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| 27 | 
  Biblio        - EH3 | 
  Biblio        - EH3 | 
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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 | 
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| 32 | 
 To do | 
 To do | 
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| 44 | 
 o HTML, scripts and front content | 
 o HTML, scripts and front content | 
| 45 | 
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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 | 
| 49 | 
     o add another short-cut for quick download | 
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| 50 | 
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     o --DONE--  add another short-cut for quick download | 
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| 52 | 
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     o --DONE--  add another short-cut | 
| 53 | 
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                   About | 
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                   Installation | 
| 55 | 
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                   Contents | 
| 56 | 
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                   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 | 
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| 62 | 
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     o --DONE--  finite-volume doesn't leap to FV figure | 
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| 64 | 
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     o -- DONE ??? --  have another go at pnmcrop et al. | 
| 65 | 
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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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| 72 | 
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| 73 | 
     o finite-volume doesn't leap to FV figure | 
          To view the altered alignment, see: | 
| 74 | 
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| 75 | 
     o have another go at pnmcrop et al. | 
             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 | 
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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 | 
| 265 | 
 >> evaluated explicitly in time | 
 >> evaluated explicitly in time | 
| 266 | 
 <- Leave it general. | 
 <- Leave it general. | 
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| 268 | 
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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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| 272 | 
 2.2 rigid-lid: | 
 2.2 rigid-lid: | 
| 273 | 
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| 417 | 
 3.14.5.4 -- 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 | 
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| 420 | 
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  o Update basic intro with one and four layer gyres | 
| 421 | 
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    - include advection options | 
| 422 | 
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    - conservation analysis | 
| 423 | 
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    - diagnostics | 
| 424 | 
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| 425 | 
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  o Four degree adjoint | 
| 426 | 
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    - both TAF and OpenAD based. | 
| 427 | 
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| 428 | 
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  o Coupled with biogeo setup | 
| 429 | 
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    - based on CCGS setup | 
| 430 | 
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| 431 | 
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| 432 | 
 >>>> From Ed | 
 >>>> From Ed | 
| 433 | 
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| 434 | 
 Here are the remaining bits for Chap 4 : | 
 Here are the remaining bits for Chap 4 : | 
| 480 | 
 exch2/                - 6.2.2 | 
 exch2/                - 6.2.2 | 
| 481 | 
 exf/                  - 6.3.4 | 
 exf/                  - 6.3.4 | 
| 482 | 
 fizhi/                - 6.4.3 | 
 fizhi/                - 6.4.3 | 
| 483 | 
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  o Including FIZHI doc | 
| 484 | 
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    - get things up to date | 
| 485 | 
 flt/                  - (PH check) | 
 flt/                  - (PH check) | 
| 486 | 
 gchem/                - 6.7.1 | 
 gchem/                - 6.7.1 | 
| 487 | 
 generic_advdiff/      - in chapter 2 (JM check) | 
 generic_advdiff/      - in chapter 2 (JM check) | 
| 527 | 
 timeave/              - retiring...... | 
 timeave/              - retiring...... | 
| 528 | 
 zonal_filt/           - chapter 2 (JM to check) | 
 zonal_filt/           - chapter 2 (JM to check) | 
| 529 | 
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| 530 | 
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  o Cost function packages | 
| 531 | 
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    - floats, weights, profiles etc... | 
| 532 | 
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| 533 | 
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| 534 | 
 list an expeiment which uses package? CNH | 
 list an expeiment which uses package? CNH | 
| 535 | 
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| 536 | 
 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  | 
 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  | 
| 539 | 
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| 540 | 
 =====  Chapter 7  =====  [EH3 editing] : | 
 =====  Chapter 7  =====  [EH3 editing] : | 
| 541 | 
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| 542 | 
 7.1.x - JMC: please add description of: | 
  + JMC: please add description of: | 
| 543 | 
         - diagstat | 
         - diagstat | 
| 544 | 
         - new temporal averaging feature | 
         - new temporal averaging feature | 
| 545 | 
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| 546 | 
 7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) | 
  + add Graphix to the list of stuff in utils/matlab (Daniel) | 
| 547 | 
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| 548 | 
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  + get bathymetry pre-processing stuff from Patrick and then describe it | 
| 549 | 
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| 550 | 
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  + add something on spgrid mesh generator | 
| 551 | 
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  o Grid generation | 
| 552 | 
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    - more explanation and some step-by-step examples | 
| 553 | 
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    - plotting grid examples | 
| 554 | 
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 7.5.2 - get bathymetry pre-processing stuff from Patrick | 
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         and then describe it | 
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| 555 | 
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| 556 | 
 add something on spgrid mesh generator (maybe)? | 
  + add in gmaze PV calculation scripts plus write up on how it is calculated | 
| 557 | 
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      http://mitgcm.org/cgi-bin/viewcvs.cgi/MITgcm_contrib/gmaze_pv/ | 
| 558 | 
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| 559 | 
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| 560 | 
 andrea | 
 andrea | 
| 567 | 
 10. Under development | 
 10. Under development | 
| 568 | 
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| 569 | 
 Constantinos LCML | 
 Constantinos LCML | 
| 570 | 
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  o Legend/LCML examples and explanation | 
| 571 | 
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    - examples and explanation! | 
| 572 | 
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| 573 | 
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| 574 | 
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| 575 | 
 Bibliography | 
 Bibliography | 
| 576 | 
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| 577 | 
  tidy up from misc - .tex | 
  tidy up from misc - .tex | 
| 578 | 
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| 579 | 
  | 
 Also | 
| 580 | 
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| 581 | 
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 a link to the new manual | 
| 582 | 
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 should appear on the front page (even if it's under construction). | 
| 583 | 
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| 584 | 
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 updating: | 
| 585 | 
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 http://mitgcm.org/r2_web_testing/latest/code_reference/callTree.html | 
| 586 | 
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 which points to a 1.5 years old code. Would be good to generate a | 
| 587 | 
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 new one, and even better, to try to keep it up-to-date. | 
| 588 | 
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