testing/latest |
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o add another short-cut for quick download |
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o --DONE-- add another short-cut for quick download |
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o --DONE-- add another short-cut |
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About |
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Installation |
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Contents |
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Overview |
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Tutorials (broken) |
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Browse Code |
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o --DONE-- words on http://mitgcm.org/r2_web_testing/latest change to |
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o --DONE-- finite-volume doesn't leap to FV figure |
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o -- DONE ??? -- have another go at pnmcrop et al. |
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| 66 |
o add another short-cut |
I've tried making a small change in latex2html which fixes |
| 67 |
About |
the oddball-lower-alignment issue that we were seeing with |
| 68 |
Installation |
most in-line expressions (that is, math embedded in text). |
| 69 |
Contents |
The fix results in some things being slightly raised but I |
| 70 |
Overview |
thin this is more asthetically pleasing than being somewhat |
| 71 |
Tutorials (broken) |
lowered as before. --EH3 |
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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" |
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o finite-volume doesn't leap to FV figure |
To view the altered alignment, see: |
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o have another go at pnmcrop et al. |
http://eddy.csail.mit.edu/r2/latest/ |
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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 |
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o Latex |
o Latex |
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Chapter 1 - CNH |
Chapter 1 - CNH |
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>> evaluated explicitly in time |
>> evaluated explicitly in time |
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<- Leave it general. |
<- Leave it general. |
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o Time-stepping outline |
| 269 |
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- what gets called when |
| 270 |
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| 271 |
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2.2 rigid-lid: |
2.2 rigid-lid: |
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| 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 |
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| 278 |
2.3 linear free-surface: |
2.3 linear free-surface: |
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- add ref(+link) to S/R names: |
- add ref(+link) to S/R names: |
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- add ref(+link) to Crank-Nickelson section 2.9.1 |
- add ref(+link) to Crank-Nickelson section 2.9.1 <- DONE |
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| 282 |
2.4 Adams-Bashforth |
2.4 Adams-Bashforth |
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- 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 |
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| 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 |
| 404 |
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| 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 |
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| 407 |
3.4 - refer to sections 3.8 - 3.18 (now says 3.8 - 3.10) |
3.11.3.1 - refers to figures and equations, links are broken |
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3.4.1 - links to the following experiments don't exist or are broken: |
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exp2 - should link to section 3.9 |
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hs94.cs-32x32x5 - link to section 3.12 |
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add 'convection' to the list, link to section 3.13 |
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add 'plume on slope` to the list, link to section 3.14 |
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add '??' link to section 3.15 |
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add 'dic_example on slope` to the list, link to section 3.16 |
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add '??' link to section 3.17 |
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add 'offline' and link to section 3.18 |
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clean up others and make links where they are needed |
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3.4.2 - text suggests to see section 2 for details about what is in the 'code' |
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and 'input' directories - should refer to the examples in this section |
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- add 'build' bullet - this is where the model is compiled and exectuable lives |
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3.5 - add some little text when talking about 'optfiles' to refer to the tools/build_options |
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as the place where they live (add a link?) |
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3.6.1 - Add some general 'approach' text - ie, output is controlled either by the |
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'data' file in the input directory or by the data.[pkg name] file for any |
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package running. And there is some default behavior when the 'state' dumps |
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are written. |
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3.6.1.2 - needs to be moved to inside section 3.6.2 |
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All the 'overview' sections need some reference to the name of the experiment in |
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the verification directory |
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3.10 - in title, 4 degrees - degree symbol is a subscript, not a superscript |
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- is this experiment in the list from section 3.4??? |
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3.10.3.1 - refers to figures and equations, links are broken |
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3.11.3.2 - line 43: link to equation is broken |
3.12.3.2 - line 43: link to equation is broken |
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- 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? |
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| 413 |
3.12.4.1 - line 34 - link to equation is broken |
3.13.4.1 - line 34 - link to equation is broken |
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- lines 60,61 - 1st (take out the 'r' in the superscript) |
- lines 60,61 - 1st (take out the 'r' in the superscript) |
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| 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 |
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3.15.1 - reference to 'fourth experiment' should be removed |
o Update basic intro with one and four layer gyres |
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- include advection options |
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- conservation analysis |
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- diagnostics |
| 424 |
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3.16.4 - strange formatting, presence of '>' symbols - remove them |
o Four degree adjoint |
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- both TAF and OpenAD based. |
| 427 |
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3.17.3 - unknown verification directory pointed to - also: no link from list in sec 3.4 |
o Coupled with biogeo setup |
| 429 |
3.17.3.1 - nothing filled in under file input/data - needs description |
- based on CCGS setup |
| 430 |
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3.18.2 - point to section 2 for details - need hyperlink |
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3.19.1 - text (2 places) says that section 3.5 called for compile in 'input' directory - not true! |
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section 3.5 has the 'build' directory in the example |
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3.20.1 - link to doc at end of section points to this section |
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3.20.2 - link to doc at end of section points to this section |
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offline - duplicate inputs, what is it, tidy up cfc v. |
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other offline. JM thinks these need tidying up. |
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Which of the following are which tutorial? |
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adjustment.128x64x1 |
