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Editors |
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Overall - JM, AM, PH, CNH, EH3 |
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Front content - EH3 |
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Chapter 1 - CNH |
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Chapter 2 - JMC |
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Chapter 3 - AM |
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Chapter 4 - CNH |
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Chapter 5 - PH |
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Chapter 6 - AM |
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Chapter 7 - EH3 |
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Chapter 8 - PH |
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Chapter 9 - CNH (Applications) |
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Chapter 10 - JMC (Under development chapter) |
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Biblio - EH3 |
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31 |
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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Add an "Under development, chapter" - shortish description of what |
Add an "Under development, chapter" - shortish description of what |
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is available (last chapter) |
is available (last chapter) |
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- add in example latex for formatting author names in different pieces. |
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this aknowledges peoples contributions and gives ref for who |
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to talk to. |
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o HTML, scripts and front content |
o HTML, scripts and front content |
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- pick a URL |
- pick a URL |
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TBD |
TBD |
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- mitgcm.org very front page. |
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o too many clicks to get to model manual. |
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make doc link go to mitgcm.org/r2_web_testing/latest |
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and add "HowTo" reference etc... to /latest page |
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- mitgcm.org/r2_web_testing/latest |
- mitgcm.org/r2_web_testing/latest |
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o add another short-cut for quick download |
o add another short-cut for quick download |
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Tutorials (broken) |
Tutorials (broken) |
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Browse Code |
Browse Code |
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o mitgcm.org (front content) [DONE] |
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Get Code (where does this go to?) |
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get rid of * CVS current bullet |
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make HTML-enabled CVS code browser leap to MITgcm/MITgcm |
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o authors |
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John, Alistair, Jean-Michel, Patrick, Andrea, Steph, Helen, |
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Martin, Baylor, Dimitris, David, Ed, Mick, Chris, Constantinos, |
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Gael - others? |
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o words on http://mitgcm.org/r2_web_testing/latest |
o words on http://mitgcm.org/r2_web_testing/latest |
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change to |
change to |
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"access on-line Auser manual/A and Atable of contents/A |
"access on-line Auser manual/A and Atable of contents/A |
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to add: mention the angle of the grid direction relative to |
to add: mention the angle of the grid direction relative to |
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Eastward, Northward direction. |
Eastward, Northward direction. |
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+ mention horizGridFile= in file "data" (PARM04) |
+ mention horizGridFile= in file "data" (PARM04) |
320 |
- add cylindrical grid description |
- add cylindrical polar grid description |
321 |
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 |
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344 |
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 |
345 |
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 |
346 |
scaling (not cos()2) |
scaling (not cos()2) |
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- need to reference the smag/leith section. |
348 |
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2.13.6 Vertical dissipation |
2.13.6 Vertical dissipation |
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- mention the implicit vertical viscosity option and ref to section 2.5 |
- mention the implicit vertical viscosity option and ref to section 2.5 |
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2.16 & 2.17 & 2.18 : |
2.16 & 2.17 & 2.18 : |
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- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
- add 1rst Order upwind option & DST-2 (Lax-Wendroff) options |
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- fix equations 2.202 & 2.203 (thanks to Martin) |
367 |
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368 |
2.20.2 mercator, non-dimensional Equations: |
2.20.2 mercator, non-dimensional Equations: |
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- does not use std notation |
- does not use std notation |
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- would be better as an appendix of section 2.20: |
- would be better as an appendix of section 2.20: |
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(e.g changing the tile to: |
(e.g changing the tile to: |
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- talk to Baylor |
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Appendix: non-dimensional Equations on Spherical-Polar grid.) |
Appendix: non-dimensional Equations on Spherical-Polar grid.) |
374 |
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JM |
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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 |
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major and has experience editing/proofing technical papers. I |
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could print out a copy and ask her to read it and suggest |
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improvements. |
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- missing references (if you point me towards URLs, I'll add them |
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to the bibliography): |
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\ref{ref hoe and hill, ecmwf} |
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\ref{magicgarden} |
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\ref{IBMLAPI} |
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\ref{Memorychannel} |
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\ref{hoe-hill:99} |
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- There are a few empty sub-sections at the end of Chap 4 that |
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should either be commented out or fleshed out. |
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and thats about it for Chap 4. |
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Add more to quick links on front page |
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Chapter 6 |
