| 538 | 
  | 
  | 
| 539 | 
    the master package diagram does not appear in the document | 
    the master package diagram does not appear in the document | 
| 540 | 
  | 
  | 
 | 
    pkg/ptracers doesn't seem to have any documentation (see packages list below) | 
  | 
 | 
                 martin volunteered - get martin to ask steph | 
  | 
 | 
  | 
  | 
 | 
  | 
  | 
| 541 | 
 Master list of packages (add this to beginning of chap 6) | 
 Master list of packages (add this to beginning of chap 6) | 
| 542 | 
  | 
  | 
| 543 | 
 admtlm/               - autodiff (chapter 5) | 
 admtlm/               - autodiff (chapter 5) | 
| 562 | 
 ebm/                  - (check with PH) | 
 ebm/                  - (check with PH) | 
| 563 | 
 ecco/                 - chapter 8 | 
 ecco/                 - chapter 8 | 
| 564 | 
 embed_files/          - add something to chapter 7 | 
 embed_files/          - add something to chapter 7 | 
 | 
 ex3/                  - move to contrib (EH) | 
  | 
| 565 | 
 exch2/                - 6.2.2 | 
 exch2/                - 6.2.2 | 
| 566 | 
 exf/                  - 6.3.4 | 
 exf/                  - 6.3.4 | 
| 567 | 
 fizhi/                - 6.4.3 | 
 fizhi/                - 6.4.3 | 
| 568 | 
 flt/                  - in chapter 2 (JM check) | 
 flt/                  - (PH check) | 
| 569 | 
 gchem/                - 6.7.1 | 
 gchem/                - 6.7.1 | 
| 570 | 
 generic_advdiff/      - in chapter 2 (JM check) | 
 generic_advdiff/      - in chapter 2 (JM check) | 
| 571 | 
 ggl90/                - nothing, (Martin?) | 
 ggl90/                - nothing, (Martin?) | 
| 572 | 
 gmredi/               - in chapter 2 (JM check). also need | 
 gmredi/               - in chapter 2 (JM check). also need | 
| 573 | 
                         Ferrari & Mc tapering | 
                         Ferrari & Mc transition zone stuff (Samar doing this) | 
| 574 | 
  | 
                         get dfer to read this | 
| 575 | 
 grdchk/               - grdchk (chapter 5 - check with PH) | 
 grdchk/               - grdchk (chapter 5 - check with PH) | 
| 576 | 
 gridalt/              - 6.2.4 | 
 gridalt/              - 6.2.4 | 
| 577 | 
 kpp/                  - 6.3.2 | 
 kpp/                  - 6.3.2 | 
| 578 | 
 land/                 - 6.4.2 (not connected to code - JM to fix) | 
 land/                 - 6.4.2 (not connected to code Rong's notes - JM to fix) | 
| 579 | 
 matrix/               - Samar | 
 matrix/               - Samar | 
| 580 | 
 mdsio/                - 7.3.1 | 
 mdsio/                - 7.3.1 | 
| 581 | 
 mnc/                  - 7.2.1 | 
 mnc/                  - 7.2.1 | 
| 584 | 
 mom_vecinv/           - in chapter 2 (JM check) | 
 mom_vecinv/           - in chapter 2 (JM check) | 
| 585 | 
 monitor/              - 7.4 | 
 monitor/              - 7.4 | 
| 586 | 
 my82/                 - nothing, (martin?) | 
 my82/                 - nothing, (martin?) | 
| 587 | 
 obcs/                 - 6.3 (needs a check) | 
 obcs/                 - 6.3 (needs a check - ask PH to read) | 
| 588 | 
 ocn_compon_interf/    - 6.6 (no content yet) | 
 ocn_compon_interf/    - 6.6 (no content yet) | 
| 589 | 
 offline/              - nothing, tutorials that need work but no package   section entry | 
 offline/              - nothing, tutorials that need work but no package   section entry | 
| 590 | 
  | 
                         trivial to document (CNH to do) | 