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adjustment.cs-32x32x1 |
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advect_cs |
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advect_xy |
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advect_xz |
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aim.5l_cs |
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aim.5l_Equatorial_Channel |
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aim.5l_LatLon |
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biogeo |
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bottom_ctrl_5x5 |
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cfc_example |
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cpl_aim+ocn |
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dome |
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exp2 |
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exp4 |
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exp5 |
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fizhi-cs-32x32x10 |
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fizhi-cs-aqualev20 |
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fizhi-gridalt-hs |
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flt_example |
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front_relax |
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global1x1_tot |
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global2x2_tot |
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global_ocean.90x40x15 |
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global_ocean.cs32x15 |
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global_ocean.cubed32x32x30 |
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global_ocean_ebm |
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global_with_exf |
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hs94.128x64x5 |
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hs94.1x64x5 |
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hs94.cs-32x32x5 |
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ideal_2D_oce |
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internal_wave |
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inverted_barometer |
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lab_sea |
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matrix_example |
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MLAdjust |
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natl_box |
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natl_box_adjoint |
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OpenAD |
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rotating_tank |
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solid-body.cs-32x32x1 |
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tidal_basin_2d |
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tutorial_baroclinic_gyre |
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tutorial_barotropic_gyre |
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tutorial_cfc_offline |
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tutorial_deep_convection |
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tutorial_global_oce_biogeo |
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tutorial_global_oce_in_p |
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tutorial_global_oce_latlon |
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tutorial_global_oce_optim |
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tutorial_held_suarez_cs |
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tutorial_offline |
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tutorial_plume_on_slope |
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tutorial_tracer_adjsens |
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vermix |
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| 431 |
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| 432 |
>>>> From Ed |
>>>> From Ed |
| 433 |
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| 451 |
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| 452 |
Chapter 6 |
Chapter 6 |
| 453 |
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| 454 |
the master package diagram does not appear in the document |
the master package diagram does not appear in the document <- done |
| 455 |
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(<- needs an update: e.g. atm2d, salt_plume, shelfice ...) |
| 456 |
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| 457 |
Master list of packages (add this to beginning of chap 6) |
Master list of packages (add this to beginning of chap 6) |
| 458 |
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(<- needs an update: e.g. atm2d, salt_plume, shelfice ...) |
| 459 |
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| 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 |
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| 532 |
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o Cost function packages |
| 533 |
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- floats, weights, profiles etc... |
| 534 |
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| 535 |
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| 536 |
list an expeiment which uses package? CNH |
list an expeiment which uses package? CNH |
| 537 |
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| 538 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
| 541 |
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|
| 542 |
===== Chapter 7 ===== [EH3 editing] : |
===== Chapter 7 ===== [EH3 editing] : |
| 543 |
|
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| 544 |
7.1.x - JMC: please add description of: |
+ JMC: please add description of: |
| 545 |
- diagstat |
- diagstat |
| 546 |
- new temporal averaging feature |
- new temporal averaging feature |
| 547 |
|
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| 548 |
7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) |
+ update the RW / MDSIO description |
| 549 |
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-> new meta file |
| 550 |
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-> list all RW S/R that one should use instead of calling directly MDSIO |
| 551 |
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| 552 |
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+ add Graphix to the list of stuff in utils/matlab (Daniel) |
| 553 |
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| 554 |
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+ get bathymetry pre-processing stuff from Patrick and then describe it |
| 555 |
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| 556 |
7.5.2 - get bathymetry pre-processing stuff from Patrick |
+ add something on spgrid mesh generator |
| 557 |
and then describe it |
o Grid generation |
| 558 |
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- more explanation and some step-by-step examples |
| 559 |
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- plotting grid examples |
| 560 |
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| 561 |
add something on spgrid mesh generator (maybe)? |
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| 562 |
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+ add in gmaze PV calculation scripts plus write up on how it is calculated |
| 563 |
|
http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/ |
| 564 |
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| 565 |
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| 566 |
andrea |
andrea |
| 573 |
10. Under development |
10. Under development |
| 574 |
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| 575 |
Constantinos LCML |
Constantinos LCML |
| 576 |
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o Legend/LCML examples and explanation |
| 577 |
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- examples and explanation! |
| 578 |
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| 579 |
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| 580 |
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| 581 |
Bibliography |
Bibliography |
| 582 |
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| 583 |
tidy up from misc - .tex |
tidy up from misc - .tex |
| 584 |
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| 585 |
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Also |
| 586 |
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| 587 |
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a link to the new manual |
| 588 |
|
should appear on the front page (even if it's under construction). |
| 589 |
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| 590 |
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updating: |
| 591 |
|
http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html |
| 592 |
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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 |
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Parent Directory
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Revision Log
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Revision Graph
| 
Patch