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the master package diagram does not appear in the document |
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pkg/ptracers doesn't seem to have any documentation (see packages list below) |
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Master list of packages (add this to beginning of chap 6) |
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admtlm/ - autodiff (chapter 5) |
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aim/ - retired |
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aim_compon_interf/ - 6.6 (no content yet) |
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aim_ocn_coupler/ - 6.6 (no content yet) |
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aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
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atm_common/ - 6.6 (no content yet) |
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autodiff/ - autodiff (chapter 5) |
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bulk_force/ - 6.3.3 |
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cal/ - 6.3.5 |
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cd_code/ - chapter 2 (JM check) |
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cfc/ - not sure |
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chronos/ - AM to check |
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compon_communic/ - 6.6 (no content yet) |
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cost/ - not sure, check with PH |
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ctrl/ - not sure, check with PH |
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debug/ - JM may do something in chapter 7 (utilities) |
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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 |
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ex3/ - rename to exch3 |
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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 |
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generic_advdiff/ - in chapter 2 (JM check) |
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ggl90/ - nothing, (Martin?) |
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gmredi/ - in chapter 2 (JM check). also need |
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Ferrari & Mc tapering |
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grdchk/ - grdchk (chapter 5 - check with PH) |
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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) |
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matrix/ - Samar |
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mdsio/ - 7.3.1 |
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mnc/ - 7.2.1 |
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mom_common/ - in chapter 2 (JM check) |
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mom_fluxform/ - in chapter 2 (JM check) |
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mom_vecinv/ - in chapter 2 (JM check) |
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monitor/ - 7.4 |
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my82/ - nothing, (martin?) |
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obcs/ - 6.3 (needs a check) |
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ocn_compon_interf/ - 6.6 (no content yet) |
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offline/ - nothing, tutorials that need work but no package section entry |
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opps/ - nothing, (martin?) |
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pp81/ - nothing, (martin?) |
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profiles/ - GAEL |
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ptracers/ - JM + SD to write something |
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rbcs/ - talk to steph |
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runclock/ - runclock |
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rw/ - not sure |
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sbo/ - text in sbo_descruption.tex but not linked into |
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part6 |
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seaice/ - 6.5.2 - no equations, dimitris has promised some |
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shap_filt/ - chapter 2, JM to check |
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shelfice/ - nothing yet (martin?) |
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solver/ - empty |
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sphere/ - chapter 5 or 8 (PH to check) |
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therm_seaice/ - empty |
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thsice/ - 6.5.1 (JM to update?) |
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timeave/ - retiring...... |
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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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6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
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Figure 6.8 is missing |
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375 |
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376 |
>>>> From Andrea |
Diagrams of grid locations etc.... and what variables and output files |
377 |
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and/or netcdf variable names are not very easy to figure out and follow. |
378 |
to do list for chap 7: |
It would be good to redo and extend these diagrams and align with GRID.h |
379 |
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content. |
380 |
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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" |
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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 |
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7.5.2 - empty |
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381 |
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382 |
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JM |
383 |
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andrea |
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384 |
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385 |
>>>> From Andrea |
>>>> From Andrea |
386 |
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389 |
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390 |
Almost all of the 'math mode' text is dropped down as subscripts |
Almost all of the 'math mode' text is dropped down as subscripts |
391 |
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divide chapter 3 more clearly into 2 sections? |
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(ie, 3.1-3.6 are more informational, 3.8- 3.18 are examples, and |
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then 3.19 and 3.20 are informational again - rearrange subsections?) |
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392 |
3.1 - don't need a link to the outside of the document (remove it) |
3.1 - don't need a link to the outside of the document (remove it) |
393 |
- link to htdig is broken |
- link to htdig is broken |
394 |
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434 |
are written. |
are written. |
435 |
3.6.1.2 - needs to be moved to inside section 3.6.2 |
3.6.1.2 - needs to be moved to inside section 3.6.2 |
436 |
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3.7 - this section is superfluous - remove it -OR- put the tutorial sections (3.8-3.18) |
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underneath this one and leave the text for 3.7 in place |
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437 |
All the 'overview' sections need some reference to the name of the experiment in |
All the 'overview' sections need some reference to the name of the experiment in |