| 591 | 
 opps/                 - nothing, (martin?) | 
 opps/                 - nothing, (martin?) | 
| 592 | 
 pp81/                 - nothing, (martin?) | 
 pp81/                 - nothing, (martin?) | 
| 593 | 
 profiles/             - GAEL | 
 profiles/             - GAEL | 
| 594 | 
 ptracers/             - JM + SD to write something | 
 ptracers/             - JM + SD + Martin to write something (nothing for this | 
| 595 | 
 rbcs/                 - talk to steph | 
                           at the moment) | 
| 596 | 
 runclock/             - runclock | 
                         AM has diagnostics table for this. | 
| 597 | 
 rw/                   - not sure | 
 rbcs/                 - CNH to talk to steph | 
| 598 | 
  | 
 runclock/             - runclock - CNH | 
| 599 | 
  | 
 rw/                   - not sure - going to stay says JMC. quick IO calls | 
| 600 | 
  | 
                         JMC to write a quick note for that. | 
| 601 | 
 sbo/                  - text in sbo_descruption.tex but not linked into | 
 sbo/                  - text in sbo_descruption.tex but not linked into | 
| 602 | 
                         part6 | 
                         part6 - CNH | 
| 603 | 
 seaice/               - 6.5.2 - no equations, dimitris has promised some | 
 seaice/               - 6.5.2 - no equations, dimitris has promised some | 
| 604 | 
 shap_filt/            - chapter 2, JM to check | 
 shap_filt/            - chapter 2, JM to check | 
| 605 | 
 shelfice/             - nothing yet (martin?) | 
 shelfice/             - nothing yet (martin?) | 
| 606 | 
 solver/               - empty | 
 solver/               - empty (go away?) | 
| 607 | 
 sphere/               - chapter 5 or 8 (PH to check) | 
 sphere/               - chapter 5 or 8 (PH to check) | 
| 608 | 
 therm_seaice/         - empty | 
 therm_seaice/         - empty (go away?) | 
| 609 | 
 thsice/               - 6.5.1 (JM to update?) | 
 thsice/               - 6.5.1 (JM to update?) | 
| 610 | 
 timeave/              - retiring...... | 
 timeave/              - retiring...... | 
| 611 | 
 zonal_filt/           - chapter 2 (JM to check) | 
 zonal_filt/           - chapter 2 (JM to check) | 
| 612 | 
  | 
  | 
| 613 | 
 Possible for chap 7 - Daniels grafix/ stuff | 
 list an expeiment which uses package? CNH | 
| 614 | 
  | 
  | 
| 615 | 
 Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. | 
 [DONE]Need to get packages to contain their available diagnostics (i.e. calls to DIAGNOSTICS_ADD). these are listed in stdout when pacakages are started. | 
 | 
  | 
  | 
 | 
 Figure 6.8 is missing | 
  | 
| 616 | 
  | 
  | 
| 617 | 
 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  | 
 6.3.1.7 Tapering: Large, Danabasoglu and Doney, JPO 1997  | 
| 618 | 
  Figure 6.8 is missing | 
  Figure 6.8 is missing | 
| 633 | 
 andrea | 
 andrea | 
| 634 | 
  | 
  | 
| 635 | 
  | 
  | 
| 636 | 
 9. Model uses | 
 9. Publications using MITgcm | 
| 637 | 
    Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... | 
    Spall, Gianmaria, Legg, Dewar, Cessi, Cournelle, Follows, Adcroft, etc... | 
| 638 | 
    (check in support for more names) | 
    (check in support for more names) | 
| 639 | 
  | 
  | 
| 640 | 
  | 
 10. Under development | 
| 641 | 
  | 
  | 
| 642 | 
  | 
  | 
| 643 | 
  | 
 Bibliography | 
| 644 | 
  | 
  | 
| 645 | 
  | 
  tidy up from misc - .tex |