438 |
the verification directory |
the verification directory |
439 |
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470 |
offline - duplicate inputs, what is it, tidy up cfc v. |
offline - duplicate inputs, what is it, tidy up cfc v. |
471 |
other offline. JM thinks these need tidying up. |
other offline. JM thinks these need tidying up. |
472 |
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473 |
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Which of the following are which tutorial? |
474 |
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adjustment.128x64x1 |
475 |
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adjustment.cs-32x32x1 |
476 |
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advect_cs |
477 |
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advect_xy |
478 |
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advect_xz |
479 |
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aim.5l_cs |
480 |
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aim.5l_Equatorial_Channel |
481 |
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aim.5l_LatLon |
482 |
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biogeo |
483 |
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bottom_ctrl_5x5 |
484 |
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cfc_example |
485 |
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cpl_aim+ocn |
486 |
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dome |
487 |
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exp2 |
488 |
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exp4 |
489 |
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exp5 |
490 |
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fizhi-cs-32x32x10 |
491 |
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fizhi-cs-aqualev20 |
492 |
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fizhi-gridalt-hs |
493 |
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flt_example |
494 |
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front_relax |
495 |
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global1x1_tot |
496 |
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global2x2_tot |
497 |
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global_ocean.90x40x15 |
498 |
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global_ocean.cs32x15 |
499 |
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global_ocean.cubed32x32x30 |
500 |
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global_ocean_ebm |
501 |
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global_with_exf |
502 |
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hs94.128x64x5 |
503 |
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hs94.1x64x5 |
504 |
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hs94.cs-32x32x5 |
505 |
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ideal_2D_oce |
506 |
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internal_wave |
507 |
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inverted_barometer |
508 |
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lab_sea |
509 |
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matrix_example |
510 |
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MLAdjust |
511 |
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natl_box |
512 |
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natl_box_adjoint |
513 |
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OpenAD |
514 |
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rotating_tank |
515 |
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solid-body.cs-32x32x1 |
516 |
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tidal_basin_2d |
517 |
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tutorial_baroclinic_gyre |
518 |
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tutorial_barotropic_gyre |
519 |
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tutorial_cfc_offline |
520 |
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tutorial_deep_convection |
521 |
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tutorial_global_oce_biogeo |
522 |
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tutorial_global_oce_in_p |
523 |
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tutorial_global_oce_latlon |
524 |
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tutorial_global_oce_optim |
525 |
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tutorial_held_suarez_cs |
526 |
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tutorial_offline |
527 |
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tutorial_plume_on_slope |
528 |
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tutorial_tracer_adjsens |
529 |
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vermix |
530 |
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531 |
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>>>> From Ed |
532 |
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533 |
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Here are the remaining bits for Chap 4 : |
534 |
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535 |
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- missing references (if you point me towards URLs, I'll add them |
536 |
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to the bibliography): |
537 |
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\ref{ref hoe and hill, ecmwf} |
538 |
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\ref{magicgarden} |
539 |
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\ref{IBMLAPI} |
540 |
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\ref{Memorychannel} |
541 |
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\ref{hoe-hill:99} |
542 |
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543 |
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- There are a few empty sub-sections at the end of Chap 4 that |
544 |
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should either be commented out or fleshed out. |
545 |
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546 |
9. Model uses |
and thats about it for Chap 4. |
547 |
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548 |
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549 |
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Add more to quick links on front page |
550 |
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551 |
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Chapter 6 |
552 |
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553 |
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the master package diagram does not appear in the document |
554 |
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555 |
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Master list of packages (add this to beginning of chap 6) |
556 |
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557 |
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admtlm/ - autodiff (chapter 5) |
558 |
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aim/ - retired |
559 |
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aim_compon_interf/ - 6.6 (no content yet)(Daniel + JM) |
560 |
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aim_ocn_coupler/ - 6.6 (no content yet) |
561 |
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aim_v23/ - 6.4.1 (content needs fixing - JM to do) |
562 |
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atm_common/ - nothing in this package (6.4.1 related) |
563 |
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autodiff/ - autodiff (chapter 5) |
564 |
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bulk_force/ - 6.3.3 |
565 |
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cal/ - 6.3.5 |
566 |
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cd_code/ - chapter 2 (JM check add a reference to paper, |
567 |
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mention parameter in data) |
568 |
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cfc/ - not sure (CNH to talk to Steph and Helen) |
569 |
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chronos/ - AM to check (not being used - Andrea to kill it) |
570 |
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compon_communic/ - 6.6 (no content yet)(Daniel + JM) |
571 |
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cost/ - not sure, check with PH |
572 |
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ctrl/ - not sure, check with PH |
573 |
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debug/ - JM may do something in chapter 7 (utilities) |
574 |
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diagnostics/ - 7.1 |
575 |
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dic/ - 6.7.2 |
576 |
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ebm/ - (check with PH) |
577 |
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ecco/ - chapter 8 |
578 |
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embed_files/ - add something to chapter 7 |
579 |
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exch2/ - 6.2.2 |
580 |
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exf/ - 6.3.4 |
581 |
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fizhi/ - 6.4.3 |
582 |
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flt/ - (PH check) |
583 |
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gchem/ - 6.7.1 |
584 |
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generic_advdiff/ - in chapter 2 (JM check) |
585 |
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ggl90/ - nothing, (Martin?) |
586 |
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gmredi/ - in chapter 2 (JM check). also need |
587 |
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Ferrari & Mc transition zone stuff (Samar doing this) |
588 |
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get dfer to read this |
589 |
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grdchk/ - grdchk (chapter 5 - check with PH) |
590 |
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gridalt/ - 6.2.4 |
591 |
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kpp/ - 6.3.2 |
592 |
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land/ - 6.4.2 (not connected to code Rong's notes - JM to fix) |
593 |
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matrix/ - Samar |
594 |
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mdsio/ - 7.3.1 |
595 |
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mnc/ - 7.2.1 |
596 |
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mom_common/ - in chapter 2 (JM check) |
597 |
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mom_fluxform/ - in chapter 2 (JM check) |
598 |
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mom_vecinv/ - in chapter 2 (JM check) |
599 |
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monitor/ - 7.4 |
600 |
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my82/ - nothing, (martin?) |
601 |
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obcs/ - 6.3 (needs a check - ask PH to read) |
602 |
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ocn_compon_interf/ - 6.6 (no content yet) |
603 |
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offline/ - nothing, tutorials that need work but no package section entry |
604 |
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trivial to document (CNH to do) |
605 |
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opps/ - nothing, (martin?) |
606 |
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pp81/ - nothing, (martin?) |
607 |
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profiles/ - GAEL |
608 |
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ptracers/ - JM + SD + Martin to write something (nothing for this |
609 |
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at the moment) |
610 |
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AM has diagnostics table for this. |
611 |
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rbcs/ - CNH to talk to steph |
612 |
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runclock/ - runclock - CNH |
613 |
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rw/ - not sure - going to stay says JMC. quick IO calls |
614 |
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JMC to write a quick note for that. |
615 |
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sbo/ - text in sbo_descruption.tex but not linked into |
616 |
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part6 - CNH |
617 |
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seaice/ - 6.5.2 - no equations, dimitris has promised some |
618 |
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shap_filt/ - chapter 2, JM to check |
619 |
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shelfice/ - nothing yet (martin?) |
620 |
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solver/ - empty (go away?) |
621 |
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sphere/ - chapter 5 or 8 (PH to check) |
622 |
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therm_seaice/ - empty (go away?) |
623 |
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thsice/ - 6.5.1 (JM to update?) |
624 |
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timeave/ - retiring...... |
625 |
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zonal_filt/ - chapter 2 (JM to check) |
626 |
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627 |
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list an expeiment which uses package? CNH |
628 |
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629 |
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6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997 |
630 |
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Figure 6.8 is missing |
631 |
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632 |
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633 |
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===== Chapter 7 ===== [EH3 editing] : |
634 |
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635 |
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7.1.1 - links to section 7.1.4: the text of the first |
636 |
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one should read "see MITgcm Kernel Diagnostics Menu" |
637 |
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the links are pointing to the proper place |
638 |
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639 |
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7.5.1 - add Graphix to the list of stuff in utils/matlab (Daniel) |
640 |
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641 |
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7.5.2 - get bathymetry pre-processing stuff from Patrick |
642 |
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and then describe it |
643 |
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644 |
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645 |
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andrea |
646 |
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647 |
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648 |
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9. Publications using MITgcm --> "Previous Applications of MITgcm" |
649 |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... |
650 |
(check in support for more names) |
(check in support for more names) |
651 |
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652 |
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10. Under development |
653 |
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654 |
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655 |
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Bibliography |
656 |
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657 |
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tidy up from misc - .tex |